Insight into mechanism of small molecule inhibitors of the MDM2-p53 interaction: molecular dynamics simulation and free energy analysis.

[1]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[2]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[3]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[4]  Peter L. Cummins,et al.  Computer-aided drug design: A free energy perturbation study on the binding of methyl-substituted pterins and N5-deazapterins to dihydrofolate reductase , 1993, J. Comput. Aided Mol. Des..

[5]  J M Thornton,et al.  LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. , 1995, Protein engineering.

[6]  M. Sanner,et al.  Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.

[7]  A. Levine.  p53, the Cellular Gatekeeper for Growth and Division , 1997, Cell.

[8]  D. Lane,et al.  The p53 tumour suppressor gene , 1998, The British journal of surgery.

[9]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[10]  A. Levine,et al.  Surfing the p53 network , 2000, Nature.

[11]  P A Kollman,et al.  Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. , 2000, Journal of molecular biology.

[12]  P A Kollman,et al.  An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. , 2001, Journal of the American Chemical Society.

[13]  C. Renner,et al.  Chalcone derivatives antagonize interactions between the human oncoprotein MDM2 and p53. , 2001, Biochemistry.

[14]  P. Kollman,et al.  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. , 2001, Journal of the American Chemical Society.

[15]  Min Wu,et al.  The initial evaluation of non-peptidic small-molecule HDM2 inhibitors based on p53-HDM2 complex structure. , 2002, Cancer letters.

[16]  P. Chène.  Inhibiting the p53–MDM2 interaction: an important target for cancer therapy , 2003, Nature Reviews Cancer.

[17]  D. Case,et al.  Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. , 2003, Journal of molecular biology.

[18]  Joshua A. Kritzer,et al.  Helical β-Peptide Inhibitors of the p53-hDM2 Interaction , 2004 .

[19]  Richard H. Henchman,et al.  Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. , 2004, Biophysical journal.

[20]  Oliver Zerbe,et al.  Using a β‐Hairpin To Mimic an α‐Helix: Cyclic Peptidomimetic Inhibitors of the p53–HDM2 Protein–Protein Interaction , 2004 .

[21]  Using a b-Hairpin To Mimic an a-Helix : Cyclic Peptidomimetic Inhibitors of the p 53 – HDM 2 Protein – Protein Interaction , 2004 .

[22]  L. Vassilev,et al.  In Vivo Activation of the p53 Pathway by Small-Molecule Antagonists of MDM2 , 2004, Science.

[23]  D. Case,et al.  Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models. , 2004, Journal of the American Chemical Society.

[24]  J. Deschamps,et al.  Structure-based design of potent non-peptide MDM2 inhibitors. , 2005, Journal of the American Chemical Society.

[25]  B. Kuhn,et al.  Validation and use of the MM-PBSA approach for drug discovery. , 2005, Journal of medicinal chemistry.

[26]  S. Sebti,et al.  Terphenyl-based helical mimetics that disrupt the p53/HDM2 interaction. , 2005, Angewandte Chemie.

[27]  H. Carlson,et al.  Computational studies and peptidomimetic design for the human p53–MDM2 complex , 2004, Proteins.

[28]  Maxwell D Cummings,et al.  Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells. , 2005, Journal of medicinal chemistry.

[29]  L. Vassilev.  p53 Activation by small molecules: application in oncology. , 2005, Journal of medicinal chemistry.

[30]  Renxiao Wang,et al.  A computational analysis of the binding affinities of FKBP12 inhibitors using the MM‐PB/SA method , 2006, Proteins.

[31]  D. Parks,et al.  Benzodiazepinedione inhibitors of the Hdm2:p53 complex suppress human tumor cell proliferation in vitro and sensitize tumors to doxorubicin in vivo , 2006, Molecular Cancer Therapeutics.

[32]  Kevin E. Riley,et al.  Insights into the strength and origin of halogen bonding: the halobenzene-formaldehyde dimer. , 2007, The journal of physical chemistry. A.

[33]  Craig W Lindsley,et al.  Small molecule protein-protein inhibitors for the p53-MDM2 interaction. , 2007, Current topics in medicinal chemistry.

[34]  Tingjun Hou,et al.  Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance. , 2007, Journal of medicinal chemistry.

[35]  John Z H Zhang,et al.  Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study. , 2008, Chemistry.

[36]  Shaomeng Wang,et al.  Targeting the MDM2-p53 Interaction for Cancer Therapy , 2008, Clinical Cancer Research.

[37]  Ye Mei,et al.  Efficient bond function basis set for π‐π interaction energies , 2008, J. Comput. Chem..

[38]  Ye Mei,et al.  Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding. , 2008, The journal of physical chemistry. B.

[39]  Xin Huang,et al.  Discovery and optimization of chromenotriazolopyrimidines as potent inhibitors of the mouse double minute 2-tumor protein 53 protein-protein interaction. , 2009, Journal of medicinal chemistry.

[40]  Shaomeng Wang,et al.  Small-molecule inhibitors of the MDM2-p53 protein-protein interaction to reactivate p53 function: a novel approach for cancer therapy. , 2009, Annual review of pharmacology and toxicology.

[41]  Xinguo Liu,et al.  A computational analysis of the binding model of MDM2 with inhibitors , 2010, J. Comput. Aided Mol. Des..

[42]  Chandra S Verma,et al.  Differential binding of p53 and nutlin to MDM2 and MDMX: Computational studies , 2010, Cell cycle.

[43]  Ye Mei,et al.  Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding. , 2010, Journal of the American Chemical Society.

[44]  Qinggang Zhang,et al.  Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: Free energy calculation and molecular dynamic simulation , 2010, Journal of molecular modeling.

[45]  Wei Wang,et al.  Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery , 2010, Cell cycle.

[46]  Arjel D. Bautista,et al.  Bridged beta(3)-peptide inhibitors of p53-hDM2 complexation: correlation between affinity and cell permeability. , 2010, Journal of the American Chemical Society.

[47]  Charles C. David,et al.  Essential dynamics of proteins using geometrical simulations and subspace analysis , 2012 .

[48]  P. Chène.  INHIBITING THE p 53 – MDM 2 INTERACTION : AN IMPORTANT TARGET FOR CANCER THERAPY , 2022 .