More effective COVID-19 drug treatments enabled through enhanced understanding of viral protein

In the ongoing fight against the disruptive virus, a breakthrough has been made through study and research

BY SEAN TARRY

Aswe enter into year three of the COVID-19 pandemic era—a frame of time that has restricted social activities and blighted economic progress in communities all across the globe—studies being conducted with the help of the Canadian Light Source at the University of Saskatchewan are enabling scientists to make meaningful breakthroughs.

Molecular biologist; Mark Paetzel, who conducts his research at Simon Fraser University, along with University of British Columbia structural biologist Natalie Strynadka, and colleagues Jaeyong Lee, Calem Kenward and Liam Worrall, have recently been studying a significant protein and its underlying structure and characteristics in order to determine the reasons that makes it such an attractive target for antiviral drugs.

Significant breakthrough

Like many RNA viruses, explains Paetzel, SARS-CoV-2 synthesizes a significant number of its proteins as one long polypeptide chain called a polyprotein. A critical step in the virus’s replication and assembly is the dicing of this polyprotein into the individual functional viral proteins. SARS-CoV-2 uses a protease called main protease (M Pro ) to essentially cut itself out of the polyprotein and to cut at nine other positions along the polyprotein. The intramolecular self-cleavage reaction of M Pro results in the protease having the specificity residues required for its self-cleavage at its own carboxy-terminus. He says that the work he and the team have conducted have revealed a number of important insights.

“Previously, we captured crystal structures of M Pro bound to the carboxy-terminus of neighbouring molecules within the crystal due to the high local effective concentration within the crystal,” he says. “This provided insights into how Mpro recognizes its own C-terminus and how it can chop its way out of the polyprotein by recognizing its carboxyterminal tail. In our latest work, we have used site-directed mutagenesis to change the Mpro carboxy-terminal tail to each of the polyprotein cut-site sequences. We have managed the capture of these cut-sites bound within the active site of Mpro. These structures have revealed how the Mpro active site structurally adapts to each polyprotein cleavage site.”

Disabling replication

In addition, Paetzel says that through the work and research conducted, he and his colleagues learned that the protein in question is remarkably adaptable, highlighted most significantly by the way in which it binds other target proteins inside of a pocket that opens and closes like a trap of sorts, enabling it to accommodate the wide variety of differently shaped proteins it has to bind with and cut. Through this discovery, it was revealed that by blocking the protein, the virus’ ability to replicate is disabled.

Enhanced drug treatments

As Paetzel points out, the work and study that’s been conducted thus far has yielded a number of revelations concerning the protein that has resulted in an enhanced understanding of its behaviour.

And, it’s an enhanced understanding that the molecular biologist believes will benefit COVID-19 drug treatments and their effectiveness going forward, allowing drug developers to design new treatments that can take advantage of the protein’s flexibility.

“Mpro is an important target for antiviral drugs,” he asserts. “By having more structural information on how Mpro recognizes all its polyprotein cut sites, medical chemists can design drugs that bind with greater specificity and affinity, and this may lead to a more effective drug with fewer side effects and drug resistance. Knowing all the different ways that the enzyme active site interacts with its cleavage sites will provide valuable insights for drug design.”

Applicable to other viruses

It’s important to note that the discovery made by Paetzel and his colleagues not only poses the potential to improve drug treatments related to the COVID-19 virus, but can be applicable to a number of other viruses as well. It’s a breakthrough that he acknowledges is a profound one, perhaps benefitting drug researchers and manufacturers, as well as healthcare workers, for some time to come.

“This in crystallo high-local effective concentration strategy for producing structures of viral protease complexes with their cleavage sites is applicable to any virus that produces its gene products as a polyprotein,” he explains.

The power of the Canadian Light Source

In order to execute the work and study that enabled this breakthrough, Paetzel and his colleagues leveraged the powerful X-rays of the CMCF-BM beamline at the Canadian Light Source at the University of Saskatchewan. Paetzel describes the technologies available at the facility as “vital” toward achieving the study’s results and in gaining their enhanced understanding of the protein and its behaviour. Most significantly, he explains, it enabled the research team to conduct the screening of the more than 500 protein crystals that was required in order to find the ones they were looking for.

“Access to the CMCF-BM beamline at CLS was critical to the success of this project,” he says. “We had to screen many crystals to find those that had the cleavage-site bound within the active-site. The intensity and resolution of the X-rays and the speed of the data collection available at CLS made this project possible, enabling us to more efficiently analyze the many crystals needed to capture these complexes.”