Just over two years ago, Myriad Proteomics was launched as a collaborative venture between Myriad Genetics, Hitachi, and Oracle. The three firms contributed a total of $185 million to launch the initiative, with the goal of mapping the entire human proteome and packaging it as a commercial database by 2004.
Soon afterwards, however, it became apparent that “the database model was going out of date,” said Sudhir Sahasrabudhe, CSO of Myriad Proteomics. So the company quietly retooled its business model while continuing with its original plan: “plugging away and generating protein-protein interaction data,” Sahasrabudhe said.
Now, thanks to a high-throughput pipeline that spits out around 6,000 yeast-two-hybrid experiments per week, the company has compiled 42,000 non-redundant protein-protein interaction pairs — enough to provide a preliminary view of protein activity in “all the major organ systems in the human body,” Sahasrabudhe said. Armed with this information, Myriad Proteomics has embarked upon its new and improved mission: mining its own database to deliver biologically relevant information on drug targets and lead compounds for pharmaceutical partners.
“We still continue to believe that there is a discovery opportunity in the data, but the bar has been set higher,” Sahasrabudhe said. “It’s no longer enough to just generate primary data…We have to look at it and ask, ‘Do we know more about the disease biology than we did previously?’” According to Sahasrabudhe, the company has spent the past two years asking that question of its own data, and has emerged with an unqualified “yes” in response. In particular, he said, Myriad Proteomics has uncovered “new targets and new ways to think about neurodegeneration and cell proliferation” within its database, and plans to move these discoveries further downstream.
The company has recently purchased compound libraries and ahigh-throughput screening platform and set up an assay development group to identify lead compounds for its targets.
The House that Proteomics Built
Myriad Proteomics’ 91 employees are housed in a year-old 34,000 square-foot facility in Salt Lake City stocked with automated plating and colony-picking robots, ABI MALDI/TOF-TOF mass spectrometers, and other high-throughput proteomics equipment. With the “daunting task” of implementing a customized LIMS recently completed, Sahasrabudhe said the company is now ready to put its technology to work.
Using a combination of proteomics technologies, including “medium-throughput” mass spectrometry to gather more information about interactions that the “random” yeast-two-hybrid experiments detect, the company has fleshed out its interaction database to depict not just pathways, but biological networks, Sahasrabudhe said. The company has developed several “network explorer” software tools to help navigate its database and access publicly available resources. Researchers can visualize a particular protein-protein interaction within the context of a larger network, retrieve all the functional information about each protein in the public databases, and check to see if additional interaction data is available across other species, such as yeast. The company refers to its ongoing pathway and network maps as “storyboards,” which are revised when new interaction data becomes available from its own experiments or from the public domain.
Sahasrabudhe said that Myriad Proteomics has just begun “active discussions” with a number of potential pharmaceutical customers for drug discovery collaborations based around its technology platform and its database. If anything, the demise of the biological database model has worked in the company’s favor to this point, he noted, because potential customers are frustrated with the amount of work required to sift through other resources that are little more than “data dumps.”
In addition, Sahasrabudhe said, the company is experiencing some demand for its database as a standalone product via a subscription model — a possibility that he said the company certainly won’t turn away, but won’t consider betting its future survival on.