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

ChemMedChem. 2018 Sep 19;13(18):1949-1956. doi: 10.1002/cmdc.201800377. Epub 2018 Aug 21.


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 (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.

Keywords: epigenetic modulators; lysine demethylase inhibition; natural products; total synthesis; tripartin.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Products / chemical synthesis
  • Biological Products / chemistry
  • Biological Products / pharmacology*
  • Dose-Response Relationship, Drug
  • Enzyme Inhibitors / chemical synthesis
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology*
  • HCT116 Cells
  • Humans
  • Hydrocarbons, Chlorinated / chemical synthesis
  • Hydrocarbons, Chlorinated / chemistry
  • Hydrocarbons, Chlorinated / pharmacology*
  • Indans / chemical synthesis
  • Indans / chemistry
  • Indans / pharmacology*
  • Jumonji Domain-Containing Histone Demethylases
  • Molecular Structure
  • Structure-Activity Relationship
  • Tumor Cells, Cultured


  • Biological Products
  • Enzyme Inhibitors
  • Hydrocarbons, Chlorinated
  • Indans
  • tripartin
  • Jumonji Domain-Containing Histone Demethylases
  • KDM4A protein, human