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Researchers Begin Merging Bio-, Cheminformatics In Race Down the Drug Discovery Superhighway


FOR YEARS bioinformaticists and cheminformaticists inhabited distinct realms of the scientific universe. But over the past year, a handful of companies have announced mergers, acquisitions, and partnerships that indicate that the walls separating the two disciplines are coming down.

“There is a lot of data coming out of the various experiments,” said Prasad Kodali, a senior informaticist at NetGenics. “On one hand, you have a whole human genome sequence, and on the other hand, you have ultra high-throughput screening where you screen almost a million compounds a day. To get the most out of this, and understand the various mechanisms involved, you have to combine bioinformatics and cheminformatics.”

Nobody yet knows how exactly this marriage of bioinformatics and cheminformatics is going to work. The two fields use different languages and protocols. For example, “activity” in cheminformatics refers to a molecule that interacts with a substrate, whereas “activity” in bioinformatics refers to all activities of an organism or component of it. On top of this, the two fields have solved some of the same problems in different ways.

For Lion Bioscience, the solution is a partnership with an outside company. Earlier this month, Bayer announced a $25 million deal to support an alliance between Lion and cheminformatics veteran Tripos to develop an integrated life science “pharmacophore” informatics platform for the German pharmaceutical giant.

The integrated platform will link Tripos’ MetaLayer enterprise-wide cheminformatics portal and application with SRS, Lion’s bioinformatics integration platform, which Lion installed at Bayer as part of an earlier 1999 partnership.

“This deal signals a paradigm shift, in going from tools in bioinformatics to process,” said Lion CEO Friedrich von Bohlen. “The key of future acceleration for drug discovery is not so much on the tools side as on the process side. What does it help if you have a Ferrari, but only 200 yards of highway to drive it on?”

Powerful high-throughput screening, molecular modeling, and genomic database analysis tools are the Ferrari. And the highway, von Bohlen says, “is where bio- and cheminformatics merge.”


While the $25 million deal gives Lion a head start in this race, it is far from the only serious entry.

Pharmacopeia molecular modeling subsidiary Molecular Simulations ramped up construction on its stretch of the highway using an acquisition strategy. In February, MSI acquired cheminformatics provider Synopsys Scientific Systems for $25 million. Then in early September, it purchased Oxford Molecular Group’s bioinformatics GCG software products and technologies.

When announcing both deals, Pharmacopeia chairman Joseph Mollica specified that these acquisitions comprised part of a strategy to offer customers an integrated system of tools for drug discovery.

Additionally, some bioinformatics and cheminformatics players have begun to cover the other half of the equation themselves.

In August 1999, bioinformatics software developer NetGenics announced it was developing an integrated drug discovery informatics platform for Pfizer. This platform, which it has just completed, uses a “federated database” or a virtual database, that allows users to do a cross-source query, where they can simultaneously pull up information from divergent platforms, such as a legacy chemical library, a single-nucleotide polymorphism library, and a sequence database.

This federated database is part of NetGenics’ flexible modular approach to integration of bio- and cheminformatics.

“Most of the informatics groups in the pharmaceutical industry have built their own informatics applications,” Kodali said. “We can use our components, their components, and third-party components.”

Since this project, NetGenics has augmented its portfolio of components by acquiring two cheminformatics programs, ChemSymphony and MetaSymphony, from FamilyGenetix.


On the other end of the equation, cheminformatics companies like SciTegic, a San Diego-based startup founded by two former MSI employees, have ventured into drug discovery informatics platforms.

SciTegic, with about a dozen employees, is not big enough to acquire or lure in a bioinformatics partner. So instead of integrating existing platforms, it has employed a strategy of building its own uniform platform from scratch.

“We thought it was going to be very difficult for an existing company to develop a next-generation system unencumbered by the legacy systems in place,” said SciTegic CEO Mathew Hahn. “It’s difficult for an existing company to make new software that undercuts its existing software.

SciTegic’s platform works on the principle of “data pipelining,” a program that draws information from diverse databases and “mines the data as if it were one physical entity,” Hahn said. This approach, he said, is quicker than rival companies’ strategies of integrating existing bioinformatics and cheminformatics software platforms.

“At MSI we went through four total mergers, and integration is a painful, slow process,” he said. “Down the road, there will be lots of competition, and the companies that will be successful will be those that can bridge the gap between bioinformatics and cheminformatics quickly.”

SciTegic has a long way to go before it bridges this gap between bioinformatics and cheminformatics. It has already sold and installed its informatics tools at Agouron Pharmaceuticals, and has three other finished, but as-yet unannounced deals, Hahn said. But it is still primarily a cheminformatics system.

Meanwhile, Lion’s von Bohlen said his company, along with Tripos, is negotiating several other bioinformatics-cheminformatics deals. “It’s not only pharma, but ag bio and larger biotech companies are interested,” he said. “We’re in discussions with other companies on solutions they didn’t even know we were capable of doing.”

—Marian Moser Jones

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