Coevolution and subsite decomposition for the design of resistance-evading HIV-1 protease inhibitors

Journal of Molecular Biology

Volumn 287, Issue 1, 1999, Pages 77-92

  Rosin, Christopher D ^a,b   Belew, Richard K ^b   Walker, Wynn L ^a   Morris, Garrett M ^a   Olson, Arthur J ^a   Goodsell, David S ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

AIDS therapy; Coevolution; Computer aided drug design; Drug resistance; HIV 1 protease

Indexed keywords

ISOLEUCINE; LEUCINE; PHENYLALANINE; PROTEINASE; PROTEINASE INHIBITOR; VALINE;

ARTICLE; CONTROLLED STUDY; DRUG DESIGN; DRUG STRUCTURE; ENZYME SUBUNIT; NONHUMAN; PRIORITY JOURNAL; VIRUS RESISTANCE;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0033583083     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2579     Document Type: Article

References (23)

1. Chou K.-C., Tomasselli A. G., Reardon I. M., Heinrikson R. L. Predicting human immunodeficiency virus protease cleavage sites in proteins by a discriminant function method. Proteins: Struct. Funct. Genet. 24:1996;51-72.
2. Darke P. L., Huff J. R. HIV protease as an inhibitor target for the treatment of AIDS. Advan. Pharmacol. 25:1994;399-455.
3. Deeks S. G., Smith M., Holodniy M., Kahn J. O. HIV-1 protease inhibitors: a review for clinicians. J. Am. Med. Assoc. 277:1997;145-153.
4. Erickson J. W., Burt S. K. Structural mechanisms of HIV drug resistance. Annu. Rev. Pharmacol. Toxicol. 36:1996;545-571.
5. Gulnik S. V., Suvorov L. I., Liu B., Yu B., Anderson B., Mitsuya H., Erickson J. W. Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure. Biochemistry. 34:1995;9282-9287.
6. Jerison H. J. Evolution of the Brain and Intelligence. 1973;Academic Press, New York.
7. Kempf D. J. Progress in the discovery of orally bioavailable inhibitors of HIV protease. Perspect. Drug Discov. Design. 2:1995;427-436.
8. Lee T., Laco G. S., Torbett B. E., Fox H. S., Lerner D. L., Elder J. H., Wong C.-H. Analysis of the S3 and S3′ subsite specificities of FIV protease; development of a broad-based protease inhibitor efficacious against FIV, SIV and HIV in vitro and ex vivo. Proc. Natl Acad. Sci. USA. 95:1998;939-944.
9. Mitchell M. An Introduction to Genetic Algorithms. 1996;MIT Press, Cambridge.
10. Pettitt S. C., Simsic J., Loeb D. D., Everitt L., Hutchison C. A., Swanstrom R. Analysis of retroviral protease cleavage sites reveals two types of cleavage sites and the structural requirements of the P1 amino acid. J. Biol. Chem. 266:1991;14539-14547.
11. Poorman R. A., Tomasselli A. G., Heinrikson R. L., Kezdy F. J. A cumulative specificity model for proteases from human immunodeficiency virus types 1 and 2, inferred from statistical analysis of an extended substrate data base. J. Biol. Chem. 266:1991;14554-14561.
12. Reynolds C. W. Competition, coevolution, and the game of tag. Brooks R. A. Artificial Life IV. 1994;MIT Press, Cambridge.
13. Rose J. R., Babe L. M., Craik C. S. Defining the level of HIV-1 protease activity required for HIV-1 particle maturation and infectivity. J. Virol. 69:1995;2751-2758.
14. Rosin C. D., Belew R. K. A competitive approach to game learning. Blum A., Kearns M. Ninth Annual Conference on Computational Learning Theory. 1996;292-302 Association for Computing Machinery, New York.
15. Rosin C. D., Belew R. K. New methods for competitive coevolution. Evolutionary Comput. 5:1997;1-29.
16. Rosin C. D., Belew R. K., Morris G. M., Olson A. J., Goodsell D. S. Coevolutionary analysis of resistance-evading peptidomimetic inhibitors of HIV-1 protease. Proc. Natl Acad. Sci. USA. 96:1998a;1369-1374.
17. Rosin C. D., Belew R. K., Morris G. M., Olson A. J., Goodsell D. S. Computational coevolution of antiviral drug resistance. Adami C., Belew R. K., Kitano H., Taylor C. E. Sixth Annual Conference on Artifical Life. 1998b;81-90 MIT Press, Cambridge.
18. Sippl M. J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5:1995;229-235.
19. Skalka A. M. Retroviral proteases: first glimpses at the anatomy of a processing machine. Cell. 56:1989;911-913.
20. Tang J., Hartsuck J. A. A kinetic model for comparing proteolytic processing activity and inhibitor resistance potential of mutant HIV-1 proteases. FEBS Letters. 367:1995;112-116.
21. West M. L., Fairlie D. P. Targeting HIV-1 protease: a test of drug-design methodologies. Trends Pharmacol. Sci. 16:1995;67-75.
22. Wlodawer A., Erickson J. W. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62:1993;543-585.
23. Zhang Y.-M., Imamichi H., Imamichi T., Lane H. C., Falloon J., Vasudevachari M. B., Salzman N. P. Drug resistance during indinavir therapy is caused by mutations in the protease gene and its Gag substrate cleavage sites. J. Virol. 71:1997;6662-6670.