Defining the mechanism of action and enzymatic selectivity of psammaplin A against its epigenetic targets

J Med Chem. 2012 Feb 23;55(4):1731-50. doi: 10.1021/jm2016182. Epub 2012 Feb 9.


Psammaplin A (11c) is a marine metabolite previously reported to be a potent inhibitor of two classes of epigenetic enzymes: histone deacetylases and DNA methyltransferases. The design and synthesis of a focused library based on the psammaplin A core has been carried out to probe the molecular features of this molecule responsible for its activity. By direct in vitro assay of the free thiol generated upon reduction of the dimeric psammaplin scaffold, we have unambiguously demonstrated that 11c functions as a natural prodrug, with the reduced form being highly potent against HDAC1 in vitro (IC(50) 0.9 nM). Furthermore, we have shown it to have high isoform selectivity, being 360-fold selective for HDAC1 over HDAC6 and more than 1000-fold less potent against HDAC7 and HDAC8. SAR around our focused library revealed a number of features, most notably the oxime functionality to be important to this selectivity. Many of the compounds show significant cytotoxicity in A549, MCF7, and W138 cells, with the SAR of cytotoxicity correlating to HDAC inhibition. Furthermore, compound treatment causes upregulation of histone acetylation but little effect on tubulin acetylation. Finally, we have found no evidence for 11c functioning as a DNMT inhibitor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Antineoplastic Agents / chemical synthesis
  • Antineoplastic Agents / chemistry
  • Antineoplastic Agents / pharmacology*
  • Cell Line, Tumor
  • Crystallography, X-Ray
  • DNA (Cytosine-5-)-Methyltransferases / antagonists & inhibitors
  • Dimerization
  • Disulfides / chemical synthesis
  • Disulfides / chemistry
  • Disulfides / pharmacology*
  • Drug Screening Assays, Antitumor
  • Epigenesis, Genetic*
  • Histone Deacetylase Inhibitors / chemical synthesis
  • Histone Deacetylase Inhibitors / chemistry
  • Histone Deacetylase Inhibitors / pharmacology*
  • Histones / metabolism
  • Humans
  • Isoenzymes / antagonists & inhibitors
  • Models, Molecular
  • Prodrugs / chemical synthesis
  • Prodrugs / chemistry
  • Prodrugs / pharmacology*
  • Structure-Activity Relationship
  • Tubulin / metabolism
  • Tyrosine / analogs & derivatives*
  • Tyrosine / chemical synthesis
  • Tyrosine / chemistry
  • Tyrosine / pharmacology


  • Antineoplastic Agents
  • Disulfides
  • Histone Deacetylase Inhibitors
  • Histones
  • Isoenzymes
  • Prodrugs
  • Tubulin
  • psammaplin A
  • Tyrosine
  • DNA (Cytosine-5-)-Methyltransferases