ArticleACS omega2021
Molecular Dynamics Study of Conformational Changes of Tankyrase 2 Binding Subsites upon Ligand Binding.
Article in ACS omega, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Ligand-specific conformational dynamics and interaction landscapes of hnRNPA2B1 reveal a structural basis for its functional regulation.Current research in structural biology · 2026Article
- Deconstruction of Dual-Site Tankyrase Inhibitors Provides Insights into Binding Energetics and Suggests Critical Hotspots for Ligand Optimization.Journal of medicinal chemistry · 2025Article
- Direct Determination of Ratios of All Conformations and Their Lifetimes for Small Flexible Molecules from Molecular Dynamics Simulations: 1,3-Propanediol in an Aqueous Environment.Molecules (Basel, Switzerland) · 2025Article
- Unlocking nature's antidiabetic potential: computer-aided discovery of α-amylase and α-glucosidase inhibitors inIn silico pharmacology · 2025Article
- Virtual screening, molecular dynamics simulations, andFrontiers in veterinary science · 2025Article
- Systematic computational strategies for identifying protein targets and lead discovery.RSC medicinal chemistry · 2024Review
- Phytochemical Analysis and Evaluation of Antioxidant and Antimicrobial Properties of Essential Oils and Seed Extracts ofPharmaceuticals (Basel, Switzerland) · 2024Article
- Unveiling the Mechanisms of EGCG-p53 Interactions through Molecular Dynamics Simulations.ACS omega · 2024Article
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- Applications of Molecular Dynamics Simulations in Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms.ACS chemical biology · 2023Article
- A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.Journal of chemical information and modeling · 2023Article
- In Silico Discovery of Small-Molecule Inhibitors Targeting SARS-CoV-2 Main Protease.Molecules (Basel, Switzerland) · 2023Article
- Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states.The Journal of chemical physics · 2023Article
- Structure-based virtual screening and molecular dynamics studies to explore potential natural inhibitors against 3C protease of foot-and-mouth disease virus.Frontiers in veterinary science · 2023Article
- Study of the Molecular Dynamics Stability in the Inhibitory Interaction of Tenofovir Disoproxil Fumarate against CTLA-4 in Chronic Hepatitis B Patients.Medical archives (Sarajevo, Bosnia and Herzegovina) · 2023Article
- Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies.Scientific reports · 2022Article
- Fludarabine, a Potential DNA-Dependent RNA Polymerase Inhibitor, as a Prospective Drug against Monkeypox Virus: A Computational Approach.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Enzyme ChE, cholinergic therapy and molecular docking: Significant considerations and future perspectives.International journal of immunopathology and pharmacologyReview
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
The interactions between proteins and ligands are involved in various biological functions. While experimental structures provide key static structural information of ligand-unbound and ligand-bound proteins, dynamic information is often insufficient for understanding the detailed mechanism of protein-ligand binding. Here, we studied the conformational changes of the tankyrase 2 binding pocket upon ligand binding using molecular dynamics simulations of the ligand-unbound and ligand-bound proteins. The ligand-binding pocket has two subsites: the nicotinamide and adenosine subsite. Comparative analysis of these molecular dynamics trajectories revealed that the conformational change of the ligand-binding pocket was characterized by four distinct conformations of the ligand-binding pocket. Two of the four conformations were observed only in molecular dynamics simulations. We found that the pocket conformational change on ligand binding was based on the connection between the nicotinamide and adenosine subsites that are located adjacently in the pocket. From the analysis, we proposed the protein-ligand binding mechanism of tankyrase 2. Finally, we discussed the computational prediction of the ligand binding pose using the tankyrase 2 structures obtained from the molecular dynamics simulations.
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Registered trials
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