Inhibition of Zinc-Dependent Histone Deacetylases with a Chemically Triggered Electrophile

Abstract

Unbiased binding assays involving small-molecule microarrays were used to identify compounds that display unique patterns of selectivity among members of the zinc-dependent histone deacetylase family of enzymes. A novel, hydroxyquinoline-containing compound, BRD4354, was shown to preferentially inhibit activity of HDAC5 and HDAC9 in vitro. Inhibition of deacetylase activity appears to be time-dependent and reversible. Mechanistic studies suggest that the compound undergoes zinc-catalyzed decomposition to an ortho-quinone methide, which covalently modifies nucleophilic cysteines within the proteins. The covalent nature of the compound-enzyme interaction has been demonstrated in experiments with biotinylated probe compound and with electrospray ionization-mass spectrometry.

Zinc as a Gatekeeper of Immune Function

“…Zinc supplementation augmented TGF-β-induced Smad 2/3 signaling and thereby FoxP3 expression [ 168 ]. Proteasomal degradation of FoxP3 involves the histone deacetylase Sirtuin-1 (Sirt1), which is inhibited by zinc as was shown for other histone deacetylases as well [ 72 , 169 ]. Another important, zinc dependent molecule in Treg cell development is interferon regulatory factor (IRF)-1, as it is able to repress FoxP3 activity [ 170 ].…”

Histone deacetylase (HDAC) 9: versatile biological functions and emerging roles in human cancer

“…The development of selective HDAC9 inhibitors has been particularly challenging due to the high degree of sequence homology exhibited by zinc-dependent HDACs. Boskovic et al [143] identified a novel, hydroxyquinolinecontaining compound, BRD4354, that is capable of a preferential reversible and time-dependent inhibition of HDAC5 and HDAC9. However, there are currently no reports detailing the in vivo inhibitory efficacy of this compound, and no natural substrates of class IIa HDACs, including HDAC9, have been identified yet [144].…”

Fragment-based covalent ligand discovery

“…For instance, the incorporation of masked thiol-reactive fragments into commonly used cysteinedirecting library that could be triggered under precisely defined physiological conditions has recently been shown as a viable option to diversify the cysteine-directing library. 118,119 We expect that further expansion of the covalent fragment chemical space will occur as the efforts move towards targeting alternative residues beyond cysteines, as we discussed above. Projecting forward, the identification of covalent fragments modifying those protein nucleophiles (lysine, serine, histidine, tyrosine, methionine, glutamic acid etc.)…”