Diamond Concise Annual Review 2021/22

30 31 D I A M O N D L I G H T S O U R C E A N N U A L R E V I E W 2 0 2 1 / 2 2 D I A M O N D L I G H T S O U R C E A N N U A L R E V I E W 2 0 2 1 / 2 2 Supporting International COVID-19 Research D iamond has continued to give international COVID-19 researchers high priority access to beamtime throughout the year, despite lockdown restrictions. Over the past year, 530 shifts were delivered across all instruments for COVID-19 research. The work taking place at Diamond is grouped into projects developing understanding of the virus structure and function, new vaccine design and efficiency, new therapy and drug development. Understanding how the virus operates Several studies continued to develop detailed understanding of the SARS- CoV-2 viral mechanisms and structure. These fundamental research efforts have already resulted in the licensing of several vaccines which have been rolled out to millions around the world in rapid vaccination programmes. In addition, neutralising monoclonal antibodies (mAbs) have been developed. A research group led by Professor Peijun Zhang maintained their work on unlocking the structure of the SARS-CoV-2 virus 1 . The team used the cryo-EM facilities at eBIC to investigate viral replication. Their approach gave a holistic view of SARS-CoV-2 infection from the whole cell to individual molecules. The study confirms the value of cryo-EM and soft X-ray tomography as techniques to investigate whole cell morphology. Professor Jonathan Grimes (Diamond Fellow) worked in collaboration with several Oxford University colleagues on two projects studying coronavirus mechanisms. The first aimed to improve understanding of the mechanism of coronavirus RNA capping which is poorly understood 2 . In the second study a group performed further characterisation of the virus using biochemical techniques 3 . This work highlighted domains that could be possible targets for antiviral drugs and identified several drugs and molecules that could be developed or re-purposed. Efficacy of the vaccine The rapid development of vaccines and mAbs against COVID-19 through intensive international collaboration has been one of the positive highlights of the pandemic. Although current vaccines elicit neutralising antibody responses to the virus spike derived from early isolates, new strains have emerged with multiple mutations. Many studies are assessing the impact of these therapies against the new variants of the virus and the ability of these different variants to evade antibody responses . Recent studies include data collected automatically at Diamond on macromolecular crystallography beamline I03. A large international group studied the ability of mAbs and convalescent and vaccine sera to neutralise two Delta variant viruses that spread globally 4 . The group used beamline I03 at Diamond to determine the crystal structures of the variants. Although neutralisation of both viruses was reduced compared with earlier strains there was no evidence of widespread antibody escape. The Beta variant has been particularly difficult to neutralise using serum induced by the early pandemic. To understand this, an international collaboration performed a study to understand its antigenic landscape 5 . The study included an in-depth structure-function analysis of potent mAbs from volunteers infected with the Beta variant. Structural analyses took place using data gathered on beamline I03 to assist the development of future vaccination strategies. This group also performed analysis on different variants 6 . Structural analysis at Diamond showed that mAbs neutralise all three variants. In another recent paper in Cell an international research group studied the neutralisation of Omicron by a large panel of sera collected from early infected individuals and those vaccinated with three doses of the Oxford/Astra Zeneca or Pfizer vaccines 7 . The study revealed Omicron to be structurally similar but the most antigenically distant variant and that the variant escaped neutralisation by most mAbs. However, the researchers showed that protection from severe infection will be maintained and that a third vaccine dose is effective in boosting neutralisation titres against Omicron. Drug development (repurposing and new drugs) To defeat the current pandemic and manage the impact of SARS-CoV-2 in the future, a combination of new drugs, repurposed drugs and other therapies will be required. Diamond is playing a key role supporting research groups around the world to develop effective therapies. Major screening studies are taking place to identify new drug candidates, repurposed antivirals are being investigated and there is ongoing development of vaccines to tackle new variants. A research collaboration between Diamond, Exscientia (Oxford), Scripps Research Institute in California and Leuven University aimed to accelerate the path to clinical trials for potential antiviral treatments. The group conducted extensive experimental screens of the drug repurposing ReFRAME library 8 which identified two potential drug candidates, the caspase-1 inhibitor SDZ 224015 and tarloxotinib, a clinical stage epidermal growth factor receptor inhibitor. Diffraction data were collected from crystals cryo-cooled at Diamond with X-ray diffraction data collected at beamlines I04-1 and I24. A collaboration between Diamond and Israeli research groups designed a computational pipeline to help identify irreversible inhibitors based on structures of targets with non-covalent binders 9 . The so-called covalentiser was developed to identify covalent analogues of non-covalent binders. The group used a pre-compiled database of covalentiser results to discover several covalent kinase inhibitors and a potent covalent COVID-19 protease inhibitor. Co-crystal structural data were collected on beamline I04-1 to confirm the computational model. Other therapies An international team continued their work on neutralising single domain antibodies (nanobodies) which have significant potential as an effective treatment against COVID-19 10 . Their small size and stability mean they can be formulated for respiratory administration with improved bioavailability, easier administration, and improved therapeutic compliance. Four nanobodies were found that neutralised the virus in vitro with picomolar potency. X-ray crystallography diffraction data were collected and processed at beamlines I03, I04 and I24 at Diamond. Cryo-EM results were obtained at eBIC. Treatment with a single dose of the most potent nanobody prevented disease progression in a hamster model. It was suggested that combinations of nanobodies targeting different epitopes may improve resilience in combating new variants of the virus. References 1. Mendonça L. et al . DOI: 10.1038/s41467-021-24887-y 2. Walker A. et al . DOI: 10.1093/nar/gkab1160 3. Baddock H. et al . DOI: 10.1093/nar/gkab1303 4. Liu C. et al . DOI: 10.1016/j.cell.2021.06.02 5. Liu C. et al . DOI: 10.1016/j.chom.2021.11.013 6. Dejnirattisai W. et al . DOI: 10.1016/j.cell.2021.03.055 7. Dejnirattisai W. et al. DOI: 10.1016/j.cell.2021.12.046 8. Redhead M. et al . DOI: 10.1038/s41598-021-92416-4 9. Zaidman D. et al . DOI: 10.1016/j.chembiol.2021.05.018 10.Huo J. et al . DOI: 10.1038/s41467-021-25480-z Image of beamline I03. The Titan Krios is a state-of-the-art fully automated electron microscope designed for rapid, stable, high-resolution data collection on frozen-hydrated samples. Crystal structure of SARS-CoV-2 M pro with a pre-clinical candidate from the COVID Moonshot bound (shown in yellow). The COVID Moonshot, of which Diamond is a founding member, has received funding of £8 million fromWellcome, on behalf of the COVID-19 Therapeutics Accelerator to develop a globally accessible antiviral.