The Many Roles of Computation in Drug Discovery

Science

Volumn 303, Issue 5665, 2004, Pages 1813-1818

  Jorgensen, William L ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; PROTEINS; SCREENING;

DRUG DISCOVERY; VIRTUAL SCREENING;

DRUG PRODUCTS;

6 CHLORO 4 (2 CYCLOPROPYLVINYL) 3,4 DIHYDRO 4 TRIFLUOROMETHYL 2(1H) QUINAZOLINONE; ATENOLOL; CELECOXIB; CHLORPROMAZINE; CIPROFLOXACIN; CYCLOOXYGENASE 1; CYCLOOXYGENASE 2; DELAVIRDINE; DRUG; EFAVIRENZ; EMIVIRINE; ESTROGEN RECEPTOR; ETRAVIRINE; GYRASE INHIBITOR; LIGAND; N [4 CHLORO 3 (3 METHYL 2 BUTENYLOXY)PHENYL] 2 METHYL 3 FURANCARBOTHIOAMIDE; NEVIRAPINE; PLASMA PROTEIN; PROTEIN; RJC 02097; RJC 03066; RNA DIRECTED DNA POLYMERASE INHIBITOR; ROFECOXIB; THYMIDINE KINASE; UNCLASSIFIED DRUG;

PHARMACEUTICAL INDUSTRY;

CELL MEMBRANE PERMEABILITY; CHEMISTRY; COMPUTER; COMPUTER PROGRAM; CRYSTAL STRUCTURE; DRUG ABSORPTION; DRUG BIOAVAILABILITY; DRUG DESIGN; DRUG DISTRIBUTION; DRUG EXCRETION; DRUG METABOLISM; DRUG SOLUBILITY; DRUG STRUCTURE; HIGH THROUGHPUT SCREENING; HYBRID; HYDROPHILICITY; LIGAND BINDING; MODEL; MOLECULAR MECHANICS; PRIORITY JOURNAL; REVIEW; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; COMPUTERS; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; PROTEINS; SOFTWARE;

EID: 1642357706     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1096361     Document Type: Review

References (68)

1. L. W. Hardy, A. Malikayil, Curr. Drug. Discov. 15, (2003).
2. B. E. Maryanoff, J. Med. Chem. 47, 769 (2004).
3. A. T. Brunger et al., Acta Crystallogr. D 54, 905 (1998).
4. T. D. Penning et al., J. Med. Chem. 40, 1347 (1997).
5. J. B. Hester et al., J. Med. Chem. 44, 1099 (2001).
6. P. G. Welling, Pharmacokinetics - Processes, Mathematics, and Applications (American Chemical Society, Washington, DC, ed. 2, 1997).
7. J. Licinio, M.-L. Wong, Eds., Pharmacogenomics: The Search for Individualized Therapies (Wiley-VCH, 2002).
8. R. P. Herzberg, A. J. Pope, Curr. Opin. Chem. Biol. 4, 445 (2000).
9. H.-J. Böhm et al., J. Med. Chem. 43, 2664 (2000).
10. R. Lahana, Drug Discov. Today 4, 447 (1999).
11. W. P. Walters, H. T. Stahl, H. A. Murcko, Drug Discov. Today 3, 160 (1998).
12. B. K. Shoicket, S. L. McGovern, B. Wei, J. J. Irwin, Curr. Opin. Chem. Biol. 6, 439 (2002).
13. J. F. Blake, E. R. Laird, Annu. Rep. Med Chem. 38, 305 (2003).
14. V. J. Gillet, P. Willett, J. Bradshaw, D. V. S. Green, J. Chem. Inf. Comput. Sci. 39, 169 (1999).
15. R. D. Taylor, P. J. Jewsbury, J. W. Essex, J. Comput. Aided Mol. Des. 16, 151 (2002).
16. T. N. Doman et al., J. Med. Chem. 45, 2213 (2002).
17. A. M. Paiva et al., Biochim. Biophys. Acta 1545, 67 (2001).
18. T. J. A. Ewing, I. D. Kuntz, J. Comput. Chem. 18, 1175 (1997).
19. M. Rarey, B. Kramer, T. Lengauer, G. Klebe, J. Mol. Biol. 261, 470 (1996).
20. Glide (Schrödinger Inc., New York, 2003).
21. G. Jones et al., J. Mol. Biol. 267, 727 (1997).
22. P. S. Charifson, J. J. Corkery, M. A. Murcko, W. P. Walters, J. Med. Chem. 42, 5100 (1999).
23. C. Bissantz, G. Folkers, D. Rognan, J. Med. Chem. 43, 4759 (2000).
24. C. Perez, A. R. Ortiz, J. Med. Chem. 44, 3768 (2001).
25. R. Wang, J. Med. Chem. 46, 2287 (2003).
26. P. Willett, J. Chem. Inf. Comput. Sci. 38, 983 (1998).
27. QikProp, v. 2.1 (Schrödinger Inc., New York, 2003).
28. QikSim, v. 2.1 (Schrödinger Inc., New York, 2003).
29. H.-J. Böhm, J. Comput. Aided Mol. Des. 6, 61 (1992).
30. V. J. Gillet et al., J. Chem. Inf. Comput. Sci. 34, 207 (1994).
31. H. M. Vinkers et al., J. Med. Chem. 46, 2765 (2003).
32. I. Muegge, Med. Res. Rev. 23, 302 (2003).
33. C. A. Lipinski, F. Lombardo, B. W. Dominy, P. J. Feeney, Adv. Drug Deliv. Rev. 23, 3 (1997).
34. C. A. Lipinski, J. Pharmacol. Toxicol. Methods 44, 235 (2000).
35. W. P. Walters, M. A. Murcko, Adv. Drug Deliv. Rev. 54, 255 (2002).
36. W. J. Egan, K. M. Merz, Jr, J. J. Baldwin, J. Med. Chem. 43, 3867 (2000).
37. W. L. Jorgensen, E. M. Duffy, Adv. Drug Deliv. Rev. 54, 355 (2002).
38. M. S. Lesney, Today's Chemist at Work, 27 (2004).
39. J. Taskinen, J. Yliruusi, Adv. Drug Deliv. Rev. 55, 1163 (2003).
40. J. M. Luco, J. Chem. Inf. Comput. Sci. 39, 396 (1999).
41. Ajay, G. W. Bemis, M. A. Murcko, J. Med. Chem. 42, 4942 (1999).
42. J. D. Irvine et al., J. Pharm. Sci. 88, 28 (1999).
43. G. Colmenarejo, A. Alvarez-Pedraglio, J.-L. Lavandera, J. Med. Chem. 44, 4370 (2001).
44. A. Cavalli, E. Poluzzi, F. De Ponti, M. Recanatini, J. Med. Chem. 45, 3844 (2002).
45. E. De Clercq, Med. Res. Rev. 22, 531 (2002).
46. P. A. Kollman, Chem. Rev. 93, 2395 (1993).
47. M. L. Lamb, W. L. Jorgensen, Curr. Opin. Chem. Biol. 1, 449 (1997).
48. H. Gohlke, G. Klebe, Angew. Chem. Int. Ed. Engl. 41, 2644 (2002).
49. M. L. Plount-Price, W. L. Jorgensen, J. Am. Chem. Soc. 122, 9455 (2000).
50. M. L. Plount-Price, W. L. Jorgensen, Bioorg. Med. Chem. Lett. 11, 1541 (2001).
51. D. Ostrovsky, M. Udier-Blagović, W. L. Jorgensen, J. Med. Chem. 46, 5691 (2003).
52. R. C. Rizzo, D.-P. Wang, J. Tirado-Rives, W. L. Jorgensen, J. Am. Chem. Soc. 122, 12898 (2000).
53. D.-P. Wang, R. C. Rizzo, J. Tirado-Rives, W. L. Jorgensen, Bioorg. Med. Chem. Lett. 11, 2791 (2001).
54. M. Udier-Blagović, J. Tirado-Rives, W. L. Jorgensen, J. Am. Chem. Soc. 125, 6016 (2003).
55. J. Tirado-Rives, W. L. Jorgensen, J. Am. Chem. Soc. 112, 2773 (1990).
56. C. Mattos, Trends Biochem. Sci. 27, 203 (2002).
57. J. Aqvist, C. Medina, J.-E. Sammuelsson, Protein Eng. 7, 385 (1994).
58. B. O. Brandsdal et al., Adv. Prot. Chem. 66, 123 (2003).
59. H. A. Carlson, W. L. Jorgensen, J. Phys. Chem. 99, 10667 (1995).
60. S. S. Wesolowski, W. L. Jorgensen, Bioorg. Med. Chem. Lett. 12, 267 (2002).
61. R. C. Rizzo et al., J. Med. Chem. 45, 2970 (2002).
62. M. Udier-Blagović, E. K. Watkins, J. Tirado-Rives, W. L. Jorgensen, Bioorg. Med. Chem. Lett. 13, 3337 (2003).
63. Y. Tominaga, W. L. Jorgensen, J. Med. Chem., in press.
64. I. Massova, P. A. Kollman, J. Am. Chem. Soc. 121, 8133 (1999).
65. R. Zhou et al., J. Phys. Chem. B 105, 10388 (2001).
66. T. Simonson, G. Archontis, M. Karplus, Acc. Chem. Res. 35, 430 (2002).
67. J. Regan et al., J. Med. Chem. 45, 2994 (2002).
68. The author is grateful to his co-workers for their dedication and to the N5F and the NIH for research support.