Abstract

Structural studies suggest that the c-Abl protein kinase domain exists in two conformations; an active and an inactive form. There are many inhibitors which bind this tyrosine kinase in both forms. Many of these kinase inhibitors are in clinical trials too. The inhibition potency of these inhibitors is a common topic of discussion. In the present study we have taken a library of eight different inhibitors and docked those using GLIDE. After GLIDE docking we have also calculated induced fit results. The validity of the docking scores was compared to the post-docking score calculated by the Molecular mechanics-gernalised Boltzman/ surface area (MM-GB/SA) approach. During this process, Imatinib and Nilotinib showed very similar scores and binding energy. A comparative study of all eight inhibitors suggest that Imatinib and Nilotinib have the best binding scores and hence, they can be considered as the best drugs relative to PHA, VX6, PD3, PD5, P17 and Dasatinib. Our findings provide further rationale for considering kinase conformation in the design of kinase inhibitors.

Key words: Docking, scoring, binding affinity.