Early De-risking: Human Cell-Based Proteomic Analysis to Identify Off-Target Proteins Associated with Targeted Protein Degradation (S16-3)

Targeted protein degraders (TPD) have the ability to alter the abundance of endogenous proteins. Currently available in vitro secondary pharmacology assays may be inadequate to predict off-target protein degradation by TPDs. We developed a novel in vitro assay where off-target proteins of interest were systematically prioritized from the entire human proteome based on phenotypes from the latest genetic and pharmacological evidence. This “selected off-target proteome” (SOTP) includes over 5,000 proteins. Algorithmic selection of hosting cell lines using transcriptome data identified a panel of four lines that covered 80% of the SOTP at the transcriptomics level. Primary and induced pluripotent stem cells (iPSC)-derived human cells were analyzed to improve SOTP coverage. In summary, we were able to conduct unbiased and biologically relevant screening for off-target proteins to influence the interpretation of nonclinical findings from conventional toxicology and safety pharmacology studies.