One drug to inhibit them all—all coronaviruses, that is, or at least the three evaluated in a recent study, namely, SARS-CoV-2, SARS-CoV-1, and MERS-CoV. According to the study, these deadly coronaviruses hijack the same host pathways. Consequently, all these coronaviruses could be targeted by the same antiviral drugs. The trick is to find drugs that interfere with crucial, highly conserved virus-host protein interactions.

Such interactions were mapped by an international team of almost 200 researchers, including researchers from over a dozen academic institutions and four companies (Aetion, a developer of analytics software; Synthego, a genome engineering company; Beam Therapeutics, a company that develops genetic medicines through the use of base editing; and HeathVerity, a company that links and de-identifies patient data).

The study’s lead investigator was Nevan Krogan, PhD, director of the Quantitative Biosciences Institute (QBI) at the School of Pharmacy at the University of California, San Francisco. “In unique and rapid fashion, we were able to bridge biological and functional insights with clinical outcomes,” said Krogan, who is also a senior investigator at Gladstone Institutes.

Krogan and colleagues presented their findings October 15 in Science, in an article titled, “Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.” The article describes how the scientists used proteomics, cell biology, virology, genetics, structural biology, biochemistry, and clinical and genomic information to provide a holistic view of SARS-CoV-2 and other coronaviruses’ interactions with infected host cells.

“[We] carried out comparative viral-human protein-protein interaction and viral protein localization analysis for all three viruses,” wrote the article’s authors. “Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 Orf9b, an interaction we structurally characterized using cryo-EM.”

In addition, using the molecular insights gained from this multidisciplinary, systematic study of coronaviruses, the scientists performed an analysis of medical records of approximately 740,000 patients with documented SARS-CoV-2 infection. In this analysis, the scientists were especially interested in identifying “important molecular mechanisms and potential drug treatments that merit further molecular and clinical study.”

Prior studies had identified more than 300 host cell proteins that can interact with SARS-CoV-2 proteins. In the current study, the investigators extended this work to SARS-CoV-1 and MERS-CoV.

Interestingly, the team found that the mitochondrial outer membrane protein Tom70 interacts with both SARS-CoV-1 and SARS-CoV-2 protein Orf9b. Tom70 is normally involved in the activation of mitochondrial antiviral-signaling protein (MAVS) and is essential for an antiviral innate immune response. Orf9b, by binding to the substrate recognition site of Tom70, inhibits Tom70’s interaction with heat shock protein 90 (Hsp90), which is key for its function in the interferon pathway and induction of apoptosis upon virus infection.

In a collaboration among more than 60 scientists in the QCRG led by Klim Verba and Oren Rosenberg at QBI, the structure of Orf9b bound to the active site of Tom70 was determined by cryoelectron microscopy (cryoEM) to a remarkable three-angstrom resolution. A noteworthy and rare finding showed that Orf9b, when by itself, forms a dimer and structurally a beta sheet, but exists as an alpha helix when bound to Tom70.

Using the structural image of the bound proteins, the scientists were able to discover that a key residue in the interaction with Hsp90 is moved out of position, suggesting that Orf9b may modulate key aspects of the immune response, interferon, and apoptosis signaling via Tom70. The functional significance and regulation of the Orf9b-Tom70 interaction require further experimental elucidation. This interaction, however, which is conserved between SARS-CoV-1 and SARS-CoV-2, could have value as a pan-coronavirus therapeutic target.

Using the three coronavirus interactomes as a guide, the team performed CRISPR and RNA interference (RNAi) knockouts of the putative host 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 the virus and used this list to prioritize evaluation of drug candidates.

Among these were the receptor for the inflammatory signaling molecule IL-17, which has been identified in numerous studies as an important indicator of disease severity; prostaglandin E synthase 2 (encoded by PTGES2), which functionally interacts with the Nsp7 protein in all three viruses; and sigma receptor 1, an interactor of Nsp6 from SARS-CoV-1 and SARS-CoV-2, which the group previously showed was a promising drug target in the laboratory setting.

It was at this point that the team analyzed the medical billing data from the approximately 740,000 people who tested positive for SARS-CoV-2 or were presumptively positive. In the outpatient setting, SARS-CoV-2-positive, new users of indomethacin, a non-steroidal anti-inflammatory drug (NSAID) that targets PGES-2, were less likely than matched new users of celecoxib, an NSAID that does not target PGES-2, to require hospitalization or inpatient services.

In the inpatient setting, again leveraging the medical billing data, the group compared the effectiveness of typical antipsychotics, namely haloperidol, which have activity against sigma receptor 1, versus atypical antipsychotics, which do not. Half as many new users of typical antipsychotics compared to new users of atypical antipsychotics progressed to the point of requiring mechanical ventilation. Typical antipsychotics can have significant adverse effects, but other sigma receptor 1-targeting drugs exist and more still are in development.

“It is critical to note that the number of patients taking each of these compounds represent small, non-interventional studies,” commented 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.”

“These analyses demonstrate how biological and molecular information are translated into real-world implications for the treatment of COVID-19 and other viral diseases,” said Pedro Beltrao, PhD, a corresponding author of the study and group leader at EMBL’s European Bioinformatics Institute. “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.”

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