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Volumn 46, Issue , 2013, Pages 132-139

Molecular dynamics simulations studies and free energy analysis on inhibitors of MDM2-p53 interaction

Author keywords

Binding free energy; Conformational mobility; MD simulations; MDM2 p53 interaction; MM GBSA

Indexed keywords

BINDING FREE ENERGY; CONFORMATIONAL MOBILITY; MD SIMULATION; MDM2-P53 INTERACTION; MM-GBSA;

EID: 84887051563     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.10.005     Document Type: Article
Times cited : (19)

References (41)
  • 2
    • 0030941458 scopus 로고    scopus 로고
    • P53, the cellular gatekeeper for growth and division
    • DOI 10.1016/S0092-8674(00)81871-1
    • A.J. Levine p53, the cellular gatekeeper for growth and division Cell 88 1997 323 331 (Pubitemid 27131374)
    • (1997) Cell , vol.88 , Issue.3 , pp. 323-331
    • Levine, A.J.1
  • 5
    • 0141482040 scopus 로고    scopus 로고
    • Antisense therapy targeting MDM2 oncogene in prostate cancer: Effects on proliferation, apoptosis, multiple gene expression, and chemotherapy
    • DOI 10.1073/pnas.1934692100
    • Z. Zhang, M. Li, H. Wang, S. Agrawal, and R. Zhang Antisense therapy targeting MDM2 oncogene in prostate cancer: effects on proliferation, apoptosis, multiple gene expression, and chemotherapy Proc. Natl. Acad. Sci. U. S. A. 100 2003 11636 11641 (Pubitemid 37205988)
    • (2003) Proceedings of the National Academy of Sciences of the United States of America , vol.100 , Issue.20 , pp. 11636-11641
    • Zhang, Z.1    Li, M.2    Wang, H.3    Agrawal, S.4    Zhang, R.5
  • 6
    • 84866739593 scopus 로고    scopus 로고
    • Discovery of novel dihydroimidazothiazole derivatives as p53-MDM2 protein-protein interaction inhibitors: Synthesis, biological evaluation and structure-activity relationships
    • M. Miyazaki, H. Kawato, H. Naito, M. Ikeda, M. Miyazaki, M. Kitagawa, T. Seki, S. Fukutake, M. Aonuma, and T. Soga Discovery of novel dihydroimidazothiazole derivatives as p53-MDM2 protein-protein interaction inhibitors: synthesis, biological evaluation and structure-activity relationships Bioorg. Med. Chem. Lett. 22 2012 6338 6342
    • (2012) Bioorg. Med. Chem. Lett. , vol.22 , pp. 6338-6342
    • Miyazaki, M.1    Kawato, H.2    Naito, H.3    Ikeda, M.4    Miyazaki, M.5    Kitagawa, M.6    Seki, T.7    Fukutake, S.8    Aonuma, M.9    Soga, T.10
  • 7
    • 0037317840 scopus 로고    scopus 로고
    • Inhibiting the p53-MDM2 interaction: An important target for cancer therapy
    • DOI 10.1038/nrc991
    • P. Chène Inhibiting the p53-MDM2 interaction: an important target for cancer therapy Nat. Rev. Cancer 3 2003 102 109 (Pubitemid 37328877)
    • (2003) Nature Reviews Cancer , vol.3 , Issue.2 , pp. 102-109
    • Chene, P.1
  • 8
    • 35048895357 scopus 로고    scopus 로고
    • Targeting protein-protein interactions: Lessons from p53/MDM2
    • DOI 10.1002/bip.20741
    • J.K. Muurray, and S.H. Gellman Targeting protein-protein interactions: lessons from p53/MDM2 Biopolymers 88 2007 657 686 (Pubitemid 47556148)
    • (2007) Biopolymers - Peptide Science Section , vol.88 , Issue.5 , pp. 657-686
    • Murray, J.K.1    Gellman, S.H.2
  • 9
    • 84860469117 scopus 로고    scopus 로고
    • The central valine concept provides an entry in a new class of non peptide inhibitors of p53-MDM2 interaction
    • P. Furet, P. Chène, A. De Pover, T.S. Valat, J.H. Lisztwan, J. Kallen, and K. Masuya The central valine concept provides an entry in a new class of non peptide inhibitors of p53-MDM2 interaction Bioorg. Med. Chem. Lett. 22 2012 3498 3502
    • (2012) Bioorg. Med. Chem. Lett. , vol.22 , pp. 3498-3502
    • Furet, P.1    Chène, P.2    De Pover, A.3    Valat, T.S.4    Lisztwan, J.H.5    Kallen, J.6    Masuya, K.7
  • 10
    • 84872323081 scopus 로고    scopus 로고
    • Structural ensemble of an intrinsically disordered polypeptide
    • J. Mittal, T.H. Yoo, G. Georqiou, and T.M. Truskett Structural ensemble of an intrinsically disordered polypeptide J. Phys. Chem. B. 117 2013 118 124
    • (2013) J. Phys. Chem. B. , vol.117 , pp. 118-124
    • Mittal, J.1    Yoo, T.H.2    Georqiou, G.3    Truskett, T.M.4
  • 11
    • 53049108040 scopus 로고    scopus 로고
    • Targeting the MDM2-p53 interaction for cancer therapy
    • S. Shangary, and S.M. Wang Targeting the MDM2-p53 interaction for cancer therapy Clin. Cancer Res. 14 2008 5318 5324
    • (2008) Clin. Cancer Res. , vol.14 , pp. 5318-5324
    • Shangary, S.1    Wang, S.M.2
  • 12
    • 47649096991 scopus 로고    scopus 로고
    • Structural biology of the tumor suppressor p53
    • A.C. Joerger, and A.R. Fersht Structural biology of the tumor suppressor p53 Annu. Rev. Biochem. 77 2008 557 582
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 557-582
    • Joerger, A.C.1    Fersht, A.R.2
  • 14
    • 3142781225 scopus 로고    scopus 로고
    • Small-molecule inhibitors of protein-protein interactions: Progressing towards the dream
    • M.R. Arkin, and J.A. Wells Small-molecule inhibitors of protein-protein interactions: progressing towards the dream Nat. Rev. Drug Discovery 3 2004 301 317 (Pubitemid 38499758)
    • (2004) Nature Reviews Drug Discovery , vol.3 , Issue.4 , pp. 301-317
    • Arkin, M.R.1    Wells, J.A.2
  • 15
    • 65249100143 scopus 로고    scopus 로고
    • Small-molecule inhibitors of the MDM2-p53 protein-protein interaction to reactivate p53 function: A novel approach for cancer therapy
    • S. Shangary, and S.M. Wang Small-molecule inhibitors of the MDM2-p53 protein-protein interaction to reactivate p53 function: a novel approach for cancer therapy Annu. Rev. Pharmacol. Toxicol. 49 2009 223 241
    • (2009) Annu. Rev. Pharmacol. Toxicol. , vol.49 , pp. 223-241
    • Shangary, S.1    Wang, S.M.2
  • 16
    • 34548780897 scopus 로고    scopus 로고
    • Efficient p53 activation and apoptosis by simultaneous disruption of binding to MDM2 and MDMX
    • DOI 10.1158/0008-5472.CAN-07-1140
    • B. Hu, D.M. Gilkes, and J. Chen Efficient p53 activation and apoptosis by simultaneous disruption of binding to MDM2 and MDMX Cancer Res. 67 2007 8810 8817 (Pubitemid 47437457)
    • (2007) Cancer Research , vol.67 , Issue.18 , pp. 8810-8817
    • Hu, B.1    Gilkes, D.M.2    Chen, J.3
  • 17
    • 65949087007 scopus 로고    scopus 로고
    • High affinity interaction of the p53 peptide-analogue with human Mdm2 and Mdmx
    • A. Czarna, G.M. Popowicz, A. Pecak, S. Wolf, G. Dubin, and T.A. Holak High affinity interaction of the p53 peptide-analogue with human Mdm2 and Mdmx Cell Cycle 8 2009 1176 1184
    • (2009) Cell Cycle , vol.8 , pp. 1176-1184
    • Czarna, A.1    Popowicz, G.M.2    Pecak, A.3    Wolf, S.4    Dubin, G.5    Holak, T.A.6
  • 19
    • 76249126943 scopus 로고    scopus 로고
    • Structure-based design of high affinity peptide inhibiting the interaction of p53 with MDM2 and MDMX
    • J. Phan, Z.Y. Li, A. Kasprzak, B.Z. Li, S. Sebti, W. Guida, E. Schönbrunn, and J.D. Chen Structure-based design of high affinity peptide inhibiting the interaction of p53 with MDM2 and MDMX J. Biol. Chem. 285 2010 2174 2183
    • (2010) J. Biol. Chem. , vol.285 , pp. 2174-2183
    • Phan, J.1    Li, Z.Y.2    Kasprzak, A.3    Li, B.Z.4    Sebti, S.5    Guida, W.6    Schönbrunn, E.7    Chen, J.D.8
  • 20
    • 2142813682 scopus 로고
    • Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
    • W.F. van Gunsteren, and H.J. Berendsen Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry Angew. Chem. Int. Ed. 29 1990 992 1023
    • (1990) Angew. Chem. Int. Ed. , vol.29 , pp. 992-1023
    • Van Gunsteren, W.F.1    Berendsen, H.J.2
  • 22
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • DOI 10.1038/nsb0902-646
    • M. Karplus, and J.A. McCammon Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 2002 646 652 (Pubitemid 34977295)
    • (2002) Nature Structural Biology , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 23
    • 0347949637 scopus 로고    scopus 로고
    • Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
    • J.M. Swanson, R.H. Henchman, and J.A. McCammon Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy Biophys. J. 86 2004 67 74 (Pubitemid 38067436)
    • (2004) Biophysical Journal , vol.86 , Issue.1 , pp. 67-74
    • Swanson, J.M.J.1    Henchman, R.H.2    McCammon, J.A.3
  • 24
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • DOI 10.1021/ja003834q
    • J. Wang, P. Morin, and P.A. Kollman Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binging mode to HIV-1 RT of efavirenz by docking and MM-PBSA J. Am. Chem. Soc. 123 2001 5221 5230 (Pubitemid 32910665)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.22 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 25
    • 0034789590 scopus 로고    scopus 로고
    • An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis
    • DOI 10.1021/ja003164o
    • W. Wang, W.A. Lim, A. Jakalian, J. Wang, R. Luo, C.I. Bayly, and P.A. Kollman An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis J. Am. Chem. Soc. 123 2001 3986 3994 (Pubitemid 32899485)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.17 , pp. 3986-3994
    • Wang, W.1    Lim, W.A.2    Jakalian, A.3    Wang, J.4    Wang, J.5    Luo, R.6    Bayly, C.I.7    Kollman, P.A.8
  • 26
    • 33748442331 scopus 로고    scopus 로고
    • A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method
    • DOI 10.1002/prot.21044
    • Y. Xu, and R. Wang A computational analysis of the binding affinities of FKBP12 inhibitors using the MM PB/SA method Proteins 50 2006 1058 1068 (Pubitemid 44420944)
    • (2006) Proteins: Structure, Function and Genetics , vol.64 , Issue.4 , pp. 1058-1068
    • Xu, Y.1    Wang, R.2
  • 27
    • 84867648701 scopus 로고    scopus 로고
    • Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: Insights from molecular dynamics simulation and free energy analysis
    • L. Chen, J.L. Zhang, L.Y. Yu, Q.C. Zheng, W.T. Chu, Q. Xue, H.X. Zhang, and C.C. Sun Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis J. Phys. Chem. B. 116 2012 12415 12425
    • (2012) J. Phys. Chem. B. , vol.116 , pp. 12415-12425
    • Chen, L.1    Zhang, J.L.2    Yu, L.Y.3    Zheng, Q.C.4    Chu, W.T.5    Xue, Q.6    Zhang, H.X.7    Sun, C.C.8
  • 28
    • 84855332585 scopus 로고    scopus 로고
    • Insight into mechanism of small molecule inhibitors of the MDM2-p53 interaction: Molecular dynamics simulation and free energy analysis
    • J.Z. Chen, J.N. Wang, B.S. Xu, W.L. Zhu, and G.H. Li Insight into mechanism of small molecule inhibitors of the MDM2-p53 interaction: molecular dynamics simulation and free energy analysis J. Mol. Graph. Model. 30 2011 46 53
    • (2011) J. Mol. Graph. Model. , vol.30 , pp. 46-53
    • Chen, J.Z.1    Wang, J.N.2    Xu, B.S.3    Zhu, W.L.4    Li, G.H.5
  • 29
    • 77955653070 scopus 로고    scopus 로고
    • A computational analysis of the binding model of MDM2 with inhibitors
    • G. Hu, D. Wang, X. Liu, and Q. Zhang A computational analysis of the binding model of MDM2 with inhibitors J. Comput. Aided Mol. Des. 24 2010 687 697
    • (2010) J. Comput. Aided Mol. Des. , vol.24 , pp. 687-697
    • Hu, G.1    Wang, D.2    Liu, X.3    Zhang, Q.4
  • 30
    • 10844238962 scopus 로고    scopus 로고
    • Computational studies and peptidomimetic design for the human p53-MDM2 complex
    • DOI 10.1002/prot.20275
    • H. Zhong, and H.A. Carlson Computational studies and peptidomimetic design for the human p53-MDM2 complex Proteins 58 2005 222 234 (Pubitemid 39665633)
    • (2005) Proteins: Structure, Function and Genetics , vol.58 , Issue.1 , pp. 222-234
    • Zhong, H.1    Carlson, H.A.2
  • 31
    • 79952588669 scopus 로고    scopus 로고
    • Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
    • T. Hou, J. Wang, Y. Li, and W. Wang Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations J. Chem. Inf. Model. 51 2011 69 82
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 69-82
    • Hou, T.1    Wang, J.2    Li, Y.3    Wang, W.4
  • 32
    • 84862818017 scopus 로고    scopus 로고
    • The evolution of HLA-B*3501 binding affinity to variable immunodominant NP(418-426) peptides from 1918 to 2009 pandemic influenza A virus: A molecular dynamics simulation and free energy calculation study
    • J. Guo, X. Wang, H. Sun, H. Liu, Y. Shen, and X. Yao The evolution of HLA-B*3501 binding affinity to variable immunodominant NP(418-426) peptides from 1918 to 2009 pandemic influenza A virus: a molecular dynamics simulation and free energy calculation study Chem. Biol. Drug Des. 79 2012 1025 1032
    • (2012) Chem. Biol. Drug Des. , vol.79 , pp. 1025-1032
    • Guo, J.1    Wang, X.2    Sun, H.3    Liu, H.4    Shen, Y.5    Yao, X.6
  • 33
    • 0043245780 scopus 로고    scopus 로고
    • Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    • H. Gohlke, C. Kiel, and D.A. Case Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes J. Mol. Biol. 330 2003 891 913
    • (2003) J. Mol. Biol. , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, C.2    Case, D.A.3
  • 34
    • 84887434803 scopus 로고    scopus 로고
    • http://www.rcsb.org/pdb/home/home.do
  • 36
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comp. Phys. 23 1977 327 341
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 37
    • 0017620929 scopus 로고
    • Numerical integration. A method for improving solution stability in models of the circulation
    • T.G. Coleman, H.C. Mesick, and R.L. Darby Numerical integration: a method for improving solution stability in models of the circulation Ann. Biomed. Eng. 5 1977 322 328 (Pubitemid 8284433)
    • (1977) Annals of Biomedical Engineering , vol.5 , Issue.4 , pp. 322-328
    • Coleman, T.G.1    Mesick, H.C.2    Darby, R.L.3
  • 38
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems
    • T. Darden, D. York, and L. Pedersen Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 40
    • 71549116815 scopus 로고    scopus 로고
    • Modulation of p53 binding to MDM2: Computational studies reveal important roles of Tyr100
    • S. Dastidar, D. Lane, and C. Verma Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100 BMC Bioinform. 10 15 2009 S6
    • (2009) BMC Bioinform. , vol.10 , Issue.15 , pp. 6
    • Dastidar, S.1    Lane, D.2    Verma, C.3
  • 41
    • 53849128197 scopus 로고    scopus 로고
    • Multiple peptide conformations give rise to similar binding affinities: Molecular simulations of p53-MDM2
    • S. Dastidar, D. Lane, and C. Verma Multiple peptide conformations give rise to similar binding affinities: molecular simulations of p53-MDM2 J. Am. Chem. Soc. 130 2008 13514 13515
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 13514-13515
    • Dastidar, S.1    Lane, D.2    Verma, C.3


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