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Assessing the Suitability of Deubiquitylases As Substrates For Targeted Protein Degradation

Tong, J.; Watkins, J. M.; Burke, J.; Kodadek, T.

2025-06-14 biochemistry
10.1101/2025.06.13.659525 bioRxiv
Show abstract

The development of selective inhibitors of Deubiquitylase enzymes (DUBs) is difficult due to a high level of homology in the active sites of the {approx} 100 such enzymes in the human proteome. A potential way to achieve this in a more facile manner would be to develop PROTACs 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.

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