Structure guided discovery of small molecule ligands targeting the oncomiR-1 NPSL2 hairpin

NPSL2 is a stem loop element within the oncomiR-1 polycistronic primary microRNA (miRNA) cluster. NPSL2 is predicted to mediate conformational rearrangements within oncomiR-1 to regulate the biogenesis of certain miRNA elements within the cluster. The regulatory role of NPSL2 makes it a promising target for small molecule ligands, which we explored through structure-based small molecule ligand discovery. Starting with an NMR-derived ensemble of NPSL2 structures, we identified ligandable cavities within NPSL2 using RNACavityMiner. We then used molecular docking to screen the ZINC library against these cavities to identify potential small molecule hits. A sampling of commercially available compounds from the initial hits were purchased for experimental characterization by saturation transfer difference (STD) and heteronuclear single quantum coherence (HSQC) NMR spectroscopy. This approach led to the identification and characterization of at least eight compounds that bind preferentially within the internal loop of NPSL2. Importantly, this workflow, which combined virtual screening and experimental validation, can be used to identify small molecules that bind to any known RNA three-dimensional structure.