By shining an “incredibly bright light” on a key viral protein, researchers are shedding new light on potential targets for antiviral drugs, including those aimed at treating COVID-19.
Simon Fraser University (SFU) molecular biologist Mark Paetzel leads the Paetzel Lab at SFU, where he and his team study the 3D-structure and mechanisms of viral and bacterial proteolytic enzymes. This research aids in the design of anti-viral and anti-bacterial treatments to inhibit the activities of these enzymes.
For a recent study, he worked with Natalie Strynadka, a structural biologist at the University of British Columbia (UBC) and UBC researchers Jaeyong Lee, Calem Kenward and Liam Worrall to study the characteristics of the enzyme Main Protease (Mpro) from the virus SARS-CoV-2.
The researchers used a powerful beam of light (known as synchrotron radiation) from the University of Saskatchewan’s Canadian Light Source (CLS)—a national research facility that produces the brightest light in the country—to study Mpro, a central enzyme in the virus’s replication.
Many RNA viruses, like SARS-CoV-2 synthesize most of their non-structural proteins as one long chain, called a polyprotein, which it cleaves—or splits up—into individual units afterwards. The researchers found that Mpro is remarkably adaptable; the pocket where it binds the target polyprotein can open and close like a catcher’s mitt to accommodate the wide variety of different protein sequences it must specifically recognize, bind and cleave.
These findings may shed new light on understanding how Mpro is able to be very specific, has the ability to cleave at only 11 specific sites within the SARS-CoV-2 polyprotein, but is also adaptable enough to accommodate different recognition sequences at each cleavage site.
Their paper, X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation was recently published in Nature Communications.
We spoke with professor Paetzel about his research.
Can you explain why this finding is so significant?
The discovery is significant since Mpro is an important target for antiviral drugs. Blocking Mpro disables the virus’s ability to replicate. Learning more about how the protease binds to its targets will help drug developers design new treatments that can take advantage of the protein’s flexibility, potentially making them more effective at fighting the virus with fewer side effects and with potentially less downstream effects of drug resistance induced by future mutations of the virus.
How did you single out and observe the atomic-level details of a viral protein? Can you describe what you observed?
Mpro must first cut itself out of the polyprotein using two different recognition sequences, one at the end of the preceding protein and one at the end of Mpro itself. The resulting free Mpro retains a recognition sequence at its tail.
Before SARS-CoV-2 arrived, my lab had been working on a different viral protease where we observed that the enzyme was able to bind the recognition sequence located at the end of the enzyme within its own active site.
We proposed that we could change the sequence at the tail of Mpro to the sequences for the nine other polyprotein cleavage sites and bind each to the Mpro active site.
We crystallized the Mpro with the various recognition sequences in conditions such that the sequences were bound within the active site of Mpro. We then used the technique of X-ray crystallography to determine the three-dimensional structure of each of the enzyme-recognition sequence complexes and observed the atomic details of their interactions.
How important to this research is the use of the Canadian Light Source (CLS) research facility?
The powerful X-rays available from the synchrotron facilities were essential for the success of this project. The CLS houses 22 beamlines with spectral ranges that provide different elemental information, and it is the brightest such light in Canada. We have used beamline CMCF-BM at the CLS as well as beamlines 23-ID-B and 23-ID-D at the Advanced Photon Source at Argonne National Laboratory in Chicago, and beamlines 5.0.1 and 5.0.2 at the Advanced Light Source at Lawrence Berkeley National Laboratory in California.
How do you share this information with the laboratories involved in the manufacture of antiviral drugs?
All the atomic coordinates and data for this project are deposited in the RCSB Protein Data Bank at: https://www.rcsb.org.
For more read the Canadian Light Source article: Better understanding of viral protein could lead to more effective COVID drug treatments with fewer side effects
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