Computer modeling for interaction of ligands and receptors and their applications in drug design

Progress in Chemistry

Volumn 10, Issue 4, 1998, Pages

  Jiang, Hualiang ^a   Hu, Zengjian ^a   Chen, Jianzhong ^a   Gu, Jiande ^a   Zhu, Weiliang ^a   Chen, Kaixian ^a   Ji, Ruyun ^a  

^a SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

Author keywords

Drug design; Ligand receptor interaction; Molecular modeling; Theoretical calculation

Indexed keywords

EID: 3242869182     PISSN: 1005281X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (78)

1. Lybrand T P, Curr. Opin. Struct. Biol., 1995, 5, 224-228.
2. Kollman P A, Curr. Opin. Struct. Biol., 1994, 4, 240-245.
3. Kubinyi H. Burger's Medicinal Chemistry and Drug Discovery, Fifth Edition, Vol. 1: Principles and Practice (ed. Wolff M E), John Wiley & Sons, Inc., New York, 1995, 497-571.
4. Kenneth M M Jr, Curr, Opin. Struct. Biol., 1993, 3, 234-240.
5. Colman P M, Curr. Opin. Struct. Biol., 1994, 4, 868-874.
6. Greer J, Erickson J W, Baldwin J J, Varney M D, J. Med. Chem., 1994, 37, 1035-1054.
7. Johnson M S, Srinivasan N, Sowdhamini R, Blundell T L, Crit. Rev. Biochem. Mol. Biol., 1994, 29, 1-68.
8. Kontoyianni M, Lybrand T P, Perspect. Drug Discov. Des., 1993, 1, 291-300.
9. Greer J, Method. Enzym., 1991, 202, 239-252.
10. Thornton J M, Swindells M B, Molecular Structures in Biology (eds. Diamond R, Koetzle T F, Drout K, Richardson J S), Oxford, New York, 1993.
11. Spellmeyer D C, Swope W C, Perspect. Drug Discov. Des., 1993, 1, 359-370.
12. Olson A J, Morris G M, Perspect. Drug Discov. Des., 1993, 1, 329-344.
13. Boyd D B, Milosevich S A F, Perspect. Drug Discov. Des., 1993, 1, 345-358.
14. Andrews P R, Craik D J, Martin J L, J. Med. Chem., 1984, 27, 1648-1657.
15. Blaney J M, Dixon J S, Perspect. Drug Discov. Des., 1993, 1, 301-320.
16. Whittle P J, Annu. Rev. Biophys. Biomol. Struct., 1994, 23, 349-375.
17. Kuntz I D, Blaney J M, Oatley S J, Langridge R, Ferrin T E, J. Mol. Biol., 1982, 161, 269-288.
18. Connolly M L, Science, 1983, 221, 709-713.
19. Lewis R A, Method. Enzym., 1991, 202, 126-156.
20. Allen F H, Bellard S, Brice M D, Cartwright B A, Doubleday A, Higgs H, Hummelink T, Hummelink-Peters B G, Kennard O, Motherwell W D S, Rodgers J R, Watson D G, Acta Crystallogr., 1979, B35, 2331-2339.
21. Bolin J T, Fellman D J, Matthews D A, Hamlin R C, Hraut J, J. Biol. Chem., 1982, 257, 13650 -13662.
22. Böhm H J, J. Comput.-Aided Mol. Des., 1992, 6, 593-606.
23. Fersht A R, Shi J, Knill-Jones J, Lowe D M, Willkinson A J, Blow D M, Brick P, Carter P, Waye M M Y, Winter G, Nature, 1985, 314, 235-238.
24. Bohacek R S, McMartin C, J. Med. Chem., 1992, 35, 1671-1684.
25. Jiang H L, Chen K X, Tang Y, Chen J Z, Li Q, Yang Y S, Wang Q M, Ji R Y, J. Med. Chem., 1997, 40, 3085-3090.
26. Jiang H L, Chen K X, Tang Y, Chen J Z, Li Q, Wang Q M, Ji R Y, Acta Pharmacol. Sin., 1997, 18(1), 36-44.
27. Jiang H L, Chen K X, Tang Y, Chen J Z, Li Q, Wang Q M, Ji R Y, Chin. Chem. Lett., 1996, 7 (3), 252-256.
28. Blaney J M, Weiner P K, J. Am. Chem. Soc., 1982, 104, 6424-6434.
29. Darden T, Blaney J M, Ann. N. Y. Acad. Sci., 1986, 482, 249-250.
30. Kuyper L, Davis S, LeBlanc H, Advances in Gene Technology: Protein Engineering and Production, ICSU Short Receptors, vol. 8 (ed. Brew K), IRL Press, Oxford, 1988, 190.
31. Kollman P, Chem. Rev., 1993, 93, 2395-2417.
32. Lee C, Curr. Opin. Struct. Biol., 1992, 2, 217-222.
33. Gerber P R, Mark A E, Van Gausteren W F, J. Computer-Aided Mol. Des., 1993, 7, 305-323.
34. Van Gunsteren W F, King P M, Mark A E, Quart. Rev. Biophys., 1994, 27, 435-481.
35. Wong C F, McCammon J A, J. Am. Chem. Soc., 1986, 108, 3830-3832.
36. Bash P A, Singh U C, Langridge R, Kollman P A, Science, 1987, 236, 564-568.
37. Merz K M, Kollman P A, J. Am. Chem. Soc., 1989; 111, 5649-5658.
38. Morgan B P, Scholtz J M, Ballinger M D et al., J. Am. Chem. Soc., -1991, 113, 197-307.
39. Merz K M, Murcko M A, Kollman P A, J. Am. Chem. Soc., 1991, 113, 4484-4490.
40. Menziam M C, Reynolds C A, Richards W G, J. Chem. Soc., Chem. Commun., 1989, 853-855.
41. Hoops S C, Anderson K W, Merz K M, J. Am. Chem. Soc., 1991, 113, 8262-8270.
42. Rao B G, Singh U C, J. Am. Chem. Soc., 1991, 113, 6735-6750.
43. Reddy M R, Viswanadhan V N, Weinstein J N, Proc. Natl. Acad. Sci. USA, 1991, 88, 10287-10291.
44. Reddy M R, Kalish V, Palmer C et al., Paper Presented at Spring ACS Meeting in Denver, 1993.
45. Ferguson D M, Radmer R J, Kollman P A, J. Med. Chem., 1991, 34, 2654-2659.
46. Tropsha A, Hermans J, J. Protein Eng., 1992, 5, 29-33.
47. Cieplak P, Kollman P A, J. Comput. -Aided. Mol. Des., 1993, 7, 291-304.
48. Cummins P L, Ramnarayan K, Singh U C et al., J. Am. Chem. Soc., 1991, 113, 8247-8256.
49. Fleischman S H, Brooks C L, Proteins, 1990, 7, 52-61.
50. Brooks C L, Fleischman S H, J. Am. Chem. Soc., 1990, 112, 3307-3312.
51. McDonald J J, Brooks C L, J. Am. Chem. Soc., 1991, 113, 2295-2301.
52. McDonald J J, Brooks C L, J. Am. Chem. Soc., 1992, 114, 2062-2072.
53. Caldwell J W, Agard D A, Kollman P A, Proteins, 1991, 10, 140-148.
54. Hirono S, Kollman P A, J. Mol. Biol., 1990, 212, 193-207.
55. Rao S N, Singh U C, Bash P A, Kollman P A; Nature, 1987, 328, 551-553.
56. Hwang J K, Warshel A, Biochemistry, 1987, 26, 2669-2673.
57. Mizushima N, Spellmeger D, J. Biol. Chem., 1991, 266, 11801-11809.
58. Computer Simulation of Biomolecular Systems; Theoretical and Experimental Applications, Vol. 2, Part 41 Computation of Free Energy (eds. Van Gunsteren W F, Weiner P K), ESCOM, New York, 1990.
59. Warshel A, Levitt M, J. Mol. Biol., 1976, 103, 227-249.
60. Field M J, Bash P A, Karplus M, J. Comput. Chem., 1990, 11, 700-733.
61. Gao J, Xia X, Science, 1992, 258, 631-635.
62. Warshel A, Computer Modeling of Chemical Reactions in Enzymes and Solutions, John Wiley and Sons, Inc., New York, 1991.
63. Aqvist J, Warshel A, Chem. Rev., 1993, 93, 2523-2544.
64. Gresh N, Caverle P, Pullman A, Theoret. Chim. Acta, 1984, 20, 1-20.
65. Elock A H, Lyne P D, Mulholland A J, Mandra A, Richards W G, J. Am. Chem. Soc., 1995, 117, 4706-4707.
66. Waszowycz B, Hillier I H, Gensmantel N, Payling D W, J. Chem. Soc., Perkin Trans., I 1991, (2), 225-230.
67. Waszowycz B, Hillier I H, Gensmantel N, Payling D W, J. Chem. Soc., Perkin Trans. I, 1991, (12), 2025-2032.
68. Bash P A, Field M J, Davenport R C, Petako G A et al., Biochemistry, 1991, 30, 5826-5832.
69. Knowles J R, Albery W J, Acc. Chem. Rev., 1977, 10, 105-111.
70. Aqvist J, Warshel A, J. Mol. Biol., 1992, 224, 7-14.
71. Aqvist J, Fothergill M, Warshel A, J. Am. Chem. Soc., 1993, 115, 631-635.
72. Jann J, Protein: Struct., Fund., and Genet., 1995, 21, 20-39.
73. DeWitte R S, Shakhnovich E I, J. Am. Chem. Soc., 1997, 118, 11733-11744.