RICHLAND, Wash.-Scientists were pleased when they learned more about how the common cold gains a foothold in the body, identifying key cellular checkpoints that are important targets of the virus.
But the real excitement extends far beyond the cold virus, which is a coronavirus like MERS-CoV or COVID-causing SARS-CoV-2. The team hopes its work will help protect people against multiple viruses by helping open up a new front in the fight to stop viral pathogens.
Rather than focusing on how to attack a specific virus directly-as antiviral drugs today work-researchers at the Department of Energy's Pacific Northwest National Laboratory want to protect the body against many viruses. The idea is to fortify the body's defenses against multiple invaders in one fell swoop, not to stop only the threat at hand.
"A virus thrives by taking over the cellular machinery of its host, hijacking normal processes to churn out copies of itself," said John Melchior, a biochemist and a corresponding author of a Sept. 12 paper in the Journal of Proteome Research. "We want to identify and then fortify the molecular complexes that are susceptible to many invading viruses-to stop viruses before they have a chance to take over the cell.
"Instead of going after the virus itself, we manipulate the control points in the cell to battle the virus," said Melchior.
Virologist Amy Sims, the co-corresponding author of the study, said the approach is a new way to fight many kinds of coronaviruses, from those that cause usually minor symptoms like a cold to those that cause severe diseases like COVID-19 and ARDS (acute respiratory distress syndrome).
"This approach offers a pathway for using a single drug to stop multiple types of viruses," said Sims. "When you target only the virus, it can produce strains that readily escape antiviral medications. But by targeting key functions in the host cell that the virus needs to replicate, and by turning off those host functions, we hope to eliminate the escape route most viruses use to cause disease."
Melchior, Sims and colleagues have adapted a newer technique that pinpoints proteins whose conformation, or shape, has changed. In the current study, they looked at human cells infected by HCoV-229E, a virus that causes the common cold.
The technique, called limited proteolysis-based mass spectrometry or LiP-MS, determines not just the changes in abundance of thousands of different proteins present in a sample but also which proteins have changed shape. For a protein, shape is everything, determining its function and regulating which molecular partners it can interact with and when.
Targeting molecules to stop multiple viruses
The PNNL team identified eight targets of the virus, including two molecular assemblies that are key control points involved in RNA processing. In both cases, the virus usurps the normal function in the cell and then takes control of the cellular machinery to make more copies of itself. The team showed that by blocking the virus from interacting with those molecular assemblies, the ability of the virus to replicate in the human lung cells where it normally thrives was reduced.
One molecular target is Nop-56, which gives a chemical stamp of approval to let the body know that a given strand of RNA is legitimate. With that chemical approval in hand, a cellular unit known as the ribosome makes the strand's protein product. When the cold virus hijacks Nop-56, human RNA is destroyed, normal proteins are not made-and rogue viral proteins are approved instead.
The spliceosome C-complex is another important target. The molecule helps cells edit RNA strands by removing non-essential regions within RNA. When the virus commandeers the molecular assembly, it again diverts the body from making its normal proteins and instead makes its own proteins that go on to hurt the host.
Picture a drone factory in a country at war, turning out products to defend itself. Imagine that a foreign invader takes over the factory, halts production and then uses the factory to turn out its own drones that are used to attack the home country. That's similar to what happens when a virus invades a person.
"We hope our work provides a list of common molecular targets that sets the foundation for the development of drugs that could block not just one but many viruses that cause disease," said Snigdha Sarkar, a postdoctoral fellow and first author of the paper.
"Viruses can mutate quickly, and that poses a problem when targeting a virus directly," she added. "That obstacle is removed if you target proteins that many viruses rely upon in the host."
Now, the PNNL team is exploring existing compounds that have been shown by scientists at Oregon Health & Science University to have antiviral potential. The team is also using artificial intelligence to rapidly identify compounds that could affect the molecular targets that its technology identified.
The work was funded by PNNL's Predictive Phenomics Initiative, an effort to understand how factors beyond the genetic code determine the traits of people, plants and all living things. The research holds promise for the bioeconomy, human health and other areas. Understanding the molecular steps involved when the environment changes-such as when a viral infection occurs-and then predicting the outcomes from those changes is at the heart of the initiative.
In addition to Melchior, Sarkar and Sims, authors include Song Feng, Hugh Mitchell, Madelyn Berger, Tong Zhang, Isaac Attah, Chelsea Hutchinson-Bunch, Victoria Prozapas, Kristin Engbrecht and Stephanie King.
