Zinc-Dependent HDAC Inhibitors

Crystal structures of a histone deacetylase-like protein (HDLP) and HDAC8 have confirmed a general pharmacophore model for HDAC inhibitors, comprising a cap joined by a hydrophobic linker to a zinc-binding group (ZBG). This model is exemplified by SAHA and the natural product HDACi Trichostatin A (TSA) 2. 

Since the identification of hydroxamic acids as potent bidentate ZBGs, an enormous range of hydroxamic acid inhibitors based on this model has been developed and is described in numerous reviews and therefore will not be dealt with in depth here [17]. Instead, the focus of this report will be on efforts to improve on these 1st generation inhibitors, specifically to improve biological and physicochemical characteristics, such as pharmacokinetics and bioavailability and to achieve isoform selectivity. 

In a simultaneous attempt to screen for further non-hydroxamate ZBGs, this team focussed on potentially bidentate ZBGs and identified a SAHA-like compound with a mercaptoacetamide functionality, which had an HDAC enzyme 

Different oxidation states of sulfur have also been explored, particularly sulf-ones and sulfonamides as transition state analogs of lysine deacetylation, but without much success. The monodentate SAHA-like methyl sulfoxide 7 proved most potent, but still with an enzyme IC50 of only 48 pM and indications of HDAC/TDAC selectivity in cellular assays [28]. 

Benzamides e.g. MS-275 8 are one of the more common hydroxamic acid alternatives but are often less potent. Recent exceptions to this pattern include substituted pyridyl [29] and thiazolyl [30] benzamides, such as 9 and 10 with HDAC1 enzyme IC50s of 19nM and 29 nM, respectively and series of benzamides substituted with other heterocycles, such as indazoles [31] and benzo [l,2,4]thiadiazines [32], many with HDAC2 IC50s of 50 nM. The addition of 

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Regardless of their origin, the structures of most inhibitors of the zinc-dependent HDAC inhibitors can be easily rationalized. They conform to the classical medicinal chemistry dogma for modulating hydrolase enzymes with a catalytic metal at the active site by competitive reversible inhibitors. Such compounds have two key features ... 

Before our work [39], only one catalytic mechanism for zinc dependent HDACs has been proposed in the literature, which was originated from the crystallographic study of HDLP [47], a histone-deacetylase-like protein that is widely used as a model for class-I HDACs. In the enzyme active site, the catalytic metal zinc is penta-coordinated by two asp residues, one histidine residues as well as the inhibitor [47], Based on their crystal structures, Finnin et al. [47] postulated a catalytic mechanism for HDACs in which the first reaction step is analogous to the hydroxide mechanism for zinc proteases zinc-bound water is a nucleophile and Zn2+ is five-fold coordinated during the reaction process. However, recent experimental studies by Kapustin et al. suggested that the transition state of HDACs may not be analogous to zinc-proteases [48], which cast some doubts on this mechanism. 

R., Gallinari, P. et al. (2004) Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDACS, complexed with a hydroxamic acid inhibitor. Proceedings of the National Academy of Sciences of the United States of America, 101 (42), 15064-15069. 

In the recent literature, many examples of A/BPs containing benzophenones can be found. A first example concerns the study of HDACs. These enzymes catalyze the hydrolysis of acetylated lysine amine side chains in histones and are thus involved in the regulation of gene expression. There are approximately 20 human HDACs, which are divided into three classes (I, II, and III). Class I and II HDACs are zinc-dependent metallohydrolases that do not form a covalent bond with their substrates during their catalytic process, which is similar to MMPs. It has been found that hydroxamate 65 (SAHA, see Fig. 5) is a potent reversible inhibitor of class I and II HDACs. In 2007, Cravatt and coworkers reported the transformation of SAHA into an A/BP by installment of a benzophenone and an alkyne moiety, which resulted in SAHA-BPyne (66) [73]. They showed that the probe can be used for the covalent modification and enrichment of several class I and class II HDACs from complex proteomes in an activity-dependent manner. In addition, they identified several HDAC-associated proteins, possibly arising from the tight interaction with HDACs. Also, the probe was used to measure differences in HDAC content in human disease models. Later they reported the construction of a library of related probes and studied the differences in HDAC labeling [74], Their most... 

Macrocyclic Inhibitors of Zinc-dependent Histone Deacetylases (HDACs)... 

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