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COVID-19 Proteomics Study Identifies Existing Compounds as Potential Antivirals

This story has been corrected to note that a single arm of a Brazilian hydroxychloroquine trial was ended over cardiotoxicity concerns but that the rest of the trial has continued. We regret the error.

NEW YORK – An international consortium of researchers has used protein interaction studies to identify antiviral agents that could be effective against SARS-CoV-2.

Detailed in a study published on Thursday in Nature, the effort identified 332 interactions between SARS-CoV-2 proteins and human proteins and 69 agents that could be used to target those interactions.

The researchers also tested a number of those agents in viral assays run by laboratories at Mount Sinai Hospital in New York and the Pasteur Institute in Paris and identified two broad mechanisms of SARS-CoV-2 inhibition — disrupting translation and targeting the host Sigma1 and Sigma2 receptors. Additionally, they identified several approved drugs as well as preclinical agents that appeared to have strong antiviral effects.

The study, a version of which was published in March as a preprint, used an experimental setup and techniques developed by the lab of senior author Nevan Krogan, a professor of cellular molecular pharmacology at the University of California, San Francisco's Quantitative Biosciences Institute and the Gladstone Institute of Data Science and Biosciences.

The researchers generated protein expression plasmids for 26 of the 29 proteins that are predicted to be produced by SARS-CoV-2, based on its genome, and transfected these plasmids into human HEK293T cells. After the proteins were expressed, they lysed the cells and pulled out the viral proteins via affinity purification, following by mass spectrometry to identify human proteins that were bound to them.

They then explored what molecules might disrupt these interactions by looking for ligands of the human interacting proteins using chemoinformatics and literature searches, identifying 69 agents targeting 63 of the human interactors.

Using this information, the Mount Sinai and Pasteur Institute teams performed viral assays, screening 47 of the 69 identified compounds along with an additional 28 molecules identified independently of the protein interaction experiments. Through this work, they found that translation inhibitors and ligands of the Sigma1 and Sigma2 receptors were particularly effective at reducing SARS-CoV-2 infectivity.

Among the Sigma1 and Sigma2 ligands tested was the anti-malarial drug hydroxychloroquine, which has been used to treat COVID-19 patients and is in clinical trials as a treatment for the virus. Some patients have suffered cardiotoxicity from hydroxychloroquine, however. In the case of a Brazilian trial looking at hydroxychloroquine treatment for COVID-19, researchers ended a high-dose arm of the trial early due to the observation of an increase in irregular ECGs in patients in that arm, though the other arms have continued.

The US Food and Drug Administration has issued a notice cautioning against use of hydroxychloroquine for treating COVID-19 due to reports of patient heart rhythm problems.

On a conference call accompanying the release of the paper, Krogan said the researchers had found that the drug binds more potently to a receptor in heart tissue than it does to the Sigma1 and Sigma2 receptors, which could be the cause of the observed cardiotoxicity. He noted that another agent the researchers tested, the preclinical molecule PB28, binds to the Sigma receptors without the off-target effects observed with hydroxychloroquine while also proving in the viral assays to be 20 times more effective at killing SARS-CoV-2.

Another known Sigma1 and Sigma2 ligand is progesterone, which Krogan noted could help explain the observation that on average, men suffer more severe infections than women.

He also highlighted the finding that the over-the-counter cough suppressant dextromethorphan appeared, at least in in vitro assays, to have a virus-promoting effect and suggested that caution should be used in recommending it for COVID-19 patients until more research can be conducted.

Krogan said that the identification of two separate mechanisms – translation and the Sigma1 and 2 receptors – for attacking SARS-Cov-2 was significant as he believed it was likely that "at the end of the day, a treatment that will be successful is a combinatorial treatment where you are adding multiple drugs like a cocktail."

He said that he and his colleagues have shared their data with a range of drugmakers, government authorities, and public health officials and that several pharma firms are taking some of the identified agents into clinical trials to evaluate their antiviral effectiveness and therapeutic index.