Design, Synthesis, and Biological Evaluation of Potent and Selective Class IIa Histone Deacetylase (HDAC) Inhibitors as a Potential Therapy for Huntington’s Disease

Abstract

Inhibition of class IIa histone deacetylase (HDAC) enzymes have been suggested as a therapeutic strategy for a number of diseases, including Huntington's disease. Catalytic-site small molecule inhibitors of the class IIa HDAC4, -5, -7, and -9 were developed. These trisubstituted diarylcyclopropanehydroxamic acids were designed to exploit a lower pocket that is characteristic for the class IIa HDACs, not present in other HDAC classes. Selected inhibitors were cocrystallized with the catalytic domain of human HDAC4. We describe the first HDAC4 catalytic domain crystal structure in a "closed-loop" form, which in our view represents the biologically relevant conformation. We have demonstrated that these molecules can differentiate class IIa HDACs from class I and class IIb subtypes. They exhibited pharmacokinetic properties that should enable the assessment of their therapeutic benefit in both peripheral and CNS disorders. These selective inhibitors provide a means for evaluating potential efficacy in preclinical models in vivo.

Potent, Selective, and CNS-Penetrant Tetrasubstituted Cyclopropane Class IIa Histone Deacetylase (HDAC) Inhibitors

“…Cyclopropanation of the methyl cinnamate derived from 1 as previously described, 6 followed by deprotonation of the racemic intermediate 2 using LDA (1.1−3 equiv) and quenching with an appropriate electrophile (MeI, CCl 4 or NFSI) 14 afforded the tetrasubstituted cyclopropane. The desired isomer was isolated by flash chromatography.…”

“…We recently reported the structure-based design of trisubstituted cyclopropane class IIa-selective HDAC inhibitors as potential therapeutics in HD. 6 This improved selectivity was driven by exploiting a selectivity pocket ( Figure 1, shown with compound 13) that is not present in the class I HDAC isoforms. This pocket is formed as a consequence of a tyrosine-histidine substitution.…”

“…6−10 The majority of class IIa HDAC activity in the Jurkat E6.1 cell line is derived from HDAC4. 6 Biochemical HDAC isoform selectivity was compared to the difference in activity in the cell assays between the Lys-Ac (class I/IIb-specific) and the Lys-TFA (class IIa/ HDAC8-specific) substrates.…”

“…6 Further improvements in biochemical potency and pharmacokinetics were targeted. The design of these molecules was inspired by the expectation that a fluorine atom alpha to the hydroxamic acids may increase their acidity.…”

“…6 It was assumed that direct glucuronidation would be their principal route of clearance, presumably via Oglucuronidation of the hydroxamic acid, and that the contribution of oxidative metabolism to the overall clearance of these molecules would be small. Compounds with very short half-lives (<5 min) in mouse liver microsomes were not progressed.…”