ArticleHeliyon2020
Application of per-residue energy decomposition to identify the set of amino acids critical for
Article in Heliyon, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- Chitosan Oligosaccharides Modulate Macrophage Inflammatory Signaling: Molecular Docking and Transcriptomic Evidence.International journal of molecular sciences · 2026Article
- Mechanistic Insights into Human Defensin Antimicrobial Activity from Membrane Simulations.The Journal of membrane biology · 2026Article
- Dual Inhibition of COX-2/5-LOX Through Novel Hybrids of NSAIDs and Peptides: Insights from Molecular Dynamics Simulation and Per-Residue Decomposition.ChemistryOpen · 2026Article
- Computational strategies for unraveling insights from known inhibitors for further lead optimization: A case study on Celecoxib analogues.Scientific reports · 2026Article
- In Silico Analysis of CMolecules (Basel, Switzerland) · 2025Article
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- Magic shotgun approach to anti-inflammatory pharmacotherapy: Synthesis of novel thienopyrimidine monomers/heterodimer as dual COX-2 and 15-LOX inhibitors endowed with potent antioxidant activity.European journal of medicinal chemistry · 2023Article
- Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors.International journal of molecular sciences · 2023Article
- In Silico Drug Repurposing Approach: Investigation ofMolecules (Basel, Switzerland) · 2022Article
- Decoding molecular recognition of inhibitors targeting HDAC2 via molecular dynamics simulations and configurational entropy estimation.PloS one · 2022Article
- Repurposing of FDA Approved Drugs Against SARS-CoV-2 Papain-Like Protease: Computational, Biochemical, andFrontiers in microbiology · 2022Article
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Authors and funding
2 authors.
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Abstract
The enormous magnitude of scientific research carried out in the field of NSAIDs and cyclooxygenases (COXs) is known. They are crucial in pain management. COX-2 inhibitors have evolved over the years; from traditional NSAIDs to isoform-specific. The present study is aimed to identify a cluster of amino acids in the catalytic site whose energy contribution can better explain COX-2 inhibitory activity accurately than the binding energy of the whole protein. Initially, MD simulations (25 ns) and MM-PBSA calculations were performed for 8 diarylheterocyclic inhibitors. Per-residue energy decomposition studies were carried out to elucidate the energy contribution of each amino acid, and their correlation with COX-2 inhibitory activity was enumerated. A cluster of catalytic amino acids whose free energy sum has a high correlation with biological data was identified. The cluster of Gln178, Ser339, Tyr341, Arg499, Phe504, Val509 and Ala513 showed the correlation of -0.60. Further, the study was extended to a total of 26 COX-2 inhibitors belonging to different classes to validate the applicability of the cluster of amino acids identified. Results clearly suggest that the cluster of amino acids identified provide accurate screening method, and can be applied to predict COX-2 inhibitory activity of small molecules.
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