There are several ways to explore the structure of protein targets and their molecular interactions, including x-ray crystallography, NMR, and computational methods, and a number of companies have made these the focus of their business.
Now a small startup company called ExSAR is adding a new tool to this commercial toolbox: hydrogen/deuterium exchange followed by mass spectrometry. The technology enables users to measure the exchange between hydrogen in proteins and deuterium in the surrounding solution, explained Patrick Griffin, ExSAR’s CSO and executive vice president for research. Users can identify specific sites where a hydrogen exchange has occurred by analyzing peptides derived from the protein by LC-MS, and can then create an H/D exchange map. An interaction of a protein with a ligand, or a change in its conformation, alters the deuterium exchange rate. Based on this information, researchers can deduce the binding mode, or the nature of a conformational change.
This ability makes H/D exchange-mass spec a good tool for lead optimization, according to Griffin, who joined the company last year from Merck Research Laboratories, where he headed a group of 40 scientists as senior director of molecular profiling proteomics and basic chemistry analytical support. Besides the study of small molecule-protein interactions, applications include antibody-protein interactions and conformational studies of protein therapeutics. As a proof-of-concept study, ExSAR has characterized the solution structure of human growth hormone and the effect of different stabilizers on the protein structure.
While the method of hydrogen/deuterium exchange followed by mass spectrometry is not new, ExSAR claims to be the first company to commercialize it for applications in drug discovery. Moreover, the company has developed a high-throughput platform, according to Eric Pflanzer, ExSAR's director for business development. Besides a number of trade secrets and proprietary software, ExSAR holds three patents: US patent No. 6,331,400, “Method for characterization of the fine structure of protein binding sites;” No. 6,291,189, “Methods for the high-resolution identification of solvent-accessible amide hydrogens in polypeptides or proteins and for characterization of the fine structure of protein binding sites;” and 5,658,739, “Method for characterization of the fine structure of protein binding sites.”
According to Griffin, the technology has a number of advantages compared to x-ray crystallography and NMR: It is solution-based and only requires microgram amounts of protein for a complete study, and its throughput is “compatible with medicinal chemistry efforts,” he said, adding that there is “no limitation to the type, size, or nature of the target.”
The company, which has a staff of fewer than 10, was founded in 1998 by Mark Fisher, a New York-based venture capitalist, and Virgil Woods, an associate professor of medicine at the University of California, San Diego. First run as a “virtual company” under the “working titles” of Thermaphore Sciences, then Carta Proteomics, it initially sponsored proof-of-concept studies in the groups of Wood and of Vernon Anderson, a professor of biochemistry and chemistry at Case Western Reserve University. These studies are still ongoing.
Last summer, the company opened shop in Monmouth Junction, NJ, under its new name, ExSAR, which stands for exchange structure activity relationships. “For deal-doing, it’s a great place to be,” said Pflanzer, given the proximity to several pharmaceutical companies, as well as investment companies in New York City.
According to Pflanzer, the company received seed funding from New York-based MBF Capital as well as early-stage venture capital “in the seven figure range” from Princeton, NJ-based Johnston Associates and a handful of other investors. For example, Carta Proteomics in 2001 received a $1.5 million investment from Johnston Associates, whose president, Robert Johnston, is ExSAR's CEO. In addition, the company won a $100,000 STTR grant from NIGMS in 2001 entitled “Hydroxyl radical mapping of protein interfaces,” which funds research in Anderson's group, and holds a number of matching grants “from California institutions,” according to Pflanzer. Several other NIH applications are currently under review, he added.
ExSAR's business plan involves both in-house use of the technology for drug development and partnerships with pharmaceutical and biopharmaceutical companies. Internally, ExSAR focuses primarily on nuclear receptors, an area Griffin was “intimately involved in” while at Merck.
Collaborations start as industry-sponsored pilot research agreements that may develop into strategic alliances, said Pflanzer, who declined to reveal whether any partnerships with industry exist at the moment.
He did outline the company's strategy for the rest of the year, though: to continue with internal projects, raise more funds, announce a partnership with another company, and increase staff. Talks with a number of companies are ongoing, he said, and while many pharmaceutical companies have explored H/D exchange techniques in-house before, not many seem to have used it successfully: “When we talk to them, they tell us ‘we failed, that’s why we are talking to you now,’” said Pflanzer.