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Biobase to Lead $4M EU Project to Create In Silico 'Toolbox' for Drug Development

Biobase said this week that it has been tapped to lead a €3 million ($4 million) European Union research project that aims to develop a “toolbox” that will integrate bioinformatics and cheminformatics software with experimental -omics platforms such as transcriptomics, proteomics, and metabolomics. 
The three-year project, called Net2Drug, was awarded under the EU’s 6th Framework Program. In addition to Biobase, participants include Spain’s Progenika Biopharma, the University of Helsinki, the Fraunhofer Institute of Toxicology and Experimental Medicine, the University of Göttingen Medical School, Russia’s Institute of Systems Biology, the Institute of Biomedical Chemistry at the Russian Academy of Medical Sciences, the Karolinska Institute, and the Italian National Research Council’s Institute of Biomedical Technologies.
Edgar Wingender, president and CSO of Biobase, said that the collaborative effort grew out of a “network that we’ve built up for many, many years of scientific collaboration.”
Wingender said that Biobase’s databases and software tools will form the bioinformatics backbone for the project.
The first step of the effort will be integrating the various experimental and computational platforms of the various participants, Wingender said. Then the collaborators will apply the combined suite of tools to breast cancer as a proof of principle.
In terms of the analytical workflow, Wingender said that the researchers will first run a battery of transcriptomics, proteomics, and metabolomics experiments on normal cells and cancer cells in order to identify the molecular underpinnings of different tumor types.
Then, the data will be analyzed in the context of biological pathways in order to identify potential “master nodes” in the regulatory network that controls expression of the genes of interest.
Next, cheminformatics tools will come into play in order to identify small molecules that might be able to control the activity of these key nodes.
“Then it goes back to the laboratory, of course, for validation,” Wingender said.
“At the end, if everything runs optimally, then we can not only come up with the hypothesis for a crucial drug target, but even with a potential lead structure that would be a good starting point to develop a drug,” he said.

“At the end, if everything runs optimally, then we can not only come up with the hypothesis for a crucial drug target, but even with a potential lead structure that would be a good starting point to develop a drug.”

Wingender said that some tools developed under the project will be available in the public domain, but said that “the integrated toolbox as such” will be commercialized.
Biobase expects to develop some new technology during the course of the project, but Wingender declined to provide details other than noting that it will involve “some innovative elements from the area of artificial intelligence.”
Wingender said that the project serves as an important validation of Biobase’s technology, particularly in downstream drug development and clinical applications, where the company’s products are not very well established.
In addition, he said, “some of the real innovative methods in bioinformatics or cheminformatics may then find their way into our product portfolio later on.”
He noted, however, that the publicly funded project is a riskier undertaking than the company would carry out with its own R&D funds. “Some parts of the project may fail — that’s the risk in research,” he said.
“In the worst case, if we [only] integrate what we have already, that would be very useful,” he said, “but the potential goes far beyond that.”

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