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Proteomics Startup Caprotec Opens Shop With $6.6M in Venture Funding

This article has been updated from a previous version, which incorrectly stated that the protein analysis market is worth $300 billion instead of $3 billion.
With €4.5 million [$6.6 million] in private equity funding, proteomics start-up Caprotec Bioanalyticals is gearing up to hit the streets with a technology its founder and CEO said will isolate proteins for analysis that otherwise would be missed.
The Berlin-based company also plans to raise another €1.5 million in a second round of private-equity financing by the end of the month that will enable it in January to move into a new facility in the city, equipped with 2,500 square feet of research space and 3,300 square feet of administrative space, according to CEO Hubert Köster.
Caprotec’s technology, called CCMS, is based on tri-functional molecules called capture compounds, which Köster said offers a new way to examine protein interactions.
CCMS can be used to define and confirm drug targets and to discover off-target proteins that cause side effects, thus “enabling subsequent drug structure optimization,” Köster and colleagues report in a paper describing the technology, published in the Nov. 3 issue of Assay and Drug Development Technologies.
A selectivity function that is part of the platform allows the capture compound to reversibly interact by affinity with proteins, while a reactivity function forms a covalent bond outside the affinity bonding site. Finally, a sorting, or pullout, function allows captured proteins to be isolated from cellular lysate to be analyzed by mass spectrometry and characterized by database queries.
Within the $3 billion protein analysis market, just about every major player in the space has chemistry for protein detection. According to Köster, the advantage of the CCMS technology is that “you can purify [molecules of interest] and identify them and characterize them so that you exactly know their authenticity, which is not the case if you use, let’s say, affinity chromatography.”
Another advantage is that the capture compound forms a covalent bond, allowing researchers to identify off-target proteins, he said.
“We also capture weak interacting proteins because we fix them to the capture compound, so you cannot really wash them out,” Köster said. With affinity chromatography, “if you are looking for unknown proteins, you don’t know which the best conditions [are] to keep them on the matrix,” he added.
CCMS complements other existing technologies, such as affinity chromatography and 2D gel electrophoresis, to allow new ways to analyze the proteome, he said.
The technology has been used by Caprotec in a collaboration with an undisclosed “big-five” pharmaceutical firm to discover with which proteins a drug candidate interacts.
Caprotec’s €4.5 million VC round was led by the VC Fonds Berlin, which is managed by the Investitionsbank Berlin Beteiligungsgesellschaft. ERP Startfonds and private investors, including Evotec co-founder Heinrich-Maria Schulte, participated in the round.
Most of Caprotec’s management team and its five-member board of directors and scientific board are in place, Köster said, and the company is now in the process of building its research team of mass spectrometrists, chemists, biochemists, and bioinformaticists.
During the second quarter of 2008, the company’s first commercial product, its Methylome Kit for isolating, identifying, and characterizing DNA-, RNA-, and protein-methyl transferases from tissue samples, is expected to hit the market.
No Interest in Mass Spec
If Köster’s name is familiar it’s because he has a long history in the biotech world. Before founding Caprotec, he had started or co-founded four other biotech firms, including in 1994 Sequenom, whose MassArray SNP-genotyping platform is based on mass spec, and prior to that in 1987 Milligen/Biosearch, where he and others designed systems to synthesize peptides and sequence proteins.

“The key … is reducing the complexity of the proteome, and then you can use mass spectrometry. Otherwise, you are swimming in a sea of information.”

Though Sequenom is a DNA analysis firm, Köster said that “it was clear to me that it’s very important to link SNP analysis, for example, with the proteins.” So after taking Sequenom public in 1997 in the third-largest biotech initial public offering on the Nasdaq exchange that year, he sought to move Sequenom into the proteomics space “and combine genomics and proteomics.”
At the time, though, the company’s board of directors didn’t agree with his vision, and after leaving Sequenom and finding himself “intellectually bored,” Köster again began exploring technology that can analyze complex protein mixtures. Caprotec is the result of that exploration.
According to Köster, who founded Caprotec with about $6 million of his own money, one thing he was not interested in was mass spectrometry. While he called the technology “wonderful,” he said the chemistry was not at a point to take full advantage of the instruments.
"The key ... is reducing the complexity of the proteome, and then you can use mass spectrometry, Köster said. “Otherwise, you are swimming in a sea of information.”
With the Methylome Kit expected to become available next year, the company should be generating revenues in its first year of operation, Köster said. During the next four years, Caprotec should be generating €15 million to €20 million annually in revenues, which would enable it to reach break-even.
In a field littered with the carcasses of failed or floundering proteomics and protein-analysis firms, Köster’s timeline for break-even may seem ambitious. But he said that CCMS’ selectivity function is a critical one because it will allow Caprotec to develop additional kits in the future.
“We can very quickly develop a family of kits which are designed to isolate identify, and characterize different proteins, or different protein classes,” he said. “That’s why we think we can build up very quickly a catalogue business of different kits designed for different protein classes.”
Eventually, Köster said he envisions creating a diagnostics division within the company that uses the CCMS technology to discover and profile protein biomarkers, as well as a unit that uses the platform to help pharmaceutical companies improve the efficacy of their drugs “by understanding the interaction of drugs in the protein space, [and] reengineering the drugs to remove side effects.”

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