Slide 1

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 2

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 3

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 4

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 5

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 6

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

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47


Slide 7

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 8

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 9

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 10

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 11

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 12

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 13

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 14

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 15

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 16

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 17

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 18

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 19

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 20

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 21

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 22

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 23

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 24

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 25

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 26

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 27

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 28

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 29

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 30

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 31

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 32

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 33

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 34

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 35

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 36

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 37

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 38

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 39

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 40

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 41

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 42

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 43

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 44

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 45

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 46

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

Modern Methods in Drug Discovery WS10/11

7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47


Slide 47

Modern Methods in Drug Discovery
Aims of this course:
• comprehensive knowledge about all
processes in the drug discovery pipeline

• in particular in silico methods of drug design

1st Lecture

Modern Methods in Drug Discovery WS10/11

1

flow of information in a
drug discovery pipeline
bioinformatics

Covered by this lecture
1st Lecture

Modern Methods in Drug Discovery WS10/11

2

medicinal chemistry
organic synthesis
biopharmaceutical aspects
(tissue models, non-oral administration)
clinical aspects
molecular modelling theory
homology modelling theory
docking basics and applications
computational chemistry
genome, proteome, metabolome
bioethics and patent law

1st Lecture

Modern Methods in Drug Discovery WS10/11

other lectures available

Related topics not covered by this lecture

3

Required knowledge
Use of tools for sequence analysis, e.g. BLAST, CLUSTALW
Use of visualizing tools, e.g. RASMOL, BALL, VMD, SPDBV
homology modelling, e.g. Swiss-Model, WHATIF, …
file format converters: Openbabel

recommended courses:
Softwarewerkzeuge der Bioinformatik
Computational Chemistry
Bioinformatics I + II
Test your personal knowledge: See selftestWS06.pdf
Actual applications during the excerices:
multiple alignment, homology in sequences
simple homology modelling
protein-ligand interactions
database queries (using SMARTS with Openbabel)
1st Lecture

Modern Methods in Drug Discovery WS10/11

4

What is drug discovery ?
rational and targeted search for new drugs
Therapeutic Target
Lead Discovery
Lead Optimization
drug design
Clinical Candidate
Commerical Drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

5

typical targets (I)

contribution to the human genome and marketed drugs

1st Lecture

Modern Methods in Drug Discovery WS10/11

6

typical targets (II)
drug targets by biochemical class
Enzymes
47%

GPCRs
30%

Ion Channels
7%

DNA
1%
Intergrins
1%
Miscellaneous
2%

Other Receptors
4%

Transporters
4%
Nuclear
Receptors
4%

Fractional content of marketed drugs according to their
biochemical targets
data: Hopkins & Groom, Nat.Rev.Drug.Disc. 1 (2002) 727
1st Lecture

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7

preliminary schedule (lectures)
1. Introduction, overview, recap
of chemical structures

8. target identification, animal
models

2. typical diseases

9. cytochrom P450,
polymorphisms,
transporters

3. properties of drugs and their
mode of action

4. Substance databases and
bioisosteric compounds
5. QSAR, statistics and
descriptors
6. ADME models
7. metabolism and toxicology

1st Lecture

10. more complex diseases
malaria, obesity
11. in silico prediction of
molecular properties
12. current trends,
disease vs. lifestyle drugs
doping

Modern Methods in Drug Discovery WS10/11

8

preliminary schedule (exercises)
Biweekly in the CIP-Pool (building E 1.3 room 1.04 )
computer account and access card required
•

chemical structures of drugs

•

enzyme-ligand interactions, analysis of .pdb files

•

substance databases and SMARTS queries

•

ADME properties

•

QSAR, statistics and descriptor handling

•

orthologue targets in model organisms

•

other online tools

1st Lecture

Modern Methods in Drug Discovery WS10/11

9

compound data bases
present substance libraries
ACD
>100,000 chemicals
World Drug Index 58,000 compounds
USAN
<10,000 in clinical trial
virtual library
100,000 compounds

Pubchem

> 3,000,000 compounds

commercial
company in house
NCBI

Investment per new chemical entity: >500,000 $
New chemical entities per year: ca. 15
1st Lecture

Modern Methods in Drug Discovery WS10/11

10

Methods of Combinatorial Synthesis for
High Throughput Screening (HTS)
S
Cl

H

R1
N

N

R2

H

S

+

R3
H

1st Lecture

R4

O

R4

R3

R2
N
R1

Modern Methods in Drug Discovery WS10/11

N
+ H 2O , H C l

11

Selection of compounds for High
Throughput Screening (HTS)

R2

R1

N

1st Lecture

R3

Modern Methods in Drug Discovery WS10/11

12

Predictive ADME

Absorption
Distribution
Metabolism
Elimination

1st Lecture

Pharmacokinetic
Bioavailability

Modern Methods in Drug Discovery WS10/11

13

For each actual marketed
drug (new chemical enitity,
NCE) there have been more
than 1000 substances that
underwent screened in vitro.
Without the use of available
computer-based ADMET
filters, this number would be
even larger.

1st Lecture

Modern Methods in Drug Discovery WS10/11

Upto 10 years

From the pipeline until the commerical launch

14

Why is the prediction of ADME parameters
that important ?

Reasons that lead to failure or withdrawl of a potential drug

1st Lecture

Modern Methods in Drug Discovery WS10/11

15

pharmacokinetics and bioavailability

1st Lecture

Modern Methods in Drug Discovery WS10/11

16

Descriptors based on molecular properties
used to predict ADME properties
logP water/octanol partitioning coefficient
Lipinski‘s rule of five
topological indices
polar surface area
similary / dissimilarity

QSAR quantitative structure activity relationship
QSPR quantitative structure property rel.

1st Lecture

Modern Methods in Drug Discovery WS10/11

17

metabolism
(bio-)chemical reactions of xenobiotics in the body
First pass effect:
Extensive metabolization of mainly lipophilic molecules,
such with MW>500, or those that have a specific affinity
to certain transporters, during the first passage through
the liver
Phase I:
Oxidation, reduction and hydrolysis 
esp. cytochrome P450 enzymes
Phase II:
Conjugation with small molecules (e.g. glutamine)
Phase III:
elimination by transporters
1st Lecture

Modern Methods in Drug Discovery WS10/11

18

cytochrome P450 enzymes
Flavin monooxygenase isoenzme
Alcohol dehydrogenase
Aldehyde oxidase
Monoamine dehydrogenase (MAO)

CYP
D ru g -R + O 2
NADPH

1st Lecture

Redoxactivity is enabled
by a iron-containing
porphyrin in the active
site

D ru g -O R + H 2 O
NADP

Modern Methods in Drug Discovery WS10/11

19

cytochrome P450 gene families

Human 14+
Molluscs 1
CYP450

Plants 22
Insects 3

Fungi 11

1st Lecture

Bacteria 18
Yeasts 2

Modern Methods in Drug Discovery WS10/11

Nematodes 3

20

cytochrome P450 polymorphism
„Every human is (more or less) different “
Determination of the phenotype by the actual activity or
the amount of the expressed enzyme.
In contrast, the genotype is determined by the individual
DNA sequence.
Thus, the same genotype enables several different
phenotypes
According to their metabolic activity of CYP there is a
classification into normal (extensive metabolizer), weak (poor
metabolizer), und accelerated (ultra-rapid metabolizer)
metabolism.
Lit: K. Nagata et al. Drug Metabol. Pharmacokin 3 (2002) 167
1st Lecture

Modern Methods in Drug Discovery WS10/11

21

genotyping of CYP P450 alleles
By using immobilized, synthetic copies of P450 nucleotides,
the Affymetrix company (USA) has developped mircoarrays
(gene chips) that allow the identification of all clinically
relevant alleles.

1st Lecture

Modern Methods in Drug Discovery WS10/11

22

Prediction of molecular properties (I)
The keynote of rational drug design
The general question is:
What is the connection between the biological space
(activity) and the chemical space (structure) ?

How are we able to make structure-based prediction ?
 QSAR and QSRP, regression analysis
 decision trees, machine learning algorithms
 other statistical methods

1st Lecture

Modern Methods in Drug Discovery WS10/11

23

Prediction of molecular properties (II)

observables

What are molecular properties?

1st Lecture

molecular weight MW (from the sum formula C12H11N3O2)
melting point
boiling point
vapour pressure
solubility (in water)
charge
dipole moment
Directly computable
from the electronic
polarizability
wave function of a
ionization potential
molecule
electrostatic potential

Modern Methods in Drug Discovery WS10/11

24

BBB-model with 12 descriptors
Descriptors mainly from QM calculations: electrostatic
surface, principal components of molecular geometry,
H-bond properties
2 .5

2

2

r = 0 .8 6 6 , a d j. r = 0 .8 4 4 , s e = 0 .3 0 8 , n = 9 0

p re d icte d lo g B B

1 .5

0 .5

CNS+

-0 .5

CNS–

-1 .5

-2 .5
-2 .5

-1 .5

-0 .5

0 .5

1 .5

2 .5

o b se rve d lo g B B

Lit: M. Hutter J.Comput.-Aided.Mol.Des. 17 (2003) 415.
1st Lecture

Modern Methods in Drug Discovery WS10/11

25

Cycle of optimization in the
drug discovery pipeline

Source: D.K. Agrafiotis et al. Nature.Rev.Drug.Discov. 1 (2002) 337.
1st Lecture

Modern Methods in Drug Discovery WS10/11

26

Accompanying books and further reading (I)
Andrew R. Leach*
Molecular Modelling. Principles and Applications
2nd edition, Prentice Hall, 2001

Rolf Knippers*
Molekulare Genetik
8. Auflage, Thieme, 2001
The Merck Index*
13th edition, Merck & CO., Inc., 2001
J.M. Berg, L. Stryer
Biochemie, Spektrum Verlag
Biochemistry, W.H. Freeman & Co Ltd.
*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

27

Accompanying books and further reading (II)
Gerhard Klebe
Wirkstoffdesign
2. Auflage, Spektrum Akad. Verlag, 2009

C.A. Orengo, D.T. Jones, J.M. Thornton
Bioinformatics
Genes, Proteins & Computers
1st ed., Bios Scientific Publishers, 2003
A.R. Leach, V. Gillet
An Introduction to Chemoinformatics
revised ed., Springer, 2007

*Available in the „Semesterapparat“
1st Lecture

Modern Methods in Drug Discovery WS10/11

28

Further hands-on tools
Molecular model sets / Molekülbaukasten

Commerically available at various price ranges
General remark: The lecturer does not endorse
any of the mentioned books/software/products.
Enquiries are welcome.
1st Lecture

Modern Methods in Drug Discovery WS10/11

29

Other useful software to make nice pictures
Chemical structures
and other objects:
Isis Draw
www.mdli.com
Windows

Protein structures:
PyMOL
www.pymol.org
Linux, Mac OS X, Windows

1st Lecture

Modern Methods in Drug Discovery WS10/11

30

Requirements to obtain the „Schein“
and the credit points
1. 50% of all accomplishable points from the home work. Two
thirds (66.7%) of all assignments must be returned. The
assignments have to be handed in until the beginning of
the next exercise unit.
2. 50% of all accomplishable points from the final exam taking
place at the end of the lecture period. If necessary,
repeated (written) exam or oral exam.

1st Lecture

Modern Methods in Drug Discovery WS10/11

31

1st assignment (I)
Refer to a prescription medicine of your own choice
Write down the active ingridient
Try to find out its molecular structure:

http://pubchem.ncbi.nlm.nih.gov/

1st Lecture

Modern Methods in Drug Discovery WS10/11

32

1st assignment (II)

1st Lecture

Modern Methods in Drug Discovery WS10/11

33

1st assignment (III)

Explain why the medicine has a completely different name
compared to the actual substance.
Try to find out some information about its molecular target:

e.g. using PubMed http://www.ncbi.nlm.nih.gov
or consult the Merck Index.
1st Lecture

Modern Methods in Drug Discovery WS10/11

34

Representation of chemical structures (I)
The valence electrons of the atoms are
pairwise grouped together
H
.
.
.
.
H C..H
.
.
H

H
.
.

H
H

C
H

H

H
.
.

..
C .. C
.
.
.
.
H
H

H

H
C
H

C
H

Lewis structures reflect covalent bonds between
atoms in a molecule

1st Lecture

Modern Methods in Drug Discovery WS10/11

35

Representation of chemical structures (II)
(electron) lone pairs are often not shown for clarity
H
.
.
.
.
.
H N .
.
.
H

H
H

H

N

H

H

H

octet rule and hypervalent atoms
H
H

N

+

H

+

O

N

H

O

H

N

H
O

H

S

O

+

+

H

O

1st Lecture

Equal bond lengths !

H

H

O

N

C
O

O
O

O

P

O

O

Modern Methods in Drug Discovery WS10/11

36

Representation of chemical structures (III)
Also carbon atoms are often omitted
H
H
H

C

H
C

H

H
C

C

H

H

H
H

C

C
H

H

C
C

C
C

H

H
H
H
H
C

C

H
H
C

H H

H

C

C
H

H
C

H

H

Corners and end of lines denote carbon atoms saturated with
the appropriate number of hydrogen atoms

1st Lecture

Modern Methods in Drug Discovery WS10/11

37

Representation of chemical structures (IV)
Stereochemistry
H

F

Solid wedges denote atoms in front
of the plane,dashed wedges
denote atoms behind

C
H3C

Cl

Four different substituents at a carbon atom cause
chirality
H

F
C

H3C

1st Lecture

H

F
C

Cl

Cl

C H3

Modern Methods in Drug Discovery WS10/11

38

Representation of chemical structures (V)
Particular for more complex molecules, these structural
drawings provide more clarity than a picture of an
actual 3D representation does.
OH

H
N

N

OH

H
C H3

Exercise: Construct this molecule using a molecular model set.
Specify the chiral carbon atoms.

1st Lecture

Modern Methods in Drug Discovery WS10/11

39

Bond distances and bond dissociation energies (I)

longer,
weaker

bond distance [Å] Do [kJ/mol] (homolytic cleavage)
H–H
0.742
432
C–H
1.09 ± 0.01
411 ± 7
C–C
1.54
345
C=C
1.34 - 1.40*
602 ± 21 *aromatic bond
C≡C
1.20
835
C–N
1.47
305
longer
C=N
1.35
615
H
C≡N
1.16
887
He
Li Be B C N O F Ne
C–O
1.43
358
N a M g Al S i P
S C l Ar
K C a G a G e As S e B r K r
C=O
1.20
526
R b S r In S n S b T e I X n
C–Si 1.85
318
C s B a T l P b B i P o At R n
C–P
1.84
264
Adapted from: J.E.Huheey
C–S
1.82
272
Inorganic Chemistry, Wiley.
C=S
1.60
577 ± 21
1st Lecture

Modern Methods in Drug Discovery WS10/11

40

Bond distances and bond dissociation energies (II)
bond distance [Å]
C–F
1.35
C–Cl 1.77
C–Br 1.94
C–I
2.14
C–H
1.09
O–H
0.96
N–H
1.01
S–H
1.34
N–N
1.45
N=N
1.25
N–O
1.40
N=O
1.21
P–O
1.63
P=O ≈1.50
1st Lecture

Do [kJ/mol]
485
327
285
213
411 non-polar hydrogen
459
polar hydrogens,
exchangable in
386 ± 8
polar solvents
363 ± 5
247 ± 13
418
201
607
≈335
≈544

reason:
N, O, and S are more
electronegative than C;
heterolytic cleavage
that leads to ions

Modern Methods in Drug Discovery WS10/11

41

Bond angles (I)
Strongly dependend on the hybridization
180°
1 0 9 .5 °
C

+ 3

=

sp 3

120°

C

C

sp 2 + p

C

C

sp + 2 p

2p

2s

 -b o n d s

-b o n d s

The C–C -bond is formed by overlap of the 1s orbitals

These are hybrizided atomic orbitals. Do not confuse with
molecular orbitals (=linear combination of atomic orbitals)
1st Lecture

Modern Methods in Drug Discovery WS10/11

42

Molecular Orbitals
MO = linear combination of atomic orbitals (LCAO)
-bond of ethylene H2C=CH2
E



pz

pz


The 2 combinations usually result in one bonding
and one anti-bonding MO
1st Lecture

Modern Methods in Drug Discovery WS10/11

43

Bond angles (II)
Extreme deviations from ideal bond angles
cyclo p ro p a n e

cu b a n e
H

H
C

H

H
1 0 9 .5 °

C

H

H
C

C
H C

C

H

H

58° C

H

H

C
C

H
C
H

cyclo p ro p e n e

C

60°

C
90°

C
H

64°

H

H
H

C

1 0 9 .5 °

H

120°

1 0 9 .5 °

gives rise to strain energy in small rings

→ problems in force fields. More than one atom type
per hybridization needed.
1st Lecture

Modern Methods in Drug Discovery WS10/11

44

Chiral atoms
Further elements showing chirality/stereochemistry
the lone pair behaves like a substituent
H
H

N

H

H
N

Fast exchange at room temperature,
but slow at 77K

H

H

O
P
R2

O

R3

R3

O

O

R2

R1

R1

phosphorus inverts even slower

P

O
S
R2

O
R1

S

O

S
R1

R1

R2

R2

sulfoxides,
sulfinic esters, etc

Furthermore: As, Si, ..., compounds with transition elements,
esp. octahedral metal complexes
1st Lecture

Modern Methods in Drug Discovery WS10/11

45

Isomers
May have different
number and kind
of bonds

Molecules that
have the same
number of atoms

1 stereo center
2 stereo centers

Source: enhanced from wikipedia
Exercise: Which kind of computational method(s) allow(s) to
calculate differences in energy between the respective isomers ?
1st Lecture

Modern Methods in Drug Discovery WS10/11

46

is stereochemistry important ?
chiral drugs
pure
chiral
synthetic 3%
pure
natural
products 28%

achiral or
racemic
natural
products <1%

racemic
synthetic 24%

achiral
synthetic 45%

Data from 1982: Böhm, Klebe & Kubinyi, Wirkstoffdesign
1st Lecture

Modern Methods in Drug Discovery WS10/11

47