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Volumn 12, Issue 2, 2016, Pages 851-860

Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1

Author keywords

[No Author keywords available]

Indexed keywords

8-OXODGTPASE; ANTINEOPLASTIC AGENT; CRIZOTINIB; DNA LIGASE; PHOSPHATASE; PROTEIN BINDING; PYRAZOLE DERIVATIVE; PYRIDINE DERIVATIVE;

EID: 84957939855     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.5b00973     Document Type: Article
Times cited : (42)

References (56)
  • 1
    • 80052806086 scopus 로고    scopus 로고
    • Structure Based Drug Design of Crizotinib (PF-02341066), a Potent and Selective Dual Inhibitor of Mesenchymal-Epithelial Transition Factor (c-MET) Kinase and Anaplastic Lymphoma Kinase (ALK)
    • Cui, J. J.; Tran-Dubé, M.; Shen, H.; Nambu, M.; Kung, P. P.; Pairish, M.; Jia, L.; Meng, J.; Funk, L.; Botrous, I. Structure Based Drug Design of Crizotinib (PF-02341066), a Potent and Selective Dual Inhibitor of Mesenchymal-Epithelial Transition Factor (c-MET) Kinase and Anaplastic Lymphoma Kinase (ALK) J. Med. Chem. 2011, 54, 6342-6363 10.1021/jm2007613
    • (2011) J. Med. Chem. , vol.54 , pp. 6342-6363
    • Cui, J.J.1    Tran-Dubé, M.2    Shen, H.3    Nambu, M.4    Kung, P.P.5    Pairish, M.6    Jia, L.7    Meng, J.8    Funk, L.9    Botrous, I.10
  • 8
    • 38349091489 scopus 로고    scopus 로고
    • Well-tempered metadynamics: A smoothly converging and tunable free-energy method
    • Barducci, A.; Bussi, G.; Parrinello, M. Well-tempered metadynamics: A smoothly converging and tunable free-energy method Phys. Rev. Lett. 2008, 100, 020603 10.1103/PhysRevLett.100.020603
    • (2008) Phys. Rev. Lett. , vol.100 , pp. 020603
    • Barducci, A.1    Bussi, G.2    Parrinello, M.3
  • 10
    • 84876214497 scopus 로고    scopus 로고
    • Funnel metadynamics as accurate binding free-energy method
    • Limongelli, V.; Bonomi, M.; Parrinello, M. Funnel metadynamics as accurate binding free-energy method Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 6358-6363 10.1073/pnas.1303186110
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 6358-6363
    • Limongelli, V.1    Bonomi, M.2    Parrinello, M.3
  • 11
    • 18744372751 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding free energy from computer simulations
    • Woo, H.-J.; Roux, B. Calculation of absolute protein-ligand binding free energy from computer simulations Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 6825-6830 10.1073/pnas.0409005102
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 6825-6830
    • Woo, H.-J.1    Roux, B.2
  • 13
    • 79960220436 scopus 로고    scopus 로고
    • Combined metadynamics and umbrella sampling method for the calculation of ion permeation free energy profiles
    • Zhang, Y.; Voth, G. A. Combined metadynamics and umbrella sampling method for the calculation of ion permeation free energy profiles J. Chem. Theory Comput. 2011, 7, 2277-2283 10.1021/ct200100e
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2277-2283
    • Zhang, Y.1    Voth, G.A.2
  • 14
    • 84905503390 scopus 로고    scopus 로고
    • P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape
    • Sun, H.; Li, Y.; Tian, S.; Wang, J.; Hou, T. P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape PLoS Comput. Biol. 2014, 10, e1003729 10.1371/journal.pcbi.1003729
    • (2014) PLoS Comput. Biol. , vol.10
    • Sun, H.1    Li, Y.2    Tian, S.3    Wang, J.4    Hou, T.5
  • 15
    • 79952354508 scopus 로고    scopus 로고
    • The hidden energetics of ligand binding and activation in a glutamate receptor
    • Lau, A. Y.; Roux, B. The hidden energetics of ligand binding and activation in a glutamate receptor Nat. Struct. Mol. Biol. 2011, 18, 283-287 10.1038/nsmb.2010
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 283-287
    • Lau, A.Y.1    Roux, B.2
  • 16
    • 79960258119 scopus 로고    scopus 로고
    • Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values
    • Søndergaard, C. R.; Olsson, M. H.; Rostkowski, M.; Jensen, J. H. Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values J. Chem. Theory Comput. 2011, 7, 2284-2295 10.1021/ct200133y
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2284-2295
    • Søndergaard, C.R.1    Olsson, M.H.2    Rostkowski, M.3    Jensen, J.H.4
  • 18
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
    • Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model J. Phys. Chem. 1993, 97, 10269-10280 10.1021/j100142a004
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.3    Kollman, P.A.4
  • 22
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092 10.1063/1.464397
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 23
    • 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 10.1016/0021-9991(77)90098-5
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 24
    • 36449007836 scopus 로고
    • Constant-pressure molecular-dynamics simulation-the Langevin piston method
    • Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. Constant-pressure molecular-dynamics simulation-the Langevin piston method J. Chem. Phys. 1995, 103, 4613-4621 10.1063/1.470648
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, B.R.4
  • 26
    • 58149299971 scopus 로고    scopus 로고
    • Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
    • Laio, A.; Gervasio, F. L. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science Rep. Prog. Phys. 2008, 71, 126601 10.1088/0034-4885/71/12/126601
    • (2008) Rep. Prog. Phys. , vol.71 , pp. 126601
    • Laio, A.1    Gervasio, F.L.2
  • 27
  • 28
    • 34249071886 scopus 로고    scopus 로고
    • A bias-exchange approach to protein folding
    • Piana, S.; Laio, A. A bias-exchange approach to protein folding J. Phys. Chem. B 2007, 111, 4553-4559 10.1021/jp067873l
    • (2007) J. Phys. Chem. B , vol.111 , pp. 4553-4559
    • Piana, S.1    Laio, A.2
  • 29
    • 33750040264 scopus 로고    scopus 로고
    • Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
    • Bussi, G.; Gervasio, F. L.; Laio, A.; Parrinello, M. Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics J. Am. Chem. Soc. 2006, 128, 13435-13441 10.1021/ja062463w
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 13435-13441
    • Bussi, G.1    Gervasio, F.L.2    Laio, A.3    Parrinello, M.4
  • 30
    • 84889648332 scopus 로고    scopus 로고
    • Free-energy landscape of protein oligomerization from atomistic simulations
    • Barducci, A.; Bonomi, M.; Prakash, M. K.; Parrinello, M. Free-energy landscape of protein oligomerization from atomistic simulations Proc. Natl. Acad. Sci. U. S. A. 2013, 110, E4708-E4713 10.1073/pnas.1320077110
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. E4708-E4713
    • Barducci, A.1    Bonomi, M.2    Prakash, M.K.3    Parrinello, M.4
  • 32
    • 84876721020 scopus 로고    scopus 로고
    • Capture and Quality Control Mechanisms for Adenosine-5′-triphosphate Binding
    • Li, L.; Martinis, S. A.; Luthey-Schulten, Z. Capture and Quality Control Mechanisms for Adenosine-5′-triphosphate Binding J. Am. Chem. Soc. 2013, 135, 6047-6055 10.1021/ja308044w
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 6047-6055
    • Li, L.1    Martinis, S.A.2    Luthey-Schulten, Z.3
  • 34
    • 80054991841 scopus 로고    scopus 로고
    • Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism
    • Berteotti, A.; Barducci, A.; Parrinello, M. Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism J. Am. Chem. Soc. 2011, 133, 17200-17206 10.1021/ja202849a
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 17200-17206
    • Berteotti, A.1    Barducci, A.2    Parrinello, M.3
  • 36
    • 33847142225 scopus 로고    scopus 로고
    • CAVER: a new tool to explore routes from protein clefts, pockets and cavities
    • Petřek, M.; Otyepka, M.; Banáš, P.; Košinová, P.; Koča, J.; Damborský, J. CAVER: a new tool to explore routes from protein clefts, pockets and cavities BMC Bioinf. 2006, 7, 316 10.1186/1471-2105-7-316
    • (2006) BMC Bioinf. , vol.7 , pp. 316
    • Petřek, M.1    Otyepka, M.2    Banáš, P.3    Košinová, P.4    Koča, J.5    Damborský, J.6
  • 37
    • 84884570151 scopus 로고    scopus 로고
    • Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches
    • Sun, H.; Li, Y.; Li, D.; Hou, T. Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches J. Chem. Inf. Model. 2013, 53, 2376-2389 10.1021/ci400188q
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 2376-2389
    • Sun, H.1    Li, Y.2    Li, D.3    Hou, T.4
  • 38
    • 84876549284 scopus 로고    scopus 로고
    • Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches
    • Pan, P.; Li, Y.; Yu, H.; Sun, H.; Hou, T. Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches J. Chem. Inf. Model. 2013, 53, 997-1006 10.1021/ci400066x
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 997-1006
    • Pan, P.1    Li, Y.2    Yu, H.3    Sun, H.4    Hou, T.5
  • 39
    • 84935829072 scopus 로고    scopus 로고
    • Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations
    • Sun, H.; Tian, S.; Zhou, S.; Li, Y.; Li, D.; Xu, L.; Shen, M.; Pan, P.; Hou, T. Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations Sci. Rep. 2015, 5, 8457 10.1038/srep08457
    • (2015) Sci. Rep. , vol.5 , pp. 8457
    • Sun, H.1    Tian, S.2    Zhou, S.3    Li, Y.4    Li, D.5    Xu, L.6    Shen, M.7    Pan, P.8    Hou, T.9
  • 40
    • 84894152562 scopus 로고    scopus 로고
    • Adaptive biasing combined with Hamiltonian replica exchange to improve umbrella sampling free energy simulations
    • Zeller, F.; Zacharias, M. Adaptive biasing combined with Hamiltonian replica exchange to improve umbrella sampling free energy simulations J. Chem. Theory Comput. 2014, 10, 703-710 10.1021/ct400689h
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 703-710
    • Zeller, F.1    Zacharias, M.2
  • 42
    • 84878680599 scopus 로고    scopus 로고
    • The pore of voltage-gated potassium ion channels is strained when closed
    • Fowler, P. W.; Sansom, M. S. The pore of voltage-gated potassium ion channels is strained when closed Nat. Commun. 2013, 4, 1872 10.1038/ncomms2858
    • (2013) Nat. Commun. , vol.4 , pp. 1872
    • Fowler, P.W.1    Sansom, M.S.2
  • 43
    • 84883744307 scopus 로고    scopus 로고
    • Recovery from slow inactivation in K+ channels is controlled by water molecules
    • Ostmeyer, J.; Chakrapani, S.; Pan, A. C.; Perozo, E.; Roux, B. Recovery from slow inactivation in K+ channels is controlled by water molecules Nature 2013, 501, 121-124 10.1038/nature12395
    • (2013) Nature , vol.501 , pp. 121-124
    • Ostmeyer, J.1    Chakrapani, S.2    Pan, A.C.3    Perozo, E.4    Roux, B.5
  • 46
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. the method
    • Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 1992, 13, 1011-1021 10.1002/jcc.540130812
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Rosenberg, J.M.2    Bouzida, D.3    Swendsen, R.H.4    Kollman, P.A.5
  • 47
    • 0035277126 scopus 로고    scopus 로고
    • Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
    • Souaille, M.; Roux, B. t. Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations Comput. Phys. Commun. 2001, 135, 40-57 10.1016/S0010-4655(00)00215-0
    • (2001) Comput. Phys. Commun. , vol.135 , pp. 40-57
    • Souaille, M.1    Roux, B.T.2
  • 48
    • 42149194240 scopus 로고    scopus 로고
    • Adaptive biasing force method for scalar and vector free energy calculations
    • Darve, E.; Rodríguez-Gómez, D.; Pohorille, A. Adaptive biasing force method for scalar and vector free energy calculations J. Chem. Phys. 2008, 128, 144120-144132 10.1063/1.2829861
    • (2008) J. Chem. Phys. , vol.128 , pp. 144120-144132
    • Darve, E.1    Rodríguez-Gómez, D.2    Pohorille, A.3
  • 49
    • 77950102787 scopus 로고    scopus 로고
    • Exploring multidimensional free energy landscapes using time-dependent biases on collective variables
    • Hénin, J.; Fiorin, G.; Chipot, C.; Klein, M. L. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables J. Chem. Theory Comput. 2010, 6, 35-47 10.1021/ct9004432
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 35-47
    • Hénin, J.1    Fiorin, G.2    Chipot, C.3    Klein, M.L.4
  • 50
    • 52449099841 scopus 로고    scopus 로고
    • Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel
    • Dehez, F.; Pebay-Peyroula, E.; Chipot, C. Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel J. Am. Chem. Soc. 2008, 130, 12725-12733 10.1021/ja8033087
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 12725-12733
    • Dehez, F.1    Pebay-Peyroula, E.2    Chipot, C.3
  • 51
    • 78650608765 scopus 로고    scopus 로고
    • How do sterols determine the antifungal activity of amphotericin B? Free energy of binding between the drug and its membrane targets
    • Neumann, A.; Baginski, M.; Czub, J. How do sterols determine the antifungal activity of amphotericin B? Free energy of binding between the drug and its membrane targets J. Am. Chem. Soc. 2010, 132, 18266-18272 10.1021/ja1074344
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 18266-18272
    • Neumann, A.1    Baginski, M.2    Czub, J.3
  • 52
    • 84861210523 scopus 로고    scopus 로고
    • Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations
    • Wereszczynski, J.; McCammon, J. A. Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 7759-7764 10.1073/pnas.1117441109
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 7759-7764
    • Wereszczynski, J.1    McCammon, J.A.2
  • 53
    • 35348911804 scopus 로고    scopus 로고
    • On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases
    • Faraldo-Gómez, J. D.; Roux, B. On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 13643-13648 10.1073/pnas.0704041104
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 13643-13648
    • Faraldo-Gómez, J.D.1    Roux, B.2
  • 54
    • 84873135773 scopus 로고    scopus 로고
    • Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
    • Lin, Y.-L.; Meng, Y.; Jiang, W.; Roux, B. Explaining why Gleevec is a specific and potent inhibitor of Abl kinase Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 1664-1669 10.1073/pnas.1214330110
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 1664-1669
    • Lin, Y.-L.1    Meng, Y.2    Jiang, W.3    Roux, B.4
  • 55
    • 84885131303 scopus 로고    scopus 로고
    • Computational Analysis of the Binding Specificity of Gleevec to Abl, c-Kit, Lck, and c-Src Tyrosine Kinases
    • Lin, Y.-L.; Roux, B. Computational Analysis of the Binding Specificity of Gleevec to Abl, c-Kit, Lck, and c-Src Tyrosine Kinases J. Am. Chem. Soc. 2013, 135, 14741-14753 10.1021/ja405939x
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 14741-14753
    • Lin, Y.-L.1    Roux, B.2
  • 56
    • 84872165531 scopus 로고    scopus 로고
    • Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
    • Gumbart, J. C.; Roux, B.; Chipot, C. Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy? J. Chem. Theory Comput. 2013, 9, 794-802 10.1021/ct3008099
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 794-802
    • Gumbart, J.C.1    Roux, B.2    Chipot, C.3


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