(UPDATED: See below.)

5am-venture-logo.gifA few weeks ago, we broke the news that 5AM Ventures is nurturing a stealthy startup called — for now — ImmunoNewco. The trail led back to the Danish biotech Borean Pharma, which is developing protein-based drugs against autoimmune conditions, and which may be in the process of transferring some or all of its programs to ImmunoNewco.

5AM partners stopped responding to calls and email when I asked them about Borean — information that emerged thanks to the incautious LinkedIn profile, since edited, of a former Borean employee — and that naturally just sparked my curiosity. Now, with the assistance of a very useful database at the California Department of Corporations, I’ve managed to dig up some additional details.

According to this ImmunoNewco filing (PDF link) with the department, it appears that the startup is headed by Phyllis Whiteley, formerly VP of business development and licensing at Perlegen Sciences and now an entrepreneur-in-residence at 5AM. Perlegen, which spun out of gene-chip maker Affymetrix, has long been focused on personalizing medical treatments to an individual’s genetic profile. In particular, Perlegen wants to salvage failed or otherwise unsuccessful drugs by using genetic scans to determine which patients are most likely to benefit or avoid side effects — a concept known formally as “pharmacogenomics.”

Whiteley, who’s named as president of ImmunoNewco in the company’s California filings, appears to have worked at Perlegen for about three years — she was hired in late 2004 and apparently left sometime last year (her signature is on an ImmunoNewco filing from last October, although her replacements at Perlegen weren’t named until two weeks ago). She has a long history of negotiating drug-licensing deals and gave an interesting interview on Perlegen’s strategy to Pharmacogenomics Reporter in 2005.

It’s entirely possible that Whiteley is involved strictly because of her business skill at acquiring drug cast-offs from other companies. But if all these pieces really fit together — and I have to stress that this is only speculation at this point — it’s beginning to look as though one or more of Borean’s drugs didn’t work out, but that the folks behind ImmunoNewco think they can be salvaged via pharmacogenomics. I tried to reach Whiteley, but she’s not listed in 5AM’s voicemail directory and their operator seems to have taken the afternoon off.

What does all this amount to? At this point, frankly, not a whole lot beyond a stealthy company that’s fun to noodle with. I happen to agree with Seth Levine’s partners that stealth is overrated as a business strategy, although of course VC firms like 5AM are well within their rights to keep whatever secrets they want to keep. But we’re also within our rights as journalists to pull on threads and see where they lead. Puzzles are fun, dammit.

UPDATE: Puzzles are also extremely satisfying when they start to come together. Borean’s Web site has been replaced with a blank page referring inquiries to “Katherine Bowdish, PhD.” in San Diego. I called Bowdish, who declined to speak on the record but hinted that there may be new developments shortly, so stay tuned.

Bowdish co-founded Prolifaron, a San Diego biotech focused on — guess what? — antibody engineering technology. That company was acquired by Alexion in 2000, where Bowdish eventually became a senior VP in charge of antibody technology. You can read her capsule biography here.

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