Grid computing guiding malaria drug discovery

[CAPE TOWN; CARACAS] Scientists are using grids — high-speed computing networks — as a large-scale and cheaper way to kick-start new drug development against malaria parasites.

Wide In Silico Docking On Malaria (WISDOM) links a network of high-power computers that ‘match’ the structures of known chemical compounds with three-dimensional structural data describing important metabolic proteins from the parasite.

Using virtual screening researchers can suggest promising new weak points within the protein for drug designers to target.

They have already screened one well-known target enzyme and a promising new enzyme found in malaria parasites against 4.3 million compounds. The results are published in Malaria Journal this month (1 May)

”Computers are especially useful in finding the best sources for new drugs — so we can tackle multi-drug resistance as the parasite evolves to survive existing drugs,” said bioinformatics researcher and PhD student Marli Botha, of South Africa’s Council for Scientific and Industrial Research, a co-author of the study and one of only two African researchers involved.

Disease laboratories in under-resourced countries can use this open-source information to run effective and inexpensive small-scale drug design programmes, said co-author Giulio Rastelli, from Italy’s University of Modena and Reggio Emilia.

In future, said lead researcher Vinod Kasam, from the Clermont-Ferrand particle physics laboratory in France, the computer will ‘hit’ multiple targets simultaneously, speeding up the process and reducing costs even more.

Virtual screening’ is not just cost-effective; it produces a vast library of information which can be used by other researchers in other aspects of malaria research, according to co-author Raul Isea from Venezuela’s Biosciences and Molecular Medicine Centre at the Advanced Studies Institute Foundation.

And computer-based drug design projects are already helping find new drugs against HIV/AIDS, flu, polio and other diseases. Virtual screening should also be ideal for combating the fourteen neglected diseases listed by the WHO.

”We want to draw attention to the opportunity offered by this grid-enabled virtual screening approach for producing short lists of particularly promising molecules, which can be tested in the laboratory at a reduced cost,” says Martin Hofmann-Apitius, from the Fraunhofer Institute for Algorithms and Scientific Computing in Germany, who helped to create and supervise the study.

Grids also form a convenient global platform for exchanging the chemical data produced, said Vincent Breton, a founder of the WISDOM and several other grid initiatives.

Link to full article in Malaria Journal [2.56MB]