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GeneGo's Deals with MDL and RMA Signal Growing Demand for Pathway Tools for Downstream Apps

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GeneGo has recently signed two agreements that indicate the market for pathway informatics tools is expanding well beyond its traditional base in genomics and early discovery.

This week, the company said that it is collaborating with Elsevier MDL to integrate its MetaCore and MetaDrug pathway-analysis systems with MDL's DiscoveryGate suite of online cheminformatics databases, which includes information on more than 16 million chemical compounds.

That agreement followed the company's announcement last week that Reproductive Medicine Associates of New Jersey had licensed MetaCore, marking the first use of the platform in a healthcare setting.

"Typically, the market that MetaCore was mostly directed to before was early research and drug discovery," Andrej Bugrim, COO of GeneGo, told BioInform. "Now, we're moving a little bit up the food chain to the medicinal chemistry area, the early clinical or preclinical trials area, where people are working mostly with the molecules and their state of mind rotates around the molecules rather than, say, differentially expressed genes as scientists in early discovery do."

Physicians also present a market opportunity, Bugrim said, "because clinical physicians mostly think about drugs and their effects, so that's another area where people who have the drug and the chemical structure as their starting point can go into MetaCore and look at what this drug can do."


"We were hoping that preclinical or clinical trials would be our next market area, so we were not yet really thinking about going all the way to actual practitioners."

Bugrim said that physicians other than those at RMA have expressed interest in using MetaCore • a trend that has actually caught the company by surprise. "It seems to be a big jump," he acknowledged. "We were pretty much in early drug discovery groups so far, maybe toxicogenomics groups in some companies, and we were hoping that preclinical or clinical trials would be our next market area, so we were not yet really thinking about going all the way to actual practitioners," he said.

"But nevertheless we see some interest in this area, and we'll see where that's going."

The agreement with MDL will give GeneGo customers access to comprehensive information about small molecules involved in biological pathways, while giving MDL customers the ability to view their lead compounds within the context of molecular pathways.

The agreement could raise GeneGo's profile among medicinal chemists and provide entry to "a whole new layer in pharmaceutical companies that could be potential users of MetaCore," Bugrim said.

MetaCore and MetaDrug already provide some information on bioactive chemicals • MetaCore includes information on endogenous metabolites and known drugs while MetaDrug is targeted toward xenobiotics and their interactions with molecules • but Bugrim noted that the chemical information in MDL's databases is much more comprehensive than anything available in GeneGo's pathway products.

Researchers can use pathway analysis to identify a compound of interest in MetaCore or MetaDrug, and then use DiscoveryGate to find compounds with a similar structure but with different characteristics, he said.

"Pathway analysis started as analysis of microarray data originally," Bugrim said, "But what we are seeing now is that different data types and the integration of different data types are starting to make sense in the context of pathway analysis."

This trend, he said, is driving adoption of pathway tools downstream.

Ingenuity Systems, another pathway informatics vendor, is seeing a similar pull for its products in downstream applications.

Last October, Wyeth extended its licensing agreement for Ingenuity Pathways Analysis. At the time, Steve Howes, senior director of bioinformatics at Wyeth Research, said that the company was planning on using the software "in translational medicine initiatives," including biomarker discovery, as part of a pharmacogenomics study [BioInform 10-31-05].

Bugrim said that pharmacogenomics may be one driver for the interest GeneGo is seeing from medical practitioners. "I think some of the advanced physicians are starting to think in terms of personalized medicine, and although it's not a big industry yet, maybe [some are] looking at what's going on in individual patients, so for that they need a tool like MetaCore so they can get some of their data into it."

In a statement, RMA said that it planned to use MetaCore to analyze gene expression data from human oocytes and blastomers and that it was seeking a system with curated content in the area of reproduction that was "capable of concurrent analysis of multiple patients' datasets."

Officials from RMA could not be reached to provide additional information on their use of the software.

• Bernadette Toner ([email protected])

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