ArticleJournal of molecular modeling2026
Molecular docking and molecular dynamics investigation of novels thiazolopyrimidines binding to canonical and alternative allosteric sites of kinesin Eg5.
Article in Journal of molecular modeling, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
contextHuman kinesin Eg5 is essential for bipolar spindle assembly, and most allosteric inhibitors bind to the canonical pocket formed by the α2 helix, loop 5, and the α3 helix. Eleven thiazolo[3,2-a]pyrimidinethiones were evaluated as ligands for two sites in Eg5: this canonical pocket and an alternative region near loop 8. All derivatives showed favorable docking poses at both sites, with average energies of -7.95 and -7.79 kcal.mol
methodThe Switch II segment was reconstructed with SWISS-MODEL and evaluated with PDBsum. The structures were prepared with PDB2PQR, AutoDockTools, and Open Babel. Redocking compared AutoDock Vina, QuickVina 2, and QuickVina-W, and QuickVina-W with exhaustiveness 32 was selected. Six systems were simulated for 500 ns in GROMACS using the OPLS-AA/L force field, TIP3P water, and ligand parameters obtained with ACPYPE. Visual Molecular Dynamics was used for trajectory measurements, Discovery Studio Visualizer for interaction analysis, and g_mmpbsa for binding-energy estimation and per-residue decomposition.
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