Determining Cysteines Available for Covalent Inhibition Across the Human Kinome

Covalently
bound protein kinase inhibitors have been frequently
designed to target noncatalytic cysteines at the ATP binding site.
Thus, it is important to know if a given cysteine can form a covalent
bond. Here we combine a function-site interaction fingerprint method
and DFT calculations to determine the potential of cysteines to form
a covalent interaction with an inhibitor. By harnessing the human
structural kinome, a comprehensive structure-based binding site cysteine
data set was assembled. The orientation of the cysteine thiol group
indicates which cysteines can potentially form covalent bonds. These
covalent inhibitor easy-available cysteines are located within five
regions: P-loop, roof of pocket, front pocket, catalytic-2 of the
catalytic loop, and DFG-3 close to the DFG peptide. In an independent
test set these cysteines covered 95% of covalent kinase inhibitors.
This study provides new insights into cysteine reactivity and preference
which is important for the prospective development of covalent kinase
inhibitors.