A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors.

Publication Type:

Journal Article


Acta Pharm Sin B, Volume 13, Issue 12, p.4893-4905 (2023)


<p>Protein arginine methyltransferases (PRMTs) are attractive targets for developing therapeutic agents, but selective PRMT inhibitors targeting the cofactor SAM binding site are limited. Herein, we report the discovery of a noncanonical but less polar SAH surrogate YD1113 by replacing the benzyl guanidine of a pan-PRMT inhibitor with a benzyl urea, potently and selectively inhibiting PRMT3/4/5. Importantly, crystal structures reveal that the benzyl urea moiety of YD1113 induces a unique and novel hydrophobic binding pocket in PRMT3/4, providing a structural basis for the selectivity. In addition, YD1113 can be modified by introducing a substrate mimic to form a &quot;T-shaped&quot; bisubstrate analogue YD1290 to engage both the SAM and substrate binding pockets, exhibiting potent and selective inhibition to type I PRMTs (IC&nbsp;&lt;&nbsp;5&nbsp;nmol/L). In summary, we demonstrated the promise of YD1113 as a general SAH mimic to build potent and selective PRMT inhibitors.</p>

PRMT3-II710 (PDB ID: 8G2F), PRMT3-YD1113 (PDB ID: 8G2G), PRMT4-YD1113 (PDB ID: 8G2H), and PRMT4-YD1290 (PDB ID: 8G2I)