A global team based out of the University of California, San Francisco (UCSF), has developed a new paradigm in COVID-19 drug development by focusing on the host as well as the virus. The researchers created a blueprint of how SARS-CoV-2 hijacks and rewires the host during the course of infection by mapping the protein-protein interactions (PPIs) between the host and virus that can be targeted. Using this blueprint to identify a series of drugs and compounds to test, they identified key drug classes with high potential to fight COVID-19—some of which are now being entered into clinical trials. They also identified one compound commonly found in over-the-counter cough syrup that, surprisingly, helped the virus infect cells better.

The work is published in Nature in a paper titled, “A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.”

The advantage of creating this type of blueprint, noted Nevan Krogan, PhD, professor of cellular and molecular pharmacology, director of the Quantitative Biosciences Institute (QBI) at UCSF, and senior author on the paper, is that it leads with the biology. Having the PPI data helped point the team in specific directions to find useful drugs and compounds. They did not have to look at 10s or 1000s of different compounds, noted Krogan. Instead, because the map identified a subset of compounds, they knew where to start and could quickly move into robust, quantitative assays.

Another advantage to this approach is fewer concerns about the virus developing resistance to the drug. Also, it could lead to the development of pan-pathogenic strategies. Toxicity can be an issue, but that is why they are focusing on repurposed drugs—those already FDA approved or that have passed toxicity checkpoints in clinical trials.

How did they generate the map? They first studied 26 of the 29 SARS-CoV-2 proteins in isolation. The SARS-CoV-2 proteins were codon optimized and cloned into a mammalian expression vector with an affinity tag—or bait—which could be used to enable affinity purification mass spectrometry (AP-MS) based proteomics upon expression in HEK293T/17 cells. After expressing these viral proteins in the host cells, they could then purify the viral proteins in the context of their interactions with host proteins. The team used these data to generate a map of 332 PPIs between host and viral proteins. The interactome can be found online here.

Now, the researchers had their playbook to identify which PPIs to inhibit. Among the 332, 66 human proteins were found to be targeted by 69 known compounds, including 29 FDA-approved drugs, 12 drugs in clinical trials, and 28 preclinical compounds. To test these drugs in vitro, the west coast team collaborated with two research groups working with SARS-CoV-2 virus in the lab; Christophe D’Enfert, PhD, professor and scientific director at the Institut Pasteur and Adolfo Garcia-Sastre, PhD, professor and director of the Global Health and Emerging Pathogens Institute at the Icahn School of Medicine at Mount Sinai.

Together, the team has tested 47 of the compounds and are working around the clock to test the rest. The Paris and NYC teams test the virus in Vero cell culture viral assays in which they first add the drug to the cells and then infect them with virus. Screening the drugs identified two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the Sigma1 and Sigma2 receptors.

To date, ten drugs have exhibited antiviral action. Protein translation inhibitors Zotatifin (currently in a Phase I trial for cancer therapy) and Ternatin-4 (plitidepsin) which is used clinically for multiple myeloma. Interestingly, the makers of both of these drugs have announced that they will be started in clinical trials for COVID-19.

Multiple drugs are known to modulate Sigma1 and Sigma2 receptors, and several of them showed efficacy against SARS-CoV-2; antihistimines (cloperastine and clemastine), antipsychotics (haloperidol and melperone), antimalarial (hydroxychloroquine), hormone (progesterone), antianxiety (siramesine), and two preclinical compounds. The team found that these Sigma1 and Sigma2 receptor modulators perturb the virus through different mechanisms than the translation inhibitors—potentially through cell stress response. They suggest that this may point to a combination drug approach, including other antivirals such as remdesivir.

All of these data have been shared with drug makers, government authorities, and public health officials.

A surprising result  

Despite looking for targets that would inhibit viral growth, the team discovered that one drug, dextromethorphan, which is used in many over-the-counter cough syrups, allowed the virus to grow better in the cells. The team noted that their observations in the laboratory setting may call for some caution to be placed on using this drug until further is known about its effect on the virus.

“We should be careful,” Brian Shoichet, PhD, professor of pharmaceutical chemistry in the UCSF school of pharmacy, stated during the press call. “These are in vitro results. They have not been shown clinically and we’re not necessarily recommending that everyone stop taking dextromethorphan, for sure.” But, he continued, “because it is a pro-viral effect, it would be wrong not to highlight it because it could be detrimental. So, more work needs to be done.”

Not your average research project

This project started a couple of months ago at the QBI when twenty-two professors came together at the beginning of March, combining their multi-disciplinary tools in a highly integrative way to study COVID-19. Krogan noted that by breaking down barriers, it is “amazing how fast science can move when we all work together.” It just takes breaking down the silos, he added.

“What most excites me about this work,” said Krogan, “is that we have been able to pull so many brilliant scientists together not just at home, but around the world to focus on a question.” This has enabled us, he asserted, to forge ahead “at an unprecedented speed to do research that normally takes years, in a few weeks. This collaboration is unlike anything I have experienced before in my career, and it is inspiring—a driving force for all of us working.”

“What has surprised me most,” Krogan told GEN, “has been the magnitude of interest and response from the world. We have seen a response not only from scientists at every corner of the globe but also from the general public. Our team of 22 scientists has been receiving encouraging messages from individuals, children, churches, even! It is an incredible feeling, to feel united as a human race, and to be fortunate enough to be part of a team that is among those who are doing their best to find a solution.” 

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