Abstract 680: Leveraging an RNA-targeting platform for the discovery of cell-active c-MYC mRNA-binding small molecules
Authors: Matthew J. Smola, Krista Marran, Sarah E. Thompson, Brittani Patterson, Roheeth K. Pavana, Caleb Sutherland, Jessica A. Sorrentino, Katherine D. Warner
Journal: Cancer Research (2024)

Abstract The MYC gene, with its oncogenic potential, has long been a formidable challenge in conventional drug discovery efforts, and its critical role in cancer progression and resistance has underscored the need for innovative therapeutic strategies. Here we demonstrate the capabilities of the Ribometrix RNA-targeting platform to modulate the c-MYC mRNA with small molecules with the aim of reducing c-MYC protein levels. Using our comprehensive platform of RNA-targeting drug discovery tools and analyses including chemical probing, structure modeling, high-purity RNA production, high-throughput screening, and biophysical characterization, we evaluated the potential to directly target c-MYC mRNA using small molecules. Our analysis revealed six high-confidence structured elements throughout the c-MYC mRNA expected to harbor tertiary structures amenable to drug-like ligand binding. Leveraging the multifaceted chemical probing and structure modeling components of our platform, we confirmed that our in vitro-transcribed RNA screening constructs adopt the same structures found in endogenous cellular c-MYC transcripts. After large-scale in vitro RNA preparation, we subjected four of these RNA elements to high-throughput screens of chemically diverse drug-like libraries using mass spectrometry affinity-selection that identified multiple chemical series with sub-micromolar affinity. We validated binding affinity using orthogonal methods including isothermal titration calorimetry and NMR. To eliminate pan-binding ligands, we evaluated of selectivity against a panel of non-target mRNA structures. Importantly, these compounds lead to rapid (4 hr) reduction of MYC protein levels in a small cell lung cancer cell line, DMS-273, with no cellular toxicity at 72 hr suggesting an on-target effect. Employing our suite of chemical probing tools, we confirmed that compounds from multiple series engage the c-MYC mRNA in cells. Medicinal chemistry efforts are ongoing to increase potency and define the precise mechanism of action in clinically relevant models. The discovery of these c-MYC mRNA-binding small molecules not only validates the utility of the Ribometrix RNA-targeted small molecule discovery platform but also showcases its potential in tackling traditionally 'undruggable' targets and provides a promising avenue for developing novel anti-cancer therapies. As we learn more about the intricacies of c-MYC mRNA biology and further refine effective small molecules, our results provide practical insights into previously-unknown vulnerabilities of MYC and present tangible opportunities for advancing targeted cancer therapies. Citation Format: Matthew J. Smola, Krista Marran, Sarah E. Thompson, Brittani Patterson, Roheeth K. Pavana, Caleb Sutherland, Jessica A. Sorrentino, Katherine D. Warner. Leveraging an RNA-targeting platform for the discovery of cell-active c-MYC mRNA-binding small molecules [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 680.