Project Summary/Abstract In recent years, computing speed has exponentially increased; however, the potential of computational ap- proaches to accelerate drug discovery has not been fully realized. Our long-term goal is to develop and ap- ply computational tools to advance structure-based drug design. The objective of this proposal is to apply new computational protocols based on the cutting-edge molecular simulation and quantum calculation tools to tackle several critical topics in the rational design of reversible and targeted covalent inhibitors (TCI) of kinases. Kinases phosphorylate a third of the proteome and deregulation of kinase functions is a major strategy to modulate cancer, autoimmune and inflammatory conditions. In recent years, reversible and covalent kinase inhibitors are gaining FDA approvals at a rapidly growing speed. Supported by our new tool developments, pilot studies, unpublished preliminary data, as well as working hypothe- ses, we will pursue three specific aims: 1) conduct kinome and proteome wide computational profiling studies to identify covalent targetable sites; 2) elucidate the reaction mechanisms and structure-reversibility relationships for chemical warhead design; and 3) elucidate the mechanisms controlling selectivity and kinetics of reversible kinase inhibitors. The outcomes of the studies will guide the current efforts in TCI discovery for kinases and the search for new druggable targets; provide detailed knowledge for attenuating reactivity and reversibility of chemical warheads to minimize toxicity; and offer new strategies to improve selectivity and kinetic parameters of reversible inhibitors. Successful completion of the project will allow us to build a computational platform to advance structure-based drug design and expand the current therapeutic target space.