posted on 2023-01-05, 16:34authored byAlexander Hanzl, Eleonora Barone, Sophie Bauer, Hong Yue, Radosław P. Nowak, Elisa Hahn, Eugenia V. Pankevich, Anna Koren, Stefan Kubicek, Eric S. Fischer, Georg E. Winter
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.