About the Project
To address this major unmet medical need, we have been funded by a Wellcome Trust Pathfinder Award to use a combination of computer-aided molecular design coupled with synthetic chemistry and an EBOV mini-genome assay (which allows EBOV replication to be measured at BSL2), to design and validate small molecules targeted to a conserved hydrophobic pocket in the EBOV nucleocapsid protein (NP). This pocket binds a peptide from the N-terminus of the VP35 cofactor, and this interaction is essential for EBOV gene expression and thus viral replication. Excitingly, this approach yielded a number of small molecules that selectively inhibited EBOV gene expression with nanomolar EC50 values (1).
This studentship will build on these studies by applying an analogous approach to a second critical interaction in virus replication – between EBOV NP and the VP30 phosphoprotein. The interface between these two proteins has also been structurally characterised. The student will use bespoke in silico drug programmes developed in Leeds (e.g. SPROUT) to interrogate this structural information and design and synthesise small molecules with the potential to interfere with this interaction. The activity of these will then be tested using an established EBOV mini-genome assay.
Further characterisation of the compounds will involve exploiting the biophysical and structural facilities available within FBS and the Astbury Centre. For example the effects of compounds of the structure of the NP-VP30 complex will be analysed using X-ray crystallography and/or NMR, binding affinities will be determined using surface plasmon resonance (SPR) or isothermal calorimetry (ITC). EBOV NP has been reported to form ring structures that are visible using electron microscopy (EM) – the effects of compounds on these higher order structures will be investigated using cryo-EM via the state-of-the-art Titan Krios microscopes in the Astbury BioStructure laboratory. With our collaborators at Porton Down and University of Texas Medical Branch, Galveston, promising lead compounds will also be tested against infectious EBOV (in BSL4).
Active compounds will also be useful as biological tools to further our understanding of EBOV replication, for example by probing the role of the EBOV NP:VP30 interaction at different stages in the virus lifecycle (such as mRNA transcription, genome replication and protein translation).
The project will thus provide the possibility of training in a unique interdisciplinary set of skills – a combination of in silico drug design/synthetic chemistry, molecular biology, cell biology, virology and biophysical/structural techniques. The precise combination of approaches will depend on both the interests of the student but also the outcomes of the initial compound activity screen. Importantly, the variety of approaches means that both flexibility and contingency strategies are built in to this project. The supervisors have a strong record of collaboration in the area of antiviral development exemplified by previous studies on hepatitis C virus (2,3)
Candidates should have, or be expecting, a 2.1 or above at undergraduate level in a relevant field. If English is not your first language, you will also be required to meet our language entry requirements. The PhD is to start in Oct 2018.
Please apply online here https://studentservices.leeds.ac.uk/pls/banprod/bwskalog_uol.P_DispLoginNon
Include project title and supervisor name, and upload a CV and transcripts.
2) Shaw J, Harris M and Fishwick CWG. Identification of a lead like inhibitor of the hepatitis C virus non-structural NS2 autoprotease. Antiviral Res 124:54-60 2015
3) Shaw J, Fishwick CWG and Harris M. Epoxide based inhibitors of the hepatitis C virus non-structural 2 autoprotease. Antiviral Res 117 20-26 2015
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