International Team of Scientists Identifies Common Vulnerabilities Across Coronaviruses

Nevan Krogan talks with the QBI COVID-19 team

Nevan Krogan (center), PhD, and his collaboration of scientists around the world have fast-tracked efforts to find the proteins in cells that get highjacked by COVID-19. Photo by Susan Merrell

In research published Oct. 15 in Science, an international team of almost 200 researchers from 14 leading institutions in six countries studied the three lethal coronaviruses SARS-CoV-2, SARS-CoV-1 and MERS-CoV in order to identify commonly hijacked cellular pathways and detect promising targets for broad coronavirus inhibition.

In addition, using molecular insights gained from this multidisciplinary, systematic study of coronaviruses, the group analyzed medical records of approximately 740,000 patients with SARS-CoV-2, assessing clinical outcomes in these patients to uncover approved therapeutics with potential for rapid deployment. These results demonstrate how molecular information can be translated into real-world implications for the treatment of COVID-19, an approach that can ultimately be applied to other diseases in the future. 

“This far-reaching international study elucidates for the first time commonalities and, importantly, vulnerabilities, across coronaviruses, including our current challenge with the SARS-CoV-2 pandemic,” said Nevan Krogan, PhD, director of the Quantitative Biosciences Institute (QBI) at the UC San Francisco School of Pharmacy, senior investigator at Gladstone Institutes, and lead investigator of the study. “In unique and rapid fashion, we were able to bridge biological and functional insights with clinical outcomes, providing an exemplary model of a differentiated way to conduct research into any disease, rapidly identify promising treatments and advancing knowledge in the fields of both science and medicine. This body of work was only made possible through the collaborative efforts of senior scientific thought leaders and teams of next-generation researchers at premier institutions across the globe.”

The collaboration included academic and private sector scientists from UCSF, QBI’s Coronavirus Research Group (QCRG), Gladstone Institutes, EMBL’s European Bioinformatics Institute (EMBL-EBI) in Cambridge, England, Georgia State University, Icahn School of Medicine at Mount Sinai in New York, Institut Pasteur in Paris, Cluster of Excellence CIBSS at the University of Freiburg in Germany, University of Sheffield in the UK, and other institutions, as well as from Aetion, which makes software for analysis of real-world data, and genome engineering company Synthego. 

Cross-Coronavirus Study of Protein Function

Building on previous work published in both Nature and Cell, the researchers studied SARS-CoV-2, SARS-CoV-1 and MERS-CoV comprehensively, using biochemical, proteomic, genetic, structural, bioinformatic, virological and imaging approaches to identify conserved target proteins and cellular processes across coronaviruses. Leveraging a SARS-CoV-2 map, or “interactome,” documenting how SARS-CoV-2 proteins interact with their target human host cell proteins, the team built protein-protein interaction maps for SARS-CoV-1 and MERS-CoV, highlighting several key cellular processes that are shared across all three coronaviruses. These common pathways and protein targets represent high-priority targets for therapeutic interventions for this and future pandemics.

“Working diligently since the early days of SARS-CoV-2 identification, we came together with the individual strengths of each organization to interrogate the biology and functional activities of these viruses, looking to exploit weaknesses,” said Veronica Rezelj, PhD, of Institut Pasteur. “In our latest study, we augmented our knowledge base by driving down into two additional coronaviruses, elucidating mechanisms across viruses that allow potential therapeutic interventions.”

Unique Interaction Between Two Viruses and a Human Protein

The team found that a human protein called Tom70 interacts with a protein called Orf9b, which is found in both the SARS-CoV-1 and SARS-CoV-2 viruses. Tom70 is normally involved in the activation of a signaling protein known as MAVS, which is essential for an innate antiviral immune response. The team showed that when Orf9b binds to Tom70, it inhibits Tom70’s interaction a protein called Hsp90, which plays a key role in the interferon pathway and inducing protective cellular self-destruction when cells are infected by a virus.  

In a collaboration among more than 60 scientists in the QCRG led by QBI Fellow Klim Verba, PhD, and QBI’s Oren Rosenberg, MD, PhD, the structure of Orf9b bound to the active site of Tom70 was determined by cryoelectron microscopy (cryoEM) at near-atomic resolution, as well as highly unusual protein–protein interactions. The functional significance and regulation of these Orf9b–Tom70 interactions require further investigation, but because these interactions were seen in both the SARS-CoV-1 and SARS-CoV-2 viruses, a deeper understanding of these processes could have value as a pan-coronavirus therapeutic target. 

Potential Targets for Clinically Approved Therapeutics

Using the three coronavirus interactomes as a guide, the team performed CRISPR and RNA interference (RNAi) knockouts of the putative host target proteins of each virus and studied how loss of these proteins altered the ability of SARS-CoV-2 to infect human cells.

They determined that 73 of the proteins studied were important for the replication of this virus and used this list to prioritize evaluation of drug targets. Among these were the receptor for the inflammatory signaling molecule IL-17, which has been identified in numerous other studies as an important marker of COVID-19 disease severity; prostaglandin E synthase 2 (PGES2), which functionally interacts with the Nsp7 protein in all three viruses; and sigma receptor 1, which interacts with Nsp6 in both SARS-CoV-1 and SARS-CoV-2. 

Armed with this knowledge, the group performed a retrospective analysis of medical billing data from approximately 740,000 people who had tested positive for SARS-CoV-2 or were presumed to be positive. 

In the outpatient setting, SARS-CoV-2-positive patients who were newly prescribed indomethacin, a non-steroidal anti-inflammatory drug (NSAID) that targets PGES-2, were less likely to require hospitalization or inpatient services than CoV-2-positive new users of celecoxib, an NSAID that does not target PGES-2.

In the inpatient setting, again leveraging the medical billing data, the group compared the effects of two classes of antipsychotic drugs on COVID-19 outcomes. In cell culture experiments, the team found that one class, known as “typical” antipsychotics, bind sigma 1 receptors and also have antiviral activity, which atypical antipsychotic drugs, which are used for the same indication, were not found to have antiviral activity. Half as many SARS-CoV-2-positive patients who were newly prescribed typical antipsychotics progressed to the point of requiring mechanical ventilation, compared to new users of atypical antipsychotics. Typical antipsychotics can have significant adverse effects, but other sigma receptor 1–targeting drugs exist and more are in development.  

“It is critical to note that the number of patients taking each of these compounds represent small, non-interventional studies,” said Krogan. “They are nonetheless powerful examples of how molecular insight can rapidly generate clinical hypotheses and help prioritize candidates for prospective clinical trials or future drug development. A careful analysis of the relative benefits and risks of these therapeutics should be undertaken before considering prospective studies or interventions.”

Pedro Beltrao, PhD, group leader at EMBL’s European Bioinformatics Institute, said, “These analyses demonstrate how biological and molecular information are translated into real-world implications for the treatment of COVID-19 and other viral diseases. After more than a century of relatively harmless coronaviruses, in the last 20 years we have had three coronaviruses which have been deadly. By looking across the species, we have the capability to predict pan-coronavirus therapeutics that may be effective in treating the current pandemic, which we believe will also offer therapeutic promise for a future coronavirus as well.”