Theoretical studies on the molecular basis of HIV-1RT/NNRTIs interactions

References

• Barre-Sinoussi F, Chermann JC, Rey F, Nugeyre MT, Chamaret C, Gruest J, Dauguet C, Axler-Blin C, Vezinet-Brun F, Rouzinouset C, Rozenbaum W, Montagnier L. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science 1983;220:868–870.
   PubMed Web of Science ®Google Scholar
• Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA.Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 1992;256:1783–1790.
   PubMed Web of Science ®Google Scholar
• Hannongbua S, Nivesanond K, Lawtrakul L, Pungpo P, Wolschann P. 3D-Quantitative structure-activity relationships of HEPT derivatives as HIV-1 reverse transcriptase inhibitors, based on ab initio calculations. J Chem Inf Model 2001;41:848–855.
   Google Scholar
• De Clercq E. Antiviral drugs in current clinical use. J Clin Virol 2004;30:115–133.
   PubMed Web of Science ®Google Scholar
• Sarafianos SG, Das K, Hughes SH, Arnold E. Taking aim at a moving target: designing drugs to inhibit drug-resistant HIV-1 reverse transcriptases. Curr Opin Struct Biol 2004;14:716–730.
   PubMed Web of Science ®Google Scholar
• Ren J, Esnouf R, Garman E, Somers D, Ross C, Kirby I, Keeling J, Darby G, Jones Y, Stuart D, Stammers D. High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nat Struct Biol 1995;2:293–302.
   PubMedGoogle Scholar
• Das K, Clark AD, Jr Lewi, PJ, Heeres J, De Jonge MR, Koymans LMH, Vinkers HM, Daeyaert F, Ludovici DW, Kukla MJ, De Corte B, Kavash RW, Ho CY, Ye H, Lichtenstein MA, Andries K, Pauwels R, De Béthune MP, Boyer PL, Clark P, Hughes SH, Janssen PAJ, Arnold E. Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants. J Med Chem 2004;47:2550–2560.
   PubMed Web of Science ®Google Scholar
• Zhou Z, Madrid M, Evanseck JD, Madura JD. Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase. J Am Chem Soc 2005;127:17253–17260.
   PubMed Web of Science ®Google Scholar
• Rizzo RC, Udier-Blagovic´ M, Wang D-P, Watkins EK, Kroeger Smith MB, Smith RH Jr, Tirado-Rives 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.
   PubMed Web of Science ®Google Scholar
• Maggiolo F. Efavirenz. Expert Opin Pharmacother 2007;8:1137–1145.
   PubMed Web of Science ®Google Scholar
• Kehr HA, Olin JL, Love BL. Etravirine - a non-nucleoside reverse transcriptase inhibitor for the treatment of resistant HIV-1 infection. Formulary 2008;43:105–114.
   Google Scholar
• Mao C, Sudbeck EA, Venkatachalam TK, Uckun FM. Structure-based drug design of non-nucleoside inhibitors for wild-type and drug-resistant HIV reverse transcriptase. Biochem Pharmacol 2000;60:1251–1265.
   PubMed Web of Science ®Google Scholar
• Rodríguez-Barrios F, Balzarini J, Gago F. The molecular basis of resilience to the effect of the Lys103Asn mutation in non-nucleoside HIV-1 reverse transcriptase inhibitors studied by targeted molecular dynamics simulations. J Am Chem Soc 2005;127:7570–7578.
   PubMed Web of Science ®Google Scholar
• Vingerhoets J, Azijn H, Fransen E, De Baere I, Smeulders L, Jochmans D, Andries K, Pauwels R, De Bethune MP. TMC125 displays a high genetic barrier to the development of resistance: evidence from in vitro selection experiments. J Virol 2005;79:12773–12782.
   PubMed Web of Science ®Google Scholar
• Martinez-Picado J, Martinez MA. HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. Virus Res 2008;134:104–123.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Shen L, Shen J, Luo X, Cheng F, Xu Y, Chen K, Arnold E, Ding J, Jiang H. Steered molecular dynamics simulation on the binding of NNRTI to HIV-1 RT. Biophys J 2003;84:3547–3563.
   PubMed Web of Science ®Google Scholar
• Weinzinger P, Hannongbua S, Wolschann P. Molecular mechanics PBSA ligand binding energy and interaction of Efavirenz derivatives with HIV-1 reverse transcriptase. J Enzym Inhib Med Chem 2005;20:129–134.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Hopkins AL, Ren J, Esnouf RM, Willcox BE, Jones EY, Ross C, Miyasaka T, Walker RT, Tanaka H, Stammers DK, Stuart DI. 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 1996;39:1589–1600.
   PubMed Web of Science ®Google Scholar
• Caze DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Kollman PA. AMBER 9. University of California: San Francisco 2006.
   Google Scholar
• Li H, Robertson AD, Jensen JH. Very fast empirical prediction and interpretation of protein pKa values. Proteins 2005;61:704–721.
   PubMed Web of Science ®Google Scholar
• Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr TV, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03, Revision C.02. Wallingford CT, Gaussian; 2004.
   Google Scholar
• Cornell WD, Cieplak P, Bayly CI, Kollmann PA. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J Am Chem Soc 1993;115:9620–9631.
   Web of Science ®Google Scholar
• Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc 1995;117:5179–5197.
   Web of Science ®Google Scholar
• Wang JM, Wang W, Kollman PA. Antechamber: an accessory software package for molecular mechanical calculations. J Am Chem Soc 2001;222:U403–U403 (Abstr).
   Web of Science ®Google Scholar
• Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 2003;24:1999–2012.
   PubMed Web of Science ®Google Scholar
• Lee MC, Duan Y. Distinguish protein decoys by using a scoring function based on a new amber force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins 2004;55:620–634.
   PubMed Web of Science ®Google Scholar
• Jorgensen WL, Chandrasekhar J, Madura J, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926–935.
   Web of Science ®Google Scholar
• Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684–3690.
   Web of Science ®Google Scholar
• Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1997;23:327–341.
   Web of Science ®Google Scholar
• York DM, Darden TA, Pedersen LG. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J Chem Phys 1993;99:8345–8348.
   Web of Science ®Google Scholar
• Gilson MK, Sharp KA, Honig BH. Calculating the electrostatic potential of molecules in solution: method and error assessment. J Comput Chem 1987; 9:327–335.
   Web of Science ®Google Scholar
• Kottalam J, Case DA. Langevin modes of macromolecules: application to crambin and DNA hexamers. Biopolymers 1990;29:1409–1421.
   PubMed Web of Science ®Google Scholar
• Luo R, David L, Gilson MK. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem 2002;23:1244–1253.
   PubMed Web of Science ®Google Scholar
• Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc 1998;120:9401–9409.
   Web of Science ®Google Scholar
• Udier-Blagovic´ M, Tirado-Rives J, Jorgensen WL. Validation of a model for the complex of HIV-1 reverse transcriptase with nonnucleoside inhibitor TMC125. J Am Chem Soc 2003;125:6016–6017.
   PubMedGoogle Scholar
• Ren J, Chamberlain PP, Stamp A, Short SA, Weaver KL, Romines KR, Hazen R, Freeman A, Ferris RG, Andrews CW, Boone L, Chan JH, Stammers DK. Structural basis for the improved drug resistance profile of new generation benzophenone non-nucleoside HIV-1 reverse transcriptase inhibitors. J Med Chem 2008;51:5000–5008.
   PubMed Web of Science ®Google Scholar
• Hsiou Y, Ding J, Das K, Clark AD, Boyer PL, Lewi P, Janssen PAJ, Kleim JP, Rösner M, Hughes SH, Arnold E. The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance. J Mol Biol 2001;309:437–445.
   PubMed Web of Science ®Google Scholar