Development of Next-Generation Macrocyclic Histone Deacetylase Inhibitors

• Applicant: Dr. Martin Roatsch
• Subject Area: Pharmacy ; Biochemistry ; Biological and Biomimetic Chemistry
• Term: from 2017 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 388454995

Epigenetic mechanisms play a vital role in the regulation of gene expression and determine, which genes are expressed by which cells and at what times. This occurs both in healthy and, when aberrantly regulated, diseased cells. These mechanisms are manifested in chemical modifications both to DNA itself as well as to histone proteins, around which DNA is wrapped. “Eraser” enzymes that remove such marks like e.g. zinc-dependent histone deacetylases (HDACs) have been recognized as emerging drug targets, in particular in oncology. Some potent, yet unselective, inhibitors have already reached the clinic.This project aims at the development of novel inhibitors of this enzyme class based on the scaffold of azumamides, a family of naturally occurring cyclotetrapeptides. The inhibitors that will be generated in this project will investigate a novel mode of action, which does not rely on strong active site metal binding, but on disruption of protein-protein interactions of HDACs with their protein partners. Isolation of class I HDACs from their multiprotein complexes also leads to drastically reduced enzymatic activity.Structural knowledge is available about HDACs in complex with their protein partners, which positions one amino acid residue of the azumamide inhibitors in close proximity to the protein-protein interaction interface. Through chemical modifications to this residue as well as to the metal-binding residue, a library of novel azumamide derivatives will be generated and tested for their HDAC inhibition. A conceptually new in vitro assay will be established, which investigates HDAC protein-protein interactions by fluorescence polarization. This can be used to demonstrate disruption of complex formation by these inhibitors. This heretofore unexplored mechanism of inhibition allows for the introduction of selectivity with regard to HDAC subfamilies or even individual isotypes as they each have different protein complex partners. Structure-guided iterative optimization of the novel azumamides in a systematic SAR study in feedback with data from biochemical testing will yield potent dual-mechanism inhibitors. By balancing of these two mechanisms, compounds can be generated with tunable potency and selectivity for one HDAC subtype over the others. Cell culture experiments will validate the antiproliferative properties on cancer cell lines and substrate-specific changes in acetylation.The use of tetrapeptidic inhibitors of epigenetic HDAC enzymes represents a unique alternative method to temporal gene regulation. As outlined, the designed dual-mechanism compounds will allow for simultaneous inhibition of enzyme activity as well as their scaffolding function in protein-protein complexes. The enhanced biological effects that can be expected from this have the potential to make these next-generation HDAC inhibitors valuable tool compounds for the characterization of the biological role of individual enzymes as well as potential drug candidates.

• DFG Programme: Research Fellowships
• International Connection: Denmark
• Host: Professor Christian A. Olsen, Ph.D.