Abstract 6567: Affinity and cooperativity modulate ternary complex formation to drive degradation of SMARCA2

Abstract

Abstract Small molecules that hijack the ubiquitin-proteasome system to degrade target proteins have gained traction as tools for chemical biology and as promising clinical candidates. Targeted degradation strategies encompass relatively large hetero-bifunctional small molecules (hSMs) that are built from target and effector ligands joined by a linker to much smaller molecular glues that have limited affinity for the target or effector proteins outside of a ternary complex. There is good reason for medicinal chemists to move from linkered hSMs toward glue-like scaffolds. Molecular glues can be considerably smaller, e.g., the IMiDs, and thus are less likely to possess atoms and functional motifs that add up to poor permeability and higher protein binding. Guided by the principle that hSMs with reduced molecular weight will have superior druglike properties, we have used SMARCA2, a potential therapeutic target in patients that have both copies of SMARCA4 inactivated, as a test of our own ability to drive rapid target degradation in relevant models. The hetero-bifunctional degraders that resulted from our work trade conventional linkers for chemical spacers that orient SMARCA2 and VHL to promote fortuitous protein-protein contacts in the ternary complex. Following in the footsteps of previously published works, we employed surface plasmon resonance (SPR), x-ray crystallography, and molecular modeling to understand the relationships between our cell-based metrics of degrader activity and the biophysical parameters that describe the ternary complex. Consequently, we found that cooperativity (α) and ternary complex affinity (KLPT) correlated well with both DC50 and initial rate of degradation. Within our series of novel SMARCA2 degraders, compound 1 exhibited exceptional cooperativity and ternary complex affinity, α = 12.8 and KLPT = 4.7 ± 1. The result of high cooperativity and enhanced affinity was rapid and near complete SMARCA2 degradation. Treatment of a cancer cell line with compound 1 resulted in 50% of SMARCA2 being degraded in under 30 minutes, and greater than 90% degradation in 2 hours. Most importantly, the near complete degradation of SMARCA2 resulted in potent effects on SWI/SNF dependent transcription in vitro and in inhibition of tumor cell growth both in vitro and in vivo. Citation Format: Ivonne Archibeque, Ken Dellamaggiore, Karen Rex, Sudipa Ghimire-Rijal, Kaylee Choi, Smither Kate, Albert Amegadzie, Ning Chen, Xiaofen Li, Ryan Wurz, Amit Vaish, Paul Hughes, Dane Mohl. Affinity and cooperativity modulate ternary complex formation to drive degradation of SMARCA2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6567.