Abstract 404: Mechanistic characterization of selective monovalent direct degraders of SMARCA2

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Abstract SMARCA2 and SMARCA4 are essential, redundant, catalytic subunits of the multi-subunit BRG1/BRM-associated factor (BAF) complex. This complex regulates gene expression and DNA repair through chromatin remodeling activity. The paralogues SMARCA2 and SMARCA4 bind acetylated histones through their highly conserved bromodomains and alter DNA-histone contacts using ATP-dependent helicase activity. Recently, mutations in specific components of the BAF complex have been identified. Of great interest are loss of function mutations in SMARCA4, found in 5-7% of all human cancers and occur with high prevalence (∼10%) in non-small cell lung cancer (NSCLC), making these SMARCA4-deficient tumor cells highly dependent on SMARCA2 for viability. This synthetic lethal relationship may provide a unique opportunity for SMARCA2-selective degraders to block the growth of SMARCA4 deficient tumors, while sparing normal tissues. To enable degrader discovery, we focused our efforts on a monovalent direct degrader approach, where small molecules are designed to bind the target protein and induce its degradation through the recruitment of an E3 ligase complex. Initial screening hits from distinct chemical series were optimized to produce potent and selective SMARCA2 degraders. Co-treatment with a proteasome inhibitor confirmed that degradation was mediated via the ubiquitin proteasome system (UPS), and a UPS-focused CRISPR screen identified the E3 ligase responsible for compound-induced degradation of SMARCA2. Cell based protein-protein interaction (PPI) studies advanced our understanding of compound-mediated E3 ligase recruitment and provided mechanistic insights into the observed selectivity for SMARCA2 over SMARCA4. Ternary complex dynamics were further investigated in vitro via surface plasmon resonance (SPR) studies. Using a combination of co-immunoprecipitation, mass spectrometry, and point mutant studies, specific amino acids that are required for compound-induced PPI and subsequent degradation of SMARCA2 were identified. Collectively, these results highlight the discovery and characterization of novel small molecule monovalent direct degraders of SMARCA2. The detailed description of the degradation mechanism presented here provides critical insights into an efficient approach to eliminating pathogenic proteins through targeted protein degradation. Citation Format: Julia Toth, Gregory Parker, Geoffray Leriche, Tayor Kampert, Aleksandar Jamborcic, Gabrielle Blanco, Kenneth Steadman, Duc Tran, Shu You, Luis Lopez, Farhana Barmare, Kyohei Hayashi, Gang Liu, Alex Campos, Meg McCarrick, Kevin Freeman-Cook, Peggy Thompson. Mechanistic characterization of selective monovalent direct degraders of SMARCA2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 404.

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