Seeking to address the “protein expression bottleneck” of the drug discovery process, Roche Diagnostics on Monday will formally introduce a new service arm for customers: the Roche Protein Expression Group.
RPEG sells purified proteins on demand to pharma companies seeking targets for structural characterization, high-throughput screening, and assay development platforms. The group began receiving internal funding from Roche in May 2002 and opened for business as an official part of Roche Diagnostics’ US operations in Sept. 2002. RPEG delivered its first protein to a “major pharma company” in Dec. 2002, and has further contracts for protein delivery with “several top 10 pharma companies in addition to smaller biopharma companies,” according to Brian Holaway, RPEG’s head of marketing and business development.
The group, with a staff of 20 people, operates out of Roche’s Indianapolis site and has a protein chemistry lab complete with purification, chromatography and mass spec equipment — as well as RPEG’s prize device, a cell-free high-yield protein expression system. “The reason this is noteworthy is people have been trying to do cell-free production of protein for years,” Holaway said. “In the past, they did it only as an analytical tool, because the amount of protein [produced] was so small.” According to Holaway, proteins that are normally difficult to express in cell-based contexts — such as membrane, apoptotic, or toxin proteins — are produced by RPEG in milligram quantities using a variation on Roche’s Rapid Translation System cell-free protein expression platform.
Although Roche is marketing RPEG as a novel service, RTS has actually been available as a commercial product for several years. The product uses technology that Roche initially licensed from the Russian Academy of Science, and it has met with mixed reactions. “[Researchers] may tell you, ‘we used it and had a hard time getting it to work,’” Hola-way said. But he said such problems have been solved in RPEG’s system, due to higher quality reagents that the group uses that are not available commercially, and to the “know-how for cell-free [work] that wouldn’t be available to a person buying the kit” — although the device itself is the same as the one for sale.
The advantages of a cell-free expression system, according to Holaway and to the research scientists who use such a system, mainly lie in the system’s ability to produce harmful proteins at high levels that would normally kill a cell; to produce proteins that have trouble folding or solubilizing — such as membrane proteins —; and to drain or add ingredients to the reaction solution, which is composed mostly of E. coli lysate. “If the protein has a tendency to seek a hydrophobic environment, we can help the protein out by adding detergents to keep it soluble. If the protein has a tendency to not fold properly, we can add stuff like chaperone proteins that will bind the protein as it is expressed and [help it to] fold properly around it,” Holaway said.
The ability to produce these “difficult” proteins can be valuable to the drug discovery process, according to Marius Ueffing, a director at the GSF Research Center for Environment and Health in Neuherberg, Germany. “Sometimes these [difficult proteins] are the most important for drug pipelines — for example, the apoptosis proteins that are very important for cancer and very hard to express in cells. The gain with the RTS system is that it doesn’t interfere with cell physiology,” Ueffing said. Ueffing plans to use the RTS system for an upcoming antibody initiative at the German Society for Proteome Research. He has not yet tested it for himself, but is taking his recommendations from the RZPD Center, a German protein and DNA resource center. “[RZPD] uses it and also knows the limitations, but their experience with this system is positive and that encourages us to choose it,” Ueffing said.
According to Joshua LaBaer, who does work with cell-free expression in his position as director of the Harvard Medical School Insitute of Proteomics, the limitations of the cell-free system may overcome the advantages in many cases, even in the case of RPEG’s supposedly superior system. “The proof of the pudding is the quality of the protein that people get from [RPEG],” LaBaer said. “It’s not novel that there are companies who prepare protein for you, and if they can do it better, faster, cheaper by using a cell-free extract — that’s terrific. But at some level it’s going to have the same limitations that all proteins produced in bacteria will have.” Drawbacks to cell-free methods that LaBaer cited include the lack of mammalian modifications, the difficulty of making proteins larger than 100 kDa, the difficulty of purifying the protein from cell-free environments that tend to have unusually high levels of background proteins, and a broad variation in yield. What all this adds up to, according to LaBaer, is ambivalence on whether cell-free expression systems are worth bothering with at all. “The word on the street seems to be that a lot of people who started on a path to cell-free systems have started to walk away from it. The sense was, it doesn’t solve any of my problems,” LaBaer said.
The drawbacks may not matter to Roche’s pharma customers, since they are not the ones making the protein. “If Roche is doing this as a service, that’s a great thing — people will want that,” LaBaer said.
Roche Diagnostics itself doesn’t want the service. “The reason we exist is to use Roche technology to increase revenue, not to channel our resources back internally,” he said. With several pharma companies biting, Haloway is confident that this raison d’etre will be validated.