IT'S ALL IN THE PROTEINS FIRM'S WORK HELPS PHARMACEUTICAL COMPANIES DISCOVER NEW CURES.

Byline: Evan Pondel Staff Writer

WOODLAND HILLS - ProteinPathways is a mapmaker of sorts - deciphering the highways and byways of proteins to help pharmaceutical companies discover new drugs.

The medical cartographers are combining lab work with computer programs to develop what ultimately resembles a web of cellular pathways for various proteins. Ideally, the renderings are studied by pharmaceutical companies to help determine more efficient methods in combating bone cancer, osteoporosis and rheumatoid arthritis.

For more than three years, the Woodland Hills company has attempted to establish its credibility in an industry often dominated by academia and other laboratory powerhouses. With about $8 million in the bank, and a scarcity of new venture capital, the company has finally begun to attract the right community.

ProteinPathways' most recent coup is a collaboration with Merck & Co. to aid in its drug discovery efforts. Neither company would reveal the terms of the deal, although Matteo Pellegrini, ProteinPathways' president, said the alliance would certainly help the company financially.

``But, more importantly, the move helps us establish our credibility. It's more important to receive validation right now and that's why a relationship with a company like Merck is important,'' Pellegrini said.

That validation also gives Pellegrini the confidence to carry on with his part-scientific, part-theoretical line of work. The Rome-born Pellegrini's ever-so-slight accent reveals a scientist who's attempting to meld an academic past with a corporate future. The 34-year-old is unshaven, wearing sneakers, with a floppy head of hair and sleepy eyes, as if he spent the whole night in a laboratory. Still, he sits poised in a conference room, rifling through a PowerPoint presentation as if he were guiding a Fortune 500 company.

Pellegrini received his bachelor's degree summa cum laude at Columbia University, and holds a doctorate in physics from Stanford University. He focused his sights on studying the physics of cells during his postdoctoral work at the University of California, Los Angeles' Molecular Biology Institute. Incidentally, Pellegrini's father chairs the University of California, Los Angeles' physics and astronomy department.

With such a background, Pellegrini is not intimidated by the large biotechnology community that thrives in Southern California. Though he does admit it's more difficult making a name for a small company when surrounded by giants like Amgen.

The proximity of such behemoths also has its advantages.

ProteinPathways' chief executive officer and chairman is Daniel Vapnek, who served as senior vice president of research at Amgen from 1988 to 1996. A phone conversation with the executive proved Vapnek's resounding confidence in his product. He seemed more sales-like than scientific, but that's what it takes to guide a budding biotechnology company.

``How about telling you that I have several years of experience in this area instead of my age?'' joked the 64-year-old.

Vapnek received his doctorate in microbiology from the University of Miami. He then moved to Yale University's medical school as a U.S. Public Health Service fellow.

Vapnek said venture capital is a concern, given economic conditions, but he's optimistic that the company's alliance with Merck will be fruitful.

``The venture capital community has shied away from this area in the last couple of years,'' he said. ``But it seems as though the U.S. is still doing pretty well in terms of drug discovery programs.''

ProteinPathways' management team also includes Christopher Giffin, formerly an associate director of product licensing and corporate development at Thousand Oaks-based Amgen.

In a sector where academic training and professional background are integral to a startup, A.L. Burlingame, deputy editor of Molecular & Cellular Proteomics, said working with the leaders in your field is equally important.

``I personally don't think one can survive in this field without a close relationship with the people who are deeply involved. There has been a lot of research in this area, especially coming out of Canada,'' said Burlingame, who is also a professor in the University of California, San Francisco's department of pharmaceutical chemistry. ``Both academic institutions and the Canadian government are spending a lot of money on proteomics.''

Proteomics - the entire expression of proteins in a particular organism - has become the present-day equivalent of decoding the human genome. That's because while the human genome is relatively easy to understand, proteins have behaviors and properties that are vastly different, Burlingame said.

``What we're going toward is the identification of all of the proteins that are necessary for bacteria to survive,'' Burlingame said. ``And I'd say in about two to five years, we'll see more antibiotics developed from these efforts.''

Evan Pondel, [phone]

evan.pondel(at)dailynews.com

CAPTION(S):

2 photos

Photo:

(1 -- color) Matteo Pellegrini, president of ProteinPathways, is covered with a projection of a network of proteins involved in osteoporosis.

(2) Mattheo Pellegrini, president of ProteinPathways, left, and staff scientist Peter Bowers, right, work in the wet lab.

Charlotte Schmid-Maybach/Staff Photographer