Tuesday, July 21, 2015

Drugs in Clinical Pipeline: Compound 7

Compound 7 [tert-butyl (4-(3-((7-(hydroxyamino)-7-oxoheptyl)carbamoyl)isoxazol-5-yl)phenyl)carbamate] a picomolar inhibitor of Histone Deacetylases 6 (HDAC6 IC50 ~ 2 pM) was identified in a series of hydroxamate based HDAC inhibitors. The series of inhibitors contain a phenylisoxazole as the CAP group that has been synthesized using nitrile oxide cycloaddition chemistry.

The activity of Compound 7 is as follows:

IC50 (HDAC1 enzyme assay) = 271 ± 23 nM
IC50 (HDAC2 enzyme assay) = 252 ± 10 nM
IC50 (HDAC3 enzyme assay) = 0.42 ± 0.08 nM
IC50 (HDAC8 enzyme assay) = 6851 ± 707 nM
IC50 (HDAC6 enzyme assay) = 0.002 nM
IC50 (HDAC10 enzyme assay) = 90.7 ± 12 nM

Common Name: Compound 7
Synonyms:  -
IUPAC Name: tert-butyl (4-(3-((7-(hydroxyamino)-7-oxoheptyl)carbamoyl)isoxazol-5-yl) phenyl)carbamate
CAS Number: 1045792-66-2
Mechanism of Action: HDAC Inhibitor; HDAC6 Inhibitor; Histone Deacetylases 6 Inhibitor
Indication: Various Cancers; Anti-tumor Therapy
Development Stage: Investigational
Company: University of Illinois and Mayo Clinic

The design of HDAC inhibitors as novel therapeutics for the treatment of a wide range of disorders, including cancers, neurodegenerative diseases, and even malaria has generated a lot of interest. These compounds owe their action to their ability to reactivate silenced genes by modulating the condensation status of DNA. The post-translational acetylation status of chromatin is determined by the competing activities of two classes of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs), which control the acetylation of lysine residues making up the histones. In general, HATs function to acetylate lysine groups in nuclear histones, resulting in neutralization of the charges on the histones and a more open, transcriptionally active chromatin structure, while the HDACs function to deacetylate and suppress transcription (the positively charged lysine amine group interacts with the negatively charge DNA organophosphate groups to cause compaction of the chromatin structure). A shift in the balance of acetylation on chromatin may result in changes in the regulation of patterns of gene expression. Many cancers are associated with aberrant transcriptional activity and HDACs and HATs associate with transcription activators and repressors, these enzymes have been identified as attractive targets for cancer therapy. Indeed, inhibitors of the HDACs have been shown to block tumor cell growth and induce differentiation and cell death [1].

HDAC6 plays an important role in deacetylation of tubulin, hence is a huge interest in the researcher and pharma community [2]. Using X-ray crystal structure of HDAC7 (2PQP) template a HDAC6 homology model was built. Preliminary investigations of other class I and class II HDAC homology models indicate that the loop areas surrounding the CAP residues show significant differences among the various HDACs and may eventually account for the enzyme selectivity that has been observed [1].

The enzyme selectivity of compound 7 was explained on the basis of the following drug-target interactions:

1. The ZBG (zinc-binding group) hydroxamic acid group and the six methylene groups bind deep inside the narrow binding pocket.
2. The CAP region of the bound ligand appears to interact with only one side of the protein.
3. The carbonyl group of the Boc group might interact with His499, which may be important in positioning the CAP residue on the surface of the HDAC protein. Such interactions are absent with the other inhibitors included in this study and may thus explain the higher potency observed for this compound.

Compound 7 was tested against five transformed cell lines as well as against two normal cell lines. Compounds 7 is active against both the Mia Paca-2 and Panc04.03 cell lines at the 100 nM level and at the 200-300 nM level against HupT3 [1].


1. Kozikowski, A. P.; et. al. Use of the nitrile oxide cycloaddition (NOC) reaction for molecular probe generation: a new class of enzyme selective histone deacetylase inhibitors (HDACIs) showing picomolar activity at HDAC6. J Med Chem 2008, 51(15), 4370-4373.
2. Bulinski, J. C.; et. al. HDAC6 deacetylation of tubulin modulates dynamics of cellular adhesions. Journal of Cell Science 2007, 120, 1469-1479.