Over the past two decades, researchers have increasingly harnessed the power and potential of the ubiquitin-proteasome system to study and treat different diseases. Deubiquitinating enzymes (DUBs) are key components of the pathway and show immense promise as a drug target class, as they act as regulators of many cellular processes linked to human cancer. Thus, small-molecule inhibitors targeting DUBs have the potential to make a significant impact on therapeutic outcomes. However, the development of DUB inhibitors has been a challenging task due to the poor selectivity of early compounds and a limited understanding of the chemical principles required in DUB drug design. Now, Sara Buhrlage, PhD, and Jarrod Marto, PhD, from Dana-Farber Cancer Institute have published a DUB-focused platform for accelerating inhibitor discovery against the enzyme family in Nature Communications, as part of an ASPIRE award supported by The Mark Foundation for Cancer Research.
In the work, lead author Wai Cheung Chan and the team first designed and synthesized a bespoke covalent library of over 150 compounds to target the catalytic cysteine in the active site of most DUBs. This library was then screened in cell lysates by activity-based protein profiling using a mass spectrometry readout, and hits were extensively validated by biochemistry assays, intact protein mass spectrometry, cysteine profiling, and target-engagement assays in live cells. The authors identified selective hits against 23 endogenous DUBs spanning four subfamilies and developed one hit into a potent and selective probe for VCPIP1, an understudied DUB implicated in a number of key cellular processes.
The discovery of selective DUB inhibitors and chemical design principles is a major step forward in the field of targeted protein degradation and the future of cancer care. “This work addresses the need for selective chemical matter for DUBs right when interest in DUB-related applications in targeted protein degradation and stabilization is surging,” explained Chan. Indeed, Buhrlage and Marto are now expanding this work as part of a phase II of their ASPIRE award to use their platform against a novel library of noncovalent compounds. “Our work highlights the power of combining structure-guided diversification with high-content chemoproteomic primary screening to simultaneously identify hits and drive SAR against recalcitrant protein families,” explained Buhrlage. “The results set the stage for further exploration of DUB inhibitors as a promising therapeutic option for cancer care.”