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Germany's PepPerPrint to Increase Peptide Array Density, Upgrade Software


By Justin Petrone

Seeking to meet an "unmet biomedical need" to survey large numbers of peptides in a high-throughput manner, Heidelberg, Germany-based PepPerPrint will soon introduce higher-density arrays on a next-generation printer and will later this year launch a new web-based software interface that will support custom array design, according to a company official.

CEO Volker Stadler said that the spinout of the German Cancer Research Center, or DKFZ, is also developing a new microchip manufacturing process that could enable it to "significantly" improve the density of its arrays.

Stadler estimated the new microchip-based production platform could come online within three years.

Stadler spoke to BioArray News about the privately held firm's plans to expand its offering following a presentation at Select Biosciences' Advances in Microarray Technology conference, held in Dublin, Ireland, last week.

"There is an unmet biomedical need to look at large numbers of peptides, and the more probe molecules you can offer on a single chip, the greater the probability is to detect something that is, on one hand, relevant, and on the other hand, really specific," Stadler said of the firm's strategy.

"With a chip of hundreds of proteins or thousands of peptides, the possibility to identify something that is really unique is not very high," he said. "But if you have a library of 160,000 and later on 500,000 peptides, the probability to identify patterns that correlate with something" increases.

"The more markers you find that can be correlated, the higher the specificity and the uniqueness of the result will be," he added.

Officially founded in 2001, PepPerPrint is funded by a €500,000 ($650,200) investment from Germany's High-Tech Gründerfonds, plus a matching €1 million research grant. The firm's technology was developed at DKFZ and uses dry immunohistochemistry to generate arrays of thousands of peptides. Dry amino acids are first encapsulated in toner powder in a state where they cannot react or decay. They are then arrayed onto a glass slide to create peptide arrays.

Last year, the firm began offering epitope-mapping services on its arrays using a first-generation laser printer capable of printing 20 different types of amino acid toners (BAN 5/26/2009). Using this printer, toners are arrayed on a surface and then heated in a generic laboratory oven at approximately 180 degrees Fahrenheit until the dry toner powder melts away. Slides are then washed, and a second layer of amino acids is printed atop the first layer. The process repeats itself to generate peptides that are up to 15 to 20 amino acids in length.

Stadler said that the next-generation laser printer, which has been in development for over a year, will enable PepPerPrint to print 24 different amino acids to "incorporate four unnatural amino acids routinely, for example, phosphorylated diamino acids." The printer, which is being designed by Fraunhofer Institute for Manufacturing Engineering and Automation IPA in Stuttgart and KMS Automation in Schramberg, will also offer an "automatic electronic alignment system, provide higher-throughput processing, and ensure production stability," he said.

While PepPerPrint's current printer can produce arrays of 156,000 peptides on a 20x20 cm glass plate and 5,500 peptides on a standard 1x3 inch glass slide, the new printer should be able to produce 500,000 peptides on a glass plate and 20,000 peptides on a microscope slide. According to Stadler, the new printer should come online in July.

While the new printer will be able to produce higher-density chips, it will still take more than a week for the firm to synthesize a new custom chip. "We do not reinvent peptide chemistry, which means that it takes one day, including all the washing steps, to synthesize one layer of amino acid," said Stadler. "That means with a 10-mer chip, it takes ten days to get the chip from the order to the final step, though we plan to halve production time soon."

Customers for the firm's chips so far have included biotechs, pharmaceutical companies, and academics, Stadler said, but the majority of PepPerPrint's customers now are from industry. "That doesn't mean that our chips are not affordable for academia," Stadler said. "It means that we have been more successful in marketing to industry so far, though marketing with our limited capabilities is not always easy."

It is in terms of price that PepPerPrint aims to be most competitive. The company claims that it costs it €0.14 to synthesize a peptide. Berlin-based JPT Peptide Technologies, which sells a suite of peptide arrays and is PepPerPrint's most direct competitor, does not divulge pricing information on its website for comparison. Piscataway, NJ-based GenScript, another peptide array firm, charges $13 per peptide, according to its website.

Other firms offering peptide array services and kits include Lelystad, the Netherlands-based Pepscan Presto; Hayward, Calif.-based Elim Pharmaceuticals; Houston-based LC Sciences; Vancouver, Canada-based Kinexus; Madison, Wis.-based GWC Technologies, and others.


In addition to the printer upgrade, Stadler said that PepPerPrint is co-developing with Heidelberg-based Sicasys a new software package for use with its arrays. Sicasys specializes in life science-analysis tools and announced the deal with PepPerPrint in January. Stadler said the firm hopes to deliver optimized software to the market this fall.

Specifically, the new software package, branded PepSlide, should be "significantly improved in terms of flexibility," user friendliness, and will have increased spot resolution, Stadler said. More importantly, the web-based platform will enable customers to design their own arrays that will be synthesized by PepPerPrint and made available as either a service or in a kitted form

"A lot of people are still spotting their own arrays," Stadler noted. "If you can sit on your web browser, design your array, and then get the chip back in a few weeks, it becomes a much more attractive option for customers."

'Just Look at DNA Chips'

Though PepPerPrint's new printer will allow the firm to quadruple the density of its current chips, Stadler said the firm has ambitions to power research programs in diagnostics and therapeutics.

"Our goal in diagnostics is to identify for a number of diseases different peptide markers that can be correlated with a specific state of a disease," he said. "And if you look at the market at therapeutic molecules, biopharmaceuticals get more and more market share, such as monoclonal antibodies and other therapeutic proteins.

"If you model the hotspot of such a therapeutic protein with a smaller peptide or peptidomimetic molecule, the costs for such drugs and drug candidates will significantly drop," Stadler added.

To get there, the company is developing even higher density chips. PepPerPrint last year began working with the University of Heidelberg and the Karlsruhe Institute of Technology to develop a microfluidics-based peptide array platform. By pairing a microchip platform with combinatorial synthesis, the company can now print up to 40,000 peptides per square centimeter and, according to Stadler, the firm sees the microchip-based method as a way to further increase the density of its slide- and plate-based peptide arrays.

"We could use the microchip as a stamp to print toner particles on glass slides," Stadler said. "We could do 160,000 peptides on a glass microscope slide, for instance," he said. "Just look at DNA chips; it's the same question, to collect as much information as you can in one place."

Stadler declined to commit to a date for when the microchip-based method could be adopted internally, but speculated that it might take the firm three more years to optimize the process before introducing it, depending on the capabilities of PepPerPrint and the development of a more automated manufacturing process.

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