Transcript PowerPoint Presentation - Use of Thiazole in the Synthesis

Peptidomimetic Inhibitors :
An Integrated Synthetic and Theoretical
Approach to their Design
Everardo Macias,
Patrick Tomboc
Eamonn F. Healy,
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Chemistry
Department,
St. Edward’s
University,
Austin TX 78704
Abstract
Peptidomimetics represent a powerful approach to pharmaceutical
treatments based on enzymatically controlled reactions.
Peptidomimetics are simply small organic molecules that serve to
mimic the transition state of the natural substrate and thus serve to
competitively inhibit the enzyme process. We are focusing on the
design and synthesis of inhibitors for the serine protease thrombin.
Thrombin plays a critical role in the formation of insoluble fibrin that
can lead to life threatening medical conditions. Our synthetic scheme
utilizes hydroxy-aldehydes in the synthesis of polypeptide isoteres
for active site inhibition. QSAR studies aid in the understanding of
the steric and hydrophobic requirements of the enzymaticbinding
sites.
Enzyme


Thrombin, a sub-class of the
hydrolyases is a serine
protease that promotes blood
clotting
Thrombin has an active site
consisting of the catalytic
triad: Ser 195, His 57 and Asp
102
Enzyme BindingSite


In addition thrombin
has three binding
sites, labelled as S1,
S2 and S3, that
determine the
strength and
specificity of binding
The lipophilicity of
S3 has been well
determined
Peptidomimetics



Small peptide-like
molecules that mimic
transition state of
substrate and work by
competitive inhibiting
binding of the natural
substrate
Peptide analog must
be stable
Drug must be a
reversible inhibitor of
the enzyme but can be
irreversible if the
enzyme is unique to
the disease
Ph
O
NH
R
N
NH
O
NH2
N
OH
O
NH-Bu
O
MIMI CS
HY DROXY ETHY LAMI NE
I SOTERE
NH
NATURAL PEPTI DE
O
Saquinavir
Project Design



Design a polypeptide S3
isotere based on a
natural thrombin
substrate (Phe-ProArg tripeptide), shown
on the right
Optimize a
generalized scheme
for isotere synthesis
Model the S2 and S3
steric and hydrophobic
requirements
Asp102
S2
His 57
O
Ser 195
N
H2 N
NH
O
O
Gly 216
NH 2
HN
S1
NH
Asp189
Project
S3


Use Quantitative
Structure-Activity
Relationships (QSAR) to
identify optimum R2 and
R3 binding fragments
Synthesize the isotere,
shown in red on the right,
designed to mimic the
serine-195 mediated
transition state
Asp102
S2
His 57
R3
R2
N
OH
Ser 195
NH
H2 N
NH
O
O
R1
Gly 216
S1
Asp189
NH2
NH2
R
NR2
O
R
H
OH
OH
g ener ali zed isotere
NH2
NH2
ami no
acid
Retrosynthesis &
Synthesis
N
H
OH
R
R
Br
S
O
O
1. BuLi
2. Me3SiCl
NH2
NH2
OH
N
H
[H]
+
R
R
Me3Si
O
O
S
2-TST
Me
NH2
2. NaBH 4
R
NH2
1. CF3SO3Me
N
N
R
S
S
OH
OH
CuCl2
NH2
NH2
O
NaBH3CN
+
R
HNR2
R
NR2
H
OH
OH
Results
1.
N
Br
2. Me 3 SiCl
S
YIELD
N
1. BuLi
3100 cm-1, sharp; 2950 cm-1 ; 1610 cm -1, weak
IR
Me 3 Si
S
>70%
NMR
d 7.7-7.8, multiplet, 2H ; d 0.4, singlet, 9H
2-TST
2.
R
N
H
+ 2-TST
Bu4 NF
CH 2 Cl 2
YIELD
R
S
O
OH
R = CH 3
R = CH 3
IR
NMR d 7.8-7.9, multiplet, 2H ;d 3.6,multiplet,1H
d 1.2-1.5, multiplet, 4H
3.
1. CF3 SO 3 Me
N
2. NaBH 4
R
S
OH
R = CH 3
O
YIELD
R
H
3. CuCl 2
OH
R = CH 3
IR
NMR
Structure-Activity Results from Ref 2
R3
R2
Ki (nm)
CH3
benzyl (S)
17
CH3
phenethyl (R)
550
CH3
phenethyl (S)
235
CH3
phenylpropyl (R)
100
CH3
phenylpropyl (S)
4
H
benzyl (R)
1112
H
benzyl (S)
8
S3
S2
R2
S
O
N
X
R3
NH
O
O
NH 2
HN
S1
NH
QSAR
Quantitative structure-activity relationships (QSAR) represent an
attempt to correlate structural or property descriptors of compounds
with their activities. These physicochemical descriptors, including
parameters describing hydrophobicity, topology, electronic effects
and steric effects, can be determined empirically or by computational
methods. Once a correlation between structure and activity/property
is found, new compounds can be screened to select those with the
desired properties. Activities in which QSAR has found wide
application include biological assays, chemical measurements,
environmental risk assessment and de novo drug design.
QSAR Methodology
Linear regression analysis of the predicted versus observed
activity/property is most commonly used to develop the QSAR
relationship. The higher the r2 value the better the fit. The technique
of leave-one-out cross-validation, quantified as rCV, is used to assess
the predictive power of the QSAR model.
Two parameters, molecular connectivity and valence connectivity,
developed by Kier and Hall were used extensively in this study.
While these are fundamentally topological parameters they have
been shown to contain electronic as well as structural information.
Connectivity Indices
Results
Preliminary results, summarized by the plot of
the predicted (y-axis) versus experimental (xaxis) binding constants, clearly show that a
functional predictive model of the steric and
electronic requirements of the S2 and S3
binding sites can be constructed. Initial results
seem to indicate the energetic descriptors are
more useful as predictors than simple
topological properties. This work continues.
chemical sample
connecti
vity
index 0
log P
energy
steric
(kcal/mo
molar
refracti
vity
Results
Binding
Constant
Ki (nM)
(S)CH3-benzyl-BenzoThia
zole(S)
(R)CH3-phenylethl-BenzoT
hiazole
(R)CH3-phenylpropyl-Thia
23.001
2.901
10.201
131.883
18.000
23.709
3.001
22.865
136.599
550.000
21.847
2.610
40.858
125.072
100.000
(S)CH3-phenylpropyl-Thia
21.847
2.610
35.824
125.072
(R)CH3-3Fquin-Thiazole
26.372
3.188
29.088
135.393
150.000
(S)CH3-3Fquin-BenzoThia
zole(S)
(S)CH3-3Fquin-Thiazole
28.941
4.272
21.630
151.406
18.000
26.372
3.188
30.545
135.393
10.000
(S)CH3-benzyl-Thiazole2(
S)
20.433
1.817
23.388
115.870
16.000
6.000
Graph 3. Ki-QSAR-W/O-Outlier3
F = -47.976*B - 1605.799*C + 13.368*D
+ 123.102*E - 10621.018 r^2 = 0.925
rCV^2 = 0.119
F = -47.976*B - 160
F = -47.976*B - 1605.799*C + 13.368*D + 123.102*E - 10621.018
-10.954
600
r^2 = 0.925 rCV^2 = 0.119
544.609
83.202
15.910
400
50.041
300
58.192
200
69.520
2
500
1
2
3
4
5
6
7
8
(S)CH3-benzy l-Be
(R)CH3-pheny leth
(R)CH3-pheny lpro
(S)CH3-pheny lpro
(R)CH3-3Fquin-Th
(S)CH3-3Fquin-Be
(S)CH3-3Fquin-Th
(S)CH3-benzy l-Th
100
57.480
78
6
4
1
0
-100
-100
0
3
100
5
200 300 400
500 600
Binding Constant Ki (nM)
F = -47.976*B - 1605.799*C + 13.368*D + 123.102*E - 10621.018
r^2 =
chemical sample
connecti
vity
index 0
log P
energy
steric
(kcal/mo
molar
refracti
vity
Binding
Constant
Ki (nM)
(S)CH3-benzyl-BenzoThia
zole(S)
(R)CH3-phenylethl-BenzoT
hiazole
(S)CH3-phenylethl-BenzoT
hiaz.58
(R)CH3-phenylpropyl-Thia
23.001
2.901
10.201
131.883
18.000
23.709
3.001
22.865
136.599
550.000
23.709
3.001
23.749
136.599
235.000
21.847
2.610
40.858
125.072
100.000
(S)CH3-phenylpropyl-Thia
21.847
2.610
35.824
125.072
(R)CH3-3Fquin-Thiazole
26.372
3.188
29.088
135.393
150.000
(S)CH3-3Fquin-BenzoThia
zole(S)
(S)CH3-3Fquin-Thiazole
28.941
4.272
21.630
151.406
18.000
26.372
3.188
30.545
135.393
10.000
(S)CH3-benzyl-Thiazole2(
S)
20.433
1.817
23.388
115.870
16.000
Results
6.000
Graph 2. Ki-QSAR-all
F = -29.160*B - 1116.702*C + 9.582*D
+ 84.612*E - 7350.105 r^2 = 0.731
rCV^2 = -0.247
F = -29.160*B - 1116.702*C + 9.58
-3.367- 1116.702*C + 9.582*D + 84.612*E - 7350.105 r^2 = 0.731 rCV^2 = -0.247
F = -29.160*B
500
384.872
393.343
400
3
72.782
24.551
55.110
53.507
300
200
100
69.072
53.128
2
897
5
1
0
-100
-100
0
4
100
1
2
3
4
5
6
7
8
9
(S)CH3-benzy l-BenzoThiazole(S)
(R)CH3-pheny lethl-BenzoThiazole
(S)CH3-pheny lethl-BenzoThiaz.58
(R)CH3-pheny lpropy l-Thia
(S)CH3-pheny lpropy l-Thia
(R)CH3-3Fquin-Thiazole
(S)CH3-3Fquin-BenzoThiazole(S)
(S)CH3-3Fquin-Thiazole
(S)CH3-benzy l-Thiazole2(S)
6
200 300 400 500 600
Binding Constant Ki (nM)
F = -29.160*B - 1116.702*C + 9.582*D + 84.612*E - 7350.105 r^2 = 0.731 rCV^2 = -0.2
References


Alessandro Dondoni, et al.; Synthesis of TSTs and
Reactions with Carbonyl Compounds; J. Org. Chem.
1988, 53, 1748-1761
Benoit Bachand , et al.; Synthesis and StructureReactivity of Potent Bicyclic Lactam Thrombin
Inhibitors; Bioinorg. & Med. Chem. 1999, 9, 913-918
Acknowledgements

We gratefully acknowledge the support of the Welch
Foundation in the form of a Departmental Research Grant