Novel RNA-protein interactions reveal conserved SARS-CoV-2 antiviral targets

The rapid evolution of SARS-CoV-2 has presented an ongoing challenge for antiviral drug development. As the virus accumulates mutations, some of its features change, potentially reducing the effectiveness of treatments designed to recognise them.

This has prompted researchers to investigate alternative targets that are less likely to change as the virus evolves. A new study co-led by scientists at the University of California, Riverside (UCR) and the University of California, San Diego (UC San Diego) has identified previously unknown interactions between viral RNA and proteins involved in coronavirus replication and regulation.

The researchers mapped interactions across the SARS-CoV-2 genome, identifying specific sites involving the RNA-dependent RNA polymerase (RdRp) and nucleocapsid (N) protein. Disrupting these interactions significantly reduced viral replication in cell cultures.

Their findings provide an early proof of concept for targeting essential processes within the viral life cycle rather than focusing exclusively on more variable features such as the spike protein.

SARS-CoV-2 evolves very quickly, so it’s important to understand the really basic and essential machinery of the virus. If we target something essential that the virus depends on to function and can’t easily change, the virus is less likely to evolve away from it, which would lead to drug resistance.”

Joy Xiang, Assistant Professor of Biomedical Sciences, UCR’s School of Medicine

 

 

Identifying new opportunities in viral RNA

To investigate how viral proteins interact with RNA, the researchers used enhanced cross-linking and immunoprecipitation (eCLIP). This technique allowed them to map protein-RNA interactions across the viral genome rather than limiting their investigation to regions already predicted to be important.

The first key finding involved the nucleocapsid protein and the 5′ untranslated region, a section at the beginning of the viral genome that contains a complex RNA structure. Although this region is highly conserved among coronaviruses, its precise functions are not fully understood.

The researchers found that its interaction with the N protein appears to influence translation, the process through which viral RNA provides instructions for making proteins.

The second key finding involved an interaction between RdRp and the RNA encoding viral protein NSP3. RdRp is an enzyme responsible for copying the viral RNA genome, making it essential for viral replication.

This interaction suggests that viral RNA may have regulatory functions beyond simply providing a template for producing proteins.

“Viruses look simpler than humans at first glance, but there’s a lot of underlying complexity to their molecular biology we’re only just beginning to unravel,” said Gene Yeo, Professor of Cellular and Molecular Medicine at UC San Diego. “Our findings suggest that viral RNA may have a more significant role in regulating fundamental cellular processes than we previously understood.”

What does this mean for antiviral drug discovery?

The findings fit into a wider research effort to develop antivirals that target conserved components of viruses, rather than features that can change rapidly.

Existing treatments demonstrate the value of this strategy. Remdesivir, for example, targets RdRp, interfering with the virus’s ability to replicate its genetic material. Meanwhile, Paxlovid targets viral proteases, which process the long protein chains produced during infection into functional proteins.

However, the new research explores a different opportunity: disrupting the interactions between viral RNA and proteins that help coordinate the virus’s life cycle.

To investigate whether these interactions could be targeted therapeutically, the team used antisense oligonucleotides (ASOs). These are short, modified nucleic acid sequences designed to bind complementary sections of RNA, potentially blocking their interactions with other molecules or disrupting their function.

The researchers designed ASOs to bind the newly identified interaction sites. Experiments showed that blocking these regions significantly reduced viral replication in Vero cells, which are derived from African green monkey cells. Similar results were observed in human lung cells.

This is important because targeting conserved RNA structures is already an area of interest in antiviral research. A 2024 review in Nature Reviews Microbiology highlighted the development of broad-spectrum antivirals targeting conserved viral components as an important part of preparedness for future coronavirus outbreaks.

The latest findings add to this work by identifying specific RNA-protein interactions that could be investigated as potential therapeutic targets. Rather than targeting viral RNA itself, researchers may be able to interfere with the molecular relationships that allow the virus to replicate and regulate its activity.

Could the approach work against future coronaviruses?

One of the most significant implications is the possibility of developing treatments that work against multiple coronaviruses.

Some of the proteins and RNA sequences involved in the interactions identified by the researchers are conserved across coronavirus species. This means they may be less susceptible to the changes that allow individual viral variants to evade existing treatments.

For early drug discovery, identifying these conserved processes could help researchers prioritise targets with broader therapeutic potential. It could also provide a starting point for investigating whether similar interactions occur in other viruses, including those with the potential to spill over from animals into humans.

However, the findings remain at an early stage. The experiments were conducted in cell cultures, meaning more research is needed to establish whether disrupting these interactions is safe and effective in living organisms. Animal studies will therefore be an important next step before the approach can be considered for therapeutic development.

Xiang is now investigating similar RNA-protein interactions in other viruses, while Yeo’s group continues to develop technologies for mapping these molecular relationships.

“The goal is to understand these core interactions so that, eventually, drug developers can develop therapies that specifically target them,” Xiang said. “We need to understand the fundamental biology of these viruses instead of just being reactive to outbreaks. There’s value in studying these biological differences, because that understanding can give us new opportunities to develop better treatments.”