Subtype selective substrates for histone deacetylases

J Med Chem. 2004 Oct 7;47(21):5235-43. doi: 10.1021/jm0497592.


To probe the steric requirements for deacylation, we synthesized lysine-derived small molecule substrates and examined structure-reactivity relationships with various histone deacetylases. Rat liver, human HeLa, and human recombinant class I and II histone deacetylases (HDACs) as well as human recombinant NAD(+)-dependent SIRT1 (class III enzyme) were used in these studies. A benzyloxycarbonyl substituent on the alpha-amino group yielded the highest conversion rates. Replacing the epsilon-acetyl group with larger lipophilic acyl substituents led to a pronounced decrease in conversion by class I and II enzymes; the class III enzyme displayed a greater tolerance. Incubations with recombinant FLAG-tagged human HDACs 1, 3, and 6 showed a distinct subtype selectivity among small molecule substrates. The subtype selectivity of HDAC inhibitors could be predicted with these substrates and an easily obtainable mixture of HDAC subtypes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • HeLa Cells
  • Histone Deacetylases / metabolism*
  • Humans
  • In Vitro Techniques
  • Liver / drug effects
  • Liver / enzymology
  • Lysine / analogs & derivatives*
  • Lysine / chemical synthesis*
  • Lysine / pharmacokinetics
  • Rats
  • Recombinant Proteins / metabolism
  • Sirtuin 1
  • Sirtuins / metabolism
  • Stereoisomerism
  • Structure-Activity Relationship
  • Substrate Specificity


  • Recombinant Proteins
  • SIRT1 protein, human
  • Sirtuin 1
  • Sirtuins
  • Histone Deacetylases
  • Lysine