Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking

SAR and QSAR in Environmental Research

Volumn 14, Issue 4, 2003, Pages 251-264

  Chen, H F ^a,b   Dong, X C ^b   Zen, B S ^b   Gao, K ^c   Yuan, S G ^b   Panaye, A ^a   Doucet, J P ^a   Fan, B T ^a  

^a CNRS   (France)

^b SHANGHAI INSTITUTE OF ORGANIC CHEMISTRY   (China)

^c LANZHOU UNIVERSITY   (China)

Author keywords

3D QSAR; Docking; Drug design; Structure generation; Virtual screening

Indexed keywords

COMPUTATIONAL CHEMISTRY; DIAGNOSIS; MOLECULAR GRAPHICS; STRUCTURAL DESIGN; TUMORS;

3D-QSAR; BIOACTIVE COMPOUNDS; DESIGN METHOD; DOCKING; DRUG DESIGN; GENERATION SYSTEMS; QSAR MODEL; RATIONAL DRUG DESIGNS; STRUCTURE GENERATION; VIRTUAL SCREENING;

LEAD COMPOUNDS;

COLCHICINE;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER AIDED DESIGN; COMPUTER SIMULATION; DRUG DESIGN; DRUG SCREENING; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

COLCHICINE; COMPUTER SIMULATION; COMPUTER-AIDED DESIGN; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; MODELS, CHEMICAL; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0141797330     PISSN: 1062936X     EISSN: None     Source Type: Journal    
DOI: 10.1080/1062936032000101493     Document Type: Article

References (22)

1. Hong, H., Neamati, N., Wang, S.M., Nicklaus, M.C., Mazumder, A., Hzao, H., Burke, J.T.R., Pommier, Y. and Milne, G.W.A. (1997) "Discovery of HIV-1 integrase inhibitors by pharmacophore searching", J. Med. Chem. 40, 930-936.
2. Roberts, N.A., Martin, J.A., Kinchington, D., Broadhurst, A.V., Craig, J.C., Duncan, I.B., Galpin, S.A., Handa, B.K., Kay, J., Kröhn, A., Lambert, R.W., Merrett, J.H., Mills, J.S., Parkes, K.E.B., Redshaw, S., Ritchie, A.J., Taylor, D.L., Thomas, G.J. and Machin, P.J. (1990) "Rational design of peptide-based HIV-1 proteinase inhibitors", Science 248, 358-361.
3. Wlodawer, A. and Vondrasek, J. (1998) "Inhibitors of HIV-1 protease: a major success of structure-assisted drug design", Annu. Rev. Biophys. Biomol. Struct. 27, 249-284.
4. DesJarlais, R.L., Seibel, G.L., Kuntz, I.D., Montellano, P.O., Furth, P.S., Alvarez, J.C., DeCamp, D.L., Babé, L.M. and Craik, C.S. (1990) "Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease", Proc. Natl Acad. Sci. USA 87, 6644-6648.
5. Kuntz, I.D. (1992) "Structure-based strategies for drug design and discovery", Science 257, 1078-1082.
6. Matter, H. (1997) "Selecting optimally diverse compounds from structure database: a validation study of two-dimensional and three-dimensional molecular descriptors", J. Med. Chem. 40, 1219-1229.
7. Shuker, S.B., Hajduk, P.J., Meadows, R.P. and Fesik, S.W. (1996) "Discovering high-affinity ligands for proteins: SAR by NMR", Science 274, 1531-1534.
8. Chen, K.X., Jiang, H.L. and Ju, R.Y. (2000) Computer Aided Drug Design: Theory, Method and Application (Shanghai Science Technology Press, Shanghai), p. 187.
9. SYBYL, Version 6.8 (2001) St. Louis (MO): Tripos Associates Inc.
10. Holland, J.H. (1973) "Genetic algorithms and optimal allocations of trials", SIAM J. Comput. 2, 88-105.
11. Davis, L. (1991) Handbook of Genetic Algorithms (Van Nostrand Reinhold, New York), p. 385.
12. Goldberg, D.E. (1989) Genetic Algorithms in Search, Optimization & Machine Learning (Addison-Wesley, Reading, MA), p. 412.
13. Chen, H.F., Li, J.F., Yao, J.H., Yuan, S.G. and Zheng, C.Z. (2000) "Automatic generation of virtual bio-active compounds", Acta Chim. Sin. 58, 529-532.
14. Martin, Y.C., Bures, M.G., Danaher, E.A., DeLazzer, J., Lico, I. and Pavlik, P.A. (1993) "A fast new approach to pharmacophore mapping and its application of dopaminergic and benzodiazepine agoistes", J. Comput.-Aided Mol. Des. 7, 83-102.
15. Zhang, S.X., Feng, J., Kuo, S.C., Brossi, A., Hamel, E., Tropsha, A. and Lee, K.H. (2000) "Antitumor agents. 199. Three-dimensional quantitative structure-activity relationship study of the colchicine binding site ligands using comparative molecular field analysis", J. Med. Chem. 43, 167-176.
16. Ståhle, L. and Wold, S. (1988) Multivariate data analysis and experimental design in biomedical research, In: Ellis, G.P. and West, G.B., eds, Progress in Medical Chemistry (Elsevier Science Publishers, Amsterdam), p 291.
17. Cramer, I.R.D. (1993) "Partial least squares (PLS) strengths and limitations", Prespct. Drug Discov. Des. 1, 269-278.
18. Engelhardt, M. and Martens, U.M. (1998) "The implication of telomerase activity and telomere stability for replicative aging and cellular immortality", Oncol. Report 5, 1043-1052.
19. Schneider, S.R., Epplen, C., Radig, K., Oda, Y., Dralle, H., Hoang, V.C., Epplen, J.T. and Roessner, A. (1998) "On telomere shortening in soft-tissue tumors", J. Cancer Res. & Clin. Oncol. 124, 165-171.
20. Boultwood, J., Fidler, C., Shepherd, P., Watkins, F., Snowball, J., Haynes, S., Kusec, R., Gaiger, A., Littlewood, A., Peniket, A.J. and Wainscoat, J.S. (1999) "Telomere length shortening is associated with disease evolution in chronic myclogenous leukemia", Am. J. Hematol. 61, 5-9.
21. Lavery, R. (1988) The chemistry and biology of unusual DNA structures adopted by oligopurine oligopyrimidine sequences, In: Wells, R.D. and Harvey, S.C., eds, Unusual DNA Structures (Springer-Verlag, Berlin), p 189.
22. Lavery, R., Zakrzewska, K. and Sklenar, H. (1995) "JUMNA: junction minimization of nucleic acids", Comput. Phys. Commun. 91, 135-158.