Identification of LOGP values and electronegativities as structural insights to model inhibitory activity of HIV-1 capsid inhibitors - A SVM and MLR aided QSAR studies

Current Topics in Medicinal Chemistry

Volumn 12, Issue 16, 2012, Pages 1763-1774

  Sharma, Nishant ^a   Ethiraj, K R ^a   Yadav, Mukesh ^b   Anuraj Nayarisseri, S ^c   Chaurasiya, Mona ^d   Vankudavath, Raju Naik ^d   Rajender Rao, K ^d  

^a VIT UNIVERSITY   (India)

^b Softvision College   (India)

^c Bioinformatics Research Laboratory   (India)

^d NATIONAL INSTITUTE OF NUTRITION   (India)

Author keywords

AIDS; HIV 1 capsid; MLR; Non linear QSAR; QSAR; SVM. linear QSAR

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE INHIBITOR;

ARTICLE; COMPUTER PROGRAM; ELECTRONEGATIVITY; HUMAN; IC 50; KERNEL METHOD; LOGP; MODEL; MOLECULAR DOCKING; MULTIPLE LINEAR REGRESSION ANALYSIS; PHYSICAL PARAMETERS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SUPPORT VECTOR MACHINE; VALIDATION PROCESS;

CAPSID; CELL LINE; HIV-1; HUMANS; INHIBITORY CONCENTRATION 50; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84875333767     PISSN: 15680266     EISSN: 18734294     Source Type: Journal    
DOI: 10.2174/156802612803989309     Document Type: Article

References (33)

1. UNAIDS & WHO (2007). IDS Epidemic Update-Dec 06. Joint United Nations Programme on HIV/AIDS (UNAIDS) and World Health Organization (WHO) 2006.
2. Hall, H.I.; Ruiguang, S.; Rhodes P. et al., Estimation of HIV Incidence in united states. JAMA, 2008, 300, 520-529.
3. Rossmann, M. G.; Antiviral agents targeted to interact with viral capsid proteins and a possible application to human immunodeficiency virus. Proc. Natl Acad. Sci. USA, 1988, 85, 4625-4627.
4. Li, S.; Hill, Christopher P.; Sundquist Wesley I. & Finch, John T.; Image reconstructions of helical assemblies of the HIV-1 CA protein. Nature, 2000, 407, 409-413.
5. Ganser, B. K.; Li, S.; Klishko, V. Y.; Finch, John; Sundquist, t.; Assembly and analysis of conical models for the HIV-1 core. Science, 1999, 283, 80-83.
6. Briggs, J. A; Wilk, T.; Welker, R.; Krausslich, H. G.; Fuller, S. D; Structural organization of authentic, mature HIV-1 virions and cores. EMBO J., 2003, 22, 1707-1715.
7. Briggs, J. A.; Grunewald, K.; Glass, B.; Forster, F.; Krausslich, H.G.; Fuller, S.D.; The mechanism of HIV-1 core assembly: insights from three-dimensional reconstructions of authentic virions. Structure, 2006, 14, 15-20.
8. Neira Jose L, The capsid protein of human immunodeficiency virus: designing inhibitors of capsid assembly. FEBS J., 2009, 276(21), 6110-6117.
9. Curreli, F.; Zhang, H.; Zhang, X.; Pyatkin, I.; Victor, Z.; Altieri, A.; Debnath, A.K. Virtual screening based identification of novel small-molecule inhibitors targeted to the HIV-1 capsid. Bioorg. Med. Chem., 2011, 19, 77-90.
10. Wiegers, K.; Rutter, G.; Kottler, H.; Tessmer, U.; Hohenberg, H.; Krausslich, H.G.; Sequential Steps in Human Immunodeficiency Virus Particle Maturation Revealed by Alterations of Individual Gag Polyprotein Cleavage Sites, J. Virol., 1998, 72, 2846-2854.
11. Briggs, J. A.; Simon, M. N.; Gross, I.; Krausslich, H. G.; Fuller, S. D., Vogt, V. M. and Johnson, M. C. The stoichiometry of Gag protein in HIV-1. Nat. Struct. Mol. Biol., 2004, 11, 672-675.
12. Mauricio G. Mateu. The capsid protein of human immunodeficiency virus: intersubunit interactions during virus assembly. FEBS Journal., 2009, 276, 6098-6109.
13. Jin, Z.; Jin, L; Peterson, D.L., Lawson, C.L.; Model for lentivirus capsid core assembly based on crystal dimers of EIAV p26. J. Mol. Biol., 1999, 286, 83-93.
14. Briggs, J.A.; Johnson, M.C.; Simon, M.N.; Fuller, S.D.; Vogt, V. M; Cryo-electron microscopy reveals conserved and divergent features of Gag packing in immature particles of Rous sarcoma virus and human immunodeficiency virus. J. Mol. Biol., 2006, 355, 157-168.
15. Gitti, R.K.; Lee, B.M.; Walker, J.; Summers, M.F., Yoo, S.; Sundquist, W.I.; Structure of the amino-terminal core domain of the HIV-1 capsid protein. 1996, 273, 231-235.
16. Gamble, T.R.; Yoo, S.; Vajdos, F.F.; von Schwedler, U.K.; Worthylake, D.K.; Wang, H.; McCutcheon, J.P.; Sundquist, W.I.; Hill, C.P.; Structure of the carboxyl-terminal dimerization domain ofthe HIV-1 capsid protein. Science, 1997, 278, 849-853.
17. Gamble, T. R.; Vajdos, F. F.; Yoo, S.; Worthylake, D. K.; Houseweart, M.; Sundquist, W. I; Hill, C. P.; Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid. Cell, 1996, 87, 1285-1294.
18. Tama, F.; Brooks 3rd, C.L.; Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J. Mol. Biol., 2005, 345, 299-314.
19. Verkhivker, G.; Tiana, G.; Camilloni, C.; Provasi, D.; Broglia, R. A.; Atomistic simulations of the HIV-1 protease folding inhibition. Biophys. J., 2008, 95, 550-562.
20. Yu, X.; Wang, Q.; Yang, J.C.; Buch, I.; Tsai, C.J.; Ma, B.; Cheng, S.Z.; Nussinov, R.; and Zheng, J. Mutational Analysis and Allosteric Effects in the HIV-1 Capsid Protein Carboxyl-Terminal Dimerization Domain, Biomacromolecules, 2009, 10, 390-399.
21. Forshey, B.M.; von Schwedler, U.; Sundquist, W.I.; and Aiken, C.; Formation of a human immunodeficiency virus type 1 core of optimal stability is crucial for viral replication. J. Virol., 2002, 76, 5667-5677.
22. http://www.chemaxon.com/free-software/
23. http://www.vcclab.org/lab/pclient/
24. http://www.strandls.com/sarchitect/freetrial.php.
25. Pavlidis, P.; Wapinski, I.; Noble, WS; Support vector machine classification on the web. Bioinformatics, 2004, 20, 586-587.
26. Vapnik, V. N.; The nature of statistical learning theory. Verlag Springer: New York, 1999.
27. Furey, T.; Cristianini, N.; Duffy, N.; Bednarski, D.; Schummer, M.; Haussler, D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics, 2000, 16, 906-914.
28. Norinder, U.; Support vector machine models in drug design: application to drug transport processes and QSAR using simplex optimizations and variable selection. Neurocomputing, 2003, 55, 337-346.
29. Cortes, C.; Vapnik, V.; Support-Vector Networks. Mach. Learn., 1995, 20, 273-297.
30. Vapnik, V.; The Support Vector method of function estimation. U.S. Patent 5, 950, 146, 1999.
31. Scior, T.; Medina-Franco, J.L.; Do, Q.-T.; Martínez-Mayorga, K.; Yunes Rojas J. A. and Bernard, P.; How to Recognize and Workaround Pitfalls in QSAR Studies: A Critical Review, Curr. Med. Chem., 2009, 16, 4297-4313.
32. Stouch, T. R.; Kenyon, J. R.; Johnson, S. R.; Chen, X.-Q.; Doweyko, A. and Li, Y.; In Silico ADME/Tox: Why Models Fail. J. Comput.-Aided Mol., 2003, 17, 83-92.
33. Polanski, J.; Bak, A.; Gieleciak, R. and Magdziarz, T. Modeling Robust QSAR. J. Chem. Inf. Model., 2006, 46, 2310-2318.