Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability

Abstract

Background:The effect of HDAC inhibitor kinetic properties on biological function is currently unknown. Results:The kinetic rate constants of HDAC inhibitors differentially affect histone acetylation, cell viability, and gene expression. Conclusion: Evaluating HDAC inhibitor properties using histone acetylation is not predictive of their function on cellular activity. Significance: Characterizing the biological effect of different HDAC inhibitors will help to evaluate their clinical utility.

A First-in-Class Small-Molecule that Acts as a Dual Inhibitor of HDAC and PDE5 and that Rescues Hippocampal Synaptic Impairment in Alzheimer’s Disease Mice

“…Based on reported structure-activity relationships (SARs), data regarding HDAC (Kalin and Bergman, 2013;Miller et al, 2003) and PDE5 inhibition (Manallack et al, 2005), and structural information that included the X-ray co-crystal structures for the HDAC2-vorinostat complex (PDB 4LXZ) (Lauffer et al, 2013) and PDE5-sildenafil complex (PDB 1TBF) (Zhang et al, 2004), we designed and synthesized compounds to interact with both HDAC (class I and HDAC6) and PDE5. Consequently, a novel series of pyrazolopyrimidinones were designed and synthesized that bore key chemical functionalities covering the critical pharmacophoric features (Figure 1a-e and Supplementary Figure S1).…”

“…Such target compounds would have a profile of moderate HDAC class I inhibition, potent HDAC6 and PDE5 inhibition, optimal passage across the BBB, a short residence time, and a reduced half-life. In this way, the candidate drugs identified should have minimal toxicity as this is often associated with strong inhibition of HDAC class I isoforms (Robers et al, 2015) (eg, the FDA-approved potent pan-HDAC inhibitors, vorinostat and panobinostat) as well as with slow dissociation kinetics (Lauffer et al, 2013). The synergistic effect should lead to achieve a degree of histone 3 acetylation that is not possible with HDAC6-selective inhibitors (eg, Ricolinostat) and, on the other hand, these new molecules will also achieve a degree of tubulin acetylation that has been impossible to obtain with the FDA-approved class I inhibitor, valproic acid (Gurvich et al, 2004).…”

“…Nevertheless, not every isoformselective HDACi has a good safety profile and, in fact, the potency of HDACis that target each class I isoform independently (HDAC1, HDAC2, and HDAC3) is associated with cytotoxicity, whereas the inhibition of HDAC6 does not affect cell survival (Robers et al, 2015). In addition, toxicity not only depends on the inhibition of HDAC class I isoforms but it is also influenced by the compound's kinetic properties that are crucial to maintain cell viability (Lauffer et al, 2013). It has been hypothesized that a short exposure of neurons to HDACis may be sufficient to provide neuroprotection while avoiding toxicity (Langley et al, 2008).…”

“…It has been hypothesized that a short exposure of neurons to HDACis may be sufficient to provide neuroprotection while avoiding toxicity (Langley et al, 2008). In fact, HDACi with fast dissociation kinetics rates (such as hydroxamates) limit the overexpression of genes involved in cell cycle regulation and thus cytotoxicity (Lauffer et al, 2013). Moreover, in the case of memory function, an initial, rapid, and transient induction of early-immediate genes (IEGs) would be sufficient to induce long-lasting changes in memory consolidation (Sheng and Greenberg, 1990;Tzingounis and Nicoll, 2006).…”

Development of an ELISA-Based HDAC Activity Assay for Characterization of Isoform-Selective Inhibitors

“…For MS-275 only, a 3-h incubation at room temperature was used with HDAC1, 2, and 3 due to slow association kinetics. 24 A control reaction without inhibitor was also included, which contained DMSO (1 µL) in HDAC-Glo buffer (24 µL). After incubation of the inhibitor with the affixed HDAC isoform, the ELISA-based HDAC activity assay protocol was followed as described above, with addition of HDAC-Glo reagent alone (25 µL).…”