HDAC Inhibitors Inspired by Natural Products

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Cancers of the digestive organs such as the stomach, colon and the kidney are prevalent and can be very difficult to treat, thus providing a compelling rationale for the pursuit of new agents that target these types of malignancies. Emerging targets that have generated considerable interest are histone deacetylases (HDACs), a family of enzymes that is involved in chromatin remodeling and epigenetic events. There has already been considerable work in this area, largely focusing on the hydroxamate class, the first of which has gained approval for the treatment of cutaneous T-cell lymphoma. Poor selectivity between HDAC isozymes is believed to underlie much of the toxicity associated with the clinical use of current HDAC inhibitors. New HDAC inhibitors with superior activities could significantly impact the efficacy of this target in cancer. We are interested in developing a completely novel class of HDAC inhibitors with enhanced levels of selectivity. These new inhibitors are based on a natural product chemotype, the tropolone system. For centuries, the wood and extracts from taiwanhinoki (Chamaecyparis taiwanesis) and Japanese hinoki (Chamaecyparis obtuse) have been prized in Japan and China. The extracts of the tree (hinoki oil) have been valued for antibacterial and antiproliferative activity and are currently used in numerous topical agents and cosmetics. The composition of these extracts was studied in the early 1940s, leading to the identification of an unusual tropolonoid termed hinokitiol (also known as thujaplicin) that was shown to be responsible for much of the biological activity. Naturally occurring tropolones such as thujaplicin have been recognized for their ability to interact with metal ions through chelation of the ¿-hydroxy ketone and could form a versatile platform for the discovery of agents that specifically target bound metal ions such as those in metalloenzymes. In fact, we have already demonstrated that tropolone analogs are capable of inhibiting HDAC-2. In this R21 application, we aim to investigate the potential of this non-benzenoid aromatic to serve as a good lead compound for the discovery of new inhibitors of HDAC. Our preliminary analysis suggests that the unique structural features of this class offer opportunities to incorporate high levels of potency and selectivity. It is our aim to use the R21 mechanism to establish the feasibility of developing a tropolone-based lead series as HDAC inhibitors. The first specific aim will describe the synthesis of a variety of differentially substituted tropolones, approximately 40 in total, which will be evaluated in the second aim using enzymatic and cell- based assays. Preliminary metabolic stability studies will also be conducted on the top five inhibitors. In the third aim, attempts will be made to crystallize HDAC in complex with a lead inhibitor. These studies will ultimately support a structure-based drug design effort as we move forward with lead optimization. Realization of the goals outlined in this R21 application would position us with high levels of control over the key synthetic, structural and biochemical facets critical for further compound development.