Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations

Proteins: Structure, Function and Genetics

Volumn 61, Issue 2, 2005, Pages 423-432

  He, Xiao ^a   Mei, Ye ^a   Xiang, Yun ^b   Zhang, Da W ^b   Zhang, John Z H ^a,b  

^a NANJING UNIVERSITY   (China)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NEVIRAPINE; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR; VIRUS ENZYME;

ARTICLE; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; DRUG PROTEIN BINDING; ENERGY; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MOLECULAR INTERACTION; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; QUANTUM MECHANICS; VIRUS RESISTANCE;

ANTI-HIV AGENTS; BINDING SITES; COMPUTATIONAL BIOLOGY; DRUG DESIGN; DRUG RESISTANCE, VIRAL; HIV-1 REVERSE TRANSCRIPTASE; MODELS, MOLECULAR; NEVIRAPINE; POINT MUTATION; QUANTUM THEORY; REVERSE TRANSCRIPTASE INHIBITORS;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 26444446031     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20578     Document Type: Article

References (35)

1. Parker WB, White EL, Shaddix SC, Ross LJ, Buckheit Jr, KW, Germany JM, Secrist JAd, Vince R, Shannon WM, Mechanism of inhibition of human-immunodeficiency-virus type-1 reverse transcriptase and human DNA polymerase-alpha, polymerasebeta-beta, and polymerase-gamma by the 5′-triphosphates of carbovir, 3′-azido-3′-deoxythymidine, 2′,3′-dideoxyguanosine, and 3′-deoxythymidine-a novel RNA template for the evaluation of antiretroviral drugs. J Biol Chem 1991;266:1754-1762.
2. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA. Crystal-structure at 3.5Å resolution of HIV-1 reverse-transcriptase complexed with an inhibitor. Science 1992;25:1783-1790.
3. Rizzo RC, Tirado-Rives J, Jorgensen WL. Estimation of binding affinities for HEPT and nevirapine analogues with HTV-1 reverse transcriptase via Monte Carlo simulations. J Med Chem 2001;44: 145-154.
4. Mitsuya H, Yarchoan R, Broder S. Molecular targets for aids therapy. Science 1990;249:1533-1544.
5. Katz RA, Skala AM. The retroviral enzymes. Ann Rev Biochem 1994;63:133-173.
6. Wang J, Morin P, Wang W, Kollman PA. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc 2001;123: 5221-5230.
7. Kopp EB, Miglietla JJ, Shrutkowski AG, Shih CK, Grob PM, Skoog MT. Steady state kinetics and inhibition of HIV1 reverse transcriptase by a nonnucleoside dipyridodiazepinone, BI-RG-587, using a heteropolymeric template. Nature 1991;19:3035-3039.
8. Romero DL, Bussa M, Tan CK, Reusser F, Palmer JR, Poppe SM, Aristoff PA, Downery KM, So AG, Resnick L, Tarpley WG. Nonnucleoside reverse transcriptase inhibitors that potently and specifically block human immunodeficiency virus type 1 replication. Proc Natl Acad Sci USA 1991;88:8806-8810.
9. Archer RH, Wisniewski M, Bambara RA, Demeter LM. The Y181C mutant of HIV-1 reverse transcriptase resistant to nonnucleoside reverse transcriptase inhibitors alters the size distribution of RNase H cleavages. Biochemistry 2001;40:4087-4095.
10. De Clercq E. Nonnucleoside reverse transcriptase inhibitors (NNRTIs) for the treatment of human immunodeficiency virus type 1 (HIV-1) infections: strategies to overcome drug resistance development. Med Res Rev 1996;16:125-157.
11. Jonckheere H, Anne J, De Clercq E. The HIV-1 reverse transcription (RT) process as target for RT inhibitors. Med Res Rev 2000;2:129-154.
12. Bacheler LT. Resistance to nonnucleoside inhibitors of HIV-1 reverse transcriptase. Drug Resist Updates 1999;2:56.
13. Richman D, Shih CK, Lowy I, Rose J, Prodanovich P, Goff S, Griffin J. Human immunodeficiency virus type 1 mutants resistant to nonnucleoside inhibitors of reverse transcriptase arise in tissue culture. Proc Natl Acad Sci USA 1991;88:11241-11245.
14. Richman DD, Havlir D, Corbeil J, Looney D, Ignacio C, Spector SA, Sullivan J, Cheeseman S, Barringer K, Pauletti D, et al. Nevirapine resistance mutations of human immunodeficiency virus type 1 selected during therapy. J Virol 1994;68:1660-1666.
15. De Clercq E. New developments in anti-HIV chemotherapy. Biochim Biophys Acta 2002;1587:258-275.
16. Corbett JW, Ko SS, Rodgers JD, Gearhart LA, Magnus NA, Bacheler LT, Diamond S, Jeffrey S, Klabe RM, Cordova BC, Garber S, Logue K, Trainor GL, Anderson PS, Erickson-Viitanen SK. Inhibition of clinically relevant mutant variants of HIV-1 by quinazolinone non-nucleoside reverse transcriptase inhibitors. J Med Chem 2000;43:2019-2030.
17. Young SD, Britcher SF, Tran LO, Payne LS, Lumma WC, Lyle TA, Huff JR, Anderson PS, Olsen DB, Carroll SS, Pettibone DJ, O'Brien JA, Ball RG, Balani SK, Lin JH, Chen IW, Schleif WA, Sardana W, Long WJ, Byrnes VW, Emini EA. L-743,726 (DMP-266): a novel, highly potent nonnucleoside inhibitor of the human immunodeficiency virus type 1 reverse transcriptase. Antimicrob Agents Chemother 1995;39:2602-2605.
18. Sardana VV, Emini EA, Gotlib L, Graham DJ, Lineberger DW, Long WJ, Schlabach AJ, Wolfgang JA, Condra JH. Functional analysis of HIV-1 revserse transcriptase amino acids involved in resistance to multiple non-nucleoside inhibitors. J Biol Chem 1992;267:17526-17530.
19. Richman DD. Resistance of clinical isolates of human immunodeficiency virus to antiretroviral agents. Antimicrob Agents Chemother 37;1993:1207-1213,
20. Schinazi RF, Larder BA, Mellors JW. Mutations in retroviral genes associated with drug resistance; 2000-2001 update. Int Antiviral News 2000;6:65-91.
21. Maseras F, Morokuma K. IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states. J Comput Chem 1995;16: 1170-1179.
22. Nakano T, Kaminuma T, Sato T, Akiyama Y, Uebayasi M, Kitaura K. Fragment molecular orbital method: application to polypeptides. Chem Phys Lett 2000;318:614-618.
23. Zhang DW, Zhang JZH. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J Chem Phys 2003;119:3599-3605.
24. Kuno M, Hannongbua S, Morokuma K. Theoretical investigation on nevirapine and HIV-1 reverse transcriptase binding site interaction, based on ONIOM method. Chem Phys Lett 2003;380:456-463.
25. Zhang DW, Chen XH, Zhang JZH. Molecular caps for full quantum mechanical computation of peptide-water interaction energy. J Comput Chem 2003;24:1846-1852.
26. Chen XH, Zhang DW, Zhang JZH. Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules. J Chem Phys 2004;120:839-844.
27. Zhang DW, Zhang JZH. Full ab initio computation of protein-water interaction energies. J Theo Comput Chem 2004;3:43-49.
28. Zhang DW, Y. Xiang, Zhang J.Z.H. New advance in computational chemistry: Full quantum mechanical ab initio computation of streptavidin-biotin interaction energy. J Phys Chem B 2003;107: 12039-12041.
29. Zhang DW, Xiang Y, Gao AM, Zhang JZH. Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex. J Chem Phys 2004;120:1145-1148.
30. Ren J, Esnouf R, Garman E, Somers D, Ross C, Kirby I, Keeling J, Darby G, Jones Y, Stuart D, et al. High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nat Struct Biol 1995;2:293-302.
31. Ren J, Milton J, Weaver KL, Short SA, Stuart DI, Stammers DK. Structural basis for the resilience of efavirenz (DMP-266) to drug resistance mutations in HIV-1 reverse transcriptase. Structure Fold Des 2000;8:1089-1094.
32. Ren J, Nichols C, Bird L, Chamberlain P, Weaver K, Short S, Stuart DI, Stammers DK. Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors. J Mol Biol 2001;312:795-805.
33. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham III TE, Del Bolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995;91:1-41.
34. Xiang Y, Zhang JZH. Fully quantum mechanical energy optimization for protein-ligand structure. J Comput Chem 2004;25:1431-1437.
35. Rizzo RC, UdierBlagovic M, Wang DP, Watkins EK, Kroeger Smith MB, Smith Jr RH, TiradoRives J, Jorgensen WL. Prediction of activity for nonnucleoside inhibitors with HIV-1 reverse transcriptase based on Monte Carlo simulations. J Med Chem 2002;45: 2970-2987.