Oxime amides as a novel zinc binding group in histone deacetylase inhibitors: synthesis, biological activity, and computational evaluation

J Med Chem. 2011 Apr 14;54(7):2165-82. doi: 10.1021/jm101373a. Epub 2011 Mar 18.

Abstract

Several oxime containing molecules, characterized by a SAHA-like structure, were explored to select a potentially new biasing binding element for the zinc in HDAC catalytic site. All compounds were evaluated for their in vitro inhibitory activity against the 11 human HDACs isoforms. After identification of a "hit" molecule, a programmed variation at the cap group and at the linker was carried out in order to increase HDAC inhibition and/or paralogue selectivity. Some of the new derivatives showed increased activity against a number of HDAC isoforms, even if their overall activity range is still far from the inhibition values reported for SAHA. Moreover, different from what was reported for their hydroxamic acid analogues the new α-oxime amide derivatives do not select between class I and class II HDACs; rather they target specific isoforms in each class. These somehow contradictory results were finally rationalized by a computational assisted SAR, which gave us the chance to understand how the oxime derivatives interact with the catalytic site and justify the observed activity profile.

MeSH terms

  • Amides / chemical synthesis
  • Amides / chemistry*
  • Amides / metabolism
  • Amides / pharmacology*
  • Catalytic Domain
  • Histone Deacetylase Inhibitors / chemical synthesis
  • Histone Deacetylase Inhibitors / chemistry
  • Histone Deacetylase Inhibitors / metabolism
  • Histone Deacetylase Inhibitors / pharmacology
  • Histone Deacetylases / chemistry*
  • Histone Deacetylases / metabolism*
  • Humans
  • Inhibitory Concentration 50
  • Isoenzymes / chemistry
  • Isoenzymes / metabolism
  • Molecular Dynamics Simulation
  • Oximes / chemistry*
  • Quantum Theory
  • Structure-Activity Relationship
  • Zinc / metabolism*

Substances

  • Amides
  • Histone Deacetylase Inhibitors
  • Isoenzymes
  • Oximes
  • Histone Deacetylases
  • Zinc