[DDC 2021] Early Insights for Optimal Chemistry Design of Targeted Protein Degraders Using the BioMAP Human Phenotypic Platform

[DDC 2021] Early Insights for Optimal Chemistry Design of Targeted Protein
Degraders Using the BioMAP Human Phenotypic Platform
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Targeted protein degradation, a compelling new drug discovery strategy, inactivates disease-driving molecules via degradation, rather than through more conventional inhibitor approaches. Degraders are bifunctional molecules comprised of a target protein binding entity linked to an E3-ligase; this complex binds to and marks the target protein for ubiquitin-mediated degradation by the proteosome. This unique mechanism of action (MoA) leads to selective degradation of key disease-related molecules that have been difficult to inhibit using conventional approaches. Phenotypic assessments of clinically-relevant protein biomarker endpoints provide key insights to support degrader discovery programs, as the outcome of protein degradation remains a key metric to evaluate this strategy. The human-centric BioMAP® Phenotypic Platform enables
comparison of the activities of a protein degrader (MZ1) and a small molecule inhibitor (JQ1) that have the same bromodomain (BRD) target. Activity profiles were generated for each test agent based on the modulation on 148 protein-based translational biomarkers. MZ1 was highly active in multiple human primary cell systems in the BioMAP Diversity PLUS Panel. Broad cytotoxicity was detected with concentrations close to reported EC50 values from orthogonal in vitro assays, indicating that human primary cell-based systems are appropriately sensitive
and translationally relevant to assess safety profiles for these novel and complex molecule classes. Importantly, although MZ1 was significantly more active than its negative control cisMZ1, the latter was not without activity. A statistical similarity search for mechanistically similar profiles from the BioMAP Reference Database returned matches for MZ1 to other BRD degraders as well as multiple BRD small molecule inhibitors, but no compounds from other target or MoA classes. Network cluster analysis demonstrated that the BioMAP profiles of E3 ligase (cereblon)-binding drugs pomalidomide and lenalidomide were similar to each other but distinct from the degraders. At a more restrictive Pearson’s correlation coefficient, degraders and inhibitors separated into distinct mechanism classes. This study establishes the BioMAP Phenotypic Platform as a powerful tool to assess biologically distinct modes of target engagement, discern common and differentiating biomarker activities of compounds in the protein degradation space, and provide key insights on outcomes relevant to ongoing
development efforts including optimal chemistry design.