ArticleJournal of computer-aided molecular design2019
Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site.
Article in Journal of computer-aided molecular design, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 20 citations in OpenAlex.
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- Exploring the druggability of the binding site of aurovertin, an exogenous allosteric inhibitor of FFrontiers in pharmacology · 2022Article
- Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach.Scientific reports · 2021Article
- Drug repurposing and computational modeling for discovery of inhibitors of the main protease (MRSC advances · 2021Article
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- Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors.bioRxiv : the preprint server for biology · 2020Article
- Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors.International journal of molecular sciences · 2019Article
- A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform.Medicines (Basel, Switzerland) · 2019Article
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6 authors at 2 institutions in 2 countries.
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Abstract
Kallikrein-8, a serine protease, is a target for structure-based drug design due to its therapeutic potential in treating Alzheimer's disease and is also useful as a biomarker in ovarian cancer. We present a binding assessment of ligands to kallikrein-8 using a residue-wise decomposition of the binding energy. Binding of four putative inhibitors of kallikrein-8 is investigated through molecular dynamics simulation and ligand binding energy evaluation with two methods (MM/PBSA and WaterSwap). For visualization of the residue-wise decomposition of binding energies, chemical energy-wise decomposition or CHEWD is introduced as a plugin to UCSF Chimera and Pymol. CHEWD allows easy comparison between ligands using individual residue contributions to the binding energy. Molecular dynamics simulations indicate one ligand binds stably to the kallikrein-8 S1 binding site. Comparison with other members of the kallikrein family shows that residues responsible for binding are specific to kallikrein-8. Thus, ZINC02927490 is a promising lead for development of novel kallikrein-8 inhibitors.
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