Streamlined Fragment-Based Discovery Platform for Targeting Structured RNAs

Fragment-based drug discovery typically relies on specialized spectrometric methods to identify low-affinity compounds that bind to biomolecules. Here, we report a proof-of-concept study on the development of a streamlined fragment-based screening platform for small molecules targeting RNA. This method employs low molecular weight fragments appended with a diazirine reactive moiety and an alkyne tag. Upon photolysis and click chemistry with an azide-containing fluorophore, these compounds can be visualized for binding to the r(CUG) repeat expansion [r(CUG)exp] implicated in myotonic dystrophy type 1 (DM1). Fragments were found to bind the 1 × 1 nucleotide U/U internal loops formed when r(CUG)exp folds, guiding the design of homodimeric compounds capable of interacting with adjacent internal loops in a single molecule. One dimeric compound exhibited enhanced affinity and was converted into a proximity-induced covalent binder for prolonged target occupancy. This work establishes a versatile platform for targeting structured RNAs with potential applications across a variety of disease-relevant RNA targets.