UNIVERSITY PARK, Pa. — As the world shifts from trying to stop the COVID-19 pandemic to learning to live with it, safe and effective antiviral drugs are increasingly important to help combat SARS-CoV-2 infection. According to new research from Penn State, several drugs already FDA-approved for other diseases like Type 2 diabetes, hepatitis C, and HIV, may also be effective against SARS-CoV-2.
In the study, the researchers screen a set of 64 repurposed drugs selected for their ability to inhibit a specific viral protein, called a protease. A protease is an enzyme that breaks down proteins into smaller pieces. SARS-CoV-2 has two viral proteases that are essential for replication: main protease (Mpro) and papain-like protease (PLpro). These proteases are a target of many antiviral studies with small-molecule inhibitors.
“SARS-CoV-2 produces long proteins, called polyproteins, from its RNA genome that must be cleaved into individual proteins by these proteases in an ordered fashion leading to the formation of functional virus enzymes and proteins to start virus replication once it enters a cell,” explains co-lead author, Katsuhiko Murakami, a professor of biochemistry and molecular biology, in a statement. “If you inhibit one of these proteases, further spread of SARS-CoV-2 in the infected person could be stopped.”
Analyzing effectiveness of repurposed drugs against COVID-19 infection
From the panel of repurposed drugs, the team identifies 11 that affect Mpro activity and five that affect PLpro activity. The results are based on a cut-off of 50% reduction in protease activity with 90% cell viability. Researchers employed a novel antiviral screening strategy allowing them to visualize protease activity inside live human cells. The technique uses the protein-cutting activity of the viral proteases to manipulate the location of a fluorescent protein inside a cell.
“We designed the experiment so that if the compound was affecting the proteases, you would see fluorescence in certain areas of the cell,” explains first author, Anoop Narayanan.
This is the first time this type of live cell-based screening of SARS-CoV-2 protease inhibitors has been reported. The approach is advantageous because it can show how a drug affects a living cell. “Although other assays are available, we designed our novel assay so it could be conducted in live cells, which enabled us to simultaneously measure the toxicity of the inhibitors to human cells,” says co-lead author, Joyce Jose.
Using this strategy, the scientists further screened the 16 potential drugs for their ability to inhibit SARS-CoV-2 replication in human cells. After prioritizing compounds based on protease inhibition and low toxicity, the team identifies eight candidates for further study. Specifically, six inhibitors for Mpro (MG-101, Lycorine HCl, BMS-707035, Atazanavir, Lomibuvir, and Nelfinavir mesylate) and two inhibitors for PLpro (Sitagliptin and Daclastavir) were selected.
Interestingly, the group finds that MG-101 also reduces the virus’s ability to infect cells. The authors suggest this could be through inhibition of processes involved in cell entry, such as protease processing of the spike protein. When the scientists treat cells with a combination of Mpro and PLpro inhibitors, they see an additive effect on inhibition of SARS-CoV-2 replication. This effect is present without an increase in cellular toxicity.
Protection from future variants
Study authors went a step further to understand how MG-101 inhibits protease activity. Using a technique called X-ray crystallography, they obtained a high-resolution structure of MG-101 in complex with Mpro. “We were able to see how MG-101 was interacting with the active site of Mpro,” explains Manju Narwal, another author on the paper. “This inhibitor mimics the polyprotein and binds in a similar manner to the protease, thereby blocking the protease from binding to and cutting the polyprotein, which is an essential step in the virus’s replication.”
“By understanding how the MG-101 compound binds to the active site, we can design new compounds that may be even more effective,” Narwal adds.
Although this study was performed using the COVID-19 Delta variant, the authors suggest the drugs will likely be effective against future variants since viral proteases are unlikely to mutate significantly.
“The development of broad-spectrum antiviral drugs against a wide range of coronaviruses is the ultimate treatment strategy for circulating and emerging coronavirus infections,” said Jose. “Our research shows that repurposing certain FDA-approved drugs that demonstrate effectiveness at inhibiting the activities of Mpro and PLpro may be a useful strategy in the fight against SARS-CoV-2.”
This study is published in Communications Biology.