Mirror-image RNA-targeted DEL Screens
Discovering RNA-binding small molecules is a formidable challenge with immense therapeutic potential but few reported successes. Here we report the discovery of specific small molecule ligands for expansion repeat, splice site, and riboswitch targets via affinity-mediated selection of DNA-encoded libraries (DELs) against immobilized mirror-image RNA. In a model system, we demonstrate that the mirror-image strategy eliminates false enrichment caused by DNA:RNA hybridization (a major issue in previous DEL:RNA studies) and enhances the enrichment of a DNA-tagged known ligand, consistent with the well-precedented assumption that DNA:RNA hybridization only occurs between homochiral strands. For three therapeutically relevant RNA targets, we employed our DEL deck containing more than 100 billion compounds, discovered novel chemical matter, synthesized the mirrored versions of the DEL hits, and confirmed their affinity to natural RNA target in orthogonal biophysical assays. Our method makes RNA as amenable to DEL screens as other target classes and unleashes the unparalleled throughput of DEL for RNA-targeted small molecule drug discovery.