Thesis
Exploring methods to predict the susceptibility of cysteines within protein domains towards electrophiles for covalent probe discovery
- Creator
- Rights statement
- Awarding institution
- University of Strathclyde
- Date of award
- 2023
- Thesis identifier
- T17542
- Person Identifier (Local)
- 201889636
- Qualification Level
- Qualification Name
- Department, School or Faculty
- Abstract
- Covalent fragment screening is a broadening technique as multiple protein side chains can now be targeted for potential protein inhibition through varying chemistries.1 It can be difficult to understand whether a specific protein domain might be a suitable target for covalent fragment screening if it lacks a catalytic nucleophile. Regarding cysteines, chemoproteomics studies involving electrophilic compounds often lack complete information regarding the cysteine reactivity within a protein, 2 which leaves questions about which cysteines in a protein domain are actually susceptible to electrophilic modification. This thesis explores using in silico methods in combination to predict which protein constructs have cysteine thiols suitably susceptible to electrophilic modifications. An α,β-unsaturated ester-containing fragment library and the reactive compound N-ethylmaleimide were used to test this pre-screen concept by finding modifications of E3 ubiquitin ligase proteins. The use of in silico methods were briefly extended to explore this concept with hydroxyl and imidazoles in a protein and modifications by arylsulfonyl fluoride fragments. The interactions between the most promising hit fragment against an E3 ubiquitin ligase domain and multiple arylsulfonyl fluoride fragments against B cell lyphoma 6 (BCL6) protein were characterised using structural and biophysical methods. It was found that a simple scoring function appeared to indicate the protein constructs which did not return selective electrophilic modifications during fragment screening. Such pre-screen methods which help understand the best chemical strategy for probing protein surfaces for electrophilic susceptibility will be useful to guide the efficient expenditure of finite protein for the discovery of covalent site-specific tool fragments. This thesis also presents evidence for the specific binding of an arylsulfonyl fluoride fragment into a protein-protein interaction groove of BCL6. This electrophilic compound could be used as a tool compound for the discovery of further non-covalent inhibitors against BCL6.
- Advisor / supervisor
- Burley, Glenn A.
- Palmer, David S.
- Chung, Chun-wa
- Resource Type
- Note
- Previously held under moratorium in Chemistry department (GSK) from 19 October 2023 until 25 November 2025.
- The confidentiality statement on each page of this thesis DOES NOT apply
- DOI
- Funder
- Embargo Note