UF team finds Covid-19 antiviral targets

A single plate of cultured cells infected with SARS-CoV-2 stained red and viewed under magnification.
A single plate of cultured cells infected with SARS-CoV-2, the virus that causes COVID-19, stained red and viewed under magnification. The white spots are plaques that have formed where the cells have been destroyed by the virus. These cultures are part of a project that seeks to identify targets for COVID-19 drug discovery. (Image courtesy of Andrew P. Bluhm, biological scientist.)

Vaccines are a key strategy in protecting against severe COVID-19 and death. But there is a growing role for antiviral drugs as people learn to live with the coronavirus — and its variants — amid a return to work, school, and pre-pandemic activities. Researchers at the University of Florida are helping in the antiviral development process.

Antiviral drugs work in two ways. They either target the virus, termed virus-targeted antivirals, or they target host factors that the virus depends on for its replication, termed host-targeted antivirals.

“One common problem with virus-targeted antivirals is the rapid emergence of drug-resistant virus variants,” said the study’s co-senior author, Stephanie Karst, a virologist in the UF College of Medicine. “Because of this, our research team decided to focus on developing new host-targeted antivirals which should be effective against all virus variants.”

In work published today in Genome Medicine, they report on 53 host genes that represent novel druggable targets in the development of antiviral therapies for COVID-19 — and against a broad array of coronavirus types. Having broad-spectrum antiviral therapies that target host-specific processes would be useful against coronavirus genetic variants such as Omicron which are extending the COVID-19 pandemic.

“A durable broad-spectrum host-targeted antiviral may also prove effective against future variants or coronaviruses that have not yet emerged but that could be even more devastating than what we’ve seen to date,” said the study’s co-senior author, Michael Norris, a molecular biologist and bioengineer in the UF College of Liberal Arts and Sciences.

Several factors underscore the need to develop broad-spectrum antiviral therapies for COVID-19. Future variants could further erode vaccine efficacy by evading immune detection, but antiviral therapies could help lessen the severity of COVID-19 infections and symptoms. This option would be particularly helpful for people who can’t receive vaccines, such as those with compromised immune systems. Antivirals would also help relieve the burden of disease and slow transmission in regions or countries with little or no access to COVID-19 vaccines and boosters.

The multidisciplinary UF team also identified existing compounds that target many of these same genes and pathways and reduce viral growth. These antiviral compounds should be further tested as possible pan-coronavirus inhibitors, the team says, because they could potentially reduce the severity of infection across multiple coronavirus infections.

“We need every possible weapon against this virus,” said Norris, who is also a member of UF’s Emerging Pathogens Institute where the lab work was performed. “Identifying new or repurposed therapeutics is critical due to the increasing impact of new genetic coronavirus variants.”

The UF investigators used CRISPR gene editing techniques to screen for genes that help coronaviruses replicate in humans. The UF team experimentally infected cultured cells with two different types of coronaviruses: SARS-CoV-2 and OC43. The first produces COVID-19 while the second produces a relatively mild and seasonally circulating common cold.

They included OC43 to zero in on targets shared by both coronaviruses. Shared targets are needed to develop broad-spectrum antivirals that work against a variety of coronaviruses known to infect people.

Using CRISPR techniques allowed the team to rapidly screen host genes and identify the few key genes that promote coronavirus infections in mammals. This led them to pinpoint novel cellular pathways that coronaviruses use to replicate inside human cells. Inhibiting or silencing specific genes of interest allowed the team to validate the role played by these pathways in viral replication.

A schematic of the study's experimental design.
A schematic of the study’s experimental design.

“Identification of these pathways is key to designing new drugs or identifying existing inhibitors for the treatment or prevention of coronavirus infections,” said Norris. “Our work demonstrates that existing drugs can inhibit SARS-CoV-2 replication and the production of infectious particles in human lung cells.”

The research team found that two genes—EDC4 and XRN1—were found to play important roles in promoting replication pathways in both coronavirus types. These genes are part of a process known as the messenger RNA decay pathway, which helps safeguard the quality of messenger RNA. If drugs could safely target them and inhibit their role, it would limit the coronavirus’s ability to replicate and spread within a host, thereby controlling the infection and the symptoms it produces.

The UF study also identified 21 host genes previously reported in other CRISPR screening studies, which validates the technique and the strength of the findings.

Based on the host factors and biological pathways identified as involved in viral replication, the team screened existing drugs and found several that diminished COVID-19 and common cold virus OC43 replication in human airway cell culture experiments. These compounds — abemaciclib, amlexanox, harmine, nintedanib, and promethazine — will undergo further testing to determine their efficacy in treating COVID-19.

A drug that targeted these host factors could prevent infected cells from releasing more virus. This effect might buy the immune system time to mount a more effective defense, while shortening the length and severity of an infection.

“These drugs and other candidate drugs which target the host capacity to support coronavirus replication hold great promise as a novel class of antiviral agents,” said study coauthor Chris Vulpe, a professor of physiological sciences in the UF College of Veterinary Medicine.

A figure visually communicates the team's main findings.
This figure visually communicates the team’s main findings.

Acknowledgments: The investigators acknowledge the exceptional efforts of the researchers who made this work possible. They are Andrew Bluhm, Michael Norris’ lab; Marco Grodski, Stephanie Karst’s lab; Mani Tagmount, Christopher Vulpe’s lab. They also acknowledge the computational analysis of colleague Dr. Moritz Schafer at ETH Zurich.

By: DeLene Beeland