Structure-Based Development of Isoform-Selective Inhibitors of Casein Kinase 1 vs Casein Kinase 1

Specific inhibition of a single kinase isoform is a challengingtask due to the highly conserved nature of ATP-binding sites. Caseinkinase 1 (CK1) delta and epsilon share 97% sequence identity intheir catalytic domains. From a comparison of the X-ray crystal structuresof CK1 delta and CK1 epsilon, we developed a potent and highly CK1 epsilon-isoform-selectiveinhibitor (SR-4133). The X-ray co-crystal structure of the CK1 delta-SR-4133complex reveals that the electrostatic surface between the naphthylunit of SR-4133 and CK1 delta is mismatched, destabilizing the interactionof SR-4133 with CK1 delta. Conversely, the hydrophobic surface arearesulting from the Asp-Phe-Gly motif (DFG)-out conformationof CK1 epsilon stabilizes the binding of SR-4133 in the ATP-bindingpocket of CK1 epsilon, leading to the selective inhibition of CK1 epsilon.The potent CK1 epsilon-selective agents display nanomolar growth inhibitionof bladder cancer cells and inhibit the phosphorylation of 4E-BP1in T24 cells, which is a direct downstream effector of CK1 epsilon.