Systematic identification of degrader drug targets by deep proteomic screening and high-sensitivity ubiquitinomics

Targeted Protein Degradation (TPD) is an emerging therapeutic modality in which disease-causing proteins are selectively degraded by endogenous E3 ubiquitin ligases through interactions with small molecules, such as molecular glues or Proteolysis Targeting Chimeras (PROTACs).

One bottleneck in the discovery of molecular glue degrader drugs is the lack of rational drug design strategies and therefore the absence of a well-defined target space. To systematically screen such degrader drugs in a target-agnostic manner, we have developed deep proteomic screening, an MS-based screening technology with high throughput capabilities. This technology allows us to screen extensive libraries of (potential) molecular glue degrader drugs against a substantial portion of the expressed cellular proteome, generating comprehensive data matrices containing robust quantification information for over 10,000 proteins.

As proof of concept, we screened a collection of 100 molecular glue compounds, identifying numerous previously uncharacterized degrader target candidates. Following screening, degrader drug target candidates (neosubstrates) are validated by demonstrating modification by ubiquitin in cells. For this, we have developed a highly sensitive one-pot ubiquitinomics workflow that is coupled to slice-PASEF mass spectrometry.

Our screening platform thus connects neosubstrate ubiquitination to protein degradation, thereby facilitating the identification of degrader targets with high confidence.