Protein-Directed Dynamic Combinatorial Chemistry

Dynamic Combinatorial Chemistry: In Drug Discovery, Bioorganic Chemistry, and Materials Science

Volumn , Issue , 2009, Pages 43-82

  Greaney, Michael F ^a   Bhat, Venugopal T ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Disulfide bond formation powerful reaction for dynamic system construction; Enzymes to catalyze reversible reactions effective strategy for DCC; Protein directed dynamic combinatorial chemistry (DCLs)

Indexed keywords

EID: 84889464013     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470551554.ch2     Document Type: Chapter

References (51)

1. Huc, I.; Lehn, J.-M. Virtual combinatorial libraries: Dynamic generation of molecular and supramolecular diversity by self-assembly. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 2106-2110.
2. Corbett, P. T.; Leclaire, J.; Vial, L.; West, K. R.; Wietor, J.-L.; Sanders, J. K. M.; Otto, S. Dynamic combinatorial chemistry. Chem. Rev. 2006, 106, 3652-3711.
3. Otto, S.; Furlan, R. L. E.; Sanders, J. K. M. Recent developments in dynamic combinatorial chemistry. Curr. Opin. Chem. Biol. 2002, 6, 321-327.
4. Ramström, O.; Lehn, J.-M. Drug discovery by dynamic combinatorial libraries. Nat. Rev. Drug Discov. 2002, 1, 26-36.
5. Otto, S.; Furlan, R. L. E.; Sanders, J. K. M. Dynamic combinatorial chemistry. Drug Discov. Today 2002, 7, 117-125.
6. Karan, C.; Miller, B. L. Dynamic diversity in drug discovery: Putting small-molecule evolution to work. Drug Discov. Today 2000, 5, 67-75.
7. Lehn, J.-M. Dynamic combinatorial chemistry and virtual combinatorial libraries. Chem. Eur. J. 1999, 3, 2455-2463.
8. Bunyapaiboonsri, T.; Ramström, O.; Lohmann, S.; Lehn, J.-M.; Peng, L.; Goeldner, M. Dynamic deconvolution of a pre-equilibrated dynamic combinatorial library of acetylcholinesterase inhibitors. Chembiochem 2001, 2, 438-444.
9. Cousins, G. R. L.; Poulsen, S.-A.; Sanders, J. K. M. Dynamic combinatorial libraries of pseudo-peptide hydrazone macrocycles. Chem. Commun. 1999, 1575-1576.
10. Bunyapaiboonsri, T.; Ramström, H.; Ramström, O.; Haiech, J.; Lehn, J.-M. Generation of bis-cationic heterocyclic inhibitors of Bacillus subti-lis HPr kinase/phosphatase from a ditopic dynamic combinatorial library. J. Med. Chem. 2003, 46, 5803-5811.
11. Hochgürtel, M.; Kroth, H.; Piecha, D.; Hofmann, M. W.; Nicolau, C.; Krause, S.; Schaaf, O.; Sonnenmoser, G.; Eliseev, A. V. Target-induced formation of neuraminidase inhibitors from in vitro virtual combinatorial libraries. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 3382-3387.
12. Hochgürtel, M.; Biesinger, R.; Kroth, H.; Piecha, D.; Hofmann, M. W.; Krause, S.; Schaaf, O.; Nicolau, C.; Eliseev, A. V. Ketones as building blocks for dynamic combinatorial libraries: Highly active neuraminidase inhibitors generated via selection pressure of the biological target. J. Med. Chem. 2003, 46, 356-358.
13. Zameo, S.; Vauzeilles, B.; Beau, J.-M. Dynamic combinatorial chemistry: Lysozyme selects an aromatic motif that mimics a carbohydrate residue. Angew. Chem. Int. Ed. 2005, 44, 965-969.
14. Zameo, S.; Vauzeilles, B.; Beau, J.-M. Direct composition analysis of a dynamic library of imines in an aqueous medium. Eur. J. Org. Chem. 2006, 5441-5444.
15. Valade, A.; Urban, D.; Beau, J.-M. Target-assisted selection of galactosyltransferase binders from dynamic combinatorial libraries. An unexpected solution with restricted amounts of the enzyme. Chembiochem 2006, 7, 1023-1027.
16. Valade, A.; Urban, D.; Beau, J.-M. Two galactosyltransferases' selection of different binders from the same uridine-based dynamic combinatorial library. J. Comb. Chem. 2007, 9, 1-4.
17. Congreve, M. S.; Davis, D. J.; Devine, L.; Granata, C.; O'Reilly, M.; Wyatt, P. G.; Jhoti, H. Detection of ligands from a dynamic combinatorial library by X-ray crystallography. Angew. Chem. Int. Ed. 2003, 42, 4479-4482.
18. Katz, B. A.; Finer-Moore, J.; Mortezaei, R.; Rich, D. H.; Stroud, R. M. Episelection: Novel K approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface. Biochemistry 1995, 34, 8264-8280.
19. Hioki, H.; Still, W. C. Chemical evolution: A model system that selects and amplifies a receptor for the tripeptide (D)Pro(L)Val(D)Val. J. Org. Chem. 1998, 63, 904-905.
20. Otto, S.; Furlan, R. L. E.; Sanders, J. K. M. Dynamic combinatorial libraries of macrocyclic disulfides in water. J. Am. Chem. Soc. 2000, 122, 12063-12064.
21. Ramström, O.; Lehn, J.-M. In situ generation and screening of a dynamic combinatorial carbohydrate library against concanavalin A. Chembiochem 2000, 1, 41-48.
22. Ramström, O.; Lohmann, S.; Bunyapaiboonsri, T.; Lehn, J.-M. Dynamic combinatorial carbohydrate libraries: Probing the binding site of the conca-navalin A lectin. Chem. Eur. J. 2004, 10, 1711-1715.
23. Milanesi, L.; Hunter, C. A.; Sedelnikova, S. E.; Waltho, J. P. Amplification of bifunctional ligands for calmodulin from a dynamic combinatorial library. Chem. Eur. J. 2006, 12, 1081-1087.
24. Danieli, B.; Giardini, A.; Lesma, G.; Passarella, D.; Peretto, B.; Sacchetti, A.; Silvani, A.; Pratesi, G.; Zunino, F. Thiocolchicine-podophyllotoxin conjugates: Dynamic libraries based on disulfide exchange reaction. J. Org. Chem. 2006, 71, 2848-2853.
25. Erlanson, D. A.; Ballinger, M. D.; Wells, J. A. In Fragment-based approaches in drug discovery. In: Jahnke, W.; Erlanson, D. A. editors. Wiley-VCH, Weinheim, Tethering, 285-308.
26. Braisted, A. C.; Oslob, J. D.; Delano, W. L.; Hyde, J.; McDowell, R. S.; Waal, N.; Yu, C.; Arkin, M. R.; Raimundo, B. C. Discovery of a potent small molecule IL-2 inhibitor through fragment assembly. J. Am. Chem. Soc. 2003, 125, 3714-3715.
27. Erlanson, D. A.; Lam, J. W.; Wiesmann, C.; Luong, T. N.; Simmons, R. L.; Delano, W. L.; Choong, I. C.; Burdett, M. T.; Flanagan, W. M.; Lee, D.; Gordon, E. M.; O'Brien, T. O. In situ assembly of enzyme inhibitors using extended tethering. Nat. Biotechnol. 2003, 21, 308-314.
28. Hardy, J. A.; Lam, J.; Nguyen, J. T.; O'Brien, T.; Wells, J. A. Discovery of an allosteric site in the caspases. Proc. Nat. Acad. Sci. U.S.A. 2004, 101, 12461-12466.
29. Buck, E.; Bourne, H.; Wells, J. A. Site-specific disulfide capture of agonist and antagonist peptides on the C5a receptor. J. Biol. Chem. 2005, 280, 4009-4012.
30. Buck, E. ; Wells, J. A. Disulfide trapping to localize small-molecule agonists and antagonists for a G protein-coupled receptor. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2719-2724.
31. Erlanson, D. A.; Braisted, A. C.; Raphael, D. R.; Randal, M.; Stroud, R. M.; Gordon, E. M.; Wells, J. A. Site-directed ligand discovery. Proc. Nat. Acad. Sci. U.S.A. 2000, 97, 9367-9372.
32. Swann, P. G.; Casanova, R. A.; Desai, A.; Frauenhoff, M. M.; Urbancic, M.; Slomczynska, U.; Hopfinger, A. J.; Le Breton, G. C.; Venton, D. L. Nonspecific protease-catalyzed hydrolysis/synthesis of a mixture of peptides: Product diversity and ligand amplification by a molecular trap. Biopolymers 1997, 40, 617-625.
33. I?-catalyzed transamidation of tertiary amides. J. Am. Chem. Soc. 2008, 130, 647-654.
34. Eldred, S. E.; Stone, D. A.; Gellman, S. H.; Stahl, S. S. Catalytic transamidation under moderate conditions. J. Am. Chem. Soc. 2003, 125, 3422-3423.
35. Bell, C. M.; Kissounko, D. A.; Gellman, S. H.; Stahl, S. S. Catalytic metathesis of simple secondary amides. Angew. Chem. Int. Ed. 2007, 46, 761-763.
36. Lins, R. J.; Flitsch, S. L.; Turner, N. J.; Irving, E.; Brown, S. A. Enzymatic generation and in situ screening of a dynamic combinatorial library of sialic acid analogues. Angew. Chem. Int. Ed. 2002, 41, 3405-3407.
37. Lins, R. J.; Flitsch, S. L.; Turner, N. J.; Irving, E.; Brown, S. A. Generation of a dynamic combinatorial library using sialic acid aldolase and in situ screening against wheat germ agglutinin. Tetrahedron 2004, 60, 771-780.
38. Cheeseman, J.D.;Corbett, A.D.;Shu, R.;Croteau, J.;Gleason, J.L.;Kazlauskas, R. J. Amplification of screening sensitivity through selective destruction: Theory and screening of a library of carbonic anhydrase inhibitors. J. Am. Chem. Soc. 2002, 124, 5692-5701.
39. Corbett, A. D. ; Cheeseman, J. D. ; Kazlauskas, R. J. ; Gleason, J. L. Pseudodynamic combinatorial libraries: A receptor-assisted approach for drug discovery. Angew. Chem. Int. Ed. 2004, 43, 2432-2436.
40. Eliseev, A. V.; Nelen, M. I. Use of molecular recognition to drive chemical evolution. 1. Controlling the composition of an equilibrating mixture of simple arginine receptors. J. Am. Chem. Soc. 1997, 119, 1147-1148.
41. Eliseev, A. V.; Nelen, M. I. Use of molecular recognition to drive chemical evolution. 2. Mechanisms of an automated genetic algorithm implementation. Chem. Eur. J. 1998, 4, 825-834.
42. Nicolaou, K. C.; Hughes, R.; Cho, S. K.; Winssinger, N.; Smethurst, C.; Labischinski, H.; Endermann, R. Angew. Chem. Int. Ed. 2000, 39, 3823-3828.
43. Giger, T.; Wigger, M.; Audétat, S.; Benner, S. A. Libraries for receptor-assisted combinatorial synthesis (RACS). The olefin metathesis reaction. Synlett 1998, 688-691.
44. Poulsen, S.-A.; Bornaghi, L. F. Fragment-based drug discovery of carbonic anhydrase II inhibitors by dynamic combinatorial chemistry utilizing alkene cross metathesis. Bioorg. Med. Chem. 2006, 14, 3275-3284.
45. Jordan, J. P.; Grubbs, R. H. Small-molecule N-heterocyclic-carbene-containing olefin-metathesis catalysts for use in water. Angew. Chem. Int. Ed. 2007, 46, 5152-5155.
46. Shi, B.; Greaney, M. F. Reversible Michael addition of thiols as a new tool for dynamic combinatorial chemistry. Chem. Commun. 2005, 886-888.
47. Shi, B.; Stevenson, R.; Campopiano, D. J.; Greaney, M. F. Discovery of glutathione S-transferase inhibitors using dynamic combinatorial chemistry. J. Am. Chem. Soc. 2006, 128, 8459-8467.
48. van Bladeren, P. J. Glutathione conjugation as a bioactivation reaction. Chem. Biol. Int. 2000, 129, 61-76.
49. Sakai, S.; Shigemasa, Y.; Sasaki, T. A self-adjusting carbohydrate ligand for GalNAc specific lectins. Tetrahedron Lett. 1997, 38, 8145-8148.
50. Sakai, S.; Shigemasa, Y.; Sasaki, T. Iron(II)-assisted assembly of trivalent GalNAc clusters and their interactions with GalNAc-specific lectins. Bull. Chem. Soc. Jpn. 1999, 72, 1313-1319.
51. Goral, V.; Nelen, M. I.; Eliseev, A. V.; Lehn, J.-M. Double-level "orthogonal" dynamic combinatorial libraries on transition metal template. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 1347-1352.