Using X-ray images to study virus proteins
Alke Meents points to an orange robot arm. “It can automatically remove a sample from a cooling vessel every three minutes and place it in a measuring device,” says the researcher from the German Electron-Synchotron (DESY) in Hamburg. “The sample is then subjected to extremely intense X-ray radiation from our PETRA III storage ring.” This gives experts a precise picture of how the atoms in the sample are arranged. This procedure is called crystal structure analysis, it benefits a wide variety of disciplines, from chemistry and biology to solid state physics and geophysics to materials research. At the moment, the method is playing a special role: It is helping researchers at DESY and the Helmholtz Centre Berlin (HZB) to understand the inner workings of the new coronavirus and identify promising substances for new medications.
An important point of attack is the so-called main protease of SARS-CoV-2. This protein plays a key role in the reproduction of the virus in the human body. “If we could find an active substance to block this enzyme, we could stop the virus,” says Meents. Scientists at both DESY and HZB are searching for medications that fit into the active center of the virus enzyme so well that they really clog it up, rendering it inactive.
Key protein identified
The conditions for such a discovery were established at HZB back in February at the BESSY II storage ring in Berlin. “At the time, a team led by Rolf Hilgenfeld of the Universität zu Lübeck succeeded in determining the exact structure of the main protease,” says HZB researcher Manfred Weiss. “They started by growing the protein into tiny crystals.” The team then analyzed the crystals using the high-intensity X-ray beam generated in the BESSY II accelerator by electrons traveling almost at the speed of light when they are directed through a special magnet. This revealed the precise structure of the key enzyme – right down to the atom.
The search for potential active ingredients could then begin in Hamburg and Berlin. The experts are pursuing different, complementary strategies: At DESY in Hamburg, Alke Meents’s team is attempting to find out whether the main protease might react to an active substance that is already known. “To do this, we crystallize the coronavirus protein with the active substance in question and use an X-ray beam to see whether the substance binds to the protein,” says Meents. At HZB in Berlin, Manfred Weiss and his colleagues are focusing on the suitability of relatively small molecules that are not established medications yet. “Based on the results of the crystal structure analysis, we can use a computer to determine whether it is possible to design similar molecules that are even more suitable,” Weiss writes.
Lockdown at the storage rings
The experiments have been conducted under unusual conditions. “In March, the coronavirus shutdown forced us to stop operating our accelerator altogether,” says HZB user coordinator Astrid Brandt. “But we left it in standby mode for the coronavirus research so we could power it up again within 24 hours.” A special fast-track procedure in Berlin and Hamburg allowed it to be accessed without any red tape. Measurements could begin just a few days after the research teams submitted their proposal.
For other teams that are not involved in coronavirus research, the accelerator shutdowns in Hamburg and Berlin have, of course, been a loss. In all, several hundred experts have been unable to perform their experiments. “We will make up for all the measuring times we had to cancel,” says Antje Vollmer, Head of User Coordination at HZB. “And we will also provide particularly fast access for urgent projects in the future.”
Both X-ray facilities have resumed operation, albeit with restrictions: With a few exceptions, users cannot travel to the facilities themselves. Instead, they have to send their samples to Hamburg or Berlin, where the permanent staff conducts the experiments. Despite these restrictions, the crisis has also presented certain opportunities. “Coronavirus will cause a number of permanent changes at our Center,” says DESY head Helmut Dosch. “We are considering fundamental changes to the way user operation is organized.”
Lessons from the coronavirus
It is conceivable that, in the future, even more experiments will be controlled remotely. The vision is for users to send their samples to the accelerator and control the experiment from an office at their own facility – much like a surgeon who operates a surgical robot via the internet. “We may even be able to use artificial intelligence to adjust the accelerator remotely, optimizing it to meet the requirements of the task at hand,” says Dosch. “We are currently discussing this in great detail.”
And the search for new substances to fight the coronavirus? The experiments at the X-ray facilities in Berlin and Hamburg are returning promising results. “We have found four or five candidates that dock with the coronavirus enzyme,” says Manfred Weiss of HZB. “We are now looking for related substances that can bind to it a little more firmly.” And at DESY, the team has succeeded in measuring 7,700 protein crystals in a very short time – a real hive of activity. “This has revealed more than forty substances that bind to the main protease. Two of them are particularly promising and very surprising candidates,” Meents is happy to report. The candidates will now go through various laboratory tests to determine whether they can actually stop the virus from reproducing, thereby knocking out the coronavirus protein.
Particle accelerators: Large-scale modern research facilities
Scientists use particle accelerators to decode the structures of a wide variety of materials. To do so, they also use synchrotrons, which are ring-shaped facilities in which charged elementary particles are greatly accelerated to gain high levels of kinetic energy. As they go around the ring, the electrons emit radiation, which scientists use in a targeted manner to identify points of attack in proteins, for example, and search for active substances.
The Helmholtz Centre Berlin operates the BESSY II electron storage ring, which focuses on soft X-rays and is unique in Germany. The facility complements the PETRA III storage ring at DESY in Hamburg, which also serves the hard X-ray spectrum and is among the brightest storage ring-based X-ray radiation sources in the world.
The accelerator facility at the GSI Helmholtz Centre for Heavy Ion Research in Darmstadt is also contributing to overcoming the coronavirus pandemic. The GSI researchers are using high-energy heavy ions instead of gamma rays to kill the virus. Unlike conventional methods, this leaves the virus shell largely intact. The inactivated virus specimens are then tested in order to develop a new vaccine.