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Volumn 55, Issue 24, 2010, Pages 2677-2683

Molecular dynamics simulations exploring drug resistance in HIV-1 proteases

Author keywords

drug resistance; HIV 1 protease; hydrogen bonds; hydrophobic interactions; molecular dynamics simulations

Indexed keywords

CERCOPITHECINE HERPESVIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 77955836275     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1007/s11434-010-3257-6     Document Type: Article
Times cited : (13)

References (28)
  • 1
    • 77955819671 scopus 로고    scopus 로고
    • UNAIDS. Annual Report 2009
    • UNAIDS. Annual Report 2009, http://data. unaids. org/pub/Report/2010/2009_annual_report_en. pdf.
  • 2
    • 0034751827 scopus 로고    scopus 로고
    • Genotypic and phenotypic evidence of different drug-resistance mutation patterns between B and non-B subtype isolates of human immunodeficiency virus type 1 found in Brazilian patients failing HAART
    • Caride E, Hertogs K, Larder B, et al. Genotypic and phenotypic evidence of different drug-resistance mutation patterns between B and non-B subtype isolates of human immunodeficiency virus type 1 found in Brazilian patients failing HAART. Virus Genes, 2001, 23: 193-202.
    • (2001) Virus Genes , vol.23 , pp. 193-202
    • Caride, E.1    Hertogs, K.2    Larder, B.3
  • 3
    • 33846798356 scopus 로고    scopus 로고
    • Hydrophobic sliding: A possible mechanism for drug resistance in human immunodeficiency virus type 1 protease
    • Foulkes-Murzycki J E, Scott W R, 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    Scott, W.R.2    Schiffer, C.A.3
  • 4
    • 0014220976 scopus 로고
    • On the size of the active site in protease. II. Carboxypeptidase-A
    • Abramowitz N, Schechter I, Berger A. On the size of the active site in protease. II. Carboxypeptidase-A. Biochem Biophys Res Commun, 1967, 29: 862-867.
    • (1967) Biochem Biophys Res Commun , vol.29 , pp. 862-867
    • Abramowitz, N.1    Schechter, I.2    Berger, A.3
  • 5
    • 0014211618 scopus 로고
    • On the size of the active site in protease. I. Papain
    • Schechter I, Berger A. On the size of the active site in protease. I. Papain. Biochem Biophys Res Commun, 1967, 27: 157-162.
    • (1967) Biochem Biophys Res Commun , vol.27 , pp. 157-162
    • Schechter, I.1    Berger, A.2
  • 6
    • 0344593433 scopus 로고    scopus 로고
    • The relation between baseline HIV drug resistance and response to antiretroviral therapy: Re-analysis of retrospective and prospective studies using a standardized data analysis plan
    • DeGruttola V, Dix L, Aquila D R, et al. The relation between baseline HIV drug resistance and response to antiretroviral therapy: Re-analysis of retrospective and prospective studies using a standardized data analysis plan. Antivir Ther, 2000, 5: 41-48.
    • (2000) Antivir Ther , vol.5 , pp. 41-48
    • Degruttola, V.1    Dix, L.2    Aquila, D.R.3
  • 7
    • 0033572954 scopus 로고    scopus 로고
    • AIDS-related opportunistic illnesses occurring after initiation of potent antiretroviral therapy: The Swiss HIV cohort study
    • Ledergerber B, Egger M, Erard V, et al. AIDS-related opportunistic illnesses occurring after initiation of potent antiretroviral therapy: The Swiss HIV cohort study. Jama, 1999, 82: 2220-2226.
    • (1999) Jama , vol.82 , pp. 2220-2226
    • Ledergerber, B.1    Egger, M.2    Erard, V.3
  • 8
    • 34248586556 scopus 로고    scopus 로고
    • Structural characterization of B and non-B subtypes of HIV-protease: Insights into the natural susceptibility to drug resistance development
    • Sanches M, Krauchenco S, Martins N H, et al. Structural characterization of B and non-B subtypes of HIV-protease: Insights into the natural susceptibility to drug resistance development. J Mol Biol, 2007, 369: 1029-1040.
    • (2007) J Mol Biol , vol.369 , pp. 1029-1040
    • Sanches, M.1    Krauchenco, S.2    Martins, N.H.3
  • 10
    • 0002098417 scopus 로고    scopus 로고
    • The development/application of "minimalist"organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data
    • Kollman P A, Cornell W D, Chipot C, et al. The development/application of "minimalist"organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. Comp Simulat Biolog Syst, 1997, 3: 83-96.
    • (1997) Comp Simulat Biolog Syst , vol.3 , pp. 83-96
    • Kollman, P.A.1    Cornell, W.D.2    Chipot, C.3
  • 11
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen W L, Madura J D, Impey R W, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys, 1983, 79: 926-935.
    • (1983) J Chem Phys , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Madura, J.D.2    Impey, R.W.3
  • 12
    • 2942532422 scopus 로고    scopus 로고
    • Development and testing of a general amber force field
    • Wang J, Wolf R M, Caldwell J W, et al. Development and testing of a general amber force field. J Comput Chem, 2004, 25: 1157-1174.
    • (2004) J Comput Chem , vol.25 , pp. 1157-1174
    • Wang, J.1    Wolf, R.M.2    Caldwell, J.W.3
  • 13
    • 33646940952 scopus 로고
    • Numerical integration of Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Rychaert J P, Berendsen H J C. Numerical integration of Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Comput Phys, 1977, 23: 327-341.
    • (1977) Comput Phys , vol.23 , pp. 327-341
    • Rychaert, J.P.1    Berendsen, H.J.C.2
  • 14
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems
    • Darden T, 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    Pedersen, L.2
  • 15
    • 33847129220 scopus 로고    scopus 로고
    • 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design
    • Wang J F, Wei D Q, Li L, et al. 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem Biophys Res Commun, 2007, 355: 513-519.
    • (2007) Biochem Biophys Res Commun , vol.355 , pp. 513-519
    • Wang, J.F.1    Wei, D.Q.2    Li, L.3
  • 16
    • 34249993539 scopus 로고    scopus 로고
    • Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP
    • Wang J F, Wei D Q, Lin Y, et al. Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem Biophys Res Commun, 2007, 359: 323-329.
    • (2007) Biochem Biophys Res Commun , vol.359 , pp. 323-329
    • Wang, J.F.1    Wei, D.Q.2    Lin, Y.3
  • 17
    • 38849107581 scopus 로고    scopus 로고
    • Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design
    • Wang J F, Wei D Q, Chen C, et al. Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design. Protein Pept Lett, 2008, 15: 27-32.
    • (2008) Protein Pept Lett , vol.15 , pp. 27-32
    • Wang, J.F.1    Wei, D.Q.2    Chen, C.3
  • 18
    • 59149104827 scopus 로고    scopus 로고
    • Pharmacogenomics and personalized use of drugs
    • Wang J F, Wei D Q, Chou K C. Pharmacogenomics and personalized use of drugs. Curr Top Med Chem, 2008, 8: 1573-1579.
    • (2008) Curr Top Med Chem , vol.8 , pp. 1573-1579
    • Wang, J.F.1    Wei, D.Q.2    Chou, K.C.3
  • 19
    • 59149083761 scopus 로고    scopus 로고
    • Drug candidates from traditional Chinese medicine
    • Wang J F, Wei D Q, Chou K C. Drug candidates from traditional Chinese medicine. Curr Top Med Chem, 2008, 8: 1656-1665.
    • (2008) Curr Top Med Chem , vol.8 , pp. 1656-1665
    • Wang, J.F.1    Wei, D.Q.2    Chou, K.C.3
  • 20
    • 62349108804 scopus 로고    scopus 로고
    • Structure of cytochrome P450s and personalized drug
    • Wang J F, Zhang C C, Chou K C, et al. Structure of cytochrome P450s and personalized drug. Curr Med Chem, 2009, 16: 232-244.
    • (2009) Curr Med Chem , vol.16 , pp. 232-244
    • Wang, J.F.1    Zhang, C.C.2    Chou, K.C.3
  • 21
    • 67651102915 scopus 로고    scopus 로고
    • Molecular dynamics studies on the interactions of PTP1B with inhibitors: From the first phosphate-binding site to the second one
    • Wang J F, Gong K, Wei D Q, et al. Molecular dynamics studies on the interactions of PTP1B with inhibitors: From the first phosphate-binding site to the second one. Protein Eng Des Sel, 2009, 22: 349-355.
    • (2009) Protein Eng Des Sel , vol.22 , pp. 349-355
    • Wang, J.F.1    Gong, K.2    Wei, D.Q.3
  • 22
    • 69249222514 scopus 로고    scopus 로고
    • Insights from investigating the interactions of adamantane-based drugs with the M2 proton channel from the H1N1 swine virus
    • Wang J F, Wei D Q, Chou K C. Insights from investigating the interactions of adamantane-based drugs with the M2 proton channel from the H1N1 swine virus. Biochem Biophys Res Commun, 2009, 388: 413-417.
    • (2009) Biochem Biophys Res Commun , vol.388 , pp. 413-417
    • Wang, J.F.1    Wei, D.Q.2    Chou, K.C.3
  • 23
    • 70450224653 scopus 로고    scopus 로고
    • Insights into the molecular switch mechanism of human Rab5a from molecular dynamics simulations
    • Wang J F, Chou K C. Insights into the molecular switch mechanism of human Rab5a from molecular dynamics simulations. Biochem Biophys Res Commun, 2009, 390: 608-612.
    • (2009) Biochem Biophys Res Commun , vol.390 , pp. 608-612
    • Wang, J.F.1    Chou, K.C.2
  • 24
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace A C, Laskowski R A, Thornton J M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng, 1995, 8: 127-134.
    • (1995) Protein Eng , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 25
    • 0001059812 scopus 로고
    • Quantitative structure-activity relationships and the unnamed science
    • Hansch C. Quantitative structure-activity relationships and the unnamed science. Acc Chem Res, 1993, 26: 147-153.
    • (1993) Acc Chem Res , vol.26 , pp. 147-153
    • Hansch, C.1
  • 26
    • 0000652554 scopus 로고    scopus 로고
    • Comparative QSAR: Toward a deeper understanding of chemicobiological interactions
    • Hansch C, Hoekman D, Gao H. Comparative QSAR: Toward a deeper understanding of chemicobiological interactions. Chem Rev, 1996, 96: 1045-1076.
    • (1996) Chem Rev , vol.96 , pp. 1045-1076
    • Hansch, C.1    Hoekman, D.2    Gao, H.3
  • 27
    • 77955787967 scopus 로고    scopus 로고
    • Physicians Desk Reference. Montvale, USA: Medical Ergonomics Data Production Company, 1995.
  • 28
    • 0033778181 scopus 로고    scopus 로고
    • Crystal structure of an in vivo HIV-1 protease mutant in complex with saquinavir: Insights into the mechanism of drug resistance
    • Hong L, Zheng X C, Hartsuck J A, et al. Crystal structure of an in vivo HIV-1 protease mutant in complex with saquinavir: Insights into the mechanism of drug resistance. Protein Sci, 2000, 9: 1898-1904.
    • (2000) Protein Sci , vol.9 , pp. 1898-1904
    • Hong, L.1    Zheng, X.C.2    Hartsuck, J.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.