A study out of UMBC, published in Nature Communications, reveals how enteroviruses—including pathogens that cause polio, encephalitis, myocarditis, and the common cold—initiate replication by hijacking host-cell machinery. The research fills a knowledge gap on this critical step and could pave the way for a new class of antiviral drugs that are effective against multiple viruses.

“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,” says senior author Deepak Koirala, associate professor of chemistry and biochemistry. Building on his group’s discovery of a crucial cloverleaf structure in the viral RNA, their latest paper, led by first author Naba Krishna Das, Ph.D. ’25, chemistry, has now shown how the cloverleaf recruits proteins to assemble the replication complex. 

Seeing the bigger picture

Enteroviruses carry a small RNA genome that must do double duty: make viral proteins and copy itself to produce new viruses. A key player is a viral protein called 3CD. One half (3C) cuts the complete string of amino acids encoded by the virus’s RNA into individual proteins. The other half (3D) is an RNA polymerase—the enzyme that copies the viral RNA. Human cells don’t have anything like this polymerase, so the virus has to bring its own.

Deepak Koirala (center) discusses his team’s research with Senali Dansou ’23, biochemistry and molecularbiology (left), and Alisha Patel ’25, biochemistry and molecular biology, and a coauthor on the new paper. (Marlayna Demond ’11/UMBC)

“We previously determined the structure of the RNA alone, and other groups determined the structure of 3C and 3D separately, but now we’ve captured the structure of the RNA and proteins together, so we know how they are interacting,” Koirala explains. “We found that it’s the 3C domain of 3CD that binds to the viral RNA, and then it recruits the other components to assemble the replication complex.”

The same complex also works as an on-off switch: when 3CD is attached, the virus copies its RNA; when it lets go, the RNA can be read to make proteins instead.

The team also settled a debate by showing that two complete 3CD molecules (bringing two RNA polymerases) bind to the RNA independently, rather than forming a single fused pair. Why two are needed is still a mystery, but the picture is now clear.

Koirala lab members Alisha Patel, Deepak Koirala, Naba Krishna Das, and Jeffrey Vogt ’23, biochemistry and molecular biology, compare the growth on petri dishes. (Marlayna Demond ’11/UMBC)

New antiviral targets

Perhaps most exciting, the seven types of enteroviruses the paper investigated all employed a very similar binding mechanism and RNA cloverleaf structure. The extent of this conservation implies the RNA cloverleaf is very important for replication, and any mutations would likely derail it. That means the RNA and RNA-protein interface is likely to be stable over time across enteroviruses, making it an even more promising drug target—and opening the door to the tantalizing prospect of a “universal” drug targeting all enteroviruses. 

Drugs disrupting 3C and 3D activity are already in development, but “now we have another layer to test,” Koirala says. “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.”

“Viruses are so, so clever. Their entire genome is equivalent to about one mRNA sequence in humans, yet they are so effective,” Koirala says. His latest work demonstrates “why we need to investigate this basic science—so that it can be translated into developing drugs targeting pathogens that cause so many harmful diseases.”