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With New $2.6M Grant, Pronota Looks Beyond Protein Identification to Validation

With a €1.87 million ($2.58 million) grant from the Belgian government, Pronota plans to hasten development of its biomarker discovery platform.
The Ghent, Belgium-based company announced the grant last week from the Flanders government, which it plans to use to build upon its core technology, MASStermind, to include biomarker validation, and to extend the company’s biomarker discovery programs, Pronota CEO Nick McCooke told ProteoMonitor this week.
“It’s always important to get this sort of funding. It supplements the equity funding that we get, [and] it extends the run rate,” he said. The latest grant comes on top of grants totaling €1.7 million from the government last year to develop the MASStermind platform, which combines mass spectrometry techniques, chromatic fractionation, and data interpretation.
Since its founding in 2004, Pronota — which until November was called Peakadilly — has relied on providing protein analysis services to other companies, particularly drug firms and diagnostic companies. It also has been engaged in its own biomarker discovery work.
But the company is now looking to drive the discovery process downstream by further developing its validation platform.
“Increasingly, we’re looking to supplement [MASStermind] because clearly if you’re going to discover biomarkers, you’re best to start with an unbiased discovery approach and then you validate with other platforms [that] are hypothesis driven and high throughput,” McCooke said.
The idea is to come up with a hit list of candidate biomarkers from the discovery process, then to process and refine that list.
“You don’t get biomarker candidates raw out of a discovery platform,” he said. “It’s a multi-stage process, and so in order to get the complete story, you have to take that hit list and further process it in terms of validating, verifying those discoveries using another technology in the same samples.”
During the past 12 months, McCooke said, the company has put much of its energy into getting the MASStermind platform to meet performance goals in terms of its throughput and ability to discover low-abundance protein biomarkers in serum. Those have been met, he said, and next week the company is scheduled to publicly announce the performance milestone.
Now the company is shifting focus from discovery to validation, aided in part by the funding announced a week ago.
“Part of that funding is to further develop that whole pipeline,” McCooke said. To date, most of the company’s investment has been “biased toward the initial discovery stage,” McCooke said. But with performance goals for the MASStermind reached, “the goal for us is to have a verification/validation platform that is compatible with the discovery platform.
“In other words, our goal is to discover biomarkers of low abundance in the discovery platform,” he said. “Then the validation platform must be capable of the sensitivity levels relevant to that.”
Aside from saying the validation platform is mass spec-based, McCooke declined to provide further details about it. The platform doesn’t yet even have a name.
The company also will be using the funding for its internal biomarker discovery program, which is based not on any specific diseases but rather on the clinical utility of the biomarkers.
As McCooke explains it, Pronota has a system to score biomarkers based on “a whole load of different characteristics” including its clinical need, the market opportunity for a biomarker, and the availability of clinical samples.
“We’ve also come from a scientific or biological point of view, thinking about the nature of the disease or the clinical context, whether it’s likely there will be detectable biomarkers in the blood, and whether we’ll be able to see biomarkers in blood at concentration levels that are appropriate for discovery,” he said.
“When we first started on this process, I perhaps naively imagined that it would probably lead to a disease focus,” McCooke said. “But it actually hasn’t worked out that way. We’ve really spent quite a lot of time looking at particular clinical applications where we think a biomarker has significant value.”
Let’s Get Some Money
The funding from the Flanders government comes as Pronota is in the midst of its second act as a business entity. In March 2006, Koen Kas, founder of Pronota, was replaced as CEO by McCooke, and reassigned as CSO of the company.
McCooke had been the founding CEO of Solexa, a company that developed gene sequencing technologies that was acquired by Illumina in January.

“We raised enough money. Along with grant money, and along with more revenue money we hope to generate over the next couple of years, we hope to be able to push a run rate at a decent rate.”

According to McCooke, Pronota’s board made the change after deciding that someone with more business experience was needed to push the company forward. For the first time, the company also began pursuing venture capital.
Last August, Pronota closed its Series A financing, raising €14.5 million. Investors included Johnson & Johnson Development, GIMV, Life Science Partners, KBC Private Equity, and Baekeland Fonds II, the venture capital fund of the Ghent University Association.
Some of that funding helped pay for instruments such as mass spectrometers, chromatographers, and robotic instruments, while some went toward developing the MASStermind platform.
In November, the company dropped its former identity, Peakadilly, and adopted its current name [See PM 11/30/06].
As chief executive at Pronota, McCooke said his primary job is setting a goal for everyone to follow — in Pronota’s case, getting MASStermind to meet its performance goals.
“At the highest level, it’s having a very clear focus on what we’re trying to achieve, which is understood by everybody,” he said. “There’s a point in a company’s evolution where it has to put in place processes and management capability, goal-driven project structure. You have to have a strong focus on goals and how those are going to be achieved.”
Last month, the company also appointed for the first time a business-development director, Huw Davies, formerly the program manager for Ciphergen Biosystems’ operations in the UK, Ireland, and the Netherlands.
“Most of the business that came our way — it sounds terrible — was largely people knocking on our door,” McCooke said. “Now we are being more proactive and [using] Huw out there to knock on doors.”
For now, at least, the company is comfortable with the funds in its war chest and doesn’t foresee having to do another funding round until the end of 2009, McCooke said.

“We raised enough money. Along with grant money, and along with more revenue money we hope to generate over the next couple of years, we hope to be able to push a run rate at a decent rate,” he said.

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