Investigating the structural dynamics and inhibition of the cysteine proteases of SARS-CoV-2 and related coronaviruses

The project focuses on developing a fundamental mechanistic understanding of viral proteases crucial for coronavirus replication. The recent outbreak of respiratory disease COVID-19, caused by coronavirus SARS-CoV-2, has caused a worldwide pandemic of unprecedented scale. SARS-CoV-2 relies on two viral proteases, the Papain-like and main proteases (PL^pro and M^pro), for the breakdown of polypeptides into individual functional proteins. Aside from proteolytic functions, PL^pro is also involved in deubiquitination and deISG15lation activities, proposed to regulate the host response to viral infections. Due to their essential role in viral replication, these enzymes have become key targets for drug discovery, with an orally administered M^pro inhibitor recently being approved by the European Medicines Agency and UK regulators.

Both proteases use multiple substrates, however, the molecular basis and dynamics underlying their different substrate selectivities are poorly understood. More generally, from a mechanistic, inhibition, enzyme engineering, and an evolutionary perspective, the role of correlated motions during enzymatic catalysis is currently a field of high interest.

This project aims to investigate the fundamentals behind the catalysis through a combination of biochemical assays and cutting-edge structural biology, in particular using time resolved (tr) crystallography employing synchrotron and XFEL sources. These tr-studies rely on the use of microcrystal slurries to enable rapid mixing of substrates with enzymes at room temperature and a serial data collection approach to mitigate radiation damage. The small size of these microcrystals benefits from the higher photon flux available at XFELs during data collection. Additionally, this study aims to explore the use of photocleavable sites in engineered peptide substrates to control the initiation of the reaction.

The overall goal of this project is to provide structural snapshots of the reaction coordinates of both PL^pro and M^pro during catalysis, which enhances the fundamental understanding of enzyme catalysis and will provide a comprehensive structural framework for drug discovery.

This is a joint project between the University of Oxford and Diamond Light Source.

Attributes of suitable applicants:

Applicants should be trained in biochemistry, biophysics or chemistry and have an interest in enzyme mechanisms and biophysics. Self-motivation, scientific curiosity, and the ability to work well as part of a team are important.

NB:

This project is supported through the Oxford Interdisciplinary Bioscience Doctoral Training Partnership (DTP) studentship programme. The student recruited to this project will join a cohort of students enrolled in the DTP’s interdisciplinary training programme, and will participate in the training and networking opportunities available through the DTP. For further details, please visit www.biodtp.ox.ac.uk. The DTP and its associated partner organisations aim to create a community that is innovative, inclusive and collaborative, in which everyone feels valued, respected, and supported, and we encourage applications from a diverse range of qualified applicants.