Mechanistic understanding and inhibitor design strategies for non-mevalonate pathway TPP-dependent enzymes

In this 4-year BBSRC iCASE PhD studentship between the University of Leeds and Syngenta PLC, you will investigate the structure, function and mechanism of plant enzymes important to the agriscience industry. The project, which is co-supervised in the Astbury Centre for Structural Molecular Biology, University of Leeds by Professors Alex Breeze and Frank Sobott, builds on previous collaboration between Syngenta and the University of Leeds to further elucidate the mechanistic biology and modes of inhibition of non-mevalonate pathway TPP-dependent enzymes including 1-deoxy-D-xylulose-5-phosphate synthase (DXS). The outcome will be an enhanced understanding of potential inhibitor design strategies and mechanisms, that in turn may lead to the development of improved herbicidal agents targeting this pathway.

Plants employ a range of distinct biosynthetic and metabolic strategies for photosynthesis and isoprenoid biosynthesis. A number of the enzymes that catalyse key steps in plant biosynthetic pathways utilise thiamine pyrophosphate (TPP) as a cofactor. TPP-dependent enzymes typically catalyse reactions involving the transfer or removal of carbonyl-containing units from pathway intermediates. A prominent example is 1-deoxy-D-xylulose 5-phosphate synthase (DXS), the key control point of the methylerythritol 4-phosphate (MEP) or ‘non-mevalonate’ pathway for isoprenoid biosynthesis. Given its absence in animals, this pathway is considered a potentially attractive target for development of herbicides.

Despite belonging to a generally well-understood class of enzymes, mechanistic understanding of DXS and its inhibition is still relatively limited, at least in part because structure determination, particularly of substrate-, catalytic intermediate-, product- or inhibitor-bound forms by X-ray crystallography has proved to be quite challenging. We propose to use cutting-edge ultra-high field methyl NMR and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to build on our earlier work. Specifically, we will transfer our methyl NMR approach based on the E. coli DXS system to orthologue(s) from plant species that will be more relevant model systems for herbicidal inhibitor development. In addition to NMR, we will use structural MS (HDX-MS, fast photochemical oxidation of proteins (FPOP)-MS and ion-mobility spectrometry- (IMS)-MS to map the binding sites and modes of interaction of substrates, catalytic / transition state intermediates and inhibitors. Molecular modelling based on existing PDB structures and AlphaFold2 structural models will be used as a basis for incorporating our experimentally-derived restraints. With these tools and mechanistic understanding in hand, there may be an opportunity for the student to further characterise a series of fragment binders of DXS in collaboration with collaborators at the University of Cambridge. Because of the nature of the project, we are seeking academically-strong candidates with an interest in and aptitude for structural biology and biophysics (NMR, HDX-MS etc.) and with a sound understanding of biological chemistry.

You will benefit from close collaboration between Syngenta and the University of Leeds including regular virtual and in-person meetings during the project. Thus, you will learn from the combined experience of the academic and industrial supervisors, as well as understand the applied nature of the project, aimed at discovering new herbicides to support growers to produce food in a sustainable manner.

You will also have the opportunity to visit the Jealott’s Hill site at Syngenta several times during the project, where you will be integrated into the Herbicide Bioscience group and have an opportunity to learn the process of agrochemical discovery from early hit generation, through lead optimization to candidate selection You will be encouraged to present your work at an annual conference hosted at the Jealott’s Hill site and to network with other students, academics and Syngenta staff and collaborators.

Eligibility: 

You should hold a first degree equivalent to at least a UK upper-second class honours degree or a MSc degree in a relevant subject.

Applicants whose first language is not English must provide evidence that their English language is sufficient to meet the specific demands of their study. The Faculty of Biological Sciences minimum requirements in IELTS and TOEFL tests are:

• British Council IELTS - score of 6.0 overall, with no element less than 5.5
• TOEFL iBT - overall score of 87 with the listening and reading element no less than 20, writing element no less than 21 and the speaking element no less than 22.

How to apply:

To apply for this project applicants should complete an online application form and attach the following documentation to support their application. 

• a full academic CV
• degree certificate and transcripts of marks
• Evidence that you meet the University's minimum English language requirements (if applicable).

To help us identify that you are applying for this studentship please ensure you provide the following information on your application form;

• Select PhD in Biological Sciences as your programme of study
• When asked for source of funding please make it clear that you are applying for a "White Rose BBSRC DTP iCASE Studentship"
• Give the full project title and name the supervisors listed in this advert.

If you have any further queries regarding this opportunity, please contact [Email Address Removed]