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Volumn 8, Issue 6, 2013, Pages 1223-1231

Small molecule regulation of protein conformation by binding in the flap of HIV protease

Author keywords

[No Author keywords available]

Indexed keywords

ARACHIDONATE 5 LIPOXYGENASE ACTIVATING PROTEIN; BENZOTRIPT; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; INDOLE 6 CARBOXYLIC ACID; UNCLASSIFIED DRUG;

EID: 84879761645     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb300611p     Document Type: Article
Times cited : (30)

References (48)
  • 2
    • 79451471817 scopus 로고    scopus 로고
    • UNAIDS. (2010), Joint United Nations Programme on HIV/AIDS (UNAIDS), Geneva, Switzerland
    • UNAIDS. (2010) UNAIDS report on the global AIDS epidemic 2010, Joint United Nations Programme on HIV/AIDS (UNAIDS), Geneva, Switzerland.
    • UNAIDS Report on the Global AIDS Epidemic 2010
  • 3
    • 46049096099 scopus 로고    scopus 로고
    • Viral reservoirs, residual viremia, and the potential of highly active antiretroviral therapy to eradicate HIV infection
    • Shen, L. and Siliciano, R. F. (2008) Viral reservoirs, residual viremia, and the potential of highly active antiretroviral therapy to eradicate HIV infection J. Allergy. Clin. Immunol. 122, 22-28
    • (2008) J. Allergy. Clin. Immunol. , vol.122 , pp. 22-28
    • Shen, L.1    Siliciano, R.F.2
  • 5
    • 73549092917 scopus 로고    scopus 로고
    • Fifteen years of HIV protease inhibitors: Raising the barrier to resistance
    • Wensing, A. M., van Maarseveen, N. M., and Nijhuis, M. (2009) Fifteen years of HIV protease inhibitors: raising the barrier to resistance Antiviral Res. 85, 59-74
    • (2009) Antiviral Res. , vol.85 , pp. 59-74
    • Wensing, A.M.1    Van Maarseveen, N.M.2    Nijhuis, M.3
  • 6
    • 0032918170 scopus 로고    scopus 로고
    • Perspectives of non-nucleoside reverse transcriptase inhibitors (NNRTIs) in the therapy of HIV-1 infection
    • De Clercq, E. (1999) Perspectives of non-nucleoside reverse transcriptase inhibitors (NNRTIs) in the therapy of HIV-1 infection Farmaco 54, 26-45
    • (1999) Farmaco , vol.54 , pp. 26-45
    • De Clercq, E.1
  • 7
    • 64849113665 scopus 로고    scopus 로고
    • Trapping moving targets with small molecules
    • Lee, G. M. and Craik, C. S. (2009) Trapping moving targets with small molecules Science 324, 213-215
    • (2009) Science , vol.324 , pp. 213-215
    • Lee, G.M.1    Craik, C.S.2
  • 8
    • 33748955158 scopus 로고    scopus 로고
    • Ultra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114
    • Kovalevsky, A. Y., Liu, F., Leshchenko, S., Ghosh, A. K., Louis, J. M., Harrison, R. W., and Weber, I. T. (2006) Ultra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114 J. Mol. Biol. 363, 161-173
    • (2006) J. Mol. Biol. , vol.363 , pp. 161-173
    • Kovalevsky, A.Y.1    Liu, F.2    Leshchenko, S.3    Ghosh, A.K.4    Louis, J.M.5    Harrison, R.W.6    Weber, I.T.7
  • 9
    • 54549105456 scopus 로고    scopus 로고
    • Solution kinetics measurements suggest HIV-1 protease has two binding sites for darunavir and amprenavir
    • Kovalevsky, A. Y., Ghosh, A. K., and Weber, I. T. (2008) Solution kinetics measurements suggest HIV-1 protease has two binding sites for darunavir and amprenavir J. Med. Chem. 51, 6599-6603
    • (2008) J. Med. Chem. , vol.51 , pp. 6599-6603
    • Kovalevsky, A.Y.1    Ghosh, A.K.2    Weber, I.T.3
  • 10
    • 54249109408 scopus 로고    scopus 로고
    • Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease
    • Kovalevsky, A. Y., Louis, J. M., Aniana, A., Ghosh, A. K., and Weber, I. T. (2008) Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease J. Mol. Biol. 384, 178-192
    • (2008) J. Mol. Biol. , vol.384 , pp. 178-192
    • Kovalevsky, A.Y.1    Louis, J.M.2    Aniana, A.3    Ghosh, A.K.4    Weber, I.T.5
  • 11
    • 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., and Schiffer, C. A. (2002) Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes Structure 10, 369-381
    • (2002) Structure , vol.10 , pp. 369-381
    • Prabu-Jeyabalan, M.1    Nalivaika, E.2    Schiffer, C.A.3
  • 13
    • 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, A. L., Lin, J. H., and McCammon, J. A. (2004) 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. 13, 1108-1123
    • (2004) Protein Sci. , vol.13 , pp. 1108-1123
    • Perryman, A.L.1    Lin, J.H.2    McCammon, J.A.3
  • 21
    • 0034483901 scopus 로고    scopus 로고
    • Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
    • Scott, W. R. and Schiffer, C. A. (2000) Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance Structure 8, 1259-1265
    • (2000) Structure , vol.8 , pp. 1259-1265
    • Scott, W.R.1    Schiffer, C.A.2
  • 22
    • 0037634016 scopus 로고    scopus 로고
    • A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex
    • Katoh, E., Louis, J. M., Yamazaki, T., Gronenborn, A. M., Torchia, D. A., and Ishima, R. (2003) A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex Protein Sci. 12, 1376-1385
    • (2003) Protein Sci. , vol.12 , pp. 1376-1385
    • Katoh, E.1    Louis, J.M.2    Yamazaki, T.3    Gronenborn, A.M.4    Torchia, D.A.5    Ishima, R.6
  • 23
    • 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, D. I., Ishima, R., Jacob, J., Wang, Y. X., Kustanovich, I., Louis, J. M., and Torchia, D. A. (2002) Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations Protein Sci. 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
  • 24
    • 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, D. I., Wang, Y. X., Louis, J. M., and Torchia, D. A. (1999) Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function Struct. Folding Des. 7, 1047-1055
    • (1999) Struct. Folding Des. , vol.7 , pp. 1047-1055
    • Ishima, R.1    Freedberg, D.I.2    Wang, Y.X.3    Louis, J.M.4    Torchia, D.A.5
  • 25
    • 34548737701 scopus 로고    scopus 로고
    • Interflap distances in HIV-1 protease determined by pulsed EPR measurements
    • Galiano, L., Bonora, M., and Fanucci, G. E. (2007) Interflap distances in HIV-1 protease determined by pulsed EPR measurements J. Am. Chem. Soc. 129, 11004-11005
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 11004-11005
    • Galiano, L.1    Bonora, M.2    Fanucci, G.E.3
  • 26
    • 44949121782 scopus 로고    scopus 로고
    • Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments
    • Ding, F., Layten, M., and Simmerling, C. (2008) Solution structure of HIV-1 protease flaps probed by comparison of molecular dynamics simulation ensembles and EPR experiments J. Am. Chem. Soc. 130, 7184-7185
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 7184-7185
    • Ding, F.1    Layten, M.2    Simmerling, C.3
  • 27
    • 70350052784 scopus 로고    scopus 로고
    • Subtype polymorphisms among HIV-1 protease variants confer altered flap conformations and flexibility
    • Kear, J. L., Blackburn, M. E., Veloro, A. M., Dunn, B. M., and Fanucci, G. E. (2009) Subtype polymorphisms among HIV-1 protease variants confer altered flap conformations and flexibility J. Am. Chem. Soc. 131, 14650-14651
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 14650-14651
    • Kear, J.L.1    Blackburn, M.E.2    Veloro, A.M.3    Dunn, B.M.4    Fanucci, G.E.5
  • 28
    • 70349153078 scopus 로고    scopus 로고
    • Monitoring inhibitor-induced conformational population shifts in HIV-1 protease by pulsed EPR spectroscopy
    • Blackburn, M. E., Veloro, A. M., and Fanucci, G. E. (2009) Monitoring inhibitor-induced conformational population shifts in HIV-1 protease by pulsed EPR spectroscopy Biochemistry 48, 8765-8767
    • (2009) Biochemistry , vol.48 , pp. 8765-8767
    • Blackburn, M.E.1    Veloro, A.M.2    Fanucci, G.E.3
  • 30
    • 61749086002 scopus 로고    scopus 로고
    • Dynamics of ″flap″ structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy
    • Torbeev, V. Y., Raghuraman, H., Mandal, K., Senapati, S., Perozo, E., and Kent, S. B. (2009) Dynamics of ″flap″ structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy J. Am. Chem. Soc. 131, 884-885
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 884-885
    • Torbeev, V.Y.1    Raghuraman, H.2    Mandal, K.3    Senapati, S.4    Perozo, E.5    Kent, S.B.6
  • 31
    • 0035314020 scopus 로고    scopus 로고
    • 1.9 A X-ray study shows closed flap conformation in crystals of tethered HIV-1 PR
    • Pillai, B., Kannan, K. K., and Hosur, M. V. (2001) 1.9 A X-ray study shows closed flap conformation in crystals of tethered HIV-1 PR Proteins 43, 57-64
    • (2001) Proteins , vol.43 , pp. 57-64
    • Pillai, B.1    Kannan, K.K.2    Hosur, M.V.3
  • 32
    • 77952055764 scopus 로고    scopus 로고
    • X-ray snapshot of HIV-1 protease in action: Observation of tetrahedral intermediate and short ionic hydrogen bond SIHB with catalytic aspartate
    • Das, A., Mahale, S., Prashar, V., Bihani, S., Ferrer, J. L., and Hosur, M. V. (2010) X-ray snapshot of HIV-1 protease in action: observation of tetrahedral intermediate and short ionic hydrogen bond SIHB with catalytic aspartate J. Am. Chem. Soc. 132, 6366-6373
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 6366-6373
    • Das, A.1    Mahale, S.2    Prashar, V.3    Bihani, S.4    Ferrer, J.L.5    Hosur, M.V.6
  • 34
    • 84857804736 scopus 로고    scopus 로고
    • Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease
    • Mittal, S., Cai, Y., Nalam, M. N. L., Bolon, D. N. A., and Schiffer, C. A. (2012) Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease J. Am. Chem. Soc. 134, 4163-4168
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 4163-4168
    • Mittal, S.1    Cai, Y.2    Nalam, M.N.L.3    Bolon, D.N.A.4    Schiffer, C.A.5
  • 35
    • 70349335348 scopus 로고    scopus 로고
    • Resistance mechanism revealed by crystal structures of unliganded nelfinavir-resistant HIV-1 protease non-active site mutants N88D and N88S
    • Bihani, S. C., Das, A., Prashar, V., Ferrer, J. L., and Hosur, M. V. (2009) Resistance mechanism revealed by crystal structures of unliganded nelfinavir-resistant HIV-1 protease non-active site mutants N88D and N88S Biochem. Biophys. Res. Commun. 389, 295-300
    • (2009) Biochem. Biophys. Res. Commun. , vol.389 , pp. 295-300
    • Bihani, S.C.1    Das, A.2    Prashar, V.3    Ferrer, J.L.4    Hosur, M.V.5
  • 36
    • 11144356514 scopus 로고    scopus 로고
    • A phenylnorstatine inhibitor binding to HIV-1 protease: A geometry, protonation, and subsite-pocket interactions analyzed at atomic resolution
    • Brynda, J., Rezacova, P., Fabry, M., Horejsi, M., Stouracova, R., Sedlacek, J., Soucek, M., Hradilek, M., Lepsik, M., and Konvalinka, J. (2004) A phenylnorstatine inhibitor binding to HIV-1 protease: a geometry, protonation, and subsite-pocket interactions analyzed at atomic resolution J. Med. Chem. 47, 2030-2036
    • (2004) J. Med. Chem. , vol.47 , pp. 2030-2036
    • Brynda, J.1    Rezacova, P.2    Fabry, M.3    Horejsi, M.4    Stouracova, R.5    Sedlacek, J.6    Soucek, M.7    Hradilek, M.8    Lepsik, M.9    Konvalinka, J.10
  • 38
    • 37249005205 scopus 로고    scopus 로고
    • The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability
    • Niesen, F. H., Berglund, H., and Vedadi, M. (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability Nat. Protoc. 2, 2212-2221
    • (2007) Nat. Protoc. , vol.2 , pp. 2212-2221
    • Niesen, F.H.1    Berglund, H.2    Vedadi, M.3
  • 39
    • 80255138809 scopus 로고    scopus 로고
    • A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network
    • Rücker, P., Horn, A., Meiselbach, H., and Sticht, H. (2011) A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network J. Mol. Model. 17, 2693-2705
    • (2011) J. Mol. Model. , vol.17 , pp. 2693-2705
    • Rücker, P.1    Horn, A.2    Meiselbach, H.3    Sticht, H.4
  • 40
    • 34648815160 scopus 로고    scopus 로고
    • Free-solution, label-free molecular interactions studied by back-scattering interferometry
    • Bornhop, D. J., Latham, J. C., Kussrow, A., Markov, D. A., Jones, R. D., and Sorensen, H. S. (2007) Free-solution, label-free molecular interactions studied by back-scattering interferometry Science 317, 1732-1736
    • (2007) Science , vol.317 , pp. 1732-1736
    • Bornhop, D.J.1    Latham, J.C.2    Kussrow, A.3    Markov, D.A.4    Jones, R.D.5    Sorensen, H.S.6
  • 41
    • 64749106155 scopus 로고    scopus 로고
    • Free-solution label-free detection of alpha-Crystallin chaperone interactions by back-scattering interferometry
    • Latham, J. C., Stein, R. A., Bornhop, D. J., and McHaourab, H. S. (2009) Free-solution label-free detection of alpha-Crystallin chaperone interactions by back-scattering interferometry Anal. Chem. 81, 1865-1871
    • (2009) Anal. Chem. , vol.81 , pp. 1865-1871
    • Latham, J.C.1    Stein, R.A.2    Bornhop, D.J.3    McHaourab, H.S.4
  • 42
    • 79953839803 scopus 로고    scopus 로고
    • Label-free quantification of membrane-ligand interactions using backscattering interferometry
    • Baksh, M. M., Kussrow, A. K., Mileni, M., Finn, M. G., and Bornhop, D. J. (2011) Label-free quantification of membrane-ligand interactions using backscattering interferometry Nat. Biotechnol. 29, 357-360
    • (2011) Nat. Biotechnol. , vol.29 , pp. 357-360
    • Baksh, M.M.1    Kussrow, A.K.2    Mileni, M.3    Finn, M.G.4    Bornhop, D.J.5
  • 43
    • 79551529077 scopus 로고    scopus 로고
    • Universal sensing by transduction of antibody binding with backscattering interferometry
    • Kussrow, A., Baksh, M. M., Bornhop, D. J., and Finn, M. G. (2011) Universal sensing by transduction of antibody binding with backscattering interferometry ChemBioChem 12, 367-370
    • (2011) ChemBioChem , vol.12 , pp. 367-370
    • Kussrow, A.1    Baksh, M.M.2    Bornhop, D.J.3    Finn, M.G.4
  • 44
    • 84855932989 scopus 로고    scopus 로고
    • Interferometric methods for label-free molecular interaction studies
    • Kussrow, A., Enders, C. S., and Bornhop, D. J. (2011) Interferometric methods for label-free molecular interaction studies Anal. Chem. 84, 779-792
    • (2011) Anal. Chem. , vol.84 , pp. 779-792
    • Kussrow, A.1    Enders, C.S.2    Bornhop, D.J.3
  • 47
    • 13844312649 scopus 로고    scopus 로고
    • ZINC: A free database of commercially available compounds for virtual screening
    • Irwin, J. J. and Shoichet, B. K. (2005) ZINC: a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45, 177-182
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 48
    • 0141726877 scopus 로고    scopus 로고
    • A 'rule of three' for fragment-based lead discovery?
    • Congreve, M., Carr, R., Murray, C., and Jhoti, H. (2003) A 'rule of three' for fragment-based lead discovery? Drug Discovery Today 8, 876-877
    • (2003) Drug Discovery Today , vol.8 , pp. 876-877
    • Congreve, M.1    Carr, R.2    Murray, C.3    Jhoti, H.4


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