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Volumn 79, Issue 7, 2011, Pages 2282-2290

Binding to the open conformation of HIV-1 protease

Author keywords

AIDS; Drug design; Ligand binding; Molecular dynamics; Protein flexibility

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE ALPHA; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE BETA; PYRROLIDINE DERIVATIVE; UNCLASSIFIED DRUG;

EID: 79958766155     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23054     Document Type: Article
Times cited : (13)

References (29)
  • 2
    • 64649102226 scopus 로고    scopus 로고
    • Darunavir: a review of its use in the management of HIV infection in adults
    • McKeage K, Perry CM, Keam SJ. Darunavir: a review of its use in the management of HIV infection in adults. Drugs 2009; 69: 477-503.
    • (2009) Drugs , vol.69 , pp. 477-503
    • McKeage, K.1    Perry, C.M.2    Keam, S.J.3
  • 3
    • 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
  • 4
    • 33846635484 scopus 로고    scopus 로고
    • Targeting structural flexibility in HIV-1 protease inhibitor binding
    • Hornak V, Simmerling C. Targeting structural flexibility in HIV-1 protease inhibitor binding. Drug Discov Today 2007; 12: 132-138.
    • (2007) Drug Discov Today , vol.12 , pp. 132-138
    • Hornak, V.1    Simmerling, C.2
  • 5
    • 0036147844 scopus 로고    scopus 로고
    • Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations
    • Freedberg DI, Ishima R, Jacob J, Wang YX, Kustanovich I, Louis JM, Torchia DA. Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Sci 2002; 11: 221-232.
    • (2002) Protein Sci , vol.11 , pp. 221-232
    • Freedberg, D.I.1    Ishima, R.2    Jacob, J.3    Wang, Y.X.4    Kustanovich, I.5    Louis, J.M.6    Torchia, D.A.7
  • 6
    • 0033200247 scopus 로고    scopus 로고
    • Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function
    • Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA. Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure 1999; 7: 1047-1055.
    • (1999) Structure , vol.7 , pp. 1047-1055
    • Ishima, R.1    Freedberg, D.I.2    Wang, Y.X.3    Louis, J.M.4    Torchia, D.A.5
  • 8
    • 37349127373 scopus 로고    scopus 로고
    • Insights into a mutation-assisted lateral drug escape mechanism from the HIV-1 protease active site
    • Sadiq AK, Wan S, Coveney PV. Insights into a mutation-assisted lateral drug escape mechanism from the HIV-1 protease active site. Biochemistry 2007; 46: 14865-14877.
    • (2007) Biochemistry , vol.46 , pp. 14865-14877
    • Sadiq, A.K.1    Wan, S.2    Coveney, P.V.3
  • 9
    • 0032127391 scopus 로고    scopus 로고
    • Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease
    • Rick SW, Erickson JW, Burt SK. Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease. Proteins 1998; 32: 7-16.
    • (1998) Proteins , vol.32 , pp. 7-16
    • Rick, S.W.1    Erickson, J.W.2    Burt, S.K.3
  • 10
    • 1842454635 scopus 로고    scopus 로고
    • HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs
    • Perryman AL, Lin JH, McCammon JA. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci 2004; 13: 1108-1123.
    • (2004) Protein Sci , vol.13 , pp. 1108-1123
    • Perryman, A.L.1    Lin, J.H.2    McCammon, J.A.3
  • 11
    • 54849414837 scopus 로고    scopus 로고
    • Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors
    • Böttcher J, Blum A, Dörr S, Heine A, Diederich WE, Klebe G. Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors. ChemMedChem 2008; 3: 1337-1344.
    • (2008) ChemMedChem , vol.3 , pp. 1337-1344
    • Böttcher, J.1    Blum, A.2    Dörr, S.3    Heine, A.4    Diederich, W.E.5    Klebe, G.6
  • 12
    • 52049093435 scopus 로고    scopus 로고
    • A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket
    • Damm KL, Ung PM, Quintero JJ, Gestwicki JE, Carlson HA. A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket. Biopolymers 2008; 89: 643-652.
    • (2008) Biopolymers , vol.89 , pp. 643-652
    • Damm, K.L.1    Ung, P.M.2    Quintero, J.J.3    Gestwicki, J.E.4    Carlson, H.A.5
  • 13
    • 10844257486 scopus 로고    scopus 로고
    • Solvation influences flap collapse in HIV-1 protease
    • Meagher KL, Carlson HA. Solvation influences flap collapse in HIV-1 protease. Proteins:Struct Funct Genet 2005; 58: 119-125.
    • (2005) Proteins:Struct Funct Genet , vol.58 , pp. 119-125
    • Meagher, K.L.1    Carlson, H.A.2
  • 16
    • 79958766816 scopus 로고    scopus 로고
    • Canada: Chemical Computing Group, Inc.
    • MOE. Montreal, Canada: Chemical Computing Group, Inc.; 2008.
    • (2008) MOE. Montreal
  • 18
    • 0001041959 scopus 로고    scopus 로고
    • Fast, efficient generation of high-quality atomic Charges. AM1-BCC model: I. Method
    • Jakalian A, Bush BL, Jack DB, Bayly CI. Fast, efficient generation of high-quality atomic Charges. AM1-BCC model: I. Method. J Comput Chem 2000; 21: 132-146.
    • (2000) J Comput Chem , vol.21 , pp. 132-146
    • Jakalian, A.1    Bush, B.L.2    Jack, D.B.3    Bayly, C.I.4
  • 22
    • 79958769452 scopus 로고    scopus 로고
    • Ann Arbor, MI: University of Michigan
    • Lerner M. APBS plugin. Ann Arbor, MI: University of Michigan; 2004.
    • (2004) APBS plugin
    • Lerner, M.1
  • 24
    • 33846823909 scopus 로고
    • Particle Mesh Ewald-an N.Log(N) method for Ewald Sums in large systems
    • Darden T, York D, Pedersen L. Particle Mesh Ewald-an N.Log(N) method for Ewald Sums in large systems. J Chem Phys 1993; 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 25
    • 36649006642 scopus 로고    scopus 로고
    • Clustering molecular dynamics trajectories: I. Characterizing the performance of different clustering algorithms
    • Shao J, Tanner SW, Thompson N, Cheatham TE. Clustering molecular dynamics trajectories: I. Characterizing the performance of different clustering algorithms. J Chem Theory Comput 2007; 3: 2312-2334.
    • (2007) J Chem Theory Comput , vol.3 , pp. 2312-2334
    • Shao, J.1    Tanner, S.W.2    Thompson, N.3    Cheatham, T.E.4
  • 26
    • 0017953820 scopus 로고
    • A cluster separation measure. Pattern analysis and machine intelligence
    • Davies DL, Bouldin DW. A cluster separation measure. Pattern analysis and machine intelligence. IEEE Trans on PAMI 1979; 1: 224-227.
    • (1979) IEEE Trans on PAMI , vol.1 , pp. 224-227
    • Davies, D.L.1    Bouldin, D.W.2
  • 27
    • 84972893020 scopus 로고
    • A dendrite method for cluster analysis
    • Calinski T, Harabasz J. A dendrite method for cluster analysis. Commun Stat 1974; 3: 1-27.
    • (1974) Commun Stat , vol.3 , pp. 1-27
    • Calinski, T.1    Harabasz, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.