Docking, molecular dynamics and quantitative structure-activity relationship studies for HEPTs and DABOs as HIV-1 reverse transcriptase inhibitors

Journal of Molecular Modeling

Volumn 18, Issue 5, 2012, Pages 2185-2198

  Mao, Yating ^a   Li, Yan ^a   Hao, Ming ^a   Zhang, Shuwei ^a   Ai, Chunzhi ^b  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

Author keywords

3D QSAR; DABO; Docking; HEPT; HIV 1 RT inhibitor; MD

Indexed keywords

1 [(2 HYDROXYETHOXY)METHYL] 6 (PHENYLTHIO)THYMINE; 1 [(2 HYDROXYETHOXY)METHYL] 6 (PHENYLTHIO)THYMINE DERIVATIVE; DIHYDROALKOXYBENZYLOXOPYRIMIDINE DERIVATIVE; LYSINE; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR; TRYPTOPHAN; TYROSINE; UNCLASSIFIED DRUG; VALINE;

ARTICLE; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; COMPUTER MODEL; DRUG CONFORMATION; DRUG STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; HYDROPHOBICITY; ISOMER; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

AMINO ACIDS; ANTI-HIV AGENTS; BINDING SITES; DRUG DESIGN; HIV REVERSE TRANSCRIPTASE; HIV-1; HUMANS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PYRIMIDINONES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REVERSE TRANSCRIPTASE INHIBITORS; THYMINE;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84861229590     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1236-8     Document Type: Article

References (46)

1. John PB, François P, Patrick G (2011) Global trends in AIDS mortality. In: Richard GR, Eileen MC (eds) The international handbook of adult mortality. Springer, New York, pp 171-183
2. Barre-Sinoussi F, Chermann JC, Rey F, Nugeyre MT, Chamaret S, Gruest J, Dauguet C, Axler-Blin C, Vezinet-Brun F, Rouzioux C, Rozenbaum W, Montagnier L (1983) Isolation of a Tlymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science 220:868-871 (Pubitemid 13080157)
3. Gallo RC, Sarin PS, Gelmann EP, Robert-Guroff M, Richardson E, Kalyanaraman VS, Mann D, Sidhu GD, Stahl RE, Zolla-Pazner S, Leibowitch J, Popovic M (1983) Isolation of human T-cell leukemia virus in acquired immune deficiency syndrome (AIDS). Science 220:865-867 (Pubitemid 13080156)
4. Morris MC, Robert-Hebmann V, Chaloin L, Mery J, Heitz F, Devaux C, Goody RS, Divita G (1999) A new potent HIV-1 reverse transcriptase inhibitor. A synthetic peptide derived from the interface subunit domains. J Biol Chem 274:24941-24946
5. Gait MJ, Karn J (1995) Progress in anti-HIV structure-based drug design. Trends Biotechnol 13:430-438
6. Benbrik E, Chariot P, Bonavaud S, Ammi-SaId M, Frisdal E, Rey C, Gherardi R, Barlovatz-Meimon G (1997) Cellular and mitochondrial toxicity of zidovudine (AZT), didanosine (ddI) and zalcitabine (ddC) on cultured human muscle cells. J Neurol Sci 149:19-25 (Pubitemid 27196376)
7. De Clercq E (1993) HIV-1-specific RT inhibitors: highly selective inhibitors of human immunodeficiency virus type 1 that are specifically targeted at the viral reverse transcriptase. Med Res Rev 13:229-258 (Pubitemid 23114516)
8. Hopkins AL, Ren J, Esnouf RM, Willcox BE, Jones EY, Ross C, Miyasaka T, Walker RT, Tanaka H, Stammers DK, Stuart DI (1996) Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors. J Med Chem 39:1589-1600
9. Ren J, Esnouf R, Garman E, Somers D, Ross C, Kirby I, Keeling J, Darby G, Jones Y, Stuart D et al (1995) High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nat Struct Biol 2:293-302
10. Geretti AM (2006) Resistance to non-nucleoside reverse transcriptase inhibitors. Antiretroviral Resistance in Clinical Practice. Mediscript, London, Chapter 2
11. De Clercq E (2009) Anti-HIV drugs: 25 compounds approved within 25 years after the discovery of HIV. Int J Antimicrob Agents 33:307-320
12. De Clercq E (2009) The history of antiretrovirals: key discoveries over the past 25 years. Rev Med Virol 19:287
13. De Clercq E (2011) A 40-year journey in search of selective antiviral chemotherapy. Annu Rev Pharmacol Toxicol 51:1-24
14. Van de Waterbeemd H (1995) Introduction In Chemometric Methods in Drug Design. Chemometric Methods in Drug Design. VCH, Weinheim, chapter 1
15. Hao M, Li Y, Zhang S-W, Yang W (2011) Investigation on the binding mode of benzothiophene analogues as potent factor IXa (FIXa) inhibitors in thrombosis by CoMFA, docking and molecular dynamic studies. J Enzyme Inhib Med Chem. doi:10.3109/14756366.2011.554414
16. Liu J, Li Y, Zhang S, Xiao Z, Ai C (2011) Studies of new fused benzazepine as selective dopamine D3 receptor antagonists using 3D-QSAR, molecular docking and molecular dynamics. Int J Mol Sci 12:1196-1221
17. Zhang B, Li Y, Zhang H, Ai C (2010) 3D-QSAR and molecular docking studies on derivatives of MK-0457, GSK1070916 and SNS-314 as inhibitors against Aurora B kinase. Int J Mol Sci 11:4326-4347
18. Cramer RD, 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
19. 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 (Pubitemid 24379702)
20. Baba M, Tanaka H, De Clercq E, Pauwels R, Balzarini J, Schols D, Nakashima H, Perno CF, Walker RT, Miyasaka T (1989) Highly specific inhibition of human immunodeficiency virus type 1 by a novel 6-substituted acyclouridine derivative. Biochem Biophys Res Commun 165:1375-1381 (Pubitemid 20029862)
21. De Clercq E (1999) Perspectives of non-nucleoside reverse transcriptase inhibitors (NNRTIs) in the therapy of HIV-1 infection. II. Farmaco 54:26-45 (Pubitemid 29187015)
22. Campiani G, Ramunno A, Maga G, Nacci V, Fattorusso C, Catalanotti B, Morelli E, Novellino E (2002) Non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors: Past, present, and future perspectives (2002). Curr Pharm Design 8:615-657 (Pubitemid 34406406)
23. Artico M, Massa S, Mai A, Marongiu EM, Piras G, Tramontano E, Colla LP (1993) 3,4-Dihydro-2-alkoxy-6-benzyl-4-oxopyrimidines (DABOs): a new class of specific inhibitors of human immunodeficiency virus Type 1. Antiviral chemistry & chemotherapy, vol 4. International Medical Press, London, pp 361-368 (Pubitemid 23341334)
24. He Y, Chen F, Yu X, Wang Y, De Clercq E, Balzarini J, Pannecouque C (2004) Nonnucleoside HIV-1 reverse transcriptase inhibitors; part 3. Synthesis and antiviral activity of 5-alkyl-2- [(aryl and alkyloxyl-carbonylmethyl)thio]- 6-(1-naphthylmethyl) pyrimidin-4(3H)-ones. Bioorg Chem 32:536-548 (Pubitemid 39504948)
25. Ji L, Chen F-E, Feng X-Q, De Clercq E, Balzarini J, Pannecouque C (2006) Non-nucleoside HIV-1 reverse Transcriptase inhibitors, part 7. Synthesis, antiviral activity, and 3D-QSAR investigations of novel 6-(1-naphthoyl) HEPT analogues. Chem Pharm Bull 54:1248-1253 (Pubitemid 44351515)
26. Meng G, Chen FE, De Clercq E, Balzarini J, Pannecouque C (2003) Nonnucleoside HIV-1 reverse transcriptase inhibitors: Part I. Synthesis and structure-activity relationship of 1-alkoxymethyl- 5-alkyl-6-naphthylmethyl uracils as HEPT analogues. Chem Pharm Bull (Tokyo) 51:779-789 (Pubitemid 41694779)
27. Sun GF, Chen XX, Chen FE, Wang YP, De Clercq E, Balzarini J, Pannecouque C (2005) Nonnucleoside HIV-1 reverse-transcriptase inhibitors, part 5. Synthesis and anti-HIV-1 activity of novel 6- naphthylthio HEPT analogues. Chem Pharm Bull (Tokyo) 53:886-892 (Pubitemid 41327674)
28. Sun GF, Kuang YY, Chen FE, De Clercq E, Balzarini J, Pannecouque C (2005) Non-nucleoside HIV reverse transcriptase inhibitors, part 6[1]: synthesis and anti-HIV activity of novel 2- [(arylcarbonylmethyl)thio]-6-arylthio DABO analogues. Arch Pharm (Weinheim) 338:457-461 (Pubitemid 41564255)
29. Wang Y, Chen FE, Balzarini J, De Clercq E, Pannecouque C (2008) Non-nucleoside HIV-1 reverse-transcriptase inhibitors. Part 10. Synthesis and anti-HIV activity of 5-alkyl-6-(1-naphthylmethyl) pyrimidin-4(3H)-ones with a mono- or disubstituted 2- amino function as novel 'dihydro-alkoxy-benzyl- oxopyrimidine' (DABO) analogues. Chem Biodivers 5:168-176 (Pubitemid 351201004)
30. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron 36:3219-3228
31. Zhu Y-Q, Lei M, Lu A-J, Zhao X, Yin X-J, Gao Q-Z (2009) 3DQSAR studies of boron-containing dipeptides as proteasome inhibitors with CoMFA and CoMSIA methods. Eur J Med Chem 44:1486-1499
32. Deshpande S, Jaiswal S, Katti SB, Prabhakar YS (2011) CoMFA and CoMSIA analysis of tetrahydroquinolines as potential antimalarial agents. SAR QSAR Environ Res 1:1-16
33. Gerhard K (2002) Comparative molecular similarity indices analysis: CoMSIA. In: Hugo K, Gerd F, Yvonne CM (eds) 3D QSAR in Drug Design. Springer, New York, pp 87-104
34. Todeschini R, Consonni V, Mauri A, Pavan M (2004) DRAGON - Software for the calculation of molecular descriptors. Rel. 5.2 for Windows. Talete srl, Milano, Italy
35. Klebe G (1994) The use of composite crystal-field environments in molecular recognition and the de Novo design of protein ligands. J Mol Biol 237:212-235 (Pubitemid 24182235)
36. Caballero J, Quiliano M, Alzate-Morales JH, Zimic M, Deharo E (2011) Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H- pyrrolo[2,3-b]pyridin-4-yloxy)aniline, and 4-(4- amino-2-fluorophenoxy)-2- pyridinylamine derivatives as c-Met kinase inhibitors. J Comput Aided Mol Des 25:349-369
37. Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: A message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43-56
38. Lindahl E, Hess B, Van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306-317 (Pubitemid 36153547)
39. Aalten DMF, Bywater R, Findlay JBC, Hendlich M, Hooft RWW, Vriend G (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J Comput Aided Mol Des 10:255-262 (Pubitemid 126712820)
40. Schuttelkopf AW, van Aalten DMF (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr Sect D Biol Crystallogr 60:1355-1363 (Pubitemid 41079731)
41. Berendsen HFC, Postma JPM,Van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Inermolecular forces. Reidel, Dordrecht, pp 331-342
42. Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: A new molecular dynamics method. J Appl Phys 52:7182-7190 (Pubitemid 12456820)
43. Lin JH, Perryman AL, Schames JR, McCammon JA (2002) Computational drug design accommodating receptor flexibility: The relaxed complex scheme. J Am Ceram Soc 124:5632-5633 (Pubitemid 34533490)
44. Estrada E (1995) Edge adjacency relationships and a novel topological index related to molecular volume. J Chem Inf Comput Sci 35:31-33
45. Estrada E (1995) Edge adjacency relationships in molecular graphs containing heteroatoms: a new topological index related to molar volume. J Chem Inf Comput Sci 35:701-707
46. Meng G, Chen FE, De Clercq E (2003) Interactive study between two types of 1-[2-(Hydroxyethoxy)methyl]-6-naphthylmethylthymines and HIV-1 reverse transcriptase. Chin J Process Eng 3:24-28