Computer-aided molecular design of highly potent HIV-1 RT inhibitors: 3D QSAR and molecular docking studies of efavirenz derivatives

SAR and QSAR in Environmental Research

Volumn 17, Issue 4, 2006, Pages 353-370

  Pungpo, P ^a   Saparpakorn, P ^b   Wolschann, P ^c   Hannongbua, S ^b  

^a UBON RATCHATHANI UNIVERSITY   (Thailand)

^b KASETSART UNIVERSITY   (Thailand)

^c UNIVERSITY OF VIENNA   (Austria)

Author keywords

3D QSAR; CoMFA; CoMSIA; Docking; Efavirenz; NNRTIs

Indexed keywords

BINDING ENERGY; COMPUTATIONAL CHEMISTRY; MOLECULAR GRAPHICS; MOLECULAR ORBITALS; X RAY CRYSTALLOGRAPHY;

3D-QSAR; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE SIMILARITIES; COMPARATIVE SIMILARITY INDEX ANALYSE; DOCKING; EFAVIRENZ; HIV-1 REVERSE TRANSCRIPTASE; INDEX ANALYSIS; NNRTI; SIMILARITY INDICES;

LIGANDS;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33747758048     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/10629360600884520     Document Type: Article

References (31)

1. E. de Clercq. Med. Res. Rev., 22, 531 (2002).
2. R.M. Gulick. Clin. Microbiol. Infect., 9, 186 (2003).
3. C. Tantillo, J. Ding, A. Jacobo-Molina, R.G. Nanni, P.L. Boyer, S.H. Hughes, R. Pauwels, K. Andries, P.A. Jannsen, E. Arnold. J. Mol. Biol., 243, 369 (1994).
4. D. Richman, C.K. Shih, I. Lowy, J. Rose, P. Prodanovich, S. Goff, J. Griffin. Proc. Nat. Acad. Sci. U.S.A., 88, 11241 (1991).
5. S.D. Young, S.F. Britcher, L.O. Tran, L.S. Payne, W.C. Lumma, T.A. Lyle, J.R. Huff, P.S. Anderson, D.B. Olsen, S.S. Carroll, D.J. Pettibone, J.A. O'Brien, R.G. Ball, S.K. Balani, J.H. Lin, I-W. Chen, W.A. Schleif, V.V. Sardana, W.J. Long, V.W. Byrnes, E.A. Emini. Antimicrob. Agents Chemother., 39, 2602 (1995).
6. L. Bacherler, S. Jeffrey, G. Hanna, R. D'Aquila, L. Wallace, K. Logue, B. Cordova, K. Hertogs, B. Larder, R. Buckery, D. Baker, K. Gallagher, H. Scarnati, R. Tritch, C. Rizzo. J. Virol., 75, 4999 (2001).
7. J.W. Corbett, S.S. Ko, J.D. Rodgers, L.A. Gearhart, N.A. Magnus, L.T. Bacheler, S. Diamond, S. Jeffrey, R.M. Klabe, B.C. Cordova, S. Garber, K. Logue, G.L. Trainor, P.S. Anderson, S.K. Erickson-Viitanen. J. Med. Chem., 43, 2019 (2000).
8. J.W. Corbett, S. Pan, J.A. Markwalder, B.C. Cordova, R.M. Klabe, S. Garber, J.D. Rodgers, S.K. Erickson-Vitanen. Bioorg. Med. Chem. Lett., 11, 211 (2001).
9. A.J. Cocuzza, D.R. Chidester, B.C. Cordova, S. Jeffrey, R.L. Parsons, L.T. Bacheler, S. Erickson-Viitanen, G.L. Trainor, S.S. Ko. Bioorg. Med. Chem. Lett., 11, 1177 (2001).
10. A.J. Cocuzza, D.R. Chidester, B.C. Cordova, R.M. Klabe, S. Jeffrey, S. Diamond, C.A. Weigelt, S.S. Ko, L.T. Bacheler, S. Erickson-Viitanen, J.D. Rodgers. Bioorg. Med. Chem. Lett., 11, 1389 (2001).
11. J. Ren, J. Milton, K.L. Weaver, S.A. Short, D.I. Stuart, D.K. Stammers. Structure, 8, 1089 (2000).
12. J. Lindberg, S. Sigurosson, S. Lowgren, H.O. Andersson, C. Sahlberg, R. Noreen, K. Fridborg, H. Zhang, T. Unge. Eur. J. Biochem., 269, 1670 (2002).
13. M. Udier-Blagovic, E.K. Watkins, J. Tirado-Rives, W.L. Jorgensen. Bioorg. Med. Chem. Lett., 13, 3337 (2003).
14. F. Rodriguez-Barrios, J. Balzarini, F. Gago. J. Am. Chem. Soc., 127, 7570 (2005).
15. M.L. Barreca, A. Rao, L.D. Luca, M. Zappala, A.M. Monforte, G. Maga, C. Pannecouque, J. Balzarini, E.D. Clercq, A. Chimirri, P. Monforte. J. Med. Chem., 48, 3433 (2005).
16. R.D. Cramer III, D.E. Patterson, J.D. Bunce. J. Am. Chem. Soc., 110, 5959 (1988).
17. G. Klabe, U. Abraham, T. Mietzner. J. Med. Chem., 37, 4130 (1994).
18. H. Kubinyi, 3D QSAR in Drug Design: Theory, Methods and Applications, ESCOM Science Publishers, Leiden (1993).
19. S. Hannongbua, P. Pungpo, P. Wolschann. J. Comp.-Aided Mol. Des., 13, 563 (1999).
20. P. Pungpo, S. Hannongbua. J. Mol. Grap. Mod., 18, 581 (2000).
21. S. Hannongbua, K. Nivesanond, L. Lawtrakul, P. Pungpo, P. Wolschann. J. Chem. Inf. Compul. Sci., 41, 848 (2001).
22. R. Thaimattam, P. Daga, S. Abdul Rajjak, R. Banerjee, J. Iqbal. Bioorg. Med. Chem. Lett., 14, 6415 (2004).
23. H. Zhang, H. Li, C. Liu. J. Chem. Inf. Model., 45, 440 (2005).
24. Y. Guo, J. Xiao, Z. Guo, F. Chu, Y. Cheng, S. Wu. Bioorg. Med. Chem., 13, 5424 (2005).
25. A. Gangjee, X. Lin. J. Med. Chem., 48, 1448 (2005).
26. L.T. Bacheler, M. Paul, P.K. Jadhav, M. Otto, J. Miller. Antiviral. Chem. Chemother., 5, 111 (1994).
27. Alchemy 2000, Tripos Associates Inc., St. Louis, MO (1998).
28. M.L. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Montgomery, R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B.G. Johnson, W. Chen, M.W. Wong, J.L. Andres, M. Head-Gordon, E.S. Replongle, and J.A. Pople, GAUSSIAN 98, Gaussian, Inc. Pittsburgh, PA (1998).
29. SYBYL 6.9, TRIPOS, Assoc., Inc., St. Louis, MO (1998).
30. G. Jones, P. Wilett, R.C. Glen, A.R. Leach, R. Taylor. J. Mol. Biol., 267, 727 (1997).
31. M. Rarey, B. Kramer, T. Lengauer, G. Klebe. J. Mol. Biol., 261, 470 (1996).