Structural Basis of p97 Inhibition by the Site-Selective Anti-Cancer Compound CB-5083.

Inhibition of p97, a key player in the ubiquitin-proteasome degradation pathway, has been proposed as a treatment for cancer. This concept was nearly realized recently when a potent p97 inhibitor, CB-5083, was developed and demonstrated broad antitumor activity in various tumor models. CB-5083 functions as a competitive inhibitor that binds selectively to the ATP-binding site of the D2 domain, although both the D1 and D2 ATPase sites of p97 are highly similar. Despite its promising anti-cancer activity, CB-5083 failed its Phase I clinical trials due to an unexpected off-target effect, which necessitates further improvement of the inhibitor. In this study, we determined the crystal structure of N-terminal domain-truncated p97 in complex with CB-5083. It provides a structural basis for the specificity of CB-5083 towards the D2 domain, offers an explanation in atomic detail for the mutations that confer resistance to CB-5083, and establishes a foundation for future structure-guided efforts to develop the next generation of p97 inhibitors.