Type-II Kinase Inhibitor Docking, Screening, and Profiling Using Modified Structures of Active Kinase States

Type-it kinase inhibitors represent a class of chemicals that trap their target kinases in an inactive, so-called DFG-out state, occupying a hydrophobic pocket adjacent to the ATP binding site. These compounds are often more specific than those that target active DFG-in kinase conformal ions. Unfortunately, the discovery of novel type-H scaffolds presents a considerable challenge, partially because the lack of compatible kinase Structures makes structure-based methods inapplicable. We present a computational protocol for converting multiple available DFG-in structures of various kinases (similar to 70% of mammalian Structural kinome) into accurate and specific models of their type-II bound state. The models, described as deletion-of-loop Asp-Phe-Gly-in (DOLPHIN) kinase models, demonstrate exceptional performance in Various inhibitor discovery applications, including Compound pose prediction, screening, and in silico activity profiling. Given the abundance of the DFG-in structures, the presented approach opens possibilities for kinome-wide discovery of specific molecules targeting inactive kinase states.