Structure

Overall Secondary Structure

Due to the composition of its secondary structure, KMT is an alpha-beta protein . The helical composition includes 3 , with two residing in the SET domain and one in the C-terminal domain. The alpha helices in the SET domain are two turns while the C-terminal helix is by far the largest with 4 turns. There are also 2 in the SET domain which are each one turn. There are 21 total which reside in the N-terminal domain and the SET domain. The beta strands are primarily anti-parallel and multiple antiparallel strands are connected by and beta turns.

The of the protein is essential for the binding and stabilization of the cofactor. The

Inhibitors

Sinefungin

Sinefungin is a potent methyltransferase inhibitor that is a natural nucleoside isolated from the "Streptomyces" species ^[1]. Also referred to as adenosyl-ornithine, it is the delta (5’ adenosyl) derivative of ornithine and a structural analog of S-adenosylmethionine. Sinefungin is more stable bound in the active site than SAM due to the ability to create two additional hydrogen bonds to its amine group that are not possible with SAM’s sulfur. Sinefungin has been used experimentally to inhibit the SET 7/9 protein on peritoneal fibrosis in mice and in human peritoneal mesothelial cells ^[2]. SET 7/9 is involved in peritoneal fibrosis because it mono-methylates H3K4, which activates the transcription of fibrosis related genes. The administration of Sinefungin to mice in vitro resulted in decreased levels of methylated H3K4 (H3K4me1) protein, as well as suppressed peritoneal cell density and thickening. The decreased levels of H3K4me1 suggest that the methylation of H3K4 was inhibited by Sinefungin, as well as that inhibiting SET7/9 ameliorates peritoneal fibrosis.

Cyproheptadine

Another inhibitor of SET 7/9 is cyproheptadine, a clinically-approved anti-allergy drug that was originally developed as a serotonin and histimine antagonist. Unlike Sinefungin, it is competitive with the peptide substrates as it binds to the peptide-binding site. The nitrogen of the methylpiperdine ring of cyproheptadine forms a hydrogen bond with Thr286 as well as hydrophobic and van der Waals interactions with the residues surrounding its binding site ^[3]. The binding of cyproheptadine to the catalytic site causes conformational changes of residue Tyr337, an important residue for the formation of the lysine access channel. This movement subsequently causes a conformational change of the beta hairpin, residues 337-349. This movement ultimately generates a large hole adjacent to the lysine access channel, as well as a shift of the C-terminal helix. With the revelation of its inhibitory effects on SET7/9, cyproheptadine was used in vitro to treat breast cancer cells (MCF7 cells). SET 7/9's non-histone activities include the metylation of estrogen receptor alpha (ERa), a nuclear receptor and a transcription factor responsible for estrogen-responsive gene regulation. The methylation of ERa via SET 7/9 stabilizes it and is necessary for the activation of ERa transcriptional activity. The expression and transcriptional activity of ERa is involved in the carcinogenesis of 70% of breast cancers, making it a major target for hormone therapy. Researchers found that treating the MCF7 cells with cyproheptadine decreased ERa' expression and transcriptional activity which therefore inhibited the estrogen-dependent cell growth. These findings suggest that cyproheptadine could possibly be repurposed to breast cancer therapy in the future.