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Volumn 8, Issue 8, 2012, Pages

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; DRUG THERAPY; FREE ENERGY;

EID: 84866086808     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002665     Document Type: Article
Times cited : (15)

References (41)
  • 1
    • 0027287506 scopus 로고
    • Rational design of potent sialidase-based inhibitors of influenza virus replication
    • von Itzstein M, Wu W-Y, Kok GB, Pegg MS, Dyason JC, et al. (1993) Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature 363: 418-423.
    • (1993) Nature , vol.363 , pp. 418-423
    • von Itzstein, M.1    Wu, W.-Y.2    Kok, G.B.3    Pegg, M.S.4    Dyason, J.C.5
  • 2
    • 0031048319 scopus 로고    scopus 로고
    • Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: Design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity
    • Kim CU, Lew W, Williams MA, Liu H, Zhang L, et al. (1997) Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: Design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity. J Am Chem Soc 119: 681-690.
    • (1997) J Am Chem Soc , vol.119 , pp. 681-690
    • Kim, C.U.1    Lew, W.2    Williams, M.A.3    Liu, H.4    Zhang, L.5
  • 3
    • 25444501243 scopus 로고    scopus 로고
    • Neuraminidase inhibitors for influenza
    • Moscona A, (2005) Neuraminidase inhibitors for influenza. N Engl J Med 353: 1363-1373.
    • (2005) N Engl J Med , vol.353 , pp. 1363-1373
    • Moscona, A.1
  • 4
    • 4444369826 scopus 로고    scopus 로고
    • Resistant influenza A viruses in children treated with oseltamivir: descriptive study
    • Kiso M, Mitamura K, Sakai-Tagawa Y, Shiraishi K, Kawakami C, et al. (2004) Resistant influenza A viruses in children treated with oseltamivir: descriptive study. Lancet 364: 759-765.
    • (2004) Lancet , vol.364 , pp. 759-765
    • Kiso, M.1    Mitamura, K.2    Sakai-Tagawa, Y.3    Shiraishi, K.4    Kawakami, C.5
  • 5
    • 78649561911 scopus 로고    scopus 로고
    • Oseltamivir-resistant pandemic (H1N1) 2009 virus, South Korea
    • Yi H, Lee J-Y, Hong E-H, Kim M-S, Kwon D, et al. (2010) Oseltamivir-resistant pandemic (H1N1) 2009 virus, South Korea. Emerg Infect Dis 16: 1938-1942.
    • (2010) Emerg Infect Dis , vol.16 , pp. 1938-1942
    • Yi, H.1    Lee, J.-Y.2    Hong, E.-H.3    Kim, M.-S.4    Kwon, D.5
  • 6
    • 29144528757 scopus 로고    scopus 로고
    • Oseltamivir resistance during treatment of influenza A (H5N1) infection
    • De Jong MD, Tran TT, Truong HK, Vo MH, Smith GJD, et al. (2005) Oseltamivir resistance during treatment of influenza A (H5N1) infection. N Engl J Med 353: 2667-2672.
    • (2005) N Engl J Med , vol.353 , pp. 2667-2672
    • de Jong, M.D.1    Tran, T.T.2    Truong, H.K.3    Vo, M.H.4    Smith, G.J.D.5
  • 7
    • 27644439501 scopus 로고    scopus 로고
    • Susceptibilities of antiviral resistant influenza viruses to novel neuraminidase inhibitors
    • Mishin VP, Hayden FG, Gubareva LV, (2005) Susceptibilities of antiviral resistant influenza viruses to novel neuraminidase inhibitors. Antimicrob Agents Chemother 49: 4515-4520.
    • (2005) Antimicrob Agents Chemother , vol.49 , pp. 4515-4520
    • Mishin, V.P.1    Hayden, F.G.2    Gubareva, L.V.3
  • 8
    • 33748437791 scopus 로고    scopus 로고
    • The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design
    • Russell RJ, Haire LF, Stevens DJ, Collins PJ, Lin YP, et al. (2006) The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 443: 45-49.
    • (2006) Nature , vol.443 , pp. 45-49
    • Russell, R.J.1    Haire, L.F.2    Stevens, D.J.3    Collins, P.J.4    Lin, Y.P.5
  • 9
    • 0036894107 scopus 로고    scopus 로고
    • Mechanism by which mutations at his274 alter sensitivity of influenza A virus N1 neuraminidase to oseltamivir carboxylate and zanamivir
    • Wang MZ, Tai CY, Mende DB, (2002) Mechanism by which mutations at his274 alter sensitivity of influenza A virus N1 neuraminidase to oseltamivir carboxylate and zanamivir. Antimicrob Agents Chemother 46: 3809-3816.
    • (2002) Antimicrob Agents Chemother , vol.46 , pp. 3809-3816
    • Wang, M.Z.1    Tai, C.Y.2    Mende, D.B.3
  • 10
    • 46249111790 scopus 로고    scopus 로고
    • Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants
    • Collins PJ, Haire LF, Lin YP, Liu J, Russell RJ, et al. (2008) Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Nature 453: 1258-1261.
    • (2008) Nature , vol.453 , pp. 1258-1261
    • Collins, P.J.1    Haire, L.F.2    Lin, Y.P.3    Liu, J.4    Russell, R.J.5
  • 11
    • 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 PI, Wang YF, Tozser J, Louis JM, et al. (2005) 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 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
  • 12
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig R, (1954) High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys 22: 1420-1426.
    • (1954) J Chem Phys , vol.22 , pp. 1420-1426
    • Zwanzig, R.1
  • 13
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood JG, (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3: 300-313.
    • (1935) J Chem Phys , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 14
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices
    • Srinivasan J, Cheatham I, TE, Cieplak P, Kollman PA, Case DA, (1998) Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices. J Am Chem Soc 120: 9401-9409.
    • (1998) J Am Chem Soc , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, I.T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 15
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • Gilson MK, Given JA, Bush BL, McCammon JA, (1997) The statistical-thermodynamic basis for computation of binding affinities: A critical review. Biophys J 72: 1047-1069.
    • (1997) Biophys J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 17
    • 60349109713 scopus 로고    scopus 로고
    • Computational evaluation of protein-small molecule binding
    • Guvench O, MacKerell AD Jr, (2009) Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol 19: 56-61.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 56-61
    • Guvench, O.1    MacKerell Jr., A.D.2
  • 18
    • 36749075510 scopus 로고    scopus 로고
    • Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12
    • Chaudhury S, Sircar A, Sivasubramanian A, Berrondo M, Gray JJ, (2007) Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12. Proteins 69: 793-800.
    • (2007) Proteins , vol.69 , pp. 793-800
    • Chaudhury, S.1    Sircar, A.2    Sivasubramanian, A.3    Berrondo, M.4    Gray, J.J.5
  • 19
    • 0007836334 scopus 로고
    • Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron transfer and proton transfer reactions
    • Warshel A, (1982) Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron transfer and proton transfer reactions. J Phys Chem 86: 2218-2224.
    • (1982) J Phys Chem , vol.86 , pp. 2218-2224
    • Warshel, A.1
  • 20
  • 21
    • 0004504539 scopus 로고
    • Monte carlo simulation of differences in free energies of hydration
    • Jorgensen WL, Ravimohan C, (1985) Monte carlo simulation of differences in free energies of hydration. J Chem Phys 83: 3050-3054.
    • (1985) J Chem Phys , vol.83 , pp. 3050-3054
    • Jorgensen, W.L.1    Ravimohan, C.2
  • 22
    • 0023106632 scopus 로고
    • Calculation of the relative change in binding free energy of a protein-inhibitor complex
    • Bash PA, Singh UC, Brown FK, Langridge R, Kollman PA, (1987) Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 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
  • 23
    • 65249136476 scopus 로고    scopus 로고
    • Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: determinants of H5N1 avian influenza virus neuraminidase inhibition by peramivir
    • Lawrenz M, Baron R, McCammon JA, (2009) Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: determinants of H5N1 avian influenza virus neuraminidase inhibition by peramivir. J Chem Theory Comput 5: 1106-1116.
    • (2009) J Chem Theory Comput , vol.5 , pp. 1106-1116
    • Lawrenz, M.1    Baron, R.2    McCammon, J.A.3
  • 24
    • 79960245735 scopus 로고    scopus 로고
    • Effects of biomolecular flexibility on alchemical calculations of absolute binding free energies
    • Lawrenz M, Baron R, Wang Y, McCammon JA, (2011) Effects of biomolecular flexibility on alchemical calculations of absolute binding free energies. J Chem Theory Comput 7: 2224-2232.
    • (2011) J Chem Theory Comput , vol.7 , pp. 2224-2232
    • Lawrenz, M.1    Baron, R.2    Wang, Y.3    McCammon, J.A.4
  • 25
    • 77955813570 scopus 로고    scopus 로고
    • Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy
    • Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, et al. (2010) Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy. Proteins 78: 2523-2532.
    • (2010) Proteins , vol.78 , pp. 2523-2532
    • Lawrenz, M.1    Wereszczynski, J.2    Amaro, R.3    Walker, R.4    Roitberg, A.5
  • 26
    • 78149458812 scopus 로고    scopus 로고
    • Using selectively applied accelerated molecular dynamics to enhance free energy calculations
    • Wereszczynski J, McCammon JA, (2010) Using selectively applied accelerated molecular dynamics to enhance free energy calculations. J Chem Theory Comput 6: 3285-3292.
    • (2010) J Chem Theory Comput , vol.6 , pp. 3285-3292
    • Wereszczynski, J.1    McCammon, J.A.2
  • 27
    • 0000987552 scopus 로고
    • Treatment of rotational isomeric states. III. The use of biasing potentials
    • Straatsma TP, McCammon JA, (1994) Treatment of rotational isomeric states. III. The use of biasing potentials. J Chem Phys 101: 5032-5039.
    • (1994) J Chem Phys , vol.101 , pp. 5032-5039
    • Straatsma, T.P.1    McCammon, J.A.2
  • 28
    • 33749238080 scopus 로고    scopus 로고
    • Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant
    • Deng Y, Roux B, (2006) Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant. J Chem Theory Comput 2: 1255-1273.
    • (2006) J Chem Theory Comput , vol.2 , pp. 1255-1273
    • Deng, Y.1    Roux, B.2
  • 29
    • 36649006864 scopus 로고    scopus 로고
    • Optimization of replica exchange molecular dynamics by fast mimicking
    • Hritz J, Oostenbrink C, (2007) Optimization of replica exchange molecular dynamics by fast mimicking. J Chem Phys 127: 204104.
    • (2007) J Chem Phys , vol.127 , pp. 204104
    • Hritz, J.1    Oostenbrink, C.2
  • 30
    • 34247266675 scopus 로고    scopus 로고
    • Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface
    • Min D, Li H, Li G, Bitetti-Putzer R, Yang W, (2007) Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface. J Chem Phys 126: 144109.
    • (2007) J Chem Phys , vol.126 , pp. 144109
    • Min, D.1    Li, H.2    Li, G.3    Bitetti-Putzer, R.4    Yang, W.5
  • 31
    • 80052807977 scopus 로고    scopus 로고
    • Improved binding free energy predictions from single-reference thermodynamic integration augmented with hamiltonian replica exchange
    • Khavrutskii IV, Wallqvist A, (2011) Improved binding free energy predictions from single-reference thermodynamic integration augmented with hamiltonian replica exchange. J Chem Theory Comput 7: 3001-3011.
    • (2011) J Chem Theory Comput , vol.7 , pp. 3001-3011
    • Khavrutskii, I.V.1    Wallqvist, A.2
  • 32
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T, Baker D, (2002) A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A 99: 14116-14121.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 33
    • 63449087331 scopus 로고    scopus 로고
    • Computational studies of H5N1 influenza virus resistance to oseltamivir
    • Wang NX, Zheng JJ, (2009) Computational studies of H5N1 influenza virus resistance to oseltamivir. Protein Sci 18: 707-715.
    • (2009) Protein Sci , vol.18 , pp. 707-715
    • Wang, N.X.1    Zheng, J.J.2
  • 34
    • 80053300058 scopus 로고    scopus 로고
    • Study of Tamiflu sensitivity to variants of A/H5N1 virus using different force fields
    • Nguyen TT, Mai BK, Li MS, (2011) Study of Tamiflu sensitivity to variants of A/H5N1 virus using different force fields. J Chem Inf Model 51: 2266-2276.
    • (2011) J Chem Inf Model , vol.51 , pp. 2266-2276
    • Nguyen, T.T.1    Mai, B.K.2    Li, M.S.3
  • 36
    • 67949124553 scopus 로고    scopus 로고
    • Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized Born molecular dynamics and end-point free energy calculations
    • Amaro RE, Cheng X, Ivanov I, Xu D, McCammon JA, (2009) Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized Born molecular dynamics and end-point free energy calculations. J Am Chem Soc 131: 4702-4709.
    • (2009) J Am Chem Soc , vol.131 , pp. 4702-4709
    • Amaro, R.E.1    Cheng, X.2    Ivanov, I.3    Xu, D.4    McCammon, J.A.5
  • 38
    • 0034084991 scopus 로고    scopus 로고
    • Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
    • Massova I, Kollman PA, (2000) Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspec Drug Discov 18: 113-135.
    • (2000) Perspec Drug Discov , vol.18 , pp. 113-135
    • Massova, I.1    Kollman, P.A.2
  • 39
    • 80255127591 scopus 로고    scopus 로고
    • Prediction of zanamivir efficiency over the possible 2009 Influenza A (H1N1) mutants by multiple molecular dynamics simulations and free energy calculations
    • Pan D, Sun H, Bai C, Shen Y, Jin N, et al. (2011) Prediction of zanamivir efficiency over the possible 2009 Influenza A (H1N1) mutants by multiple molecular dynamics simulations and free energy calculations. J Mol Model 17: 2465-2473.
    • (2011) J Mol Model , vol.17 , pp. 2465-2473
    • Pan, D.1    Sun, H.2    Bai, C.3    Shen, Y.4    Jin, N.5
  • 40
    • 70349251134 scopus 로고    scopus 로고
    • How does each substituent functional group of oseltamivir lose its activity against virulent H5N1 influenza mutants?
    • Rungrotmongkol T, Udommaneethanakit T, Malaisree M, Nunthaboot N, Intharathep P, et al. (2009) How does each substituent functional group of oseltamivir lose its activity against virulent H5N1 influenza mutants? Biophys Chem 145: 29-36.
    • (2009) Biophys Chem , vol.145 , pp. 29-36
    • Rungrotmongkol, T.1    Udommaneethanakit, T.2    Malaisree, M.3    Nunthaboot, N.4    Intharathep, P.5
  • 41
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme T, Kim DE, Baker D, (2004) Computational alanine scanning of protein-protein interfaces. Sci STKE 2004: pl2.
    • (2004) Sci STKE , vol.2004
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3


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