Chemical probes identify a role for histone deacetylase 3 in Friedreich's ataxia gene silencing

Chem Biol. 2009 Sep 25;16(9):980-9. doi: 10.1016/j.chembiol.2009.07.010.

Abstract

We recently identified a class of pimelic diphenylamide histone deacetylase (HDAC) inhibitors that show promise as therapeutics in the neurodegenerative diseases Friedreich's ataxia (FRDA) and Huntington's disease. Here, we describe chemical approaches to identify the HDAC enzyme target of these inhibitors. Incubation of a trifunctional activity-based probe with a panel of class I and class II recombinant HDAC enzymes, followed by click chemistry addition of a fluorescent dye and gel electrophoresis, identifies HDAC3 as a unique high-affinity target of the probe. Photoaffinity labeling in a nuclear extract prepared from human lymphoblasts with the trifunctional probe, followed by biotin addition through click chemistry, streptavidin enrichment, and Western blotting also identifies HDAC3 as the preferred cellular target of the inhibitor. Additional inhibitors with different HDAC specificity profiles were synthesized, and results from transcription experiments in FRDA cells point to a unique role for HDAC3 in gene silencing in Friedreich's ataxia.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Drug Design
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology
  • Friedreich Ataxia / enzymology*
  • Friedreich Ataxia / genetics
  • Gene Silencing*
  • Histone Deacetylase 1 / antagonists & inhibitors
  • Histone Deacetylase 1 / metabolism
  • Histone Deacetylase 2 / antagonists & inhibitors
  • Histone Deacetylase 2 / metabolism
  • Histone Deacetylase Inhibitors / pharmacology
  • Histone Deacetylases / metabolism
  • Histone Deacetylases / physiology*
  • Humans
  • Iron-Binding Proteins / genetics
  • Iron-Binding Proteins / metabolism
  • Mice
  • Neuroprotective Agents / chemistry
  • Neuroprotective Agents / pharmacology
  • Photoaffinity Labels / chemistry
  • Pimelic Acids / chemistry
  • Pimelic Acids / pharmacology*
  • Recombinant Proteins / antagonists & inhibitors
  • Recombinant Proteins / metabolism

Substances

  • Enzyme Inhibitors
  • Histone Deacetylase Inhibitors
  • Iron-Binding Proteins
  • Neuroprotective Agents
  • Photoaffinity Labels
  • Pimelic Acids
  • Recombinant Proteins
  • frataxin
  • pimelic diphenylamide 106
  • HDAC1 protein, human
  • Histone Deacetylase 1
  • Histone Deacetylase 2
  • Histone Deacetylases
  • histone deacetylase 3