DTU Chemistry - PhD 2014

Anti-cancer Drugs Based on Epigenetic Modulation (I)

Desmethyl azumamide analogs are promising candidates for inhibition of histone deacetylases (HDACs), which are key substances in gene expression.
Histone deacetylases (HDACs) are key substances in regulation of gene expression, which is a fundamental life process. While all genetic information is stored in DNA, and the same DNA is present in all cells, not all genes will actually be expressed in all cells. The actual gene-expression is regulated by a number of processes called epigenetic mechanisms. HDACs play an important role in one of these mechanisms. They function as “erasers”, which remove certain modifications. Aberrant epigenetic processes have been associated with various forms of cancer, and HDACs have therefore become targets for new types of anticancer drugs. So far, two HDAC inhibitors have been approved by the American food and drug administration (FDA), and several compounds are in clinical trials. The thesis investigates a group of possible HDAC inhibitors, namely analogs of natural products called azumamides.

Azumamides are an interesting type of HDAC inhibitors. These macrocyclic compounds are able to interact with a variety of amino acids on the surface near the binding site. The interactions can be used to obtain selectivity for specific HDAC isozymes. Further, the azuma- mides are potent HDAC inhibitors, and since they possess a relatively weak zinc-binding group, the activity must come from interactions with the large “cap group”.

Aromatic substituents in cyclic peptides were explored, with the most challenging modifications being introduced in the β–amino acid residue. Six azumamide analogs were synthesized, all with the methyl group removed from the 2-position of the β–amino acid. Different amino acids were investigated as well as modifications to the unsaturation in the side chain. The key step in the synthetic route was a cross-metathesis on a vinyl amino acid building block, which could be readily obtained from commercially available L-aspartic acid. An optimized position for the cyclization was found, which led to a significantly improved yield.

The azumamide analogs were tested against a number of HDAC enzymes. Minor changes in activity were observed among the analogs. However, removal of the methyl group had a significant impact relative to the natural products. Compounds containing a phenylalanine and a trans olefin in the side chain were slightly less potent.

Investigations by NMR and computational techniques were performed in collaboration with the laboratories of Charlotte H. Gotfredsen and Peter Fristrup at DTU Chemistry, and these revealed that the 3D-structures of the azumamide analogs were similar to the natural compounds. Although a conclusion was not found, the preliminary docking results indicate favorable lipophilic interaction with the methyl group in the azumamides.

Largazole is another macrocyclic natural product with HDAC inhibitory activity. The compound contains a thioester functionality in the side chain, which is presumably hydrolyzed before interaction with the HDAC enzymes. To mimic the prodrug nature of largazole, compounds containing a thiol were designed as it was hypothesized that acylation with different lipids could generate compounds with improved cell-penetrating properties. A desmethylated azumamide analog containing a thiol side chain was synthesized.

Caption: TSA (magenta, space filling model) bound to histone deacetylase-like protein (PDB: 1C3R). Amino acids involved in the deacetylation are shown as sticks.

DTU Chemistry - PhD 2014
Christian A. Olsen, now Professor at University of Copenhagen

Funded by:
The project was funded by the Lundbeck Foundation. The project was related to the PhD study of Jesper Villadsen.

Link to the thesis!