—San Diego’s Amylin Pharmaceuticals says Bydureon, its new once-a-week drug for treating Type 2 diabetes can hit the market as early as next month, after the FDA cleared Bydureon. The FDA rejected the Amylin’s drug twice before. An estimated 26 million people in the United States, or roughly 8 percent of the population, have type 2 diabetes.

—San Diego’s life sciences sector has expanded since 2009, with employment increasing by more than 5,550 jobs, or 15 percent, over the past two years, according to a new economic report from Biocom, the local industry group. The comprehensive study counted more than 1,700 life sciences companies with a total of 41,937 employees throughout San Diego County in 2011, and says those numbers are expected to grow over the next two years.

—The FDA gave its approval to Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: VRTX), which has substantial operations in San Diego, for a new drug called Ivacaftor (Kalydeco), developed to treat a rare form of cystic fibrosis. The twice-a-day pill targets about 4 percent of the 30,000 patients in the U.S. with cystic fibrosis.

—Johnson & Johnson’s reorganized R&D operation in San Diego, now known as Janssen Healthcare Innovation, is trying an experiment in innovation by creating an incentive prize challenge. Janssen is offering a total of $250,000 for technology that helps improve care for patients who have just been discharged from a hospital.

—The folks who produce the quarterly MoneyTree report on venture capital funding just released a deeper dive into the details of life sciences investments. The survey shows that VC funding for life sciences increased 21 percent nationwide in 2011, with a total of $7.5 billion going into 785 deals. San Diego ranked third among metropolitan regions in terms of capital invested in the fourth quarter. The top five are Bay Area ($498 million), Boston ($384 million), San Diego Metro ($193 million), NY Metro ($98 million), and Orange County ($97 million

—Optimer Pharmaceuticals (NASDAQ: OPTR) CEO Pedro Lichtinger outlined his plans for expanding the market for the company’s first product, the antibiotic fidaxomicin (Dificid), as a preventative therapy for hospital patients at risk for a nasty intestinal infection called C. difficile. San Diego-based Optimer is planning a clinical trial to prove the drug can help prevent severe diarrhea in patients undergoing bone-marrow transplants.

—A tweet from Bob More of Frazier Healthcare Ventures prompted Luke to delve into the importance of character among life sciences leaders in his BioBeat column. “Politics pretty similar to backing CEO’s,” More said. “Newt may be smart and a good debate guy. But Newt=Smug. Never back smug,”

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Bonnie Ramsey said three years ago that a cystic fibrosis drug from Vertex Pharmaceuticals was a huge medical advance in the making, and would end up being an achievement on par with putting a man on the moon, at least for her patients.

Yesterday, she says, was the day it truly felt like she was part of a team that reached the moon-shot goal. The good news came when the FDA approved Vertex’s ivacaftor (Kalydeco) as the first drug of its kind to work by treating an underlying genetic defect for cystic fibrosis.

“It’s a really big day,” says Ramsey, a leading CF physician/scientist at Seattle Children’s Hospital and the University of Washington. “Even though it’s for a small subpopulation, the treatment paradigm has completely changed. It’s no longer about just treating the symptoms, it’s about treating the genetic defect. That’s a real game-changer.”

The drug from Cambridge, MA-based Vertex (NASDAQ: VRTX) is now FDA approved for patients age six and older who have what’s known as a Class 3 gene mutation called G551D. This mutation is found in about 4 percent of the 30,000 patients in the U.S. with cystic fibrosis. The disease, the result of various mutations to a gene called CFTR, causes the poor transfer of water and salt across cell membranes, which leads to the buildup of thick, sticky mucus in the lungs, and poor absorption of nutrients. It means patients have to endure hours a day of treatment their entire lives, and the median life expectancy is about 39 years. Doctors currently treat the symptoms of the disease, through things like inhalable antibiotics, but Vertex’s drug is the first FDA-approved therapy that works by altering an underlying disease-related protein.

Bonnie Ramsey of Seattle Children's Hospital

Ramsey has had an instrumental role in developing this drug since its infancy. As the executive director of the Cystic Fibrosis Foundation’s Therapeutic Development Network, back in 2000 she began collaborating with the drug’s original developer, San Diego-based Aurora Biosciences (later acquired by Vertex.)

Ramsey was the lead investigator of a pivotal study of 161 patients, known as Strive, which yielded results in February that laid the foundation for yesterday’s FDA approval. The study showed that patients age 12 and older on the twice-daily pill from Vertex had about a 10.6 percent absolute improvement in their ability to force out air from their lungs in one second—compared with a placebo. The effect held up over the full 48-week course of the study. Researchers also saw significant improvements in being able to gain weight, while also reducing cough, sputum production, and the incidence of pulmonary exacerbations. Side effects included headache, and upper respiratory tract infections, researchers said, although more patients dropped out of the placebo group than the drug group. A second study verified the effect in younger patients, age six and above.

What excites scientists is that the drug has a compelling foundation in biology. It is designed to … Next Page »

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[Updated: 1:25 pm] Vertex Pharmaceuticals is now officially more than just a one-hit wonder.

The Cambridge, MA-based biotech company (NASDAQ: VRTX), best known for its hepatitis C drug, has won clearance from the FDA to start selling a new twice-daily pill called ivacaftor (Kalydeco) for a rare form of cystic fibrosis. The FDA said today the Vertex drug can now be used for patients age six and older who have a gene mutation called G551D. About 1,200 patients in the U.S., or roughly 4 percent of the total population of 30,000 cystic fibrosis patients, have the mutation.

The approval came faster than expected, as Vertex turned in its application in October, and the FDA had a deadline of April 18 to complete its review. The company plans to start shipping the drug to pharmacies this week, the company said.

“Kalydeco is an excellent example of the promise of personalized medicine—targeted drugs that treat patients with a specific genetic makeup,” said FDA Commissioner Margaret Hamburg, in a statement. “The unique and mutually beneficial partnership that led to the approval of Kalydeco serves as a great model for what companies and patient groups can achieve if they collaborate on drug development.”

The new cystic fibrosis drug has been highly anticipated for years, and the application to the FDA is based on clinical trial results that arrived in February. The study of 161 patients found that patients on the Vertex drug had about a 10 percent absolute improvement in their ability to force out air from their lungs in one second—a common measure of success in treating lung disease—compared with those on a placebo. The effect lasted over the entire 48-week course of the study. Researchers also saw significant improvements in reducing cough, sputum production, and the incidence of pulmonary exacerbations. Side effects included headache, upper respiratory tract infections, nasal congestion, rash, and dizziness, although more patients on the placebo group dropped out of the study early because of side effects, Vertex said.

While the 10 percent absolute improvement in breathing ability for people with a deadly lung disease might not sound like much, it is a big step forward for the disease. Cystic fibrosis, the result of mutations to a gene called CFTR, causes the poor transfer of water and salt across cell membranes, which leads to the buildup of thick, sticky mucus in the lungs. That effectively suffocates people over time, and often ends up killing people in their late 30s or early 40s. Doctors currently treat the symptoms of the disease, but Vertex’s drug is the first FDA-approved therapy that works by altering an underlying disease-related protein.

[Updated pricing information] Based on the small patient population that has the G551D mutation, and the significant benefit the drug provides to them, Vertex set the price at $294,000 per patient per year, Nancy Wysenski, Vertex’s chief commercial officer, told analysts today on a conference call. The company estimates that about 60 percent of eligible patients have private health insurance, while the rest are covered by government insurance, Wysenski says. As is common for companies selling high-priced medications, Vertex has established programs to help get the drug to patients who can’t afford it. Vertex said it will provide free medicine to uninsured families with household incomes of less than $150,000 a year, and it will provide assistance in making co-payments for those with insurance.

“We have a strong commitment to help patients 6 and older get Kalydeco,” Wysenski said on the conference call.

The drug was developed as part of a 13-year long collaboration with the Cystic Fibrosis Foundation, which put more than $70 million into the development program, along with Vertex, and the drug’s original developer that was acquired by Vertex-San Diego-based Aurora Biosciences. Because of its support, the Cystic Fibrosis Foundation will collect a royalty on Kalydeco sales that will start in the “high-single digit” percentage of sales, and escalate to “just below the teen level” as the drug reaches undisclosed sales milestones, according to Vertex finance chief Ian Smith.

Vertex has a number of plans ongoing to expand the use of Kalydeco beyond this initial small group of patients in the U.S. The company has applied for approval in the European Union, and hopes to receive clearance there to start selling in the third quarter. It is also running a trial of the drug in patients under the age of six; as a treatment for certain other gating mutations of the CFTR gene; and in combination with other medicines that seek to correct additional mutations.

Based on the price and number of patients in the U.S., Vertex can expect peak U.S. sales from the G551D patient population of about $550 million, said analyst Mark Schoenebaum of ISI Group, in a note to clients.

Vertex shares climbed 6 percent t0 $36.90 at 1:45 pm Eastern.

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[Update: 10:40 am ET] Vertex Pharmaceuticals is getting a new CEO, as it faces tough new competition with its flagship hepatitis C drug and prepares to roll out a second new medicine for cystic fibrosis.

Cambridge, MA-based Vertex (NASDAQ: VRTX) said today that Jeff Leiden, a member of the company’s board and a managing director at Clarus Ventures in Boston, will replace Matt Emmens as president and CEO on Feb. 1. Emmens plans to remain a full-time executive chairman until May, when Vertex says he will retire from a full-time role at the company, but remain a member of the company’s board.

[Update with Emmens's age] Emmens, 60, is the former Merck executive who took over from founder Josh Boger as CEO in May 2009, as the company was finishing up clinical trials and preparing for the commercial push of a groundbreaking new therapy for hepatitis C, telaprevir (Incivek). The drug was cleared by the FDA in May, and although analysts expect it to be a billion-dollar seller, it quickly surpassed Wall Street sales expectations in its first couple quarters, allowing Vertex to report its first product-driven quarterly profit in its 22-year history.

But the hepatitis C landscape has changed in just the past couple months, as Gilead Sciences moved to acquire a competing drugmaker for $11 billion, and Vertex’s stock has plunged amid fears that it will soon be upstaged in the marketplace.

Shares jumped as high as $58 a share earlier this year, then plummeted all the way to $30.54 at yesterday’s close, leaving Vertex with a market valuation of $6.3 billion. Most of the value is based on the prospects for Incivek, although Vertex also has an application in to the FDA to start selling a new cystic fibrosis drug, ivacaftor (Kalydeco). That drug is getting a faster-than-usual six-month regulatory review, which the FDA sometimes grants to groundbreaking new medicines. The FDA deadline to finish its review is April 18.

“Under Matt’s leadership, Vertex established itself as a company capable not only of discovering important new medicines, but of successfully bringing those medicines to patients,” Leiden said in a statement. “As a member of the Vertex Board, I have been extremely impressed with the company’s ability to retain its clear focus on both groundbreaking science and improving the lives of people with serious diseases. It will be a privilege to lead Vertex at this exciting time and to further build the organization as we prepare for the global launch of our second new therapy, advance our diverse pipeline and build value for shareholders in the years ahead.”

Leiden, 56, is the former president and chief operating officer of Abbott Laboratories, where he gained experience in the highly competitive rheumatoid arthritis drug market with adalimumab (Humira).

Emmens, in a company statement, added: “I am proud of the accomplishments we have made during my almost three years at Vertex and believe the company is well-positioned to bring forward additional innovative new medicines. Jeff brings significant and broad leadership experience to Vertex, and I am confident that his understanding of the company, combined with his unique blend of scientific, commercial and financial expertise, will help Vertex deliver on its goals in the future.”

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Cambridge, MA-based Vertex Pharmaceuticals is looking to be more than another one-hit biotech wonder. The company, best known for its drug for hepatitis C introduced earlier this year, is now vying for FDA approval of a second treatment that it hopes will shake up the way physicians treat cystic fibrosis, a deadly genetic disease.

Vertex (NASDAQ: VRTX) said today it has turned in its new drug application to the FDA for clearance to sell ivacaftor (Kalydeco, aka VX-770) as a new treatment for a rare form of cystic fibrosis in the U.S. The drug, pronounced kuh-LYE-deh-koh, is designed to treat about 4 percent of the 30,000 or so people in the U.S. with cystic fibrosis who have a mutation of a gene known as G551D. The company is seeking a six-month expedited regulatory review, instead of the usual 10-month review. The FDA sometimes provides faster reviews for groundbreaking new medicines.

The new cystic fibrosis drug has been highly anticipated for years, and the application to the FDA is based heavily on clinical trial results that arrived in February. The study of 161 patients found that patients on the Vertex drug had about a 10 percent absolute improvement in their ability to force out air from their lungs in one second—a common measure of success in treating lung disease-compared with those on a placebo. The effect lasted over the entire 48-week course of the study. Side effects included headache, upper respiratory tract infections, nasal congestion, rash, and dizziness, although more patients on the placebo group dropped out of the study early because of side effects, Vertex said.

While the 10 percent absolute improvement in breathing ability for people with a deadly lung disease might not sound like much, the result is a big step forward for the disease. Cystic fibrosis, the result of a genetic mutation, causes the poor transfer of water and salt across cell membranes, which leads to the buildup of thick, sticky mucus in the lungs. That effectively suffocates people over time, and often ends up killing people in their late 30s or early 40s. Doctors currently treat the symptoms of the disease, but Vertex’s drug could become the first FDA-approved therapy that works by altering an underlying disease-related protein.

The drug was developed as part of a 13-year long collaboration with the Cystic Fibrosis Foundation, which put more than $70 million into the development program, along with Vertex, and the drug’s original developer that was acquired by Vertex—San Diego-based Aurora Biosciences.

The new CF drug will surely be expensive, given its impact for a small group of patients with a deadly disease. Vertex, like all drug companies, isn’t saying what the price will be until approval. But, naturally, there’s a fair amount of speculation about what the market will pay for such a drug. Thomas Russo, an analyst with Robert W. Baird, quoted a physician in a June research report who said the clinical results for the drug were the best she has seen in 23 years of treating CF. Russo estimates the drug will cost about $150,000 a year, and will generate about $700 million a year in annual revenues over time.

“We are quite comfortable that our model is very conservative and that VRTX’s CF franchise is still a story about potentially very sizable upside,” Russo wrote in the June 16 note.

Vertex said it plans to turn in its application for European Union approval of the new CF compound by the end of this month.

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Developing new medicines is an amazingly difficult undertaking. The research portion alone is daunting, and for those of us who have actually attempted it, humbling. A recent article reminded me just how little many people understand about the drug discovery process. The basic premise of “Pharma Needs an Innovation Intervention” was that pharma should change its focus from “finding druggable targets” to “deliver a consumer-focused product and service and a business model that goes beyond the product itself.”

Unfortunately, the article doesn’t address two critical issues; one grounded in the past, the other the future. First off, why has Big Pharma, after being one of the most profitable industries for decades, suddenly become so remarkably unproductive in coming up with new medicines? Second, if Big Pharma walked away from the difficult task of “finding druggable targets,” then who would take over the job of creating new medicines? From a business point of view, one can see a clear need to alter a revenue model that may not be working for Big Pharma any longer. However, from a practical and societal perspective, there needs to be some way of innovating new medicines, not just new business models.

I wish I could provide a definitive reason why Big Pharma, as a group, has become so unproductive in recent years. These companies are not monolithic and have distinct styles for running their businesses. To paraphrase Tolstoy’s Anna Karenina “Productive drug companies are all alike; every unproductive drug company is unproductive in its own way.” It’s easy to congregate a lineup of the usual non-productivity suspects: excessive layers of bureaucracy, fear of making the wrong (or any) decisions, entrenched industrial group-thinking, failure to recognize and support an innovative culture, and new regulatory uncertainties. I suspect that all of these concerns contribute to the productivity problem, but it’s difficult to quantitate exactly how important each of these factors really is.

I think Big Pharma is still hung over after a difficult transition from a decades-long focus on screening chemical libraries to more of a recombinant DNA/genomic biology mindset. It may very well be that after a century or so of effort, all of the “low hanging fruit” really has been picked off of the medicinal tree. Finally, consider that Big Pharma’s recent attention was focused on developing blockbuster drugs that would bring in sufficient revenues to feed their bloated organizations. Genzyme’s marked success in treating rare diseases (along with its recent acquisition by Sanofi) illustrates how that thinking has changed.

So why is coming up with new drugs so difficult? The answer is actually pretty straightforward: because biology is amazingly complex. It’s not rocket science; it’s much harder. With all due respect to the people that design and build our space vehicles, uncovering the functional role of thousands of unique biological molecules is a significantly more complicated undertaking. Twelve years is about the average length of time it takes for a single drug to be discovered, developed, tested, and approved by the FDA. Twelve years also defines the time period between the start of the space age (the launch of Sputnik 1 in 1957) and humans landing on the moon in 1969.

Even more difficult than figuring out the function of biological molecules is coming up with a way to alter, in an appropriate way, the divergent activities of selected subsets of these molecules to treat various diseases. People can be afflicted with literally thousands of different ailments. As living organisms, we reflect eons of genetic diversification and are vulnerable to rogue viruses, bacteria, fungi, and environmental pollutants. No two of us are alike, not even identical twins. People also suffer from pain, are susceptible to psychological disorders including addictions, and are at risk of unintentional side effects brought on by numerous medications. The biological and rocket sciences do share one primary characteristic: they are both very expensive, high cost-of-entry businesses. … Next Page »

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Pulmatrix, the Lexington, MA-based company with an unusual strategy for fighting diseases of the lungs, is announcing today that it has secured $14 million in a Series B1 venture round, bringing the total amount raised by the company to $60 million. All of Pulmatrix’s existing investors participated, including Polaris Venture Partners, 5AM Ventures, Arch Venture Partners, and Novartis Venture Fund.

The company also announced that it will advance its lead compound, called PUR118, as a new treatment for cystic fibrosis, and chronic obstructive pulmonary disease (COPD)—an umbrella term for diseases like emphysema and chronic bronchitis that commonly affect smokers. Recently completed Phase 1 studies in healthy volunteers showed the new drug was safe and well-tolerated, the company reports, so Pulmatrix will move the treatment into additional trials designed to measure PUR118′s effects on airway inflammation and mucus. The new cash, says CEO Robert Connelly, “will get us through these critical studies over the next 18 months, which will put us in position to plan larger, pivotal studies.”

Pulmatrix is using its technology platform, which it calls iCalm, to create aerosol treatments that attack lung ailments from three directions. First, they have positively-charged ion-based compounds, like calcium and magnesium, which stimulate the immune system to fight off many different pathogens that people breathe in all the time, like viruses and bacteria. “We have the ability to take on all comers—we can deal with any airborne infection, ” Connelly says. Secondly, the drugs produce an anti-inflammatory effect without the use of steroids-a common ingredient in many lung remedies. And finally, they help clear mucus from the lungs.

PUR118 is a dry powder that patients can inhale. Pulmatrix initially developed it as a liquid formulation, called PUR003, which patients had to inhale via a somewhat bulky machine called a nebulizer. Pulmatrix reformulated the drug so it could be used like an asthma inhaler—a far more … Next Page »

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This week we’ve seen news of acquisitions and funding, as well as longer articles on strategy and research moves for New England’s life sciences firms.

—BL Healthcare, a provider of telemedicine products that is based in Foxboro, MA, has bumped its Series A funding round up to $4.9 million, with another $2 million in equity-, debt-, and rights-based financing, an SEC filing showed.

—Luke took a look at the moves that Cambridge, MA-based Epizyme has been making in scoring deals with Big Pharma companies. GlaxoSmithKline (NYSE: GSK) paid the three-year-old biotech $20 million upfront with potentially another $630 million in milestones for a drug discovery partnership, and Japanese firm Eisai Pharmaceuticals will pump $6 million upfront and potentially $200 million in milestones into Epizyme for a collaboration to develop cancer drugs.

—Cambridge-based Vertex Pharmaceuticals (NASDAQ: VRTX) said the Phase III study of its cystic fibrosis drug, VX-770, met its primary goal among patients ages 6 to 11 of improving lung function through 24 weeks, showing that the drug is working about as well in children as it did in older patients with the genetic disorder. The 48-week study of 52 patients is still ongoing, but at 24 weeks, children on the drug showed a mean absolute improvement from baseline in lung function of 12.5 percent.

—Follica, the baldness treatment developer that got started in Boston in 2006, is working to protect its technology that uses lithium treatments to stimulate new hair growth with a patent application, filed in September and published this March. But that’s only one piece of the multiple areas of research that Follica is focusing on, CEO and president William Ju told Ryan.

—Worcester, MA-based RNA interference drug developer RXi Pharmaceuticals (NASDAQ: RXII) announced it has agreed to acquire Scottsdale, AZ-based Apthera, a developer of peptide immunotherapies for cancer. Apthera shareholders will get 4.8 million of RXi’s shares, which were valued at $1.50 before the deal. As part of the agreement, RXi CEO Noah Beerman will resign and will be replaced by RXi board member Mark Ahn.

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A debate over the sustainability of the venture biotech ecosystem continues to percolate, and the San Diego Venture Group is even planning a breakfast debate on the topic. We’ve got the rest of what’s brewin’ in life sciences too.

—San Diego’s Ligand Pharmaceuticals (NASDAQ: LGND) is pursuing a fundamentally different strategy under CEO John Higgins. Instead of trying to develop billion-dollar drugs internally, Higgins said he has acquired 60 new drug candidates through acquisitions over the past three years. He intends to generate more chances to develop successful drugs by keeping Ligand’s costs low and forging partnerships with pharmaceutical companies as soon as possible.

—Antoine Papiernik of Sofinnova Partners in Paris responded to criticism that Avalon Ventures founder Kevin Kinsella leveled against the pharmaceutical industry a few weeks ago. Papiernik says the issues that Kinsella identified as “predatory business practices” are a predictable result due to the weakness of venture-backed life science companies—and the weakness of their VC backers.

—Luke argued in his BioBeat column that Big Pharma isn’t realizing many advantages through its spate of recent consolidations. He said mega-mergers create a lot of internal bureaucratic headaches, and that companies spend months, sometimes years, trying to figure out exactly what they acquired through a merger.

—Vertex Pharmaceuticals (NASDAQ: VRTX) reported that its cystic fibrosis drug, VX-770, is working about as well in children as it did in previous trials with older patients who have the genetic disorder. The Cambridge, MA-based company, which has operations in San Diego, said the drug is intended to improve the function of a defective protein with a specific mutation called G551D.

—San Diego’s Regulus Therapeutics said it got exclusive rights from New York University to develop treatments for a couple of microRNA targets that are believed to be involved in atherosclerosis and metabolic syndrome. Financial terms of the license weren’t disclosed.

—San Diego’s Carefusion (NYSE: CFN) sold its Onsite Services business to affiliates of Seattle-based Frazier Healthcare Ventures without disclosing terms of the deal. OnSite offers medical instrument repair and instrument management programs to hospitals.

—San Diego-based Arena Pharmaceuticals (NASDAQ: ARNA) raised $35.5 million through a PIPE stock offering, a private investment in a public entity. Arena plans to use about half of the proceeds to pay off debt to Deerfield Management that comes due in June 2013. Deerfield, a New York hedge fund manager, also was the investor in the PIPE. It is buying 12.15 million common shares of Arena stock for $1.46 each and 12,150 shares of preferred shares for $1,460 each.

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Grass is growing. Birds are singing. IPOs are filing. And snow is coming tomorrow. In other words, it’s springtime in New England.

Every so often, we like to take a breath and look back at some of Xconomy’s top stories from the past few months. These are not necessarily the ones that generated the most traffic (though in some cases they are). They are stories that exemplify what we try to deliver to our readers day in and day out—real stories behind the companies, people, ideas, and trends that are shaping the future of innovation in our network of cities. What’s more, they help distinguish us from the media pack—especially the low-level din of incremental tech journalism (not to mention any schmo with a Twitter account).

For this quarter, our Boston editors’ picks range widely in topic from scrappy startups and unsung companies (Dyn, PoKos, Topera) to giants and public firms (IBM/Netezza, Alkermes, Vertex); from personal stories (Adriana Jenkins, Bliss) to broad, sweeping trends (big data, Boston vs. other innovation hubs); from historic developments (Genzyme) to quirky twists (Blank Label); and from the serious (fighting drug addiction) to the humorous (“hold on to your toupees”).

Without further ado, here are Xconomy Boston’s top 20 stories of the first quarter, sorted by sector:

Top 10 Tech Stories:

Yes, Now That Stranger Across the Bar Can Text You. No, It’s Not As Scary As It Sounds, Says Mobile App Developer PoKos

Netezza Chief Talks About “Formative” PTC Days, IBM Deal History, and the Future of Big Data

You Snooze, You Lose: 10 Boring Boston-Area Tech Companies That Are Actually Interesting

The Changing Face of Boston VC: A Chat With NextView Ventures’ David Beisel

Mass Customization, Mystery Developers, and Men’s Shirts: Blank Label Returns to Boston

EveryTrail Was “Unappreciated Gem,” Says TripAdvisor Exec: A Look Inside Today’s Acquisition

MassChallenge, With Lessons Learned, Gears Up for 2011 Startup Competition: A Definitive Debrief

Boston Vs. New York: Tech Startups and Investors Add New Spice to Classic Rivalry

2010 Startup Moves from Boston to San Francisco Offer Insights to the Perennial Coast vs. Coast Debate

Desh Deshpande on Starting Merrimack Valley Innovation Center—and Making a Global Impact from Massachusetts to India

Redstar, From ATG Founders, Reveals Funding Strategy, Sets Up Office Space, Looks to Hire Entrepreneurs

.

Top 10 Life Sciences and Energy Stories:

Former Boston Scientific Exec and UCSD Physician Team Up at Startup Topera Medical

Bill Gates Backs Nimbus, Betting on Computer-Based Drug Discovery

Agrivida, Developer of Cheap Biofuel Tech, Seeks Deals to Broaden Commercial Horizons

Vertex Nails Pivotal Study for Cystic Fibrosis, Racing Toward Market With Second Drug

Alkermes Sees Chance to Reinvent Vivitrol For Fighting Drug Addiction, Not Just Alcoholism

Genzyme, After Months of Holding Out, Agrees to be Sold to Sanofi-Aventis for $20.1B

Adriana Jenkins, Boston Biotech PR Maven, Dies from Breast Cancer at 41

Bliss Healthcare, Founded by MIT Sloan Grad, Starts New Web-Savvy Home Care Service

Amgen’s R&D Chief, Roger Perlmutter, on Why BioVex’s Cancer-Fighting Virus Is Worth $1B

Follica Co-Founder and Team Find New Clues About Male Baldness

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Vertex Pharmaceuticals (NASDAQ:VRTX) reported today positive results from an ongoing late-stage study of its cystic fibrosis drug, VX-770, that show that the drug is working about as well in children as it did in older patients with the genetic disorder.

The Cambridge, MA-based company said that the Phase III study of the drug, which aims to improve the function of a defective protein with a specific mutation called G551D, met its primary goal among patients ages 6 to 11 of improving lung function through 24 weeks. The 48-week study involving 52 patients is ongoing. At 24 weeks, children on the drug showed a mean absolute improvement from baseline in lung function of 12.5 percent, slightly better than the still-impressive 10.6 percent improvement after 24 weeks among CF patients ages 12 and up who participated in a separate Phase III study described on February 23. The lung function test used in the study measures how much air a patient can exhale in a second.

The latest study also showed improvements in weight gain and reductions in sweat chloride levels in patients who took VX-770. People with the disease, which leads to the production of thick, sticky mucus and chronic lung infections that can be fatal, often lose weight in part because of the lung infections and nutritional problems that result from the disorder. And high levels of sweat chloride in patients with the disease are a key indicator of the defective CF protein, which fails to properly transport chloride ions through cell membranes. Vertex said that adverse events during the study included respiratory issues that were observed in both patients on its drug and those who took a placebo.

The positive results from the study of children on the drug and those from the trial involving older patients bode well for Vertex as it plans to submit applications including the data for U.S. and European approval of the VX-770 in the second half of 2011. The drug could become a game-changing therapy for certain patients with CF. There are about 30,000 patients in the U.S. and 70,000 patients worldwide with the genetic disorder; about 4 percent of them in the U.S. have at least one copy of the G551D mutation.

“The data announced today are highly encouraging because children with CF tend to be healthier than adults and significant improvements in lung function may be harder to demonstrate in a clinical study,” Robert Beall, president and CEO of the Cystic Fibrosis Foundation, which has supported the development of VX-770, said in a statement. “Data from Phase 3 studies of VX-770 in people with the G551D mutation provide strong support for the concept that addressing the defective protein that leads to CF may significantly improve outcomes for patients and give hope for the future of other CF treatments that repair the basic defect of the disease.”

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There were a million arguments against healthcare reform a year ago. One was that if President Obama got his way and expanded health insurance to millions of uninsured people, and the government made a real effort to study the comparative effectiveness of drugs at high and low prices, it was really the first step toward government-imposed price controls on new prescription drugs.

Once you have government price controls, opponents argued, drugmakers will lose the windfall profits the marketplace offers today to companies that take the substantial risk to develop innovative new drugs. The U.S., in turn, would lose its competitive edge as the center of innovative pharmaceutical R&D.

Guess what happened? One year after Obama signed healthcare reform into law, drugmakers are still in the midst of a golden age. Drugmakers still command ever-higher prices for innovative new medicines. And they will almost surely continue to enjoy this kind of pricing power in the U.S. at least until the end of this decade.

The latest bit of evidence arrived last week in a report from the Government Accountability Office (GAO). The report said that brand-name drug prices climbed by an annual average of 8.3 percent from 2006 through the first quarter of 2010, compared with a 3.8 percent annual uptick in the consumer price index for overall medical goods and services. (When generics were factored in, the overall amount of spending on the 100 most commonly used drugs was a much more modest 2.6 percent annual increase, according to the GAO.)

Still, that’s a big rate of price increases for new brand-name drugs. Yet despite the evidence, plenty of people like to argue that we are starting to see a new era of “stealth” price controls that are part of healthcare reform.

When the FDA proposed the revocation of Genentech’s approval of bevacizumab (Avastin) for breast cancer in December, opponents of healthcare reform surmised the agency was actually cracking down on the drug because of its price—which isn’t the FDA’s job. The same point—about nameless, unaccountable bureaucrats exercising some hidden policy on behalf of price controls—was made in August when the FDA delayed Genentech’s application to market a supercharged version of Herceptin which is sure to have a supercharged price. And plenty of observers—me included—sensed that a hidden agenda against high-priced drugs was really driving Medicare’s decision to force Dendreon to publicly explain the safety and effectiveness of its new prostate cancer drug last November.

Whatever the true motivations are—and there are plenty of other reasons why government agencies might have made those decisions—I haven’t seen any compelling evidence that says … Next Page »

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The San Francisco Bay Area has a storied tradition as the birthplace and leading hub of biotechnology, but something curious has happened the past couple years. Most of the scientifically groundbreaking, medical-textbook rewriting, financially lucrative new biotech drugs of the 21st century are coming from somewhere else.

This dawned on me last week as I started thinking about the 20-year outlook for the Bay Area life sciences cluster, in advance of the Bay Area Life Sciences 2031 event I’m organizing in San Francisco on Wednesday evening. It forced me to think about the really innovative drugs that still have a chance to generate billions of dollars in revenue two decades from today, that will help people live longer and better lives, and that are blazing new scientific trails. I’m talking about drugs that are a scientific, clinical, and business trifecta—drugs like Gleevec, Avastin, Herceptin, and Enbrel.

Plenty of molecules in the hopper today have that kind of potential, but for the purposes of this subjective parlor game I wanted to focus on the ones that have generated proof through pivotal clinical trials, and have either recently won FDA approval or are clearly on the verge of approval. That makes for a pretty short list:

• Vertex Pharmaceuticals’ new drugs for hepatitis C and cystic fibrosis

• Human Genome Sciences’ treatment for lupus

• Dendreon’s immunotherapy for prostate cancer

• Seattle Genetics’ “empowered antibody” for rare lymphomas

• Amgen’s antibody for osteoporosis and cancer

• Plexxikon and Roche’s genetically tailored treatment for melanoma

• Genentech’s souped-up version of Herceptin for breast cancer

A couple of things jump out at me right away. Of these eight new molecules, two are coming from Boston, two are from Seattle, one is from Washington, D.C., one is from greater Los Angeles, and only the last two are from the San Francisco Bay Area. These products are important not just for shareholders, patients, and scientists, but also for their respective regions, because they stir up … Next Page »

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Targeted Genetics has been a shell of its former self for a couple years now, but today it’s officially no longer the same old Targeted Genetics.

The Seattle-based company, a one-time trailblazer in the field of gene therapy, said today it has made a slew of changes to its business, including ditching the old name in favor of a new one—AmpliPhi Biosciences (pronounced like the thing that cranks up the sound coming from a guitar).

The re-invented company, traded on the Pink Sheets, is now headquartered out of London, the home of new CEO Edward Cappabianca. AmpliPhi is the creation of the merger of Targeted Genetics and London-based Biocontrol—although the emphasis in today’s release is focused on what Biocontrol brought to the table. The new company is going to focus on bacteriophage therapies, designed to fight stubborn antibiotic-resistant bugs like Pseudomonas aeruginosa. AmpliPhi says it has nailed down research grants for part of its drug development programs, including support from the Cystic Fibrosis Foundation of America.

The new entity is still holding onto some old Targeted Genetics intellectual property, and it stands to collect royalties if any partners like Amsterdam Molecular Therapeutics, San Diego-based Celladon and Cambridge, MA-based Genzyme (NASDAQ: GENZ) are able to create new drugs that use Targeted’s techniques for delivering specific gene therapies where they need to go in cells.

Targeted Genetics had been struggling to stay afloat for two years now, as it ran out of cash and was unable to keep raising more as investors lost interest in the once highflying field of gene therapy in the 1990s. It burned through more than $315 million in investor capital during its 19-year history, leaving many investors with holdings that were basically worthless. The company did, however, leave a profound mark on the Seattle biotech community as a training ground for a generation of scientific and managerial talent. Founder and longtime CEO H. Stewart Parker recently landed a new gig as the CEO of the Infectious Disease Research Institute, bringing her business experience to the prolific global health nonprofit organization.

I’ve personally covered Targeted Genetics for almost 10 years now, and seen it experience a few highs, like the time its gene therapy showed an effect against a congenital form of blindness. There were also plenty of lows, like the time a clinical trial showed its most advanced gene therapy failed to help patients with cystic fibrosis, and when a patient died in a rheumatoid arthritis trial, raising suspicion that Targeted’s therapy was responsible (ultimately, it wasn’t).

AmpliPhi Biosciences will retain a Seattle office focusing on finance, business development, investor relations, and capitalizing on the remaining gene therapy assets, says David Poston, the longtime finance chief for Targeted Genetics. Former CEO Susan Robinson “is pursuing other Seattle-based biotech projects, which may include forming her own company,” Poston says. The new company strategy, he says, amount to “exciting times, indeed.”

We don’t have a London bureau so this will probably be my last post about the company now known as AmpliPhi.

Targeted, R.I.P.

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—Cambridge, MA-based Quanterix partnered up with Novartis Diagnostics, the unit of healthcare giant Novartis that tests the safety of 80 percent of the U.S. blood supply. Novartis will run tests to see how effective Quanterix’s device is at pinpointing a protein biomarker in the blood that is linked to an undisclosed neurological disorder. Terms of the arrangement weren’t disclosed.

—New York pharmaceutical company Forest Laboratories (NYSE: FRX) paid $1.2 billion ($30 per share) upfront to acquire Newton, MA-based Clinical Data (NASDAQ: CLDA), a drug developer that won FDA approval last month for its anti-depressant. Forest could pay another $6 per share to Clinical Data shareholders if the drug, vilazodone, hits certain sales goals over the next seven years.

—Watertown, MA-based Athenahealth (NASDAQ: ATHN) formed an alliance with Microsoft (NASDAQ: MSFT) to make the companies’ systems more compatible and easier for healthcare professionals to use together to get a single view of patient records for hospital and outpatient visits.

—Cambridge-based Vertex Pharmaceuticals (NASDAQ: VRTX) announced it had passed a pivotal clinical trial of 161 cystic fibrosis patients who were randomly assigned to the company’s VX-770 pill or  a placebo. Those who received the Vertex drug showed a 17 percent relative improvement in their ability to force out air from their lungs in one second (a measure of lung function). Vertex’s stock shot up 15 percent the morning of the news, to hit $44.03 per share at 10:14am.

—Greg took a look at iAMscientist, a Brookline, MA-based startup developing a global community and resource site for researchers and institutions in science, technology, and medicine. The company has raised $1 million in seed funding from a group that includes famed Harvard chemist George Whitesides, and more than a dozen companies, such as Genzyme.

—Cambridge-based Metamark Genetics is moving out of stealth mode, wrote my colleague Ryan, who caught up with the company’s relatively new CEO Mark Straley. The startup—which was founded by top scientists at Harvard and elsewhere—is out to release a molecular test to provide prognostic information that will help physicians make better treatment decisions.

—Waltham, MA-based lab instruments and services provider Thermo Fisher Scientific (NYSE: TMO) announced it had sold off its Athena Diagnostics and Lancaster Laboratories units for a total of $940 million in cash, to boost shareholder value. Madison, NJ-based lab testing firm Quest Diagnostics is paying $740 million for Athena, and Eurofins Scientific of Brussels, Belgium, will shell out $200 million to acquire Lancaster, a provider of contract testing and analysis services to pharmaceutical companies.

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Vertex Pharmaceuticals’ winning ways are being felt on Wall Street this morning. The Cambridge, MA-based drug developer’s (NASDAQ:VRTX) shock price was up 15 percent to $44:03 per share as of 10:14 am Eastern time today as investors reacted to positive results the firm revealed this morning from a late-stage trial of its treatment VX-770 for certain patients with cystic fibrosis. My colleague Luke Timmerman provided the details this morning of the game-changing study for certain patients with the genetic illness that causes thick mucus to build up in their lungs. The results follow the company’s impressive results from late-stage studies of its experimental treatment for hepatitis C infections, telaprevir. The company now has a market value of about $9 billion.

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Vertex Pharmaceuticals has been moving in this direction for a long time, but it can now say with confidence that it is on its way to shaking up the standard of care for not just one disease this year, but two.

The Cambridge, MA-based biotech company (NASDAQ: VRTX), which has operations in San Diego, is announcing today it has passed a pivotal clinical trial of 161 patients with cystic fibrosis who were randomly assigned to get the company’s VX-770 pill or a placebo. The study found that patients on the Vertex drug had a 17 percent relative improvement in their ability to force out air from their lungs in one second—a common measure of success in treating lung disease—compared with those on a placebo. The effect lasted over the entire 48-week course of the study. Side effects included headache, upper respiratory tract infections, nasal congestion, rash, and dizziness, although more patients on the placebo group dropped out of the study early because of side effects, Vertex said.

While 17 percent relative improvement in breathing capacity for people with a deadly lung disease might not sound like much, this result represents a watershed for a portion of the 30,000 people in the U.S. with cystic fibrosis. Vertex is valued primarily for a drug (telaprevir) that has shown an ability to double the cure rate for patients with hepatitis C liver infections, but the company could have a similar life-changing effect for many patients with this genetic disorder. Cystic fibrosis, the result of a genetic mutation, causes the buildup of thick, sticky mucus in the lungs, which suffocates people over time, allowing a typical life expectancy of about 37 years. Doctors currently treat the symptoms of the disease, but Vertex’s drug could become the first FDA-approved therapy that works by altering an underlying faulty protein at work in patients with cystic fibrosis.

This drug isn’t for everybody—it was tested in a subpopulation of just 4 percent of cystic fibrosis patients with an abnormality known as G551D—but it’s the kind of result that scientists hope they will be able to build on to expand treatment to more patients with the deadly lung disease.

The results Vertex is releasing today from a study called Strive, which will be discussed later this year at a medical meeting, are “far beyond our expectations,” Vertex said in a statement. The firm plans to put together an application before the end of this year to seek regulatory clearance in the U.S., and Europe, to start marketing VX-770.

“The results from Strive are highly encouraging for the CF community and provide scientific evidence supporting our long-standing belief that targeting the underlying defect of CF may have a profound effect on the disease,” said Robert Beall, the president and CEO of the Cystic Fibrosis Foundation, in a company statement. “We have much more to do to eliminate this disease, but these data are extremely exciting.” (The CF Foundation helped develop VX-770.)

Vertex’s trial would have been deemed a success if it delivered just 4.5 percentage points of absolute improvement in patients’ breathing, as measured by the standard clinical trial goal (forced expiratory volume in one second, or FEV1). The actual result, in absolute terms from the beginning … Next Page »

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John Flatley, a real estate developer and philanthropist, has founded an investment group called Flatley Venture Capital to back life sciences startups with potential treatments for the genetic disease cystic fibrosis. Flatley, who has a close family member with the disease, told me he launched the venture group within the last few months.

Flatley Venture Capital, unlike a traditional VC firm, isn’t primarily focused on making profits on its investments, Flatley says. The venture outfit aims to provide between $200,000 and $2 million to support biotech startups that might not otherwise be able to afford to develop their technologies for the cystic fibrosis market, which consists of 30,000 patients in the U.S. and about 70,000 worldwide—numbers that pale in comparison to the cancer and heart disease markets. Flatley only expects to break even with his investments from the fund, he says.

Flatley, the son of the late Boston-area real estate mogul Thomas Flatley, has hired a Harvard University graduate named Alex Pickett as a senior analyst to evaluate deals for the venture group. While the group hasn’t made any investments yet, Flatley says “it’s going to be a substantial fund.” He says he is already considering backing two companies, which he declined to name.

This isn’t Flatley’s first foray to help advance cystic fibrosis treatments. He previously led the creation of a nonprofit laboratory, now called the Flatley Discovery Lab, in the Charlestown neighborhood of Boston. The nonprofit effort, quietly launched in 2008, has the mission of finding new drugs for cystic fibrosis, which causes the body to produce thick mucus that leads to chronic lung infections and poor absorption of nutrients. (The median life expectancy of someone with the disease was about 37 years in 2008).

When word got out last year that Flatley had started the research lab, formerly known as … Next Page »

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We saw some meaty stories on FDA drug approval processes, new collaborations, acquisitions, and hires for Boston’s life sciences firms.

—Pfizer’s former chief of licensing Ed Harrigan started a new gig as CEO of stealthy Boston biotech Karuna Pharmaceuticals, a PureTech Ventures-incubated startup that is quietly working on schizophrenia drugs.

—Vertex Pharmaceuticals (NASDAQ: VRTX) of Cambridge, MA, announced that the FDA granted its request for a speedier review of its drug telaprevir as a new treatment for hepatitis C. The agency, which will take six months to review the drug instead of the usual 10, often grants such requests when a potentially groundbreaking or lifesaving drug is involved.

—Last week an advisory panel to the FDA suggested the agency not approve liprotamase, a pancreatic enzyme replacement therapy that Eli Lilly (NYSE: LLY) took on when it acquired Cambridge-based Alnara Pharmaceuticals last summer. This week Ryan took a look at the potential impact of that decision, with perspective from a Needham, MA-based mother of two children with cystic fibrosis, a genetic disease that typically requires patients to take enzyme replacement therapies like liprotamase. The drug is intended to produce pancreatic enzymes that patients with cystic fibrosis and other diseases lack.

—Boston Scientific, a Natick, MA-based medical devices firm, announced it had bought Atritech, which makes a device alternative to treating patients with atrial fibrillation who are at risk of stroke. Boston Scientific (NYSE: BSX) will shell out $100 million upfront for the Plymouth, MN-based firm, and as much as another $275 million in regulatory and commercial milestone fees through 2015.

—I took a look at Boston-based Sproxil, which won IBM’s SmartCamp competition last summer for its mobile product authentication technology for detecting counterfeit medicine abroad. The startup has nabbed awards at other business plan competitions and has enlisted some big-name pharmaceutical companies as customers for its service in Nigeria. Consumers can use the service to verify whether a medication they’re about to buy is the real thing.

—Cambridge-based Ironwood Pharmaceuticals (NASDAQ: IRWD) announced a new drug discovery collaboration with Redwood City, CA-based Protagonist Therapeutics. The California company will use its proprietary technology for developing peptide drugs against biological targets picked by Ironwood.

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Sometimes it takes a parent’s perspective on the regulatory process for drugs in this country to understand what is really at stake for patients.

Last week an FDA advisory panel shot down Eli Lilly’s (NYSE:LLY) enzyme therapy for cystic fibrosis that has deep roots in the Boston area. And two parents of children with cystic fibrosis, a genetic disease that typically requires people to take such treatments, say they feel like the regulators got this one wrong.

“I appreciate that they are trying very hard not to do anything bad, but the measures that they were asking us to use for this particular product were meaningless,” says Francine Healey, a Needham, MA, mother of two children with cystic fibrosis.

Cystic fibrosis, which is known for causing a buildup of thick mucus in the lungs that makes it hard to breathe, also affects people’s digestion and their ability to absorb sufficient nutrients to maintain their weight. About 30,000 patients in the U.S. have the disease, and they have a median life expectancy of about 37 years. Liprotamase—the Lilly drug that it picked up through its buyout of Cambridge, MA-based Alnara Pharmaceuticals for as much as $380 million last summer—-is intended to provide certain pancreatic enzymes that patients with the disease and other conditions need to gain nutrition from foods. Yet the FDA panel voted 9-3 last week that there wasn’t enough evidence that the drug was effective for CF patients.

The FDA is expected to say whether it will approve liprotamase by mid-April. The agency isn’t required to follow the advice of its advisory panels, but it often does.

Healey, who testified in support of the drug at the panel’s meeting last week, has since written to FDA officials to let them know she disagreed with the outcome of the hearing. Her 19-year-old son, Mike, and her 16-year-old daughter, Amanda, now take digestion supplements made with enzymes from pigs. Liprotamase is made in a microbial process and would be the first approved treatment of its kind not to use the pig enzymes.

The FDA panel voted 11-1 in favor of recommending that additional studies of the effectiveness of liprotamase be done before it is approved. The agency’s staff also noted in its analysis issued last week that liprotamase scored lower in a measure of fat absorption than the existing supplements made with pig enzymes.

Patrick Marshall, who testified at the panel as a parent with a daughter who has cystic fibrosis, says that the measure of fat absorption has never … Next Page »

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