Proteome-Wide Discovery of Degradable Proteins Using Bifunctional Molecules

Targeted protein degradation (TPD) is an emergent therapeutic strategy with the potential to circumvent challenges associated with targets unamenable to conventional pharmacological inhibition. Among TPD approaches, proteolysis-targeting chimeras (PROTACs) have shown marked advancement, with numerous candidates in clinical development. Despite their potential, most PROTACs utilize advanced small-molecule inhibitors, inherently limiting the scope of this approach. More generally, the fraction of the proteome tractable to small-molecule-induced degradation strategies is unknown. Here we describe a chemical proteomic strategy for the agnostic discovery of degradable proteins in cells using a new class of bifunctional degrader molecules called "AgnoTACs". Proteome-wide screening of 72 AgnoTACs in human cells uncovered downregulation events spanning >50 functionally and structurally diverse proteins, most of which lack chemical probes. While many events progressed through canonical degradation pathways, we also observed instances of alternative mechanisms, indicating that AgnoTACs can impact protein stability via multiple modes of action. Our findings highlight the potential of function-biased chemical libraries coupled with proteomic profiling to discover degrader starting points as well as furnish a blueprint for expanding our understanding of the chemically degradable proteome.