1. COMBINATORIAL CHEMISTRY AND DYNAMIC COMBINATORIAL CHEMISTRY Sonya Balduzzi, PhD

2. From DNA To Proteins…

3. Polymer-Supported Peptide Synthesis Merrifield, R. B. J. Am. Chem. Soc. 1963, 85, 2149.

4. Combinatorial Synthesis vs Parallel Synthesis Combinatorial Synthesis  “Split synthesis” method  Each well or reaction vessel contains many types of support- bound compounds  Biological assays are performed with mixtures of compounds  Analysis of compound mixtures requires a deconvolution procedure in order to identify an individual compound of interest Parallel Synthesis  “One-bead-one-compound” method  Each well or reaction vessel contains one type of support-bound compound  Biological assays are performed with individual compounds  Analysis of compounds which are either support-bound or free in solution

5. Polymer-Supported Synthesis

6. Polymeric Resins Resin -the polymeric matrix which forms the solid support and is inert to the reaction conditions employed during library synthesis Resin Types:  Merrifield (chloromethylpolystyrene)  Hydroxymethylpolystyrene  Aminomethylpolystyrene  TentaGel (polystyrene-poly(ethylene glycol) copolymer)  ArgoGel (polystyrene-poly(ethylene glycol) copolymer)  PEGA (poly(ethylene glycol)-polyacrylamide copolymer)

7. Linkers Linker – serves to attach the molecule of interest to the solid support Integral Linkers – the linker is part of the polymeric resin (eg. Merrifield) Nonintegral Linkers – the linker is attached to the polymeric resin in a separate step, typically via ether, amide or C-C connections – provide a more uniform degree of loading of the molecule of interest than integral linkers

8. Electrophilic Linker Cleavage

9. Nucleophilic Linker Cleavage  Nucleophilic addition to linker functionality  Base-catalyzed elimination Richard Morphy, J.; Rankovic, Z.; Rees, D. C. Tetrahedron Lett.1996, 37, 3209.

10. Photolytic Linker Cleavage PiUai, V. N. R. Synthesis 1980, 1-26.

11. Cyclative Linker Cleavage DeWitt, S. H.; Kiely, J. S.; Stankovic, C. J~; Schroeder, M. C.; Cody, D. M. R.; Pavia, M. R. Proc. Natl. Acad Sci. U. S. A. 1993, 90, 6909-6913.

12. Reductive Linker Cleavage Oxidative Linker Cleavage Kobayashi, S.; Hachiya, I.; Yasuda, M. Tetrahedron Lett. 1996,37, 5569. Michels, R.; Kato, M.; Heitz, W. Makromol. Chem. 1976, 177,2311.

13. “Traceless” Linker Plunkett, M. J.; Ellman, J, A. J. Org. Chem. 1997, 62, 2885-2893.

14. “Safety-Catch” Linker Kenner, G. W.; McDermott, J. R.; Sheppard, R. C. Chem. Commun. 1971, 636.

15. Spacer Molecules  Introduced between polymeric resin and linker molecule  Spacers serve to distance the chemistry from the solid support (immobilized catalysts)  Spacers alter both the solubility and swelling properties of the resin (eg. PEG increases the solubility of Merrifield resin in polar organic solvents)  Spacers alter the cleavage properties of the linker Page, P.; Bradley, M.; Walters, I.; Teague, S. J. Org. Chem. 1999, 64, 794.

16. Combinatorial Synthesis vs Parallel Synthesis Combinatorial Synthesis  “Split synthesis” method  Each well or reaction vessel contains many types of support- bound compounds  Biological assays are performed with mixtures of compounds  Analysis of compound mixtures requires a deconvolution procedure in order to identify an individual compound of interest Parallel Synthesis  “One-bead-one-compound” method  Each well or reaction vessel contains one type of support-bound compound  Biological assays are performed with individual compounds  Analysis of compounds which are either support-bound or free in solution

17. Combinatorial Synthesis Parallel Synthesis

18. Deconvolution of Combinatorial Libraries of Compounds The biologically active compound in a mixture of many compounds is determined  Iterative deconvolution method  Positional scanning deconvolution method  Molecular tags

19. Iterative Deconvolution Method  Method developed for analysis of peptide mixtures  The library is resynthesized in a different format  Each well or reaction vessel contains a mixture of compounds that differ at only one position

20. Combinatorial Synthesis Iterative Deconvolution

21. Molecular Tags Ohlmeyer, M. H. J.; Swanson, R. N.; Dillard, L. W.; Reader, J. C.;Asouline, G.; Kobayashi, R.; Wigler, M.; Still, W. C. Sci. U.S.A. 1993, 90, 10922.Proc. Natl. Acad.

22. Diazoketones as Molecular Tags 40 Different diazoketones can be prepared from:  10 different diols  4 different chlorophenols  vanillic acid Encoding requires predictable reactions !

23. Characterization of Compounds On solid support  IR  Enzyme-linked colorimetric assay (for peptides) (Lam, K. S.; Salmon, S. E.; Hersh, E. M.; Hruby, V. J.; Kazmierski, W. M.; Knapp, R. J. Nature 1991, 354, 82) In solution  NMR, MS, IR

24. DYNAMIC COMBINATORIAL CHEMISTRY

25. Static vs Dynamic Combinatorial Chemistry Lehn, J.-M.Chem. Eur. J. 5, 2455–2463 (1999).

26. Dynamic Combinatorial Chemistry Definition  All possible combinations of compounds are generated through reversible connection processes, either covalent or noncovalent (virtual combinatorial library)  Upon introduction of a target molecule (such as a receptor), a binding event can occur between the target and individual compounds  The compound which binds most strongly to the target will be produced in greatest quantity (amplification phenomenon) through changes in the composition of the equilibrium (adaptive phenomenon) Olof Ramström and Jean-Marie Lehn Nature Reviews Drug Discovery 2002, 1, 26

27. Dynamic Combinatorial Chemistry Advantages  DCC provides a more efficient method to produce large quantities of compounds for biological screening since individual members of the virtual combinatorial library are not actually isolated and purified prior to screening  Detection and characterization of compounds is facilitated by an increased signal strength of the strongest binding compound as a result of its amplification  Isolation of “amplified” compounds is facilitated through physical separation of the target-compound complex (dialysis)  The ability to analyze target-bound compounds would eliminate a few synthetic steps

28. Dynamic Combinatorial Chemistry Requirements  Reversible connection processes must occur between components of a library  Reversible connection processes can be covalent or noncovalent  Equilibrium between the components of a library must be reached on the same time scale as the reaction between a target molecule and the components of a library  The components of a library must have similar reactivity in order to attain thermodynamic control

29. Generation of a Virtual Combinatorial Library Casting: Receptor-induced self assembly of a complementary substrate Lehn, J.-M.Chem. Eur. J. 5, 2455–2463 (1999). Molding: Substrate-induced self assembly of a complementary receptor

30. Generation of a Virtual Combinatorial Library - Casting I. Huc, J.-M. Lehn, Proc. Natl. Acad. Sci. USA 1997, 94, 2106

31. Generation of a Virtual Combinatorial Library - Casting I. Huc, J.-M. Lehn, Proc. Natl. Acad. Sci. USA 1997, 94, 2106

32. HPLC Trace of Reaction Mixtures

33. Target-Accelerated Combinatorial Synthesis of Vancomycin Analogues Vancomycin  An antibiotic (last line of defence against gram-positive bacteria) which inhibits bacterial growth by interfering with bacterial cell wall peptidoglycan biosynthesis  Vancomycin forms 5 hydrogen bonds to the terminal Lys- D -Ala- D -Ala residue of bacterial peptidoglycan Nicolaou, K. C.; Hughes, R.; Cho, S. Y.; Winssinger, N.; Smethurst, C.; Labischinski, H.; Endermann, R. Angew. Chem. Int. Ed. 2000, 39, 3823.

34. Dimerization of Vancomycin  Monomer vancomycin bound to a peptide substrate has a greater dimerization constant than free monomeric vancomycin  The dimeric form of vancomycin has greater biological activity than the monomeric form (increased binding affinity to peptidoglycan through extended hydrogen-bonding) Nicolaou, K. C.; Hughes, R.; Cho, S. Y.; Winssinger, N.; Smethurst, C.; Labischinski, H.; Endermann, R. Angew. Chem. Int. Ed. 2000, 39, 3823.

35. Combinatorial Synthesis of Dimeric Vancomycin Analogues

36. Ac 2 - L -Lys- D -Ala- D -Ala

37. Mass Spectrometric Analysis of the Vancomycin Dimer Mixture m = 2, 3,4 C 2 -C 2 C 2 -C 3 C 3 -C 2 C 2 -C 4 C 4 -C 2 C 3 -C 3 C 3 -C 4 C 4 -C 3 C 4 -C 4

38. Correlation Between Biological Activity and Tether Length n = number of atoms between the two nitrogens MIC = minimum inhibition concentration n = 16 corresponds to the C 2 -C 2 homodimer

39. Dynamic Combinatorial Chemistry Limitations  Only reversible reactions can be employed  Equilibrium must be established under reaction conditions in which the target is stable (biological molecules have solvent and pH requirements)  There are limits on the potential size of a combinatorial library since the concentration of all the components must be sufficient for binding to the target