Compounds stop SARS-CoV-2 replication by attacking key viral enzyme

As the death toll from the COVID-19 pandemic increases, scientists around the world continue to push to develop effective treatments and a vaccine against the highly contagious respiratory virus.

Scientists at the University of South Florida Morsani School of Medicine (USF Health) recently worked with colleagues at the University of Arizona School of Pharmacy to identify several existing compounds that block the replication of the COVID-19 virus (SARS- CoV-2) within human cells grown in the laboratory. All inhibitors demonstrated potent chemical and structural interactions with a viral protein critical to the virus’s ability to proliferate.

The research team’s drug discovery study appeared June 15 in Cell research, a high impact Nature magazine.

The most promising drug candidates, including the FDA-approved hepatitis C drug boceprevir and an investigational veterinary antiviral drug known as GC-376, target the primary protease of SARS-CoV-2 (M^Pro), an enzyme that cuts proteins from a long chain that the virus produces when it invades a human cell. Without M^Pro, the virus cannot replicate and infect new cells. This enzyme had already been validated as an antiviral target for the original SARS and MERS, both genetically similar to SARS-CoV-2.

“With an infectious disease rapidly emerging as COVID-19, we don’t have time to develop new antiviral drugs from scratch,” said Yu Chen, PhD, associate professor of molecular medicine at USF Health and co-author of the article Cell Research. “Many good drug candidates are already available as a starting point. But, with new information from studies like ours and current technology, we can help design even better (reused) drugs much faster.”

Before the pandemic, Dr. Chen applied his experience in designing structure-based drugs to help develop inhibitors (drug compounds) that attack bacterial enzymes that cause resistance to certain commonly prescribed antibiotics, such as penicillin. . Now his lab focuses his advanced techniques, including X-ray crystallography and molecular coupling, on finding ways to stop SARS-CoV-2.

METER^Pro It represents an attractive target for drug development against COVID-19 due to the enzyme’s essential role in the coronavirus life cycle and the absence of a similar protease in humans, said Dr. Chen. Since people don’t have the enzyme, drugs targeting this protein are less likely to cause side effects, he explained.

The following are the four main drug candidates identified by the University of Arizona-USF Health team as the best (most powerful and specific) to fight COVID-19.These inhibitors came out on top after analyzing more than 50 existing protease compounds for possible reuse:

• Boceprevir, a medicine to treat hepatitis C, is the only one of the four compounds already approved by the FDA. The effective dose, safety profile, formulation, and how the body processes the drug (pharmacokinetics) are already known, which would greatly speed up the steps necessary to bring boceprevir to COVID-19 clinical trials, Dr. Chen said.
• GC-376, an investigational veterinary drug for a deadly strain of coronavirus in cats, which causes feline infectious peritonitis. This agent was the most powerful inhibitor of M^Pro enzyme in biochemical tests, Dr. Chen said, but before human trials can begin, it would need to be tested in animal models of SARS-CoV-2. Dr. Chen and his PhD student Michael Sacco determined the X-ray crystal structure of GC-376 bound by M^Proand characterized the molecular interactions between the compound and the viral enzyme using 3D computer modeling.
• Calpain II and XII inhibitors, cysteine ​​inhibitors investigated in the past for cancer, neurodegenerative diseases, and other conditions, also showed strong antiviral activity. Its ability to doubly inhibit both M^Pro and the calpain / cathepsin protease suggests that these compounds may include the added benefit of suppressing drug resistance, the researchers report.

All four compounds were superior to other M^Pro Inhibitors previously identified as suitable for clinical evaluation to treat SARS-CoV-2, said Dr. Chen.

A promising drug candidate, one that kills or damages the virus without destroying healthy cells, fits neatly into the unique “binding pocket” shape of the viral protein receptor. The GC-376 worked particularly well to meet (complement) the target M shape^Pro enzyme binding sites, said Dr. Chen. Using a lock (binding pocket or receiver) and a key analogy (drug), “GC-376 was by far the key with the best or tightest fit,” he added. “Our model shows how the inhibitor can mimic the original peptide substrate when it binds to the active site on the surface of the main protease of SARS-CoV-2.”

Instead of promoting viral enzyme activity, as the substrate normally does, the inhibitor significantly decreases the activity of the enzyme that helps SARS-CoV-2 make copies of itself.

Visualization of three-dimensional interactions between antiviral compounds and viral protein provides a clearer understanding of how M^Pro Complex and long-term work can lead to the design of new COVID-19 drugs, Dr. Chen said. Meanwhile, he added, the researchers focus on making first-line antiviral treatments faster by adjusting existing candidates for coronavirus drugs to improve their stability and performance.

Dr. Chen worked on the study with principal investigator Jun Wang, PhD, an assistant professor of pharmacology and toxicology at the UA. The work was supported in part by grants from the National Institutes of Health.