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Volumn 55, Issue 9, 2015, Pages 1926-1935

Binding Kinetics versus Affinities in BRD4 Inhibition

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; BIOCHEMISTRY; LIGANDS; MOLECULAR DYNAMICS; PROTEINS; THERMODYNAMICS;

EID: 84942532115     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00265     Document Type: Article
Times cited : (25)

References (60)
  • 1
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin Modifications and Their Function
    • Kouzarides, T. Chromatin Modifications and Their Function Cell 2007, 128, 693-705 10.1016/j.cell.2007.02.005
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 3
    • 79955856345 scopus 로고    scopus 로고
    • Therapeutic Prospects for Epigenetic Modulation
    • Heightman, T. D. Therapeutic Prospects for Epigenetic Modulation Expert Opin. Ther. Targets 2011, 15, 729-740 10.1517/14728222.2011.561786
    • (2011) Expert Opin. Ther. Targets , vol.15 , pp. 729-740
    • Heightman, T.D.1
  • 4
    • 79955665883 scopus 로고    scopus 로고
    • Bromodomain Coactivators in Cancer, Obesity, Type 2 Diabetes, and Inflammation
    • Denis, G. V. Bromodomain Coactivators in Cancer, Obesity, Type 2 Diabetes, and Inflammation Discovery Med. 2010, 10 (55) 489-499
    • (2010) Discovery Med. , vol.10 , Issue.55 , pp. 489-499
    • Denis, G.V.1
  • 5
    • 70149105669 scopus 로고    scopus 로고
    • The Role of Human Bromodomains in Chromatin Biology and Gene Transcription
    • Sanchez, R.; Zhou, M. M. The Role of Human Bromodomains in Chromatin Biology and Gene Transcription Curr. Opin. Drug Disc. 2009, 12, 659-665
    • (2009) Curr. Opin. Drug Disc. , vol.12 , pp. 659-665
    • Sanchez, R.1    Zhou, M.M.2
  • 6
    • 79952534189 scopus 로고    scopus 로고
    • Regulation of Chromatin by Histone Modifications
    • Bannister, A. J.; Kouzarides, T. Regulation of Chromatin by Histone Modifications Cell Res. 2011, 21, 381-395 10.1038/cr.2011.22
    • (2011) Cell Res. , vol.21 , pp. 381-395
    • Bannister, A.J.1    Kouzarides, T.2
  • 7
    • 84860371870 scopus 로고    scopus 로고
    • Combinatorial Complexity in Chromatin Structure and Function: Revisiting the Histone Code
    • Rando, O. J. Combinatorial Complexity in Chromatin Structure and Function: Revisiting The Histone Code Curr. Opin. Genet. Dev. 2012, 22, 148-155 10.1016/j.gde.2012.02.013
    • (2012) Curr. Opin. Genet. Dev. , vol.22 , pp. 148-155
    • Rando, O.J.1
  • 8
    • 15044358494 scopus 로고    scopus 로고
    • Reading Signals on the Nucleosome with A New Nomenclature for Modified Histones
    • Turner, B. M. Reading Signals on The Nucleosome with A New Nomenclature for Modified Histones Nat. Struct. Mol. Biol. 2005, 12, 110-112 10.1038/nsmb0205-110
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 110-112
    • Turner, B.M.1
  • 9
    • 0035839136 scopus 로고    scopus 로고
    • Translating the Histone Code
    • Jenuwein, T.; Allis, C. D. Translating The Histone Code Science 2001, 293, 1074-1080 10.1126/science.1063127
    • (2001) Science , vol.293 , pp. 1074-1080
    • Jenuwein, T.1    Allis, C.D.2
  • 10
    • 84859731822 scopus 로고    scopus 로고
    • Epigenetic Modifications in Cardiovascular Disease
    • Lorenzen, J. M.; Martino, F.; Thum, T. Epigenetic Modifications In Cardiovascular Disease Basic Res. Cardiol. 2012, 107, 1-10 10.1007/s00395-012-0245-9
    • (2012) Basic Res. Cardiol. , vol.107 , pp. 1-10
    • Lorenzen, J.M.1    Martino, F.2    Thum, T.3
  • 12
    • 84863621527 scopus 로고    scopus 로고
    • Cancer Epigenetics: From Mechanism to Therapy
    • Dawson, M. A.; Kouzarides, T. Cancer Epigenetics: From Mechanism to Therapy Cell 2012, 150, 12-27 10.1016/j.cell.2012.06.013
    • (2012) Cell , vol.150 , pp. 12-27
    • Dawson, M.A.1    Kouzarides, T.2
  • 13
    • 77953995002 scopus 로고    scopus 로고
    • Covalent Histone Modifications - Miswritten, Misinterpreted and Mis-Erased in Human Cancers
    • Chi, P.; Allis, C. D.; Wang, G. G. Covalent Histone Modifications-Miswritten, Misinterpreted and Mis-Erased in Human Cancers Nat. Rev. Cancer 2010, 10, 457-469 10.1038/nrc2876
    • (2010) Nat. Rev. Cancer , vol.10 , pp. 457-469
    • Chi, P.1    Allis, C.D.2    Wang, G.G.3
  • 14
    • 0033519641 scopus 로고    scopus 로고
    • Structure and Ligand of A Histone Acetyltransferase Bromodomain
    • Dhalluin, C.; Carlson, J. E.; Zeng, L.; He, C.; Aggarwal, A. K.; Zhou, M. M. Structure and Ligand of A Histone Acetyltransferase Bromodomain Nature 1999, 399, 491-496 10.1038/20974
    • (1999) Nature , vol.399 , pp. 491-496
    • Dhalluin, C.1    Carlson, J.E.2    Zeng, L.3    He, C.4    Aggarwal, A.K.5    Zhou, M.M.6
  • 15
    • 84857331171 scopus 로고    scopus 로고
    • Inhibition of Bromodomain-Mediated Protein-Protein Interactions as A Novel Therapeutic Strategy
    • Furdas, S. D.; Carlino, L.; Sippl, W.; Jung, M. Inhibition of Bromodomain-Mediated Protein-Protein Interactions as A Novel Therapeutic Strategy MedChemComm 2012, 3, 123-134 10.1039/C1MD00201E
    • (2012) MedChemComm , vol.3 , pp. 123-134
    • Furdas, S.D.1    Carlino, L.2    Sippl, W.3    Jung, M.4
  • 17
    • 84905269946 scopus 로고    scopus 로고
    • Structure-Based Virtual Screening of Novel, High-Affinity BRD4 Inhibitors
    • Muvva, C.; Singam, E. R. A.; Raman, S. S.; Subramanian, V. Structure-Based Virtual Screening of Novel, High-Affinity BRD4 Inhibitors Mol. BioSyst. 2014, 10, 2384-2397 10.1039/C4MB00243A
    • (2014) Mol. BioSyst. , vol.10 , pp. 2384-2397
    • Muvva, C.1    Singam, E.R.A.2    Raman, S.S.3    Subramanian, V.4
  • 18
    • 84899934825 scopus 로고    scopus 로고
    • Discovery of BRD4 Bromodomain Inhibitors by Fragment-Based High-Throughput Docking
    • Zhao, H. T.; Gartenmann, L.; Dong, J.; Spiliotopoulos, D.; Caflisch, A. Discovery of BRD4 Bromodomain Inhibitors by Fragment-Based High-Throughput Docking Bioorg. Med. Chem. Lett. 2014, 24, 2493-2496 10.1016/j.bmcl.2014.04.017
    • (2014) Bioorg. Med. Chem. Lett. , vol.24 , pp. 2493-2496
    • Zhao, H.T.1    Gartenmann, L.2    Dong, J.3    Spiliotopoulos, D.4    Caflisch, A.5
  • 19
    • 84870013141 scopus 로고    scopus 로고
    • Progress in the Development and Application of Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine Interactions
    • Hewings, D. S.; Rooney, T. P. C.; Jennings, L. E.; Hay, D. A.; Schofield, C. J.; Brennan, P. E.; Knapp, S.; Conway, S. J. Progress in The Development and Application of Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine Interactions J. Med. Chem. 2012, 55, 9393-9413 10.1021/jm300915b
    • (2012) J. Med. Chem. , vol.55 , pp. 9393-9413
    • Hewings, D.S.1    Rooney, T.P.C.2    Jennings, L.E.3    Hay, D.A.4    Schofield, C.J.5    Brennan, P.E.6    Knapp, S.7    Conway, S.J.8
  • 26
    • 84879692312 scopus 로고    scopus 로고
    • Does Bromodomain Flexibility Influence Histone Recognition?
    • Steiner, S.; Magno, A.; Huang, D.; Caflisch, A. Does Bromodomain Flexibility Influence Histone Recognition? FEBS Lett. 2013, 587, 2158-63 10.1016/j.febslet.2013.05.032
    • (2013) FEBS Lett. , vol.587 , pp. 2158-2163
    • Steiner, S.1    Magno, A.2    Huang, D.3    Caflisch, A.4
  • 29
    • 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
  • 34
    • 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
  • 35
    • 84871864524 scopus 로고    scopus 로고
    • Molecular Dynamics and Umbrella Sampling Study of Stabilizing Factors in Cyclic Peptide-Based Nanotubes
    • Vijayaraj, R.; Van Damme, S.; Bultinck, P.; Subramanian, V. Molecular Dynamics and Umbrella Sampling Study of Stabilizing Factors in Cyclic Peptide-Based Nanotubes J. Phys. Chem. B 2012, 116, 9922-9933 10.1021/jp303418a
    • (2012) J. Phys. Chem. B , vol.116 , pp. 9922-9933
    • Vijayaraj, R.1    Van Damme, S.2    Bultinck, P.3    Subramanian, V.4
  • 37
    • 79960707811 scopus 로고    scopus 로고
    • Characterizing the Dynamics and Ligand-Specific Interactions in the Human Leukocyte Elastase Through Molecular Dynamics Simulations
    • Estacio, S. G.; Moreira, R.; Guedes, R. C. Characterizing The Dynamics and Ligand-Specific Interactions in The Human Leukocyte Elastase Through Molecular Dynamics Simulations J. Chem. Inf. Model. 2011, 51, 1690-1702 10.1021/ci200076k
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 1690-1702
    • Estacio, S.G.1    Moreira, R.2    Guedes, R.C.3
  • 39
    • 45849120595 scopus 로고    scopus 로고
    • Understanding Ligand-Based Modulation of the Hsp90 Molecular Chaperone Dynamics at Atomic Resolution
    • Colombo, G.; Morra, G.; Meli, M.; Verkhivker, G. Understanding Ligand-Based Modulation of The Hsp90 Molecular Chaperone Dynamics at Atomic Resolution Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 7976-7981 10.1073/pnas.0802879105
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 7976-7981
    • Colombo, G.1    Morra, G.2    Meli, M.3    Verkhivker, G.4
  • 40
    • 36649006642 scopus 로고    scopus 로고
    • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    • Shao, J. Y.; Tanner, S. W.; Thompson, N.; Cheatham, T. E. Clustering Molecular Dynamics Trajectories: 1. Characterizing The Performance of Different Clustering Algorithms J. Chem. Theory Comput. 2007, 3, 2312-2334 10.1021/ct700119m
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 2312-2334
    • Shao, J.Y.1    Tanner, S.W.2    Thompson, N.3    Cheatham, T.E.4
  • 41
    • 79751535059 scopus 로고    scopus 로고
    • Povme: An Algorithm for Measuring Binding-Pocket Volumes
    • Durrant, J. D.; De Oliveira, C. A. F.; Mccammon, J. A. Povme: An Algorithm for Measuring Binding-Pocket Volumes J. Mol. Graphics Modell. 2011, 29, 773-776 10.1016/j.jmgm.2010.10.007
    • (2011) J. Mol. Graphics Modell. , vol.29 , pp. 773-776
    • Durrant, J.D.1    De Oliveira, C.A.F.2    McCammon, J.A.3
  • 42
    • 79955574923 scopus 로고    scopus 로고
    • Version 1.6; Schrödinger Llc: New York
    • The Pymol Molecular Graphics System. Version 1.6; Schrödinger Llc: New York, 2013.
    • (2013) The Pymol Molecular Graphics System
  • 43
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti Correlation-Energy Formula into A Functional of the Electron Density
    • Lee, C.; Yang, W.; Parr, R. G. Development of The Colle-Salvetti Correlation-Energy Formula Into A Functional of The Electron Density Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785-789 10.1103/PhysRevB.37.785
    • (1988) Phys. Rev. B: Condens. Matter Mater. Phys. , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 44
    • 4243553426 scopus 로고
    • Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior
    • Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100 10.1103/PhysRevA.38.3098
    • (1988) Phys. Rev. A: At., Mol., Opt. Phys. , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 45
    • 33748263629 scopus 로고    scopus 로고
    • Pseudobond Ab Initio Qm/Mm Approach and Its Applications to Enzyme Reactions
    • Zhang, Y. K. Pseudobond Ab Initio Qm/Mm Approach and Its Applications to Enzyme Reactions Theor. Chem. Acc. 2006, 116, 43-50 10.1007/s00214-005-0008-x
    • (2006) Theor. Chem. Acc. , vol.116 , pp. 43-50
    • Zhang, Y.K.1
  • 46
    • 22944472113 scopus 로고    scopus 로고
    • Improved Pseudobonds for Combined Ab Initio Quantum Mechanical/Molecular Mechanical Methods
    • Zhang, Y. K. Improved Pseudobonds for Combined Ab Initio Quantum Mechanical/Molecular Mechanical Methods J. Chem. Phys. 2005, 122, 024114 10.1063/1.1834899
    • (2005) J. Chem. Phys. , vol.122 , pp. 024114
    • Zhang, Y.K.1
  • 47
    • 0000145441 scopus 로고    scopus 로고
    • Free Energy Calculation on Enzyme Reactions with An Efficient Iterative Procedure to Determine Minimum Energy Paths on A Combined Ab Initio Qm/Mm Potential Energy Surface
    • Zhang, Y. K.; Liu, H. Y.; Yang, W. T. Free Energy Calculation on Enzyme Reactions with An Efficient Iterative Procedure to Determine Minimum Energy Paths on A Combined Ab Initio Qm/Mm Potential Energy Surface J. Chem. Phys. 2000, 112, 3483-3492 10.1063/1.480503
    • (2000) J. Chem. Phys. , vol.112 , pp. 3483-3492
    • Zhang, Y.K.1    Liu, H.Y.2    Yang, W.T.3
  • 48
    • 0001582558 scopus 로고    scopus 로고
    • A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods
    • Zhang, Y. K.; Lee, T. S.; Yang, W. T. A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods J. Chem. Phys. 1999, 110, 46-54 10.1063/1.478083
    • (1999) J. Chem. Phys. , vol.110 , pp. 46-54
    • Zhang, Y.K.1    Lee, T.S.2    Yang, W.T.3
  • 49
    • 0000394426 scopus 로고
    • Some Multistep Methods for Use in Molecular Dynamics Calculations
    • Beeman, D. Some Multistep Methods for Use In Molecular Dynamics Calculations J. Comput. Phys. 1976, 20, 130-139 10.1016/0021-9991(76)90059-0
    • (1976) J. Comput. Phys. , vol.20 , pp. 130-139
    • Beeman, D.1
  • 52
    • 84863165405 scopus 로고    scopus 로고
    • Qm/Mm Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase
    • Wu, R. B.; Gong, W. J.; Liu, T.; Zhang, Y. K.; Cao, Z. X. Qm/Mm Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase J. Phys. Chem. B 2012, 116, 1984-1991 10.1021/jp211403j
    • (2012) J. Phys. Chem. B , vol.116 , pp. 1984-1991
    • Wu, R.B.1    Gong, W.J.2    Liu, T.3    Zhang, Y.K.4    Cao, Z.X.5
  • 53
    • 79954998200 scopus 로고    scopus 로고
    • Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to the Linker Binding Channel
    • Wu, R. B.; Lu, Z. Y.; Cao, Z. X.; Zhang, Y. K. Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to The Linker Binding Channel J. Am. Chem. Soc. 2011, 133, 6110-6113 10.1021/ja111104p
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 6110-6113
    • Wu, R.B.1    Lu, Z.Y.2    Cao, Z.X.3    Zhang, Y.K.4
  • 54
    • 84913581030 scopus 로고    scopus 로고
    • Structure-Function Analysis of the Conserved Tyrosine and Diverse Pi-Stacking among Class i Histone Deacetylases: A Qm (DFT)/Mm Md Study
    • Zhou, J. W.; Xie, H. J.; Liu, Z. H.; Luo, H. B.; Wu, R. B. Structure-Function Analysis of The Conserved Tyrosine and Diverse Pi-Stacking Among Class I Histone Deacetylases: A Qm (Dft)/Mm Md Study J. Chem. Inf. Model. 2014, 54, 3162-3171 10.1021/ci500513n
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 3162-3171
    • Zhou, J.W.1    Xie, H.J.2    Liu, Z.H.3    Luo, H.B.4    Wu, R.B.5
  • 55
    • 84896262993 scopus 로고    scopus 로고
    • Concerted Cyclization of Lanosterol C-Ring and D-Ring under Human Oxidosqualene Cyclase Catalysis: An Ab Initio Qm/Mm Md Study
    • Chen, N. H.; Zhou, J. W.; Li, J. B.; Xu, J.; Wu, R. B. Concerted Cyclization of Lanosterol C-Ring and D-Ring Under Human Oxidosqualene Cyclase Catalysis: An Ab Initio Qm/Mm Md Study J. Chem. Theory Comput. 2014, 10, 1109-1120 10.1021/ct400949b
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 1109-1120
    • Chen, N.H.1    Zhou, J.W.2    Li, J.B.3    Xu, J.4    Wu, R.B.5
  • 58
    • 77958535230 scopus 로고    scopus 로고
    • Binding Kinetics and Mechanism of Action: Toward the Discovery and Development of Better and Best in Class Drugs
    • Zhang, R.; Monsma, F. Binding Kinetics and Mechanism of Action: Toward The Discovery and Development of Better and Best in Class Drugs Expert Opin. Drug Discovery 2010, 5, 1023-1029 10.1517/17460441.2010.520700
    • (2010) Expert Opin. Drug Discovery , vol.5 , pp. 1023-1029
    • Zhang, R.1    Monsma, F.2


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