New computational approaches to predict protein-ligand interactions

Structure-based Ligand Design

Volumn 6, Issue , 2008, Pages 129-142

  Böhm, Hans Joachim ^a  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

3D database; Computational methods; De novo design; Electrostatic potential; Protein binding

Indexed keywords

BINDING ENERGY; BIOCHEMISTRY; LIGANDS; PROTEINS;

3D DATABASE; COMPUTATIONAL APPROACH; DE NOVO DESIGN; DE NOVO LIGAND DESIGNS; ELECTROSTATIC POTENTIALS; LIGAND BINDING AFFINITY; PROTEIN BINDING; PROTEIN-LIGAND INTERACTIONS;

COMPUTATIONAL METHODS;

EID: 84956804076     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527612178.ch8     Document Type: Chapter

References (102)

1. Navia, M. A., and Murcko, M. A., Curr. Opin. Struct. Biol. 2,202-210 (1992)
2. Baldwin, J. J., Ponticello, G. S., Anderson, P. S., Christy, M. E., Murcko, M. A., et al., J. Med. Chem. 32, 2510-2513 (1989)
3. Appelt, K., Bacquet, R. J., Bartlett, C. A., et al., J. Med. Chem. 34,1925-1934 (1991)
4. Varney, M. D., Marzoni, G. P., Palmer, C. L., et al., J. Med. Chem. 35,663-676 (1992)
5. Reich, S. H., Fuhry, M. A. M., Nguyen, D., et al., J. Med. Chem. 35,847-858 (1992)
6. Thompson, W. J., Fitzgerald, P., Holloway, M. K., et al., J. Med. Chem. 35,1685-1701 (1992)
7. Lam, P. Y. S., Jadhav, P. K., Eyermann, C. J., et al., Science 263,380-384 (1994)
8. von Itzstein, M, Wu, W. Y., and Kok, G. B., Nature 363,418-23 (1993)
9. Mack, H., Pfeiffer, Th., Homberger, W., Bohm, H. J., and Hoffken, H. W., J. Enzyme Inhibition 9,73-86 (1995)
10. Cohen, N. C, Blaney, J. M., Humblet, C, Gund, P., and Barry, D. C, J. Med. Chem. 33, 883-894 (1990)
11. Martin, Y. C, J. Med. Chem. 35,2145-2154 (1992)
12. Wireko, F. C, Kellogg, and G. E., Abraham, D. J., J. Med. Chem. 34,758-767 (1991)
13. Kellog, G. E., Joshi, G. S., and Abraham, D. J., Med. Chem. Res. 1,444-53 (1992)
14. Nicholls, A., Sharp, K. A., and Honig, B. H., Proteins 11,281 (1991)
15. Connolly, M. L., Biopolymers 32,1215-1236 (1992)
16. Lewis, R. A., J. Comput. Aided Molec. Des. 3,133-147 (1989)
17. Kleywegt, G. J., and Jones, T. A., Acta Crystallogr. D50,178-185 (1994)
18. Goodford, P. J., J. Med. Chem. 28,849-857 (1985)
19. Boobbyer, D. N. A., Goodford, P. J., McWhinnie, P. M., and Wade, R. C, J. Med. Chem. 32, 1083-1094 (1989)
20. Tomioka, N., and Itai, A., J. Comput. Aided Molec. Des. 8,347-366 (1994)
21. Miranker, A., and Karplus, M., Proteins: Struct. Fund. Genet. 11,29-34 (1991)
22. Blaney, J. M., and Dixon, J. S., Perspect. Drug Disc. Design 1,301-319 (1993)
23. Kuntz, I. D., Meng, E. C, and Shoichet, B. K., Ace. Chem. Res. 27,117-123 (1994)
24. DesJarlais, R. L., Sheridan, R. P., Seibel, G. L., Dixon, J. S., Kuntz, I. D., and Venkataraghavan, R., J. Med. Chem. 31,722-729 (1988)
25. Meng, E. C, Shoichet, B. K., and Kuntz, I. D., J. Comp. Chem. 13,505-524 (1992)
26. Meng, E. C, Gschwend, D. A., Blaney, J. M, and Kuntz, I. D., Proteins 17,266-278 (1993)
27. Kuntz, I. D., Science 257,1078-1082 (1992)
28. Shoichet, B. K., Stroud, R. M, Santi, D. V., Kuntz, I. D., and Perry, K. M., Science 259,1445-1450 (1993)
29. Li, Z., Chen, X., Davidson, E., et al., Chemistry & Biology 1,31-37 (1994)
30. Lawrence, M. C, and Davis, P. C, Proteins 12,31-41 (1992)
31. Miller, M. D., Kearsley, S. K., Underwood, D. J., and Sheridan, R. P., J. Comput. Aided Molec. Des. 8,153-174 (1994)
32. Bohm, H. J., J. Comput. Aided Molec. Des. 8,623-632 (1994)
33. Lewis, R. A., and Leach, A. R., J. Comput. Aided Molec. Des. 8,467-175 (1994)
34. Bohm, H. J., In: Kubinyi, H., Ed. 3D-QSAR in Drug Design, Escom Science Publishers; Leiden; 386-405 (1993)
35. Verlinde, C. L. M. J., and Hoi, W. G. J., Structure 2,577-587 (1994)
36. Nishibata, Y., and Itai, A., Tetrahedron 47,8985-8990 (1991)
37. Nishibata, Y., Itai, A., J. Med. Chem. 36,2921-2928 (1993)
38. Bohacek, R. S., and McMartin, C, J. Am. Chem. Soc. 116,5560-5571 (1994)
39. Gehlhaar, D. K., Moerder, K. E., Zichi, D., Sherman, C. J., Ogden, R. C, and Freer, S. T., J. Med. Chem. 38,46-472 (1995)
40. Moon, J. B., and Howe, W. J., Proteins 11,314-328 (1991)
41. Tschinke, V., and Cohen, N. C, J. Med. Chem. 36,3863-3870 (1993)
42. Rotstein, S. H., and Murcko, M. A., J. Med. Chem. 36,1700-1710 (1993)
43. Eisen, M. B., Wiley, D. C, Karplus, M., and Hubbard, R. E., Proteins 19,199-221 (1994)
44. Caflish, A., Miranker, A., and Karplus, M., J. Med. Chem. 36,2142-2167 (1993)
45. Lewis, R. A., J. Mol. Graphics 10,66 (1992)
46. Gillet, V. J., Johnson, A. P., Mata, P., and Sike, S., Tetrahedron Comput. Methods 3,681-696 (1990)
47. Gillet, V., Johnson, P., Mata, P., Sike, S., and Williams, P., J. Comput. Aided Molec. Design 7, 127-153 (1993)
48. Mata, P., Gillet, V. J., Johnson, P., Lampreia, J., Myatt, G. J., Sike, S., and Stebbings, A. L., J. Chem. Inf. Comput. Sci. 35,479-493 (1995)
49. Rotstein, S. H., and Murcko, M. A., J. Comput. Aided Molec. Des. 7,23-43 (1993)
50. Bartlett, P. A., Shea, G. T., Telfer, S. J., and Waterman, S. In: Molecular Recognition: Chemical and Biological Problems, Roberts S. M. (Ed.), Royal Society of London; 182-196 (1989)
51. Pearlman, D. A., and Murcko, M. A., J. Comput. Chem. 14,1184-1193 (1993)
52. Lewis, R. A., and Dean, P. M., Proc. R. Soc. Lond. B236,125-140 (1989)
53. Lewis, R. A., and Dean, P. M., Proc. R. Soc. Lond. B236,141-162 (1989)
54. Chau, P. L., and Dean, P. M., J. Comput. Aided Molec. Des. 6,385-396 (1992)
55. VanDrie, J., Weininger, D., and Martin, Y. C, J. Comput Aided Molec. Des. 3,225-251 (1989)
56. Bohm, H. J., J. Comput. Aided Molec. Des. 6,61-78 (1992)
57. Bohm, H. J., J. Comput. Aided Molec. Des. 6,593-606 (1992)
58. Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink-Peters, T., Kennard, O. Motherwell, W. D. S., Rodgers, J. R., and Watson, D. G., Acta Crystallogr. B35,2331-2339 (1979)
59. Bohm, H. J., J. Comput Aided Molec. Des. 8,243-256 (1994)
60. Klebe, G., J. Mol. Biol. 237,212-235 (1994)
61. Allen, F. H., Kennard, O., and Taylor, R., Ace. Chem. Res. 16,146-153 (1983)
62. Allen, F. H., Davies, J. E., Galloy, J. J., et al., J. Chem. Inf. Comput. Set 31,187-204 (1991)
63. Pisabarro, M. T., Ortiz, A. R., Palomar, A., Cabre, F., Garcia, L., Wade, R. C, Gago, F., Mauleon, D., and Carganico, G.,J. Med. Chem. 37, 337-341 (1994)
64. The fine chemicals directory (FCD) and the available chemicals directory (ACD) are distributed by Molecular Design Ltd., San Leandro, 2132 Farallon Drive, CA 94577
65. Program CONCORD, distributed by Tripos Ass., 1699 S. Hanley Rd., St. Louis, MO 63144
66. Sadowski, J., Rudolph, C, and Gasteiger, J., Tetrahedron Comput. Methodol. 3,537 (1990)
67. Marquart, M., Walter, J., Deisenhofer, J., Bode, W., and Huber, R., Acta Crystallogr. B39480-490 (1983)
68. Mares-Guia, M., and Shaw, E., J. Biol. Chem. 240,1579-1585 (1965)
69. Recanatini, M., Klein, T., Yang, C. Z., McClarin, J., Langridge, R., and Hansch, C, Mol. Phar-macol. 29,436-446 (1986)
70. Green, N. M., Adv. Protein Chem. 29,85 (1975)
71. Babine, R. E., Bleckman, T. M., Kissinger, C. R., Showalter, R., Pelletier, L. A., Lewis, C, Tucker, K., Moomaw, E., Parge, H. E., and Villafranca, J. E., Biorg. Med. Chem. Lett. 15, 1719-1724 (1995)
72. LUDI is available from MSI Technologies, 9685 Scranton Road, San Diego, CA 92121-2
73. Wieseman T., Wiliston S., Brandts J., and Lin L., Anal. Biochem. 179,131 (1989)
74. Hitzemann, R., Trends Pharmacol. Sci. 9,408-411 (1988)
75. Hitzemann, R., Murphy, M., and Currell, J., Eur. J. Pharmacol. 108,171-177 (1985)
76. Weiland, G. A., Minnemann, G. P., and Molinoff, P. B., Mol. Pharmacol. 18, 341-347 (1980)
77. Epps, D. E., Cheney, J. Schostarez, H., Sawyer, T. K., Prairie, M., Krueger, W. C, and Mandel, F., J. Med. Chem. 33,2080 (1990)
78. Weber, P. C, Wendoloski, J. J., Panoliano, M. W., and Salemme, F. R., J. Am. Chem. Soc. 114, 3197-3200 (1992)
79. Holloway, M. K., Wai, J. M., Halgren, T. A., et al., J. Med. Chem. 38, 305-317 (1995)
80. Grootenhuis, P. D. J., and Van Galen, P. J. M., Acta Crystallogr. D51,560-566 (1995)
81. van Gunsteren, W. F., and Weiner, P. K., Computer Simulations of Biomolecular Systems, Escom; Leiden, 1989
82. Reddy, M. R., Viswanadhan, V. N., and Weinstein, J. N., Proc. Natl Acad. Sci. USA 88, 10287-10291 (1991)
83. Rao, B. G., Tilton, R. F., and Singh, U. C, J. Am. Chem. Soc. 114,4447-4452 (1992)
84. Miyamoto, S., and Kollman, P. A., Proteins 16,226-245 (1993)
85. Miyamoto, S., and Kollman, P. A., Proc. Natl Acad. Sci. USA 90,8402-8406 (1993)
86. Bash, P. A., Singh, U. C, Brown,F. K., Langridge, R., and Kollman, P. A., Science 235, 574-576, (1987)
87. Merz, K. M., and Kollman, P. A., J. Am. Chem. Soc. 111, 5649-5658 (1989)
88. Kollman, P. A., Curr. Opin. Struct. Biol. 4,240-245 (1994)
89. Warshel, A., Tao, H., Fothergill, M., and Chu, Z. T Isr. J. Chem. 34,263-256 (1994)
90. Honig, B., and Nicholls, A., Science 268,1144-1149 (1995)
91. Kang, Y. K., Gibson, K. D., Nemethy, G., and Scheraga, H. A., J. Phys. Chem. 92, 4739-4742 (1988)
92. Williams, R. L., Vila, J., Perrot, G., and Scheraga, H. A., Proteins 14,110-119 (1992)
93. Cramer, C. J., and Truhlar, D. G., J. Am. Chem. Soc. 113,8305 (1991)
94. Cramer, C. J., and Truhlar, D. G., J. Comp. Aided Molec. Des. 6,629-666 (1992)
95. Andrews, P. R., Craik, D. J., and Martin, J. L, J. Med. Chem. 27,1648-1657 (1984)
96. Vajda, S., Weng, Z., Rosenfeld, R., and DeLisi, C, Biochemistry 33,13 977-13 988 (1994)
97. Krystek, S., Stouch, T., and Novotny, J., J. Mol. Biol. 234, 661-679 (1993)
98. Horton, N., and Lewis, M., Protein Sci. 1,169-181 (1992)
99. Banner, D. W., and Hadvary, P., J. Biol. Chem. 266,20085-20093 (1991)
100. Sali, A., Veerapandian, B., Cooper, J. B., Moss, J. B., Hofmann, T., and Blundell, T. L., Proteins 12,158-170(1992)
101. Rahuel, J., Priestle, J. P., and Grutter, M. G., J. Struct. Biol. 107, 227-236 (1991)
102. Wierenga, R. K., Noble, M. E. M., and Davenport, R. C, J. Mol. Biol. 224,1115-1126 (1992)