The EGEE Grid Infrastructure Helps in Fighting the Avian Flu

During April, a collaboration of Asian and European laboratories has analysed 300,000 possible drug components against the avian flu virus H5N1 using the EGEE (Enabling Grids for E-sciencE) grid infrastructure, the implementation of which involves experts from the CESNET association. 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. With the results from the in silico screening, researches can predict which compounds and chemical fragments are most effective for blocking the active neuraminidases in case of mutations, which is especially important in the event of flue pandemic.

The drug discovery process is being greatly accelerated by using the EGEE and associated computing grid infrastructures. For the docking of 300,000 compounds against 300 different target structures of Influenza A neuraminidases, 2000 computers were used during 4 weeks in April – the equivalent of 100 years on a single computer. More than 60,000 output files with the data volume of 600 Gigabytes have been created so far and stored in a relational database. Potential drug compounds against the avian flu are now being identified and ranked according to binding energies of the docked models.

"With the help of the high-speed computing and huge data managing capabilities of the grid, possible drug components can be screened and studied very rapidly by the available computer modelling applications," says Ying-Ta Wu, biologist at the Genomics Research Center of the Academia Sinica. "This will free up medicinal chemists' time to better respond to instant, large-scale threats. Moreover, we can concentrate our biological assays in the laboratory on the most promising components, the ones we expect to have the greatest impact."

"With these results, the grid demonstrates that it is a powerful and reliable resource for scientists, opening up new research possibilities and improving existing methods," said Viviane Reding, European Commissioner responsible for Information Society and Media. "I am very grateful to see that the European flagship grid infrastructure is contributing to solving current and socially important problems such as the avian flu."

Taking advantage of the experience acquired in the previous data challenge on malaria, the grid-enabled in silico process was implemented in less than a month on three different grid infrastructures: local AuverGrid (France), European EGEE and Asian TWGrid (Taiwan). This paves the way for a virtual drug screening service at a large scale.

This drug discovery application against the avian flu virus was jointly deployed by the following institutions: Genomics Research Center, Academia Sinica, Taiwan; Academia Sinica Grid Computing Team, Taiwan; Corpuscular Physics Laboratory of Clermont-Ferrand, France; Institute for Biomedical Technologies, Italy. Collaboration was initiated with the EGEE project, the AuverGrid regional grid in Auvergne, and the TWGrid. Works were carried out in cooperation with EMBRACE (European Model for Bioinformatics Research and Community Education) Network of Excellence and the BioInfoGrid (Bioinformatics Grid Application for Life Science) project.

The CESNET association has been founded by universities and the Academy of Sciences of the Czech Republic. The association is currently financed mainly from the resources of the governmental Committee for the Research and Education and the resources of the members of the association. The association performs research and development in the area of information and communication technologies, building and developing the national gigabit optical network, CESNET2, designed for research and educational purposes. Due to the research activities and results achieved, the CESNET association acts as a representative of the Czech Republic in the project within which a pan-European network called GEANT2 is constructed, actively taking part also in the implementation of this project. Among other things, the association supports the IP mobility and roaming within the CESNET2 research network and deals with development and implementation of an "inter-domain" distributed infrastructure, providing authentication and authorization services for supporting cooperation of users registered in various home institutions.