Development of lysine acylating small molecules for covalent kinase inhibition

Rights statement
Awarding institution
  • University of Strathclyde
Date of award
  • 2021
Thesis identifier
  • T16607
Person Identifier (Local)
  • 201776699
Qualification Level
Qualification Name
Department, School or Faculty
  • Drug discovery has experienced an increasingly pronounced interest in covalent drugs. The mechanisms of action of covalent and reversible inhibitors are fundamentally different, and this must be taken into account in drug design efforts. Covalent inhibitors require careful tuning of their selectivity and reactivity profile to avoid nonspecific binding. This is essential to control the toxicity risks associated with over-reactive compounds. Although early covalent drugs such as aspirin and β-lactam antibiotics were discovered serendipitously, reports of rational design strategies in the literature have multiplied to support a recent renewed interest in covalent drug discovery. Incorporation of a reactive electrophilic warhead to a previously optimised reversible ligand is a common method to selectively inhibit a target of interest, taking advantage of pre-existing selectivity features. When applied to appropriate protein targets, covalent drugs can offer unique clinical advantages: enhanced potencies and extended duration of action, resulting in smaller and less-frequent doses. Oncology treatments have greatly benefited from the approval of novel covalent kinase inhibitors in the last decade. The most exemplified method for covalent kinase inactivation relies on Michael acceptors targeting non-conserved cysteine residues close to the active site. Despite its success in the clinic, this strategy is inherently limited to kinases bearing an accessible reactive cysteine residue. This has prompted the study of other nucleophilic residues to expand the scope of kinases amenable to covalent inhibition. Lysines in particular have been the focus of multiple research efforts. The research project described in this thesis studied the effect of small chemical modifications of the conserved catalytic lysine on kinaseactivity. We were specifically interested in alterations of the protein structure similar to post-translational modifications, such as acetylation. The objective of the project was to imitate natural cellular regulation mechanisms using covalent small molecule ligands, potentially reducing the risk of downstream toxicity from covalent inhibitors. Small molecule acylating tools were developed using activated phenolic esters as the reactive electrophiles. The covalent warheads were incorporated onto known reversible lipid kinase inhibitors. The reversible chemical templates would act as acyl group carriers, bringing the esters in close proximity to the targeted lysine. Multiple chemical series with different kinase selectivity profiles were investigated to develop covalent probes targeting PI3Kδ. Libraries of structural ester variants, including acetate esters as the smallest electrophiles explored, were examined to understand the binding rate of different acyl groups and their impact on kinase activity. Biochemical and biophysical data confirmed that PI3Kδ inhibition was directly caused by covalent lysine acylation. Due to the conserved nature of the catalytic lysine across the kinome, we believe this inhibition strategy could be applicable to a broad range of clinically relevant targets, supporting the development of novel covalent drugs and chemical biology tools.
Advisor / supervisor
  • White, Gemma
  • Campos, Sébastien
  • Patel, Vipul
Resource Type
  • Previously held under moratorium in Chemistry Department (GSK) from 31st March 2021 to 2nd June 2023.
  • The confidentiality statement on each page of this thesis DOES NOT apply
Embargo Note
  • This thesis is restricted to Strathclyde users only until 31st March 2026.