Mechanistically Defined Epoxide- and Aziridine-2-carboxamide Electrophiles Enable Stereoselective Covalent RNA Modulation

ABSTRACT RNA remains a largely untapped target for covalent small-molecule intervention due to the lack of electrophiles with predictable reactivity and stability in biological settings. Here, a mechanistically defined and tunable class of epoxide- and aziridine-2-carboxamide electrophiles that enable structure-guided covalent targeting of RNA is described. These warheads arise from an unexpected hydrolytic rearrangement of 3-chloropivalamide precursors under physiological conditions and selectively react with guanine N7, with reactivity and stability controlled by substitution pattern, linkage chemistry, and stereochemistry. Application to two distinct RNA targets demonstrates generality: epoxide- and aziridine-based ligands covalently modify pathogenic r(CUG) exp repeat RNA and disrupt RNA–protein interactions in vitro and in cells, while structure-guided placement on a flavin scaffold yields stereoselective covalent modulators of the flavin mononucleotide (FMN) riboswitch with validated reaction site and cellular activity. Together, this work establishes epoxide- and aziridine-2-carboxamides as a versatile platform for covalent RNA targeting and provides a general framework for the rational design of stereochemically controlled RNA-reactive small molecules.