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Title: Development of covalent inhibitors of KDM5B
Author: Wright, Miranda
ISNI:       0000 0004 7960 0083
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2018
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Lysine Demethylases (KDMs) represent an interesting drug target as they have been implicated in many diseases including several cancers. Reported inhibitors of KDM5 are commonly metal-chelators which bind in the cosubstrate 2-oxoglutarate (2-OG) binding site. The inhibitors are potent biochemically but suffer from poor selectivity over the closely-related KDM4 and poor cellular potency. An explanation for the large drop off in cellular activity has been attributed to competition from 2-oxoglutarate. In this thesis, I report the development of a covalent inhibitor that is potent and selective for KDM5. The inhibitors were designed with an 8-pyridopyrimidinone-based scaffold and cysteine-selective electrophiles for covalent binding to C480 in KDM5B, a non-conserved residue across the other KDM subfamilies. The compounds were rationally designed through covalent docking to ensure non-covalent interactions were maintained (Chapter 2). Numerous compounds were synthesised via a common synthetic pathway. Screening of the covalent inhibitors for time-dependent inhibition was performed using an AlphaScreen assay to determine their kinact/Ki values (Chapter 3). AlphaScreen was also used to determine whether covalent binding resulted in less competition from 2-OG and improved selectivity over the other KDM subfamilies. Covalent binding of the inhibitors to KDM5B using MS-labelling experiments was described in Chapter 4. Proof of target engagement of the covalent inhibitors with KDM5B in the cellular environment using pull-down experiments was attempted in Chapter 5. Chapter 6 describes the development of a bench-stable transfer reagent for the synthesis of trifluoromethyl sulfonimidamides. This work was undertaken while on industrial placement at Janssen Pharmaceuticals who were interested in this interesting bioisosteric replacement in their own drug discovery projects. Current methods require the formation of an unstable sulfonimidoyl fluoride so it was envisaged that this transfer reagent could be formed on large scale for the synthesis of diverse libraries of CF3-sulfonimidamides. The final chapter describes another approach towards a therapeutic for cancer. Ribonucleotide Reductase (RNR) is an enzyme essential for the synthesis of phosphorylated deoxyribonucleotides so a deoxyadenosine-based PROTAC was developed for the targeted degradation of the RRM1 subunit of RNR.
Supervisor: Brennan, Paul ; Kawamura, Akane Sponsor: Engineering and Physical Sciences Research Council
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available