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OGS Files Patent Applications on 4,000 Proteins In Symbol of Transition into Drug Development

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Oxford GlycoSciences has filed patent applications on 4,000 disease-associated proteins, protein isoforms, and their genes, accomplishing a goal the company set for itself in March 2000, the Abingdon, UK-based company said Dec. 7.

None of the applications have yet been granted, but OGS executives said reaching its goal in filing intellectual property represented a turning point in the company’s development, marking the end of a purely discovery-based phase and the start of its push to move its candidate biomarkers, drug targets, and therapeutic proteins down the drug development pipeline.

“We are still committed to our proteomics technology platform, but in terms of corporate development the market is looking for us to discover drugs and bring them into the clinic,” said Stephen Parker, OGS’ CFO.

Included in the filing on each protein are data on the amino acid sequence, corresponding gene sequence, biochemical and physiochemical properties, clinical expression, disease association, and proposed mechanisms for applying that information to patients’ needs, Parker said. The patent applications, filed in the US, Japan, and Europe, do not include structural data on individual proteins, he said.

Using its 2D gel electrophoresis-based platform, combined with labeling chemistries such as the ICAT reagent technology, OGS has identified, and now filed patent applications on proteins associated with breast, prostate, and other cancers, central nervous system diseases such as Alzheimer’s, and autoimmune diseases, OGS’ chief scientific officer Raj Parekh said in a conference call.

The company’s most promising drug targets included in the patent applications are among the 514 proteins that OGS claims are associated with cancer, according to Parker. OGS has identified five membrane proteins that are overexpressed in a combined 86 percent of all types of breast cancer, but expressed normally in other types of tissue, Parker said. The company has also discovered a novel heparanase, a protein implicated in tumor progression and angiogenesis. “We would certainly get pretty excited about those,” he said.

OGS expects to file its first Investigational New Drug application with FDA sometime next year, and “after 2002 we’ll expect to see a whole wave of [INDs] coming through,” Parker said. What remains to be seen is how many of the 4,000 proteins make the cut once OGS and its partners in drug development, NeoGenesis and Medarex, complete their antisense knockout, gain-of-function, and other target validation studies.

Beyond being able to validate its potential protein targets and biomarkers, OGS also faces intense competition from other proteomics companies also rushing to file patent applications on novel proteins. Several competitors, such as Celera Genomics and Caprion Pharmaceuticals, were skeptical of OGS’ chances for being granted patents on all its 4,000 proteins, and of the company’s chances for defending those patents in court.

“Novelty alone doesn’t cut it,” said Lloyd Segal, Caprion’s CEO. “The more function you’ve got, the more likely you are to be able to protect that patent. Anybody with money in the bank can file patents, but whether they’re going to be issued or not is a different thing.”

Indeed, many patent applications often fail to include enough credible information on how a protein is useful, said James Haley, a patent attorney at Fish & Neave, an intellectual property firm in New York. “The law of claiming chemical discoveries says you must be able to know the structure sufficiently to distinguish that protein from all others, and you must be able to say how it’s useful,” Haley said.

OGS’ Parker admitted that other companies could conceivably file patents on the same proteins as OGS, but for application to a different disease. But he added that filing patent applications is an essential element of OGS’ effort to begin moving aggressively into drug development. Success in the clinic will ultimately determine the validity of the proteomics approach, he said.

“Proteomics is to some degree viewed with a degree of skepticism; it’s the latest ''''omic, so it’s important that we show that this is something that has real power as a means to drug discovery, rather than something that gives vaguely interesting indications.”

—JSM

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