Selective ubiquitination of drug-like small molecules by the ubiquitin ligase HUWE1

The ubiquitin system regulates myriad pathways in eukaryotic physiology by modifying specific substrate proteins. The recognition of the substrates and the assembly of ubiquitin signals on them – key specificity determinants in ubiquitin signaling - are determined by the diversified class of ubiquitin ligases. It has recently emerged that certain ubiquitin ligases can modify non-protein substrates, such as sugars, lipids, and nucleotides. Here we expand this new realm of ubiquitin biology by revealing that the human cancer-associated HECT-type ubiquitin ligase HUWE1 can target drug-like small molecules. Our study focuses on a set of compounds identified as HUWE1 inhibitors, demonstrating that they act as selective substrates of their target ligase. The small-molecule ubiquitination is driven by the canonical catalytic ubiquitination cascade, linking the ubiquitin C-terminus to an essential primary amino group of the compounds. In vitro, the modification is selectively catalyzed by HUWE1 and allows the small molecules to compete with protein substrates for ubiquitination. We establish strategies to specifically detect small-molecule ubiquitination, unveiling that the inhibitors are targets of the ubiquitin system when supplied to human cells. While the cellular compound modification is promoted by HUWE1, it is not specific to it, highlighting that other ubiquitination enzymes can target exogenous small-molecule substrates. Our findings open the intriguing perspective of harnessing the ubiquitin system to transform exogenous small molecules into new chemical modalities in cells, as basic research tools or therapeutics.