Virtual screening of chemical libraries

Nature

Volumn 432, Issue 7019, 2004, Pages 862-865

  Shoichet, Brian K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL EQUIPMENT; COMPUTER APPLICATIONS; DRUG PRODUCTS; MOLECULAR STRUCTURE; SCREENING;

BIOLOGICAL STRUCTURES; COMPUTER-BASED METHODS; RECEPTOR-BOUND STRUCTURES; VIRTUAL SCREENING;

LABORATORIES;

DRUG;

CHEMISTRY;

CHEMICAL BOND; CORRELATION ANALYSIS; DRUG ACTIVITY; DRUG RESEARCH; DRUG SCREENING; DRUG TARGETING; EMPIRICISM; IC 50; LIGAND BINDING; MOLECULAR INTERACTION; NATURAL SCIENCE; PRIORITY JOURNAL; REVIEW; STRUCTURE ACTIVITY RELATION; TECHNIQUE;

COMPUTER SIMULATION; DRUG EVALUATION, PRECLINICAL; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PHARMACEUTICAL PREPARATIONS;

EID: 11144323163     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03197     Document Type: Review

References (32)

1. Beddell, C. R., Goodford, P. J., Norrington, F. E., Wilkinson, S. & Wootton, R. Compounds designed to fit a site of known structure in human haemoglobin. Br. J. Pharmacol. 57, 201-209 (1976).
2. Cohen, S. S. A strategy for the chemotherapy of infectious disease. Science 197, 431-432 (1977).
3. Itzstein, M. V. et al. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature 363, 418-423 (1993).
4. Varney, M. D. et al. Crystal-structure-based design and synthesis of Benz[cd]indole-containing inhibitors of thymidylate synthase. J. Med. Chem. 35, 663-676 (1992).
5. Kuntz, I. D. Structure-based strategies for drug design and discovery. Science 257, 1078-1082 (1992).
6. Jorgensen, W. L. The many roles of computation in drug discovery. Science 303, 1813-1818 (2004).
7. Stahura, F. L. & Bajorath, J. Virtual screening methods that complement HTS. Comb. Chem. High Throughput Screen 7, 259-269 (2004).
8. Perutz, M. F. The hemaglobin molecule. Sci. Am. 211, 64-76 (1964).
9. van Gunsteren, W. F. & Berendsen, H. J. C. Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 29, 992-1023 (1990).
10. Rizzo, R., Wang, D., Tirado-Rives, J. & Jorgensen, W. Validation of a model for the complex of HIV-1 reverse transcriptase with sustiva through computation of resistance profiles. J. Am. Chem. Soc. 122, 12898-12900 (2000).
11. Rosenfeld, R. J. et al. Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. J. Comput. Aided Mol. Des. 17, 525-536 (2003).
12. Brik, A. et al. Rapid diversity-oriented synthesis in microtiter plates for in situ screening of HIV protease inhibitors. Chembiochem. 4, 1246-1248 (2003).
13. Schapira, M. et al. Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc. Natl Acad. Sci. USA 100, 7354-7359 (2003).
14. Evers, A. & Klebe, G. Ligand-supported homology modeling of G-protein-coupled receptor sites: models sufficient for successful virtual screening. Angew. Chem. Int. Ed. Engl. 43, 248-251 (2004).
15. Shoichet, B. K., McGovern, S. L., Wei, B. & Irwin, J. J. Lead discovery using molecular docking. Curr. Opin. Chem. Biol. 6, 439-446 (2002).
16. Schneidman-Duhovny, D., Nussinov, R. & Wolfson, H. J. Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Curr. Med. Chem. 11, 91-107 (2004).
17. Wyss, P. C. et al. Novel dihydrofolate reductase inhibitors. Structure-based versus diversity-based library design and high-throughput synthesis and screening. J. Med. Chem. 46, 2304-2312 (2003).
18. Kick, E. K. et al. Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D. Chem. Biol. 4, 297-307 (1997).
19. Doman, T. N. et al. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J. Med. Chem. 45, 2213-2221 (2002).
20. Paiva, A. M. et al. Inhibitors of dihydrodipicolinate reductase, a keyenzyme of the diaminopimelate pathway of Mycobacterium tuberculosis, Biochim. Biophys. Acta. 1545, 67-77 (2001).
21. Gradler, U. et al. A new target for shigellosis; rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase. J. Mol. Biol. 306, 455-467 (2001).
22. Powers, R. A., Morandi, F. & Shoichet, B. K. Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Structure (Camb.) 10, 1013-1023 (2002).
23. Gruneberg, S., Stubbs, M. T. & Kiebe, G. Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation. J. Med. Chem. 45, 3588-3602 (2002).
24. Wei, B. Q., Baase, W. A., Weaver, L. H., Matthews, B. W. & Shoichet, B. K. A model binding site for testing scoring functions in molecular docking. J. Mol. Biol. 322, 339-355 (2002).
25. Lipinski, C. A., Lombardo, F., Dominy, B. W. & Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23, 3-25 (1997).
26. Oprea, T. I. Current trends in lead discovery: are we looking for the appropriate properties? Mol. Divers 5, 199-208 (2002).
27. McGovern, S. L., Caselli, E., Grigorieff, N. & Shoichet, B. K. A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J. Med. Chem. 45, 1712-1722 (2002).
28. Krämer, O., Hazemann, I., Podjarny, A. D. & Klebe, G. Virtual screening for inhibitors of human aldose reductase. Proteins 55, 814-823 (2004).
29. Horn, J. R. & Shoichet, B. K. Allosteric inhibition through core disruption. J. Mol. Biol. 336, 1283-1291 (2004).
30. Kaiser, J. NIH Gears up for chemical genomics. Science 304, 1728 (2004).
31. Kalyanaraman, C., Bernacki, K. & Jacobson, M. P. Virtual screening against highly charged active sites: Identifying substrates of alpha-beta barrel enzymes. Biochemistry in the press.
32. Pieper, U., Eswar, N., Stuart, A. C., Ilyin, V. A. & Sali, A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 30, 255-259 (2002).