Researchers from the European Molecular Biology Laboratory (EMBL) in Grenoble, France have determined the detailed 3-dimensional structure of part of the flu virus RNA polymerase, an enzyme that is crucial for influenza virus replication.
The scientists focused on the endonuclease part of the viral RNA polymerase which is responsible for a unique mechanism called 'cap-snatching' that allows the virus to trick its host cell into producing viral proteins.
In human cells the translation of messenger RNA (mRNA) strands into proteins requires a special structure, called the cap, at the beginning of each mRNA.
When the influenza virus infects a host cell its endonuclease "snatches" that cap from the cell's own mRNA. Another part of its RNA polymerase then uses it as the starting point for synthesising viral mRNA.
With the correct cap structure at the beginning, viral mRNA can then hijack the protein-production machinery of the infected cell to make viral proteins, which assemble into new viruses that will spread the infection.
The team led by Stephen Cusack, Head of EMBL Grenoble, analysed crystals of endonuclease from the 2009 pandemic influenza strain using the high intensity X-ray beams at the European Synchrotron Radiation Facility (ESRF).
The researchers were able to determine the 3D atomic structure of the enzyme and to visualise how several different small molecule inhibitors bind to and block its active site.
If the active site of the endonuclease is blocked by an inhibitor the enzyme cannot bind its normal substrate, the host cell mRNA, and viral replication is prevented.
The active site of the endonuclease is shaped like a cave with two metal ions at the bottom. Cusack and colleagues found that all the inhibitors they studied bind to those two metal ions but, depending on their shapes, different inhibitors bind differently to the amino-acids of the cave's walls.
"Based on this detailed structural information we can now design new synthetic chemicals which bind even more tightly to the endonuclease active site and thus will potentially be more potent inhibitors of influenza virus replication," Stephen Cusack said in a statement.
The study was published in the journal PLoS Pathogens.