Synthesis and Biological Evaluation of Tripartin, a Putative KDM4 Natural Product Inhibitor, and 1‐Dichloromethylinden‐1‐ol Analogues

Abstract

The natural product tripartin has been reported to inhibit the N-methyl-lysine histone demethylase KDM4A. A synthesis of tripartin starting from 3,5-dimethoxyphenylacrylic acid was developed, and the enantiomers were separated by chiral HPLC. We observed that both tripartin enantiomers manifested an apparent increase in H3K9me3 levels when dosed in cells, as measured by western blot analysis. Thus, there is no enantiomeric discrimination toward this natural product in terms of its effects on cellular histone methylation status. Interestingly, tripartin did not inhibit isolated KDM4A-E under our assay conditions (IC >100 μm). Tripartin analogues with a dichloromethylcarbinol group derived from the indanone scaffold were synthesized and found to be inactive against isolated recombinant KDM4 enzymes and in cell-based assays. Although the precise cellular mode of action of tripartin is unclear, our evidence suggests that it may affect histone methylation status via a mechanism other than direct inhibition of the KDM4 histone demethylases.

A New Family of Jumonji C Domain-Containing KDM Inhibitors Inspired by Natural Product Purpurogallin

“…Compound QC6352 (7) was reported to inhibit KDM4 with high efficacy in breast and colon cancer PDX models (Chen et al, 2017). Tripartin (8), the first natural histone lysine demethylase inhibitor (Kim et al, 2013;Guillade et al, 2018), has been recently re-evaluated and shown to cause substantial increase in H3K9me3 levels in HCT-116 cells by Western blot analysis, but either no inhibition or very mild inhibition when tested at 100 µM against isolated KDM4A, B, C, D, or E under standard assay conditions (Guillade et al, 2018).…”

The Clinically Used Iron Chelator Deferasirox Is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases

“…14 As JumonjiC KDMs use molecular oxygen as oxidizing agent for the demethylation reaction, a role in cellular oxygen sensing has also been discussed, e. g. for the subtype KDM6A. 15 JmjC histone demethylases have emerged as promising drug targets, 1,[16][17][18][19][20] with inhibitor discovery programs being reported by us [21][22][23][24][25][26][27] and others, [28][29][30][31][32][33][34][35] as recently reviewed. 17,19,[36][37][38][39][40] The majority of reported JmjC KDM inhibitors function by active site metal chelation and competitive displacement of the co-substrate 2OG.…”

Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer

“…Importantly, plenty of natural compounds are known to interfere with epigenetic processes; for example, flavonoids are compounds found in black raspberry (and many other plants) which inhibit DNA methyltransferase 1 (DNMT1) activity and enhance the expression of tumor suppressor genes ( Wang et al, 2013 ). Nevertheless, although there are reports about natural molecules that could interfere with KDM4 subfamily activity, no direct natural inhibitors are known so far ( Guillade et al, 2018 ).…”

“…Tripartin, a compound produced by a bacteria found in dung beetles, is the only natural inhibitor reported for the KDM4 subfamily ( Kim et al, 2013 ). However, another study showed that tripartin and its analogs increased H3K9me3 levels but did not directly interact with KDM4 proteins, suggesting that their mechanisms of action could involve other enzymes ( Guillade et al, 2018 ).…”