Identification of potential HIV-1 integrase strand transfer inhibitors: In silico virtual screening and QM/MM docking studies

SAR and QSAR in Environmental Research

Volumn 24, Issue 7, 2013, Pages 581-595

  Reddy, K K ^a   Singh, S K ^a   Tripathi, S K ^a   Selvaraj, C ^a  

^a ALAGAPPA UNIVERSITY   (India)

Author keywords

3D QSAR; HIV 1 IN pharmacophore; QM MM docking; virtual screening

Indexed keywords

COMPLEXATION; COMPUTATIONAL CHEMISTRY; MOLECULAR DYNAMICS; PHARMACODYNAMICS;

3D-QSAR; CATALYSE; DOCKING STUDIES; HIV-1 INTEGRASE; HIV-1 INTEGRASE PHARMACOPHORE; IN-SILICO; PHARMACOPHORE MODELS; PHARMACOPHORES; QM/MM DOCKING; VIRTUAL SCREENING;

HYDROGEN BONDS;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84887988777     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/1062936X.2013.772919     Document Type: Article

References (48)

1. Gottlieb, M.S., Schroff, R., Schanker, H.M., Weisman, J.D., Fan, P.T., Wolf, R.A. and Saxon, A. 1981. Pneumocystis carinii pneumonia and mucosal candidiasis in previously healthy homosexual men: Evidence of a new acquired cellular immunodeficiency. N. Engl. J. Med., 305: 1425 - 1431.
2. Masur, H., Michelis, M.A., Greene, J.B., Onorato, I., Stouwe, R.A., Holzman, R.S., Wormser, G., Brettman, L., Lange, M., Murray, H.W. and Cunningham-Rundles, S. 1981. An outbreak of community-acquired Pneumocystis carinii pneumonia: Initial manifestation of cellular immune dysfunction. N. Engl. J. Med., 305: 1431 - 1438.
3. Barre-Sinoussi, F., Chermann, J.C., Rey, F., Nugeyre, M.T., Chamaret, S., Gruest, J., Dauguet, C., Axler-Blin, C., Vezinet-Brun, F., Rouzioux, C., Rozenbaum, W. and Montagnier, L. 1983. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science, 220: 868 - 871.
4. Pandey, K.K. and Grandgenett, D.P. 2008. HIV-1 integrase strand transfer inhibitors: Novel insights into their mechanism of action. Retrovirology, 2: 11 - 16.
5. Ramkumar, K., Serrao, E., Odde, S. and Neamati, N. 2010. HIV-1 integrase inhibitors: 2007-2008 update. Med. Res. Rev., 30: 890 - 954.
6. Bushman, F.D. and Craigie, R. 1991. Activities of human immunodeficiency virus (HIV) integration protein in vitro: Specific cleavage and integration of HIV DNA. Proc. Natl. Acad. Sci. USA, 88: 1339 - 1343.
7. Seo, B.I., Uchil, V.R., Okello, M., Mishra, S., Ma, X.H., Nishonov, M., Shu, Q., Chi, G. and Nair, V. 2011. Discovery of a potent HIV integrase inhibitor that leads to a prodrug with significant anti-HIV activity. ACS Med. Chem. Lett., 2: 877 - 881.
8. Marcelin, A.G., Ceccherini-Silberstein, F., Perno, C.F. and Calvez, V. 2009. Resistance to novel drug classes. Curr. Opin. HIV AIDS, 4: 531 - 537.
9. Ceccherini-Silberstein, F., Malet, I., D'Arrigo, R., Antinori, A., Marcelin, A.G. and Perno, C.F. 2009. Characterization and structural analysis of HIV-1 integrase conservation. AIDS Rev., 11: 17 - 29.
10. Chow, S.A., Vincent, K.A., Ellison, V. and Brown, P.O. 1992. Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science, 255: 723 - 726.
11. Goodarzi, G., Im, G.J., Brackmann, K. and Grandgenett, D. 1995. Concerted integration of retrovirus-like DNA by human immunodeficiency virus type 1 integrase. J. Virol., 69: 6090 - 6097.
12. Kukolj, G. and Skalka, A.M. 1995. Enhanced and coordinated processing of synapsed viral DNA ends by retroviral integrases in vitro. Genes Dev., 9: 2556 - 2567.
13. Hayouka, Z., Rosenbluh, J., Levin, A., Loya, S., Lebendiker, M., Veprintsev, D., Kotler, M., Hizi, A., Loyter, A. and Friedler, A. 2007. Inhibiting HIV-1 integrase by shifting its oligomerization equilibrium. Proc. Natl. Acad. Sci. USA, 104: 8316 - 8321.
14. Goldgur, Y., Craigie, R., Cohen, G.H., Fujiwara, T., Yoshinaga, T., Fujishita, T., Sugimoto, H., Endo, T., Murai, H. and Davies, D.R. 1999. Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: A platform for antiviral drug design. Proc. Natl. Acad. Sci. USA, 96: 13040 - 13043.
15. Marchand, C., Maddali, K., Metifiot, M. and Pommier, Y. 2010. HIV-1 IN inhibitors, update and perspectives. Curr. Top. Med. Chem., 9 (2009): 1016 - 1037.
16. Cai, M., Zheng, R., Caffrey, M., Craigie, R., Clore, G.M. and Gronenborn, A.M. 1997. Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. Nat. Struct. Biol., 4: 567 - 577.
17. Dyda, F., Hickman, A.B., Jenkins, T.M., Engelman, A., Craigie, R. and Davies, D.R. 1994. Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases. Science, 266: 1981 - 1986.
18. Engelman, A. and Craigie, R. 1992. Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J. Virol., 66: 6361 - 6369.
19. Esposito, D. and Craigie, R. 1999. HIV integrase structure and function. Adv. Virus Res., 52: 319 - 333.
20. Masuda, T. 2011. Non-enzymatic functions of retroviral integrase: The next target for novel anti-HIV drug development. Front. Microbiol., 2: 210
21. Reddy, K.K., Singh, S.K., Dessalew, N., Tripathi, S.K. and Selvaraj, C. 2012. Pharmacophore modelling and atom-based 3D-QSAR studies on N-methyl pyrimidones as HIV-1 integrase inhibitors. J. Enzyme Inhib. Med. Chem., 27: 339 - 347.
22. Ojha, P.K. and Roy, K. 2011. Exploring QSAR, pharmacophore mapping and docking studies and virtual library generation for cycloguanil derivatives as PfDHFR-TS inhibitors. Med. Chem., 7: 173 - 199.
23. Lu, S.H., Wu, J.W., Liu, H.L., Zhao, J.H., Liu, K.T., Chuang, C.K., Lin, H.Y., Tsai, W.B. and Ho, Y. 2011. The discovery of potential acetylcholinesterase inhibitors: A combination of pharmacophore modeling, virtual screening, and molecular docking studies. J. Biomed. Sci., 18: 8
24. Phase, version 3.3, Schrödinger LLC, New York, NY, 2011; software available at http://www.schrodinger.com.
25. Dixon, S.L., Smondyrev, A.M., Knoll, E.H., Rao, S.N., Shaw, D.E. and Friesner, R.A. 2006. PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J. Comput. Aided Mol. Des., 20: 647 - 671.
26. Dixon, S.L., Smondyrev, A.M. and Rao, S.N. 2006. PHASE: A novel approach to pharmacophore modeling and 3D database searching. Chem. Biol. Drug Des., 67: 370 - 372.
27. Dror, O., Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. and Wolfson, H.J. 2009. Novel approach for efficient pharmacophore-based virtual screening: method and applications. J. Chem. Inf. Model., 49: 2333 - 2343.
28. Yang, S.Y. 2010. Pharmacophore modeling and applications in drug discovery: Challenges and recent advances. Drug Discov. Today, 15: 444 - 450.
29. Tang, J., Maddali, K., Dreis, C.D., Sham, Y.Y., Vince, R., Pommier, Y. and Wang, Z. 2011. 6-Benzoyl-3-hydroxypyrimidine-2,4-diones as dual inhibitors of HIV reverse transcriptase and integrase. Bioorg. Med. Chem. Lett., 21: 2400 - 2402.
30. Tang, J., Maddali, K., Metifiot, M., Sham, Y.Y., Vince, R., Pommier, Y. and Wang, Z. 2011. 3-Hydroxypyrimidine-2,4-diones as an inhibitor scaffold of HIV integrase. J. Med. Chem., 54: 2282 - 2292.
31. LigPrep, version 2.5, Schrödinger LLC, New York, NY, 2011; software available at http://www.schrodinger.com.
32. Jorgensen, W.L., Maxwell, D.S. and Tirado-Rives, J. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 118: 11225 - 11236.
33. Lipinski, C.A., Lombardo, F., Dominy, B.W. and Feeney, P.J. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev., 46: 3 - 26.
34. Glide, version 5.7, Schrödinger LLC, New York, NY, 2011; software available at http://www.schrodinger.com.
35. Friesner, R.A., Banks, J.L., Murphy, R.B., Halgren, T.A., Klicic, J.J., Mainz, D.T., Repasky, M.P., Knoll, E.H., Shelley, M., Perry, J.K., Shaw, D.E., Francis, P. and Shenkin, P.S. 2004. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem., 47: 1739 - 1749.
36. Prime, version 3.1, Schrödinger LLC, New York, NY, 2012; software available at http://www.schrodinger.com
37. Canvas, version 1.4, Schrödinger LLC, New York, NY, 2011; software available at http://www.schrodinger.com.
38. Tanimoto T. IBM internal report 1957. November; 1957.
39. Duan, J., Dixon, S.L., Lowrie, J.F. and Sherman, W. 2010. Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods. J. Mol. Graph. Model., 29: 157 - 170.
40. Sastry, M., Lowrie, J.F., Dixon, S.L. and Sherman, W. 2010. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. J. Chem. Inf. Model., 50: 771 - 784.
41. Schrödinger Suite 2011 QM-Polarized Ligand Docking protocol; Glide version 5.7, Schrödinger LLC, New York, NY, 2011; Jaguar version 7.8, Schrödinger LLC, New York, NY, 2011; QSite version 5.7, Schrödinger LLC, New York, NY, 2011; software available at http://www.schrodinger.com
42. Cho, A.E., Guallar, V., Berne, B.J. and Friesner, R. 2005. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J. Comput. Chem., 26: 915 - 931.
43. S. Tripathi, C. Selvaraj, S. Singh, and K. Reddy, Molecular docking, QPLD, and ADME prediction studies on HIV-1 integrase leads, Med. Chem. Res. (2012), pp. 1-13.
44. Desmond Molecular Dynamics System, version 3.1, D. E. Shaw Research, New York, NY, 2012. Maestro-Desmond Interoperability Tools, version 3.1, Schrödinger, New York, NY, 2012.
45. Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J. and Sherman, W. 2010. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J. Chem. Theory Comput., 6: 1509 - 1519.
46. Guo, Z., Mohanty, U., Noehre, J., Sawyer, T.K., Sherman, W. and Krilov, G. 2010. Probing the alpha-helical structural stability of stapled p53 peptides: Molecular dynamics simulations and analysis. Chem. Biol. Drug Des., 75: 348 - 359.
47. Tropsha, A. 2010. Best practices for QSAR model development, validation, and exploitation. Molec. Inf., 29: 476 - 488.
48. Alves, C.N., Marti, S., Castillo, R., Andres, J., Moliner, V., Tunon, I. and Silla, E. 2008. A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid. Biophysics J, 94: 2443 - 2451.