Investigation of a squaramide motif as a bioisostere of the amino-acid group of S-adenosyl-L-methionine and its functional impact on RNA methylation
Jiajin Du, Batoul Mahcene, Valerii Martynov, Elisa Frezza, Christelle Vasnier, Luc Ponchon, Dylan Coelho, Frédéric Bonhomme, Emmanuelle Braud, Mélanie Ethève‐Quelquejeu, Bruno Sargueil
Abstract
Methyltransferases (MTases) are enzymes that methylate biomolecules like proteins, DNA, RNA, lipids, and small molecules, mostly using S-adenosyl-L-methionine (SAM) as a methyl donor. MTases have emerged as promising drug targets, and SAM analogues are widely employed to investigate their involvement in diseases and to develop effective drug therapies. We designed and synthesized stable SAM analogues with a squaramide moiety mimicking the methionine side chain. These compounds were tested on the two human m⁶A RNA MTases METTL3/14 and METTL16. While these SAM analogues failed to support catalytic activity, they exhibited potent inhibitory effects on the METTL3/14 activity. Surprisingly, some of these compounds demonstrated remarkable potency (KI = 3 nM) and specificity, likely attributed to the unique properties of the squaramide motif. Docking studies showed they bind METTL3/14 cofactor pocket similarly to SAM, allowing us to make new hypothesis on the catalytic mechanism. Our synthetic method expands the structural diversity of SAM analogues, providing a foundation for developing selective RNA MTase inhibitors. SAM-dependent methyltransferases (MTases) are crucial enzymes involved in various biological processes and are considered promising drug targets. Here, the authors synthesize SAM analogues with a squaramide moiety mimicking the methionine side chain, demonstrating potent and specific inhibitory effects on RNA MTase METTL3/14 activity.