4.3 Article

Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Chemistry, Multidisciplinary

Gaussian accelerated molecular dynamics: Principles and applications

Jinan Wang et al.

Summary: Gaussian accelerated molecular dynamics (GaMD) is a robust computational method that accelerates biomolecular simulations by adding a harmonic boost potential, allowing for energetic reweighting via cumulant expansion to accurately reconstruct free energy landscapes. Hybrid schemes with other enhanced sampling methods have been introduced to further improve sampling and free energy calculations, enabling efficient characterization of biomolecular dynamics and interactions.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2021)

Article Chemistry, Medicinal

Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis

Jianzhong Chen et al.

Summary: The mutations G12V and D33E in K-Ras significantly alter the flexibility of SW1 and SW2, as well as affecting their correlated motions relative to the P-loop and each other, leading to a tuning of K-Ras activity. Analysis of free energy landscapes also reveals the conformational disorders in SW1 and SW2, which may impact the binding of guanine nucleotide exchange factors or effectors to K-Ras, with instability in hydrogen-bonding interactions being a key factor.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Multidisciplinary Sciences

Potential anti-COVID-19 agents, cepharanthine and nelfinavir, and their usage for combination treatment

Hirofumi Ohashi et al.

Summary: The study identified cepharanthine and nelfinavir as potential antiviral agents against SARS-CoV-2, with different modes of action. A synergistic effect was observed when these two drugs were used in combination, shortening the time until viral clearance. Further evaluation of the anti-SARS-CoV-2 activity of cepharanthine and nelfinavir is warranted.

ISCIENCE (2021)

Article Biochemistry & Molecular Biology

Binding of Inhibitors to BACE1 Affected by pH-Dependent Protonation: An Exploration from Multiple Replica Gaussian Accelerated Molecular Dynamics and MM-GBSA Calculations

Jianzhong Chen et al.

Summary: In this study, the effect of pH-dependent protonation on inhibitor binding to BACE1 was investigated using molecular simulations and analyses. Results showed that pH-dependent protonation significantly influences the binding abilities of inhibitors to BACE1, altering hydrogen bonding interactions and structural flexibility. Higher pH conditions were found to enhance the binding abilities of inhibitors to BACE1, providing valuable insights for the design of potent BACE1 inhibitors.

ACS CHEMICAL NEUROSCIENCE (2021)

Article Biology

Conformational transformation of switch domains in GDP/K-Ras induced by G13 mutants: An investigation through Gaussian accelerated molecular dynamics simulations and principal component analysis

Jianzhong Chen et al.

Summary: This study used simulations and analysis to investigate the effects of G13A, G13D, and G13I mutations on conformational transformations of K-Ras switch domains. The results indicate that these mutations increase structural flexibility, alter correlated motion modes, and enhance total motion strength of K-Ras compared to the wild-type.

COMPUTERS IN BIOLOGY AND MEDICINE (2021)

Article Biology

Binding mechanism of inhibitors to p38α MAP kinase deciphered by using multiple replica Gaussian accelerated molecular dynamics and calculations of binding free energies

Jianzhong Chen et al.

Summary: The study utilized MR-GaMD simulations and MM-GBSA method to investigate the binding mechanisms of three inhibitors to p38α, showing significant conformational changes and suggesting potential efficient target residues for potent inhibitors towards p38α.

COMPUTERS IN BIOLOGY AND MEDICINE (2021)

Article Chemistry, Multidisciplinary

Insights into effect of the Asp25/Asp25MODIFIER LETTER PRIME protonation states on binding of inhibitors Amprenavir and MKP97 to HIV-1 protease using molecular dynamics simulations and MM-GBSA calculations

Y. X. Yu et al.

Summary: The protonation states of Asp25/Asp25' significantly affect the conformational changes and inhibitor bindings of HIV-1 protease (PR). Dynamics analysis confirms the strong impact of Asp25/Asp25' protonation states on the conformational dynamics of the flaps in PR, while binding free energy calculations show a clear enhancement in inhibitor bindings due to these protonation states.

SAR AND QSAR IN ENVIRONMENTAL RESEARCH (2021)

Article Chemistry, Multidisciplinary

Molecular mechanism concerning conformational changes of CDK2 mediated by binding of inhibitors using molecular dynamics simulations and principal component analysis

S. S. Liang et al.

Summary: In this study, MD simulations and PC analysis were used to explore the binding mechanisms and conformational changes of three inhibitors (1PU, CDK, 50Z) to CDK2. The results showed significant impacts of inhibitors on the internal dynamics, movement patterns, and conformational changes of CDK2. CDK exhibited the strongest binding to CDK2 among the three inhibitors, primarily through hydrogen bonding interactions and hydrophobic interactions.

SAR AND QSAR IN ENVIRONMENTAL RESEARCH (2021)

Article Chemistry, Physical

Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease

Troy W. Whitfield et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Physical

Identifying hot spots of inhibitor-CDK2 bindings by computational alanine scanning

Juan Zhao et al.

CHEMICAL PHYSICS LETTERS (2020)

Article Biochemical Research Methods

Optimizing the refinement of merohedrally twinned P61 HIV-1 protease-inhibitor cocrystal structures

Gordon J. Lockbaum et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics

Jianzhong Chen et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2020)

Article Biochemistry & Molecular Biology

Conformational landscape of non-B variants of HIV-1 protease: A pulsed EPR study

Trang T. Tran et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2020)

Article Chemistry, Physical

Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics

Jianzhong Chen et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2020)

Article Biochemistry & Molecular Biology

Electrostatic interaction-mediated conformational changes of adipocyte fatty acid binding protein probed by molecular dynamics simulation

Fangfang Yan et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2019)

Article Chemistry, Medicinal

Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease

Gordon J. Lockbaum et al.

ACS INFECTIOUS DISEASES (2019)

Article Chemistry, Physical

Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease

Florian Leidner et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Biochemistry & Molecular Biology

Molecular Dynamics Exploration of Selectivity of Dual Inhibitors 5M7, 65X, and 65Z toward Fatty Acid Binding Proteins 4 and 5

Fangfang Yan et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2018)

Article Biochemistry & Molecular Biology

Exploring molecular mechanism of allosteric inhibitor to relieve drug resistance of multiple mutations in HIV-1 protease by enhanced conformational sampling

Jianzhong Chen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2018)

Review Biochemistry & Molecular Biology

Recent Developments and Applications of the MMPBSA Method

Changhao Wang et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2018)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Multidisciplinary Sciences

Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease

Ayseguel Oezen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Chemistry, Multidisciplinary

In silico models for predicting vector control chemicals targeting Aedes aegypti

J. Devillers et al.

SAR AND QSAR IN ENVIRONMENTAL RESEARCH (2014)

Article Chemistry, Physical

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Romelia Salomon-Ferrer et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Multidisciplinary

An overview of the Amber biomolecular simulation package

Romelia Salomon-Ferrer et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2013)

Article Biochemistry & Molecular Biology

Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease

Nancy M. King et al.

ACS CHEMICAL BIOLOGY (2012)

Article Chemistry, Physical

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

Bill R. Miller et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Andreas W. Goetz et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Biochemistry & Molecular Biology

Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir

Parimal Kar et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2012)

Article Biochemistry & Molecular Biology

Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding

Ming-Jun Yang et al.

JOURNAL OF STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease

Zhigang Liu et al.

PROTEIN JOURNAL (2011)

Article Pharmacology & Pharmacy

Lopinavir/Ritonavir A Review of its Use in the Management of HIV-1 Infection

Jamie D. Croxtall et al.

Review Pharmacology & Pharmacy

Atazanavir A Review of its Use in the Management of HIV-1 Infection

Katherine F. Croom et al.

Article Chemistry, Multidisciplinary

Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study

Emilia L. Wu et al.

CHEMISTRY-A EUROPEAN JOURNAL (2008)

Review Pharmacology & Pharmacy

Lopinavir/ritonavir: a protease inhibitor for HIV-1 treatment

Patricia Barragan et al.

EXPERT OPINION ON PHARMACOTHERAPY (2008)

Article Biochemistry & Molecular Biology

Structural Evidence for Effectiveness of Darunavir and Two Related Antiviral Inhibitors against HIV-2 Protease

Andrey Y. Kovalevsky et al.

JOURNAL OF MOLECULAR BIOLOGY (2008)

Article Chemistry, Multidisciplinary

HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants

Michael D. Altman et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Article Biochemistry & Molecular Biology

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

Delphine C. Bas et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Evaluating the potency of HIV-1 protease drugs to combat resistance

Tingjun Hou et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Mechanism of drug resistance revealed by the crystal structure of the unliganded HIV-1 protease with F53L mutation

Fengling Liu et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Review Biochemistry & Molecular Biology

Very fast empirical prediction and rationalization of protein pKa values

H Li et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Review Chemistry, Multidisciplinary

The Amber biomolecular simulation programs

DA Case et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Review Pharmacology & Pharmacy

Fosamprenavir: advancing HIV protease inhibitor treatment options

S Becker et al.

EXPERT OPINION ON PHARMACOTHERAPY (2004)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

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

A Onufriev et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)

Article Chemistry, Multidisciplinary

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

A Jakalian et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)

Article Multidisciplinary Sciences

Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance

W Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Chemistry, Physical

Langevin stabilization of molecular dynamics

JA Izaguirre et al.

JOURNAL OF CHEMICAL PHYSICS (2001)

Article Biochemistry & Molecular Biology

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

W Wang et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)