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Volumn 6, Issue 6, 2011, Pages

Hydrogen bonding penalty upon ligand binding

Author keywords

[No Author keywords available]

Indexed keywords

EPHRIN RECEPTOR B4 INHIBITOR; LIGAND; MOLECULAR SCAFFOLD; PROTEIN; PROTEIN INHIBITOR; UNCLASSIFIED DRUG; WATER;

EID: 79959222106     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0019923     Document Type: Article
Times cited : (102)

References (42)
  • 1
    • 0021107943 scopus 로고
    • Site-directed mutagenesis as a probe of enzyme structure and catalysis: tyrosyl-tRNA synthetase cysteine-35 to glycine-35 mutation
    • Wilkinson AJ, Fersht AR, Blow DM, Winter G, (1983) Site-directed mutagenesis as a probe of enzyme structure and catalysis: tyrosyl-tRNA synthetase cysteine-35 to glycine-35 mutation. Biochemistry 22: 3581-3586.
    • (1983) Biochemistry , vol.22 , pp. 3581-3586
    • Wilkinson, A.J.1    Fersht, A.R.2    Blow, D.M.3    Winter, G.4
  • 2
    • 0019969022 scopus 로고
    • Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding
    • Winter G, Fersht AR, Wilkinson AJ, Zoller M, Smith M, (1982) Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding. Nature 299: 756-758.
    • (1982) Nature , vol.299 , pp. 756-758
    • Winter, G.1    Fersht, A.R.2    Wilkinson, A.J.3    Zoller, M.4    Smith, M.5
  • 3
    • 0021251828 scopus 로고
    • A large increase in enzyme-substrate affinity by protein engineering
    • Wilkinson AJ, Fersht AR, Blow DM, Carter P, Winter G, (1984) A large increase in enzyme-substrate affinity by protein engineering. Nature 307: 187-188.
    • (1984) Nature , vol.307 , pp. 187-188
    • Wilkinson, A.J.1    Fersht, A.R.2    Blow, D.M.3    Carter, P.4    Winter, G.5
  • 4
    • 0036835460 scopus 로고    scopus 로고
    • Integration of virtual and high-throughput screening
    • Bajorath J, (2002) Integration of virtual and high-throughput screening. Nat Rev Drug Discov 1: 882-894.
    • (2002) Nat Rev Drug Discov , vol.1 , pp. 882-894
    • Bajorath, J.1
  • 5
    • 0035002134 scopus 로고    scopus 로고
    • Virtual screening: an effective tool for lead structure discovery?
    • Langer T, Hoffmann RD, (2001) Virtual screening: an effective tool for lead structure discovery? Curr Pharm Des 7: 509-527.
    • (2001) Curr Pharm Des , vol.7 , pp. 509-527
    • Langer, T.1    Hoffmann, R.D.2
  • 6
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A, (1995) Classical electrostatics in biology and chemistry. Science 268: 1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 7
    • 0346971105 scopus 로고    scopus 로고
    • Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
    • Feig M, Onufriev A, Lee MS, Im W, Case DA, et al. (2004) Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem 25: 265-284.
    • (2004) J Comput Chem , vol.25 , pp. 265-284
    • Feig, M.1    Onufriev, A.2    Lee, M.S.3    Im, W.4    Case, D.A.5
  • 8
    • 77950503976 scopus 로고    scopus 로고
    • Virtual screening: an endless staircase?
    • Schneider G, (2010) Virtual screening: an endless staircase? Nat Rev Drug Discov 9: 273-276.
    • (2010) Nat Rev Drug Discov , vol.9 , pp. 273-276
    • Schneider, G.1
  • 9
    • 33750124980 scopus 로고    scopus 로고
    • Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
    • Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, et al. (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49: 6177-6196.
    • (2006) J Med Chem , vol.49 , pp. 6177-6196
    • Friesner, R.A.1    Murphy, R.B.2    Repasky, M.P.3    Frye, L.L.4    Greenwood, J.R.5
  • 10
    • 12144289984 scopus 로고    scopus 로고
    • Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    • Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47: 1739-1749.
    • (2004) J Med Chem , vol.47 , pp. 1739-1749
    • Friesner, R.A.1    Banks, J.L.2    Murphy, R.B.3    Halgren, T.A.4    Klicic, J.J.5
  • 11
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang R, Lu Y, Wang S, (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46: 2287-2303.
    • (2003) J Med Chem , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 12
    • 77949797550 scopus 로고    scopus 로고
    • Ligand-protein cross-docking with water molecules
    • Thilagavathi R, Mancera RL, (2010) Ligand-protein cross-docking with water molecules. J Chem Inf Model 50: 415-421.
    • (2010) J Chem Inf Model , vol.50 , pp. 415-421
    • Thilagavathi, R.1    Mancera, R.L.2
  • 13
    • 41649096077 scopus 로고    scopus 로고
    • Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model
    • Kolb P, Huang D, Dey F, Caflisch A, (2008) Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model. J Med Chem 51: 1179-1188.
    • (2008) J Med Chem , vol.51 , pp. 1179-1188
    • Kolb, P.1    Huang, D.2    Dey, F.3    Caflisch, A.4
  • 14
    • 0032227735 scopus 로고    scopus 로고
    • The role of tyrosine phosphorylation in cell growth and disease
    • Hunter T, (1998) The role of tyrosine phosphorylation in cell growth and disease. Harvey Lect 94: 81-119.
    • (1998) Harvey Lect , vol.94 , pp. 81-119
    • Hunter, T.1
  • 15
    • 70349263942 scopus 로고    scopus 로고
    • The ephrinB2/EphB4 axis is dysregulated in osteoprogenitors from myeloma patients and its activation affects myeloma bone disease and tumor growth
    • Pennisi A, Ling W, Li X, Khan S, Shaughnessy JD Jr, et al. (2009) The ephrinB2/EphB4 axis is dysregulated in osteoprogenitors from myeloma patients and its activation affects myeloma bone disease and tumor growth. Blood 114: 1803-1812.
    • (2009) Blood , vol.114 , pp. 1803-1812
    • Pennisi, A.1    Ling, W.2    Li, X.3    Khan, S.4    Shaughnessy Jr., J.D.5
  • 16
    • 77954114200 scopus 로고    scopus 로고
    • High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors
    • Zhou T, Caflisch A, (2010) High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors. ChemMedChem 5: 1007-1014.
    • (2010) ChemMedChem , vol.5 , pp. 1007-1014
    • Zhou, T.1    Caflisch, A.2
  • 17
    • 33845668264 scopus 로고    scopus 로고
    • Design and effective synthesis of novel templates, 3,7-diphenyl-4-amino-thieno and furo-[3,2-c]pyridines as protein kinase inhibitors and in vitro evaluation targeting angiogenetic kinases
    • Miyazaki Y, Nakano M, Sato H, Truesdale AT, Stuart JD, et al. (2007) Design and effective synthesis of novel templates, 3,7-diphenyl-4-amino-thieno and furo-[3,2-c]pyridines as protein kinase inhibitors and in vitro evaluation targeting angiogenetic kinases. Bioorg Med Chem Lett 17: 250-254.
    • (2007) Bioorg Med Chem Lett , vol.17 , pp. 250-254
    • Miyazaki, Y.1    Nakano, M.2    Sato, H.3    Truesdale, A.T.4    Stuart, J.D.5
  • 18
    • 43049114977 scopus 로고    scopus 로고
    • Inhibitors of the tyrosine kinase EphB4. Part 1: Structure-based design and optimization of a series of 2,4-bis-anilinopyrimidines
    • Bardelle C, Cross D, Davenport S, Kettle JG, Ko EJ, et al. (2008) Inhibitors of the tyrosine kinase EphB4. Part 1: Structure-based design and optimization of a series of 2,4-bis-anilinopyrimidines. Bioorg Med Chem Lett 18: 2776-2780.
    • (2008) Bioorg Med Chem Lett , vol.18 , pp. 2776-2780
    • Bardelle, C.1    Cross, D.2    Davenport, S.3    Kettle, J.G.4    Ko, E.J.5
  • 19
    • 70350072332 scopus 로고    scopus 로고
    • Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4)
    • Lafleur K, Huang D, Zhou T, Caflisch A, Nevado C, (2009) Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). J Med Chem 52: 6433-6446.
    • (2009) J Med Chem , vol.52 , pp. 6433-6446
    • Lafleur, K.1    Huang, D.2    Zhou, T.3    Caflisch, A.4    Nevado, C.5
  • 21
    • 0021828928 scopus 로고
    • Hydrogen bonding and biological specificity analysed by protein engineering
    • Fersht AR, Shi JP, Knill-Jones J, Lowe DM, Wilkinson AJ, et al. (1985) Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314: 235-238.
    • (1985) Nature , vol.314 , pp. 235-238
    • Fersht, A.R.1    Shi, J.P.2    Knill-Jones, J.3    Lowe, D.M.4    Wilkinson, A.J.5
  • 22
    • 0001125401 scopus 로고
    • Structural Effects on Rates and Equilibria. 15. Hydrogen-Bonded Intermediates and Stepwise Mechanisms for Proton-Exchange Reactions between Oxygen-Atoms in Hydroxylic Solvents
    • Hine J, (1972) Structural Effects on Rates and Equilibria. 15. Hydrogen-Bonded Intermediates and Stepwise Mechanisms for Proton-Exchange Reactions between Oxygen-Atoms in Hydroxylic Solvents. J Am Chem Soc 94: 5766-&.
    • (1972) J Am Chem Soc , vol.94 , pp. 5766
    • Hine, J.1
  • 23
    • 0006474999 scopus 로고
    • Role of C-H. O Hydrogen-Bonds in the Coordination of Water-Molecules - Analysis of Neutron-Diffraction Data
    • Steiner T, Saenger W, (1993) Role of C-H. O Hydrogen-Bonds in the Coordination of Water-Molecules- Analysis of Neutron-Diffraction Data. J Am Chem Soc 115: 4540-4547.
    • (1993) J Am Chem Soc , vol.115 , pp. 4540-4547
    • Steiner, T.1    Saenger, W.2
  • 26
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Bohm HJ, (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 8: 243-256.
    • (1994) J Comput Aided Mol Des , vol.8 , pp. 243-256
    • Bohm, H.J.1
  • 27
    • 2342593131 scopus 로고    scopus 로고
    • Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
    • Morozov AV, Kortemme T, Tsemekhman K, Baker D, (2004) Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A 101: 6946-6951.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 6946-6951
    • Morozov, A.V.1    Kortemme, T.2    Tsemekhman, K.3    Baker, D.4
  • 28
    • 84986505827 scopus 로고
    • Validation of the General-Purpose Quanta(R)3.2/Charmm(R) Force-Field
    • Momany FA, Rone R, (1992) Validation of the General-Purpose Quanta(R)3.2/Charmm(R) Force-Field. J Comput Chem 13: 888-900.
    • (1992) J Comput Chem , vol.13 , pp. 888-900
    • Momany, F.A.1    Rone, R.2
  • 30
    • 0020475509 scopus 로고
    • Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
    • Warwicker J, Watson HC, (1982) Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J Mol Biol 157: 671-679.
    • (1982) J Mol Biol , vol.157 , pp. 671-679
    • Warwicker, J.1    Watson, H.C.2
  • 31
    • 0032096837 scopus 로고    scopus 로고
    • Continuum Solvation Model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
    • Im W, Beglov D, Roux B, (1998) Continuum Solvation Model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Computer Physics Communications 111: 59-75.
    • (1998) Computer Physics Communications , vol.111 , pp. 59-75
    • Im, W.1    Beglov, D.2    Roux, B.3
  • 32
    • 0036682024 scopus 로고    scopus 로고
    • Probing the ATP ribose-binding domain of cyclin-dependent kinases 1 and 2 with O(6)-substituted guanine derivatives
    • Gibson AE, Arris CE, Bentley J, Boyle FT, Curtin NJ, et al. (2002) Probing the ATP ribose-binding domain of cyclin-dependent kinases 1 and 2 with O(6)-substituted guanine derivatives. J Med Chem 45: 3381-3393.
    • (2002) J Med Chem , vol.45 , pp. 3381-3393
    • Gibson, A.E.1    Arris, C.E.2    Bentley, J.3    Boyle, F.T.4    Curtin, N.J.5
  • 33
    • 18744397820 scopus 로고    scopus 로고
    • Design and synthesis of potent, orally bioavailable dihydroquinazolinone inhibitors of p38 MAP kinase
    • Stelmach JE, Liu L, Patel SB, Pivnichny JV, Scapin G, et al. (2003) Design and synthesis of potent, orally bioavailable dihydroquinazolinone inhibitors of p38 MAP kinase. Bioorg Med Chem Lett 13: 277-280.
    • (2003) Bioorg Med Chem Lett , vol.13 , pp. 277-280
    • Stelmach, J.E.1    Liu, L.2    Patel, S.B.3    Pivnichny, J.V.4    Scapin, G.5
  • 34
    • 71749117560 scopus 로고    scopus 로고
    • Non-hinge-binding pyrazolo[1,5-a]pyrimidines as potent B-Raf kinase inhibitors
    • Berger DM, Torres N, Dutia M, Powell D, Ciszewski G, et al. (2009) Non-hinge-binding pyrazolo[1,5-a]pyrimidines as potent B-Raf kinase inhibitors. Bioorg Med Chem Lett 19: 6519-6523.
    • (2009) Bioorg Med Chem Lett , vol.19 , pp. 6519-6523
    • Berger, D.M.1    Torres, N.2    Dutia, M.3    Powell, D.4    Ciszewski, G.5
  • 35
    • 77249141072 scopus 로고    scopus 로고
    • Pyridinylquinoxalines and pyridinylpyridopyrazines as lead compounds for novel p38 alpha mitogen-activated protein kinase inhibitors
    • Koch P, Jahns H, Schattel V, Goettert M, Laufer S, (2010) Pyridinylquinoxalines and pyridinylpyridopyrazines as lead compounds for novel p38 alpha mitogen-activated protein kinase inhibitors. J Med Chem 53: 1128-1137.
    • (2010) J Med Chem , vol.53 , pp. 1128-1137
    • Koch, P.1    Jahns, H.2    Schattel, V.3    Goettert, M.4    Laufer, S.5
  • 36
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell DS, Olson AJ, (1990) Automated docking of substrates to proteins by simulated annealing. Proteins 8: 195-202.
    • (1990) Proteins , vol.8 , pp. 195-202
    • Goodsell, D.S.1    Olson, A.J.2
  • 37
    • 0346951125 scopus 로고
    • Determination of Net Atomic Charges Using a Modified Partial Equalization of Orbital Electronegativity Method. 1. Application to Neutral Molecules as Models for Polypeptides
    • No KT, Grant JA, Scheraga HA, (1990) Determination of Net Atomic Charges Using a Modified Partial Equalization of Orbital Electronegativity Method. 1. Application to Neutral Molecules as Models for Polypeptides. Journal of Physical Chemistry 94: 4732-4739.
    • (1990) Journal of Physical Chemistry , vol.94 , pp. 4732-4739
    • No, K.T.1    Grant, J.A.2    Scheraga, H.A.3
  • 38
    • 33751553791 scopus 로고
    • Determination of Net Atomic Charges Using a Modified Partial Equalization of Orbital Electronegativity Method. 2. Application to Ionic and Aromatic-Molecules as Models for Polypeptides
    • No KT, Grant JA, Jhon MS, Scheraga HA, (1990) Determination of Net Atomic Charges Using a Modified Partial Equalization of Orbital Electronegativity Method. 2. Application to Ionic and Aromatic-Molecules as Models for Polypeptides. Journal of Physical Chemistry 94: 4740-4746.
    • (1990) Journal of Physical Chemistry , vol.94 , pp. 4740-4746
    • No, K.T.1    Grant, J.A.2    Jhon, M.S.3    Scheraga, H.A.4
  • 39
    • 13844312649 scopus 로고    scopus 로고
    • ZINC-a free database of commercially available compounds for virtual screening
    • Irwin JJ, Shoichet BK, (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
  • 41
    • 70349755625 scopus 로고    scopus 로고
    • Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction
    • Yang CY, Sun H, Chen J, Nikolovska-Coleska Z, Wang S, (2009) Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. J Am Chem Soc 131: 13709-13721.
    • (2009) J Am Chem Soc , vol.131 , pp. 13709-13721
    • Yang, C.Y.1    Sun, H.2    Chen, J.3    Nikolovska-Coleska, Z.4    Wang, S.5
  • 42
    • 1942453243 scopus 로고    scopus 로고
    • Ligand efficiency: a useful metric for lead selection
    • Hopkins AL, Groom CR, Alex A, (2004) Ligand efficiency: a useful metric for lead selection. Drug Discov Today 9: 430-431.
    • (2004) Drug Discov Today , vol.9 , pp. 430-431
    • Hopkins, A.L.1    Groom, C.R.2    Alex, A.3


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