Solving the structure of the SARS-CoV-2 main protease: from synthetic gene to crowdsourced drug discovery project


As part of a huge, international team effort, scientists at the Diamond Light Source (Instruct Centre UK) solved a new structure of SARS-CoV-2 main protease (Mpro), triggering a full X-ray fragment-based drug discovery project.

Efforts began in late January 2020, when researchers at the Diamond Light Source were contacted by scientists in China. The research team of Zihe Rao and Haitao Yang at ShanghaiTech University had worked rapidly to determine the crystal structure of the novel SARS-CoV-2 main protease in complex with a covalent inhibitor (N3) at 2.16 Å (PDB ID: 6LU7). The next challenge was to obtain and characterise ligand-free crystals of the main protease. Using a length of DNA synthesised using the published protease sequence, the team at Diamond cloned the full-length protein to obtain crystals of the unliganded enzyme for analysis by X-ray diffraction. On the macromolecular crystallography beamline I04-1 at the Diamond Light Source, the main protease crystals diffracted to high resolution, allowing the scientists to solve the crystal structure of the free main protease to 1.25 Å (PDB ID: 6YB7). Crucially, the structure revealed that the active site of SARS-CoV-2 main protease was empty and solvent-accessible, making it an ideal candidate for fragment screening.


SARS-CoV-2 Mpro Single Crystal Crystallography from Diamond Light Source on Vimeo.

Using the SARS-CoV-2 main protease reference structure, a huge crystal-based fragment screen was undertaken at the XChem facility at the Diamond Light Source. The XChem screening experiment, combined with a mass spectrometry screen of covalent fragments at the Weizmann Institute of Science (Instruct Centre IL), yielded over 60 fragment hits with structures of fragment-protein complexes. The fragment screening motivated a huge computational effort to design inhibitor compounds of SARS-CoV-2 main protease including a crowdsourcing initiative. In the first round of submissions, 1900 structures were submitted by 300 contributors. It is hoped that the combined internal and external efforts to design inhibitor compounds will facilitate the development of effective drug against COVID-19.



To be published:

COVID-19 main protease with unliganded active site 

Owen, C.D., Lukacik, P., Strain-Damerell, C.M., Douangamath, A., Powell, A.J., Fearon, D., Brandao-Neto, J., Crawshaw, A.D., Aragao, D., Williams, M., Flaig, R., Hall, D., McAauley, K., Stuart, D.I., von Delft, F., Walsh, M.A.


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