Kinesins are key microtubule-associated motor proteins involved in intracellular transport as well as in the assembly of the mitotic spindle. Kinesin-5 (Eg5) and kinesin-12 (KIF15) have proven crucial regulators of bipolarity of the spindle and therefore have become potential anticancer targets. Although small molecules monastrol, terpendole E, and HR22C16 have established the proof of concept, small-molecule therapeutics so far have been hampered by solubility, metabolic clearance, neurotoxicity, as well as non-specificity. Given the limitations of small molecules, there is an imperative need for novel modalities possessing the ability to selectively impair kinesin activity with enhanced safety profiles. Herein, an integrated computational approach toward the design and optimization of peptide inhibitors for kinesins was described. Druggable sites in kinesin motor domains as well as protein-protein interfaces were determined using crystal structures as well as cryo-EM structures. A library of peptides was assembled as well as screened by using the application of structure-based virtual screening as well as molecular docking. Molecular dynamics simulation as well as free energy perturbation was then used in the optimization of peptide-kinesin interactions. Lead candidates were optimized further using in silico chemical modifications (cyclization, non-natural residue incorporation) as well as ADMET and pharmacokinetic profiling. Our findings identify some optimized peptide scaffolds that exhibit robust kinesin-5 and kinesin-12 binding stability at their best conformations, displaying higher selectivity and drug-like properties when compared with the available small-molecule inhibitors. Such findings not only validate the potential for peptide-mediated kinesin inhibition but also provide an applicable computational workflow for rational peptide drug discovery against protein-protein interfaces.
Bake et al. (2026) studied this question.