METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes

• Published in: ChemMedChem Vol. 16; no. 19; pp. 3035 - 3043
• Main Authors: Moroz‐Omori, Elena V., Huang, Danzhi, Kumar Bedi, Rajiv, Cheriyamkunnel, Sherry J., Bochenkova, Elena, Dolbois, Aymeric, Rzeczkowski, Maciej D., Li, Yaozong, Wiedmer, Lars, Caflisch, Amedeo
• Format: Journal Article
• Language: English
• Published: WEINHEIM Wiley 06.10.2021; Wiley Subscription Services, Inc; John Wiley and Sons Inc
• Subjects: Caco-2 Cells; Cell lines; Chemistry, Medicinal; Dose-Response Relationship, Drug; Enantiomers; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; epitranscriptomics; Humans; leukemia; Life Sciences & Biomedicine; m6A; Methylase; Methylation; Methyltransferases - antagonists & inhibitors; Methyltransferases - metabolism; METTL3; Molecular Structure; mRNA; N6-methyladenosine; Pharmacology & Pharmacy; RNA methyltransferase inhibitor; RNA modification; RNA, Small Interfering - chemistry; RNA, Small Interfering - pharmacology; Science & Technology; Selectivity; Structure-Activity Relationship; leukemia; METHYLATION; MESSENGER-RNA; epitranscriptomics; METTL3; m6A; RNA methyltransferase inhibitor; EXPRESSION
• ISSN: 1860-7179; 1860-7187
• DOI: 10.1002/cmdc.202100291

The methylase METTL3 is the writer enzyme of the N6‐methyladenosine (m6A) modification of RNA. Using a structure‐based drug discovery approach, we identified a METTL3 inhibitor with potency in a biochemical assay of 280 nM, while its enantiomer is 100 times less active. We observed a dose‐dependent reduction in the m6A methylation level of mRNA in several cell lines treated with the inhibitor already after 16 h of treatment, which lasted for at least 6 days. Importantly, the prolonged incubation (up to 6 days) with the METTL3 inhibitor did not alter levels of other RNA modifications (i. e., m1A, m6Am, m7G), suggesting selectivity of the developed compound towards other RNA methyltransferases. Writer's block: We developed and characterized a small‐molecule inhibitor of m6A writer METTL3 by protein crystallography, biochemical and cellular assays. It shows high‐nanomolar potency in the biochemical assay, good selectivity against a panel of protein methyltransferases and kinases, and it reduced m6A/A ratio in mRNAs of different cell lines. In addition, we confirmed the selectivity of our compound towards other RNA methyltransferases in living cells.