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GeneFormatics Expects to Announce Slew of Deals in Near Future

NEW YORK, Oct. 4 – GeneFormatics, which announced a major deal with three Bruker affiliates on Wednesday, expects to unveil a number of deals towards the end of the month designed to further enhance its technological capabilities as it looks for ways to improve the drug discovery process.

“The deal with the Bruker companies is one piece of a jigsaw puzzle that will help us to put our NMR efforts on steroids,” John Chiplin, CEO of GeneFormatics, told GenomeWeb. "GeneFormatics is trying to provide a high-throughput approach to NMR.”

“There will be more announcements toward the end of this month,” he said.

On Wednesday, GeneFormatics announced that it had penned deals with Bruker BioSpin for nuclear magnetic resonance spectroscopy technology, with Bruker AXS for X-ray single crystal diffraction systems, and with Bruker Daltonics for Matrix Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry machines. Chiplin said that the NMR piece of the deal was the leading piece.

NMR techniques exploit the way different atoms within a protein’s molecular structure resonate, use the measurements of these resonances to determine distances between atoms, and model protein structures based on these distances.

Under the terms of the deal, San Diego-based GeneFormatics will acquire an unspecified number of Bruker machines for use in its proteomics effort. 

“We took a look at a few other companies but we felt that the Bruker group of companies were ahead of the pack,” Chiplin said. “The technology developed by Bruker allows you to get much better sensitivity in your NMR experiment by improving the signal-to-noise ratio.”

In exchange for GeneFormatics commitment to Bruker, the Bruker companies will contribute to GeneFormatics’ next round of private financing. GeneFromatics, which has so far raised $28 million in private investments, said it would also make an equity investment in Bruker AXS and Bruker Daltonics. The companies did not disclose the size of the equity investments.

The Bruker companies will also benefit from the deal by having certain rights to incorporate findings from GeneFormatics' work to improve their technology, Chiplin said. And GeneFormatics, which currently has 65 employees, will also become a test site for new mass spectrometry, x-ray crystallography, and NMR spectroscopy technologies developed by the Bruker companies.

GeneFormatics uses a “function first” in silico approach to structural proteomics. While some companies employ threading models, homology models, or ab initio models to determine a protein’s structure and function, Chiplin said that researchers at GeneFormatics take a “best-tool-for-the-job” approach.

“Our belief is that we can get several orders of magnitude higher by combining the technologies,” Chiplin said.

Representatives of the Bruker companies seemed to agree.

“What’s important here is that GeneFormatics is coming at this with a new approach,” Mark Chaykovsky, executive vice president of Bruker BioSpin, told GenomeWeb. “In the past it’s been create the sequence, do the function, and then get the structure. They are starting with the in silico approach that will allow companies to screen the proteins and analyze them based on what’s interesting.”

Other protein structure determination companies such as Structural Genomix and Syrrx are both focused on streamlining the labor-intensive process of x-ray crystallography, in which proteins are isolated, then crystallized and zapped with x-ray beams.

Earlier this year, GeneFormatics acquired Structure Function Genomics, a Princeton, N.J.-based company that has developed high-throughput NMR techniques for determining protein structure. GeneFormatics of San Diego also has a commercial license deal with Rutgers University for NMR spectroscopy technology developed by Gaetano Montelione’s lab at Rutgers. Montelione is a leader in NMR and a principal member of Structure Function Genomics.

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