Dynamic template-assisted strategies in fragment-based drug discovery

Trends in Biotechnology

Volumn 27, Issue 9, 2009, Pages 512-521

  Schmidt, Marco F ^a,b   Rademann, Jörg ^a,b  

^a LEIBNIZ INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG DISCOVERY; DRUG DISCOVERY PROCESS; DRUG LEADS; DYNAMIC SCREENING; DYNAMIC TEMPLATES; FRAGMENT DETECTION; FRAGMENT-BASED METHODS; HIGH-AFFINITY BINDERS; HIGH-THROUGHPUT SCREENING; LIGAND ASSEMBLIES; ON DYNAMICS; PROTEIN TARGETS;

BINDERS;

LIGANDS;

ENZYME INHIBITOR; PROTEINASE INHIBITOR; SEVERE ACUTE RESPIRATORY SYNDROME VACCINE;

BINDING AFFINITY; COMBINATORIAL CHEMISTRY; DRUG INDUSTRY; DRUG MANUFACTURE; DRUG RESEARCH; DRUG SCREENING; DRUG STRUCTURE; DRUG SYNTHESIS; DRUG TARGETING; ENZYME SUBSTRATE; FRAGMENTATION REACTION; HIGH THROUGHPUT SCREENING; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN TARGETING; REVIEW; STRUCTURE ANALYSIS;

DRUG DISCOVERY; DRUG EVALUATION, PRECLINICAL; HUMANS; LIGANDS; PROTEIN BINDING; PROTEINS;

EID: 68749088518     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2009.06.001     Document Type: Review

References (55)

1. Schreiber S.L. Small molecules: the missing link in the central dogma. Nat. Chem. Biol. 1 (2005) 64-66
2. Drews J. Strategic trends in the drug industry. Drug Discov. Today 8 (2003) 411-420
3. Drews J. Innovation deficit revisited: reflections on the productivity of pharmaceutical R&D. Drug Discov. Today 3 (1998) 491-494
4. Drews J., and Ryser S. The role of innovation in drug development. Nat. Biotechnol. 15 (1997) 1318-1319
5. Brown D. Future pathways for combinatorial chemistry. Mol. Divers. 2 (1996) 217-222
6. Jencks W.P. On the attribution and additivity of binding energies. Proc. Natl. Acad. Sci. U. S. A. 78 (1981) 4046-4050
7. Fink T., et al. Virtual exploration of the small-molecule chemical universe below 160 daltons. Angew. Chem. Int. Ed. 44 (2005) 1504-1508
8. Bohacek R.S., et al. The art and practice of structure-based drug design: a molecular modeling perspective. Med. Res. Rev. 16 (1996) 3-50
9. Hann M.M., and Opera T.I. Pursuing the lead likeness concept in pharmaceutical research. Curr. Opin. Chem. Biol. 8 (2004) 255-263
10. Andrews P.R., et al. Functional group contributions to drug-receptor interactions. J. Med. Chem. 27 (1984) 1648-1657
11. Hopkins A.L., et al. Ligand efficiency: a useful metric for lead selection. Drug Discov. Today 9 (2004) 430-431
12. Kuntz I.D., et al. The maximal affinity of ligands. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 9997-10002
13. Hajduk P.J., and Greer J. A decade of fragment-based drug design: strategic advances and lessons learned. Nat. Rev. Drug Discov. 6 (2007) 211-219
14. Shuker S.B., et al. Discovery high-affinity ligands for proteins: SAR by NMR. Science 274 (1996) 1531-1534
15. Nienaber V.L., et al. Discovering novel ligands for macromolecules using X-ray crystallographic screening. Nat. Biotechnol. 18 (2000) 1105-1108
16. Blundell T.L., et al. High-throughput crystallography for lead discovery in drug design. Nat. Rev. Drug Discov. 1 (2002) 45-54
17. Blundell T.L., and Patel S. High-throughput X-ray crystallography for drug discovery. Curr. Opin. Pharmacol. 4 (2004) 490-496
18. Neumann T., et al. SPR-based fragment screening: advantages and applications. Curr. Top. Med. Chem. 7 (2007) 1630-1642
19. Freire E. Isothermal titration calorimetry: controlling binding forces in lead optimization. Drug Discov. Today Technol. 1 (2004) 295-299
20. Ciulli A., et al. Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate. ChemBioChem 9 (2008) 2606-2611
21. Whitty A. Cooperativity and biological complexity. Nat. Chem. Biol. 4 (2008) 435-439
22. Huc I., and Lehn J.-M. Virtual combinatorial libraries: dynamic generation of molecular and supramolecular diversity by self-assembly. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 2106-2110
23. Lehn J.-M. Dynamic combinatorial chemistry and virtual libraries. Chem. Eur. J. 5 (1999) 2455-2463
24. Corbett P.T., et al. Dynamic combinatorial chemistry. Chem. Rev. 106 (2006) 3652-3711
25. Erlanson D.A., et al. Tethering: fragment-based drug discovery. Annu. Rev. Biophys. Biomol. Struct. 33 (2004) 199-223
26. Erlanson D.A., et al. Site-directed ligand discovery. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 9367-9372
27. Erlanson D.A., et al. In situ assembly of enzyme inhibitors using extended tethering. Nat. Biotechnol. 21 (2003) 308-314
28. Cancilla M.T., et al. Discovery of an Aurora kinase inhibitor through site-specific dynamic combinatorial chemistry. Bioorg. Med. Chem. Lett. 18 (2008) 3978-3981
29. Vongvilai P., et al. Dynamic combinatorial resolution: direct asymmetric lipase-mediated screening of a dynamic nitroaldol library. Angew. Chem. Int. Ed. 46 (2007) 948-950
30. Angelin M., et al. Tandem driven dynamic combinatorial resolution via Henry-iminolactone rearrangement. Chem. Commun. (2008) 768-770
31. Maly D.J., et al. Combinatorial target-guided ligand assembly: identification of potent subtype-selective c-Src inhibitors. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 2419-2424
32. Corbett A.D., et al. Pseudodynamic combinatorial libraries: a receptor-assisted approach for drug discovery. Angew. Chem. Int. Ed. 43 (2004) 2432-2436
33. Cheeseman J.D., et al. Amplification of screening sensitivity through selective destruction: theory and screening of a library of carbonic anhydrase inhibitors. J. Am. Chem. Soc. 124 (2002) 5693-5701
34. Corbett A.D., and Gleason J.L. Preparation of active esters on solid support for aqueous-phase peptide coupling. Tetrahedron Lett. 43 (2002) 1369-1372
35. Angelin M., et al. Crystallization-induced secondary selection from a tandem driven dynamic combinatorial resolution process. J. Org. Chem. 73 (2008) 3593-3595
36. Nicolaou K.C., et al. Target-accelerated combinatorial synthesis and discovery of highly potent antibiotics effective against vancomycin-resistant bacteria. Angew. Chem. Int. Ed. 39 (2000) 3823-3828
37. Hu X., et al. Bcl-XL-templated assembly of its own protein-protein interaction modulator from fragments decorated with thio acids and sulfonyl azides. J. Am. Chem. Soc. 130 (2008) 13820-13821
38. Nguyen R., and Huc I. Using an enzyme's active site to template inhibitors. Angew. Chem. Int. Ed. 40 (2001) 1774-1776
39. Bourne Y., et al. Freeze-frame inhibitor captures acetylcholinesterase in a unique conformation. Proc. Natl. Acad. Sci. U. S. A. 101 (2003) 1449-1454
40. Whiting M., et al. Inhibitors of HIV-1 protease by using in situ click chemistry. Angew. Chem. Int. Ed. 45 (2006) 1435-1439
41. Patterson A.W., et al. Substrate activity screening (SAS): a general procedure for the preparation and screening of a fragment-based non-peptidic protease substrate library for inhibitor discovery. Nat. Protoc. 2 (2007) 424-433
42. Wood W.J., et al. Substrate activity screening: a fragment-based method for the rapid identification of non peptidic proteasae inhibitors. J. Am. Chem. Soc. 127 (2005) 15521-15527
43. Schmidt, M.F. et al. (2009) Selective identification of cooperatively binding fragments in a high-throughput ligation assay enables development of a picomolar caspase-3 inhibitor. Angew. Chem. Int. Ed. 48, July 23 [Epub ahead of print]
44. Schmidt M.F., et al. Sensitized detection of inhibitory fragments and iterative development of non-peptidic protease inhibitors by dynamic ligation screening. Angew. Chem. Int. Ed. 47 (2008) 3275-3278
45. pro) inhibitors. ChemBioChem 7 (2006) 1048-1055
46. Hochgürtel M., et al. Ketones as building blocks for dynamic combinatorial libraries: highly active neuramidase inhibitors generated via selection pressure of the biological target. J. Med. Chem. 46 (2003) 356-358
47. Congreve M.S., et al. Detection of ligands from a dynamic combinatorial library by X-ray crystallography. Angew. Chem. Int. Ed. 42 (2003) 4479-4482
48. Ludlow R.F., and Otto S. Two-vial. LC-MS identification of ephedrine receptors from a solution-phase dynamic combinatorial library of over 9000 compounds. J. Am. Chem. Soc. 130 (2008) 12218-12219
49. Ramström O., and Lehn J.-M. In situ generation and screening of a dynamic combinatorial carbohydrate library against Concanavalin A. ChemBioChem 1 (2000) 41-48
50. Inglese J., and Benkovic S.J. Multisubstrate adduct inhibitors of glycinamide ribonucleotide transformylase: synthetic and enzyme-assembled. Tetrahedron 47 (1991) 2351-2364
51. Lewis W.G., et al. Click chemistry in situ: acetylcholinesterase as a reaction vessel for the selective assembly of a femtomolar inhibitor from an array of building blocks. Angew. Chem. Int. Ed. 41 (2002) 1053-1057
52. Kolb H.C., et al. Click chemistry: diverse chemical function from a few good reactions. Angew. Chem. Int. Ed. 40 (2001) 2004-2021
53. Soellner M.B., et al. Fragment-based substrate activity screening method for the identification of potent inhibitors of the Mycobacterium tuberculosis phosphatase PtpB. J. Am. Chem. Soc. 126 (2007) 9613-9615
54. El-Dashan A., et al. C-Acylation of polymeric phosphoranylidene acetates for C-terminal variation of peptide carboxylic acids. Org Lett. 15 (2007) 949-952
55. Hochgürtel M., et al. Target-induced formation of neuramidase inhibitors from in vitro virtual combinatorial libraries. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 3382-3387