Mechanistic Insights into Harmine-Mediated Inhibition of Human DNA Methyltransferases and Prostate Cancer Cell Growth

Abstract

Mammalian DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B, are key DNA methylation enzymes and play important roles in gene expression regulation. Dysregulation of DNMTs is linked to various diseases and carcinogenesis, and therefore except for the two approved anticancer azanucleoside drugs, various non-nucleoside DNMT inhibitors have been identified and reported. However, the underlying mechanisms for the inhibitory activity of these non-nucleoside inhibitors still remain largely unknown. Here, we systematically tested and compared the inhibition activities of five non-nucleoside inhibitors toward the three human DNMTs. We found that harmine and nanaomycin A blocked the methyltransferase activity of DNMT3A and DNMT3B more efficiently than resveratrol, EGCG, and RG108. We further determined the crystal structure of harmine in complex with the catalytic domain of the DNMT3B-DNMT3L tetramer revealing that harmine binds at the adenine cavity of the SAM-binding pocket in DNMT3B. Our kinetics assays confirm that harmine competes with SAM to competitively inhibit DNMT3B-3L activity with a K i of 6.6 μM. Cell-based studies further show that harmine treatment inhibits castration-resistant prostate cancer cell (CRPC) proliferation with an IC50 of ∼14 μM. The CPRC cells treated with harmine resulted in reactivating silenced hypermethylated genes compared to the untreated cells, and harmine cooperated with an androgen antagonist, bicalutamide, to effectively inhibit the proliferation of CRPC cells. Our study thus reveals, for the first time, the inhibitory mechanism of harmine on DNMTs and highlights new strategies for developing novel DNMT inhibitors for cancer treatment.

Integrative analyses of DNA methylase expression and related immune landscape in Prostate Cancer

“…As de novo methyltransferases, DNMT3B are more biased towards methylating unmethylated CpG dinucleotides 26 . Studies have shown that when the adenine cavity of the SAM-binding pocket in DNMT3B is bound, its enzyme activity decreases, thus limiting the proliferation of prostate cancer 27 . The remaining DNA methyltransferases are generally thought to lack cytosine methyltransferase activity, although DNMT3L can increase the binding capacity of DNMT3B to the methyl donor S-adenosyl-L-methionine (SAM) to increase their activity 28 .…”

Research progress on the antitumor effects of harmine

“…found that harmine inhibited prostate cancer cell growth by blocking mammalian DNMT activity. Harmine competitively binds to the SAM-binding site of the adenine domain in DNMT3B, thereby inhibiting the activity of the DNMT3B-3L complex and limiting prostate cancer cell proliferation ( 41 ). Therefore, harmine can serve as an important cell cycle regulator that inhibits tumor cell proliferation and exhibits antitumor activity.…”