Synthesis and biological evaluation of tripartin, a putative KDM4 natural product inhibitor, and 1-dichloromethylinden-1-ol analogues

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 the H3K9me3 levels when dosed in cells, as measured by Western blot analysis. Thus, there is no enantiomeric discrimination towards 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 (IC50 > 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.