Abstract 6869: A quantitative, conformation-driven screening approach for identification of RNA-targeting small molecule modulators of MYC expression in cancer

Abstract Targeting RNA molecules that encode for undruggable proteins involved in cancer is an emerging strategy for small molecule drug development. While a handful of compounds have entered the clinic, progress has been slow due to longstanding challenges in identifying molecules that are both functional and selective. Wayfinder Biosciences has developed an RNA-based sensor technology that addresses these bottlenecks and deployed it to discover compounds that bind to structured elements in the MYC mRNA, which is deregulated in a majority of human cancers. The MYC 5’ UTR is known to contain RNA structures that regulate translation of the c-Myc protein. Using Wayfinder’s proprietary computational pipeline, we selected three targetable RNA motifs and designed Wayfinder sensors for each. Wayfinder sensors couple folding of the target RNA motif to folding of a fluorogenic RNA domain and are designed to only generate fluorescence when the target RNA adopts a specific conformation. By screening compound libraries against our sensors, we can identify small molecules that selectively bind to each target RNA structure. Notably, one of the MYC motifs we selected represents an alternative conformation that we predict will inhibit interaction with regulatory RNA-binding proteins, enabling us to discover a novel class of modulators of MYC expression. We screened a panel of sensors encoding the MYC elements or off-target RNA structures against a library of 50, 000 drug-like small molecules to identify compounds that selectively target each MYC motif. Hits were validated via dose-response experiments and surface plasmon resonance, an orthogonal biophysical method. Top binders were tested for their ability to reduce cell viability and c-Myc protein levels in a small cell lung cancer cell line (NCI-H82) and a mesothelioma cell line (MSTO-211H), both of which harbor large MYC gene amplifications. To date, we have identified multiple hit series that bind to the MYC 5’ UTR and modulate c-Myc protein levels, leading to significantly reduced proliferation of Myc-amplified cancer cells. Together, our results validate the ability of Wayfinder’s platform to identify selective RNA-binding small molecules that engage their target in in vitro models and offer promise for development of cancer therapeutics. Top compounds from this study are currently undergoing medicinal chemistry optimization for potency and selectivity in preclinical models. Future studies will focus on defining the indication space that can be addressed by our MYC-targeting molecules and further characterizing their antiproliferative mechanism of action. Citation Format: Michelle Kriner, Chuhern Hwang, Brett Israels, Fusayo Koyanagi, Isha Gupta, Wanling Kratzman, Jason Fontana, David Sparkman-Yager. A quantitative, conformation-driven screening approach for identification of RNA-targeting small molecule modulators of MYC expression in cancer [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 6869.