Discovery of a First-in-Class Inhibitor of the PRMT5–Substrate Adaptor Interaction

Abstract

PRMT5 and its substrate adaptor proteins (SAPs), pICln and Riok1, are synthetic lethal dependencies in MTAP-deleted cancer cells. SAPs share a conserved PRMT5 binding motif (PBM) which mediates binding to a surface of PRMT5 distal to the catalytic site. This interaction is required for methylation of several PRMT5 substrates, including histone and spliceosome complexes. We screened for small molecule inhibitors of the PRMT5–PBM interaction and validated a compound series which binds to the PRMT5–PBM interface and directly inhibits binding of SAPs. Mode of action studies revealed the formation of a covalent bond between a halogenated pyridazinone group and cysteine 278 of PRMT5. Optimization of the starting hit produced a lead compound, BRD0639, which engages the target in cells, disrupts PRMT5–RIOK1 complexes, and reduces substrate methylation. BRD0639 is a first-in-class PBM-competitive inhibitor that can support studies of PBM-dependent PRMT5 activities and the development of novel PRMT5 inhibitors that selectively target these functions.

Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction–Reconstruction and Fragment-Growing Approach

“…Also, viral proteins from several viruses are methylated by PRMTs, − including SARS-CoV-2 nucleocapsid (N) protein, the methylation of which at residues R95 and R177 is crucial for viral replication . Indeed, over the past 15 years the medicinal chemistry community has paid a growing attention to PRMTs, ,,− in particular to PRMT5 (with a few inhibitors in clinical trials) ,− and to type I enzymes (both pan-type I ,− and selective ,− ).…”

The Influence of Arginine Methylation in Immunity and Inflammation

“…This inhibitor was shown to effectively outcompete binding between PRMT5 and RIOK1, inhibiting the methylation of certain PRMT5 substrates dependent on RIOK1 interaction. 135 A new potent and selective PRMT5 inhibitor that binds to the MTA-bound PRMT5 complex has also been developed. MRTX1719 has been shown to inhibit PRMT5 activity exclusively in MTAP negative cells.…”

Structure-Aided Design, Synthesis, and Biological Evaluation of Potent and Selective Non-Nucleoside Inhibitors Targeting Protein Arginine Methyltransferase 5

“…PRMT5 consists of two binding pockets in the SAM-dependent methyltransferase domain, including a SAM binding pocket and a substrate peptide binding pocket, which provide two options for the development of PRMT5 inhibitors. Indeed, many efforts have been made to discover PRMT5 inhibitors by targeting one of these two pockets. − As shown in Figure , compound 2 ( EPZ015666 ) is the first reported highly potent and orally bioavailable PRMT5 inhibitor, with an IC 50 of 22 nM in a biochemical assay . Kinetic experiments showed that it was competitive with the peptide substrate and uncompetitive with SAM.…”

“…Accordingly, synthetic lethal inhibitors of the PRMT5 . MTA complex were discovered for the treatment of MTAP-deleted cancers, providing an option for therapeutic intervention. ,− …”