Lysosomal Degradation of MicroRNA-21 Precursor by a Small-Molecule Chimera

Abstract

Non-coding RNAs (ncRNAs) are key regulators of cancer progression and have emerged as promising therapeutic targets. However, current approaches for targeting oncogenic ncRNAs remain limited, and expanding the repertoire of cellular degradation pathways available for selective ncRNA elimination remains a significant challenge. Here, we report lysosomal RNA-degrading chimeras (LyRACs), bifunctional small molecules that recruit the autophagosome-associated protein LC3B to direct precursor microRNA-21 (pre-miR-21) toward lysosomal degradation. Structure-guided screening of full-length pre-miR-21 identified dovitinib as the RNA-recognition module; subsequent in vitro binding analyses defined the structural basis of dovitinib’s recognition of pre-miR-21 and revealed exploitable chemical space for ligand optimization. Conjugation of dovitinib to the LC3B recruiter GW5074 via optimized linkers yielded DPG-3, which simultaneously engages pre-miR-21 and LC3B to form a ternary complex and promotes selective pre-miR-21 degradation through the autophagy-lysosome pathway, resulting in potent anti-proliferative activity in hepatocellular carcinoma (HCC) cells. In head-to-head comparisons, DPG-3 achieved more pronounced depletion of pre-miR-21 and mature miR-21-5p than dovitinib-RiboTAC, accompanied by stronger inhibition of HCC cell proliferation. Collectively, these findings establish lysosome-directed RNA degradation as an attractive strategy for suppressing oncogenic ncRNAs through direct small-molecule recognition and provide a structural framework for optimizing RNA-binding ligands and expanding the scope of chemically induced RNA degradation.