The Origin of Diazonamide

Transcript The Origin of Diazonamide

Diazonamide A: The Long Story of a Misunderstood Molecule

Seminar presented by Elisia Villemure February 14, 2008 1

The Origin of Diazonamide

 Isolated from the colonial ascidian

Diazona angulata

 Collected from the ceilings of caves along the northwest coast of Siquijor Island in the Philippines Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 2

Why Is this Molecule So Interesting?

Over the years, many groups focused their efforts towards the synthesis of Diazonamide A. Only K. C. Nicolaou’s and P. G. Harran’s groups had been able to complete the total synthesis of the molecule.

Initially proposed structure

 Diazonamide A has a IC 50 of 2-5 nM against 4 human cancer cell lines (Diazonamide A is more potent than Diazonamide B)  Molecule is trapped as a single atropisomer because of its rigidity  Macrolactam unit  Macrocyclic Heterocyclic core  Quaternary center at the center of the molecule Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 3

Structure Determination of Diazonamide A and B

Structures determined by William Fenical (Scripps Institution of Oceanography) And Jon Clardy (Cornell University) in 1991 Diazonamide A Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 Diazonamide B 4

Strategy for Structure Elucidation

Jaspars, M Nat. Prod. Rep. 1999 , 16, 241 Pretsch, E.; Toth, G.; Munk, M. E. ; Baddertscher, M.

Computer-Aided Structure Elucidation

, Wiley-VCH

2002

, 279 p.

Evidence of the Presence of an Hemiacetal in Diazonamide A and B

Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 6

Evidence on the Structure of Diazonamide A and B

Diazonamide A Diazonamide B

Similarity in the 2 structures

 1 H, 13 C NMR, UV and IR indicate an identical polycyclic nucleus  UV shows evidence of their high degree of unsaturation Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 7

Evidences on the Structure of Diazonamide A and B

Diazonamide A Diazonamide B MS (M + H – H 2 O): C 40 H 35 N 6 O 6 Cl 2  + 5 Carbons  + 11 Hydrogens  + 1 Nitrogen  + 1 Oxygen C 35  H 24 N 5 O 5 Cl 2 Br + 1 Bromine

An valine extra residue fits the differences in the molecular formula and coincides with NMR assignment

Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 8

Crystal Structure of Diazonamide B

Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 9

First Synthesis by Harran’s Group

In 2001, P. G. Harran published the first synthesis of ‘’Diazonamide A’’.

Spectroscopic data didn’t match the natural product assignment!!!

24 step synthesis

Revision of the structure is proposed!

Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4765 10

Structural Misassignment in Literature

A search in the literature between January 1990 to April 2004 revealed 300 structural revisions of natural products Kinamycin C: (+)-tolyporphin A: Wiedemannic Acid Sauer, E., Barriault, L. Org. Lett. 2004 , 19, 3329 Nicolaou, K. C. Angew. Chem., Int. Ed. 2005 , 44, 1012 11

Diazonamide Structure Revision

In 2001, P. G. Haran’s group published the structure revision of Diazonamide Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770 12

X-Ray Crystallography

Scattered X-Ray Incident X-Ray X-Ray generator Electron cloud Crystal Atom Nucleus Diffraction pattern 

Every atom scatters X-Ray differently depending on its size



Hydrogen atoms are almost invisible in X-Ray

Clegg, W.; Blake, A.J.; Gould, R.O.; Main, P.

Crystal Structure Analysis Principles and Practice

, Oxford Science Publication

2001

, 265p.

Massa, W.

Crystal Structure Determination

, Spinger

2004

, 210 p.

X-Ray X-Ray Crystallography Phasing Fitting Crystal Diffraction patterns Electron density map

1- The crystal is mounted in the X-Ray beam and rotated 2- The crystal is irradiated by X-Ray (typical wavelength: 1 Å (0.1 nm)) 3- Multiple diffraction patterns are obtained 4- Phasing :2D images are converted into a 3D model of the density of electrons by mathematic calculations 5- Fitting: Electron density map is converted into a atomic model

Atomic model

Clegg, W.; Blake, A.J.; Gould, R.O.; Main, P.

Crystal Structure Analysis Principles and Practice

, Oxford Science Publication

2001

, 265p.

Massa, W.

Crystal Structure Determination

, Spinger

2004

, 210 p.

X-Ray X-Ray Crystallography Phasing Fitting Crystal Diffraction patterns Electron density map Atomic model Thermal ellipsoids atomic model:

 Represents the probability of finding the electrons around the atom as it vibrates.

 High probability = More precise atomic model = Smaller ellipsoids Thermal ellipsoids size:

Debye-Waller factor (B-factor):

-Accounting for the thermal motion of the atom - Numeric representation of the size of the ellipsoid Clegg, W.; Blake, A.J.; Gould, R.O.; Main, P.

Crystal Structure Analysis Principles and Practice

, Oxford Science Publication

2001

, 265p.

Massa, W.

Crystal Structure Determination

, Spinger

2004

, 210 p.

X-Ray Crystallography



Collected information

 Structure in the space  Stereochemistry  Bond lengths  Bond angles Debye-Waller factor (B-factor) Clegg, W.; Blake, A.J.; Gould, R.O.; Main, P.

Crystal Structure Analysis Principles and Practice

, Oxford Science Publication

2001

, 265p.

Massa, W.

Crystal Structure Determination

, Spinger

2004

, 210 p.

Diazonamide Structure Revision

C8 (4.33) C7 (4.49) C10 (4.83) C12 (4.83) C17 (4.53) O2 (5.46) C11 (5.13) O3 (7.42) Natural Diazonamide bicyclic core Typical C –O bond distances: 1.353-1.409 Å Typical C –N bond distances: 1.365-1.411 Å C7 –O2 bond length: 1.371 Å C17 –O3 bond length: 1.433 Å Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770 17

Diazonamide Structure Revision

C8 (4.33) C7 (4.49) C10 (4.83) C12 (4.83) C17 (4.53) O2 (5.46) C11 (5.13) O3 (7.42) Natural Diazonamide bicyclic core  O3 has a large thermal motion compared with O2  X-Ray analysis of the synthetic Diazonamide B B (eq) : O2 = 6.00 Å 2 O3 = 5.35 Å 2

The bond length and the B-factor are consistent the hypothesis of O3 being a Nitrogen

Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770 18

Diazonamide Structure Revision

C8 (4.33) C7 (4.49) C10 (4.83) C12 (4.83) C17 (4.53) O2 (5.46) C11 (5.13) O3 (7.42) Natural Diazonamide bicyclic core In X-Ray, the scattering power of an atom is proportional to its atomic number. Neighboring atoms in the periodic table differ slightly from one another, like O and N Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770 19

Comparison of the Assignments

Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770 20

Diazonamide Structure Revision

To be consistent with the molecular formula, C 40 H 35 N 6 O 6 Cl 2 , one oxygen atom is missing and there is one extra nitrogen 5 oxygens 7 nitrogens 21 Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770

Diazonamide Structure Revision

Acid digests of diazonamide A do not produce valine, but indicates the presence of two isopropyl groups  N7 protons are reported as a sharp one-proton doublet  C37 resonates at 76,9 ppm. Considerably downfield for a typical valine (~62 ppm)

These observations are consistent with C37 substituent being an alcohol rather than an amine

Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770 22

Diazonamide Structure Revision

Dehydrated form of the originally proposed structure Compound Natural diazonamide A GI 50 (nM) 8 C37-

16 C37-

Growth inhibition determined for human adenocacinoma OVCAR-3

191 Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 470 23

Find the differences!

Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12888 Nicolaou, K. C. Angew. Chem., Int. Ed. 2002 , 41, 3495 Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770

Later validated by total synthesis

Diazonamide A Timeline Discovery

Fenical, W.; Clardy, J. J. Am. Chem. Soc. 1991 , 113, 2303 Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4765 Harran, P. G. Angew. Chem., Int. Ed. 2001 , 40, 4770 Nicolaou, K. C. Angew. Chem., Int. Ed. 2002 , 41, 3495 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12888 Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 Harran, P. G. Angew. Chem., Int. Ed. 2003 , 42, 4961 25

Nicolaou’s Synthetic Strategy

Formation of the Heterocyclic core Macrolactamization Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 26

Retrosynthetic Analysis of Diazonamide A

Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 27

Retrosynthetic Analysis of Diazonamide A

Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 28

Retrosynthetic Analysis of Diazonamide A

Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 29

Synthesis of Indole-Oxazole Building Block

Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 10162 Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 30

Synthesis of Indole-Oxazole Building Block

Li, J. J.

Name Reactions in Heterocyclic Chemistry

, Wiley-Interscience

2005

, 557p.

Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 31

Synthesis of Indole-Oxazole Building Block

Miyaura, N. J. Org. Chem. 1995 , 60, 7508 Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 32

Synthesis of the Aryl Bromide Coupling Partner

Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 33

Synthesis of the Aryl Bromide Coupling Partner

Padwa, A. J. Am Chem. Soc. 1975 , 97, 1837 Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 34

Synthesis of the Aryl Bromide Coupling Partner

Nicolaou, K. C. Angew. Chem., Int. Ed. 2003 , 42, 1753 Nicolaou, K. C. J. Am. Chem. Soc. 2004 , 126, 12897 35