Indirect Ubiquitination: Noncovalent Ubiquitin Tethering Independent of Endogenous Ubiquitination Machinery for Targeted Protein Degradation

Heterobifunctional degrader molecules that hijack endogenous E3 ubiquitin ligases have attracted attention for the rapid and irreversible knock-down of target proteins via ubiquitination. However, the formation of appropriately oriented E3 ligase–target complexes is required for efficient ubiquitination of the target, which complicates the molecular optimization and leads to acquired drug resistance caused by the loss of E3 ligase activity and mutations at the E3–target interfaces. Here, we report on indirect ubiquitination as a chemical strategy for ubiquitination of the target substrate independent of endogenous ubiquitination machinery. Comprising a ligand molecule and a ubiquitin moiety, the designed chimeric molecule enables the non-covalent ubiquitination of target proteins, which lead to the proteasomal degradation of recombinant and endogenous proteins. Indirect ubiquitination offers a design platform for tethering of proteolytic ubiquitin-based modifiers independent of endogenous ubiquitination enzymes and expands the scope of targeted protein degradation that has been limited by the complexity and impairment of the activity of the endogenous ubiquitination machinery.