[Updated: 3:47 pm] Amylin Pharmaceuticals and Alkermes have gone to the FDA twice before to seek approval of their new diabetes drug, and been turned back, but now the persistence has paid off. The FDA has cleared their once-weekly injectable diabetes drug for sale in the U.S.

San Diego-based Amylin (NASDAQ: AMLN) and Dublin- and Waltham, MA-based Alkermes (NASDAQ: ALKS) today won clearance to start selling exenatide once-weekly (Bydureon) in the U.S., according to a letter posted on the FDA website. The approval came after the agency held up the application twice before—first in March 2010, and again in October 2010, saying it needed further assurance that the drug doesn’t cause an irregular heart rhythm known as QT prolongation. The companies expressed confidence back in July that the issue had been resolved, based on results of an additional clinical trial. The drug won approval in Europe back in June.

[Updated with added detail on Alkermes royalty] The long-awaited U.S. approval is vital to future of Amylin, as it started investing back in 2005 in a $500 million Ohio factory to mass-produce the new drug. Amylin’s fortunes have become even more tied to Bydureon since November, when longtime partner Eli Lilly bowed out of a collaboration to co-market the drug. Alkermes, which provided technology that made the drug last long enough in the bloodstream to turn it into a once-weekly injection, will pick up an 8 percent royalty on sales of the first 40 million units sold in a single year, and a 5.5 percent royalty once sales exceed 40 million units in a single calendar year. While there is competition from Novo Nordisk’s liraglutide (Victoza) as a once-daily injection for diabetes, and various other oral pills and injectable insulin, the new drug from Amylin and Alkermes is the first treatment that can be injected as little as once a week. Amylin has been marketing the original form of exenatide (Byetta) as a twice-daily injectable since 2005.

About 25 million people in the U.S. have the disease, and numbers are growing fast as the nation’s obesity rate continues to surge. The new Amylin drug could generate $1.25 billion in peak U.S. sales in 2018, said Cory Kasimov, an analyst with JP Morgan, in a note to clients on Nov. 11.

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Development deals, clinical advances, startup funding, and new hires made up the New England life sciences news this week.

—Chelsea, MA-based Civitas Therapeutics, a spinout from the Waltham, MA, biotech Alkermes (NASDAQ: ALKS), said that its inhaled form of the Parkinson’s disease drug L-dopa performed well in a Phase 1 clinical trial. The study aimed to test the drug’s safety and whether the drug’s delivery to the lungs gets it into the bloodstream in levels that produce a therapeutic outcome.

—Serial biotech entrepreneurs Bob Langer (of MIT) and Omid Farokhzad (of Harvard Medical School) have founded their newest company, Blend Therapeutics, alongside MIT professor Stephen Lippard. Blend is reportedly backed by Flagship Ventures, New Enterprise Associates, and NanoDimension.

—Cambridge-based genomics analysis startup Knome named former NormOxys CEO Martin Tolar its new chief executive and landed a new contract from Johns Hopkins University.

—Watertown, MA-based Forma Therapeutics announced a cancer drug discovery partnership with Johnson & Johnson’s (NYSE: JNJ) Janssen Biotech, worth up to $700 million over time. That’s less than a week after Forma’s $65 million partnership with Boehringer Ingelheim was announced.

—Warp Drive Bio came out of the woodwork this week with $125 million in funding, and hopes to examine the genetic makeup of plants, animals, and other organisms to find hot new drugs. Cambridge-based Warp is backed by Boston firm Third Rock Ventures, Greylock Partners, and French pharmaceutical giant Sanofi, and has an elite roster of founders, including Harvard genomics expert George Church.

—Cambridge-based Flagship Ventures surpassed its initial $250 million expectation for its fourth fund, announcing the fund closed at $270 million. It will focus on investments in the life sciences and cleantech sectors.

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Chelsea, MA-based Civitas Therapeutics announced today that its inhaled form of L-dopa—the drug that many Parkinson’s disease patients take to relieve shaking and other debilitating symptoms—performed well in a Phase 1 clinical trial. The trial was designed to test whether the drug, called CVT-301, is safe, and whether delivering it to the lungs gets it into the bloodstream at levels that are likely to produce a therapeutic outcome. So far, so good, the company says. Civitas will present comprehensive data from the study at a future scientific gathering.

Civitas seems to have passed a small, but important, first test for CVT-301. In 2011, Civitas was spun out from Waltham, MA-based Alkermes (NASDAQ: ALKS), which had recently abandoned plans to develop an inhaled insulin product for diabetes. Civitas started up with $20 million in financing from Canaan Partners and Longitude Capital, and a state-of-the-art, 90,000 square foot manufacturing and R&D facility that it inherited from Alkermes. “Right when we walked in, we were in brand spanking new labs,” says Glenn Batchelder, co-founder and CEO of Civitas.

The idea behind Civitas was, in the most basic terms, to find a better use for the technology that Alkermes and its development partner Eli Lilly (NYSE: LLY) spent millions to develop. Inhaled insulin didn’t gain traction in the diabetes market, Batchelder says, because the devices that were initially developed were large and clunky, and therefore not very convenient for patients to carry around. More importantly, he says, inhaled insulin “didn’t have a clinical benefit” over injected insulin. “That was a learning.”

Civitas pursued L-Dopa because of the potential for an inhaled form of the drug to surpass the pill form in both convenience and performance, Batchelder told Xconomy during a December tour of the company’s headquarters. The pill form of L-dopa works, but some patients have to take it several times a day to see any impact, and it can be difficult to control how much of the drug gets into the bloodstream. “Food affects the variability,” Batchelder says. “They never know how much of the drug is getting to the blood. There’s also variability in how long it takes for the drug to produce an effect. Some people stop living their lives because the pills don’t solve the problem.”

CVT-301 is a fine powder that’s delivered via a small, plastic inhaler similar to an asthma inhaler. Civitas only had to make a few small adjustments to the diabetes inhaler to ensure the device would be easy enough for Parkinson’s patients to handle, Batchelder says. ”You just breathe in, and the powder goes into the lungs,” he says. “No matter how hard you breathe, you get the same exact dose.” The device, unlike some of the early insulin inhalers that were developed, is small and discreet. “It’s five plastic parts, two springs, and a staple,” Batchelder says. According to the company’s statement, CVT-301 delivered consistently precise doses during the Phase 1 trial, and the drug was immediately absorbed into the body.

Civitas is developing CVT-301 with the help of New York-based Michael J. Fox Foundation for Parkinson’s Research, which announced on November 29 that it had awarded a grant of undisclosed size to the company. And Civitas inherited most of the manufacturing equipment it needs—not to mention tons of supplies—from Alkermes. During the recent tour, Batchelder and Civitas’ chief scientific officer Rick Batycky pointed out a cavernous room on the ground floor, which is serving as a holding pen for fillers, solvents, and other lab supplies, until it’s needed for commercial manufacturing. “The labs are outfitted with everything they need,” Batycky says. “When they run out, they just come here. It’s like going to Wal-Mart. It’s very valuable. We haven’t needed to buy a lot.”

If all goes well in future trials, Civitas hopes to file for approval in 2015, Batchelder says. With so much of the manufacturing infrastructure already in place, it won’t be hard to get up and running fast, he says. “That’s the beauty of having this facility,” he says. “It gives us the ability to scale this up and commercialize the drug. We wouldn’t have been able to create that as a small company.”

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San Diego-based Zogenix (NASDAQ: ZGNX) has an update today on its development of an extended-release and acetaminophen-free formulation of the painkiller, hydrocodone bitartrate, which the company plans to market as Zohydro oral capsules.

After agreeing on submission requirements for its reformulated drug in a series of meetings with regulators at the FDA, Zogenix says it plans to submit its new drug application for Zohydro by mid-May. The company says it is seeking clearance under a section of the Food and Drug Act that allows a new drug candidate to rely on studies already published in the scientific literature or the FDA’s own finding of safety and effectiveness of a previously approved drug product.

In its statement today, Zogenix says Zohydro is being evaluated for the management of moderate-to-severe chronic pain in patients requiring around-the-clock opioid therapy for an extended period. If approved, Zohydro could be the first extended-release hydrocodone therapy available without acetaminophen, which is associated with an increased risk of liver toxicity when used in high doses over time.

The formulation relies on proprietary extended-release technology that was developed by Alkermes (NASDAQ: ALKS), the drugmaker based in Dublin, Ireland, that Zogenix chose as its chemistry and manufacturing controls (CMC) partner.

If the NDA is approved, Zogenix has said it could begin marketing the drug as early as 2013. The company estimates that more than 128 million prescriptions are written in the U.S. each year for hydrocodone drugs, a potential $7.5 billion market opportunity.

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Medical device makers, drug developers, charity foundations, and health IT startups rounded out the New England life sciences news pot this week.

—Cambridge, MA-based MedicalRecords.com is raising $500,000 to put toward the development of its website, which connects sellers of electronic medical records software with doctors looking to adopt the technology.

—Rib-X Pharmaceuticals, a New Haven, CT-based antibiotics developer with two drugs in clinical trials, filed documents with the SEC indicating its intent to go public. The company, founded in 2000, has developed a drug-discovery platform based around an atomic, three-dimensional picture of the interactions between the antibiotics and the bacteria they target.

—The Michael J. Fox Foundation for Parkinson’s Research awarded grant money to Chelsea, MA-based Civitas Therapeutics, a startup working to improve the standard treatment for Parkinson’s disease. Patients usually take the drug, levodopa (L-dopa), in pill form, but Civitas is developing a version that they could inhale to get quicker, more precise doses of the medication. The company, spun out by the Waltham, MA, biotech Alkermes (NASDAQ: ALKS) will test the inhalable drug in a pair of clinical trials over the next year.

—Mundipharma will provide $50 million to Cambridge-based Infinity Pharmaceuticals in 2013 to support the development of Infinity (NASDAQ: INFI) drug candidates, like IPI-145, a molecule that’s being designed to treat blood cancers and inflammatory conditions. Infinity and Mundipharma first inked a collaboration deal in 2008, in which Mundipharma and its Stamford, CT-based affiliate Purdue Pharma, the maker of the drug oxycodone (Oxycontin), said they would pay $75 million to Infinity to access the company’s research and development capabilities.

—Cambridge-based Idera Pharmaceuticals regained the rights to a cancer drug it was previously co-developing with Merck KGaA, until the German drugmaker cancelled the collaboration this past July. Merck will continue an ongoing clinical trial of the drug, IMO-2055, in combination with Eli Lilly’s cetuximab (Erbitux) in 104 patients with a form of head and neck cancer, and Idera will reimburse the company for about 1.8 million Euros in expenses associated with the trial across 12 months. Idera (NASDAQ: IDRA) will own the data from that trial and other clinical studies Merck helped conduct and finance.

—A bioreactor made by Holliston, MA-based Harvard Bioscience was recently used in the world’s first two synthetic trachea implantations. Harvard’s InBreath Bioreactor helped create the tracheas by using the patients’ own stem cells. The company (NASDAQ: HBIO) has been around for 110 years as a maker of scientific instruments such as pumps and glassware for drug research, but it’s expanding its presence in the regenerative medicine field.

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The holiday weekend didn’t seem to slow New England deals making down.

—MedicalRecords, a Cambridge, MA-based startup connecting doctors with sellers of health record software, is working on raising its first outside funding round. It’s got about 60 percent of a targeted $500,000 round committed, from investors like Ty Danco and Peter Bordes.

—New Haven, CT-based antibiotics developer Rib-X Pharmaceuticals filed federal documents that reveal its plans to go public. The company has raised $208.4 million in venture funding and recently inked a partnership with Sanofi that could be worth as much as $772 million.

—Mundipharma will provide more than $50 million in funding in 2013 to Cambridge-based Infinity Pharmaceuticals as an expansion of a drug development partnership first inked in 2008. The money will go to developing drug candidates from Infinity (NASDAQ: INFI) such as IPI-145, which is being designed to target blood cancers and inflammatory conditions.

—VMTurbo, a Waltham, MA-based virtualization management software developer, announced that it had wrapped up a $10 million Series B investment led by its return backers Bain Capital Ventures and Highland Capital Partners. The new funding will go to product development, customer support, sales, and marketing.

—Skyhook Wireless has inked a deal to get its location-finding technology into the new Norton Anti-Theft Web service, from Mountain View, CA-based Symantec (NASDAQ: SYMC). The Norton service enables people to lock, locate, and, ideally, recover a lost or stolen Windows-based laptop, and Android smartphone or tablet, with Skyhook’s technology that use GPS, WiFi and cellular signals to track a device.

—ChoiceStream, a Cambridge-based developer of software for personalizing e-commerce shopping experiences for consumers, raised $8.7 million of a targeted $12.3 million equity and options offering, an SEC filing showed.

—Boston-based Summit Partners led a $10 million investment LogiXML, a maker of Web-based business intelligence software. Other LogiXML investors include Grotech Ventures and Updata Partners.

—Civitas, a Chelsea, MA-based spinout of the biotech Alkermes (NASDAQ: ALKS), will get an undisclosed grant award from the Michael J. Fox Foundation for Parkinson’s Reseach to put towards development of an inhaled form of the Parkinson’s treatment levodopa (L-dopa).

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For decades, people with Parkinson’s disease have been taking L-dopa pills to keep symptoms of the neurodegenerative disease under control. But now the Michael J. Fox Foundation is betting that a new form of the drug can be inhaled into the lungs to provide fast relief when the old standby isn’t getting the job done.

The New York-based Michael J. Fox Foundation for Parkinson’s Research is announcing today it is providing an undisclosed grant award to help Chelsea, MA-based Civitas Therapeutics develop an inhaled form of levodopa (L-dopa) for Parkinson’s disease. Civitas plans to use the Fox Foundation support, along with its $20 million Series A investment from earlier this year, to run a pair of clinical trials over the next year that will seek to prove that an inhalable L-dopa can be a viable alternative to the pill form. The first clinical trial of the drug, CVT-301, is set to begin before year’s end, says Civitas CEO Glenn Batchelder.

Patients with Parkinson’s tend to take L-dopa pill about three times a day, to try to keep a steady amount of the drug in the bloodstream. Take too much, and it won’t do much good, and it can cause side effects. Too little means that the telltale symptoms like tremors and stiffness start to appear. Various companies have tried other ways to deliver steady doses of the drug, through skin patches or infusion-based medicines, with little to show for it. If Civitas, a spinoff from Waltham, MA-based Alkermes (NASDAQ: ALKS), can create an inhalable form, it could end up providing a quick and steady dose for those instances when the pills don’t work. The demand for such a treatment could be big, since about 1 million people in the U.S. suffer from Parkinson’s.

“People have been trying to deliver L-dopa, the gold standard treatment, for 40 years,” says Batchelder. “We believe this is the technology that will really make a difference.” Todd Sherer, the CEO of the Michael J. Fox Foundation, added in a statement that L-dopa delivery challenges “represent a critical unmet need in Parkinson’s disease.”

Civitas CEO Glenn Batchelder

Civitas has a lot more resources than the typical venture-backed startup might have to pursue this kind of challenge. The company is housed in a Chelsea, MA, facility that represents more than $100 million of investment, which Alkermes built up years ago to make inhalable insulin for diabetics through a partnership with Eli Lilly (NYSE: LLY). Lilly scrapped that program in 2008, which got people thinking about what other inhalable drugs could be made there. By January, the assets were spun out into a new company, Civitas Therapeutics, which secured $20 million in a financing co-led by Canaan Partners and Longitude Capital.

The key challenge that Civitas is facing is with what you could call drug transportation. The existing L-dopa pills are swallowed and make their way into the intestines, where they get absorbed into the bloodstream. Sometimes the amount of drug concentration that actually gets into the blood can be erratic, however, because L-dopa can get blocked in the digestive tract when there are large protein molecules from food that get in the way, Batchelder says.

“Orally, it goes in, and it may get into your blood in 30 or 60 or 90 minutes, or maybe not much will get in at all,” Batchelder says. “Through the lungs, you can get precise dose.”

Civitas will have to prove … Next Page »

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San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN)) and Eli Lilly today called a cease-fire to litigation that began earlier this year, and outlined an agreement to end the alliance they formed in 2002 to commercialize exenatide (Byetta), Amylin’s diabetes drug. A replay of Amylin’s conference call with analysts about the deal is available here.

Amylin sued Lilly in federal court in May, alleging that Lilly had violated their agreement to develop and market exenatide after Lilly agreed to work with a new partner, Boehringer Ingelhiem, to commercialize linagliptin (Tradjenta), a competing diabetes drug.

The deal reflects just how much a drug development partnership with a Big Pharma is worth to a small biotech. Amylin agreed to take over the development and commercialization of exenatide, beginning with the U.S. market on Nov. 30, and to make a one-time, upfront payment of $250 million to Indianapolis, IN-based Lilly. Amylin also agreed to share 15 percent of its worldwide exenatide revenue until Amylin has made aggregate payments of $1.2 billion, plus accrued interest.

The deal makes no mention of a third party in the drug development partnership, Waltham, MA-based Alkermes (NASDAQ: ALKS). In an e-mail this morning Amylin spokeswoman Anne Erickson says, “Our relationship with Alkermes does not change because of today’s announcement.  Alkermes has provided the microsphere drug delivery technology for Bydureon and will receive a royalty on global sales.”

Under their agreement, Amylin will gradually assume responsibility for marketing exenatide as well as a long-lasting version of exenatide (Bydureon) in foreign markets over the next two years. The former partners agreed to work together, market-by-market, to make the transition, and Amylin agreed to pay Lilly as much as $60 million to ensure that Lilly won’t lose money on “exenatide-related activities” during the transition period.

Dan Bradbury

Just over a year ago, the U.S. Food and Drug Administration said the once-weekly version of exenatide required additional data to determine what effect, if any, the drug might have on a particular heartbeat arhythmia in patients enrolled in the the clinical trials. That data was collected and the new drug application was re-submitted to the FDA in July. If the one-injection-weekly version of exenatide fails to win FDA approval by June 30, 2014, the companies agreed that Amylin’s global revenue-sharing obligations will end, and Amylin will continue to pay Lilly a flat 8 percent of global net sales of all exenatide products.

In their joint statement, Amylin CEO Dan Bradbury says, “We anticipate working with one or more partners outside the U.S. in order to maximize the global potential of this innovative molecule and achieve greater operational flexibility and efficiency. This clarity of focus will provide us with an enhanced opportunity to increase shareholder value.”

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It seems that IT news has dominated this week, so we’re bringing you a short and sweet roundup of life sciences funding and drug development news from around New England.

—Cambridge, MA-based Ironwood Pharmaceuticals (NASDAQ: IRWD) and New York-based Forest Laboratories (NYSE: FRX) announced that they submitted a new drug application to the FDA for their irritable bowel syndrome treatment, linaclotide. The application included data from safety studies and four placebo-controlled clinical trials of patients with IBS with constipation and chronic constipation.

—Boston-based T1D Exchange, funded by a three-year $26 million grant from the charitable trust set up by hotel heiress Leona Helmsley and her husband, is launching a social media site for diabetes patients, called Glu. T1D got started in September 2010 as a clinical registry service focused on connecting diabetes patients and researchers.

—T2 Biosystems of Lexington, MA, nabbed a $23 Series D investment from new investor Aisling Capital, with participation from its return backers Flagship Ventures, Polaris Venture Partners, Flybridge Capital Partners, Physic Ventures, Partners Healthcare, Arcus Ventures, RA Capital, Camros Capital, and WS Investments. T2 said it will put the funding toward development and clinical trials for its diagnostic machine that it says can identify biological substances such as proteins, small molecules, viruses, and DNA more quickly and cheaply than traditional optical-based technology.

—The FDA has set a deadline of January 28 to complete its newly updated review of exenatide once-weekly (Bydureon), a once-weekly injectable diabetes medicine from San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN), Indianapolis-based Eli Lilly (NYSE: LLY), Waltham, MA-based Alkermes (NASDAQ: ALKS).

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San Diego’s life sciences community was teeming with news over the past week. We’ve got it all cultivated for you.

—Shares of San Diego’s Adventrx Pharmaceuticals (NYSE Amex: ANX) plunged by more than 55 percent after the biotech company said the FDA refused to approve its new lung-cancer drug vinorelbine injectable emulsion (Exelbine) until a key bio-equivalence trial is repeated. Adventrx CEO Brian Culley has said the company has enough capital to shift its focus to other drugs in its pipeline.

—Qualcomm’s (NASDAQ: QCOM) wireless health team hit the halfway mark today in an eight-week fitness challenge that has equipped 32 employees with wireless monitors and weight scales to help increase their activity and lose weight. I posted a Q&A with Qualcomm’s Don Jones, who also posted this update today on the Qualcomm blog. A Qualcomm spokesman tells me the 32 participants have burned a total of roughly 1.9 million calories and lost a total of 48.5 pounds.

—Pfizer added UC San Diego Health Sciences to its network of drug discovery innovation centers that includes prominent research institutions in Boston, New York, and San Francisco. UC San Diego Health Sciences’ partnership agreement with Pfizer could be worth as much as $50 million over the next five years.

—The La Jolla Institute for Allergy & Immunology officially opened a new center today that is focused on RNA interference technology, and is intended to operate as a collaborative and open resource for the scientific community in San Diego and elsewhere. The RNAi Center was funded by a $12.6 million grant from the National Institutes of Health. If scientists make discoveries of potential clinical benefit, “the natural next step would be to seek partnering opportunities for clinical translation and potential drug development,” said Steve Wilson, the center’s executive director and chief technology officer.

—Former SKY MobileMedia CEO Naser Partovi introduced a year-old startup that provides outpatient management software called Wellaho. Partovi told me that Wellaho operates a HIPAA-compliant social media network around the chronically ill, and which is tailored to the needs of that patient. “You can’t just join Wellaho,” Partovi says. “It must be prescribed for you by your doctor.”

—San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN) and Japan’s Takeda Pharmaceuticals said they are halting further development of pramlintide/metreleptin for the treatment of obesity. Their program was in mid-stage development as a … Next Page »

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San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN), Indianapolis-based Eli Lilly (NYSE: LLY), and Waltham, MA-based Alkermes (NASDAQ: ALKS) said today that the FDA has set a deadline of Jan. 28 to complete its review of the newly updated application for exenatide once-weekly (Bydureon). The companies are seeking FDA clearance to start marketing the new product as the first once-weekly injectable medicine for diabetes patients in the U.S. The drug was approved in the European Union in June.

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[Updated 8/4/11, 6:55 pm. See below.] San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN) and Japan’s Takeda Pharmaceutical threw in the towel today, saying they are discontinuing development of pramlintide/metreleptin for the treatment of obesity.

[Updated 8/4/11, 6:55 pm to clarify explanation] Observers feared something like this might happen in March, when Takeda and Amylin suspended a clinical trial examining the safety and effectiveness of the compound, which combines pramlintide, an analog of the natural hormone Amylin, with metreleptin, an analog of human leptin. The program was in mid-stage development as a formulation for twice-a-day injection. The partners halted the study voluntarily to investigate antibody-related findings with metreleptin in two patients who had been participating in a broader obesity trial.

A spokeswoman for Amylin, however, tells me in an email this evening, “the joint decision to discontinue the pramlintide/metreleptin program was not related to the March announcement, but rather to the reasons specified in this afternoon’s press release.”

In their statement, the companies said their joint decision was based on a commercial reassessment of their prospects as well as “evolving dynamics” within the field of obesity therapeutics. Amylin and Takeda plan to evaluate other assets for treating obesity under the terms of their existing collaboration agreement. The two companies signed that agreement in late 2009, a partnership deal that was once valued at more than $1 billion for Amylin.

Amylin CEO Dan Bradbury told Luke in January the company was still working on getting the right formulation of metreleptin and pramlintide before moving to a late-stage clinical trial.

[Updated 8/4/11, 6:55 pm to correct nature of single heart study required by FDA] Amylin said earlier this week it had re-submitted its application to the FDA for another drug—exenatide once-weekly (Bydureon)—with two partners, Indianapolis-based Eli Lilly (NYSE: LLY), and Waltham, MA-based Alkermes (NASDAQ: ALKS). In an unexpected move last October, the FDA refused to approve exenatide once-weekly for sale to U.S. diabetes patients until the partners conducted a study focused on an irregular heart rhythm known as QT prolongation.

In their statement today, Amylin and Takeda said the abandoned study was not expected to require either company to revise its latest financial guidance for their respective 2011 fiscal years.

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If there’s a common thread in San Diego’s biotech news over the past week, it would be perseverance. If you can persist with our briefing, you’ll see what I mean.

—Cambridge, MA-based Vertex, (NASDAQ: VRTX), which has a sizable presence in San Diego, said it generated $74.5 million in second-quarter sales of telaprevir (Incivek), its new drug for treating hepatitis C. Wall Street analysts had expected the number would be less than half that.

—San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN), Indianapolis-based Eli Lilly (NYSE: LLY), and Waltham, MA-based Alkermes (NASDAQ: ALKS) re-submitted an application to the FDA to market exenatide, its new, once-a-week version of Bydureon.

—San Diego-based Arena Pharmaceuticals, (NASDAQ: ARNA), which sustained a major setback last October when the FDA refused to clear its obesity drug, reported results from a recent study that could address part of the FDA’s objections. Arena said its weight-loss drug lorcaserin (Lorqess) was found in cerebrospinal fluid at much lower concentrations in human beings than in rats. The company plans to address each of the concerns raised by the FDA about its drug.

—San Diego-based BrainCells Inc., which has raised at least $77 million in venture capital since it was founded in 2003, has raised nearly $1 million in a planned financing of $14 million. But BrainCells is moving forward without CEO James Schoeneck, who joined the company more than five years ago, and Carrolee Barlow, who was the chief scientific officer. Consultant Robert Williamson has been serving as the company’s acting CEO.

—There’s a new venture firm in town, called Moore Venture Partners. Terry Moore told me he can make a difference in helping San Diego’s underserved startup community with even a small fund of $10 million to $15 million. Moore plans to invest in both tech and life sciences startups, and participated in last year’s $26.5 million Series B financing at San Diego-based Astute Medical.

—San Diego-based Illumina (NASDAQ: ILMN) said it is working with the University of Oxford to sequence the whole genomes of 500 people with a range of life-threatening genetic diseases or disorders that pose major challenges in diagnosis, treatment, and care. The team plans to recruit patients from Oxford’s clinical community in an effort to identify genetic mutations that could be used to diagnose their diseases and optimize treatment.

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We saw several headlines surrounding clinical development by New England-area drugmakers this week.

—Weston, MA-based Biogen Idec (NASDAQ: BIIB) said that it nabbed a conditional approval from the European Commission to market a long-acting version of fampridine (Fampyra) to adult patients with multiple sclerosis who have walking disability. The agency has also asked Biogen to commission a study exploring the benefits, beyond improved walking speed, of the therapy—which Biogen said it had planned to do post-marketing.

—Xconomy East Coast biotechnology editor Arlene Weintraub wrote about how Watertown, MA-based EnVivo Pharmaceuticals is charging ahead with development of its Alzheimers drug—despite negative data reported by Eli Lilly in a drug trial of its own similar compound. EnVivo began Phase 1 testing on June 1 of its compound, EVP-0962, which reduced brain inflammation caused by Alzheimer’s, reversed behavioral defects, and appeared to have a better safety profile than gamma secretase inhibitors (which the Lilly drug is), during animal trials.

—Also perserverent, Cerulean Pharmaceuticals of Cambridge, MA, is pushing ahead with its nanotechnology for drug delivery. The company began a trial this month of its cancer nanoparticle drug and is also continuing development of its technology for the field of RNA interference—which has struggled to realize its potential in the form of successful drugs.

—Natick, MA-based Boston Scientific (NASDAQ: BSX) announced second-quarter sales of nearly $2 billion and earnings of $.17 per share—beating Wall Street predictions by about a dime. The medical devices firm also announced plans to repurchase $1 billion of its common shares and (the day before its earnings announcement) revealed that it will be investing $150 million over five years in a manufacturing facility in China and will be upping its employee head count in the country.

—San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) and Waltham, MA-based Alkermes (NASDAQ: ALKS) resubmitted their application for the FDA’s approval to market their drug exenatide once-weekly (Bydureon) as a new treatment for diabetes in the U.S. The FDA, which had previously asked the two biotechs to submit data indicating the drug doesn’t have an effect on abnormal heart rhythms known as the QT interval, will have about six months to review the application.

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San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN), Indianapolis-based Eli Lilly (NYSE: LLY), and Waltham, MA-based Alkermes (NASDAQ: ALKS) said today that they have re-submitted an application to the FDA, for clearance to start marketing exenatide once-weekly (Bydureon) as a new treatment for diabetes in the U.S. The agency turned down an earlier application, asking the companies to produce more data showing the drug doesn’t have an effect on abnormal heart rhythms known as the QT interval. The new application includes such a study, which the companies reported on earlier this month. The FDA will likely have six months to complete its review of the application, the companies said. If approved, analysts expect the drug could generate billions in annual U.S. sales.

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New England biotechs and devices firms have been active in nabbing partnerships, landing investments, and progressing with clinical programs this week.

—Syndax Pharmaceuticals, an epigenetics startup out of Waltham, MA, revealed three sets of data on its lung cancer drug at the Study of Lung Cancer conference this week. The drug, entinostat, is in Phase 2 clinical testing, and acts against certain enzymes that influence specific epigenetic alterations that drive cancer growth and drug tolerance. Syndax aims to combine the drug with other cancer drugs to treat tumors that haven’t responded to other therapies.

—Xconomy national biotech editor Luke Timmerman caught up with Alkermes CEO Richard Pops about his plans to turn the Waltham, MA-based company into a biotech powerhouse. Alkermes (NASDAQ: ALKS), Luke wrote, has seen its stock climb about 30 percent since it announced its plans in May to buy Elan Drug Technologies for $960 million.

—Rib-X Pharmaceuticals could pocket about $772 million through a research and licensing agreement it inked with Sanofi (NYSE: SNY) surrounding Rib-X’s RX-04 program for the treatment of resistant Gram-negative and resistant Gram-positive infections. Sanofi payed $10 million upfront, with another potential $9 million to come in research milestones. Each product selected through the program could earn Rib-X up to $186 million in a mix of development, regulatory, and commercial milestones.

—Cambridge, MA-based obesity drug developer Zafgen nabbed a $33 million Series C financing led by existing investors such as Third Rock Ventures and Atlas Venture, to put toward advancing its lead drug candidate through Phase 2 clinical trials. The deal doubles Zafgen’s funding pot to $66 million.

—Maynard, MA-based Allegro Diagnostics, which is developing a platform for the early detection of lung cancer, said that it added another $5.4 million in Series A extension financing, from existing investors Kodiak Venture Partners and Catalyst Health Ventures

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The diabetes drug that people are counting on at Amylin Pharmaceuticals, Eli Lilly, and Alkermes has passed a crucial test that the FDA demanded almost 10 months ago.

San Diego-based Amylin (NASDAQ: AMLN), along with its partners, said today that exenatide once-weekly (Bydureon) didn’t appear to cause an irregular heart rhythm, known as QT prolongation, when it was studied in healthy individuals at both normal, and higher-than-normal doses. The study compared 75 people who were randomly assigned to get the new drug, or a placebo. Full study details weren’t released in today’s statement, but the companies said they plan to present the data at a future medical meeting, and submit the results for publication.

Investors and researchers are watching this study carefully because this drug seeks to replace a twice-daily injection with a once-weekly shot—raising the potential of a more convenient medicine for patients, and a steadier way to control blood sugar in people’s daily lives. Amylin shares jumped 10 percent in after-hours trading after the announcement.

“The findings of this thorough QT study are clear. Exenatide did not lead to QT prolongation, even at very high concentrations in the blood,” Christian Weyer, Amylin’s senior vice president of R&D, said in a statement. “This study was designed in accordance with existing guidelines and in consultation with the FDA. We are confident in these results and will continue to work toward making Bydureon available to patients in the U.S. as soon as possible.”

The FDA delayed the original application for approval of Bydureon last October, when it asked the companies for more data on the drug’s effect on QT prolongation. The new data will be packaged together and shipped off to the FDA for review sometime before the end of September, the companies said. Amylin has the most at stake in the FDA’s decision, since it only has two other approved products and the new drug is supposed to be its major profit driver for the future. But Waltham, MA-based Alkermes (NASDAQ: ALKS), the company with technology that makes the diabetes drug last long enough in the blood to enable once-weekly injections, also has a lot at stake. Alkermes stands to collect an 8 percent royalty on worldwide sales of the drug, without having to pay expenses for marketing or manufacturing.

The market clearly has potential to be lucrative for all the companies. Demand for new diabetes treatments is surging as an estimated 25 million people in the U.S. suffer from the disease, and incidence is expected to climb for years as more people develop complications from obesity. Jefferies & Co. analyst Thomas Wei forecasted, in a June 27 note to clients, that the drug has potential to generate U.S. sales of about $2.38 billion in 2016. The product was cleared for sale in Europe by regulators there last month.

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Richard Pops went on hiatus for a while as CEO of Alkermes, and when he returned in September 2009, he vowed to put the company back in “building mode.” It could have been dismissed as rah-rah rhetoric, but over the past couple of months, the investment community has started to rally behind Pops’ bold plan to build Alkermes into a much bigger, more stable company.

Waltham, MA-based Alkermes (NASDAQ: ALKS) has enjoyed a bull run ever since May 9, seeing its shares climb more than 30 percent after unveiling plans for a $960 million takeover of Ireland-based Elan Drug Technologies. There are moving parts to any acquisition, sometimes in the fine print, but investors have been warm to this deal from the start. By obtaining the 400-person unit of Elan, Alkermes is putting together a portfolio of 25 commercial products-five of which have potential to be cash cows well into the 2020s. The “new” Alkermes is supposed to be consistently profitable, have more than $450 million in annual revenue, and offer a diversified lineup of products that can help protect it from any potential hiccups (regulatory, commercial, manufacturing or other) that can damage a company that counts on just one or two drugs.

Ultimately, it’s about taking the company up a notch, into the league of Big Biotechs where investors care not just about scientific “blue-sky” possibilities, but also how much money you can make each year, and how durable all the legs really are on the company stool.

“At first blush, Wall Street’s reaction was ‘Aha, I get it, it’s financially transformative,” Pops said during a lunch meeting a couple weeks ago in downtown Boston. “You go from a money-losing biotech company to one that’s growing revenues, growing margins, growing cash flows for a long time.”

Richard Pops

The acquisition of Elan Drug Technologies, which will technically reincorporate Alkermes into a Dublin-based company, still has to pass a vote of shareholders, which is expected sometime before the end of September. But no real opposition has emerged, or even much bearish sentiment, so this looks like it’s basically a done deal. As Cory Kasimov, a biotech analyst with JP Morgan put it in a May 9 note to clients, “ALKS has been one of our favorite mid-cap biotechs, and at first glance, this development further entrenches our view.”

To understand what’s going on here, a little background on the “old” Alkermes is needed. The company is best known for its technology that helps make biotech drugs remain stable for longer periods of time in the bloodstream, enabling them to be given as less-frequent injections. The company in its current form gets more than 80 percent of its revenue today from one product—Johnson & Johnson’s long-lasting version of risperidone (Risperdal Consta) for treating schizophrenia and bipolar disorder.

Alkermes also has high hopes that its delivery technology will generate significant cash with a new treatment to help wean people off addiction to opioid-based painkillers (Vivitrol), and a long-awaited new treatment for diabetes—Amylin Pharmaceuticals and Eli Lilly’s exexatide once-weekly (Bydureon).

Before this deal was announced, Alkermes bears on Wall Street had plenty to chew on. Vivitrol has generated a lot of optimism among drug-treatment officials, but it hasn’t yet translated into … Next Page »

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It was not a week for a lot of life sciences news, but what we’ve got is pretty interesting. Judge for yourselves; our roundup begins now.

—A global survey of venture capitalists released this week reveals substantial pessimism among VCs about venture investment levels in U.S. life sciences startups over the next five years. The annual survey by The National Venture Capital Association and Deloitte shows that 81 percent of the VCs polled expect biopharmaceutical investments in the U.S. to stay the same (51 percent) or decrease (30 percent) through 2016. In the medical device and equipment sector, 76 percent anticipate funding will stay the same (52 percent) or drop (24 percent). Their attitude toward China is just the opposite; with 100 percent of the VCs polled saying biopharmaceutical investments in China will rise (83 percent) or stay the same (17 percent). Nobody thought biopharma funding will decline in China. On medical devices and equipment, 93 percent anticipate investment levels will increase (77 percent) or stay the same (16 percent.)

—European Union drug regulators approved the once-weekly injectable version of exenatide (Bydureon) for treating type-2 diabetes, providing a shot in the arm to San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN) and its partners-Indianapolis-based Eli Lilly (NYSE: LLY) and Waltham, MA-based Alkermes (NASDAQ: ALKS). The FDA declined to approve Bydureon for the U.S. market eight months ago, asking the companies to run a thorough study that evaluated effects of bigger doses on patients’ heart rates.

—Peppi Prasit, who left Amira Pharmaceuticals in November, appears to have started another San Diego biotech, Inception 1, which has raised $5 million in venture funding, according to a recent regulatory filing. Prasit, who was Amira’s co-founder and chief scientific officer, is identified in the filing as an executive and director. There isn’t much additional information disclosed. Versant Ventures partner Bradley Bolzon is listed as a director and San Diego’s Thomas Coll is listed as an executive.

—San Diego’s industrial biotech, Genomatica, received the EPA’s annual Green Chemistry Challenge Award. Genomatica has genetically engineered a type of bacteria to consume sugar in fermentation tanks and produce 1,4-Butanediol (BDO), an intermediate “building block” chemical needed to make spandex and various plastics.

—Carlsbad, CA-based GenMark Diagnostics (NASDAQ: GNMK) said it arranged a secondary offering of its stock to the public at a price of $4.25 a share that was intended to raise at lease $30 million. The company makes automated DNA and RNA diagnostics testing systems.

—San Diego’s Anaphore named former Fate Therapeutics CEO and Sanderling Ventures managing director Paul Grayson as its new CEO. He replaces founding CEO Kathy Bowdish, who will stay on as an Anaphore consultant.

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San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) and its partners—Indianapolis-based Eli Lilly (NYSE: LLY) and Waltham, MA-based Alkermes (NASDAQ: ALKS)—said today that their once-weekly injectable version of exenatide (Bydureon) was cleared for sale in Europe as a treatment for diabetes. The drug’s introduction has been delayed by regulators in the U.S., who have asked for more data on the drug’s potential effect on an abnormal heart rhythm known as QT prolongation. The companies said today they expect to respond to the FDA’s questions later this year. Amylin, Lilly, and Alkermes are all counting on this drug to become a future profit driver, as it represents the first once-weekly injectable medicine for diabetes, which often requires many more needlesticks.

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