Researchers have identified a molecular mechanism that enteroviruses exploit to reproduce inside human cells, potentially paving the way for drugs that could fight multiple viruses in this dangerous family at once.
A team at the University of Maryland, Baltimore County discovered how viruses like polio, the common cold, encephalitis, and myocarditis hijack cellular machinery to copy themselves. The work, led by associate professor Deepak Koirala and recent Ph.D. graduate Naba Krishna Das, was published in Nature Communications and reveals a critical vulnerability shared across these pathogens.
"My lab has been really motivated to understand how RNA viruses produce their proteins inside the cell and multiply their genome to make more virus particles," Koirala said. The team built on earlier discoveries of a cloverleaf shaped structure within viral RNA, showing how that structure recruits the proteins needed to launch replication.
The Machinery Behind Viral Reproduction
Enteroviruses carry incredibly compact RNA genomes that must accomplish two tasks simultaneously. The viral RNA must direct production of viral proteins while also serving as a template for creating new copies of the virus itself.
The genome's instructions focus mainly on structural proteins, but they also encode specialized proteins for replication. The most critical is a fusion protein called 3CD, which functions in two parts. The 3C domain cuts long amino acid chains into separate proteins the virus needs. The 3D domain acts as an RNA polymerase, an enzyme that copies viral RNA. Unlike human cells, which lack this type of polymerase, viruses must manufacture their own.
The researchers used X-ray crystallography to visualize how the RNA cloverleaf and 3CD protein interact. They also employed isothermal titration calorimetry, which measures heat released when molecules bind, and biolayer interferometry, which tracks molecular attachment duration using light interference patterns.
"We previously determined the structure of the RNA alone, and other groups determined the structure of 3C and 3D, but now we've captured the structure of the RNA and proteins together, so we know how they are interacting," Koirala explained. "We found that it's the 3C domain of 3CD that binds to the RNA in the viral genome, and then it recruits the other components, such as host protein PCBP2, to assemble the replication complex."
The experiments revealed something unexpected. Two full 3CD molecules, each carrying its own RNA polymerase, bind side by side on the viral RNA. Previous research had proposed they formed a single fused pair instead, settling a longstanding scientific debate about viral assembly.
Most intriguingly, the researchers found this molecular system functions like a switch. When 3CD is attached to the RNA, the virus copies its genome. When the protein detaches, the RNA becomes available for producing viral proteins instead. Scientists still do not fully understand why two copies are needed, but the study provides a much clearer picture of how replication begins.
The work reveals a second discovery with major implications: the mechanism appeared nearly identical across all seven enteroviruses the team examined. The viruses shared virtually identical RNA cloverleaf structures and binding behavior, suggesting this RNA structure is absolutely essential to viral survival. Significant mutations would likely disrupt replication, making it a potentially stable drug target across many enteroviruses at once.
"Viruses are so, so clever. Their entire genome is equivalent to about one mRNA sequence in humans, yet they are so effective," Koirala said. The similarity across different viruses hints at why this structure has remained unchanged through evolution.
Drugs targeting 3C and 3D proteins are already in development, but the new findings suggest another strategy entirely. "Now we have another layer to test," Koirala said. "What if we target the RNA, or the RNA-protein interface, so that we break the interaction? That is another opportunity. Now that we have high-resolution structures, you can precisely design drug molecules to target them."
The potential for broad spectrum antivirals represents a significant shift. Rather than developing separate drugs for polio, rhinoviruses, and other enteroviruses individually, researchers could create medications that disrupt a single shared vulnerability across the entire viral family.
Author Jessica Williams: "This discovery matters because it targets something viruses can't easily change without dying, which means resistance becomes far less likely than with drugs hitting protein targets alone."
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