Chemical probes identify a role for histone deacetylase 3 in Friedreich's ataxia gene silencing.
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.
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Chunping
C
Xu
Elisabetta
E
Soragni
C James
CJ
Chou
David
D
Herman
Heather L
HL
Plasterer
James R
JR
Rusche
Joel M
JM
Gottesfeld
D000818:Animals; D002460:Cell Line; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D005621:Friedreich Ataxia / Q000201:enzymology* / Q000235:genetics; D020868:Gene Silencing; D056284:Histone Deacetylase 1 / Q000037:antagonists & inhibitors / Q000378:metabolism; D056464:Histone Deacetylase 2 / Q000037:antagonists & inhibitors / Q000378:metabolism; D056572:Histone Deacetylase Inhibitors / Q000494:pharmacology; D006655:Histone Deacetylases / Q000378:metabolism / Q000502:physiology*; D006801:Humans; D033862:Iron-Binding Proteins / Q000235:genetics / Q000378:metabolism; D051379:Mice; D018696:Neuroprotective Agents / Q000737:chemistry / Q000494:pharmacology; D019920:Photoaffinity Labels / Q000737:chemistry; D010867:Pimelic Acids / Q000737:chemistry / Q000494:pharmacology*; D011994:Recombinant Proteins / Q000037:antagonists & inhibitors / Q000378:metabolism; D000096923:Frataxin; D000099186:Histone Deacetylase 3
D004791:Enzyme Inhibitors; D056284:Histone Deacetylase 1; D056464:Histone Deacetylase 2; D056572:Histone Deacetylase Inhibitors; D006655:Histone Deacetylases; D033862:Iron-Binding Proteins; D018696:Neuroprotective Agents; D019920:Photoaffinity Labels; D010867:Pimelic Acids; D011994:Recombinant Proteins; D000096923:Frataxin; D000099186:Histone Deacetylase 3; C535010:pimelic diphenylamide 106; C110550:HDAC1 protein, human