A Potent, Selective and Cell‐Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3)

Abstract

] These authors contributed equally to this work.Supporting information for this article (including detailed synthetic procedures and compound characterization as well as methods for scaffold hopping, crystallization, structure determination, bio-chemical assays, SPR, ITC, PRMT3 InCELL Hunter assay, cellular PRMT3 assay, cell viability assay, and mouse PK studies) is available on the WWW under http://dx

Chemical Biology of Protein Arginine Modifications in Epigenetic Regulation

“…165 Optimization of the initial hit compounds revealed inhibitor 39 . 166 Notably, this inhibitor is noncompetitive with respect to both SAM and the peptide substrate and binds to an allosteric site present in PRMT3 (Figure 41). This compound is highly selective for PRMT3, and detailed structural analyses showed that 39 binds to an allosteric pocket at the base of the dimerization arm between two PRMT3 subunits.…”

“…It is thought that 39 induces conformational constraints on this α-helix that prevent formation of a catalytically competent state. 166 The isoquinoline moiety of 39 forms a buried hydrogen bond with T466, the urea group forms hydrogen bonds with the side chains of E422 and R39, and the pyrrolidine amide pushes against the α-helix (Figure 41). To test the in vivo efficacy, 39 was evaluated for target engagement using an InCELL Hunter assay.…”

Inhibitors of Protein Methyltransferases as Chemical Tools

“…Besides the SAM/substrate-competitive inhibitors, a distinct set of PMT inhibitors were developed to target the allosteric sites of PMTs that are less obvious but essential for enzyme catalysis [46, 47]. It has been well documented that the methyltransferase activities of certain PMTs depend upon the participation of the residues remote from their catalytic sites.…”

“…Such examples include the dimerization arm of PRMT3 or the formation of a higher-order complex with their partner proteins ( e.g. MLL1 and EZH2) [37, 46, 47]. Dimerization of PRMT3 occurs through extensive interactions between the outer surface of the SAM-binding domain of one PRMT3 subunit and the three-helix arm extending from β-barrel domain of the neighboring PRMT3 subunit [46].…”

“…MLL1 and EZH2) [37, 46, 47]. Dimerization of PRMT3 occurs through extensive interactions between the outer surface of the SAM-binding domain of one PRMT3 subunit and the three-helix arm extending from β-barrel domain of the neighboring PRMT3 subunit [46]. A cavity at the base of the dimerization arm, which is more than 15 Å away from PRMT3’s catalytic site, was determined to be the target site of SGC707 (Figure 4), a PRMT3-specific inhibitor [46].…”