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With Axys Acquisition Complete, Celera Integrates Chemistry with Proteomics

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Last week, at a briefing for analysts held at the Pierre Hotel in Manhattan, Celera officials offered a more detailed description of how this would occur.

Specifically, Patterson and other Celera executives, including Craig Venter, Celera’s president and chief scientific officer, laid out how newly-acquired Axys Pharmaceuticals would contribute its capabilities in structural biology and chemistry to Patterson’s proteomics platform. Axys, now known as Celera South San Francisco, disclosed last week that it has arranged pilot study projects with Graffinity, a Heidelberg, Germany-based developer of protein arrays, and Syrrx, the San Diego-based drug discovery company specializing in high-throughput x-ray crystallography of proteins.

In addition to the potential partnerships with Graffinity and Syrrx, Celera has also established a chemical proteomics group at its new South San Francisco facility. To lead the group, Celera last month hired Matthew Bogyo, a biochemist at the University of California, San Francisco, said Mike Venuti, a former Axys executive now serving as the general manager of Celera South San Francisco. Bogyo’s lab resides in a new building completed last month that currently provides space for 60 medicinal chemists.

Proteins with potential

Bogyo’s academic research group has specialized in designing small peptides that interact with cysteine proteases and other proteins. Cysteine proteases have also been the subject of Axys’ attention; last week Celera South San Francisco extended a collaboration with Merck to develop small molecule inhibitors to Cathepsin K, a cysteine protease associated with osteoporosis-related bone resorption.

To assist Patterson’s efforts to analyze and identify only those proteins with potential as druggable targets, Bogyo will attempt to design chemical affinity agents that only screen for similar proteases and kinases, Venuti said. Once these protein targets are identified via Celera’s proteomics platform, Bogyo and other Celera scientists can refine the affinity agents for use as potential small molecule therapeutics, Patterson added.

Celera’s pilot project with Graffinity will also investigate ways to “distinguish proteins amenable to small molecule intervention,” said Venuti. The collaboration is aimed at using surface plasmon resonance to study how proteins bound to a chip interact with a library of small molecules, he said.

With Syrrx, Celera plans to determine how useful the structural biology company’s platform for high-throughput x-ray crystallography helps identify protein targets useful for structure-based drug design. Celera chose to work with Syrrx, rather than some other structural biology company, because Syrrx has technology for studying a broader range of proteins and protein complexes, Venuti said. “The way they’ve developed their technology leaves them relatively unbiased in their approach to protein families,” he said, “but we’re doing a pilot study to see if it’s as fair as it sounds.” Exact financial terms of the deal were not disclosed, but Celera said it would make research and development payments to Syrrx.

Picking up the pace

Applera, Celera’s parent company, held the meeting with analysts to discuss plans for Celera Diagnostics, a joint venture between Applied Biosystems and Celera Genomics. The Alameda, Calif.-based diagnostics venture will attempt to commercialize biomarkers that Celera discovers using proteomics and genome sequencing. Currently all of Celera’s proteins with potential as markers, targets, or therapeutics are at the preclinical stage, said Venter.

Venter added that Celera is not focusing on identifying secreted proteins, because other pharmaceutical companies “have mined [secreted proteins] for the last decade without finding anything.” Instead, the company’s proteomics effort is targeted toward membrane proteins that are differentially expressed in certain disease cells, such as cancer cells, as well as other proteins differentially expressed in cellular compartments, according to Stephen Hoffman, Celera’s senior vice president for biologics. Hoffman recently joined Celera from the US Navy, where he directed research on malaria.

Celera is not looking to acquire new technical capabilities, Venter said, because the company’s focus will now be on extracting pharmaceutical products from its existing platform. “Now that we’ve built the technology, we need to increase the pace of discovery,” he said.

The company has not ruled out acquiring additional expertise in downstream drug development, said Applera CEO Tony White, who also spoke with analysts at the meeting.

— JSM

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