Mechanistic and Structural Insights on Difluoromethyl-1,3,4-oxadiazole Inhibitors of HDAC6

Int J Mol Sci. 2024 May 28;25(11):5885. doi: 10.3390/ijms25115885.

Abstract

Histone deacetylase 6 (HDAC6) is increasingly recognized for its potential in targeted disease therapy. This study delves into the mechanistic and structural nuances of HDAC6 inhibition by difluoromethyl-1,3,4-oxadiazole (DFMO) derivatives, a class of non-hydroxamic inhibitors with remarkable selectivity and potency. Employing a combination of nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) kinetic experiments, comprehensive enzymatic characterizations, and X-ray crystallography, we dissect the intricate details of the DFMO-HDAC6 interaction dynamics. More specifically, we find that the chemical structure of a DMFO and the binding mode of its difluoroacetylhydrazide derivative are crucial in determining the predominant hydrolysis mechanism. Our findings provide additional insights into two different mechanisms of DFMO hydrolysis, thus contributing to a better understanding of the HDAC6 inhibition by oxadiazoles in disease modulation and therapeutic intervention.

Keywords: DFMO hydrolysis; LC-MS; NMR; X-ray crystallography; difluoroacetylhydrazide (DFAcH); difluoromethyl-1,3,4-oxadiazole (DFMO); enzyme kinetics; histone deacetylase 6 (HDAC6); non hydroxamic inhibitors.

MeSH terms

  • Crystallography, X-Ray
  • Histone Deacetylase 6* / antagonists & inhibitors
  • Histone Deacetylase 6* / chemistry
  • Histone Deacetylase 6* / metabolism
  • Histone Deacetylase Inhibitors* / chemistry
  • Histone Deacetylase Inhibitors* / pharmacology
  • Humans
  • Kinetics
  • Models, Molecular
  • Oxadiazoles* / chemistry
  • Oxadiazoles* / pharmacology
  • Protein Binding
  • Structure-Activity Relationship

Substances

  • Oxadiazoles
  • Histone Deacetylase 6
  • Histone Deacetylase Inhibitors
  • HDAC6 protein, human
  • 1,3,4-oxadiazole

Grants and funding

NMR experiments: carried out at the Department of Biotechnology and Biosciences, University of Milano-Bicocca, and X-ray crystallography experiments, carried out at Selvita S.A., Poland, were sponsored by Italfarmaco S.p.A.