Class II HDACs

HDAC8 lies close to the phylogenetic boundary between the class I and class II HDACs (Buggy et al, 2000 Hu et al, 2000). It is a PKA substrate and its phosphorylation, contrary to the phosphorylation-mediated gain of function of all HDACs, is associated with decreased activity (Lee et al, 2004). 

HDAC9 is the predominant member of the class II HDAC family expressed in heart (Zhang et al, 2002). Its major product was shown to encode the splice variant MEF2-interacting transcription repressor/histone deacetylase-related protein (MITRIHDRP), which lacks the enzymatic domain but forms complexes with both HDACI and HDAC3 (Zhou et al, 2000 Zhou et al, 2001) and has been recently implicated in skeletal muscle chromatin acetylation and gene expression under motor innervation control (Mejat et al, 2005). 

Like Class I HDACs, all Class II HDACS are inhibited by trichostatin A (TSA). However, unlike other family members, HDAC6 is uniquely resistant to the potent HDAC inhibitors trapoxin-B (Furumai et al, 2001) and sodium butyrate as a... 

One of the first HDAC inhibitors to be identified and characterized was sodium butyrate, where it was found to alter the histone acetylation state (Riggs et al, 1977), and further determined to inhibit HDAC activity both in vitro and in vivo (Candido et al, 1978). Almost a decade later trichostatin A (TSA), a fungistatic antibiotic, was found to induce murine erythroleukemia cell differentiation (Yoshida et al, 1987). To date, a wide range of molecules have been described that inhibit the activity of Class I and Class II HDAC enzymes, and with a few exceptions, can be divided into structural classes including (1) small-molecule hydroxamates, such as TSA, suberoylanilide hydroxamic acid (SAHA), scriptaid and oxamflatin (2) short-chain fatty-acids, such as sodium butyrate, sodium phenylbutyrate and valproic acid (VPA) (3) cyclic tetrapeptides, such as apicidin, trapoxin and the depsipeptide FK-228 and (4) benzamides, such as MS-275 and Cl-994 (for reviews see Remiszewski et al, 2002 Miller et al, 2003). Some of these molecules are represented in Fig. 4. 

Apart from this HDACs are also associated with a number of other epigenetic repression mechanisms including histone methylation, polycomb group of proteins and DNA methylation (discussed later). The class II HDACs have been found to be involved in muscle development, particularly HDAC 5 and 9 knockouts or mutants show evidence of cardiac hypertrophy in a age or stress dependent manner (Zhang et al, 2002 Chang et al, 2004). 

The crystal structure of FB188 HDAH (histone deacetylase-like amidohydrolase from Bordetella/Alcaligenes strain FB188), a baderial class II HDAC homolog. 

Although no structure of class II HDAC has been solved in complex with an acetylated peptide, the structure of FB188 H DAH bound to an acetate molecule, the deacetylation reaction product, showed that the acetate was bound to the Zn ion [48]. A17-A long channel was found in FB188 HDAH, leading from the bottom of the active site cavity to the protein surface, and was proposed to function as an exit tunnel for the acetate, as previously proposed for HDLP [41, 44]. 

Fischle, W., Dequiedt, F., Hendzel, M.J., Guenther, M.G., Lazar, M.A., Voelter, W. and Verdin, E. (2002) Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR. Molecular Cell, 9 (1), 45-57. 

So far 18 different members of HDACs have been discovered in humans and classified into four classes based on their homology to yeast histone deacetylases [33]. Class I includes four different subtypes (HDACl, 2, 3, 8), class II contains six subtypes tvhich are divided into two subclasses class Ila with subtypes HDAC4, 5, 7, 9 and class Ilb with HDAC6, 10. Class I and class II HDAC share significant structural homology, especially within the highly conserved catalytic domains. HDACs 6 and 10 are unique as they have two catalytic domains. HDACll is referred to as class IV. While the activity of class I, II and IV HDACs depends on a zinc based catalysis mechanism, the class III enzymes, also called sirtuins, require nicotinamide adenine dinucleotide as a cofactor for their catalysis. 

Even though it is currently unclear whether any of the side effects observed in the clinic with the current pan-HDAC inhibitors are hnked to inhibition of the class-II HDACs, these observations, nevertheless, triggered the quest for HDAC isotype specific inhibitors, which will be further discussed below. 

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... 

Class IV HDAC 11 is most closely related to the class I family but also displays common characteristics with class II HDACs. The low overall homology to either of these classes has resulted in a separate classification. HDAC 11 is highly expressed in heart, brain, testis, muscle, and kidney cells and is predominantly located in the nucleus [28]. This deacetylase has short N- and C-terminal extensions little is known about its function. 

Fischle W et al (2002) Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR. Mol Cell 9(l) 45-57... 

Class I and Class II HDACs as Drug Discovery Targets 1697... 

Compared to other classes of HDAC inhibitors, the depsipeptides exhibit two impressive features. Firstly, they are highly potent with IC50S in the low nanomolar range. Secondly, they are significantly more active against class I HDACs compared to class II HDACs. Fortuitously, it is the former that are more heavily implicated in cancer and cardiac hypertrophy. On the other hand, the depsipeptides are structurally the most complicated class of HDAC inhibitors. Their elaborate framework has apparently deterred the pharmaceutical industry from the preparation of unnatural analogs and the iterative improvement of their properties. The Fujisawa and Yamanouchi patents only cover the natural products and so far only academic groups have described the total synthesis of depsipeptides. 

---