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WISDOM’S New Fight Against Malaria

The WIDSOM initiative went into top gear with its latest drug discovery challenge, which finished 31 January with an average of 80,000 compounds analysed each hour on the EGEE Grid infrastructure. In total, the challenge processed over 140 million possible docking arrangements between drug compounds and target proteins of the malaria parasite.

This virtual screening challenge of the international WISDOM (World-wide In Silico Docking On Malaria) initiative between 1 October and 31 January targeted compounds that are of interest for drug discovery against neglected diseases. WISDOM uses in silico docking techniques, where researchers use computing systems to compute the probability that potential drugs will dock with a target protein.

This lets researchers rule out the vast majority of potential drugs, so that they can concentrate on the most promising compounds in laboratory tests. This speeds up the screening process and reduces the cost of new drug development to treat diseases such as malaria.

“The impact of WISDOM goes much beyond malaria,” declared Doman Kim, Director of the Bioindustry and Technology Institute at Jeonnam National University in Korea. “The method developed can be extended to all diseases and this opens exciting industrial perspectives. Until now, the search for new drugs in the academic sector was done at a relatively small scale, whereas the WISDOM approach allows a systematic inquiry of all the potentially interesting molecules.”

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This challenge was the consequence of the first, very successful large scale in silico docking, which ran on the EGEE Grid in summer 2005, when WISDOM docked over 41 million compounds in just six weeks, the equivalent of 80 years work for a single PC. The WISDOM team identified some 5000 interesting compounds, from which they found three interesting families of molecules that could be effective against the malaria parasite. Laboratories at the University of Modena, CNRS in France and CNR-ITB in Italy are now carrying out more advanced studies of the molecules using molecular dynamics. Following those studies, the enzymology laboratory of the Jeonnam National University in Korea will test them in vitro.

A second computing challenge targeting Avian Flu in April and May 2006 has significantly raised the interest of the biomedical research community. Laboratories in France, Italy, Venezuela and South Africa proposed targets for the second challenge against neglected diseases.

The WISDOM endeavour would be impossible without the support from BioSolveIT, a German firm who provided more than 6000 free floating licenses for their commercial docking program FlexX. "The WISDOM programme is very interesting and BioSolveIT is happy to sponsor this work,” says Dr Christian Lemmen, CEO of BioSolveIT. “The initiative takes full advantage of the speed and accuracy of FlexX – demonstrating the potential of the virtual screening technique in the search for drugs against neglected diseases.” Due to the initial success of the data challenge, the company even decided to extend the FlexX license for several weeks which allowed studying a new target.

In addition to the computing power that the EGEE Grid provided, AuverGrid, EELA, EUChinaGRID, EUMedGRID and South East Asia Grid all provided additional resources. The Embrace and BioinfoGRID projects are contributing to the development of a virtual, in silico screening pipeline that will allow researchers to select, for any given target protein, the most active molecules out of the millions of compounds commercially available.

Over the 10 weeks of the challenge, the project used the equivalent of 420 years of computing power of a single PC. Up to 5000 computers were used simultaneously in 27 countries, generating a total of 2000GB of useful data.

Hannelore Hammerle | alfa
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