Exploring the CAP and the ZBG functionalities of HDAC inhibitors with a phenyl-4-yl-acrylohydroxamic acids scaffold

Regulation of gene expression is mediated by several mechanisms such as DNA methylation, ATP-dependent chromatin remodeling, and post-translational modifications of histones. The latter mechanism includes dynamic acetylation and deacetylation of lysine residues present in the tail of core histones. Acetylation is executed by histone acetyltransferases (HATs) and is reversed by histone deacetylases (HDACs). Inhibition of HDACs causes histone hyperacetylation with transcriptional activation of genes associated with cell cycle arrest or apoptosis in tumor cells. Well characterized HDAC inhibitors typically contain three structural features that are thought to be required for optimal activity: an aromatic cap group (CAP), a linker chain and a zinc binding group (ZBG). Based on molecular modeling studies, we have developed a series of hydroxamic acid-based compounds, characterized by a cinnamic spacer capped with a substituted phenyl group.1 Here we report our recent efforts to optimize drug-target interaction by modification of the cap group and the ZBG-functionality. Molecular docking was used to predict the optimal conformation of different molecules in the active site of a representative isoform from class I (HDAC2, sharing 85% sequence identity and 93% of sequence homology with HDAC1) and class II (HDAC6). Whereas most of the candidates with alternative Zn-binding groups were less effective than the parent hydroxamic acid, selected compounds modified in the cap region showed an activity towards HDAC1, 2 and 6 in the low µM range, assessed through a fluorimetric assay. One of the compounds was further tested in vitro and in vivo in a colon carcinoma model and showed significant proapoptotic and antitumor activity.