Assessing Lysine and Cysteine Reactivities for Designing Targeted Covalent Kinase Inhibitors

Ruibin Liu, Zhi Yue, Cheng-Chieh Tsai, and Jana Shen
J. Am. Chem. Soc., 2019
DOI: 10.1021/jacs.8b13248

Targeted covalent inhibitor design is gaining increasing interest and acceptance. A typical covalent kinase inhibitor design targets a reactive cysteine; however, this strategy is limited due to the low abundance of cysteine and acquired drug resistance from point mutations. Inspired by the recent development of lysine-targeted chemical probes, we asked if nucleophilic (reactive) catalytic lysines are common based on the published crystal structures of the human kinome. Using a newly developed pKa prediction tool based on continuous constant pH molecular dynamics, the catalytic lysines of 8 unique kinases from various human kinase groups were retro- and prospectively predicted to be nucleophilic, when kinase is in the rare DFG-in/aC-out type of conformation. Importantly, other reactive lysines as well as cysteines at various locations were also identified. Based on the finding, we proposed a new strategy based on modification of selective type II reversible kinase inhibitors to discover highly selective, lysine-targeted covalent inhibitors. Traditional covalent drugs were discovered serendipitously; the presented tool, which can assess the reactivities of any potentially targetable residues, may assist and accelerate the rational discovery of new covalent inhibitors. Another significant finding of the work is that lysines and cysteines in kinases may adopt neutral and charged states at physiological pH, respectively. This finding may shift the current paradigm of computational studies of kinases, which assume standard protonation states.