Structural Bioinformatics-Based Design of Selective, Irreversible Kinase Inhibitors

TLDR

The active sites of 491 human protein kinase domains are highly conserved, making selective inhibitor design a formidable challenge. Using structural bioinformatics, we identified two selectivity filters—a threonine and a cysteine—at defined positions in the active site of p90 ribosomal protein S6 kinase (RSK). A fluoromethylketone inhibitor that exploits both filters potently and selectively inactivated RSK1 and RSK2, and kinases lacking one filter were resistant but became sensitive when the second filter was introduced, showing that two distinct amino acids are sufficient to confer inhibitor sensitivity.

Abstract

The active sites of 491 human protein kinase domains are highly conserved, which makes the design of selective inhibitors a formidable challenge. We used a structural bioinformatics approach to identify two selectivity filters, a threonine and a cysteine, at defined positions in the active site of p90 ribosomal protein S6 kinase (RSK). A fluoromethylketone inhibitor, designed to exploit both selectivity filters, potently and selectively inactivated RSK1 and RSK2 in mammalian cells. Kinases with only one selectivity filter were resistant to the inhibitor, yet they became sensitized after genetic introduction of the second selectivity filter. Thus, two amino acids that distinguish RSK from other protein kinases are sufficient to confer inhibitor sensitivity.