Promising COVID-19 Antibodies Examined Using Cryo-EM and X-ray Crystallography

Curbing the COVID-19 pandemic will rely on vaccines. But, they will take time to develop, test and manufacture, and distribute. Some researchers, given the urgent and immediate need for tools to help combat the spread, are looking to neutralizing antibodies to fill in some of the gaps. An international team, led by Davide Corti, PhD, senior vice president of antibody research at Vir Biotechnology and David Veesler, PhD, assistant professor at the University of Washington, has been working on a complementary approach. They are working to identify neutralizing antibodies that could be used as a preventative treatment or as a post-exposure therapy.

Their latest findings, which include data gathered at Berkeley National Laboratory’s Advanced Light Source (ALS), indicate that antibodies derived from SARS survivors could potentially block entry of SARS-CoV-2 and other closely related coronaviruses into host cells. In a study published this week in Nature, titled “Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody,” the scientists noted that the most promising candidate antibody is already on an accelerated development path toward clinical trials.

“We are very excited to have found this potent neutralizing antibody that we hope will participate in ending the COVID-19 pandemic,” said Veesler.

Leveraging the immune system

Previous research on coronaviruses shows that neutralizing antibodies last one or two years. In addition, scientists can manufacture pharmaceutical quantities of identical antibodies so long as they know the protein sequence. Mass-produced antibodies may then be given to people who do not yet have any of their own antibodies against that particular pathogen.

Soon after SARS-CoV-2 emerged in late 2019, Veesler and his colleagues began screening for potential neutralizing antibodies among those identified from SARS and MERS survivors in 2003 and 2013, respectively. Their previous research on the SARS- and MERS-causing coronaviruses revealed that some neutralizing antibodies produced in response to those diseases were also effective against closely related coronaviruses. So, they suspected that several might inhibit SARS-CoV-2, which is very closely related to SARS-CoV.

The screening yielded eight antibodies that can bind to the SARS-CoV-2 spike glycoprotein found on the viral surface, composed of proteins with attached carbohydrates, that facilitates entry into the host cell. Multiple studies have suggested that the spike glycoprotein is the main target for both neutralizing antibodies and vaccines. Further tests narrowed the field to reveal one SARS-CoV antibody, called S309, that successfully neutralizes SARS-CoV-2.

Mapping the structure

To understand how this antibody hinders the spike protein, and to gather the information necessary to reproduce it, the team used cryo-electron microscopy (cryo-EM) and X-ray crystallography performed at ALS beamline 5.0.2., which is managed by the Berkeley Center for Structural Biology (BCSB). The ALS—a Department of Energy (DOE) user facility open to both industry and commercial teams—is a particle accelerator called a synchrotron that produces extremely bright beams of light from infrared to X-rays. The beams are directed into beamlines to support a wide range of scientific techniques, including protein crystallography. Operation of the ALS to conduct this research was supported in part by the U.S. Department of Energy National Virtual Biotechnology Laboratory, a consortium of DOE National laboratories with core capabilities relevant to the threats posed by COVID-19, and funded under the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

Using cryo-electron microscopy and binding assays, the authors wrote, “we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment.” Antibody cocktails including S309, they continued, “further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants.”

“David’s group is a more recent user of the BCSB beamlines,” said Marc Allaire, a biophysicist in Berkeley Lab’s Biosciences Area and head of the BCSB. “In 2018, they used the ALS to examine the spike glycoproteins of other coronaviruses and investigate how potential antibodies bind to them, and when it became clear that SARS-CoV-2 was a threat we were able to give the team priority time to use the beamlines.” The group used the ALS in early February and on March 31 they analyzed crystallized samples of S309.

“I have been in the field for quite a while and I am still fascinated by the power of protein crystallography,” Allaire added. In crystallography, a beam of X-ray light aimed at crystallized samples generates diffraction patterns. The intensities of the diffracted spots are then measured and used to reconstruct a 3D map of a molecule’s atomic structure. Beamline 5.0.2 is a specialized crystallography beamline that has been in operation for 20 years supporting a broad spectrum of structural biology studies and drug discovery. “We feel privileged to be contributing to David and Davide’s amazing effort and the promise of S309.”

These results pave the way for using S309- and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease.