ArticleInternational journal of molecular sciences2025
Enhancing HDAC Inhibitor Screening: Addressing Zinc Parameterization and Ligand Protonation in Docking Studies.
Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Beyond the Score: Fixed-Budget Benchmarking of Virtual Screening Integration Strategies for Decision-Centric Drug Discovery.International journal of molecular sciences · 2026Article
- Phytochemical, Antimicrobial, Insect-Repellent, and Molecular Docking Profiles of Gamma-IrradiatedMicroorganisms · 2026Article
- Interpretable QSAR, External PubChem Validation, and Coordination-Aware Docking Enable Tiered Prioritization of Carbonic Anhydrase I Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Mechanistic multiscale modeling identifies putative natural tri-target candidates of MAO-B, LRRK2 and A₂A for Parkinson's disease.Scientific reports · 2026Article
- Design, synthesis, antiproliferative assessments, and computational studies of new quinolin-2(1Frontiers in chemistry · 2025Article
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Authors and funding
6 authors.
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Abstract
Precise binding free-energy predictions for ligands targeting metalloproteins, especially zinc-containing histone deacetylase (HDAC) enzymes, require specialized computational approaches due to the unique interactions at metal-binding sites. This study evaluates a docking algorithm optimized for zinc coordination to determine whether it could accurately differentiate between protonated and deprotonated states of hydroxamic acid ligands, a key functional group in HDAC inhibitors (HDACi). By systematically analyzing both protonation states, we sought to identify which state produces docking poses and binding energy estimates most closely aligned with experimental values. The docking algorithm was applied across HDAC 2, 4, and 8, comparing protonated and deprotonated ligand correlations to experimental data. The results demonstrate that the deprotonated state consistently yielded stronger correlations with experimental data, with R
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