Studying the selectivity of a targeted small molecule degrading a hypoxia-associated non-coding RNA

Small molecule targeted recruitment of nucleases to RNA is a powerful method to affect RNA biology. Inforna, a sequence-based design approach to target RNA, enables the design of small molecules that bind and cleave RNA in a selective and substoichiometric manner. Herein, we investigate the ability of RNA targeted degradation to improve the selectivity of small molecules targeting RNA. The microRNA-210 hairpin precursor (pre-miR-210) is overexpressed in hypoxic cancers. Previously, a small molecule (Targapremir-210, TGP-210) targeted this RNA in cells, but with only a 5-fold window for DNA binding. Appendage of a nuclease recruitment module onto TGP-210 locally recruited ribonuclease L onto pre-miR-210, triggering its degradation. The chimera has enhanced selectivity compared to TGP-210 with nanomolar binding to the pre-miR-210, but no DNA binding, and is broadly selective for affecting RNA function in cells. Importantly, it cleaved pre-miR-210 substoichiometrically and induced apoptosis in breast cancer cells. Examination of small molecule-treated (TGP-210-RL) or vehicle-treated (DMSO) hypoxic MDA-MB-231 cells in biological triplicates