Assessing the suitability of deubiquitylases as substrates for targeted protein degradation

The development of selective inhibitors of deubiquitylase enzymes (DUBs) is difficult due to a high level of homology in the active sites of the ≈100 such enzymes in the human proteome. A potential way to achieve this in a more facile manner would be to develop proteolysis-targeting chimera (PROTAC) or molecular glues that engage the target DUB in a less conserved region outside of the catalytic domain. However, this raises the concern that auto-deubiquitylation would make DUBs poor substrates for this modality. Here, we describe a chemical genetics system to evaluate this issue. We find that some DUBs are readily degradable via the Ubiquitin-proteasome pathway, and some are not. Of the latter category, some resist turnover through auto-deubiquitylation, and some are simply poor proteasome substrates.