Rapid Access to Photoswitchable RNA Binders: Fluorination Enhances Protein Rescue by Exon Inclusion

Targeting RNA is a rich, yet largely untackled opportunity for controlling biological functions, with high potential for therapeutic intervention. However, it remains inherently challenging. Beyond RNA structural diversity, functional RNA motifs are frequently context-dependent and transient, complicating the rational design of selective small-molecule binders. We here develop novel photoswitchable ligands to target RNA. They offer highly desirable, precise intervention by enabling light-controlled regulation of both direct RNA interactions and downstream events. Unfortunately, access to such photoswitchable RNA molecular tools is scarce, requiring complex and lengthy synthesis routes. We present a readily adaptable platform for the straightforward synthesis of photoswitchable RNA binders capable of targeting pre-mRNA and restoring functional survival motor neuron (SMN) protein levels by rescuing exon inclusion. Evaluation of our compounds demonstrated that both fluorination and heteroaryl groups (e.g., benzo- and thioxozaole) enhance binding affinity to the targeted dsRNA with in-cellulo activity. Importantly, molecular recognition and structure-activity relationships were rationalized through a combination of computational studies and NMR spectroscopy.