• In the coronavirus SARS-CoV-2 is an enzyme called the main protease, which drives its replication once it infects the human cell. For the first time, scientists have completed a 3D map that reveals the location of every atom in the molecule of this enzyme. 
  • As Covid-19 cases surge again in several countries, this 3D mapping will allow scientists to better understand how the coronavirus behaves, and how it can be stopped.
  • The mapping was done by researchers at the Oak Ridge National Laboratory under the US Department of Energy. The results are published in the Journal of Biological Chemistry.
  • SARS-CoV-2 expresses long chains of proteins. When these chains are broken down and cut into smaller strands, it enables the virus to reproduce. This task is performed by the main protease. Its structure: two identical protein molecules held together by hydrogen bonds. If a drug can be developed that inhibits or blocks the protease activity, it will prevent the virus from replicating and spreading to other cells in the body.
  • Researchers used a technique called neutron crystallography. The site containing the amino acids where the protein chains are cut, these experiments revealed, is in an electrically charged reactive state — not in a resting or neutral state, contrary to previously held beliefs. Second, researchers mapped the location of each hydrogen atom in the places where drug inhibitors could bind to the protease enzyme, as well as the electrical charges of the associated amino acids.  
  • Previous research published in Nature Communications creates a complete atomic structure of the protease enzyme. The new research builds on that.
  • The team will now use the newly obtained information to investigate the binding properties of drug molecule candidates to produce improved Covid-19 therapeutics.

The research is novel In several ways. It is the first time anyone has obtained a neutron structure of a coronavirus protein. The researchers said it is also the first time anyone has looked at this class of protease enzymes using neutrons. Further, the fact that the protein chains are cut at a site that is in an electrically charged reactive state, rather than neutral, was a surprise finding.