Design, Synthesis And Molecular Function Of Histone Deacetylase Inhibitors

The acetylation state of core histones modulated by histone acetyl transferase (HAT) and histone deacetylase (HDAC) plays a fundamental role in the regulation of gene expression. Abnormal increase in the activity of HDACs has been linked to the development of human cancers, since it results in the transcriptional repression of some tumor suppressor genes. HDAC inhibitors (HDACIs) can inhibit the overpressed HDACs and induce growth arrest, cell proliferation, and apoptosis in tumour cells. HDACIs thus have potential use in cancer therapy, and have become an attractive class of anticancer agent. In this research, some novel HDACIs were designed by computer-aided drug design (CADD) method and then synthesized. The interaction mechanisms of HDACs with inhibitors were explored.Firstly, several derivatives from L-2-amino-7-bromoheptanoic acid and L-2-amino-8-bromooctanoic acid were designed as HDACIs based on the structure feature and interaction mechanism. All synthesized compounds exhibited HDAC-inhibitory and anticancer activities at low concentrations, and had greater affinity toward HDAC1and HDAC2than HDAC8. The introduction of a benzyloxycarbonyl group to the surface recognition domain of these compounds enhanced their HDAC-inhibition ability. Molecular modeling studies were conducted to elucidate the interactions between inhibitors and different class I HDACs isoforms (HDAC2and8). It indicated that coordination of zinc ion, formation of hydrogen bond and hydrophobic interaction between inhibitors and HDACs were essential for the HDAC-inhibitory activities of these compounds. The benzyloxycarbonyl group largely increased the interactions between inhibitors and HDACs. There were five or six methylenes in the linker domains, and the introduction of amide group or ester group into the surface recognition domains had little effect on their affinity to HDACs. Molecular modeling revealed that the zinc ion in the bottom of the active pocket of HDACs coordinated six atoms in the HDAC-inhibitor complexes. The hydrogen bond, hydrophobic effect and π-π interaction between inhibitors and HDACs were essential for the binding. Interaction between each of the compounds and HDAC2involved an additional hydrogen bond compared to the interaction between the same compound with HDAC8. Leu276of HDAC2provided more favorable contribution to the binding than corresponding Met274of HDAC8.Based on the results obtained above, some L-2-amino-8-bromooctanoic acid-based HDACIs were designed and synthesized. All compounds exhibited potent HDAC-inhibitory and anticancer activities, and two of them were at the same level as Trichostatin A (TSA). Structure-activity relationship study showed that the introduction of2-amino-4-phenylthiazole or9-methyleneoxy-fluorenyl group into the surface recognize domain could largely increase the inhibitory activity against HDACs. Molecular modeling studies indicated that2-amino-4-phenylthiazole and9-methyleneoxy-fluorenyl groups could enhance the interactions between HDACIs and enzyme, and reduce the binding free energy.Some cyclic tetrapeptide inhibitors in that the thiol group was worked as metal binding domains were designed, and the interactions between these inhibitors and both class I and class II HDACs (HDAC2and4) were explored by molecular modeling method. The results showed that the L-Phe residue in the surface recognition domain was important in binding to HDACs. The binding mode of inibitor to HDAC2and HDAC4was similar, but had some differences. The coordination number of the zinc ion in the active site in HDAC2-and HDAC4-inhibitor complexes were identical. The metal binding domain of the inhibitors was strongly bonded to HDAC2by a hydrogen bond, and the surface recognition domain of the inhibitors formed two weaker hydrogen bonds to HDAC4. This may be the reason for the similar inhibitory activities of these cyclic tetrapeptides to class Ⅰ and Ⅱ HDACs.Lastly, to understand the interactions between HDAC8and inhibitors, including pan-inhibitors that inhibit many HDACs isoforms and selective inhibitors with no linker domain, molecular docking and molecular dynamics simulations were conducted. The results indicated that when inhibitors with large cap groups bound to the active pocket of HDAC8, Phe152and Met274shifted from their initial positions and the entrance of the active pocket would become more open, resulting in the formation of sub-pocket. For "linkerless" HDACIs, the position of the cap group may have a large effect on their activities. Furthermore, some HDAC8-selective inhibitors were designed. The results of molecular docking and molecular dynamics simulations indicated that all compounds could bind to HDAC8.To sum up, a series of novel and potent HDACIs were designed and synthesized. Some HDAC8-selective inhibitors were designed by molecular modeling method. The interactions between the same inhibitor and different class Ⅰ HDACs isoforms, and between a cyclic tetrapeptide inhibitor and HDACs in class Ⅰ and class Ⅱ were explored by molecular modeling studies. The data generated from this study would allow us to design some potent and selective HDACIs.