PARIS, Dec 18 - The yeast two-hybrid method, first developed in 1989 by Stanley Fields, has provided the basis for a swift, high-throughput industrial process used to make protein-protein interaction maps. Established companies such as CuraGen and Myriad have each adapted the methodology and use it as part of their respective drug discovery platforms.
Now Hybrigenics of Paris is hoping that its technique, which uses protein fragments rather than whole proteins, will dominate the next generation of high-throughput yeast two-hybrid screening techniques.
As part of those plans Hybrigenics is currently using the $17 million from its recent private equity financing to develop its yeast two-hybrid screening program, which along with its PIM (protein interaction map) Rider software, is designed to accelerate the drug discovery process.
By fragmenting cDNA, Hybrigenics aims to study the interactions between carefully selected “bait” proteins or protein fragments and millions of “prey” fragments. Because of the fragmentation, Hybrigenics says the technique allows it to easily identify the domain responsible for each putative protein interaction. Once an interaction is identified, a domain’s location can be determined by sequencing the bit of cDNA that gave rise to the protein fragment.
Vincent Schachter, director of bioinformatics research at Hybrigenics, said the company’s method offers a qualitative advantage over other methods by lessening the number of false positives and false negatives and allowing the scoring of protein interactions according to their reliability.
“ Hybrigenics' high throughput assay captures an average of five interactions per protein on large protein sets, consistent with results obtained by the best low-throughput procedures on small sets of proteins, ” Schachter said. “We save time and achieve more with less interaction studies without sacrificing quality or reproducibility.”
“We test a bait protein against millions of fragments [from thousands of proteins] in parallel,” he added.
In order to process the vast amount of data, Hybrigenics is bioinformatics intensive, with 15 of the company’s 30 scientists dedicated to bioinformatics. This group has developed PIM Rider, a proprietary interactive mapping and analysis tool that makes protein-protein interactions easier to visualize and explore. PIM Rider also includes a unique feature that gives a statistical indication of the degree of confidence in each mapped interaction.
Fragmenting Proteins Has Pros and Cons
While Hybrigenics still has to prove its commercial viability, there are indications that some of the more established companies are adapting the fragmentation method, at least for some of their studies.
Bruce Taillon, group leader for engineering and technology development at CuraGen, said that his company utilizes fragmentation as a targeted approach in instances where specific proteins are singled out as being potentially important. He did, however, endorse the whole protein method, noting the speed at which his company is blazing away.
CuraGen finished the yeast protein interaction map for 6,000 proteins in a mere six weeks and has since accelerated the pace. The company, which published the first protein interaction map of an entire model organism, Saccharomyces cerevisiae, expects to do tens of thousands of proteins in 2001.
A source familiar with the yeast two-hybrid technique said that Hybrigenics’ fragmentation model might have some advantages over the whole protein techniques employed by CuraGen and Myriad, especially regarding false negatives. The source, who requested anonymity, said, for example, that cDNA for some whole proteins might not get transcribed in the yeast simply because they are too bulky to get into the nucleus.
Another possible problem with whole protein studies is that a whole protein is much more likely to be toxic to yeast than a fragment of protein, thus making it impossible to measure the protein’s interactions using yeast.
The same source warned, however, about a potential disadvantage: two protein fragments may interact while the whole proteins they came from may not. Such a scenario would lead to false positives.
Eric Neumann, chief scientific officer and vice president of life science informatics at 3rd Millenium, put it this way: “We're getting a lot of smoking guns and the question is, 'Is one method getting us more data than another?’”
That’s a question still waiting for an answer.
In the meantime, Hybrigenics, which says it has completed a map of the Helicobacter pylori genome and has done significant work on yeast, is planning to map thousands of proteins next year, measuring billions of protein-protein fragment interactions. It is also hoping to secure a commercial deal.
So far, Hybrigenics is only involved in a number of collaborative relationships with academic groups and biotech companies, including Lynx Therapeutics and XTL Biopharmaceuticals. Both of these latter deals might prove to have commercial significance.
Together with gene expression company Lynx, Hybrigenics is trying to identify targets for obesity.
“There is synergy to be had by bringing our two technologies alongside each other,” said Norrie Russell, CEO of Lynx, noting that Hybrigenic’s founder and CEO, Donny Strosberg, is a world leader in obesity and metabolism.
Lynx will identify relevant genes by screening entire cDNA libraries taken from normal and differentiated adipose cells using its Megasort technology. Genes found to be expressed differently in different kinds of adipose cells will be sent to Hybrigenics for protein interaction mapping and target identification.
And Hybrigenics has also teamed up with XTL, a British biotechnology company, to design drug candidates for hepatitis C virus. Hybrigenics will use protein maps and bioinformatics to provide drug leads and XTL will use its human HCV mouse model in an effort to find the best strategy to treat the disease. The companies plan to share equal responsibility in the discovery and marketing of any new HCV treatment.
While Hybrigenics has yet to post a franc in revenues, Schachter spoke confidently about the likelihood of the company signing up customers in 2001. He indicated that a publication validating its technology is in the works and hinted at the possibility that Hybrigenics’ first pharmaceutical customer agreements may be completed and made public soon.