ArticleJournal of computer-aided molecular design2017
Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR.
Article in Journal of computer-aided molecular design, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- International Union of Basic and Clinical Pharmacology CXIII: Nuclear Receptor Superfamily-Update 2023.Pharmacological reviews · 2023Review
- Human Endocrine-Disrupting Effects of Phthalate Esters through Adverse Outcome Pathways: A Comprehensive Mechanism Analysis.International journal of molecular sciences · 2023Article
- Multi-dimensional structural footprint identification for the design of potential scaffolds targeting METTL3 in cancer treatment from natural compounds.Journal of molecular modeling · 2023Article
- Unveiling the Inhibitory Potentials of Peptidomimetic Azanitriles and Pyridyl Esters towards SARS-CoV-2 Main Protease: A Molecular Modelling Investigation.Molecules (Basel, Switzerland) · 2023Article
- Insights into glycosidic bond specificity of an engineered selective α-L-rhamnosidase N12-Rha via activity assays and molecular modelling.AMB Express · 2022Article
- Time to target the circadian clock for drug discovery.Trends in biochemical sciences · 2022Review
- The role of REV-ERB in NASH.Acta pharmacologica Sinica · 2022Article
- Targeting Nuclear Receptors for TImmunometabolism · 2022Article
- Phthalate's multiple hormonal effects and their supplementary dietary regulation scheme of health risks for children.Environmental science and pollution research international · 2022Article
- Systematic Structure-Based Search for Ochratoxin-Degrading Enzymes in Proteomes from Filamentous Fungi.Biomolecules · 2021Article
- Review
- Doxorubicin Encapsulation in Carbon Nanotubes Having Haeckelite or Stone-Wales Defects as Drug Carriers: A Molecular Dynamics Approach.Molecules (Basel, Switzerland) · 2021Article
- Enhanced Biodegradation of Phthalic Acid Esters' Derivatives by Plasticizer-Degrading Bacteria (International journal of environmental research and public health · 2020Article
- Carbon Nanotubes Having Haeckelite Defects as Potential Drug Carriers. Molecular Dynamics Simulation.Molecules (Basel, Switzerland) · 2019Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The knowledge of the free energy of binding of small molecules to a macromolecular target is crucial in drug design as is the ability to predict the functional consequences of binding. We highlight how a molecular dynamics (MD)-based approach can be used to predict the free energy of small molecules, and to provide priorities for the synthesis and the validation via in vitro tests. Here, we study the dynamics and energetics of the nuclear receptor REV-ERBα with its co-repressor NCoR and 35 novel agonists. Our in silico approach combines molecular docking, molecular dynamics (MD), solvent-accessible surface area (SASA) and molecular mechanics poisson boltzmann surface area (MMPBSA) calculations. While docking yielded initial hints on the binding modes, their stability was assessed by MD. The SASA calculations revealed that the presence of the ligand led to a higher exposure of hydrophobic REV-ERB residues for NCoR recruitment. MMPBSA was very successful in ranking ligands by potency in a retrospective and prospective manner. Particularly, the prospective MMPBSA ranking-based validations for four compounds, three predicted to be active and one weakly active, were confirmed experimentally.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.