Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies

No abstract is available for this paper.

• Publication year

  2017

• Venue

  Journal of Biomolecular Structure and Dynamics

• Publication date

  2017-03-01

• Fields of study

  Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1080/07391102.2016.1165736PMID 26982261
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.

  2018cited by this paper
• Understanding the Dual Inhibition of COX-2 and Carbonic Anhydrase-II by Celecoxib and CG100649 Using Density Functional Theory Calculations and other Molecular Modelling Approaches.

  2015cited by this paper
• Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring.

  2014cited by this paper
• Free energy calculations to estimate ligand-binding affinities in structure-based drug design.

  2014cited by this paper
• Integrated approach to structure-based enzymatic drug design: molecular modeling, spectroscopy, and experimental bioactivity.

  2014cited by this paper
• Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set.

  2014cited by this paper
• g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations

  2014cited by this paper
• Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models.

  2013cited by this paper
• Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations.

  2013cited by this paper
• Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models.

  2012cited by this paper
• iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS).

  2012influential reference
• Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

  2012cited by this paper
• Structure and Ligand Based Drug Design Strategies in the Development of Novel 5-LOX Inhibitors

  2012cited by this paper
• iAPBS: a programming interface to the adaptive Poisson–Boltzmann solver

  2012cited by this paper
• Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

  2011cited by this paper
• Docking and Molecular Dynamics Calculations of Pyrrolidinone Analog MMK16 Bound to COX and LOX Enzymes

  2011cited by this paper
• SwissParam: A fast force field generation tool for small organic molecules

  2011cited by this paper
• R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

  2011cited by this paper
• Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

  2011cited by this paper
• Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

  2010cited by this paper
• Modeling the binding modes of stilbene analogs to cyclooxygenase-2: a molecular docking study

  2010cited by this paper
• The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

  2010cited by this paper
• AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

  2009cited by this paper
• Eicosanoids in inflammation and cancer: the role of COX-2

  2009cited by this paper
• PubChem: Integrated Platform of Small Molecules and Biological Activities

  2008cited by this paper
• GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

  2008cited by this paper
• Evolution of nonsteroidal anti-inflammatory drugs (NSAIDs): cyclooxygenase (COX) inhibition and beyond.

  2008cited by this paper
• Molecular Determinants for the Selective Inhibition of Cyclooxygenase-2 by Lumiracoxib*

  2007cited by this paper
• An Evidence-Based Update on Nonsteroidal Anti-Inflammatory Drugs

  2007cited by this paper
• Computer aided drug design approaches to develop cyclooxygenase based novel anti-inflammatory and anti-cancer drugs.

  2007cited by this paper
• Ligand Coordinate Analysis of SC-558 from the Active Site to the Surface of COX-2: A Molecular Dynamics Study

  2006cited by this paper
• Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

  2006cited by this paper
• Cardiovascular Risk Associated With Celecoxib in a Clinical Trial for Colorectal Adenoma Prevention

  2006cited by this paper
• Future of COX2 inhibitors

  2005cited by this paper
• Thermostat Algorithms for Molecular Dynamics Simulations

  2005cited by this paper
• Cardiovascular events associated with rofecoxib in a colorectal adenoma chemoprevention trial.

  2005cited by this paper
• Advanced Computer Simulation

  2005cited by this paper
• A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6

  2004cited by this paper
• Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition.

  2004cited by this paper
• Relationship Between Selective Cyclooxygenase-2 Inhibitors and Acute Myocardial Infarction in Older Adults

  2004cited by this paper
• Comparison of lumiracoxib with naproxen and ibuprofen in the Therapeutic Arthritis Research and Gastrointestinal Event Trial (TARGET), reduction in ulcer complications: randomised controlled trial.

  2004cited by this paper
• COX-2 and beyond: approaches to prostaglandin inhibition in human disease

  2003cited by this paper
• A Novel Mechanism of Cyclooxygenase-2 Inhibition Involving Interactions with Ser-530 and Tyr-385*

  2003cited by this paper
• Expression of cyclooxygenase-2 in rat testis.

  2003cited by this paper
• Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

  2003cited by this paper
• Characterization of celecoxib and valdecoxib binding to cyclooxygenase.

  2003cited by this paper
• COX-3, a cyclooxygenase-1 variant inhibited by acetaminophen and other analgesic/antipyretic drugs: Cloning, structure, and expression

  2002cited by this paper
• The coxibs, selective inhibitors of cyclooxygenase-2.

  2001cited by this paper
• GROMACS 3.0: a package for molecular simulation and trajectory analysis

  2001cited by this paper
• Molecular dynamics simulation of the interaction of 5-keto substituted 7-tert-butyl-2 , 3-dihydro-3 , 3-dimethylbenzofuran derivatives with cyclooxygenase-2

  2001cited by this paper
• The coxibs, selective inhibitors of cyclooxygenase-2.

  2001cited by this paper
• Comparison of upper gastrointestinal toxicity of rofecoxib and naproxen in patients with rheumatoid arthritis. VIGOR Study Group.

  2000cited by this paper
• Automated docking and molecular dynamics simulations of nimesulide in the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 (COX-2)

  2000cited by this paper
• Gastrointestinal toxicity with celecoxib vs nonsteroidal anti-inflammatory drugs for osteoarthritis and rheumatoid arthritis: the CLASS study: A randomized controlled trial. Celecoxib Long-term Arthritis Safety Study.

  2000cited by this paper
• Analysis of Binding Affinities for Celecoxib Analogues with COX-1 and COX-2 from Combined Docking and Monte Carlo Simulations and Insight into the COX-2/COX-1 Selectivity

  2000cited by this paper
• The Protein Data Bank

  2000cited by this paper
• The discovery of rofecoxib, [MK 966, Vioxx, 4-(4'-methylsulfonylphenyl)-3-phenyl-2(5H)-furanone], an orally active cyclooxygenase-2-inhibitor.

  1999cited by this paper
• Cyclooxygenases 1 and 2.

  1998cited by this paper
• Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices

  1998cited by this paper
• LINCS: A linear constraint solver for molecular simulations

  1997cited by this paper
• Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents

  1997cited by this paper
• Altered sensitivity of aspirin-acetylated prostaglandin G/H synthase-2 to inhibition by nonsteroidal anti-inflammatory drugs.

  1997cited by this paper
• Synthesis and biological evaluation of the 1,5-diarylpyrazole class of cyclooxygenase-2 inhibitors: identification of 4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]benze nesulfonamide (SC-58635, celecoxib).

  1997cited by this paper
• Characterization of Prostaglandin G/H Synthase 1 and 2 in rat, dog, monkey, and human gastrointestinal tracts.

  1996cited by this paper
• Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents

  1996cited by this paper
• Prostaglandin synthase 2.

  1996cited by this paper
• Involvement of Arginine 120, Glutamate 524, and Tyrosine 355 in the Binding of Arachidonate and 2-Phenylpropionic Acid Inhibitors to the Cyclooxygenase Active Site of Ovine Prostaglandin Endoperoxide H Synthase-1 (*)

  1996cited by this paper
• Flexibility of the NSAID binding site in the structure of human cyclooxygenase-2

  1996cited by this paper
• Prostaglandin endoperoxide synthases-1 and -2.

  1995cited by this paper
• GROMACS: A message-passing parallel molecular dynamics implementation

  1995influential reference
• The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1

  1994influential reference
• A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char

  1993cited by this paper
• Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

  1993cited by this paper
• Dexamethasone inhibits mitogen induction of the TIS10 prostaglandin synthase/cyclooxygenase gene.

  1992cited by this paper
• Gastrointestinal damage associated with the use of nonsteroidal antiinflammatory drugs.

  1992cited by this paper
• Expression of a mitogen-responsive gene encoding prostaglandin synthase is regulated by mRNA splicing.

  1991cited by this paper
• Selective regulation of cellular cyclooxygenase by dexamethasone and endotoxin in mice.

  1990cited by this paper
• Comparison of simple potential functions for simulating liquid water

  1983cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper

• Computational strategies for unraveling insights from known inhibitors for further lead optimization: A case study on Celecoxib analogues

  2026cites this paper
• Binding interactions of resveratrol and luteolin with bovine serum albumin: Insights into enhancing their stability

  2026cites this paper
• Unlocking the Potential of Papuan Red Fruit (Pandanus conoideus Lamk): A Comprehensive Exploration of Its Role in COVID-19 Inhibition Through Molecular Docking and Molecular Dynamics Simulation

  2025cites this paper
• Binding interaction between rice bran albumin and sweet potato leaves polyphenol: Multi-spectroscopic and simulated molecular docking analysis.

  2025cites this paper
• Explore the binding mechanism and dynamic variation of pea protein isolate-rutin complexes to effectively improve the foam performance of pea protein isolate.

  2025cites this paper
• Sustainable one-pot synthesis, digital ADMET modelling, DFT analysis, molecular docking and biological screening of dibutyl((5-hydroxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)(aryl)methyl) phosphonates

  2025cites this paper
• Repurposing major metabolites of lamiaceae family as potential inhibitors of α-synuclein aggregation to alleviate neurodegenerative diseases: an in silico approach

  2025cites this paper
• Computational Comparison of the Binding Affinity of Selective and Nonselective NSAIDs to COX-2 Using Molecular Docking

  2025cites this paper
• Evaluation of the therapeutic potentials of natural compounds against Eimeria tenella hexokinase for poultry coccidiosis: bioinformatics and in-silico study

  2025cites this paper
• MOLECULAR DOCKING INSIGHTS INTO PROBIOTICS SAKACIN P AND SAKACIN A AS POTENTIAL INHIBITORS OF THE COX-2 PATHWAY FOR COLON CANCER THERAPY

  2025cites this paper
• Discovery of non-peptide GLP-1r natural agonists for enhancing coronary safety in type 2 diabetes patients

  2024cites this paper
• Unveiling the potential of recently FDA-approved drugs as quorum sensing inhibitors against P. Aeruginosa using high-performance computational techniques

  2024cites this paper
• New insights into protein–protein interaction modulators in drug discovery and therapeutic advance

  2024cites this paper
• Mechanism of flavonols for binding protein and inhibiting cell activity: Regulation by B-ring hydroxyl groups and Cu(II) coordination

  2024cites this paper
• Exploration of binding mechanism of whey protein isolate and proanthocyanidin: Spectroscopic analysis and molecular dynamics simulation.

  2024cites this paper
• Computational Screening of T-Muurolol for an Alternative Antibacterial Solution against Staphylococcus aureus Infections: An In Silico Approach for Phytochemical-Based Drug Discovery

  2024cites this paper
• Flavonoid compound of red fruit papua and its derivatives against sars-cov-2 mpro: An in silico approach

  2024influential citation
• Unravelling Phyto-Compound Therapeutics against SRC Protein via FGF Pathway Targeting-A Comprehensive Approach Integrating Omics Data Analysis, Network Pharmacology, Virtual Screening, and Molecular Dynamics.

  2024cites this paper
• Postharvest ripening of newly harvested corn: Weakened interactions between starch and protein.

  2024cites this paper
• Identification of Potential Inhibitors of Three NDM Variants of Klebsiella Species from Natural Compounds: A Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Study.

  2024cites this paper
• “A Comprehensive Review on Selective Dual Inhibitor NSAID - Polmacoxib”

  2024influential citation
• Molecular docking and dynamics analysis of halogenated imidazole chalcone as anticancer compounds

  2023cites this paper
• Molecular docking and molecular dynamics simulation analysis of bioactive compounds of Cichorium intybus L. seed against hepatocellular carcinoma

  2023cites this paper
• Innovative screening for functional improved aromatic amine derivatives: Toxicokinetics, free radical oxidation pathway and carcinogenic adverse outcome pathway.

  2023cites this paper
• Molecular Structure-Based Screening of the Constituents of Calotropis procera Identifies Potential Inhibitors of Diabetes Mellitus Target Alpha Glucosidase

  2022cites this paper
• Computational Analysis and Biological Activities of Oxyresveratrol Analogues, the Putative Cyclooxygenase-2 Inhibitors

  2022cites this paper
• PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications

  2022cites this paper
• Exploring the binding mechanism of pumpkin seed protein and apigenin: Spectroscopic analysis, molecular docking and molecular dynamics simulation

  2022cites this paper
• Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study

  2022cites this paper
• A probable means to an end: exploring P131 pharmacophoric scaffold to identify potential inhibitors of Cryptosporidium parvum inosine monophosphate dehydrogenase

  2021cites this paper
• Component Identification of Phenolic Acids in Cell Suspension Cultures of Saussurea involucrata and Its Mechanism of Anti-Hepatoma Revealed by TMT Quantitative Proteomics

  2021cites this paper
• Structure-based identification of novel scaffolds as potential HIV-1 entry inhibitors involving CCR5

  2021cites this paper
• Identification of potential inhibitors of Schistosoma mansoni purine nucleoside phosphorylase from neolignan compounds using molecular modelling approaches

  2021cites this paper
• A Mechanistic Probe into the Dual Inhibition of T. cruzi Glucokinase and Hexokinase in Chagas Disease Treatment – A Stone Killing Two Birds?

  2021cites this paper
• A hybrid platform featuring nanomagnetic ligand fishing for discovering COX-2 selective inhibitors from aerial part of Saussurea laniceps Hand.-Mazz.

  2021cites this paper
• Discrimination of Naturally-Occurring 2-Arylbenzofurans as Cyclooxygenase-2 Inhibitors: Insights into the Binding Mode and Enzymatic Inhibitory Activity

  2020cites this paper
• Arylidene analogues as selective COX-2 inhibitors: synthesis, characterization, in silico and in vitro studies

  2020cites this paper
• Application of per-residue energy decomposition to identify the set of amino acids critical for in silico prediction of COX-2 inhibitory activity

  2020influential citation
• Molecular Basis of P131 Cryptosporidial-IMPDH Selectivity—A Structural, Dynamical and Mechanistic Stance

  2020cites this paper
• Screening of potential drug for Alzheimer’s disease: a computational study with GSK-3 β inhibition through virtual screening, docking, and molecular dynamics simulation

  2020cites this paper
• Computational Investigation on the p53–MDM2 Interaction Using the Potential of Mean Force Study

  2020cites this paper
• Identification of new potential cyclooxygenase-2 inhibitors: insight from high throughput virtual screening of 18 million compounds combined with molecular dynamic simulation and quantum mechanics

  2020cites this paper
• Identification of novel NAD(P)H dehydrogenase [quinone] 1 antagonist using computational approaches

  2020cites this paper
• Interpretations on the Interaction between Protein Tyrosine Phosphatase and E7 Oncoproteins of High and Low-Risk HPV: A Computational Perception

  2020cites this paper
• Deciphering the ‘Elixir of Life’: Dynamic Perspectives into the Allosteric Modulation of Mitochondrial ATP Synthase by J147, a Novel Drug in the Treatment of Alzheimer's Disease

  2019cites this paper
• Pharmacophore modeling, multiple docking, and molecular dynamics studies on Wee1 kinase inhibitors

  2019cites this paper
• Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations

  2019cites this paper
• A crystallographic and theoretical study of an (E)-2-Hydroxyiminoethanone derivative: prediction of cyclooxygenase inhibition selectivity of stilbenoids by MM-PBSA and the role of atomic charge

  2019cites this paper
• Recent Developments and Applications of the MMPBSA Method

  2018cites this paper
• Solving the riddle: Unraveling the mechanisms of blocking the binding of leukotoxin by therapeutic antagonists in periodontal diseases

  2018cites this paper
• Docking-based 3D-QSAR (CoMFA, CoMFA-RG, CoMSIA) study on hydroquinoline and thiazinan-4-one derivatives as selective COX-2 inhibitors

  2018cites this paper
• MM-PBSA and per-residue decomposition energy studies on 7-Phenyl-imidazoquinolin-4(5H)-one derivatives: Identification of crucial site points at microsomal prostaglandin E synthase-1 (mPGES-1) active site.

  2018cites this paper
• Deciphering the crucial residues involved in heterodimerization of Bak peptide and anti-apoptotic proteins for apoptosis

  2018cites this paper
• Characterizing the Binding Interactions between DNA-Binding Proteins, XPA and XPE: A Molecular Dynamics Approach

  2018cites this paper
• Discover potential inhibitors for PFKFB3 using 3D-QSAR, virtual screening, molecular docking and molecular dynamics simulation

  2018cites this paper
• Does Size Really Matter? Probing the Efficacy of Structural Reduction in the Optimization of Bioderived Compounds – A Computational “Proof-of-Concept”

  2018cites this paper
• Across the blood-brain barrier: Neurotherapeutic screening and characterization of naringenin as a novel CRMP-2 inhibitor in the treatment of Alzheimer's disease using bioinformatics and computational tools

  2018cites this paper
• Computational insights into the origin of decrease/increase in potency of N-CDPCB analogues toward FTO

  2017cites this paper
• sars-cov-2 mpro: An in silico approach

  year unknowncites this paper