Molecular docking and molecular dynamics investigation of novels thiazolopyrimidines binding to canonical and alternative allosteric sites of kinesin Eg5.

CONTEXT: Human 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-1 for the loop 5 and loop 8 sites, respectively, whereas monastrol favored loop 5 by 1.6 kcal.mol-1. Compounds 1a and 2d remained associated with both sites during 500 ns simulations, with ligand root-mean-square deviations between 1.00 and 1.53 Å. MM-PBSA estimates ranged from -26.02 to -22.92 kcal.mol-1, compared with -22.14 kcal.mol-1 for monastrol. RMSF calculations revealed site- and ligand-dependent redistribution of mobility in loop 5, loop 8, Switch I, Switch II, the microtubule-binding site, the cover-neck bundle, and the neck linker. These results indicate that this scaffold is promising for the exploration of alternative allosteric sites in Eg5, although experimental confirmation is required. METHOD: The 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.