X-ray Screening Identifies Promising Drugs for Treatment of COVID-19

A team of researchers, including scientists from the MPSD, has identified several candidates for drugs against the SARS-CoV-2 coronavirus using the PETRA III X-ray light source from Germany’s Electron Synchrotron (DESY). They bind to an important protein of the virus and could thus be the basis for a drug against Covid-19. In a so-called X-ray screening, the DESY-led research team tested nearly 6,000 known active substances that already exist for the treatment of other diseases. After measuring about 7,000 samples, the team was able to identify a total of 37 substances that bind to the main protease (Mpro) of the SARS-CoV-2 virus, as the scientists report online today in the journal Science. Seven of these substances inhibit the activity of the protein and thus slow down the multiplication of the virus. Two of them do this so promisingly that they are currently under further investigation in preclinical studies. This drug screening – probably the largest of its kind – also revealed a new binding site on the virus’s main protease that drugs can attach to.

Unlike vaccines, which help healthy people defend themselves against the virus, drug research looks for drugs that slow or stop the virus from propagating in the bodies of people who are already infected. Viruses cannot reproduce by themselves. Instead, they introduce their own genetic material into their host’s cells and cause them to produce new viruses. Proteins such as the virus’s main protease play an important role in this process. Protease cuts protein chains produced by the host cell according to the blueprint of the virus genetic material into smaller parts necessary for the virus to reproduce. If the main protease can be blocked, the cycle may be interrupted; the virus can no longer reproduce and the infection is defeated.

Beamline P11 from DESY’s PETRA III research light source specializes in structural biology studies. Here, the three-dimensional structure of proteins can be imaged with atomic precision. The research team led by DESY physicist Alke Meents used this special capability to examine several thousand active substances to see if and how they ‘stick’ to the main protease – the first important step to block it. Like a key in a lock, the drug molecule fits into a binding center of the protease. Since these active substances have already been approved for the treatment of humans or are currently being tested, suitable candidates to combat SARS-CoV-2 could be used in clinical trials significantly faster, saving months or years of drug development.

The robotic equipment at the beamline processed each of the more than 7,000 measurements in just about three minutes each. Using automated data analysis, the team was able to quickly separate the chaff from the chaff. “Using a high-throughput method, we were able to find a total of 37 active substances that bind with the main protease,” says Meents, who initiated the experiments.

Lourdu Xavier, a co-author of the International Max Planck Research School IMPRS-UFAST study at MPSD, describes the process: “The challenging part was screening 6000+ drugs using the monocrystalline screening method. It required several dozen people to work around the clock for a few weeks growing crystals, soaking them with drugs, fishing, freezing and loading the crystals into the robotic station for X-ray examination. It was a marathon cum relay. “says Lourdu Xavier.” It was a fantastic team effort and I am happy that we found several bound drugs.

“As these exciting results come in to preclinical studies, we are also well equipped to gain deeper insights into the room temperature dynamics of the allosteric drug-binding mechanism using XFEL pulses, which can provide millions of diffraction patterns in a short time. time.”

In a next step, the researchers at the Bernhard Nocht Institute for Tropical Medicine investigated whether these active substances inhibit or even prevent virus replication in cell cultures and how compatible they are for the host cells. As a result, the number of suitable active ingredients has been reduced to seven, two of which were particularly striking. “The active ingredients Calpeptin and Pelitinib clearly showed the highest antivirality with good cell compatibility. Our collaboration partners have therefore already started preclinical research with these two substances, ”explains DESY researcher Sebastian Günther, lead author of the Science publication.

In their drug research using protein crystallography, the researchers did not examine fragments of potential drugs as is usually the case, but entire molecules of the drug. However, during the process, the team of more than 100 scientists also discovered something completely unexpected: They found a binding site on the main protease that was completely unknown until then. “It was not only a nice surprise that we were able to discover a new drug binding site on the main protease – a result that can really only be achieved with a synchrotron light source such as PETRA III – but that even one of the two promising drug candidates binds exactly to this site. ”Says Christian Betzel of the University of Hamburg, co-initiator of the study.

“Even if the two most promising candidates fail clinical trials, the 37 compounds that bind to the main protease provide a valuable database for drug development based on them,” explains Patrick Reinke, DESY researcher and co-author of the publication. .

Reference: “X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease” by Sebastian Günther, Patrick YA Reinke, Yaiza Fernández-García, Julia Lieske, Thomas J. Lane, Helen M. Ginn, Faisal HM Koua, Christiane Ehrt , Wiebke Ewert, Dominik Oberthuer, Oleksandr Yefanov, Susanne Meier, Kristina Lorenzen, Boris Krichel, Janine-Denise Kopicki, Luca Gelisio, Wolfgang Brehm, Ilona Dunkel, Brandon Seychell, Henry Gieseler, Brenna Norton-Bakero, Beatri-Bakero Pérez, Martin Domaracky, Sofiane Saouane, Alexandra Tolstikova, Thomas A. White, Anna Hänle, Michael Groessler, Holger Fleckenstein, Fabian Trost, Marina Galchenkova, Yaroslav Gevorkov, Chufeng Li, Salah Awel, Ariana Peck, Miriam Barthelmess, Frank Schluenzen, Paulraj Lourdu Xavier, Nadine Werner, Hina Andaleeb, Najeeb Ullah, Sven Falke, Vasundara Srinivasan, Bruno Alves França, Martin Schwinzer, Hévila Brognaro, Cromarte Rogers, Diogo Melo, Joanna J. Zaitseva-Doyle, Juraj Knoska, Gisel E. Peña- Murill o, Ai da Rahmani Mashhour, Vincent Hennicke, Pontus Fischer, Johanna Hakanpää, Jan Meyer, Philip Gribbon, Bernhard Ellinger, Maria Kuzikov, Markus Wolf, Andrea R. Beccari, Gleb Bourenkov, David von Stetten, Guillaume Pompidor, Isabel Bento, Saravanan Panneerselvam, Ivars Karpics, Thomas R. Schneider, Maria Marta Garcia-Alai, Stephan Niebling, Christian Günther, Christina Schmidt, Robin Schubert, Huijong Han, Juliane Boger, Diana CF Monteiro, Linlin Zhang, Xinyuanyuan Sun, Jonathan Pletzer-Zelgert, Jan Wollenhaupt, Christian G. Feiler, Manfred S. Weiss, Eike-Christian Schulz, Pedram Mehrabi, Katarina Karnicar, Aleksandra Usenik, Jure Loboda, Henning Tidow, Ashwin Chari, Rolf Hilgenfeld, Charlotte Uetrecht, Russell Cox, Andrea Zaliani, Tobias Beck, Matthias Rarey, Stephan Günther, Dusan Turk, Winfried Hinrichs, Henry N. Chapman, Arwen R. Pearson, Christian Betzel and Alke Meents, April 2, 2021, Science.
DOI: 10.1126 / science.abf7945

Researchers from DESY, the MPSD, the Universities of Hamburg and Lübeck, the Bernhard Nocht Institute of Tropical Medicine, the Fraunhofer Institute for Translational Medicine and Pharmacology, the Heinrich Pette Institute, the European XFEL, the European Molecular Biology Laboratory EMBL, the Max Planck Society, the Helmholtz-Zentrum Berlin and other institutions were involved in the work. In addition to the experiments at the P11 measuring station, measurements were also carried out at the EMBL measuring stations P13 and P14 on PETRA III.