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Volumn 55, Issue 5, 2012, Pages 2035-2047

Binding affinity prediction for ligands and receptors forming tautomers and ionization species: Inhibition of mitogen-activated protein kinase-activated protein kinase 2 (MK2)

Author keywords

[No Author keywords available]

Indexed keywords

BENZOTHIOPHENE DERIVATIVE; MITOGEN ACTIVATED PROTEIN KINASE 1; PROTEIN SERINE THREONINE KINASE INHIBITOR; PYRIDINE DERIVATIVE;

EID: 84858011865     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm201217q     Document Type: Article
Times cited : (32)

References (72)
  • 1
    • 0029894013 scopus 로고    scopus 로고
    • The properties of known drugs. 1. Molecular frameworks
    • Bemis, G. W.; Murcko, M. A. The properties of known drugs. 1. Molecular frameworks J. Med. Chem. 1996, 39, 2887-2893
    • (1996) J. Med. Chem. , vol.39 , pp. 2887-2893
    • Bemis, G.W.1    Murcko, M.A.2
  • 4
    • 0042665956 scopus 로고    scopus 로고
    • Quantitative identification of the protonation state of histidines in vitro and in vivo
    • Shimba, N.; Serber, Z.; Ledwidge, R.; Miller, S. M.; Craik, C. S.; Doetsch, V. Quantitative identification of the protonation state of histidines in vitro and in vivo Biochemistry 2003, 42, 9227-9234
    • (2003) Biochemistry , vol.42 , pp. 9227-9234
    • Shimba, N.1    Serber, Z.2    Ledwidge, R.3    Miller, S.M.4    Craik, C.S.5    Doetsch, V.6
  • 5
    • 79955017879 scopus 로고    scopus 로고
    • Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH
    • Vila, J. A.; Arnautova, Y. A.; Vorobjev, Y.; Scheraga, H. A. Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 5602-5607
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 5602-5607
    • Vila, J.A.1    Arnautova, Y.A.2    Vorobjev, Y.3    Scheraga, H.A.4
  • 7
    • 0000214368 scopus 로고
    • NMR study of the tautomerism of porphyrin including the kinetic HH/HD/DD isotope effects in the liquid and the solid state
    • Braun, J.; Koecher, M.; Schlabach, M.; Wehrle, B.; Limbach, H. H.; Vogel, E. NMR study of the tautomerism of porphyrin including the kinetic HH/HD/DD isotope effects in the liquid and the solid state J. Am. Chem. Soc. 1994, 116, 6593-6604
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 6593-6604
    • Braun, J.1    Koecher, M.2    Schlabach, M.3    Wehrle, B.4    Limbach, H.H.5    Vogel, E.6
  • 8
    • 0002594455 scopus 로고    scopus 로고
    • Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    • Sponer, J.; Leszczynski, J.; Hobza, P. Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases Biopolymers 2001, 61, 3-31
    • (2001) Biopolymers , vol.61 , pp. 3-31
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 9
    • 7744225390 scopus 로고    scopus 로고
    • Acid-base properties of purine residues and the effect of metal ions: Quantification of rare nucleobase tautomers
    • Sigel, H. Acid-base properties of purine residues and the effect of metal ions: Quantification of rare nucleobase tautomers Pure Appl. Chem. 2004, 76, 1869-1886
    • (2004) Pure Appl. Chem. , vol.76 , pp. 1869-1886
    • Sigel, H.1
  • 10
    • 67749135405 scopus 로고    scopus 로고
    • Promotion of rare nucleobase tautomers by metal binding
    • Lippert, B.; Gupta, D. Promotion of rare nucleobase tautomers by metal binding Dalton Trans. 2009, 4619-4634
    • (2009) Dalton Trans. , pp. 4619-4634
    • Lippert, B.1    Gupta, D.2
  • 12
    • 0035868922 scopus 로고    scopus 로고
    • Excited-state intramolecular proton transfer in 10-hydroxybenzo[ h ]quinoline
    • Chou, P. T.; Chen, Y. C.; Yu, W. S.; Chou, Y. H.; Wei, C. Y.; Cheng, Y. M. Excited-state intramolecular proton transfer in 10-hydroxybenzo[ h ]quinoline J. Phys. Chem. A 2001, 105, 1731-1740
    • (2001) J. Phys. Chem. A , vol.105 , pp. 1731-1740
    • Chou, P.T.1    Chen, Y.C.2    Yu, W.S.3    Chou, Y.H.4    Wei, C.Y.5    Cheng, Y.M.6
  • 14
    • 60349127442 scopus 로고    scopus 로고
    • QM/MM methods for biomolecular systems
    • Senn, H. M.; Thiel, W. QM/MM methods for biomolecular systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 1198-1229
    • Senn, H.M.1    Thiel, W.2
  • 15
    • 33748584863 scopus 로고    scopus 로고
    • Mechanisms and free energies of enzymatic reactions
    • Gao, J.; Ma, S.; Major, D. T.; Nam, K.; Pu, J.; Truhlar, D. G. Mechanisms and free energies of enzymatic reactions Chem. Rev. 2006, 106, 3188-3209
    • (2006) Chem. Rev. , vol.106 , pp. 3188-3209
    • Gao, J.1    Ma, S.2    Major, D.T.3    Nam, K.4    Pu, J.5    Truhlar, D.G.6
  • 16
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Aqvist, J.; Medina, C.; Samuelsson, J. E. A new method for predicting binding affinity in computer-aided drug design Protein Eng. 1994, 7, 385-391
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 17
    • 0029557441 scopus 로고
    • Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations
    • Hansson, T.; Aqvist, J. Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations Protein Eng. 1995, 8, 1137-1144
    • (1995) Protein Eng. , vol.8 , pp. 1137-1144
    • Hansson, T.1    Aqvist, J.2
  • 18
    • 0001382020 scopus 로고    scopus 로고
    • Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions
    • Aqvist, J. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions J. Comput. Chem. 1996, 17, 1587-1597
    • (1996) J. Comput. Chem. , vol.17 , pp. 1587-1597
    • Aqvist, J.1
  • 19
    • 0001389474 scopus 로고
    • An extended linear response method for determining free energies of hydration
    • Carlson, H. A.; Jorgensen, W. L. An extended linear response method for determining free energies of hydration J. Phys. Chem. 1995, 99, 10667-10673
    • (1995) J. Phys. Chem. , vol.99 , pp. 10667-10673
    • Carlson, H.A.1    Jorgensen, W.L.2
  • 20
    • 0030906731 scopus 로고    scopus 로고
    • Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method
    • Jones-Hertzog, D. K.; Jorgensen, W. L. Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method J. Med. Chem. 1997, 40, 1539-1549
    • (1997) J. Med. Chem. , vol.40 , pp. 1539-1549
    • Jones-Hertzog, D.K.1    Jorgensen, W.L.2
  • 21
    • 0033135425 scopus 로고    scopus 로고
    • Estimation of the binding affinities of FKBP12 inhibitors using a linear response method
    • Lamb, M. L.; Tirado-Rives, J.; Jorgensen, W. L. Estimation of the binding affinities of FKBP12 inhibitors using a linear response method Bioorg. Med. Chem. 1999, 7, 851-860
    • (1999) Bioorg. Med. Chem. , vol.7 , pp. 851-860
    • Lamb, M.L.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 22
    • 0033557303 scopus 로고    scopus 로고
    • What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
    • Wang, W.; Wang, J.; Kollman, P. A. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins. 1999, 34, 395-402
    • (1999) Proteins. , vol.34 , pp. 395-402
    • Wang, W.1    Wang, J.2    Kollman, P.A.3
  • 23
    • 23944459025 scopus 로고    scopus 로고
    • A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands
    • Khandelwal, A.; Lukacova, V.; Comez, D.; Kroll, D. M.; Raha, S.; Balaz, S. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands J.Med. Chem. 2005, 48, 5437-5447
    • (2005) J.Med. Chem. , vol.48 , pp. 5437-5447
    • Khandelwal, A.1    Lukacova, V.2    Comez, D.3    Kroll, D.M.4    Raha, S.5    Balaz, S.6
  • 24
    • 34548808607 scopus 로고    scopus 로고
    • QM/MM linear response method distinguishes ligand affinities for closely related metalloproteins
    • Khandelwal, A.; Balaz, S. QM/MM linear response method distinguishes ligand affinities for closely related metalloproteins Proteins 2007, 69, 326-339
    • (2007) Proteins , vol.69 , pp. 326-339
    • Khandelwal, A.1    Balaz, S.2
  • 25
    • 33947262611 scopus 로고    scopus 로고
    • Improved estimation of ligand/macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods
    • Khandelwal, A.; Balaz, S. Improved estimation of ligand/macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods J.Comput-Aided. Mol. Des. 2007, 21, 131-137
    • (2007) J.Comput-Aided. Mol. Des. , vol.21 , pp. 131-137
    • Khandelwal, A.1    Balaz, S.2
  • 32
    • 33244471768 scopus 로고    scopus 로고
    • MAPKAP kinases, MKs-two's company, three's a crowd
    • Gaestel, M. MAPKAP kinases, MKs-two's company, three's a crowd Nature Rev. Mol. Cell Biol. 2006, 7, 120-130
    • (2006) Nature Rev. Mol. Cell Biol. , vol.7 , pp. 120-130
    • Gaestel, M.1
  • 34
    • 27744522930 scopus 로고    scopus 로고
    • Potential adverse effects associated with inhibition of p38α/β MAP Kinases
    • Dambach, D. M. Potential adverse effects associated with inhibition of p38α/β MAP Kinases Curr. Top. Med. Chem. 2005, 5, 929-939
    • (2005) Curr. Top. Med. Chem. , vol.5 , pp. 929-939
    • Dambach, D.M.1
  • 36
    • 0033571681 scopus 로고    scopus 로고
    • Estimation of microscopic, zwitterionic ionization constants, isoelectric point and molecular speciation of organic compounds
    • Hilal, S. H.; Karickhoff, S. W.; Carreira, L. A. Estimation of microscopic, zwitterionic ionization constants, isoelectric point and molecular speciation of organic compounds Talanta 1999, 50, 827-840
    • (1999) Talanta , vol.50 , pp. 827-840
    • Hilal, S.H.1    Karickhoff, S.W.2    Carreira, L.A.3
  • 38
    • 0027477251 scopus 로고
    • Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins
    • Gilson, M. K. Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins Proteins 1993, 15, 266-282
    • (1993) Proteins , vol.15 , pp. 266-282
    • Gilson, M.K.1
  • 39
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. Prediction of pH-dependent properties of proteins J. Mol. Biol. 1994, 238, 415-436
    • (1994) J. Mol. Biol. , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 41
    • 0042840900 scopus 로고    scopus 로고
    • Modeling protonation equilibria in biomolecules
    • In; van Gunsteren, W. F. Weiner, P. K. Wilkinson, A. J. Springer: New York, Vol.
    • Gilson, M. K. Modeling protonation equilibria in biomolecules. In Computer Simulation of Biomolecular Systems; van Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A. J., Eds.; Springer: New York, 1997; Vol. 3, pp 199-222.
    • (1997) Computer Simulation of Biomolecular Systems , vol.3 , pp. 199-222
    • Gilson, M.K.1
  • 42
    • 0031670370 scopus 로고    scopus 로고
    • a calculations: Conformational averaging versus the average structure
    • a calculations: Conformational averaging versus the average structure Proteins 1998, 33, 145-158
    • (1998) Proteins , vol.33 , pp. 145-158
    • Van Vlijmen, H.W.T.1    Schaefer, M.2    Karplus, M.3
  • 43
    • 8444247565 scopus 로고    scopus 로고
    • a shifts in proteins using a combination of molecular mechanical and continuum solvent calculations
    • a shifts in proteins using a combination of molecular mechanical and continuum solvent calculations J. Comput. Chem. 2004, 25, 1865-1872
    • (2004) J. Comput. Chem. , vol.25 , pp. 1865-1872
    • Kuhn, B.1    Kollman, P.A.2    Stahl, M.3
  • 47
    • 62749167980 scopus 로고    scopus 로고
    • a calculations with extensive side chain rotamer sampling
    • a calculations with extensive side chain rotamer sampling J.Comput. Chem. 2009, 30, 2231-2247
    • (2009) J.Comput. Chem. , vol.30 , pp. 2231-2247
    • Song, Y.F.1    Mao, J.J.2    Gunner, M.R.3
  • 50
    • 0037013143 scopus 로고    scopus 로고
    • The conformational plasticity of protein kinases
    • Huse, M.; Kuriyan, J. The conformational plasticity of protein kinases Cell 2002, 109, 275-282
    • (2002) Cell , vol.109 , pp. 275-282
    • Huse, M.1    Kuriyan, J.2
  • 51
    • 0037473497 scopus 로고    scopus 로고
    • Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
    • Vreven, T.; Morokuma, K.; Farkas, O.; Schlegel, H. B.; Frisch, M. J. Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints J. Comput. Chem. 2003, 24, 760-769
    • (2003) J. Comput. Chem. , vol.24 , pp. 760-769
    • Vreven, T.1    Morokuma, K.2    Farkas, O.3    Schlegel, H.B.4    Frisch, M.J.5
  • 53
    • 84978704285 scopus 로고    scopus 로고
    • Gaussian Inc. Wallingford, CT 06492, USA.
    • Frisch, M. J. Gaussian 09, version A.1; Gaussian Inc., Wallingford, CT 06492, USA, 2011.
    • (2011) Gaussian 09, Version A.1
    • Frisch, M.J.1
  • 55
    • 84858065125 scopus 로고    scopus 로고
    • Frontline Systems Inc. Incline Village, NV, USA.
    • Premier Solver Platform version 10.5; Frontline Systems Inc.: Incline Village, NV, USA, 2011.
    • (2011) Premier Solver Platform Version 10.5
  • 56
    • 84858052342 scopus 로고    scopus 로고
    • Tripos Inc. St. Louis, MO, USA.
    • Sybyl-X version 1.1; Tripos Inc.: St. Louis, MO, USA, 2010.
    • (2010) Sybyl-X Version 1.1
  • 57
    • 11644266970 scopus 로고
    • Electronic population analysis on LCAO-MO [linear combination of atomic orbital-molecular orbital] molecular wave functions. i
    • Mulliken, R. S. Electronic population analysis on LCAO-MO [linear combination of atomic orbital-molecular orbital] molecular wave functions. I J. Chem. Phys. 1955, 23, 1833-1840
    • (1955) J. Chem. Phys. , vol.23 , pp. 1833-1840
    • Mulliken, R.S.1
  • 58
    • 84858035521 scopus 로고    scopus 로고
    • Schrödinger: LLC Portland, OR, USA.
    • Jaguar; Schrödinger: LLC Portland, OR, USA, 2003.
    • (2003) Jaguar
  • 59
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. III. The role of exact exchange
    • Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 1993, 98, 5648-5652
    • (1993) J. Chem. Phys. , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 60
    • 33745770836 scopus 로고
    • Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms scandium to mercury
    • Hay, P. J.; Wadt, W. R. Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms scandium to mercury J. Chem. Phys. 1985, 82, 270-283
    • (1985) J. Chem. Phys. , vol.82 , pp. 270-283
    • Hay, P.J.1    Wadt, W.R.2
  • 61
    • 0006073669 scopus 로고
    • Ab initio effective core potentials for molecular calculations. Potentials for main group elements sodium to bismuth
    • Wadt, W. R.; Hay, P. J. Ab initio effective core potentials for molecular calculations. Potentials for main group elements sodium to bismuth J. Chem. Phys. 1985, 82, 284-298
    • (1985) J. Chem. Phys. , vol.82 , pp. 284-298
    • Wadt, W.R.1    Hay, P.J.2
  • 62
    • 0036890275 scopus 로고    scopus 로고
    • Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
    • Ren, P.; Ponder, J. W. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations J. Comput. Chem. 2002, 23, 1497-1506
    • (2002) J. Comput. Chem. , vol.23 , pp. 1497-1506
    • Ren, P.1    Ponder, J.W.2
  • 64
    • 84858038783 scopus 로고    scopus 로고
    • Gaussian Inc. Wallingford, CT 06492, USA.
    • GaussView version 5.0; Gaussian Inc.: Wallingford, CT 06492, USA, 2011.
    • (2011) GaussView Version 5.0
  • 65
    • 84885509901 scopus 로고    scopus 로고
    • Getting the most out of ONIOM: Guidelines and pitfalls
    • In; Matta, C. F. Wiley-VCH: New York
    • Clemente, F. R.; Vreven, T.; Frisch, M. J. Getting the most out of ONIOM: guidelines and pitfalls. In Quantum Biochemistry; Matta, C. F., Ed.; Wiley-VCH: New York, 2010; pp 61-83.
    • (2010) Quantum Biochemistry , pp. 61-83
    • Clemente, F.R.1    Vreven, T.2    Frisch, M.J.3
  • 66
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 2006, 65, 712-725
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 70
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n -alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n -alkanes J. Comput. Phys. 1977, 23, 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 71
    • 0004014257 scopus 로고
    • Department of Biochemistry and Molecular Biology, University College London: London.
    • Hubbard, S. J.; Thornton, J. M. NACCESS; Department of Biochemistry and Molecular Biology, University College London: London, 1993.
    • (1993) NACCESS
    • Hubbard, S.J.1    Thornton, J.M.2
  • 72
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B.; Richards, F. M. The interpretation of protein structures: Estimation of static accessibility J. Mol. Biol. 1971, 55, 379-400
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2


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