Large-scale research facilities in Lund help tackle SARS CoV-2 viral genome replication machinery

Ribbon diagram of SARS CoV-2 Nsp10
Figure 2: Ribbon diagram of SARS CoV-2 Nsp10 in its unbound form. Nsp10 contains two zinc fingers (zinc ions are shown as grey spheres). Photo: ESS

An international collaboration between the UK’s UCL School of Pharmacy, Lund Protein Production Platform at Lund University, and ESS - through it's DEMAX laboratory, have initiated bio-physical and structural studies of three non-structural proteins from the novel coronavirus, SARS CoV-2, the causative agent of COVID-19.

The Deuteration & Macromolecular Crystallisation (DEMAX) platform at ESS has been offering prioritised access to laboratory services for scientists and researchers working on COVID-19-related research projects. Under this call, a research project on viral proteins was accepted and the research team recently managed to solve, and have now started to analyse, one of these proteins, Nsp10, with the help of the BioMAX beamline at MAX IV Laboratory.

Crystals of SARS CoV-2 Nsp10

Figure 1a (left): Photo of crystallisation drop showing many hexagonal-shaped crystals of SARS CoV-2 Nsp10. Figure 1b (right): Single crystal of Nsp10 frozen on a 0.08mm loop (BioMAX beamline, MAX IV laboratory).

Photos: ESS & MAX IV

To be able to find an efficient drug, which prohibits the novel coronavirus from causing the disease COVID-19, one important aim is to understand how to block the virus from replicating its genomic material. By doing so, the virus will ‘die out’ over time as it fails to reproduce or make infectious particles. One way of obtaining this knowledge is to use X-rays to obtain an image of the structure of the proteins involved in this process. 

Zoe Fisher, Group Leader for Deuteration & Macromolecular Crystallisation at ESS, examines

Zoe Fisher, Group Leader for Deuteration & Macromolecular Crystallisation at ESS. 

Photo: Indressa Gustafsson

There are 16 non-structural proteins (NSPs) in SARS CoV-2 that play important roles in viral replication and transcription. The virus has proof-reading capabilities and the proteins involved are possible drug targets.

Interfering with the virus’s ability to replicate and produce a mature, infectious virus capsid is a key focus for many international researchers. High-resolution crystallographic studies play an important role in finding either new inhibitors or, studying how existing drugs can be repurposed to block the novel coronavirus.

There are several proteins involved with proofreading of the viral RNA and its protection by RNA cap methylation, ensuring RNA replication. The research team’s studies focus on three of these: Nsp10, Nsp14, and Nsp16. A key part of this work is to establish crystallisation conditions to enable high-throughput fragment-based screening in the search for novel small molecule inhibitors that can block the viral replication cycle.

Recently, the research team had success and were able to produce crystals of one of these proteins, Nsp10 (Figure 1). Using rapid access, the data was collected remotely at the BioMAX beamline at MAX IV to approx. 2.6 Å resolution. The structure was determined and structural analysis is ongoing (Figure 2). The other work on Nsp14 and 16 also continues and the research team are working towards crystal structures of those as well.

Mounting crystals at MAX IV Laboratory's BioMAX beam line

A student mounts crystals at MAX IV Laboratory's BioMAX beam line.

Photo: MAX IV, 2018

The ultimate goal for this research project is to obtain high resolution X-ray crystal structures of these proteins alone or in complex with each other to enable the search for small molecule inhibitors that disrupt their activity. These structural studies will also be complemented with other biophysical characterisation experiments such thermal stability, microscale thermophoresis and solution scattering studies using X-rays and neutrons.

When ESS is open to neutron users, we will be able to offer researchers access to instrumentation and beamtime to pursue scientific research and investigations with the help of neutron rays. According to Dr. Zoë Fisher, group Leader for DEMAX at ESS, "Neutron protein crystallography of these viral proteins in complex with inhibitors can reveal atomic level details of hydrogen atoms and binding interactions that could be crucial for understanding - and potentially improving - on inhibitor binding. Small angle scattering of different complexes of these proteins in solution could also help understand the behaviour and shape of the molecules under physiological conditions. "

This project is an international collaboration between Prof. Frank Kozielski (Main PI, School of Pharmacy, University College London), Dr. Wolfgang Knecht (Lund Protein Production Platform (LP3), Lund University) and Dr. Zoë Fisher (DEMAX, European Spallation Source ERIC, Lund).

It is supported by the MAX IV rapid access call COVID-19,, and the ESS DEMAX call for prioritised projects related to COVID-19 research.
Acknowledgements: We also need to thank all Lund Protein Production Platform (LP3) staff for excellent support and performing all experiments. We thank MAX IV Laboratory for rapid beamtime access at BioMAX through its COVID-19 response actions. We thank the BioMAX beamline staff for excellent support. We acknowledge the support of the project by the ESS for projects related to COVID-19 as well as to Lund University and its faculties for support to LP3.