Proteome-Wide Discovery of Degradable Proteins Using Bifunctional Molecules

Forrest, I.; Conway, L. P.; Jadhav, A. M.; Gathmann, C.; Chiu, T.-Y.; Chaheine, C. M.; Estrada, M.; Shrestha, A.; Reitsma, J.; Warder, S. E.; Vasudevan, A.; McLoughlin, S. M.; Parker, C. G.

doi:10.1101/2025.03.21.644652

bioRxiv · 10.1101/2025.03.21.644652

Proteome-Wide Discovery of Degradable Proteins Using Bifunctional Molecules

Forrest, I.·Conway, L. P.·Jadhav, A. M.·Gathmann, C.·Chiu, T.-Y.·Chaheine, C. M.·Estrada, M.·Shrestha, A.·Reitsma, J.·Warder, S. E.·Vasudevan, A.·McLoughlin, S. M.·Parker, C. G.

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Abstract

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 PROTAC-type strategies is unknown. Here, we describe a chemical proteomic strategy for the agnostic discovery of degradable human 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. 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.

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Forrest, I., Conway, L. P., Jadhav, A. M., Gathmann, C., Chiu, T.-Y., Chaheine, C. M., Estrada, M., Shrestha, A., Reitsma, J., Warder, S. E., Vasudevan, A., McLoughlin, S. M., Parker, C. G.. 2025-03-22. Proteome-Wide Discovery of Degradable Proteins Using Bifunctional Molecules. https://doi.org/10.1101/2025.03.21.644652

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