Do active site conformations of small ligands correspond to low free-energy solution structures?

Journal of Computer-Aided Molecular Design

Volumn 12, Issue 6, 1998, Pages 563-572

  Vieth, Michal ^a,b   Hirst, Jonathan D ^a   Brooks III, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b ELI LILLY AND COMPANY   (United States)

Author keywords

Anchor points; Conformational search; Ligand binding

Indexed keywords

BINDING ENERGY; LIGANDS; PHARMACODYNAMICS;

ACTIVE SITE; ANCHOR POINT; CONFORMATIONAL SEARCH; ENERGY SOLUTIONS; ENERGY STRUCTURES; LIGAND BINDING; LOWER ENERGIES; SOLUTION CONFORMATIONS; SOLUTION STRUCTURES; SYSTEMATIC SEARCHES;

FREE ENERGY;

LIGAND;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; ELECTRICITY; SOLUTION AND SOLUBILITY;

BINDING SITES; ELECTROSTATICS; LIGANDS; MOLECULAR STRUCTURE; SOLUTIONS;

EID: 0032197018     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008055202136     Document Type: Article

References (41)

1. Clark, D.E., Westhead, D.R., Sykes, R.A. and Murray, C.W., J. Comput.-Aided Mol. Design, 10 (1996) 397.
2. Martin, Y.C., J. Med. Chem., 35 (1992) 2145.
3. Wang, S., Zaharewitz, D.W., Sharma, R., Marquez, V.E., Lewin, N.B., Du, L., Blumberg, P.M. and Milne, G.W., J. Med. Chem., 37 (1994) 4479.
4. Kiyama, R., Honma, T., Hayashi, K., Ogawa, M., Hara, M., Fujimoto, M. and Fujishita, T.J., J. Med. Chem., 38 (1995) 2728.
5. Klebe, G., J. Mol. Biol., 237 (1994) 212.
6. Hodgkin, E.E., Miller, A. and Whittaker, M., J. Comput.-Aided Mol. Design, 7 (1993) 515.
7. Dammkoehler, R.A., Karasek, S.F., Shands, E.F. and Marshall, G.R., J. Comput.-Aided. Mol. Design, 3 (1989) 3.
8. Dammkoehler, R.A., Karasek, S.F., Shands, E.F. and Marshall, G.R., J. Comput.-Aided Mol. Design, 9 (1995) 491.
9. Jones, G., Willet, P. and Glen, R.C., J. Comput.-Aided Mol. Design, 9 (1995) 532.
10. Mayer, D., Naylor, C.B., Motoc, I. and Marshall, G.R., J. Comput.-Aided Mol. Design, 1 (1987) 3.
11. Sheridan, R.P., Nilakantan, R., Dixon, J.S. and Venkataraghavan, R., J. Med. Chem., 29 (1986) 899.
12. Schwyzer, R., Biopolymers, 37 (1995) 5.
13. Fisher, E. and Thierfelder, H., Berl. Dtsh, Chem. Ges., 27 (1894) 2985.
14. Jorgensen, W.L., Science, 254 (1991) 954.
15. Patten, P.A., Gray, N.S., Yang, P.L., Marks, C.B., Wedemayer, G.J., Boniface, J.J., Stevens, R.C. and Schultz, P.G., Science, 271 (1996) 1086.
16. Böhm, H.-J. and Klebe, G., Angew. Chem. Int. Ed. Engl., 35 (1996) 2588.
17. Nicklaus, M.C., Shaomeng, W., Driscoll, J.S. and Milne, W.A., Bioorg. Med. Chem., 3 (1995) 411.
18. Klebe, G. In Burgi, H.B. and Dunitz, J.D. (Eds.) Structure Correlation, VCH, Weinheim, 1994, p. 543.
19. Allen, F.H. In Domenicano, A. and Hargittai, I. (Eds.) Accurate Molecular Structures, Oxford University Press, Oxford, 1992, p. 355.
20. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
21. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., J. Comput. Chem., 4 (1983) 187.
22. Quanta, Molecular Simulations Inc., San Diego, CA, 1997.
23. Gaussian 94, Gaussian, Inc., Pittsburgh, PA, 1995.
24. Vieth, M., Parameter files for ligands are available through anonymous ftp from ftp.scripps.edu/ficio/parameters/ or from our web site at www.scripps.edu/brooks/ficio/parameters/param.html, 1997.
25. Miranker, A. and Karplus, M., Proteins, 11 (1991) 29.
26. Cerius2, Molecular Simulations Inc., San Diego, CA, 1997.
27. Catalyst, Molecular Simulations Inc., San Diego, CA, 1997.
28. Jain, A.K. and Dubes, R.C., Algorithms for clustering data, Prentice Hall, Englewood Cliffs, NJ, 1988.
29. Warwicker, J. and Watson, H.C., J. Mol. Biol., 157 (1982) 671.
30. Edinger, S.R., Cortis, C., Shenkin, P.S. and Friesner, R.A., J. Phys. Chem., B101 (1997) 1190.
31. Allen, F.H., Bellard, S., Brice, M.D., Cartwright, B.A., Doubleday, A., Higgs, A., Hummelink-Peters, T., Kennard, O., Motherwell, W.D.S., Rodgers, J.R. and Watson, D.G., Acta Crystallogr., 35 (1979) 2331.
32. Weber, P.C., Ohlendorf, D.H., Wendoloski, J.J. and Salemme, F.R., Science, 243 (1989) 85.
33. Segal, D.M., Padlan, E.A., Cohen, G.H., Rudikoff, S., Potter, M. and Davies, D.R., Proc. Natl. Acad. Sci. USA, 71 (1974) 4298.
34. Weis, W.I., Brünger, A.T., Skehel, J.J. and Wiley, D.C., J. Mol. Biol., 212 (1990) 737.
35. Robbins, A.H. and Stout, C.D., Proc. Natl. Acad. Sci. USA, 86 (1989) 3639.
36. Noble, M.E.M., Wierenga, R.K., Lambeir, A.M., Opperdoes, F.R., Thunnissen, A.M.W.H., Kalk, K.H., Groendijk, H. and Hol, W.G.J., Proteins, 10 (1991) 50.
37. Walter, J., Steigemann, W., Singh, T.P., Bartunik, H., Bode, W. and Huber, R., Acta Crystallogr. B, 38 (1982) 1462.
38. Christianson, D.W. and Lipscomb, W.N., Proc. Natl. Acad. Sci. USA, 83 (1986) 7568.
39. Holden, H.M. and Matthews, B.W., J. Biol. Chem., 263 (1988) 3256.
40. Leslie, A.G.W., J. Mol. Biol., 213 (1990) 167.
41. Tronrud, D.E., Monzingo, A.F. and Matthews, B.W., Eur. J. Biochem., 157 (1986) 261.