E3-Specific Degrader Discovery by Dynamic Tracing of Substrate Receptor Abundance

• Published in: Journal of the American Chemical Society 2023-01, Vol.145 (2), p.1176-1184
• Main Authors: Hanzl, Alexander, Barone, Eleonora, Bauer, Sophie, Yue, Hong, Nowak, Radosław P., Hahn, Elisa, Pankevich, Eugenia V., Koren, Anna, Kubicek, Stefan, Fischer, Eric S., Winter, Georg E.
• Format: Article
• Language: English
• Subjects: Carrier Proteins - metabolism; Humans; Protein Processing, Post-Translational; Proteolysis; Ubiquitin-Protein Ligases - metabolism; Ubiquitination
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/jacs.2c10784

Targeted protein degradation (TPD) is a new pharmacology based on small-molecule degraders that induce proximity between a protein of interest (POI) and an E3 ubiquitin ligase. Of the approximately 600 E3s encoded in the human genome, only around 2% can be co-opted with degraders. This underrepresentation is caused by a paucity of discovery approaches to identify degraders for defined E3s. This hampers a rational expansion of the druggable proteome and stymies critical advancements in the field, such as tissue- and cell-specific degradation. Here, we focus on dynamic NEDD8 conjugation, a post-translational, regulatory circuit that controls the activity of 250 cullin RING E3 ligases (CRLs). Leveraging this regulatory layer enabled us to develop a scalable assay to identify compounds that alter the interactome of an E3 of interest by tracing their abundance after pharmacologically induced auto-degradation. Initial validation studies are performed for CRBN and VHL, but proteomics studies indicate broad applicability for many CRLs. Among amenable ligases, we select CRLDCAF15 for a proof-of-concept screen, leading to the identification of a novel DCAF15-dependent molecular glue degrader inducing the degradation of RBM23 and RBM39. Together, this strategy empowers the scalable identification of degraders specific to a ligase of interest.