Chemical Proteomic Discovery of Isotype-Selective Covalent Inhibitors of the RNA Methyltransferase NSUN2.

Abstract

5-Methylcytosine (m5 C) is an RNA modification prevalent on tRNAs, where it can protect tRNAs from endonucleolytic cleavage to maintain protein synthesis. The NSUN family (NSUN1-7 in humans) of RNA methyltransferases are capable of installing the methyl group onto the C5 position of cytosines in RNA. NSUNs are implicated in a wide range of (patho)physiological processes, but selective and cell-active inhibitors of these enzymes are lacking. Here, we use cysteine-directed activity-based protein profiling (ABPP) to discover azetidine acrylamides that act as stereoselective covalent inhibitors of human NSUN2. Despite targeting a conserved catalytic cysteine in the NSUN family, the NSUN2 inhibitors show negligible cross-reactivity with other human NSUNs and exhibit good proteome-wide selectivity. We verify that the azetidine acrylamides inhibit the catalytic activity of recombinant NSUN2, but not NSUN6, and demonstrate that these compounds stereoselectively disrupt NSUN2-tRNA interactions in cancer cells, leading to a global reduction in tRNA m5 C content. Our findings thus highlight the potential to create isotype-selective and cell-active inhibitors of NSUN2 with covalent chemistry targeting a conserved catalytic cysteine.

• Authors: Yongfeng Tao, Jan G Felber, Zhongyu Zou, Evert Njomen, Jarrett R Remsberg, Daisuke Ogasawara, Chang Ye, Bruno Melillo, Stuart L Schreiber, Chuan He, David Remillard, Benjamin F Cravatt
• Journal: Angewandte Chemie (International ed. in English) (Angew Chem Int Ed Engl) Pg. e202311924 (Nov 01 2023) ISSN: 1521-3773 [Electronic] Germany
• PMID: 37909922 (Publication Type: Journal Article)
• Copyright: © 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.