Histone deacetylase (HDAC) inhibitor kinetic rate constants correlate with cellular histone acetylation but not transcription and cell viability

J Biol Chem. 2013 Sep 13;288(37):26926-43. doi: 10.1074/jbc.M113.490706. Epub 2013 Jul 29.


Histone deacetylases (HDACs) are critical in the control of gene expression, and dysregulation of their activity has been implicated in a broad range of diseases, including cancer, cardiovascular, and neurological diseases. HDAC inhibitors (HDACi) employing different zinc chelating functionalities such as hydroxamic acids and benzamides have shown promising results in cancer therapy. Although it has also been suggested that HDACi with increased isozyme selectivity and potency may broaden their clinical utility and minimize side effects, the translation of this idea to the clinic remains to be investigated. Moreover, a detailed understanding of how HDACi with different pharmacological properties affect biological functions in vitro and in vivo is still missing. Here, we show that a panel of benzamide-containing HDACi are slow tight-binding inhibitors with long residence times unlike the hydroxamate-containing HDACi vorinostat and trichostatin-A. Characterization of changes in H2BK5 and H4K14 acetylation following HDACi treatment in the neuroblastoma cell line SH-SY5Y revealed that the timing and magnitude of histone acetylation mirrored both the association and dissociation kinetic rates of the inhibitors. In contrast, cell viability and microarray gene expression analysis indicated that cell death induction and changes in transcriptional regulation do not correlate with the dissociation kinetic rates of the HDACi. Therefore, our study suggests that determining how the selective and kinetic inhibition properties of HDACi affect cell function will help to evaluate their therapeutic utility.

Keywords: Binding Kinetics; Cell Cycle; Cell Death; Crystallography; Gene Expression; Histone Deacetylase; Histone Deacetylase Inhibitors; Histone Modification.

Publication types

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

MeSH terms

  • Acetylation
  • Benzamides / chemistry
  • Binding, Competitive
  • Cell Line, Tumor
  • Cell Survival / drug effects
  • Gene Expression Regulation, Enzymologic*
  • Gene Expression Regulation, Neoplastic*
  • Histone Deacetylase Inhibitors / chemistry*
  • Histones / chemistry*
  • Humans
  • Hydroxamic Acids / chemistry
  • Inhibitory Concentration 50
  • Kinetics
  • Oligonucleotide Array Sequence Analysis
  • Protein Binding
  • Pyridines / chemistry
  • Transcription, Genetic
  • Vorinostat


  • Benzamides
  • Histone Deacetylase Inhibitors
  • Histones
  • Hydroxamic Acids
  • Pyridines
  • entinostat
  • trichostatin A
  • Vorinostat

Associated data

  • PDB/4LXZ
  • PDB/4LY1