Development of lysine-targeted irreversible inhibitors of PI3Kδ

Dalton, Samuel E.

Thesis

Development of lysine-targeted irreversible inhibitors of PI3Kδ

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Creator

Dalton, Samuel E.

Rights statement

Strathclyde Thesis Copyright

Awarding institution

University of Strathclyde

Date of award

2018

Thesis identifier

T15980

Person Identifier (Local)

201474584

Qualification Level

Doctoral (Postgraduate)

Qualification Name

Doctor of Philosophy (PhD)

Department, School or Faculty

Department of Pure and Applied Chemistry

Abstract

Targeted covalent inhibition of poorly conserved cysteine residues for kinase inhibition has increased in popularity over recent years. Whilst these inhibitors are often highly successful, studies have shown that only ~40% of human kinases are amenable to this approach. Furthermore, cysteine point-mutations present common resistance mechanisms to these drugs. This thesis explores the concept of targeting the catalytically essential lysine of the kinase, which is conserved throughout the human kinome, for selective covalent inhibition. The validity of this approach is exemplified with the lipid kinase phosphoinositide 3-kinase delta (PI3Kδ), as it has been implicated in a range of diseases, and is not amenable to traditional cysteine-targeting. An activated ester motif was identified that was able to covalently modify this lysine residue, on non-selective scaffolds. These scaffolds were then optimised by exploration of the hingebinder, back-pocket, and electrophilic warhead to afford a series of indazole-based inhibitors that showed nanomolar potency and >100-fold selectivity in biochemical assays. The best series of inhibitors were then progressed to a full kinetic analysis to understand the mechanism of binding to PI3Kδ. The lead inhibitor, possessing a para-fluorophenolic ester warhead, showed evidence of target engagement in CD4+ T-cells in the sub-nanomolar range with an extended duration of action. Additionally, this inhibitor showed minimal off-target engagement in chemoproteomic studies in Ramos cells. In summary, this thesis discloses the development of the first selective irreversible inhibitor of PI3Kδ. This supports the hypothesis that covalent inhibition of kinases can be achieved by targeting a highly conserved lysine residue, opening the door to covalent targeting of kinases not possessing reactive cysteine residues. Additionally, this inhibitor may have applications in the design of long-acting therapeutics for kinase-mediated diseases. Finally, this concept may also offer a way of overcoming cysteine point-mutations as an acquired resistance mechanism to currently available targeted covalent inhibitors.

Advisor / supervisor