Molecular modeling study of HIV-1 gp120 attachment inhibitors

Medicinal Chemistry Research

Volumn 21, Issue 8, 2012, Pages 1892-1904

  Gadhe, Changdev G ^a   Kothandan, Gugan ^a   Madhavan, Thirumurthy ^a   Cho, Seung Joo ^a  

^a Chosun University   (South Korea)

Author keywords

CoMFA; CoMSIA; Docking; gp120; HIV 1

Indexed keywords

GLYCOPROTEIN GP 120; INDOLE GLYOXAMIDE DERIVATIVE; PROTEIN INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; BIOLOGICAL ACTIVITY; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; DRUG POTENCY; DRUG STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; INHIBITION KINETICS; MOLECULAR DOCKING; MOLECULAR MODEL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; THREE DIMENSIONAL QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP;

EID: 84866091499     PISSN: 10542523     EISSN: 15548120     Source Type: Journal    
DOI: 10.1007/s00044-011-9711-4     Document Type: Article

References (39)

1. Bandres JC, Wang QF, O'Leary J, Baleaux F, Amara A, Hoxie JA, Zolla-Pazner S, Gorny MK (1998) Human immunodeficiency virus (HIV) envelope binds to CXCR4 independently of CD4, and binding can be enhanced by interaction with soluble CD4 or by HIV envelope deglycosylation. J Virol 72:2500-2504
2. Barbaro G, Scozzafava A, Mastrolorenzo A, Supuran CT (2005) Highly active antiretroviral therapy: current state of the art, new agents and their pharmacological interactions useful for improving therapeutic outcome. Curr Pharm Des 11:1805-1843
3. Barré-Sinoussi F, Chermann JC, Rey F, Nugeyre MT, Chamaret S, Gruest J, Dauguet C, Axler-Blin C, Vézinet-Brun F, Rouzioux C, Rozenbaum W, 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. Blair WS, Lin PF, Meanwell NA, Wallace OB (2000) HIV-1 entry-an expanding portal for drug discovery. Drug Discov Today 5:183-194
5. Borkow G, Lapidot A (2005) Multi-targeting the entrance door to block HIV-1. Curr Drug Targets Infect Disord 5:3-15
6. Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, Harrison SC (2005) Structure of an unliganded simian immunodeficiency virus gp120 core. Nature 433:834-841
7. Cramer RD III (1993) Partial least squares (PLS): its strengths and limitations. Perspect Drug Discov Des 1:269-278
8. Cramer RD III, Patterson DE, Bunce JD (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110:5959-5967
9. De Clercq E (1995) Toward improved anti-HIV chemotherapy: therapeutic strategies for intervention with HIV infections. J Med Chem 38:2491-2517
10. Dunn WJ III, Wold S, Edlund U, Hellberg S, Gasteiger J (1984) Multivariate structure-activity relationships between data from a battery of biological tests and an ensemble of structure descriptors: the PLS method. Quant Struct Act Relat 3:131-137
11. Gallo RC, Salahuddin SZ, Popovic M, Shearer GM, Kaplan M, Haynes BF, Palker TJ, Redfield R, Oleske J, Safai B, White G, Foster P, Markham PD (1984) Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS. Science 224:500-503
12. Guo Q, Ho HT, Dicker I, Fan L, Zhou N, Friborg J, Wang T, McAuliffe BV, Wang HG, Rose RE, Fang H, Scarnati HT, Langley DR, Meanwell NA, Abraham R, Colonno RJ, Lin PF (2003) Biochemical and genetic characterizations of a novel human immunodeficiency virus type 1 inhibitor that blocks gp120-CD4 interactions. J Virol 77:10528-10536
13. Harrison SC (2005) Mechanism of membrane fusion by viral envelope proteins. Adv Virus Res 64:231-261
14. Klebe G, Abraham U, Mietzner T (1994) Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J Med Chem 37:4130-4146
15. Kong R, Tan JJ, Ma XH, Chen WZ, Wang CX (2006) Prediction of the binding mode between BMS-378806 and HIV-1 gp120 by docking and molecular dynamics simulation. Biochim Biophys Acta 1764:766-772
16. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA (1998) Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393:648-659
17. Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, Sodroski J, Hendrickson WA (2000) Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure 8:1329-1339
18. Lin PF, Blair W, Wang T, Spicer T, Guo Q, Zhou N, Gong YF, Wang HG, Rose R, Yamanaka G, Robinson B, Li CB, Fridell R, Deminie C, Demers G, Yang Z, Zadjura L, Meanwell N, Colonno R (2003) A small molecule HIV-1 inhibitor that targets the HIV-1 envelope and inhibits CD4 receptor binding. Proc Natl Acad Sci USA 100:11013-11018
19. Lu P, Wei X, Zhang R (2010) CoMFA and CoMSIA studies on HIV-1 attachment inhibitors. Eur J Med Chem 45:1792-1798
20. Lucas GM, Cheever LW, Chaisson RE, Moore RD (2001) Detrimental effects of continued illicit drug use on the treatment of HIV-1, infection. J Acquir Immune Defic Syndr 27:251-259
21. Madani N, Perdigoto AL, Srinivasan K, Cox JM, Chruma JJ, LaLonde J, Head M, Smith AB III, Sodroski JG (2004) Localized changes in the gp120 envelope glycoprotein confer resistance to human immunodeficiency virus entry inhibitors BMS-806 and # 155. J Virol 78:3742-3752
22. Meanwell NA, Wallace OB, Wang H, Deshpande M, Pearce BC, Trehan A, Yeung KS, Qiu Z, Wright JJ, Robinson BA, Gong YF, Wang HG, Blair WS, Shi PY, Lin PF (2009) Inhibitors of HIV-1, attachment. Part 3: A preliminary survey of the effect of structural variation of the benzamide moiety on antiviral activity. Bioorg Med Chem Lett 19:5136-5139
23. Moore JP, Doms RW (2003) The entry of entry inhibitors: a fusion of science and medicine. Proc Natl Acad Sci USA 100:10598-10602
24. Richman DD (2001) HIV chemotherapy. Nature 410:995-1001
25. Ruppert J, Welch W, Jain AN (1997) Automatic identification and representation of protein binding sites for molecular docking. Protein Sci 6:524-533
26. Rusconi S, Scozzafava A, Mastrolorenzo A, Supuran CT (2004) New advances in HIV entry inhibitors development. Curr Drug Targets Infect Disord 4:339-355
27. Ryser HJ, Flückiger R (2005) Progress in targeting HIV-1 entry. Drug Discov Today 10:1085-1094
28. Schän A, Madani N, Klein JC, Hubicki A, Ng D, Yang X, Smith AB III, Sodroski J, Freire E (2006) Binding thermodynamics of a small-molecular-weight CD4 mimetic to HIV-1 gp120. Biochemistry 45:10973-10980
29. Si Z, Madani N, Cox JM, Chruma JJ, Klein JC, Schän A, Phan N, Wang L, Biorn AC, Cocklin S, Chaiken I, Freire E, Smith AB III, Sodroski JG (2004) Small-molecule inhibitors of HIV-1 entry block receptor-induced conformational changes in the viral envelope glycoproteins. Proc Natl Acad Sci USA 101:5036-5041
30. Stricher F, Martin L, Barthe P, Pogenberg V, Mechulam A, Menez A, Roumestand C, Veas F, Royer C, Vita C (2005) A highthroughput fluorescence polarization assay specific to the CD4, binding site of HIV-1 glycoproteins based on a fluoresceinlabelled CD4 mimic. Biochem J 390:29-39
31. Teixeira C, Serradji N, Maurel F, Barbault F (2009) Docking and 3DQSAR studies of BMS-806 analogs as HIV-1 gp120 entry inhibitors. Eur J Med Chem 44:3524-3532
32. Tripos Inc. (1699) South Hanley Road, St. Louis, 63144
33. UNAIDS (2008) Report on the global HIV/AIDS epidemic 2008: executive summary. http://www.unaids.org/en/KnowledgeCentre/HIVData/GlobalReport/2008/. Accessed 29 Aug 2010
34. Wang T, Zhang Z, Wallace OB, Deshpande M, Fang H, Yang Z, Zadjura LM, Tweedie DL, Huang S, Zhao F, Ranadive S, Robinson BS, Gong YF, Ricarrdi K, Spicer TP, Deminie C, Rose R, Wang HG, Blair WS, Shi PY, Lin PF, Colonno RJ, Meanwell NA (2003) Discovery of 4-benzoyl-1-[(4-methoxy-1H-yrrolo [2, 3-b] pyridin-3-yl) oxoacetyl]-2-(R)-methylpiperazine (BMS-378806): a novel HIV-1 attachment inhibitor that interferes with CD4-gp120 interactions. J Med Chem 46:4236-4239
35. Wignot TM, Stewart RP, Schray KJ, Das S, Sipos T (2004) In vitro studies of the effects of HAART drugs and excipients on activity of digestive enzymes. Pharm Res 21:420-427
36. Wold S, Sjästräm M, Eriksson L (2001) PLS-regression: a basic tool of chemometrics. Chemom Intell Lab Syst 58:109-130
37. Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, Hendrickson WA, Sodroski JG (1998) The antigenic structure of the HIV gp120 envelope glycoprotein. Nature 393:705-711
38. Xiang SH, Kwong PD, Gupta R, Rizzuto CD, Casper DJ, Wyatt R, Wang L, Hendrickson WA, Doyle ML, Sodroski J (2002) Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein. J Virol 76:9888-9899
39. Yang Z, Zadjura L, D'Arienzo C, Marino A, Santone K, Klunk L, Greene D, Lin PF, Colonno R, Wang T, Meanwell N, Hansel S (2005) Preclinical pharmacokinetics of a novel HIV-1 attachment inhibitor BMS-378806 and prediction of its human pharmacokinetics. Biopharm Drug Dispos 26:387-402