메뉴 건너뛰기




Volumn 2, Issue 11, 2010, Pages 2509-2535

Molecular basis for drug resistance in HIV-1 protease

Author keywords

Drug resistance; HIV 1 protease; Protease inhibitors; Structure based drug design; Substrate envelope

Indexed keywords

AMPRENAVIR; ATAZANAVIR; DARUNAVIR; FOSAMPRENAVIR; GAG PROTEIN; INDINAVIR; LOPINAVIR; LOPINAVIR PLUS RITONAVIR; NELFINAVIR; POL PROTEIN; PROTEINASE; PROTEINASE INHIBITOR; RITONAVIR; SAQUINAVIR; TIPRANAVIR;

EID: 79952171610     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v2112509     Document Type: Article
Times cited : (114)

References (128)
  • 1
    • 54249158122 scopus 로고    scopus 로고
    • The Joint United Nations Program on HIV/AIDS (UNAIDS), UNAIDS/08.25E/JC1510E; UNAIDS: Geneva, Switzerland
    • The Joint United Nations Program on HIV/AIDS (UNAIDS). 2008 Report on the Global AIDS Epidemic; UNAIDS/08.25E/JC1510E; UNAIDS: Geneva, Switzerland, 2008.
    • (2008) 2008 Report On the Global AIDS Epidemic
  • 2
    • 73549088708 scopus 로고    scopus 로고
    • Molecular basis of human immunodeficiency virus drug resistance: An update
    • Menendez-Arias, L. Molecular basis of human immunodeficiency virus drug resistance: An update. Antivir. Res. 2010, 85, 210-231.
    • (2010) Antivir. Res , vol.85 , pp. 210-231
    • Menendez-Arias, L.1
  • 3
    • 35348992176 scopus 로고    scopus 로고
    • Protease inhibitor resistance in HIV-infected patients: Molecular and clinical perspectives
    • Martinez-Cajas, J.L.; Wainberg, M.A. Protease inhibitor resistance in HIV-infected patients: Molecular and clinical perspectives. Antivir. Res. 2007, 76, 203-221.
    • (2007) Antivir. Res , vol.76 , pp. 203-221
    • Martinez-Cajas, J.L.1    Wainberg, M.A.2
  • 4
    • 73549092917 scopus 로고    scopus 로고
    • Fifteen years of HIV Protease Inhibitors: Raising the barrier to resistance
    • Wensing, A.M.; van Maarseveen, N.M.; Nijhuis, M. Fifteen years of HIV Protease Inhibitors: Raising the barrier to resistance. Antivir. Res. 2010, 85, 59-74.
    • (2010) Antivir. Res , vol.85 , pp. 59-74
    • Wensing, A.M.1    van Maarseveen, N.M.2    Nijhuis, M.3
  • 5
    • 77249134151 scopus 로고    scopus 로고
    • Twenty-six years of anti-HIV drug discovery: Where do we stand and where do we go
    • Mehellou, Y.; De Clercq, E. Twenty-six years of anti-HIV drug discovery: Where do we stand and where do we go? J. Med. Chem. 2010, 53, 521-538.
    • (2010) J. Med. Chem , vol.53 , pp. 521-538
    • Mehellou, Y.1    de Clercq, E.2
  • 11
    • 0028846226 scopus 로고
    • Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme
    • Kim, E.E.; Baker, C.T.; Dwyer, M.D.; Murcko, M.A.; Rao, B.G.; Tung, R.D.; Navia, M.A. Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme. J. Am. Chem. Soc. 1995, 117, 1181-1182.
    • (1995) J. Am. Chem. Soc , vol.117 , pp. 1181-1182
    • Kim, E.E.1    Baker, C.T.2    Dwyer, M.D.3    Murcko, M.A.4    Rao, B.G.5    Tung, R.D.6    Navia, M.A.7
  • 15
    • 19544386471 scopus 로고    scopus 로고
    • TMC114, a novel human immunodeficiency virus type 1 protease inhibitor active against protease inhibitor-resistant viruses, including a broad range of clinical isolates
    • De Meyer, S.; Azijn, H.; Surleraux, D.; Jochmans, D.; Tahri, A.; Pauwels, R.; Wigerinck, P.; de Bethune, M.P. TMC114, a novel human immunodeficiency virus type 1 protease inhibitor active against protease inhibitor-resistant viruses, including a broad range of clinical isolates. Antimicrob. Agents Chemother. 2005, 49, 2314-2321.
    • (2005) Antimicrob. Agents Chemother , vol.49 , pp. 2314-2321
    • de Meyer, S.1    Azijn, H.2    Surleraux, D.3    Jochmans, D.4    Tahri, A.5    Pauwels, R.6    Wigerinck, P.7    de Bethune, M.P.8
  • 19
    • 0035958773 scopus 로고    scopus 로고
    • Overview of the effectiveness of triple combination therapy in antiretroviral-naive HIV-1 infected adults
    • Bartlett, J.A.; DeMasi, R.; Quinn, J.; Moxham, C.; Rousseau, F. Overview of the effectiveness of triple combination therapy in antiretroviral-naive HIV-1 infected adults. AIDS 2001, 15, 1369-1377.
    • (2001) AIDS , vol.15 , pp. 1369-1377
    • Bartlett, J.A.1    Demasi, R.2    Quinn, J.3    Moxham, C.4    Rousseau, F.5
  • 22
    • 0346025675 scopus 로고    scopus 로고
    • Pharmacological and therapeutic properties of ritonavir-boosted protease inhibitor therapy in HIV-infected patients
    • Zeldin, R.K.; Petruschke, R.A. Pharmacological and therapeutic properties of ritonavir-boosted protease inhibitor therapy in HIV-infected patients. J. Antimicrob. Chemother. 2004, 53, 4-9.
    • (2004) J. Antimicrob. Chemother , vol.53 , pp. 4-9
    • Zeldin, R.K.1    Petruschke, R.A.2
  • 23
    • 67649631240 scopus 로고    scopus 로고
    • Approaches to the design of HIV protease inhibitors with improved resistance profiles
    • Gulnik, S.V.; Eissenstat, M. Approaches to the design of HIV protease inhibitors with improved resistance profiles. Curr. Opin. HIV AIDS 2008, 3, 633-641.
    • (2008) Curr. Opin. HIV AIDS , vol.3 , pp. 633-641
    • Gulnik, S.V.1    Eissenstat, M.2
  • 24
    • 67649628164 scopus 로고    scopus 로고
    • New approaches to HIV protease inhibitor drug design II: Testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors
    • Nalam, M.N.L.; Schiffer, C.A. New approaches to HIV protease inhibitor drug design II: Testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors. Curr. Opin. HIV AIDS 2008, 3, 642-646.
    • (2008) Curr. Opin. HIV AIDS , vol.3 , pp. 642-646
    • Nalam, M.N.L.1    Schiffer, C.A.2
  • 25
    • 38949203748 scopus 로고    scopus 로고
    • Design of HIV protease inhibitors targeting protein backbone: An effective strategy for combating drug resistance
    • Ghosh, A.K.; Chapsal, B.D.; Weber, I.T.; Mitsuya, H. Design of HIV protease inhibitors targeting protein backbone: An effective strategy for combating drug resistance. Acc. Chem. Res. 2008, 41, 78-86.
    • (2008) Acc. Chem. Res , vol.41 , pp. 78-86
    • Ghosh, A.K.1    Chapsal, B.D.2    Weber, I.T.3    Mitsuya, H.4
  • 26
    • 67649946397 scopus 로고    scopus 로고
    • Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: Synthesis, biological evaluation, and protein-ligand X-ray studies
    • Ghosh, A.K.; Leshchenko-Yashchuk, S.; Anderson, D.D.; Baldridge, A.; Noetzel, M.; Miller, H.B.; Tie, Y.; Wang, Y.F.; Koh, Y.; Weber, I.T.; Mitsuya, H. Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: Synthesis, biological evaluation, and protein-ligand X-ray studies. J. Med. Chem. 2009, 52, 3902-3914.
    • (2009) J. Med. Chem , vol.52 , pp. 3902-3914
    • Ghosh, A.K.1    Leshchenko-Yashchuk, S.2    Anderson, D.D.3    Baldridge, A.4    Noetzel, M.5    Miller, H.B.6    Tie, Y.7    Wang, Y.F.8    Koh, Y.9    Weber, I.T.10    Mitsuya, H.11
  • 28
    • 0345358532 scopus 로고    scopus 로고
    • Lysine sulfonamides as novel HIV-protease inhibitors: Optimization of the Nepsilon-acyl-phenyl spacer
    • Stranix, B.R.; Sauve, G.; Bouzide, A.; Cote, A.; Sevigny, G.; Yelle, J. Lysine sulfonamides as novel HIV-protease inhibitors: Optimization of the Nepsilon-acyl-phenyl spacer. Bioorg. Med. Chem. Lett. 2003, 13, 4289-4292.
    • (2003) Bioorg. Med. Chem. Lett , vol.13 , pp. 4289-4292
    • Stranix, B.R.1    Sauve, G.2    Bouzide, A.3    Cote, A.4    Sevigny, G.5    Yelle, J.6
  • 30
    • 0031804609 scopus 로고    scopus 로고
    • Inhibitors of HIV-1 protease: A major success of structure-assisted drug design
    • Wlodawer, A.; Vondrasek, J. Inhibitors of HIV-1 protease: A major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 249-284.
    • (1998) Annu. Rev. Biophys. Biomol. Struct , vol.27 , pp. 249-284
    • Wlodawer, A.1    Vondrasek, J.2
  • 37
    • 0036121219 scopus 로고    scopus 로고
    • Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes
    • Prabu-Jeyabalan, M.; Nalivaika, E.A.; Schiffer, C.A. Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes. Structure 2002, 10, 369-381.
    • (2002) Structure , vol.10 , pp. 369-381
    • Prabu-Jeyabalan, M.1    Nalivaika, E.A.2    Schiffer, C.A.3
  • 38
    • 5444247213 scopus 로고    scopus 로고
    • Combating susceptibility to drug resistance: Lessons from HIV-1 protease
    • King, N.M.; Prabu-Jeyabalan, M.; Nalivaika, E.A.; Schiffer, C.A. Combating susceptibility to drug resistance: Lessons from HIV-1 protease. Chem. Biol. 2004, 11, 1333-1338.
    • (2004) Chem. Biol , vol.11 , pp. 1333-1338
    • King, N.M.1    Prabu-Jeyabalan, M.2    Nalivaika, E.A.3    Schiffer, C.A.4
  • 39
    • 6344231715 scopus 로고    scopus 로고
    • Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor
    • King, N. M.; Prabu-Jeyabalan, M.; Nalivaika, E. A.; Wigerinck, P.; de Bethune, M. P.; Schiffer, C. A. Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor. J. Virol. 2004, 78, 12012-12021.
    • (2004) J. Virol , vol.78 , pp. 12012-12021
    • King, N.M.1    Prabu-Jeyabalan, M.2    Nalivaika, E.A.3    Wigerinck, P.4    de Bethune, M.P.5    Schiffer, C.A.6
  • 40
    • 55049134097 scopus 로고    scopus 로고
    • Resilience to resistance of HIV-1 protease inhibitors: Profile of darunavir
    • Lefebvre, E.; Schiffer, C.A. Resilience to resistance of HIV-1 protease inhibitors: Profile of darunavir. AIDS Rev. 2008, 10, 131-142.
    • (2008) AIDS Rev , vol.10 , pp. 131-142
    • Lefebvre, E.1    Schiffer, C.A.2
  • 41
    • 79952123638 scopus 로고    scopus 로고
    • Stanford HIV Drug Resistance Database, accessed on 20 October 2010
    • Stanford HIV Drug Resistance Database. Available online: http://hivdb.Stanford.edu (accessed on 20 October 2010).
  • 42
    • 20244387096 scopus 로고    scopus 로고
    • Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments
    • Wu, T.D.; Schiffer, C.A.; Gonzales, M.J.; Taylor, J.; Kantor, R.; Chou, S.; Israelski, D.; Zolopa, A.R.; Fessel, W.J.; Shafer, R.W. Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J. Virol. 2003, 77, 4836-4847.
    • (2003) J. Virol , vol.77 , pp. 4836-4847
    • Wu, T.D.1    Schiffer, C.A.2    Gonzales, M.J.3    Taylor, J.4    Kantor, R.5    Chou, S.6    Israelski, D.7    Zolopa, A.R.8    Fessel, W.J.9    Shafer, R.W.10
  • 43
    • 0029151345 scopus 로고
    • Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure
    • Gulnik, S.V.; Suvorov, L.I.; Liu, B.; Yu, B.; Anderson, B.; Mitsuya, H.; Erickson, J.W. Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure. Biochemistry 1995, 34, 9282-9287.
    • (1995) Biochemistry , vol.34 , pp. 9282-9287
    • Gulnik, S.V.1    Suvorov, L.I.2    Liu, B.3    Yu, B.4    Anderson, B.5    Mitsuya, H.6    Erickson, J.W.7
  • 44
    • 0031692748 scopus 로고    scopus 로고
    • Genotypic and phenotypic characterization of human immunodeficiency virus type 1 variants isolated from patients treated with the protease inhibitor nelfinavir
    • Patick, A.; Duran, M.; Cao, Y.; Shugarts, D.; Keller, M.; Mazabel, E.; Knowles, M.; Chapman, S.; Kuritzkes, D.; Markowitz, M. Genotypic and phenotypic characterization of human immunodeficiency virus type 1 variants isolated from patients treated with the protease inhibitor nelfinavir. Antimicrob. Agents Chemother. 1998, 42, 2637-2644.
    • (1998) Antimicrob. Agents Chemother , vol.42 , pp. 2637-2644
    • Patick, A.1    Duran, M.2    Cao, Y.3    Shugarts, D.4    Keller, M.5    Mazabel, E.6    Knowles, M.7    Chapman, S.8    Kuritzkes, D.9    Markowitz, M.10
  • 46
    • 2442657656 scopus 로고    scopus 로고
    • Identification of I50L as the signature atazanavir (ATV)-resistance mutation in treatment-naive HIV-1-infected patients receiving ATV-containing regimens
    • Colonno, R.; Rose, R.; McLaren, C.; Thiry, A.; Parkin, N.; Friborg, J. Identification of I50L as the signature atazanavir (ATV)-resistance mutation in treatment-naive HIV-1-infected patients receiving ATV-containing regimens. J. Infect. Dis. 2004, 189, 1802-1810.
    • (2004) J. Infect. Dis , vol.189 , pp. 1802-1810
    • Colonno, R.1    Rose, R.2    McLaren, C.3    Thiry, A.4    Parkin, N.5    Friborg, J.6
  • 47
    • 0032500125 scopus 로고    scopus 로고
    • Activity of a ritonavir plus saquinavir-containing regimen in patients with virologic evidence of indinavir or ritonavir failure
    • Deeks, S.G.; Grant, R.M.; Beatty, G.W.; Horton, C.; Detmer, J.; Eastman, S. Activity of a ritonavir plus saquinavir-containing regimen in patients with virologic evidence of indinavir or ritonavir failure. AIDS Res. Hum. Retroviruses 1998, 12, F97-F102.
    • (1998) AIDS Res. Hum. Retroviruses , vol.12
    • Deeks, S.G.1    Grant, R.M.2    Beatty, G.W.3    Horton, C.4    Detmer, J.5    Eastman, S.6
  • 49
    • 0033534115 scopus 로고    scopus 로고
    • HIV-1 genotypic resistance patterns predict response to saquinavir-ritonavir therapy in patients in whom previous protease inhibitor therapy had failed
    • Zolopa, A.R.; Shafer, R.W.; Warford, A.; Montoya, J.G.; Hsu, P.; Katzenstein, D.; Merigan, T.C.; Efron, B. HIV-1 genotypic resistance patterns predict response to saquinavir-ritonavir therapy in patients in whom previous protease inhibitor therapy had failed. Ann. Intern. Med. 1999, 131, 813-821.
    • (1999) Ann. Intern. Med , vol.131 , pp. 813-821
    • Zolopa, A.R.1    Shafer, R.W.2    Warford, A.3    Montoya, J.G.4    Hsu, P.5    Katzenstein, D.6    Merigan, T.C.7    Efron, B.8
  • 50
    • 0034056585 scopus 로고    scopus 로고
    • An alternate binding site for the P1-P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease
    • Munshi, S.; Chen, Z.; Yan, Y.; Li, Y.; Olsen, D.B.; Schock, H.B.; Galvin, B.B.; Dorsey, B.; Kuo, L.C. An alternate binding site for the P1-P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease. Acta Crystallogr. D Biol. Crystallogr. 2000, 56, 381-388.
    • (2000) Acta Crystallogr. D Biol. Crystallogr , vol.56 , pp. 381-388
    • Munshi, S.1    Chen, Z.2    Yan, Y.3    Li, Y.4    Olsen, D.B.5    Schock, H.B.6    Galvin, B.B.7    Dorsey, B.8    Kuo, L.C.9
  • 51
    • 0037223718 scopus 로고    scopus 로고
    • Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: Structural insights for better antiviral therapy
    • Prabu-Jeyabalan, M.; Nalivaika, E.A.; King, N.M.; Schiffer, C.A. Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: Structural insights for better antiviral therapy. J. Virol. 2003, 77, 1306-1315.
    • (2003) J. Virol , vol.77 , pp. 1306-1315
    • Prabu-Jeyabalan, M.1    Nalivaika, E.A.2    King, N.M.3    Schiffer, C.A.4
  • 52
    • 77956326486 scopus 로고    scopus 로고
    • Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters
    • Shen, C.H.; Wang, Y.F.; Kovalevsky, A.Y.; Harrison, R.W.; Weber, I.T. Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. FEBS J. 2010, 277, 3699-3714.
    • (2010) FEBS J , vol.277 , pp. 3699-3714
    • Shen, C.H.1    Wang, Y.F.2    Kovalevsky, A.Y.3    Harrison, R.W.4    Weber, I.T.5
  • 53
    • 50049088535 scopus 로고    scopus 로고
    • Enzymatic and structural analysis of the I47A mutation contributing to the reduced susceptibility to HIV protease inhibitor lopinavir
    • Saskova, K.G.; Kozisek, M.; Lepsik, M.; Brynda, J.; Rezacova, P.; Vaclavikova, J.; Kagan, R.M.; Machala, L.; Konvalinka, J. Enzymatic and structural analysis of the I47A mutation contributing to the reduced susceptibility to HIV protease inhibitor lopinavir. Protein Sci. 2008, 17, 1555-1564.
    • (2008) Protein Sci , vol.17 , pp. 1555-1564
    • Saskova, K.G.1    Kozisek, M.2    Lepsik, M.3    Brynda, J.4    Rezacova, P.5    Vaclavikova, J.6    Kagan, R.M.7    Machala, L.8    Konvalinka, J.9
  • 54
    • 79952140089 scopus 로고    scopus 로고
    • University of Massachusetts Medical School, Worcester, MA, USA. Unpublished work
    • Schiffer, C.A. University of Massachusetts Medical School, Worcester, MA, USA. Unpublished work, 2010.
    • (2010)
    • Schiffer, C.A.1
  • 55
    • 69249215358 scopus 로고    scopus 로고
    • Molecular characterization of clinical isolates of human immunodeficiency virus resistant to the protease inhibitor darunavir
    • Saskova, K.G.; Kozisek, M.; Rezacova, P.; Brynda, J.; Yashina, T.; Kagan, R.M.; Konvalinka, J. Molecular characterization of clinical isolates of human immunodeficiency virus resistant to the protease inhibitor darunavir. J. Virol. 2009, 83, 8810-8818.
    • (2009) J. Virol , vol.83 , pp. 8810-8818
    • Saskova, K.G.1    Kozisek, M.2    Rezacova, P.3    Brynda, J.4    Yashina, T.5    Kagan, R.M.6    Konvalinka, J.7
  • 56
    • 27144554995 scopus 로고    scopus 로고
    • Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs
    • Tie, Y.; Boross, P.I.; Wang, Y.F.; Gaddis, L.; Liu, F.; Chen, X.; Tozser, J.; Harrison, R.W.; Weber, I.T. Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs. FEBS J. 2005, 272, 5265-5277.
    • (2005) FEBS J , vol.272 , pp. 5265-5277
    • Tie, Y.1    Boross, P.I.2    Wang, Y.F.3    Gaddis, L.4    Liu, F.5    Chen, X.6    Tozser, J.7    Harrison, R.W.8    Weber, I.T.9
  • 58
    • 0037047028 scopus 로고    scopus 로고
    • Amplification of the effects of drug resistance mutations by background polymorphisms in HIV-1 protease from African subtypes
    • Velazquez-Campoy, A.; Vega, S.; Freire, E. Amplification of the effects of drug resistance mutations by background polymorphisms in HIV-1 protease from African subtypes. Biochemistry 2002, 41, 8613-8619.
    • (2002) Biochemistry , vol.41 , pp. 8613-8619
    • Velazquez-Campoy, A.1    Vega, S.2    Freire, E.3
  • 59
    • 28444482769 scopus 로고    scopus 로고
    • Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S
    • Liu, F.; Boross, P.I.; Wang, Y.F.; Tozser, J.; Louis, J.M.; Harrison, R.W.; Weber, I.T. Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S. J. Mol. Biol. 2005, 354, 789-800.
    • (2005) J. Mol. Biol , vol.354 , pp. 789-800
    • Liu, F.1    Boross, P.I.2    Wang, Y.F.3    Tozser, J.4    Louis, J.M.5    Harrison, R.W.6    Weber, I.T.7
  • 62
    • 0032574705 scopus 로고    scopus 로고
    • Molecular basis of resistance to HIV-1 protease inhibition: A plausible hypothesis
    • Luque, I.; Todd, M.J.; Gomez, J.; Semo, N.; Freire, E. Molecular basis of resistance to HIV-1 protease inhibition: A plausible hypothesis. Biochemistry 1998, 37, 5791-5797.
    • (1998) Biochemistry , vol.37 , pp. 5791-5797
    • Luque, I.1    Todd, M.J.2    Gomez, J.3    Semo, N.4    Freire, E.5
  • 63
    • 0035370444 scopus 로고    scopus 로고
    • Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes
    • Mahalingam, B.; Louis, J.M.; Hung, J.; Harrision, R.W.; Weber, I.T. Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes. Proteins 2001, 43, 455-464.
    • (2001) Proteins , vol.43 , pp. 455-464
    • Mahalingam, B.1    Louis, J.M.2    Hung, J.3    Harrision, R.W.4    Weber, I.T.5
  • 65
    • 9644281075 scopus 로고    scopus 로고
    • Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance
    • Johnston, E.; Winters, M.A.; Rhee, S.Y.; Merigan, T.C.; Schiffer, C.A.; Shafer, R.W. Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. Antimicrob. Agents Chemother. 2004, 48, 4864-4868.
    • (2004) Antimicrob. Agents Chemother , vol.48 , pp. 4864-4868
    • Johnston, E.1    Winters, M.A.2    Rhee, S.Y.3    Merigan, T.C.4    Schiffer, C.A.5    Shafer, R.W.6
  • 66
    • 33748856573 scopus 로고    scopus 로고
    • HIV-1 protease mutations and inhibitor modifications monitored on a series of complexes. Structural basis for the effect of the A71V mutation on the active site
    • Skalova, T.; Dohnalek, J.; Duskova, J.; Petrokova, H.; Hradilek, M.; Soucek, M.; Konvalinka, J.; Hasek, J. HIV-1 protease mutations and inhibitor modifications monitored on a series of complexes. Structural basis for the effect of the A71V mutation on the active site. J. Med. Chem. 2006, 49, 5777-5784.
    • (2006) J. Med. Chem , vol.49 , pp. 5777-5784
    • Skalova, T.1    Dohnalek, J.2    Duskova, J.3    Petrokova, H.4    Hradilek, M.5    Soucek, M.6    Konvalinka, J.7    Hasek, J.8
  • 67
    • 0036786493 scopus 로고    scopus 로고
    • Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations
    • Piana, S.; Carloni, P.; Rothlisberger, U. Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. Protein Sci. 2002, 11, 2393-2402.
    • (2002) Protein Sci , vol.11 , pp. 2393-2402
    • Piana, S.1    Carloni, P.2    Rothlisberger, U.3
  • 68
    • 33846798356 scopus 로고    scopus 로고
    • Hydrophobic sliding: A possible mechanism for drug resistance in human immunodeficiency virus type 1 protease
    • Foulkes-Murzycki, J.E.; Scout, W.R.P.; Schiffer, C.A. Hydrophobic sliding: A possible mechanism for drug resistance in human immunodeficiency virus type 1 protease. Structure 2007, 15, 225-233.
    • (2007) Structure , vol.15 , pp. 225-233
    • Foulkes-Murzycki, J.E.1    Scout, W.R.P.2    Schiffer, C.A.3
  • 69
    • 0038058949 scopus 로고    scopus 로고
    • Elucidation of HIV-1 protease resistance by characterization of interaction kinetics between inhibitors and enzyme variants
    • Shuman, C.F.; Markgren, P.O.; Hamalainen, M.; Danielson, U.H. Elucidation of HIV-1 protease resistance by characterization of interaction kinetics between inhibitors and enzyme variants. Antivir. Res. 2003, 58, 235-242.
    • (2003) Antivir. Res , vol.58 , pp. 235-242
    • Shuman, C.F.1    Markgren, P.O.2    Hamalainen, M.3    Danielson, U.H.4
  • 70
    • 38849209120 scopus 로고    scopus 로고
    • The contribution of naturally occurring polymorphisms in altering the biochemical and structural characteristics of HIV-1 subtype C protease
    • Coman, R.M.; Robbins, A.H.; Fernandez, M.A.; Gilliland, C.T.; Sochet, A.A.; Goodenow, M.M.; McKenna, R.; Dunn, B.M. The contribution of naturally occurring polymorphisms in altering the biochemical and structural characteristics of HIV-1 subtype C protease. Biochemistry 2008, 47, 731-743.
    • (2008) Biochemistry , vol.47 , pp. 731-743
    • Coman, R.M.1    Robbins, A.H.2    Fernandez, M.A.3    Gilliland, C.T.4    Sochet, A.A.5    Goodenow, M.M.6    McKenna, R.7    Dunn, B.M.8
  • 71
    • 0030769354 scopus 로고    scopus 로고
    • Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites
    • Zhang, Y.M.; Imamichi, H.; Imamichi, T.; Lane, H.C.; Falloon, J.; Vasudevachari, M.B.; Salzman, N.P. Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites. J. Virol. 1997, 71, 6662-6670.
    • (1997) J. Virol , vol.71 , pp. 6662-6670
    • Zhang, Y.M.1    Imamichi, H.2    Imamichi, T.3    Lane, H.C.4    Falloon, J.5    Vasudevachari, M.B.6    Salzman, N.P.7
  • 72
    • 0029899093 scopus 로고    scopus 로고
    • Second locus involved in human immunodeficiency virus type 1 resistance to protease inhibitors
    • Doyon, L.; Croteau, G.; Thibeault, D.; Poulin, F.; Pilote, L.; Lamarre, D. Second locus involved in human immunodeficiency virus type 1 resistance to protease inhibitors. J. Virol. 1996, 70, 3763-3769.
    • (1996) J. Virol , vol.70 , pp. 3763-3769
    • Doyon, L.1    Croteau, G.2    Thibeault, D.3    Poulin, F.4    Pilote, L.5    Lamarre, D.6
  • 73
    • 0034284897 scopus 로고    scopus 로고
    • Polymorphism of HIV type 1 gag p7/p1 and p1/p6 cleavage sites: Clinical significance and implications for resistance to protease
    • Bally, F.; Martinez, R.; Peters, S.; Sudre, P.; Telenti, A. Polymorphism of HIV type 1 gag p7/p1 and p1/p6 cleavage sites: Clinical significance and implications for resistance to protease. AIDS Res. Hum. Retroviruses 2000, 16, 1209-1213.
    • (2000) AIDS Res. Hum. Retroviruses , vol.16 , pp. 1209-1213
    • Bally, F.1    Martinez, R.2    Peters, S.3    Sudre, P.4    Telenti, A.5
  • 74
    • 0031846317 scopus 로고    scopus 로고
    • Resistance-associated loss of viral fitness in human immunodeficiency virus type 1: Phenotypic analysis of protease and gag coevolution in protease inhibitor-treated patients
    • Mammano, F.; Petit, C.; Clavel, F. Resistance-associated loss of viral fitness in human immunodeficiency virus type 1: Phenotypic analysis of protease and gag coevolution in protease inhibitor-treated patients. J. Virol. 1998, 72, 7632-7637.
    • (1998) J. Virol , vol.72 , pp. 7632-7637
    • Mammano, F.1    Petit, C.2    Clavel, F.3
  • 75
    • 0031748806 scopus 로고    scopus 로고
    • Novel Gag-Pol frameshift site in human immunodeficiency virus type 1 variants resistant to protease inhibitors
    • Doyon, L.; Payant, C.; Brakier-Gingras, L.; Lamarre, D. Novel Gag-Pol frameshift site in human immunodeficiency virus type 1 variants resistant to protease inhibitors. J. Virol. 1998, 72, 6146-6150.
    • (1998) J. Virol , vol.72 , pp. 6146-6150
    • Doyon, L.1    Payant, C.2    Brakier-Gingras, L.3    Lamarre, D.4
  • 78
    • 63449110982 scopus 로고    scopus 로고
    • Gag mutations strongly contribute to HIV-1 resistance to protease inhibitors in highly drug-experienced patients besides compensating for fitness loss
    • Dam, E.; Quercia, R.; Glass, B.; Descamps, D.; Launay, O.; Duval, X.; Krausslich, H.G.; Hance, A.J.; Clavel, F. Gag mutations strongly contribute to HIV-1 resistance to protease inhibitors in highly drug-experienced patients besides compensating for fitness loss. PLoS Pathog. 2009, 5, e1000345.
    • (2009) PLoS Pathog , vol.5
    • Dam, E.1    Quercia, R.2    Glass, B.3    Descamps, D.4    Launay, O.5    Duval, X.6    Krausslich, H.G.7    Hance, A.J.8    Clavel, F.9
  • 79
    • 7644230388 scopus 로고    scopus 로고
    • Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease
    • Prabu-Jeyabalan, M.; Nalivaika, E.A.; King, N.M.; Schiffer, C.A. Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease. J. Virol. 2004, 78, 12446-12454.
    • (2004) J. Virol , vol.78 , pp. 12446-12454
    • Prabu-Jeyabalan, M.1    Nalivaika, E.A.2    King, N.M.3    Schiffer, C.A.4
  • 81
    • 33646043172 scopus 로고    scopus 로고
    • Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate
    • Kolli, M.; Lastere, S.; Schiffer, C.A. Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate. Virology 2006, 347, 405-409.
    • (2006) Virology , vol.347 , pp. 405-409
    • Kolli, M.1    Lastere, S.2    Schiffer, C.A.3
  • 82
    • 70350317566 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance
    • Kolli, M.; Stawiski, E.; Chappey, C.; Schiffer, C.A. Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance. J. Virol. 2009, 83, 11027-11042.
    • (2009) J. Virol , vol.83 , pp. 11027-11042
    • Kolli, M.1    Stawiski, E.2    Chappey, C.3    Schiffer, C.A.4
  • 83
    • 0032804864 scopus 로고    scopus 로고
    • Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy
    • Nijhuis, M.; Schuurman, R.; de Jong, D.; Erickson, J.; Gustchina, E.; Albert, J.; Schipper, P.; Gulnik, S.; Boucher, C.A. Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy. AIDS 1999, 13, 2349-2359.
    • (1999) AIDS , vol.13 , pp. 2349-2359
    • Nijhuis, M.1    Schuurman, R.2    de Jong, D.3    Erickson, J.4    Gustchina, E.5    Albert, J.6    Schipper, P.7    Gulnik, S.8    Boucher, C.A.9
  • 84
    • 0034734783 scopus 로고    scopus 로고
    • Fitness of human immunodeficiency virus type 1 protease inhibitor-selected single mutants
    • Martinez-Picado, J.; Savara, A.V.; Shi, L.; Sutton, L.; D'Aquila, R.T. Fitness of human immunodeficiency virus type 1 protease inhibitor-selected single mutants. Virology 2000, 275, 318-322.
    • (2000) Virology , vol.275 , pp. 318-322
    • Martinez-Picado, J.1    Savara, A.V.2    Shi, L.3    Sutton, L.4    D'aquila, R.T.5
  • 85
    • 0032928065 scopus 로고    scopus 로고
    • Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1
    • Martinez-Picado, J.; Savara, A.V.; Sutton, L.; D'Aquila, R.T. Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1. J. Virol. 1999, 73, 3744-3752.
    • (1999) J. Virol , vol.73 , pp. 3744-3752
    • Martinez-Picado, J.1    Savara, A.V.2    Sutton, L.3    D'aquila, R.T.4
  • 86
    • 0031015475 scopus 로고    scopus 로고
    • Impaired fitness of human immunodeficiency virus type 1 variants with high-level resistance to protease inhibitors
    • Croteau, G.; Doyon, L.; Thibeault, D.; McKercher, G.; Pilote, L.; Lamarre, D. Impaired fitness of human immunodeficiency virus type 1 variants with high-level resistance to protease inhibitors. J. Virol. 1997, 71, 1089-1096.
    • (1997) J. Virol , vol.71 , pp. 1089-1096
    • Croteau, G.1    Doyon, L.2    Thibeault, D.3    McKercher, G.4    Pilote, L.5    Lamarre, D.6
  • 87
    • 0035104646 scopus 로고    scopus 로고
    • Individual contributions of mutant protease and reverse transcriptase to viral infectivity, replication, and protein maturation of antiretroviral drug-resistant human immunodeficiency virus type 1
    • Bleiber, G.; Munoz, M.; Ciuffi, A.; Meylan, P.; Telenti, A. Individual contributions of mutant protease and reverse transcriptase to viral infectivity, replication, and protein maturation of antiretroviral drug-resistant human immunodeficiency virus type 1. J. Virol. 2001, 75, 3291-3300.
    • (2001) J. Virol , vol.75 , pp. 3291-3300
    • Bleiber, G.1    Munoz, M.2    Ciuffi, A.3    Meylan, P.4    Telenti, A.5
  • 88
    • 0034632745 scopus 로고    scopus 로고
    • HIV type 1 protease cleavage site mutations and viral fitness: Implications for drug susceptibility phenotyping assays
    • Robinson, L.H.; Myers, R.E.; Snowden, B.W.; Tisdale, M.; Blair, E.D. HIV type 1 protease cleavage site mutations and viral fitness: Implications for drug susceptibility phenotyping assays. AIDS Res. Hum. Retroviruses 2000, 16, 1149-1156.
    • (2000) AIDS Res. Hum. Retroviruses , vol.16 , pp. 1149-1156
    • Robinson, L.H.1    Myers, R.E.2    Snowden, B.W.3    Tisdale, M.4    Blair, E.D.5
  • 90
    • 69449097224 scopus 로고    scopus 로고
    • Gag determinants of fitness and drug susceptibility in protease inhibitor-resistant human immunodeficiency virus type 1
    • Parry, C.M.; Kohli, A.; Boinett, C.J.; Towers, G.J.; McCormick, A.L.; Pillay, D. Gag determinants of fitness and drug susceptibility in protease inhibitor-resistant human immunodeficiency virus type 1. J. Virol. 2009, 83, 9094-9101.
    • (2009) J. Virol , vol.83 , pp. 9094-9101
    • Parry, C.M.1    Kohli, A.2    Boinett, C.J.3    Towers, G.J.4    McCormick, A.L.5    Pillay, D.6
  • 91
    • 29744469946 scopus 로고    scopus 로고
    • Reduced susceptibility to protease inhibitors (PI) in the absence of primary PI resistance-associated mutations
    • Parkin, N.; Chappey, C.; Lam, E.; Petropoulos, C. Reduced susceptibility to protease inhibitors (PI) in the absence of primary PI resistance-associated mutations. Antivir. Ther. 2005, 10, S118.
    • (2005) Antivir. Ther , vol.10
    • Parkin, N.1    Chappey, C.2    Lam, E.3    Petropoulos, C.4
  • 92
    • 79952154269 scopus 로고    scopus 로고
    • Role of Gag in HIV Resistance to Protease Inhibitors
    • Clavel, F.; Mammano, F. Role of Gag in HIV Resistance to Protease Inhibitors. Viruses 2010, 2, 1411-1426.
    • (2010) Viruses , vol.2 , pp. 1411-1426
    • Clavel, F.1    Mammano, F.2
  • 94
    • 79952150641 scopus 로고    scopus 로고
    • HIV Sequence Database, accessed on 20 October 2010
    • HIV Sequence Database. Available online: http://www.hiv.lanl.gov/ (accessed on 20 October 2010).
  • 96
    • 77956820913 scopus 로고    scopus 로고
    • The Effect of Clade Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways
    • Bandaranayake, R.M.; Kolli, M.; King, N.M.; Nalivaika, E.; Heroux, A.; Kakizawa, J.; Sugiura, W.; Schiffer, C.A. The Effect of Clade Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways. J. Virol. 2010, 84, 9995-10003.
    • (2010) J. Virol , vol.84 , pp. 9995-10003
    • Bandaranayake, R.M.1    Kolli, M.2    King, N.M.3    Nalivaika, E.4    Heroux, A.5    Kakizawa, J.6    Sugiura, W.7    Schiffer, C.A.8
  • 97
    • 33746025903 scopus 로고    scopus 로고
    • Natural polymorphisms in the protease gene modulate the replicative capacity of non-B HIV-1 variants in the absence of drug pressure
    • Holguin, A.; Sune, C.; Hamy, F.; Soriano, V.; Klimkait, T. Natural polymorphisms in the protease gene modulate the replicative capacity of non-B HIV-1 variants in the absence of drug pressure. J. Clin. Virol. 2006, 36, 264-271.
    • (2006) J. Clin. Virol , vol.36 , pp. 264-271
    • Holguin, A.1    Sune, C.2    Hamy, F.3    Soriano, V.4    Klimkait, T.5
  • 99
    • 0037825993 scopus 로고    scopus 로고
    • Patterns of point mutations associated with antiretroviral drug treatment failure in CRF01_AE (subtype E) infection differ from subtype B infection
    • Ariyoshi, K.; Matsuda, M.; Miura, H.; Tateishi, S.; Yamada, K.; Sugiura, W. Patterns of point mutations associated with antiretroviral drug treatment failure in CRF01_AE (subtype E) infection differ from subtype B infection. J. Acquir. Immune Defic. Syndr. 2003, 33, 336-342.
    • (2003) J. Acquir. Immune Defic. Syndr , vol.33 , pp. 336-342
    • Ariyoshi, K.1    Matsuda, M.2    Miura, H.3    Tateishi, S.4    Yamada, K.5    Sugiura, W.6
  • 100
    • 0028354926 scopus 로고
    • Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant
    • Lau, F.T.; Karplus, M. Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant. J. Mol. Biol. 1994, 236, 1049-1066.
    • (1994) J. Mol. Biol , vol.236 , pp. 1049-1066
    • Lau, F.T.1    Karplus, M.2
  • 101
    • 0023346161 scopus 로고
    • Free energy calculations by computer simulation
    • Bash, P.A.; Singh, U.C.; Langridge, R.; Kollman, P.A. Free energy calculations by computer simulation. Science 1987, 287, 564-567.
    • (1987) Science , vol.287 , pp. 564-567
    • Bash, P.A.1    Singh, U.C.2    Langridge, R.3    Kollman, P.A.4
  • 102
    • 0024365336 scopus 로고
    • Hidden thermodynamics of mutant proteins: A molecular dynamics analysis
    • Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M. Hidden thermodynamics of mutant proteins: A molecular dynamics analysis. Science 1989, 244, 1069-1072.
    • (1989) Science , vol.244 , pp. 1069-1072
    • Gao, J.1    Kuczera, K.2    Tidor, B.3    Karplus, M.4
  • 103
    • 0001486087 scopus 로고
    • Dynamics and Design of Enzymes and Inhibitors
    • Wong, C.F.; McCammon, J.A. Dynamics and Design of Enzymes and Inhibitors. J. Am. Chem. Soc. 1986, 108, 3830-3832.
    • (1986) J. Am. Chem. Soc , vol.108 , pp. 3830-3832
    • Wong, C.F.1    McCammon, J.A.2
  • 104
    • 0023106632 scopus 로고
    • Calculation of the relative change in binding free energy of a protein-inhibitor complex
    • Bash, P.A.; Singh, U.C.; Brown, F.K.; Langridge, R.; Kollman, P.A. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 1987, 235, 574-576.
    • (1987) Science , vol.235 , pp. 574-576
    • Bash, P.A.1    Singh, U.C.2    Brown, F.K.3    Langridge, R.4    Kollman, P.A.5
  • 105
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P.A. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395-2417.
    • (1993) Chem. Rev , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 106
    • 77956634216 scopus 로고    scopus 로고
    • Structural basis for the resilience of Darunavir (TMC114) resistance major flap mutations of HIV-1 protease
    • Purohit, R.; Sethumadhavan, R. Structural basis for the resilience of Darunavir (TMC114) resistance major flap mutations of HIV-1 protease. Interdiscip. Sci. 2009, 1, 320-328.
    • (2009) Interdiscip. Sci , vol.1 , pp. 320-328
    • Purohit, R.1    Sethumadhavan, R.2
  • 107
    • 0034084991 scopus 로고    scopus 로고
    • Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
    • Massova, I.; Kollman, P.A. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspect. Drug Discovery Des. 1999, 18, 113-135.
    • (1999) Perspect. Drug Discovery Des , vol.18 , pp. 113-135
    • Massova, I.1    Kollman, P.A.2
  • 108
    • 0347949637 scopus 로고    scopus 로고
    • Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
    • Swanson, J.M.; Henchman, R.H.; McCammon, J.A. Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 2004, 86, 67-74.
    • (2004) Biophys. J , vol.86 , pp. 67-74
    • Swanson, J.M.1    Henchman, R.H.2    McCammon, J.A.3
  • 109
    • 39749152456 scopus 로고    scopus 로고
    • Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
    • Stoica, I.; Sadiq, S.K.; Coveney, P.V. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J. Am. Chem. Soc. 2008, 130, 2639-2648.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 2639-2648
    • Stoica, I.1    Sadiq, S.K.2    Coveney, P.V.3
  • 110
    • 33947644064 scopus 로고    scopus 로고
    • Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: Mechanism for binding and drug resistance
    • Hou, T.; Yu, R. Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: Mechanism for binding and drug resistance. J. Med. Chem. 2007, 50, 1177-1188.
    • (2007) J. Med. Chem , vol.50 , pp. 1177-1188
    • Hou, T.1    Yu, R.2
  • 111
    • 0035910029 scopus 로고    scopus 로고
    • Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
    • Wang, W.; Kollman, P.A. Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 14937-14942.
    • (2001) Proc. Natl. Acad. Sci. U. S. A , vol.98 , pp. 14937-14942
    • Wang, W.1    Kollman, P.A.2
  • 112
    • 77951133082 scopus 로고    scopus 로고
    • Decomposing the Energetic Impact of Drug Resistant Mutations in HIV-1 Protease on Binding DRV
    • Cai, Y.; Schiffer, C. Decomposing the Energetic Impact of Drug Resistant Mutations in HIV-1 Protease on Binding DRV. J. Chem. Theory Comput. 2010, 6, 1358-1368.
    • (2010) J. Chem. Theory Comput , vol.6 , pp. 1358-1368
    • Cai, Y.1    Schiffer, C.2
  • 113
    • 0024239036 scopus 로고
    • A free-energy perturbation study of the binding of methotrexate to mutants of dihydrofolate reductase
    • Singh, U.C.; Benkovic, S.J. A free-energy perturbation study of the binding of methotrexate to mutants of dihydrofolate reductase. Proc. Natl. Acad. Sci. U. S. A. 1988, 85, 9519-9523.
    • (1988) Proc. Natl. Acad. Sci. U. S. A , vol.85 , pp. 9519-9523
    • Singh, U.C.1    Benkovic, S.J.2
  • 114
    • 2342648012 scopus 로고    scopus 로고
    • Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal Alchemical path, and practical solutions
    • Blondel, A. Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal Alchemical path, and practical solutions. J. Comput. Chem. 2004, 25, 985-993.
    • (2004) J. Comput. Chem , vol.25 , pp. 985-993
    • Blondel, A.1
  • 115
    • 0027218692 scopus 로고
    • Structure-based inhibitors of HIV-1 protease
    • Wlodawer, A.; Erickson, J.W. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 1993, 62, 543-585.
    • (1993) Annu. Rev. Biochem , vol.62 , pp. 543-585
    • Wlodawer, A.1    Erickson, J.W.2
  • 116
    • 0042710087 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • Massova, I.; Kollman, P.A. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. J. Am. Chem. Soc. 1999, 121, 8133-8143.
    • (1999) J. Am. Chem. Soc , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 117
    • 0035895423 scopus 로고    scopus 로고
    • Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
    • Archontis, G.; Simonson, T.; Karplus, M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. J. Mol. Biol. 2001, 306, 307-327.
    • (2001) J. Mol. Biol , vol.306 , pp. 307-327
    • Archontis, G.1    Simonson, T.2    Karplus, M.3
  • 118
    • 0035367150 scopus 로고    scopus 로고
    • Interpreting trends in the binding of cyclic ureas to HIV-1 protease
    • Mardis, K.L.; Luo, R.; Gilson, M.K. Interpreting trends in the binding of cyclic ureas to HIV-1 protease. J. Mol. Biol. 2001, 309, 507-517.
    • (2001) J. Mol. Biol , vol.309 , pp. 507-517
    • Mardis, K.L.1    Luo, R.2    Gilson, M.K.3
  • 119
    • 0036771626 scopus 로고    scopus 로고
    • Accelerated Poisson-Boltzmann calculations for static and dynamic systems
    • Luo, R.; David, L.; Gilson, M.K. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J. Comput. Chem. 2002, 23, 1244-1253.
    • (2002) J. Comput. Chem , vol.23 , pp. 1244-1253
    • Luo, R.1    David, L.2    Gilson, M.K.3
  • 120
    • 38549143261 scopus 로고    scopus 로고
    • Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease
    • Altman, M.D.; Nalivaika, E.A.; Prabu-Jeyabalan, M.; Schiffer, C.A.; Tidor, B. Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins 2008, 70, 678-694.
    • (2008) Proteins , vol.70 , pp. 678-694
    • Altman, M.D.1    Nalivaika, E.A.2    Prabu-Jeyabalan, M.3    Schiffer, C.A.4    Tidor, B.5
  • 121
    • 65249084628 scopus 로고    scopus 로고
    • Evaluation of an inverse molecular design algorithm in a model binding site
    • Huggins, D.J.; Altman, M.D.; Tidor, B. Evaluation of an inverse molecular design algorithm in a model binding site. Proteins 2009, 75, 168-186.
    • (2009) Proteins , vol.75 , pp. 168-186
    • Huggins, D.J.1    Altman, M.D.2    Tidor, B.3
  • 122
    • 42049099944 scopus 로고    scopus 로고
    • Novel method for probing the specificity binding profile of ligands: Applications to HIV protease
    • Sherman, W.; Tidor, B. Novel method for probing the specificity binding profile of ligands: Applications to HIV protease. Chem. Biol. Drug Des. 2008, 71, 387-407.
    • (2008) Chem. Biol. Drug Des , vol.71 , pp. 387-407
    • Sherman, W.1    Tidor, B.2
  • 123
    • 34250794023 scopus 로고    scopus 로고
    • Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease
    • Chellappan, S.; Kairys, V.; Fernandes, M.X.; Schiffer, C.; Gilson, M.K. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins 2007, 68, 561-567.
    • (2007) Proteins , vol.68 , pp. 561-567
    • Chellappan, S.1    Kairys, V.2    Fernandes, M.X.3    Schiffer, C.4    Gilson, M.K.5
  • 124
    • 33645767675 scopus 로고    scopus 로고
    • Substrate envelope and drug resistance: Crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease
    • Prabu-Jeyabalan, M.; King, N.M.; Nalivaika, E.A.; Heilek-Snyder, G.; Cammack, N.; Schiffer, C.A. Substrate envelope and drug resistance: Crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease. Antimicrob. Agents Chemother. 2006, 50, 1518-1521.
    • (2006) Antimicrob. Agents Chemother , vol.50 , pp. 1518-1521
    • Prabu-Jeyabalan, M.1    King, N.M.2    Nalivaika, E.A.3    Heilek-Snyder, G.4    Cammack, N.5    Schiffer, C.A.6
  • 125
    • 33845492104 scopus 로고    scopus 로고
    • Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands
    • Ali, A.; Reddy, G.S.K.K.; Cao, H.; Anjum, S.G.; Nalam, M.N.L.; Schiffer, C.A.; Rana, T.M. Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands. J. Med. Chem. 2006, 49, 7342-7356.
    • (2006) J. Med. Chem , vol.49 , pp. 7342-7356
    • Ali, A.1    Reddy, G.S.K.K.2    Cao, H.3    Anjum, S.G.4    Nalam, M.N.L.5    Schiffer, C.A.6    Rana, T.M.7
  • 127
    • 68949201698 scopus 로고    scopus 로고
    • Toward the design of mutation-resistant enzyme inhibitors: Further evaluation of the substrate envelope hypothesis
    • Kairys, V.; Gilson, M.K.; Lather, V.; Schiffer, C.A.; Fernandes, M.X. Toward the design of mutation-resistant enzyme inhibitors: Further evaluation of the substrate envelope hypothesis. Chem. Biol. Drug Des. 2009, 74, 234-245.
    • (2009) Chem. Biol. Drug Des , vol.74 , pp. 234-245
    • Kairys, V.1    Gilson, M.K.2    Lather, V.3    Schiffer, C.A.4    Fernandes, M.X.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.