In silico study on indole derivatives as anti HIV-1 agents: A combined docking, molecular dynamics and 3D-QSAR study

Archives of Pharmacal Research

Volumn 37, Issue 8, 2014, Pages 1001-1015

  Balupuri, Anand ^a   Gadhe, Changdev G ^a   Balasubramanian, Pavithra K ^a   Kothandan, Gugan ^a   Cho, Seung Joo ^a  

^a Chosun University   (South Korea)

Author keywords

CoMFA; gp120; HIV 1 entry inhibitors; MM GBSA; Molecular docking; Molecular dynamics simulation

Indexed keywords

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; GLYCOPROTEIN GP 120; GP120 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; INDOLE DERIVATIVE; PROTEIN BINDING;

CHEMICAL STRUCTURE; CHEMISTRY; DRUG EFFECTS; HUMAN IMMUNODEFICIENCY VIRUS 1; METABOLISM; MOLECULAR DOCKING; MOLECULAR DYNAMICS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REGRESSION ANALYSIS;

ANTI-HIV AGENTS; HIV ENVELOPE PROTEIN GP120; HIV-1; INDOLES; LEAST-SQUARES ANALYSIS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84889963135     PISSN: 02536269     EISSN: 19763786     Source Type: Journal    
DOI: 10.1007/s12272-013-0313-1     Document Type: Article

References (34)

1. Berger, E.A., P.M. Murphy, and J.M. Farber. 1999. Chemokine receptors as HIV-1 coreceptors: Roles in viral entry, tropism, and disease. Annual Review of Immunology 17: 657-700.
2. Blacklow, S.C., M. Lu, and P.S. Kim. 1995. Trimeric subdomain of the simian immunodeficiency virus envelope glycoprotein. Biochemistry 34: 14955-14962.
3. Bosch, M.L., P.L. Earl, K. Fargnoli, S. Picciafuoco, F. Giombini, F. Wong-Staal, and G. Franchini. 1989. Identification of the fusion peptide of primate immunodeficiency viruses. Science 244: 694-697.
4. Brasseur, R., B. Cornet, A. Burny, M. Vandenbranden, and J.M. Ruysschaert. 1988. Mode of insertion into a lipid membrane of the N-terminal HIV gp41 peptide segment. AIDS Research and Human Retroviruses 4: 83-90.
5. Clark, M., R.D. Cramer, and V.N. Opdenbosch. 1989. Validation of the general purpose Tripos 5.2 force field. Journal of Computational Chemistry 10: 982-1012.
6. Case, D.A., T.A. Darden, T.E. Cheatham III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, and K.M. Merz. 2012. AMBER 12. San Francisco: University of California.
7. Dalgleish, A.G., P.C.L. Beverley, P.R. Clapham, D.H. Crawford, M.F. Greaves, and R.A. Weiss. 1984. The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus. Nature 312: 763-767.
8. Dorr, P., M. Westby, S. Dobbs, P. Griffin, B. Irvine, M. Macartney, J. Mori, G. Rickett, C. Smith-Burchnell, and C. Napier. 2005. Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity. Antimicrobial Agents and Chemotherapy 49: 4721-4732.
9. Essmann, U., L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen. 1995. A smooth particle mesh Ewald method. Journal of Chemical Physics 103: 8577-8593.
10. Gadhe, C.G., G. Kothandan, T. Madhavan, and S.J. Cho. 2012. Molecular modeling study of HIV-1 gp120 attachment inhibitors. Medicinal Chemistry Research 21: 1892-1904.
11. Gasteiger, J., and M. Marsili. 1980. Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 36: 3219-3228.
12. Helseth, E., U. Olshevsky, D. Gabuzda, B. Ardman, W. Haseltine, and J. Sodroski. 1990. Changes in the transmembrane region of the human immunodeficiency virus type 1 gp41 envelope glycoprotein affect membrane fusion. Journal of Virology 64: 6314-6318.
13. Hornak, V., R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling. 2006. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure Function, and Bioinformatics 65: 712-725.
14. Hou, T., J. Wang, Y. Li, and W. Wang. 2011. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling 51: 69-82.
15. Kadow, J., H.G. Wang, and P.F. Lin. 2006. Small-molecule HIV-1 gp120 inhibitors to prevent HIV-1 entry: An emerging opportunity for drug development. Current Opinion in Investigational Drugs 7: 721-726.
16. Kilby, J.M., S. Hopkins, T.M. Venetta, B. Dimassimo, G.A. Cloud, J.Y. Lee, L. Alldredge, E. Hunter, D. Lambert, and D. Bolognesi. 1998. Potent suppression of HIV-1 replication in humans by T-20, a peptide inhibitor of gp41-mediated virus entry. Nature Medicine 4: 1302-1307.
17. Kong, R., J.J. Tan, X.H. Ma, W.Z. Chen, and C.X. Wang. 2006. Prediction of the binding mode between BMS-378806 and HIV-1 gp120 by docking and molecular dynamics simulation. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1764: 766-772.
18. Kowalski, M., J. Potz, L. Basiripour, T. Dorfman, W.C. Goh, E. Terwilliger, A. Dayton, C. Rosen, W. Haseltine, and J. Sodroski. 1987. Functional regions of the envelope glycoprotein of human immunodeficiency virus type 1. Science 237: 1351-1355.
19. Lasky, L.A., G. Nakamura, D.H. Smith, C. Fennie, C. Shimasaki, E. Patzer, P. Berman, T. Gregory, and D.J. Capon. 1987. Delineation of a region of the human immunodeficiency virus type 1 gp120 glycoprotein critical for interaction with the CD4 receptor. Cell 50: 975-985.
20. Lu, M., S.C. Blacklow, and P.S. Kim. 1995. A trimeric structural domain of the HIV-1 transmembrane glycoprotein. Nature Structural & Molecular Biology 2: 1075-1082.
21. Morris, G.M., D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson. 1998. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry 19: 1639-1662.
22. Morris, G.M., R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, and A.J. Olson. 2009. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry 30: 2785-2791.
23. Powell, M.J.D. 1977. Restart procedures for the conjugate gradient method. Mathematical Programming 12: 241-254.
24. Sanner, M.F. 1999. Python: A programming language for software integration and development. Journal of Molecular Graphics and Modelling 17: 57-61.
25. Teixeira, C., J.R.B. Gomes, P. Gomes, F.F. Maurel, and F. Barbault. 2011. Viral surface glycoproteins, gp120 and gp41, as potential drug targets against HIV-1: Brief overview one quarter of a century past the approval of zidovudine, the first anti-retroviral drug. European Journal of Medicinal Chemistry 46: 979-992.
26. Teixeira, C., N. Serradji, S. Amroune, K. Storck, C. Rogez-Kreuz, P. Clayette, F. Barbault, and F. Maurel. 2013. Is the conformational flexibility of piperazine derivatives important to inhibit HIV-1 replication? Journal of Molecular Graphics and Modelling 44: 91-103.
27. Teixeira, C., N. Serradji, F. Maurel, and F. Barbault. 2009. Docking and 3D-QSAR studies of BMS-806 analogs as HIV-1 gp120 entry inhibitors. European Journal of Medicinal Chemistry 44: 3524-3532.
28. Wang, J., R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case. 2004. Development and testing of a general amber force field. Journal of Computational Chemistry 25: 1157-1174.
29. Wold, S., A. Ruhe, H. Wold, and I.W. Dunn. 1984. The collinearity problem in linear regression. The partial least squares (PLS) approach to generalized inverses. SIAM Journal on Scientific and Statistical Computing 5: 735-743.
30. Wyatt, R., and J. Sodroski. 1998. The HIV-1 envelope glycoproteins: Fusogens, antigens, and immunogens. Science 280: 1884-1888.
31. Xiang, S.H., P.D. Kwong, R. Gupta, C.D. Rizzuto, D.J. Casper, R. Wyatt, L. Wang, W.A. Hendrickson, M.L. Doyle, and J. Sodroski. 2002. Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein. Journal of Virology 76: 9888-9899.
32. Yeung, K.S., Z. Qiu, Q. Xue, H. Fang, Z. Yang, L. Zadjura, C.J. D'Arienzo, B.J. Eggers, K. Riccardi, and P.Y. Shi. 2013a. Inhibitors of HIV-1 attachment. Part 7: Indole-7-carboxamides as potent and orally bioavailable antiviral agents. Bioorganic & Medicinal Chemistry Letters 23: 198-202.
33. Yeung, K.S., Z. Qiu, Z. Yin, A. Trehan, H. Fang, B. Pearce, Z. Yang, L. Zadjura, C.J. D'Arienzo, and K. Riccardi. 2013b. Inhibitors of HIV-1 attachment. Part 8: The effect of C7-heteroaryl substitution on the potency, and in vitro and in vivo profiles of indole-based inhibitors. Bioorganic & Medicinal Chemistry Letters 23: 203-208.
34. Zhan, P., W. Li, H. Chen, and X. Liu. 2010. Targeting protein-protein interactions: A promising avenue of anti-HIV drug discovery. Current Medicinal Chemistry 17: 3393-3409.