Structure of critical enzyme in flu virus replication determined
8 August 2012
The European Molecular Biology Laboratory (EMBL) in Grenoble,
France, has determined the detailed 3-dimensional structure of part of
the flu virus’ RNA polymerase, an enzyme that is crucial for
The research was done on the 2009 pandemic influenza strain but
it will help scientists to design innovative drugs against all the
different influenza strains, and potentially lead to a new class of
anti-flu drugs in the next 5-10 years.
The scientists focused on the endonuclease part of the viral RNA
polymerase. The endonuclease 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 synthesizing
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, analyzed
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 visualize 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,” explains Stephen Cusack.
“We can even try to build in anti-drug resistance by making sure the
inhibitors only contact those amino acids that the virus cannot
mutate since they are essential for the normal activity of the
Because the cap-snatching mechanism is common to all influenza
strains, new potent endonuclease inhibitors should be effective
against seasonal flu, novel pandemic strains or highly pathogenic
H5N1 bird flu. EMBL scientists are working with EMBL’s spin-off
company Savira pharmaceuticals, in partnership with Roche, to
further develop influenza inhibitors. Promising candidates will be
tested first for efficacy in cell culture, ultimately moving into
clinical trials on humans.
The study is published in: Kowalinski, E., Zubieta, C.,
Wolkerstorfer, A., Szolar, O.H.J., Ruigrok, R.W.H. & Cusack, S.
Structural analysis of specific metal chelating inhibitor binding to
the endonuclease domain of influenza pH1N1 (2009) polymerase.
PLoS Pathogens, 2 August 2012.