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International Journal of Zoology and Applied Biosciences Research Article
Pharmacophore signatures of amino acid binding pockets and their small-molecule inhibitors
Banupriya B K, Saalini Vellivel, Kiran Kumar S, Sowmiya B and Sujitha K
Year : 2025 | Pages: 427-431
Received on: 25/09/2025
Revised on: 22/10/2025
Accepted on: 23/11/2025
Published on: 01/12/2025
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Banupriya B K, Saalini Vellivel, Kiran Kumar S, Sowmiya B and Sujitha K ( 2025).
Pharmacophore signatures of amino acid binding pockets and their small-molecule inhibitors
. International Journal of Zoology and Applied Biosciences, 10( 6), 427-431.
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Abstract
Amino acid binding pockets within protein targets play a central role in molecular recognition, ligand specificity, and drug–receptor interactions. Mapping the pharmacophoric signatures of these pockets provides a rational foundation for inhibitor design, particularly in proteins where conserved residues mediate ligand engagement. This study performs a hybrid computational and literature-driven analysis to characterize the key pharmacophore features associated with amino acid binding hot-spots such as hydrogen-bond donors/acceptors, aromatic centroids, hydrophobic regions, and charged interaction sites. Using structure-based models, representative proteins containing serine, cysteine, lysine, and aspartate-dominated pockets were analyzed for their inhibitor-binding characteristics. LigandScout and PyRx-assisted pharmacophore extraction revealed recurring interaction features, including nucleophilic attack points for cysteine-targeting electrophiles, anionic acceptor sites near lysine-rich pockets, and π–π stacking motifs around aromatic residues like tryptophan. A comparative inhibitor analysis highlighted key molecular scaffolds optimized for binding selectivity. The findings provide an integrative framework for understanding residue-specific recognition and can guide future inhibitor development through pharmacophore-driven screening and rational design.
Keywords
Pharmacophore mapping, Amino acid binding pockets, Small-molecule inhibitors, Molecular docking.
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© The Author(s) 2025. This article is published by International Journal of Zoology and Applied Biosciences under the terms of the Creative Commons Attribution 4.0 International License (creativecommons.org), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
