Believe it or not, the troubles besetting Genzyme (NASDAQ: GENZ) were not the only life science stories coming out of the Boston area this week, although they sure grabbed most of the attention. So let’s get them all out of the way first:

—On Friday the 13th, the FDA said bits of steel, rubber, and fiber had been detected in vials of five major enzyme replacement drugs made by Genzyme, all manufactured at the company’s troubled Allston Landing plant in Boston. But the agency said that the problem affected only about 1 percent of Genzyme’s products, and that no serious side effects have been reported. In a statement, Genzyme said a review of its safety database “has not identified any safety concerns to suggest that patients treated with Genzyme products have been exposed to foreign particles.”

—On Monday the 16th, Genzyme got word that the FDA won’t approve its application to market its drug alglucosidase alfa (Lumizyme), a proposed treatment for Pompe disease, until the company fixes deficiencies at the Allston Landing facility, where it wants to mass-produce the drug in large batches. But Genzyme continues to make the drug in smaller batches and sell it under the name Myozyme.

—On Tuesday the 17th, shares in Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) fell 16 percent after Isis and Genzyme released the full details of joint clinical trials of mipomersen, a cholesterol-lowering drug that the two companies see as a potential successor to Pfizer’s blockbuster atorvastatin (Lipitor). The drug lowered “bad” LDL cholesterol levels by 25 percent on average, but in several patients it raised liver enzymes to triple their normal levels, indicating potential liver damage. In new trials, Genzyme and Isis say they’re going to study what side effects, if any, mipomersen causes at different doses.

—On Wednesday the 18th, Genzyme said it had decided to scrap an experimental kidney disease drug, an “advanced phosphate binder,” after a clinical trial of 349 patients showed that it was no better at ridding phosphorus from the blood of dialysis patients than Genzyme’s existing drug sevelamer carbonate (Renvela). Genzyme’s two existing phosphate binders, which generate $850 million per year in sales, go off-patent in 2014, and the company is anxious to find a next-generation treatment.

—In non-Genzyme news, Chelmsford, MA-based Zoll Medical (NASDAQ: ZOLL), which makes cardiac defibrillators and other emergency medical devices, released a CPR training app for the Apple iPhone and iPod Touch that Ryan called the “most advanced” he’s seen. The “PocketCPR” app, which provides visual and audio instructions on proper CPR technique, could help lower the death toll from sudden cardiac arrest, which kills 300,000 Americans each year.

—Alkermes (NASDAQ: ALKS) of Cambridge, MA, said a 250-patient clinical trial showed that its drug naltrexone (Vivitrol), which is already used as a treatment for alcoholism, was more effective than a placebo at treating dependence on opioids such as heroin. The company plans to ask the FDA to approve this new use of the drug next year.

—Waltham, MA-based Polaris Venture Partners contributed to a $30 million Series B venture financing round for San Diego-based stem cell startup Fate Therapeutics. Kirkland, WA-based OVP Venture Partners led the deal, which also involved Arch Venture Partners, Venrock Associates, Astellas Venture Management, and Genzyme Ventures. Fate has collected about $50 million in venture funding all told.

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Sanofi-Aventis (NYSE: SNY) hosted a large event at its R&D site in Cambridge, MA, yesterday to make its pitch for why Boston-area biotech companies should want to form partnerships with the French drug giant. It was an impressive show of force by the company, which has historically kept a lower profile in local biotech circles than some of its Big Pharma competitors.

The top brass from Sanofi were there at the firm’s Cambridge Research Center in Kendall Square. Sanofi CEO Chris Viehbacher outlined the global drug-maker’s plans to form stronger ties with biotech firms in Boston and around the world as part of a broader strategy to build a more sustainable business. Viehbacher also confirmed that Sanofi plans to form a venture capital unit to invest in biotech companies and further efforts to access innovation from outside of the company.

Sanofi, like many other Big Pharma companies, is looking outside of its organization to biotech firms for what Viehbacher called the “right brain activity” that leads to creativity and innovation. Sanofi’s shift toward more external product development efforts includes a partnership deal with Merrimack Pharmaceuticals, announced last month, focused on the Cambridge, MA-based biotech’s experimental antibody drug for cancer. There’s a good reason for this: the large and expensive internal R&D organizations of Big Pharma companies like Sanofi haven’t been productive enough. Over the next several years Sanofi is facing patent expirations on some of its biggest sellers, such as anti-clotting drug clopidogrel bisulfate (Plavix) and the sleeping pill zolpidem (Ambien).

“We all know there is a patent cliff in this industry, and it goes from 2012 to 2014,” Viehbacher said. “But my goal isn’t just to fill a sales gap,” it’s to build a sustainable business. (Viehbacher spoke to Xconomy at length in June about his strategy for building sustainable business at Sanofi.)

Sanofi has been in Massachusetts for more than a decade, but the company has been less active in partnering with biotechs in the state than other Big Pharma outfits. The company conducts a wide variety of genomic research at its Cambridge Research Center on Albany Street, and last year the firm expanded its presence in the state with its acquisition of British vaccine developer Acambis, which has operations in Cambridge and Canton, MA. This year the company has formed alliances with …Next Page »

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San Diego’s Trius Therapeutics, a venture-backed biotech developing a new antibiotic for treating acute and life-threatening bacterial infections, submitted a regulatory filing Friday to raise as much as $86 million in an initial public stock offering. It marks the third IPO filing by a company in the San Diego area so far this year.

The biotech was founded in 2004, and has posted a loss every year since then. No pricing terms were disclosed in the filing. Trius plans to list on the NASDAQ under the symbol TSRX.

The San Diego biotech passed a key Phase 2 test of its antibiotic in June, with an overall cure rate of 96 percent at three different doses for patients with complicated skin infections. The company has been looking to proceed to Phase 3 clinical trials of its antibiotic, torezolid, which Trius describes as a second-generation successor to linezolid, the Pfizer antibiotic known as Zyvox.

Even when I sat down with Trius CEO Jeff Stein seven months ago, he was looking ahead to fund its Phase 3 trials from another fundraising round, or by striking a development deal with a strategic partner.

Trius licensed torezolid from South Korea’s Dong-A Pharmaceuticals, but the company says it has developed new techniques that use antisense technology to identify other potential antibacterial drugs.

Trius says its lead antibiotic, like Pfizer’s linezolid, is particularly effective against drug-resistant strains of bacteria, such as MRSA (methicillin-resistant Staphylococcus aureus). Torezolid also appears to be more potent than linezolid, allowing for lower dosing, and can be administered intravenously. Stein told Luke an estimated 19,000 people in the U.S. die from bacterial infections each year. Total U.S. sales for the four existing antibiotics labeled for MRSA grew from $778 million in 2005 to $1.4 billion in 2008, according to Trius’ IPO filing. Sales of linezolid alone were $1.1 billion.

With the additional funding, Trius says it plans to conduct two Phase 3 clinical trials to evaluate the 200 milligram dose of torezolid for treating acute bacterial skin infections. The first trial, which is expected to begin by June 2010, is intended to evaluate the efficacy, safety, and tolerability of the dosage in adolescent and adult patients in comparison to linezolid. The second trial will begin by administering torezolid to patients intravenously and subsequently switch to oral tablets.

Trius has raised close to $51 million in venture capital, and recently secured a $19.2 million loan from a number of existing investors that is convertible to stock. According to its IPO registration, San Francisco-based Sofinnova Ventures holds a 21.3 percent stake in the company; Menlo Park, CA-based InterWest Partners holds a 17.7 percent stake; San Francisco-based Versant Partners, 17.7 percent; Westwood, MA-based Prism VentureWorks, 13.5 percent; and Kleiner Perkins Caufield Byers, 11.9 percent. None of the firms will retain their current shares following the IPO.

MaxLinear, a Carlsbad, CA, semiconductor designer, also filed for an IPO Friday. San Diego-based Bridgepoint Education went public through an IPO earlier this year.

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TEDMED had Martha, Goldie, and other celebrity speakers, but San Diego-based Amylin Pharmaceuticals broke this week’s big news when it signed up a big Japanese partner to develop its line of obesity drugs. It’s all part of your regular dose of San Diego biotech news, and it’s ready now:

—Amylin Pharmaceuticals, the San Diego-based diabetes drug specialist, announced that it has formed a partnership with Japan’s Takeda Pharmaceuticals, which agreed to carry most of the development costs for Amylin’s weight-loss drugs. In return, Takeda gets a worldwide exclusive license to eventually commercialize Amylin’s experimental obesity drugs, including the combination of pramlintide and metreleptin, and davalintide.

—After a five-year hiatus, TEDMED founder Richard Saul Wurman, and president, Marc Hodosh (who also is an Xconomist), brought the conference on medical technology, entertainment and design to San Diego’s Hotel del Coronado. TEDMED announced during the conference, which included presentations by Boston Scientific co-founder (and Xconomist) John Abele, Martha Stewart, and Goldie Hawn, that the conference will return to the same location next October.

—I only had time to attend a fraction of the presentations at TEDMED last week. One of my favorites talks, though, was delivered by Bill Davenhall, who leads the health and human services marketing team at ESRI, the Redlands, CA, giant in geographic information systems. Davenhall talked about the importance of including patients’ “place histories” as part of their medical records and raised an interesting question: Will the electronic health record systems being created today have the capability to add data in new categories—such as “geo-medicine”–that aren’t typically included in today’s patient records?

—New York-based Xenomics filed a lawsuit against San Diego-based Sequenom that alleges Sequenom misrepresented the progress in its development of a prenatal test for Downs syndrome. Xenomix says it would not have licensed its patents to Sequenom had it known the truth.

—Denise profiled San Diego-based Sirigen, an early stage medical diagnostic company that is developing technology that uses light-emitting polymers to detect bits of DNA. Sirigen founder Brent Gaylord developed the technology at UC Santa Barbara, extending the significance of UCSB physicist and Nobel laureate Alan Heeger’s discovery of conductive polymers.

—The FDA told San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) and its partner Eli Lilly the companies can now market exenatide (Byetta) as a frontline, standalone therapy for diabetes. The drug was previously approved for use with other drugs, or as a fallback option when other tretments failed.

—Vertex (NASDAQ: VRTX), the Cambridge, MA, biotech with operations in San Diego, said the latest trial of its telaprevir treatment for hepatitis C was able to attain the clinical definition of a cure in more than 80 percent of patients who got the drug. The finding is part of the mounting evidence Vertex is gathering on its quest to develop the first-of-its-kind protease inhibitor for the chronic liver disease.

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San Diego’s Ardea Biosciences (NASDAQ: RDEA) appears to have stubbed a toe in its development of RDEA 594 as a first-line treatment for gout. Data presented at a medical meeting in Philadelphia today showed the Ardea drug was no better at controlling gout than existing medications, including allopurinol, a cheap generic. During a conference call with investors today, CEO Barry Quart says Ardea’s chief focus is on developing RDEA 594 as an add-on or alternative for patients who do not respond adequately to existing drugs. Quart says the potential market for RDEA 594 remains quite large since 60 percent of gout patients do not fully improve on the mainstay drug allopurinol.

Ardea is testing its drug in combination with allopurinol and in combination with febuxostat, a newer drug marketed by Takeda under the name Uloric, Quart said. A mid-stage trial pitting RDEA 594/allopurinol against allopurinol alone in gout patients is now underway, with data expected by the end of the year. Development of the febuxostat/RDEA 594 combination is not as far along; an early-stage study is being conducted in 54 healthy volunteers to look at the safety of the drug combination. If results are good, Ardea will test the drug combination in people with gout. Quart said animal studies to date have supported the safety of the drug combinations.

Adrea still believes RDEA 594 may be useful as a standalone treatment for people who can’t tolerate or don’t benefit from allopurinol. However, developing RDEA 594 as a monotherapy is not a major focus, according to the company. “We have to be realistic,” said Ardea spokesman John Beck, noting the company has been shifting the focus of its development program for “the last couple quarters.”

Quart’s comments came as Ardea presented fresh data from clinical studies of RDEA 594 at the annual meeting of the American College of Rheumatology/ Association of Rheumatology Health Professionals. Data from a small trial of 21 gout patients shows …Next Page »

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As the flu season nears, it’s still unclear how severe the H1N1 strain of swine flu will be. But several San Diego companies are nevertheless riding a wave of investor enthusiasm for the public companies that could benefit. Get that and other biotech news here.

—The financial health of San Diego’s public life sciences companies appears to be improving, according to Luke’s recent analysis of available data about the companies’ cash balances, burn rates, and financial projections. Luke concluded that 15 of the 27 public biotechs in the San Diego area are in stronger financial shape now than they were at the end of 2008.

—After presenting highlights of a clinical trial that enrolled more than 4,000 patients, San Diego’s Arena Pharmaceuticals (NASDAQ: ARNA) says its obesity drug candidate meets at least one FDA benchmark for effectiveness and is “safe and well-tolerated.” Arena CEO Jack Lief said the company has “accomplished what we set out to accomplish.”

—San Diego-based Ambrx, which has drug development partnerships with Merck, Eli Lilly, and Merck KGaA of Germany, has signed up another major partner—Wyeth. Ambryx will work with Wyeth to create new engineered antibody drugs against multiple diseases, and since New Jersey-based Wyeth (NYSE: WYE) is in the process of being acquired by Pfizer, it means Ambryx will continue to work on the antibody partnership with Pfizer—as long as the buyout goes through.

—San Diego’s Quidel (NASDAQ: QDEL) is among five San Diego biomedical companies that have benefitted from investor interest in swine flu-related products or services in recent months. But as Denise found, not all five companies will generate much additional business if the H1N1 flu season proves to be as serious and some health officials have predicted. The official start of the flu season is Oct. 4.

—Soon after Denise’s profile of San Diego “virtual” biotech Tioga Pharmaceuticals, Luke visited virtual company VentiRx, which has employees in Seattle and San Diego. VentiRx co-founder Rob Hershberg says VentiRx has enrolled 18 patients in its first clinical trial of a drug for cancer, and so far it appears safe.

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San Diego’s Neurocrine Biosciences (NASDAQ: NBIX says it has arranged $75 million in available financing under a three-year agreement with Kingsbridge Capital, a private investment group. Neurocrine, which is developing drugs for treating endometriosis, anxiety, diabetes, and other diseases, says it is not obligated to draw on any of the available financing. The agreement enables Neurocrine to sell shares of newly issued stock to Kingsbridge, which will pay a discount of 5 to 10 percent from the stock’s market price.

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The chief medical officer of  Tioga Pharmaceuticals, a start-up working on a drug for irritable bowel syndrome, is in North Carolina. The company’s regulatory team is in San Francisco. Its chief operating officer works from an office at San Diego’s Forward Ventures, the venture capital firm that formed Tioga. He also happens to be the company’s only fulltime employee.

A weak economy has combined with product development setbacks to turn once-promising companies into virtual ones. Witness the winnowing of San Diego’s TorreyPines Therapeutics to just three employees after it sold off much of its portfolio in June.

By contrast, Tioga is virtual drug-developer by design. The company outsources all aspects of clinical development—human trials, chemistry and manufacturing, regulatory, legal and IP management—in a business model that keeps overhead to a minimum as development progresses from one phase to the next.

Forward has advocated this business model for a while, and its moment may be at hand.

“I am a big believer in this approach to doing business, especially in difficult times like these,” Forward Ventures partner Stuart Collinson told me when we chatted last week. “When you see a traditional company, and count the employees and see the buildings and all those things, it is not a good model when every dollar of capital has to be used as efficiently as possible.”

In some respects, the model can be traced back to the beginning of the biotechnology industry 33 years ago. Genentech was little more than a virtual company when it negotiated the research contract with scientists at City of Hope National Medical Center in Duarte, CA, that lead to the first genetically engineered drug.

The parallels, of course, end there. Genentech invented something entirely new, genetically engineered human insulin, and went on to become …Next Page »

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CareFusion, a medical technology company, got its official start earlier this week and is already one of the largest companies in San Diego, with 15,000 employees and $3.7 billion in annual revenue. Find out how that happened and read up on other local biotech news.

—Shares of San Diego’s Acadia Pharmaceuticals (NASDAQ: ACAD), which had run up nearly six-fold since late April on hopes for its lead experimental drug, collapsed after the biotech said Tuesday that the anti-psychosis drug, pimavanserin, had failed in a trial. Acadia’s announcement also was a blow to Biovail, the Toronto-based collaborator that had provided $30 million in funding to help develop pimavanserin for Parkinson’s patients.

—CareFusion, a San Diego medical technology company spun off by Ohio-based Cardinal Health (NYSE: CAH), officially became an independent company with shares traded on the New York Stock Exchange (NYSE: CFN). CareFusion’s business, which includes technologies created by San Diego’s Pyxis and Alaris, has about 15,000 employees and $3.7 billion in annual sales. The company’s stock was included in the S&P 500 index.

—Carlsbad, CA-based Medsphere Systems says it raised $12 million in venture funding to expand sales of its OpenVista electronic health record technology. The healthcare IT company’s announcement was among several funding deals in the San Diego region, according to a series of regulatory filings with the Securities and Exchange Commission. Those deals included:

—Aubrey, the Carlsbad, CA-based developer of advanced biosynthetic dressings for treating wounds and burns, raised nearly $3.9 million from investors and wants to raise another $2.1 million.

—Animal Cell Therapies, the San Diego company developing methods to produce and store animal stem cells, has raised $1.1 million of a planned …Next Page »

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Fallout from two of the proxy battles we followed earlier this year has become more apparent on the boards at San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN) and Cambridge, MA-based Biogen Idec (NASDAQ: BIIB), which has operations in San Diego. We’ve got that and more life sciences news.

—Diabetes drug maker Amylin Pharmaceuticals said its board selected newly elected director and former Novartis CEO Paulo Costa as chairman, a move that was supported by dissident investor Eastbourne Capital Management. At Biogen Idec, longtime R&D president Cecil Pickett decided to retire from the company and to relinquish his board seat. He’s the second director to resign from Biogen Idec’s board in two months.

—After merging in June with VGX Pharmaceuticals of Blue Bell, PA, shares of San Diego’s Inovio Biomedical (AMEX: INO) have climbed in value. But in talking with Inovio CEO J. Joseph Kim, Luke reported that Inovio’s good fortune has less to do with the synergies of combining with VGX than with Inovio’s announcement about its vaccine for the H1N1 “swine flu.”

—Lately, a number of San Diego’s drug development companies are focused on reviving or repurposing older drugs, including Cadence Pharmaceuticals, Somaxon Pharmaceuticals, and Victory Pharmaceuticals. But Denise found that getting a head start with compounds that already passed regulatory muster doesn’t necessarily reduce the odds of failure.

—San Diego’s Ligand Pharmaceuticals (NASDAQ: LGND) has agreed to acquire Neurogen in a mostly stock deal valued at $11 million, resulting in a 3 percent ownership stake for Neurogen shareholders.

—AltheaDx, a San Diego startup that provides services and technologies to streamline drug development, intends to raise $6 million in fresh venture capital, according to a recent regulatory filing. AltheaDx has raised almost $3.6 million so far.

—San Diego-based Enterprise Partners Venture Capital has renewed its commitment to Complete Genomics of Mountain View, CA. The VC firm is participating in the company’s latest $45 million venture round, along with OVP Venture Partners of Kirkland, WA. Complete Genomics intends to use the proceeds to build its own proprietary genome sequencing machines, and plans to provide its services to researchers who send in their samples.

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Biotechnology start-ups have long been seen as fearless innovators, embracing experimental technologies, like gene therapy, that big pharmaceutical companies won’t touch. But the news flow from San Diego this summer suggests the industry may have become a bit more cautious. More and more companies, it seems, are focused on reviving or repurposing older drugs – and avoiding the risks of inventing a medicine entirely from scratch.

Take Cadence Pharmaceuticals, (NASDAQ: CADX) which is developing an intravenous pain reliever containing acetaminophen, the active ingredient found in Tylenol. Another San Diego company, Somaxon Pharmaceuticals (NASDAQ:  SOMX), is working on a sleeping pill that contains the old antidepressant drug doxepin.

Then there is Avanir Pharmaceuticals (NASDAQ: AVNR), located just across the San Diego border in the Orange County community of Aliso Viejo. It hopes to market a tablet for a side effect of ALS and Parkinson’s disease that contains two existing drugs – dextromethorphan, an ingredient in over-the-counter cough medication, and quinidine, an old drug for treating irregular heart rhythms.

Working on existing drugs has some obvious advantages. Because the drugs have already been approved, companies have access to mounds of data to guide their development programs. In some cases, they may be able to forgo some pre-clinical tests or even clinical tests.

“You are dealing with known chemical entities. So from a baseline perspective, you are ahead of the curve. You do have a sense of how the compounds work, and a large amount of data,” Avanir CEO Keith Katkin tells me.

Getting a running start in this way can save start-ups many thousands or millions of dollars in research and development costs—and reduce the risk of failure. It’s a compelling strategy, particularly in an economy that has been brutal for more traditional biotechs. Over the last few months, we’ve seen La Jolla Pharmaceuticals (NASDAQ: LJPC) wind down its operations, and TorreyPines Therapeutics (NASDAQ: TPTX) announce a merger agreement to avoid a similar fate. The troubles aren’t confined to San Diego; to the north in Seattle, gene therapy pioneer Targeted Genetics (NASDAQ: TGEN) is fighting for survival.

But if the chances of losing big are lower, so are the odds of winning big.

A recycled drug isn’t likely to become a multibillion-dollar blockbuster like Genentech’s Avastin, a cancer medicine invented entirely in-house. That said, few drugs are as successful as Avastin. And the revenue potential of some reformulated drugs isn’t shabby; some analysts think Cadence’s intravenous acetaminophen could bring in $500 million a year.

So retooled drugs may become successful products – but are they innovative ones? It’s an important question to Xconomy, and I asked it of Eckard Weber, a venture …Next Page »

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San Diego’s Ligand Pharmaceuticals (NASDAQ: LGND) has agreed to acquire Branford, CT-based Neurogen, in a stock deal valued at $11 million. The transaction gives Neurogen shareholders a 3 percent ownership stake in the combined company, and a variety of contingent cash payments, such as net proceeds from the sale of Neurogen real estate. Ligand gains access to Neurogen’s existing partnerships with Merck, which includes a drug candidate for treating acute and chronic pain, an anti-histamine program, and potential drugs for boosting red and white blood cells.

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It’s been relatively slow for San Diego life sciences news, except for a flurry of funding deals for local drug development companies. Get the scoop on who’s getting money, along with some biotech profiles and more.

—CEO Steve Worland of San Diego’s Anadys Pharmaceuticals (NASDAQ: ANDS) says the company has stabilized following some mercurial advances and declines in the price of its shares. Whether or not Wall Street has been overreacting to Anadys’ announcements concerning its experimental drug for treating hepatitis C, Worland has put his efforts to find a drug development partner on hold. Instead, he’s cut payroll and raised more than $16 million so the company can carry out the next stage of its drug development plan on its own.

—One of the most ambitious life sciences startups in San Diego nowadays is Intellikine, a two-year-old drug development company that has raised $28 million this year of what could be as much as $51 million in venture capital. Intellikine co-founder and CEO Troy Wilson told Luke Intellikine company is developing drugs to block what’s known as the PI3 kinase pathway, reactions that control cell proliferation, migration, and survival. It’s a hot area because researchers have shown the pathway is involved in both cancer and autoimmune diseases.

—Several life sciences companies in the region have been busy raising capital, according to some recent filings with the federal Securities and Exchange Commission. Vista, CA-based Auspex Pharmaceuticals, which specializes in the emerging field of deuterium modification, says it raised $3 million in warrants and promissary notes that can be converted to shares of preferred stock. San Diego-based Palkion, which is developing drugs to treat anemia, has raised $2.5 million from investors. And San Diego-based Sequel Pharmaceuticals, which is developing drugs to treat a type of irregular heartbeat known as atrial fibrillation, has raised about $3 million of a planned $8.4 million round.

—Seattle biotech consultant Stewart Lyman submitted a national post that describes how the life sciences industry has entered the era of biologics—genetically engineered protein drugs made in living cells. Lyman says Big Pharma views the development of new biologics-based drugs as a smart move because generic versions of biologics-based drugs are expected to raise more concerns among regulators than generic copies of their traditional small-molecule treatments. That means generic versions of biologics appear more likely to withstand competition from generics that has done so much to undermine sales of conventional drugs.

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While San Diego has seen a big decline in VC investments this year, it’s nice to know that Domain Associates, one of the region’s most-active life sciences VCs, has raised a new fund. We’ve got the rundown on that and more news of interest to the life sciences community.

—San Diego’s life sciences community got some encouraging news earlier this week when the venture capital firm Domain Associates said it has closed Domain Partners VIII, a $500 million venture capital fund devoted exclusively to the life sciences industry. While Domain is based in Princeton, NJ, the firm maintains an office in San Diego, and many of its investments are in California.

—Seattle’s Bonnie Ramsey first learned of a cystic fibrosis drug under development by San Diego’s Aurora Biosciences nine years ago, when she was working for the Cystic Fibrosis Foundation’s Therapeutic Development Network. Aurora was later acquired by Vertex Pharmaceuticals (NASDAQ: VRTX), and now the Cambridge, MA, biotech has advanced development of Aurora’s CF drug—now known as VX-770—to the final stage of clinical trials. Luke talked at length with Ramsey, who is a clinical researcher affiliated with Seattle Children’s Hospital, and the University of Washington.

—How long should it take a company’s reconstituted board of directors to elect a new chairman? It’s taken more than two months at San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN), which was subjected to a proxy fight this spring. That’s taxing the patience of Rick Barry, the founder and portfolio manager of Eastbourne Capital Management. Barry, whose firm holds a 12.5 percent stake in Amylin and has been pushing for change at the diabetes drug specialist, told me he wants the new chairman to be chosen from one of the four newly elected directors to the company’s 12-person board.

—SpectraScience (OTCBB: [[ticker: SCIE]]), a San Diego-based maker of optical biopsy technology used to detect cancerous tissue, has raised $930,000 of a planned $5 million investment round among individual investors. The medical diagnostics company plans to use the capital to expand its sales and distribution network for equipment it has developed to search for telltale signs of cancer.

——The National Institute of Neurological Disorders and Stroke has awarded a $3.3 million grant to privately held Ichor Medical Systems of San Diego for development of a DNA vaccine for Alzheimer’s disease. The company makes it easier for cells to absorb its DNA vaccines by using an electroporation delivery system that creates temporary pores in cell membranes.

—Sequenom (NASDAQ: SQNM), the San Diego biotech developing DNA-based diagnostic tests, has maintained radio silence since it first disclosed three months ago it had uncovered R&D test data was mishandled for its much-anticipated genetic test for Down syndrome. In a recent statement, Sequenom says the company is no longer relying on previously announced test data and results, but it’s unclear if that means the company’s planned introduction is slipping further behind schedule. Sequenom had planned to introduce its SEQureDx test in June.

—Avanir Pharmaceuticals (NASDAQ: AVNR), a one-time San Diego biotech now based in Aliso Viejo, CA, said it hopes to submit results of its late-stage drug trial for treating an unusual neurological disorder to the FDA in the first half of next year. The company said this week that its drug passed a final-stage clinical trial, designed to see whether it was effective in treating involuntary bouts of laughter, crying, and other emotional outbursts.

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The price of shares in Avanir Pharmaceuticals climbed by almost 30 percent today after the onetime San Diego biotech said a late-stage clinical trial shows its drug for treating an unusual neurological disorder can substantially reduce involuntary emotional outbursts and is “generally safe and well tolerated.”

Avanir (NASDAQ: AVNR), which is now based just across the Orange County border, in Aliso Viejo, CA, announced the positive Phase III study results of its reformulated drug dextromethorphan/quinidine, or DMQ, before the market opened today. Wall Street responded with an outburst of its own, sending Avanir shares nearly 80 percent higher. That fell back later, and the stock closed in regular trading at $2.84 a share, a gain of 65 cents, or nearly 30 percent. Trading volume was almost 29.6 million shares, 35 times Avanir’s recent daily average of 845,091 shares.

As Denise reported, Avanir developed the drug, to be marketed as Zenvia, to treat unpredictable episodes of crying, laughing, and other emotional outbursts, which the company calls pseudobulbar affect, or PBA. The random outbursts often accompany brain injury or neurologic disease such as multiple sclerosis, Lou Gehrig’s Disease, or Parkinson’s.

Avanir agreed to develop and test a new formulation of the drug after the FDA raised concerns about possible cardiac side effects from quinidine, which helps metabolize the key ingredient, dextromethorphan. So the latest trial was intended to test whether the drug would still be effective with a smaller amount of quinidine.

The company said it plans to submit the phase III findings to the FDA in the first half of 2010.

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San Diego’s Acadia Pharmaceuticals (NASDAQ: ACAD) has filed a shelf registration to sell up to 7 million shares at a maximum share price of $4.17. The company, which is working on a drug to treat psychotic symptoms in Parkinson’s disease patients, anticipates that the proceeds will be used for working capital and general corporate purposes. Acadia says existing cash and anticipated payments from collaborators will fund operations through the first half of 2011.

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After a bruising proxy battle ousted Amylin Pharmaceuticals’ chairman and lead outside director, the San Diego biotech issued a statement on June 2 that seemed to signal a cease-fire with dissident shareholders (including Carl Icahn). “We look forward to working with all our new directors to bring transformational medicines to patients and to drive sustainable and profitable growth,” the company said.

But have the directors of the San Diego diabetes drug developer really been able to bury the hatchet?

One sign they may not have is the fact that in the two months since shareholders ousted chairman Joseph Cook and director James Wilson—and elected four new directors to Amylin’s 12-member board— Amylin has yet to announce a new chairman. Two of Amylin’s longtime directors, founding CEO Howard “Ted” Greene and Ginger Graham, another former CEO, were more or less forced to resign in April to make room for the company’s slate of new board candidates. Votes were cast on May 27th at Amylin’s annual shareholders meeting.

Whether that’s enough time for a corporate board to choose a new chairman is a matter of debate. Aside from telling me the company has no information concerning a new chairman, Amylin didn’t have much to say. When asked if continuing dissension is prolonging the board’s deliberations on the matter, spokeswoman Anne Erickson e-mailed this statement to me:  “Our Chairman of the Board is elected each year following our Annual Meeting of Stockholders by the newly-elected Board. With four new Directors, the Board is working together to make a thoughtful decision about this very important role to the organization. Amylin welcomes all four new Directors to the Board and looks forward to a productive working relationship.”

Those four new directors include two who were elected from the company’s slate of nominees—former Icos chairman and CEO Paul N. Clark and former Novartis CEO Paulo F. Costa. The other new directors came from the dissident camps—Alex Denner has served as a portfolio manager for Icahn, and Kathleen Behrens, a consultant and former managing director of RS Investments, was nominated by Eastbourne Capital Management of San Rafael, CA.

Since Eastbourne Capital holds a 12.5 percent stake in Amylin, I checked in with the firm’s founder and portfolio manager, Rick Barry, via e-mail:

Xconomy: Is Amylin’s board having difficulty electing a new chairman?

Rick Barry: We don’t know, but it has been over two months since the annual meeting and there is no announcement regarding a new Chairperson. This concerns us and is likely to concern all other Amylin shareholders.

X: Can you tell me which Amylin directors Eastbourne views as appropriate candidates for board chairman?

RB: Of the four newly elected independent directors, Paul Clark and Paulo Costa were selected after a rigorous process by the Company’s corporate governance committee. They were shown to have excellent qualifications and Amylin deemed them desirable additions to maximize value for all Amylin Shareholders. We too supported their election, as did an overwhelming majority of the other shareholders. We believe that either of these two individuals would be an excellent choice for Chairperson.

X: Are there any current directors that Eastbourne is unwilling to support?

RB: We believe the Board needs to be lead by someone who has a fresh perspective, unburdened by past decisions with ample time and a successful track record. We would support any of the four newly elected independent directors.

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Ichor Medical Systems, a privately held San Diego biotech, says it’s getting a $3.3 million grant award from the National Institute of Neurological Disorders and Stroke to develop a vaccine for Alzheimer’s disease. Using an electroporation delivery system that creates temporary pores in cell membranes, Ichor has been developing DNA vaccines and drugs for treating an array of diseases, including influenca, hepatitis, HIV, melanoma, and malaria.

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It might be the dog days of summer, but San Diego’s life sciences companies kept up a busy flow of cool news over the past week. Get your update here.

—Isis Pharmaceuticals, the Carlsbad, CA, biotech that specializes in so-called antisense technology, is getting ready to test a new treatment later this year for patients with an aggressive form of amyotrophic lateral sclerosis (ALS), or Lou Gehrig’s disease. Isis (NASDAQ: ISIS) is planning the first clinical trial of a treatment known as ISIS-SODRIX, a drug designed to shut down the genetic RNA machinery that enables the production of disease-causing proteins. Luke reported the treatment also could pioneer a new way of delivering antisense drugs for a variety of neurological disorders.

—San Diego’s TorreyPines Therapeutics (NASDAQ: TPTX) has agreed to a reverse merger with Novato, CA-based Raptor Pharmaceuticals. To pull off the deal, however, TorreyPines must get its shareholders to vote to approve the deal. That sounds easy enough, but TorreyPines was unable to muster enough shareholder votes in July to approve a resolution to dissolve the company.

—A Boston-area researcher said a new drug developed by San Diego’s BrainCells Inc. could someday prove effective in treating depression. The drug known as BCI-952, which combines buspirone and melatonin, was not expected to work. But it’s getting a second look after Dr. Maurizio Fava, of Massachusetts General Hospital, presented promising results in a clinical trial of 142 patients diagnosed with major depression.

—San Diego’s La Jolla Pharmaceuticals (NASDAQ: LJPC) plans to seek shareholder approval for a liquidation plan. As Denise reported, the company disclosed in a recent SEC filing that it has discharged substantially all of its obligations to creditors and is working to satisfy those that remain. The biotech also said it has settled a lawsuit with former partner BioMarin Pharmaceuticals (NASDAQ: BMRN) of Novato, CA.

—San Diego’s Inovio Biomedical (AMEX: INO) has raised $30 million from the direct sale of 11.1 million shares and 2.8 million warrants to institutional investors. Inovio is focused on the development of vaccines to prevent or treat cancers and chronic infectious diseases. The company’s delivery solutions are based on electroporation, which uses brief, controlled electrical pulses to create temporary pores in cell membranes, which makes it easier for cells to take in a useful biopharmaceutical.

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San Diego’s La Jolla Pharmaceuticals (NASDAQ:LJPC) plans to ask shareholders to approve a liquidation plan at a not-yet-scheduled special shareholders meeting, according to a recent SEC filing. The company says it has discharged substantially all of its obligations to creditors and is working to satisfy those that remain. Separately last week, the company disclosed that it settled a lawsuit with former partner BioMarin Pharmaceuticals (NASDAQ:BMRN) of Novato, CA. BioMarin had marketing rights to La Jolla’s only experimental drug, but abetimus sodium (Riquent) failed in a late-stage trial.

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