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

Abstract

Protein arginine methyltransferases (PRMTs) are important therapeutic targets, playing a crucial role in the regulation of many cellular processes and being linked to many diseases. Yet, there is still much to be understood regarding their functions and the biological pathways in which they are involved, as well as on the structural requirements that could drive the development of selective modulators of PRMT activity. Here we report a deconstruction–reconstruction approach that, starting from a series of type I PRMT inhibitors previously identified by us, allowed for the identification of potent and selective inhibitors of PRMT4, which regardless of the low cell permeability show an evident reduction of arginine methylation levels in MCF7 cells and a marked reduction of proliferation. We also report crystal structures with various PRMTs supporting the observed specificity and selectivity.

Identification of a Protein Arginine Methyltransferase 7 (PRMT7)/Protein Arginine Methyltransferase 9 (PRMT9) Inhibitor

“…31 On the contrary, the study showed that increasing the linker length is detrimental for the inhibition of PRMT6 because the resulting compounds are forced to adopt an odd distorted U-shaped conformation that reduces the favorable binding interactions with the enzyme double-E loop clamp and the arginine substrate pocket. 31 Interestingly, we observed a different trend for the inhibitory activity against PRMT7, with the shorter compound (1a, EML 734) showing an IC 50 value of 0.32 μM and a certain selectivity compared to other tested PRMTs (SI values in the range 26−227; see Figure 2). This is consistent with the restrictive and narrow active site described for PRMT7.…”

“…Yet, we previously reported that, regardless of its low cell permeability, 1h is able to induce an evident reduction of PRMT4-catalyzed arginine methylation levels in MCF-7 cells and a marked reduction of proliferation. 31 Therefore, we resolved to investigate whether the compounds can reduce the cellular level of arginine methylation catalyzed by PRMT9. Note that when SF3B2 was characterized as the methylation substrate of PRMT9, a homemade methyl-specific antibody was developed to detect PRMT9catalyzed SF3B2 methylation site (R508), namely, SF3B2 R508me2s.…”

Virtual Special Issue: Epigenetics 2022

“…There is also a report of an orally bioavailable inhibitor of the WDR5-mixed lineage leukemia (MLL) protein–protein interaction, which prevents MLL histone methyl­ransferase activity . There are additional papers reporting inhibitors of PRMT5, PRMT4, and nicotin­amide N -methyl­transferase . Compounds that bind to the EED subunit of PRC2 and that act as allosteric inhibitors of PRC2 methyl­transferase activity are disclosed.…”

Conjugates of adenosine mimetics and arginine‐rich peptides serve as inhibitors and fluorescent probes but not as long‐lifetime photoluminescent probes for protein arginine methyltransferases

“…15,16 For the design of PRMT inhibitors, both the SAM-binding site as well as the protein substrate-binding site, and the connecting catalytic groove have been extensively surveyed. [17][18][19][20][21][22][23] Furthermore, the biligand-type inhibitors that represent transition state mimetics have been reported, primarily targeting PRMT4 (CARM1), but also PRMT1 or PRMT6. 24,25 The latter compounds (sometimes also termed bisubstrate inhibitors if SAM is considered as a substrate rather than the cofactor) were constructed by linking SAM via the 5 0 -position of the sugar moiety to the side-chain of the substrate arginine protruding toward the cofactor-binding site.…”

“…The kinetic studies with PRMT1 revealed that this enzyme binds its cofactor SAM and a protein substrate in an ordered sequential manner (sequential ordered Bi–Bi kinetic mechanism) to form a ternary complex prior to the methyl transfer (Figure 1). 15,16 For the design of PRMT inhibitors, both the SAM‐binding site as well as the protein substrate‐binding site, and the connecting catalytic groove have been extensively surveyed 17–23 . Furthermore, the biligand‐type inhibitors that represent transition state mimetics have been reported, primarily targeting PRMT4 (CARM1), but also PRMT1 or PRMT6 24,25 .…”