Discovery and Mechanistic Study of a Class of Protein Arginine Methylation Inhibitors

Abstract

Protein arginine methylation regulates multiple biological processes such as chromatin remodeling and RNA splicing. Malfunction of protein arginine methyltransferases (PRMTs) is correlated with many human diseases. Thus, small molecule inhibitors of protein arginine methylation are of great potential for therapeutic development. Herein, we report a type of compound that blocks PRMT1-mediated arginine methylation at micromolar potency through a unique mechanism. Most of the discovered compounds bear naphthalene and sulfonate groups and are structurally different from typical PRMT substrates, for example, histone H4 and glycine- and arginine-rich sequences. To elucidate the molecular basis of inhibition, we conducted a variety of kinetic and biophysical assays. The combined data reveal that this type of naphthyl-sulfo (NS) molecule directly targets the substrates but not PRMTs for the observed inhibition. We also found that suramin effectively inhibited PRMT1 activity. These findings about novel PRMT inhibitors and their unique inhibition mechanism provide a new way for chemical regulation of protein arginine methylation.

Pharmacophore-Based Virtual Screening and Biological Evaluation of Small Molecule Inhibitors for Protein Arginine Methylation

“…A9 and A36 bear certain similar pharmacophore features with the previously reported inhibitors AMI-1 and NS-1 that both target the substrate of PRMT1 rather than the enzyme to execute inhibitory effect 31 . Furthermore, the kinetic pattern of PRMT1 inhibition by A9 and A36 suggest that these compounds may compete with peptide substrate.…”

“…Thus, A36 targets substrate rather than the enzyme for the inhibition, in the same manner as certain previously reported arginine methylation inhibitors. 31 …”

“…36 The assays were carried out in 0.6 mL plastic tubes at 30 °C in a reaction volume of 30 µL. The reaction buffer contained 50 mM HEPES (pH=8.0), 10mM NaCl and 1 mM DTT.…”

Chemical Biology of Protein Arginine Modifications in Epigenetic Regulation

“…151 Notably, AMI-1 forms a complex with an H4 peptide substrate, most likely via bidentate electrostatic interactions between its sulfonate groups and the arginine guanidinium groups present in the peptide substrate, thereby blocking substrate access to the PRMTs. 151 …”

New insights regarding the regulation of chemotaxis by nucleotides, adenosine, and their receptors

“…Non-hydrolyzable analogs, such as ATPγS, can also help distinguish P1-and P2-mediated effects. Caution is required in using agents such as suramin, a P2 receptor inhibitor that also interacts with other signaling components (e.g., G-proteins [106] and protein arginine methyltransferase 1 [107]). Furthermore, because cells often express multiple P1/P2 receptor subtypes, one must employ drug concentrations that are appropriate for the receptors of interest.…”