Targeting RNA degradation with small molecules: design and synthesis of selective RNA binders and development of ribonuclease targeting chimeras (RIBOTACs)

RNA has been successfully targeted by small molecules for drug discovery purposes, by taking advantage of binding sites available upon rearrangement of RNA into secondary and tertiary structures.1 A validated RNA target is pre-miR-21, a non-coding RNA, linked to various cancers and other pathologies.2 This project aims to develop selective binders to target pre-miRNA21 and in turn decrease miRNA21 levels. To identify RNA ligands, we used a virtual screening, taking advantage of RNA binders reported in literature. Those compounds were docked against different possible conformations of pre-miRNA21. Here, the best compounds were selected for further synthesis. We identified two fragments, selected for a fragment growth campaign. Indeed, by following an optimized synthetic strategy, we obtained several derivatives that have been tested for their binding affinity to the short pre-miR-21 construct by high-resolution mass spectroscopy (MS) under native conditions. Binding data from native MS will guide ongoing structure−activity relationship (SAR) studies for the expansion of ligand library and the development of more potent and selective pre-miRNA21 ligands. Subsequently, pre-miRNA21 ligands will be employed as warheads to synthesize Ribonuclease Targeting Chimeras (RIBOTACs), a class of RNA-degraders.3 RIBOTAC includes an RNA-binder conjugated by a linker to an RNase L recruiter, ultimately to induce enzymatic cleavage the RNA of Interest (ROI). (Figure 1).