Mutagenesis studies of the 14 Å internal cavity of histone deacetylase 1: insights toward the acetate-escape hypothesis and selective inhibitor design

J Med Chem. 2014 Feb 13;57(3):642-50. doi: 10.1021/jm401837e. Epub 2014 Jan 27.

Abstract

Histone deacetylase (HDAC) proteins are promising targets for cancer treatment, as shown by the approval of two HDAC inhibitors for the treatment of cutaneous T-cell lymphoma. HDAC1 in particular has been linked to cell growth and cell cycle regulation and is therefore an attractive target for anticancer drugs. The HDAC1 active site contains a hydrophobic 11 Å active-site channel, with a 14 Å internal cavity at the bottom of the active site. Several computational and biochemical studies have proposed an acetate-escape hypothesis where the acetate byproduct of the deacetylation reaction escapes via the 14 Å internal cavity. Selective HDAC inhibitors that bind to the 14 Å cavity have also been created. To understand the influence of amino acids lining the HDAC1 14 Å cavity in acetate escape and inhibitor binding, we used mutagenesis coupled with acetate competition assays. The results indicate that amino acids lining the 14 Å cavity are critical for catalytic activity and acetate competition, confirming the role of the cavity in acetate escape. In addition, these mutagenesis studies will aid in HDAC1-inhibitor design that exploits the 14 Å cavity.

Publication types

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

MeSH terms

  • Acetates / chemistry*
  • Amino Acids / chemistry
  • Antineoplastic Agents / chemistry*
  • Catalytic Domain
  • Depsipeptides / chemistry
  • Drug Design
  • Histone Deacetylase 1 / chemistry*
  • Histone Deacetylase 1 / genetics
  • Histone Deacetylase Inhibitors / chemistry*
  • Humans
  • Hydroxamic Acids / chemistry
  • Jurkat Cells
  • Molecular Docking Simulation
  • Mutation
  • Vorinostat

Substances

  • Acetates
  • Amino Acids
  • Antineoplastic Agents
  • Depsipeptides
  • Histone Deacetylase Inhibitors
  • Hydroxamic Acids
  • Vorinostat
  • romidepsin
  • Histone Deacetylase 1