Chemoproteomics reveals time-dependent binding of histone deacetylase inhibitors to endogenous repressor complexes

Area of Science:

• Biochemistry
• Molecular Biology
• Pharmacology

Background:

• Class I histone deacetylases (HDACs) are key targets for cancer and inflammation therapies.
• HDAC selectivity is challenging due to their regulation within large repressor complexes.
• Aminobenzamide inhibitors show potential for isoform and protein complex selectivity.

Purpose of the Study:

• To develop a chemoproteomics strategy to determine time-dependent inhibitor binding to endogenous HDACs and their complexes.
• To investigate the kinetic binding rates of aminobenzamide inhibitors to HDAC complexes.
• To compare the binding kinetics of aminobenzamides with other inhibitor classes, like hydroxamates.

Main Methods:

• Utilized a chemoproteomics approach to study inhibitor binding kinetics.
• Determined time-dependent association and dissociation rates for endogenous HDAC repressor complexes.
• Investigated the impact of inhibitor binding on cellular acetylation levels and isolated protein complexes.

Main Results:

• Aminobenzamide inhibitors demonstrated slow binding kinetics, dependent on their association within protein complexes.
• This binding behavior contrasts with hydroxamate-type inhibitors.
• Observed delayed cellular responses in histone acetylation and limited inhibition of HDAC activity in isolated Sin3 complexes.

Conclusions:

• Aminobenzamide inhibitor selectivity is intrinsically linked to their complex-dependent binding kinetics.
• This provides a mechanistic understanding for achieving isoform and complex-specific inhibition of Class I HDACs.
• Findings support the development of novel therapeutic strategies targeting HDACs in oncology and inflammation.