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Peptide Array-Manufacturing Breakthrough Could Breathe New Life Into DKFZ Spin-Out

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Scientists from the Fraunhofer Institute for Manufacturing Engineering and Automation IPA in Stuttgart and the German Cancer Research Center in Heidelberg recently announced that they have developed a way of mass-producing peptide arrays that is less expensive than existing methods.
 
The method, which employs a laser scanner developed by Fraunhofer, could reinvigorate a struggling seven-year-old firm founded by DKFZ researchers to provide inexpensive peptide chips to pharmaceutical and biotech companies.
 
Fraunhofer IPA scientist Stefan Güttler said that researchers from DKFZ had approached his institute with the idea to co-develop a low-cost, high-throughput method for manufacturing peptide arrays.
 
The group settled on a method pioneered by DKFZ researchers that uses dry immunohistochemistry. Dry amino acids are first encapsulated in toner powder in a state where they cannot react or decay. “Amino acids encapsulated in powders can be stored for months and processed without any reactions,” Güttler noted. They are then arrayed onto a glass slide to create peptide arrays. A paper describing the method appeared in Science in December. [Beyer M, et al. Combinatorial synthesis of peptide arrays onto a microchip. Science. 2007 Dec 21;318(5858):1888.]
 
To create arrays this way, Fraunhofer developed a special laser printer capable of printing 20 different types of amino acid toners. Güttler said that the 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.
 
The slides are then washed and a second layer of amino acids is printed atop the first layer. The process repeats itself until the researchers generate arrays of up to 160,000 peptides that are 15 to 20 amino acids in length.
 
Güttler told BioArray News last week that there is an unmet need for such arrays in the cancer research space, and that DKFZ turned to Fraunhofer because it had become clear that available printing technologies were not suitable to mass produce them.
 

“Peptide arrays would be very useful for research connected to the development of drugs, vaccines, and completely new methods of diagnosing diseases.”

“Peptide arrays would be very useful for research connected to the development of drugs, vaccines, and completely new methods of diagnosing diseases,” said Güttler. “The problem connected to this is the huge amount of peptides that are needed.”
 
Güttler said that propelling the demand was high expense and small supply of existing “state of the art” peptide chips. Today, such chips contain as many as 10,000 peptides and cost about €5 ($7.75) per peptide, meaning that a typical peptide chip would cost around $77,000. Such a price tag “would make no [financial] sense” to use the technology, “and therefore this technology plays almost no role in biomedical research,” he said.
 
Mass Production
 
Mass production became the key. Initially, the researchers considered inkjet printing, but Güttler said Fraunhofer quickly ruled out this option because it would not meet the speed and quality requirements sought by DKFZ. Moreover, the amino acids used in peptide array manufacturing had a high level of viscosity and cross-reactivity, which led to an “unreliable printing process,” Güttler said.
 
Eventually they turned to the laser printing technology. According to Güttler, Fraunhofer and DKFZ developed a prototype peptide arrayer that relies on this process, though the heating step remained manual. Using the prototype arrayer, Fraunhofer and DKFZ are able to manufacture peptide arrays at only a few cents per peptide.
 
“With this prototype [DKFZ] managed to prove that this process of production of peptide arrays works, and that the peptide arrays have the full functionality compared to those arrays produced conventionally,” Güttler said. He added that Fraunhofer and DKFZ aim to mass produce and eventually commercialize the arrayers, which could happen as early as next year.
 
The opportunities raised by the development of the new arrayer have reinvigorated PepPerPrint, a small technology shop started in 2001 by the same DKFZ scientists who helped develop the new peptide array printer.
 
Frank Breitling, a DKFZ scientist and PepPerPrint co-founder, told BioArray News last week that the company had developed the dry immunohistochemistry printing principle as far back as 1998. He said his team had hoped to secure funds to develop the printer and commercialize it earlier this decade but could not due to a difficult funding environment.
 
Now, with the Fraunhofer-designed prototype completed, Breitling said PepPerPrint is confident it should be able to secure European Union funding by the beginning of 2009 that will allow it to begin offering peptide array screening services for other companies.
 
“I am optimistic that we will get funding and get into the market,” Breitling said. “I am not sure how long it will take to penetrate the market, but at the moment we think it might make sense to develop a small-molecule-screening facility for big pharma companies.”
 
Breitling envisions PepPerPrint not only manufacturing and screening natural peptides but also creating and screening synthetic peptides. He added that recent research has hinted that such peptides can be used to treat certain diseases.
 
“We could screen right from the beginning from these partly non-natural peptides … [to see which ones] bind to interesting proteins that might be able to treat, say, pancreatic tumors,” Breitling said.
 
The IP for the dry immunohistochemistry production methodology is owned by DKFZ, while the IP rights for the laser printer are controlled by Fraunhofer. According to Breitling, it is likely that Fraunhofer will spin out a company to manufacture and sell the laser printers.
 
Because it is relatively untapped, the market for peptide arrays and arrayers has not been clearly defined. And, because of its cost, the technology has not attracted interest from the firms that dominate the DNA array market, such as Affymetrix, Illumina, or Agilent Technologies, leaving the sector to shops like Berlin-based JPT Peptide Technologies; Rockville, Md.-based 20/20 GeneSystems; and Nantes, France-based ProtNeteomix. Also, firms that sell protein arrays, like Invitrogen, Gentel Biosciences, or Sigma-Aldrich, have yet to specifically target the peptide array market.
 
Breitling said that one reason that there has yet to be large-scale adoption of commercial peptide arrays is that they are “simply unaffordable for most groups of researchers.” He attributed the cost passed on from current methods of printing as one of the main obstacles to growing the market.

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