Studies on Hydroxamates Incorporated with a Naturally Occurring Cap as Novel Selective-Spectrum Histone Deacetylase Inhibitors

Epigenetic modifications such as DNA methylation, post-translational modification of histone proteins, and chromatin remolding regulate gene expression through change of chromatin structure without change of gene sequence. Of these epigenetic processes, reversible acetylation of the chromatin histones has been widely studied. This dynamic system is controlled by the balance of the activity between histone acetyltransferases (HATs) and histone deacetylases (HDACs). Deregulation of the process may cause various forms of malignancy. Moreover, HDACs are involved with acetylation of non-histone proteins such as tubulin, p21 and p53, suggesting that these enzymes may also regular a broad spectrum of cellular events. HDAC inhibitors have been shown to exhibit anti-neoplastic effect in many types of tumor cell lines as well as in vivo models. Hence, they are validated as a strategy for treatment of cancer. All reported HDAC inhibitors contain three pharmacophoric features: a zinc-chelating group, a hydrophobic linker, and a hydrophobic cap for surface recognition. Recently we have demonstrated the effectiveness of osthole, a hydrophobic Chinese herbal compound, as the surface recognition cap incorporated into cinnamyl- (2d) or aliphatic-based (3g) hydroxamate as inhibitors of HDAC; both compounds showed significant potency against several HDAC isoforms. They also exhibited multiple significant cellular effects towards cancer cells as well as antitumor activity in xenograft model. Molecular docking analysis showed that the osthole moiety when introduced into cinnamyl hydroxamate may interact with the same hydrophobic surface pocket exploited by SAHA and it may be further modified to provide class-specific selectivity. Furthermore, by screening our compound library for HDAC8 inhibitory activity, we found that ortho-phenyl N-hydroxycinnamide (8e) showed potent and selective inhibition, which may correlated to antiproliferative activity of vascular smooth muscle. In this three-year project, we will further combine natural product chemistry, structure biology supported by Co-PI, Dr. Chang at Academia Sinica and cellular mechanism studies performed by Co-PI, Dr. Chen at NTU to achieve our goal for lead optimization based on the result as described above. This study may help us to develop HDAC inhibitor as a potential agent for treatment of cancer or other diseases related to this enzyme. Specific aim of the first year: Based on molecular docking studies on osthole-derived N-hydroxycinnamide with class IIa HDAC, we aim to develop aryl-substituted series as selective inhibitors. The co-crystal structure with HDAC4 and multiple cellular effects towards cancer cells of resulting compounds could be elucidated through this work. Specific aim of the second year: Exploiting osthole-based aliphatic hydroxamate as a lead compound, we aim to introduce 1,2,3-triazole ring into linker and investigate whether such modification could improve the inhibitory activity against specific spectrum of HDAC isoforms and cellular effects. Moreover, the structure-activity relationship (SAR) could be validated by using molecular modeling or co-crystallography. Specific aim of the third year: Based on our preliminary studies on ortho-phenyl substituted N-hydroxycinnamide, we aim to investigate whether modification made to phenyl group has effect on HDAC8 inhibition and vascular smooth muscle proliferation. The cellular mechanism associated with HDAC8 inhibition could be further clarified.