Grid attacks avian flu

During April, a collaboration of Asian and European laboratories analysed 300,000 possible drug components against the avian flu virus H5N1 using the EGEE Grid infrastructure.


Schematic presentation of the avian flu virus.


The distribution of the EGEE sites in the world on which the avian flu scan was performed.

The goal was to find potential compounds that can inhibit the activities of an enzyme on the surface of the influenza virus, the so-called neuraminidase, subtype N1. Using the Grid to identify the most promising leads for biological tests could speed up the development process for drugs against the influenza virus. Co-ordinated by CERN and funded by the European Commission, the EGEE project (Enabling Grids for E-sciencE) aims to set up a worldwide grid infrastructure for science.

The challenge of the in silico drug discovery application is to identify those molecules which can dock on the active sites of the virus in order to inhibit its action. To study the impact of small scale mutations on drug resistance, a large set of compounds was screened against the same neuraminidase target but with various, slightly different structures. With the results from the in silico screening, researchers can predict which compounds and chemical fragments are most effective for blocking the active neuraminidases in case of mutations.

The drug discovery process is being greatly accelerated by the use of the EGEE and associated computing Grid infrastructures. For the docking of 300000 compounds against eight different target structures of Influenza A neuraminidases, 2000 computers were used during four weeks in April - the equivalent of 100 years on a single computer. More than 60000 output files with a data volume of 600 Gigabytes were created and stored in a relational database. Potential drug compounds against avian flu are now being identified and ranked.

'This will free up medicinal chemists' time to better respond to instant, large-scale threats,'said Ying-Ta Wu, a biologist at the Genomics Research Center of the Academia Sinica in Taipei. 'Moreover, we can concentrate our biological assays in the laboratory on the most promising components, the ones we expect to have the greatest impact.'

This drug discovery application against the avian flu virus was jointly deployed by an international collaboration.

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