A potent and selective inhibitor of a histone demethylase

Thesis

Post-translational modifications (PTMs) to histone proteins play important roles in the regulation of gene expression. Histone lysine demethylases (KDMs) remove methyl groups from N^ϵ-amino methylated lysine residues. There are two classes of human KDMs; the flavin adenosine dinucleotide-dependent demethylases (the KDM1 subfamily) and the 2-oxoglutarate- (2OG) dependent Jumonji C (JmjC) demethylases (KDM2–7). Misregulation and mutation of histone demethylases are associated with multiple human diseases including cancer. Hence potent and selective inhibitors are of interest for investigations into the biological roles of KDMs and their relevance as targets for drug discovery. JmjC KDM inhibitors have been reported in the literature but there are few subfamily selective examples. The aim of the work described in this thesis was to design and synthesise potent and subfamily selective inhibitors of human JmjC KDMs for use as chemical probes.

An aminomethyl pyridine-4-carboxylate series that was derived from a high throughput screening hit delivered a selective, submicromolar KDM2A inhibitor. X-ray crystallographic analyses demonstrated that the aminomethyl pyridine moiety bound the active site iron revealing a novel JmjC KDM inhibitor scaffold.

A known 2,2'-bipyridine-4-carboxylate scaffold was used as a starting point for the identification of a second, novel JmjC KDM inhibitor series that contains a triazolopyridine moiety as a replacement for the bipyridine system. The triazolopyridine core was shown to bind in the 2OG binding site of KDM4A by X-ray crystallography. Optimisation of the triazole substituent gave a selective inhibitor of KDM2A/7B that is significantly more potent (KDM2A IC₅₀: 58 nM, KDM7B IC₅₀: 150 nM) than reported KDM2/7 subfamily selective inhibitors. As for many other JmjC KDM inhibitors, this compound was not found to be efficacious in a cellular assay. A variety of strategies were pursued with the aim of improving the cellular efficacy. However, only a modest effect was observed in the cellular assay (less than 25% inhibition at 100 μM). A biotinylated analogue was immobilised onto streptavidin-coated beads for chemoproteomics experiments and was found to interact with KDM2A in cell lysate.

Overall, this work resulted in the identification of two new scaffolds for JmjC KDM inhibition and in a potent and selective inhibitor of KDM2A/7B.

Authors: England, K

• DOI: 10.5287/ora-ao70ejmn6
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Subjects: Organic Chemistry; Medicinal Chemistry; Epigenetics; Chemical Biology