Automated Docking and the Search for HIV Protease Inhibitors

SAR and QSAR in Environmental Research

Volumn 8, Issue 3-4, 1998, Pages 273-285

  Olson, A J ^a   Goodsell, D S ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Automated docking; computer aided rational drug design; HIV protease inhibitors

Indexed keywords

AUTOMATED DOCKING; COMPOUND LIBRARIES; COMPUTER-AIDED; COMPUTER-AIDED RATIONAL DRUG DESIGN; DOCKING SIMULATIONS; HIV-1 PROTEASE INHIBITORS; HIV-PROTEASE INHIBITORS; RATIONAL DESIGN; RATIONAL DRUG DESIGNS; STRUCTURE-BASED;

MOLECULAR DOCKING;

PROTEINASE INHIBITOR;

CHEMISTRY; COMPUTER AIDED DESIGN; COMPUTER SIMULATION; DRUG DESIGN; METABOLISM; REVIEW; STRUCTURE ACTIVITY RELATION;

COMPUTER SIMULATION; COMPUTER-AIDED DESIGN; DRUG DESIGN; HIV PROTEASE INHIBITORS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0031600220     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/10629369808039144     Document Type: Article

References (34)

1. Ajay and Murcko, M. A., 1995. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem., 38: 4953–4967.
2. Blaney, J., and Dixon, S. J., 1993. A good ligand is hard to find. Perspect. Drug. Des., 1: 301–319.
3. Bohm, H.-J., 1992a. The computer program LUDI: A new method for the de novo design of enzyme inhibitors. J. Comput. Aided Mol. Des., 6: 61–78.
4. Bohm, H.-J., 1992b. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comp. Aided Mol. Design, 6: 593–606.
5. Bohm, H.-J., 1994. The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des., 8: 243–256.
6. Clark, D. E., and Westhead, D. R., 1996. Evolutionary algorithms in computer-aided molecular design. J. Comput. Aided Mol. Des., 10: 337–358.
7. DesJarlais, R. L., Seibel, G. L., Kuntz, I. D., Furth, P. S., Alvarez, J. C., Ortiz de Montellano, P. R., DeCamp, D. L., Babe, L. M., and Carik, S., 1990. Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc. Natl. Acad. Sci. USA, 87: 6644–6648.
8. DesJarlais, R. L., Sheridan, R. P., Dixon, J. S., Kuntz, I. D., and Venkataraghavan, R., 1986. Docking flexible ligands to macromolecular receptors by molecular shape. J. Med. Chem., 29: 2149–2153.
9. DesJarlais, R. L., Sheridan, R. P., Seibel, G. L., Dixon, J. S., Kuntz, I. D., and Venkataraghavan, R., 1988. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J. Med. Chem., 31: 722–729.
10. Goodsell, D. S., and Olson, A. J., 1990. Automated docking of substrates to proteins by simulated annealing. Prot.: Struct., Funct., Genetics, 8: 195–202.
11. Harrison, R. W., and Weber, I. T., 1994. Molecular dynamics simulations of HIV-1 protease with peptide substrate. Prot. Engin., 7: 1353–1363.
12. Hart, T. N., and Read, R. J., 1992. A multiple-start Monte Carlo docking method. Prot.: Struct., Funct. and Genetics, 13: 206–222.
13. Kuntz, I. D., Blaney, J. M., Oatley, S., Langridge, R., and Ferrin, T., 1982. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol., 161: 269–288.
14. Lam, P. Y. S., Jadav, P. K., Eyermann, C., Hodge, C. N., Lee, Y. R., Bacheloer, L. T., Meek, J. L., Otto, M. J., Rayner, M. M., Wong, Y. N., Chang, C.-H., Weber, P. C., Jackson, D. A., Sharpe, T. R., and Erickson-Viitanen, S. E., 1994. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science, 263: 380–384.
15. Leach, A. R., 1994. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol., 235: 345–356.
16. Leach, A. R., and Kuntz, I. D., 1992. Conformational analysis of flexible ligands in macromolecular receptor sites. J. Comp. Chem., 13: 730–748.
17. Lewis, R., 1990. Automated site-directed drug design: approaches to the formation of 3D molecular graphs. J. Comput. Aided Mol. Des., 4: 205–210.
18. Lewis, R., 1992. Automated site-directed drug design: a method for the generation of general three-dimensional molecular graphs. J. Mol. Graphics, 10: 131–143.
19. Liu, H., Muller-Plathe, F., and Van Gunsteren, W. F., 1996. A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease. J. Mol. Biol., 261: 454–469.
20. Miller, M. D., Sheridan, R. P., Kearsley, S. K., and Underwood, D., 1994, 1994. “Advances in automated docking applied to human immunodeficiency virus type 1 protease”. In Methods in Enzymology, 354–355. Academic Press.
21. Morris, G. M., Goodsell, D. S., Huey, R., and Olson, A. J., 1996. Distributed automated docking of flexible ligands ot proteins: parallel applications of AutoDock 2.4. J. Comp. Aided Mol. Design, 10: 293–304.
22. Pearlman, D. A., and Murcko, M., 1993. CONCEPTS: New dynamic algorithm for de novo drug suggestion. J. Comp. Chem., 14: 1184–1193.
23. Pearlman, D., and Murcko, M. A., 1996. CONCERTS: Dynamic connection of fragments as an approach to de novo ligand design. J. Med. Chem., 39: 1651–1663.
24. Pennisi, E., and Cohen, J., 1996. Eradicating HIV from a patient not just a dream?. Science, 272: 1884
25. Rosenfeld, R., Vajda, S., and DeLisi, C., 1995. Flexible docking design. Ann. Rev. Biophys. Biomol. Struct., 24: 677–700.
26. Slee, D. H., Laslo, K. L., Elder, J. H., Ollmann, I. R., Gustchina, A., Kervinen, J., Zdano, V., Wlodawer, A., and Wong, C.-H., 1995. Selectivity in the inhibition of HIV and FIV protease: Inhibitory and mechanistic studies of pyrrolidine-containing alpha-keto amide and hydroxyethylamine core structures. J. Am. Chem. Soc., 117: 11867–11878.
27. Solis, F. J., and Wets, R. J.-B., 1981. Minimization by random search techniques. Mathematical Operations Res., 6: 19–30.
28. Stouten, P., Frommel, C., Nakamura, H., and Sander, C., 1993. An effective solvation term based on atomic occupancies for use in protein simulations. Molecular Simulations, 10: 97–120.
29. Walker, W. L., Kopka, M. L., Dickerson, R. E., and Goodsell, D. S., 1997. Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method. J. Comput. Aided Mol. Des., in press
30. Weber, I. T., and Harrison, R. W., 1996. Molecular mechanics calculations on HIV-1 protease with peptide substrates correlate with experimental data. Prot. Engin., 9: 679–690.
31. Weber, L., Wallbaum, S., Broger, C., and Gubernator, K., 1995. Optimization of the biological activity of combinatorial compound libraries by a genetic algorithm. Angew. Chem. Int. Ed. Engl., 34: 2280–2282.
32. Wesson, L., and Eisenberg, D., 1992. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Prot. Sci., 1: 227–235.
33. West, M. L., and Fairlie, D. P., 1995. Targeting HIV-1 protease: a test of drug-design methodologies. Trends in Pharmacol. Sci., 16: 67–75.
34. Williams, D. H., Cox, J. P. L., Doig, A. J., Gardner, M., Gerhard, U., Kaye, P. T., Lal, A. R., Nicholls, I. A., Salter, C. J., and Mitchell, R. C., 1991. Toward the semiquantitative estimation of binding constants. Guides for peptide-peptide binding in aqueous solution. J. Am. Chem. Soc., 113: 7020–7030.