Comparison of the Deacylase and Deacetylase Activity of Zinc-Dependent HDACs

Abstract

The acetylation status of lysine residues on histone proteins has long been attributed to a balance struck between the catalytic activity of histone acetyl transferases and histone deacetylases (HDAC). HDACs were identified as the sole removers of acetyl post-translational modifications (PTM) of histone lysine residues. Studies into the biological role of HDACs have also elucidated their role as removers of acetyl PTMs from lysine residues of nonhistone proteins. These findings, coupled with high-resolution mass spectrometry studies that revealed the presence of acyl-group PTMs on lysine residues of nonhistone proteins, brought forth the possibility of HDACs acting as removers of both acyl- and acetyl-based PTMs. We posited that HDACs fulfill this dual role and sought to investigate their specificity. Utilizing a fluorescence-based assay and biologically relevant acyl-substrates, the selectivities of zinc-dependent HDACs toward these acyl-based PTMs were identified. These findings were further validated using cellular models and molecular biology techniques. As a proof of principal, an HDAC3 selective inhibitor was designed using HDAC3’s substrate preference. This resulting inhibitor demonstrates nanomolar activity and >30 fold selectivity toward HDAC3 compared to the other class I HDACs. This inhibitor is capable of increasing p65 acetylation, attenuating NF-κB activation, and thereby preventing downstream nitric oxide signaling. Additionally, this selective HDAC3 inhibition allows for control of HMGB-1 secretion from activated macrophages without altering the acetylation status of histones or tubulin.

The unraveling of substrate specificity of histone deacetylase 6 domains using acetylome peptide microarrays and peptide libraries

“…Regarding acyl specificity profiling, our data are consistent with the findings of McClure et al (51) pointing toward the narrow range of acyl modifications recognized by HDAC6. In both studies, only the formyl, acetyl, and propionyl moieties are removed from the target peptides.…”

The Process and Strategy for Developing Selective Histone Deacetylase 3 Inhibitors

“…These two compounds have IC 50 values for HDAC1 and HDAC2 higher than 10 μM, and compound 6 showed in vitro efficacy in suppressing the cancer stem cell subpopulation of triple-negative breast cancer by downregulating β-catenin [ 61 ]. McClure et al synthesized compound 8 as a selective HDAC3 inhibitor with IC 50 of 1.2 μM, 1.5 μM, and 0.08 μM for HDAC1, 2, and 3, respectively [ 62 ]. More interestingly, compound 9, which has another fluorine atom in the meta position of the amine of o -aminoanilide, shows a decrease in potency for HDACs, but a better selectivity profile for HDAC3 [ 62 ].…”

“…McClure et al synthesized compound 8 as a selective HDAC3 inhibitor with IC 50 of 1.2 μM, 1.5 μM, and 0.08 μM for HDAC1, 2, and 3, respectively [ 62 ]. More interestingly, compound 9, which has another fluorine atom in the meta position of the amine of o -aminoanilide, shows a decrease in potency for HDACs, but a better selectivity profile for HDAC3 [ 62 ]. Furthermore, the compounds bearing a fluorine atom in the ortho position of the amine or amide lose their potency for HDACs [ 62 ], indicating that the substitution pattern of o -aminoanilides contributes to their selectivity and potency for HDACs.…”

Systemic exosomal miR-193b-3p delivery attenuates neuroinflammation in early brain injury after subarachnoid hemorrhage in mice

“…Histone deacetylase inhibition has a neuro-protective effect via reducing neuroinflammation [33], reported to be beneficial with respect to neurological functions in many diseases, including Alzheimer's disease [40], Huntington's disease [41], TBI, stroke [42], and spinal cord injury [33]. Recent studies reported that HDCA3 inhibition appears to suppress NF-κB transcriptional activity by maintaining the NF-κB p65 acetylated (inactive) state and restraining the inflammatory response [33,43]. The NF-κB signaling pathway occurs in passive post-injury necrosis and in damaged cells, activating microglia to secrete inflammatory cytokines and causing amplification of the inflammatory response cascade [44,45].…”