Background
Carbohydrates are essential to human life: they play key roles in cell-cell and host-pathogen interactions, modulate cellular communication and control a range of other cellular processes. Accordingly, the incorrect assembly of carbohydrate chains (glycans), and/or problems with their breakdown, are often linked to human disease. A class of metabolic disorders called lysosomal storage disorders results from inherited deficiencies in the enzymes (glycosidases) that are responsible for the degradation of glycoconjugates in lysosomes. There is no cure for such disorders, while at the same time detailed knowledge of the underlying molecular and cellular mechanisms is in many cases lacking. Thus, there is a clear need for new probes and assays to study the relevant enzymes and their involvement in disease. Your work will enable the development and application of these enzyme probes.
This studentship is offered at York. It is part of a team of researchers across three countries.
Objectives
Activity-based probes are chemical tools that allow the specific detection of active enzyme populations in their physiological context. This project seeks to design and synthesise activity-based probes for the selective detection of two human glycosidases that are involved in lysosomal storage disorders. These probes will be used to develop assays to monitor enzyme activity in cells and tissues, providing potentially new avenues for disease diagnosis and for high-throughput discovery of novel enzyme modulators.
Experimental approach
You will synthesise a number of small molecule probes derived from the carbohydrate portion of the enzymes’ natural substrates. A variety of electrophilic traps will be explored to achieve activity-based binding to the respective target enzymes, as well as a number of different tags for visualisation and/or enrichment of labelled enzymes. You will then apply the synthesised probes to the detection of enzyme activity in cellular models of disease. Working with colleagues within the university as well as teams in Leiden (Netherlands) and Barcelona (Spain), you will also collaborate on solving 3-D structures of target proteins in complex with the probes, designing new probes based upon your observations, and developing high-throughput screening assays.
Novelty and impact
The power of activity-based probes lies in their ability to visualise the activity of specific enzymes in a native context. The effectiveness of this technology has been demonstrated on a range of other enzymes, including glycosidases involved in different lysosomal storage disorders (see https://tinyurl.com/y57vg7ac for a review). However, so far this approach has not yet been applied to the enzyme class we are targeting here. This project therefore provides a conceptually new methodology that also has potentially far reaching implications for disease diagnosis and the screening and evaluation of novel therapeutics. Aside from lysosomal storage disorders, the developed technology will also be transferable to a mechanistically related, non-lysosomal enzyme which has been identified as a target for the treatment of Alzheimer’s disease.
Training
You will receive training in synthetic organic chemistry, specialising in carbohydrate chemistry, as well as mammalian cell culture and biochemical characterisation of (labelled) enzymes. As part of the world-renowned ‘York Structural Biology Laboratory (YSBL)’, you will also be exposed to techniques in molecular biology, protein production, and modern structural biology (primarily X-ray, but CryoEM is also available). You will collaborate with Dutch and Spanish groups as part of the dynamic “Carbocentre” team which covers many aspects of activity-based probe research. You will have access to our innovative Doctoral Training in Chemistry (iDTC): cohort-based training to support the development of scientific, transferable and employability skills: https://www.york.ac.uk/chemistry/postgraduate/idtc/
The Department of Chemistry holds an Athena SWAN Gold Award and is committed to supporting equality and diversity for all staff and students: https://www.york.ac.uk/chemistry/ed/.
You should hold or expect to achieve the equivalent of at least a UK 2:1 degree in Chemistry or a related subject. Please check the entry requirements for your country: https://www.york.ac.uk/study/international/your-country/
For more project information, click on the supervisor's name above to email the supervisor. For more information about the application process, please click on email institution.
This PhD is expected to start on 1 October 2021, however an earlier start date is possible if the candidate is available.
HOW TO APPLY: to be considered for this PhD, you need to submit an application for a PhD in Chemistry by 8 February 2021 via this link: https://www.york.ac.uk/study/postgraduate/courses/apply?course=DRPCHESCHE3
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