Insight into the key features for ligand binding in Y1230 mutated c-Met kinase domain by molecular dynamics simulations

Abstract

c-Met kinase has been considered as an attractive target for developing antitumor agents. The strong interactions between Tyr1230 and the inhibitors emphasized its importance for ligand binding. The clinically related Tyr1230 mutations have made negative impacts on current c-Met kinase inhibitors, especially the exquisitely selective ones, like PF-04217903, while the multi-targeted inhibitors, like Crizotinib, were not affected so much. In this study, the protein–ligand interactions between c-Met kinase domain (wild, Y1230C and Y1230H) and these inhibitors were compared. The binding site was expanded and the post-mutated regions became solvent accessible. The heavy dependency of PF-04217903 on the interactions with Tyr1230 resulted in the steep decrease of its potency against the Y1230 mutants. It was found that the ligand entrance region contributed consistently to the binding of Crizotinib, but not PF-04217903. Additional groups substituted in the ligand entrance region with stable interactions should be beneficial for improving the inhibitory activity of PF-04217903 against the Y1230 mutants. These findings will facilitate the discovery of potent inhibitors against Y1230 mutated c-Met kinase.