Unique structure of COVID protein suggests new target for drugs
Researchers from University of Waterloo discover potential pathway to disrupt protein vital for replication of virus
By Brian OwensA protein vital to the replication of the virus that causes COVID-19, known as the main protease, or Mpro, makes a good target for antiviral drugs like remdesivir. Now researchers using the Canadian Light Source at the University of Saskatchewan have uncovered a potential new way for drugs to disrupt that protein to treat the disease.
“Mpro is a good target for drugs. If we can halt its activity, we can halt viral replication,” says Todd Holyoak, a structural biologist at the University of Waterloo.
The SARS-CoV-2 virus replicates itself in an unusual way, he says. The proteins encoded in its RNA genome get translated into one long protein called a polyprotein, which is then chopped up into its constituent parts. Mpro is the protein that does most of that chopping.
Mpro is itself a little unusual. It only functions when there are two copies of the protein stuck together (called a dimer). And it contains more of an amino acid called cysteine than most proteins. This is significant because cysteine is highly susceptible to damage from oxidation, which is a key way the body can combat infection. This should be a liability for a viral protein. Yet SARS-CoV-2 is obviously a very effective virus.
“That’s kind of a conundrum,” says Holyoak.
Earlier research by Holyoak and his colleagues found that, under oxidative conditions, Mpro protects its vulnerable cysteines by temporarily linking C117 and C145. When conditions improve, the bond breaks.
“We wanted to understand, what would the effect be of over-oxidizing one of those two cysteines? Would there be other consequences from a structural point of view?” he says.
The researchers created altered versions of the protein that had one of the cysteines replaced with aspartate, another amino acid that closely resembles the oxidized form of cysteine. They discovered that when C117 was disabled, the Mpro dimer split into two separate proteins called monomers.The team's findings are published in the journal Protein Science.
Using the CLS, they were – possibly for the time ever -- able to see the 3D structure of the Mpro monomer and found it had a very different shape than when it was part of a dimer. That, says Holyoak, could open up new ways to fight COVID-19.
Remdesivir, and other drugs in development, go after the dimer’s active site to block it from binding to and cutting up the polyprotein. It’s an effective mechanism, but the virus may eventually be able to develop a resistance to it. Instead, Holyoak envisions drugs that target the monomer version of the protein and stop it from forming the active dimer.
“If we can find molecules that can bind and stabilize the monomer form, it will never even form the dimer,” says Holyoak. “That opens up a whole new therapeutic avenue.”
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Andress, Sam, Matthew J. McLeod, and Todd Holyoak. "The C117D oxidation mimic reveals the monomeric structure of SARS‐CoV‐2 main protease." Protein Science 35, no. 9 (2026): e70753. https://doi.org/10.1002/pro.70753
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