Abstract 1283: Discovery of selective and potent BRD4 protein degraders using Plexium's DELPhe platform

Abstract

Abstract Targeted protein degradation using the endogenous Ubiquitin Proteasome System (UPS) represents a fundamentally new approach to drug discovery that potentially allows proteins that cannot be modulated by conventional small molecule inhibitors to be brought under therapeutic control. Plexium has developed the DELPhe platform, which combines solid phase synthesis of DNA encoded libraries with high-throughput ultra-miniaturized cell-based assays, to readily and cost-effectively identify both bifunctional (PROTAC) and monovalent degraders for traditionally undruggable targets including scaffolding proteins, protein-protein interactions and transcription factors. In addition to modulating previously “undruggable” proteins, degradation can lead to greater efficacy and a prolonged downstream signaling response, thereby addressing common obstacles seen with small molecule inhibitors. The bromodomain extra-terminal (BET) protein family are epigenetic readers that have been targeted using small molecule inhibitors. Compounds currently in development typically inhibit multiple BET family members. The bromodomain protein BRD4 is a transcriptional and epigenetic regulator that associates at super-enhancers, driving the expression of oncogenic proteins such as MYC that are critical for the pathogenesis of cancer. We describe here the use of Plexium's DELPhe platform to sample extensive chemical space and discover small molecule monovalent degraders that demonstrate selective and sustained degradation of BRD4. Near complete degradation was observed within 4 hours and DC50 potency of <10 nM was achieved for BRD4 without any appreciable degradation of the highly homologous BRD2 and BRD3 proteins. Degradation of BRD4 resulted in down regulation of MYC protein levels and potent anti-proliferative activity (20-200 nM) against a panel of tumor cell lines with activity superior to inhibition with the pan-BET inhibitor JQ1. Co-treatment with either proteosome or neddylation inhibitors blocked BRD4 degradation, suggesting that protein turnover is regulated by a Cullin-RING Ligase (CRL). Biochemical studies verified a direct interaction between the small molecule and BRD4, suggesting that binding promotes a conformational change that exposes key protein motifs to ubiquitination and degradation. Mutational analysis and a ubiquitin ligase-focused CRISPR screen were used to provide insights into defining the principles of degradation. Collectively, these data demonstrate that the Plexium DELPhe platform enables the discovery of selective and potent monovalent degraders of BRD4. Citation Format: Gregory S. Parker, Julia A. Toth, Geoffray Leriche, Simon Bailey, Kenneth Chng, Sara Fish, Aleks Jamborcic, Elizabeth Daniele, Erika Green, Michael Hocker, Adam Kallel, Peggy A. Thompson, Steven D. Brown, Kandaswamy Vijayan. Discovery of selective and potent BRD4 protein degraders using Plexium's DELPhe platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1283.