LENS fighting Covid-19: How neutrons will contribute

LENS and the fight against Covid-19: How neutrons will contribute

27 MAR 2020

Schematic diagram of the coronavirus particle. CREDIT: Binte Altaf

As with HIV before it, Europe’s advanced neutron sources will make an essential contribution to the fight against the SARS-CoV-2 virus.

On 26 October 1895 Louis Pasteur announced to the National Academy of Science in Paris the first successful vaccination of a 9-year-old boy infected with rabies, a viral disease that up to then was considered unavoidably fatal. Viral diseases continue to haunt humanity, as demonstrated by the current pandemic of Covid-19 that, as we write, has killed tens of thousands, is straining our health systems dangerously beyond their capacity and is a severe threat to the global economy. However, the means we have to confront our foe have improved tremendously since the times of Pasteur, and this is one of the merits of modern science. 

While Pasteur did not even know what enemy he was dealing with, SARS-CoV-2, the virus at the origin of the coronavirus disease, Covid-19, was deciphered immediately after its discovery. Its full genome sequence is available on the internet. This sequence and the processes developed in the context of genetic research are at the origin of the kits employed to test for Covid-19. The sequencing equally allowed expression of many of the proteins that make up the virus, and today—only three months after the discovery of the virus—the three-dimensional structures of these proteins are available. This structural information is already in use by pharmaceutical researchers hunting for the inhibitors that will impede the virus’s reproduction. 

Global distribution of confirmed cases of COVID-19, 27 March 2020. CREDIT: Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU)

But the global race for both a vaccine and therapeutics for Covid-19 requires more than genetic information. Modern analytical tools such as synchrotron X-ray radiation, cryo-electron microscopy and neutron scattering are indispensable for important insights into the morphology and functionality of viruses. Neutron scattering’s particular role here is to provide unique information on the chemistry of enzymatic reactions that often involve proton transfer. Recent studies on HIV-1 protease, an enzyme essential for the life-cycle of the HIV virus, perfectly illustrate the case. 

Treating the disease and stopping the virus

Proteases are like biological scissors that cleave polypeptide chains at precise locations. If the cleavage is inhibited, for example, by appropriate anti-retroviral drugs, then so-called poly-proteins remain in their original state and the machinery of virus replication is blocked. For the treatment to be efficient this inhibition has to be robust—that is, the drug occupying the active site should be strongly bound to the backbone of the protease. In this way the likelihood that treatments can be effective in the long run, despite mutations of the enzyme, is increased. Neutron crystallography data adds supplementary structural information to X-ray data by providing key details regarding hydrogen atoms, critical players in the binding of such drugs to their target enzyme through hydrogen bonding, and revealing important details of protonation and hydration. In this way neutron crystallography data can help towards the design of more effective medications. 

Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease. CREDIT: ILL/Methods in Enzymology

High-resolution X-ray data on the protease of SARS-CoV-2 are already available and efforts are being deployed to obtain crystals for neutron crystallography studies. Proteases are, however, not the only proteins where neutron crystallography can provide essential information. For example, virus spike proteins responsible for mediating the attachment and entry into human cells are of great relevance for developing therapeutic defense strategies against the virus. Here neutron crystallography can provide unique information about the precise coupling mechanism of the virus and the receptor proteins of the cell membrane.

The big picture and the moving picture

When it comes to studying the function of larger biological complexes such as assembled viruses, small angle neutron scattering becomes an important analytical tool. The technique’s capacity to distinguish specific regions (RNA, proteins and lipids) of the virus—thanks to advanced deuteration methods—enables researchers to map out the arrangement of the various components, contributing invaluable information to structural studies of SARS-CoV-2. 

While NMR and cryo-electron microscopy provide the detailed atomic-resolution structure of small biological assemblies, neutron scattering allows researchers to pan back to see the larger picture of full molecular complexes at lower resolution. Neutron scattering is also uniquely suited to determining the structure of functional membrane proteins in physiological conditions. Neutron scattering will therefore make it possible to map out the structure of the complex formed by the SARS-CoV-2 spike protein—the protein surrounding the virus—and its human receptor.

This image shows five clinical drugs superimposed in the active site of the human carbonic anhydrase II isoenzyme (hCA II). The image is based on neutron-resolved crystal structures. The active site is flanked by hydrophilic (violet) and hydrophobic (green) binding pockets that can be used to design specific drugs targeting cancer-associated hCAs. CREDIT: ORNL/Andrey Kovalevsky

A full understanding of the virus’s life cycle requires the study of the interaction of the virus with the cell membrane and the mechanism it uses to penetrate the host cell. Covid-19 is one of those viruses, like HIV, possessing a viral envelope composed of lipids, proteins and sugars. By providing information on its molecular structure and composition, the technique of neutron reflectometry helps to elucidate the precise mechanism the virus uses to penetrate the cell. This may be by direct fusion of the virus membrane with the external cell membrane, or with the plasma membrane, or, in the case that the virus is internalized, by endocytosis. Neutron reflectometry can in fact provide detailed structural information on the interaction of small protein fragments, so-called peptides, that mimic the spike protein and that are believed to be responsible for binding with the receptor of the host cell. 

Finally, we should not forget that viruses in their physiological environments are highly dynamic systems. Knowing how they move, deform and cluster is essential to the optimisation of diagnostic and therapeutic processes. Neutron spectroscopy, which is ideally suited to follow the motion of matter from the small chemical group to large macromolecular assemblies, is the tool of choice to provide this information. 

Assembling the data from all of these neutron-based analyses of the coronavirus will be essential to control its spread and limit its societal impact over the long term.

LENS facilities recognize and have quickly embraced their responsibility to contribute to the fight against Covid-19, and are fully mobilized to rapidly conduct all relevant experiments. These will take priority over all other scientific activities at the facilities. Special access channels to beam time have been put in place to allow the scientific community to respond without delay to the challenge posed by Covid-19. Details can be found on the respective sites of the LENS partners.

Budapest Neutron Center (BNC)

European Spallation Source (ESS)

Forschungszentrum Jülich (FZJ)

Institut Laue-Langevin (ILL)

ISIS Neutron & Muon Source (ISIS)

Laboratoire Léon Brillouin (LLB)

Heinz Maier-Leibnitz Zentrum (MLZ)

Paul Scherrer Institute (PSI)

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