Postgraduate research opportunities

Development of native ion mobility mass spectrometry methods to study PROTAC systems

PROTACS and other protein degraders are emerging as promising drug candidates for cancer, but their complex binding modes (simultaneous binding of two proteins) makes them difficult to study. Native mass spectrometry methods will be developed to address this bottleneck in the development of degraders as novel drugs.

Number of places

1

Funding

Home fee, Stipend

Opens

1 June 2020

Deadline

31 July 2020

Duration

36 months

Eligibility

Minimum 2.1 degree (or equivalent) in chemistry or a related subject.

Open to all UK or EU nationals.

Project Details

Small molecule inhibitors have traditionally been developed to bind to a specific protein, thereby preventing it from carrying out its function in the cell. In recent biotechnological approaches, molecules have been created that degrade a target protein, rather than inhibit it. Major advantages of protein degraders over inhibitors are the longer-lasting effects of degraders and the lower concentrations required to achieve efficacy. Moreover, degraders are applicable to a wider spectrum of proteins since binding is not limited to a specific active site. The most popular type of degraders to date are called proteolysis targeting chimeras (PROTACs), which are  bifunctional ligands that bind simultaneously to the targeted protein and an E3 ligase, bringing the proteins into a complex, so that the E3 ligase labels the targeted protein for degradation by the cell. PROTACs have been developed against a variety of medically relevant proteins, such as the tumorigenic Androgen Receptor and Estrogen Receptor, as explored in clinical trials.

A current limitation in the development of novel PROTACs is the ability to directly measure the formation of ternary complexes in a fast and efficient manner. Native mass spectrometry (nMS) is an efficient method for analysing the species present in complex mixtures involving E3 ligases, PROTACs, and substrate proteins. This is due to its ability to report on multiple binding stoichiometries present in dynamic protein mixtures, including species populated to a low extent. When coupled with ion mobility, which is a complementary gas-phase technique, different conformations of proteins or protein complexes can also be separated. This project aims to further develop nMS, ion mobility and chromatography methods for the analysis of PROTACs and other bivalent ligands. This will address the need for novel analytical techniques to study PROTAC systems, leading to better understanding and faster design of PROTACs and hence novel cancer therapies.

Techniques used:

Mass spectrometry, ion mobility, size exclusion chromatography, capillary electrophoresis, related analytical techniques.

References:

Beveridge, Rebecca, et al. "Native mass spectrometry can effectively predict PROTAC efficacy." bioRxiv (2019): 851980.

Tinworth, Christopher P., et al. "PROTAC-mediated degradation of Bruton’s tyrosine kinase is inhibited by covalent binding." ACS chemical biology 14.3 (2019): 342-347.

Hanzl, Alexander, and Georg E. Winter. "Targeted protein degradation: current and future challenges." Current Opinion in Chemical Biology 56 (2020): 35-41.

Sharon, M. and C.V. Robinson, The Role of Mass Spectrometry in Structure Elucidation of Dynamic Protein Complexes. Annual Review of Biochemistry, 2007. 76(1): p. 167-193.

Roy, M.J., S. Winkler, S.J. Hughes, C. Whitworth, M. Galant, W. Farnaby, K. Rumpel and A. Ciulli, SPR-Measured Dissociation Kinetics of PROTAC Ternary Complexes Influence Target Degradation Rate. ACS Chemical Biology, 2019. 14(3): p. 361-368.

Beveridge, Rebecca, et al. "Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding." Nature communications 7.1 (2016): 1-9.

Conditions: (e.g. experience in a specific technique, qualification)

We are looking for a motivated candidate who will ideally have experience in protein chemistry and/ or mass spectrometry.

 

Funding Details

Funding is available to cover tuition fees for Home UK or EU applicants for 3 years (from 1st of October 2020), as well as paying a stipend at the Research Council rate (estimated £15,285).

Supervisor

How to apply

To apply please send your C.V., a cover letter and details of two referees to Rebecca Beveridge. The cover letter should outline why you’re interested in this project and describe your relevant experience.