Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation (Q36329555)

13 August 2017

Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation (English)

1 reference

13 August 2017

Jianzhong Chen

1

1 reference

13 August 2017

Jinan Wang

2

1 reference

13 August 2017

Qinggang Zhang

3

1 reference

13 August 2017

Kaixian Chen

4

1 reference

13 August 2017

Weiliang Zhu

5

1 reference

13 August 2017

language of work or name

English

0 references

publication date

30 November 2015

1 reference

13 August 2017

1 reference

13 August 2017

5

1 reference

13 August 2017

17421

1 reference

Creative Commons Attribution 4.0 International

13 August 2017

start time

30 November 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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A New Quantum Calibrated Force Field for Zinc-Protein Complex

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Revealing origin of decrease in potency of darunavir and amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations

30 September 2017

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Binding modes of three inhibitors 8CA, F8A and I4A to A-FABP studied based on molecular dynamics simulation

30 September 2017

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Investigating the impact of Asp181 point mutations on interactions between PTP1B and phosphotyrosine substrate

30 September 2017

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CH-π hydrogen bonds in biological macromolecules

30 September 2017

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Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction

30 September 2017

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MDM2, MDMX and p53 in oncogenesis and cancer therapy

30 September 2017

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Simulating molecular mechanisms of the MDM2-mediated regulatory interactions: a conformational selection model of the MDM2 lid dynamics

30 September 2017

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Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization

30 September 2017

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Computational studies of difference in binding modes of peptide and non-peptide inhibitors to MDM2/MDMX based on molecular dynamics simulations

30 September 2017

1 reference

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Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies

30 September 2017

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Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

30 September 2017

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D-peptide inhibitors of the p53–MDM2 interaction for targeted molecular therapy of malignant neoplasms

30 September 2017

1 reference

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A computational analysis of the binding model of MDM2 with inhibitors

30 September 2017

1 reference

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Differential binding of p53 and nutlin to MDM2 and MDMX: computational studies

30 September 2017

1 reference

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The p53 orchestra: Mdm2 and Mdmx set the tone

30 September 2017

1 reference

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Structure-based Design of High Affinity Peptides Inhibiting the Interaction of p53 with MDM2 and MDMX

30 September 2017

1 reference

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Theoretical analysis of kinetic isotope effects on proton transfer reactions between substituted alpha-methoxystyrenes and substituted acetic acids

30 September 2017

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Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization

30 September 2017

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Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

30 September 2017

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Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization.

30 September 2017

1 reference

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Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX

30 September 2017

1 reference

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Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Elevated MDM2 boosts the apoptotic activity of p53-MDM2 binding inhibitors by facilitating MDMX degradation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Very fast prediction and rationalization of pKa values for protein-ligand complexes

30 September 2017

1 reference

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Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex

30 September 2017

1 reference

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Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

p53 in health and disease

30 September 2017

1 reference

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Senescence and tumour clearance is triggered by p53 restoration in murine liver carcinomas

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Restoration of p53 function leads to tumour regression in vivo

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Modeling the therapeutic efficacy of p53 restoration in tumors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Small-molecule inhibitors of the MDM2-p53 protein-protein interaction based on an isoindolinone scaffold

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

MDMX overexpression prevents p53 activation by the MDM2 inhibitor Nutlin.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Conformational changes of the p53-binding cleft of MDM2 revealed by molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Structure-based design of spiro-oxindoles as potent, specific small-molecule inhibitors of the MDM2-p53 interaction.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Very fast empirical prediction and rationalization of protein pKa values

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Exploring protein native states and large-scale conformational changes with a modified generalized born model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

In vivo activation of the p53 pathway by small-molecule antagonists of MDM2

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

30 September 2017

1 reference

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Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

30 September 2017

Surfing the p53 network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

MDMX: a novel p53-binding protein with some functional properties of MDM2

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding

29 June 2018

1 reference

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A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from molecular dynamics

22 September 2018

1 reference

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Ligand selectivity of estrogen receptors by a molecular dynamics study

22 September 2018

1 reference

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Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein.

22 September 2018

1 reference

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Fast and accurate computation schemes for evaluating vibrational entropy of proteins.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Molecular dynamics simulations on the mechanism of transporting methylamine and ammonia by ammonium transporter AmtB.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

High affinity interaction of the p53 peptide-analogue with human Mdm2 and Mdmx

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Protein polarization is critical to stabilizing AF-2 and helix-2' domains in ligand binding to PPAR-gamma

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Computational studies and peptidomimetic design for the human p53-MDM2 complex

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Ion solvation thermodynamics from simulation with a polarizable force field

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

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.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4663504

Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration.

22 September 2018

1 reference

https://api.crossref.org/works/10.1038%2FSREP17421

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSREP17421

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSREP17421

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSREP17421

Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

Molecular modeling and molecular dynamics simulation studies on pyrrolopyrimidine-based α-helix mimetic as dual inhibitors of MDM2 and MDMX

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/26616018

12 December 2020

Identifiers

DOI

10.1038/SREP17421

1 reference

13 August 2017

1 reference

13 August 2017

PubMed publication ID

26616018

1 reference