[ELRIG Drug Discovery EU 2021] Profiling Targeted Protein Degraders Using the BioMAP Human Phenotypic Platform Reveals Mechanistic Insights on Translational Biomarkers and Toxicity Signatures
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- ELRIG Drug Discovery EU
Targeted protein degraders represent a compelling new strategy for selectively removing disease-driving molecules through 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 modifies the target protein for subsequent ubiquitin-mediated degradation by the proteosome. This unique mechanism of action (MOA) enables selective degradation of key disease-related molecules that have been difficult to inhibit using conventional approaches. The biological outcomes of protein degradation remains a key metric to evaluate this strategy. We used the human-centric BioMAP® Phenotypic Platform to compare the activities of a protein degrader (MZ1) and a small molecule inhibitor (JQ1) that target the same bromodomain (BRD) molecule. The BioMAP Diversity PLUS® Panel of 12 human primary cell-based in vitro models, designed to recapitulate key aspects of tissue and disease states, was used to profile each agent at multiple concentrations. 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 this panel. Broad cytotoxicity was detected with concentrations close to reported EC50 values from orthogonal in vitro assays, indicating that human primary cell-based systems may be appropriately sensitive and translationally relevant to assess safety/tolerability profiles for these novel and complex molecule classes. MZ1 was significantly more active than its negative control, cisMZ1. 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 importantly, not other target or MOA classes. Pomalidomide and lenalidomide, E3 ligase (cereblon)-binding drugs, showed similar BioMAP profiles consistent with clinical reports. Evaluation for the presence of toxicity signatures within the BioMAP profiles of the tested agents revealed that all five agents were flagged for the presence of one or more signatures. 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.