If you’ve turned on your TV anytime in the last, oh, decade or so, you’ve no doubt been bombarded by ads imploring you to “ask your doctor” about Drug X. And you’re well familiar with the routine: You get treated to happy images of folks dancing, perhaps, or walking their dogs in pretty green meadows, while a soothing voice in the background tells you that Drug X may cause you to lose your ability to drive safely, lose your vision, or lose your mind.

Forgive the exaggeration but you get the picture.

Well, the FDA isn’t pleased with the pharmaceutical industry’s advertising practices. So it’s proposing a new set of rules that would not only limit the ability of drug advertisers to use so many cheerful images, but may indeed force them to place more emphasis on their products’ potential side effects.

The FDA actually proposed the new rules back in 2010. But it re-opened the matter to public comment on January 27, after it published the results from an experiment it sponsored to measure the impact of distraction on consumers’ ability to understand the risks and benefits of drugs being advertised. The rules would pertain to direct-to-consumer (DTC) ads for prescription drugs on television or radio.

The original proposal is rather bulky. But here are the basics of what the FDA is suggesting: The agency wants to amend the rules for DTC advertising to more clearly define the standards for determining whether side effects are presented in a “clear, conspicuous, and neutral manner.” For example, the new guidelines would dictate that the adds cannot include “distracting representations,” such as statements, images, or sounds that might draw the audience’s attention away from those laundry lists of potentially adverse events.

So what exactly makes an ad distracting? The FDA’s proposal doesn’t really spell it out clearly, but you can get a hint of what the agency was thinking in the newly released report on its study, which it titled, “Experimental Evaluation of the Impact of Distraction on Consumer Understanding of Risk and Benefit Information in Direct-to-Consumer Prescription Drug Television Advertisements.” The FDA planned the study to answer a number of questions. Among them: Do visual images that are positive in tone affect viewers’ ability to comprehend the risks inherent in a product? Do positive images influence how people feel about the product? And if the advertiser super-imposes text onto the images—spelling out the side effects—does that change how viewers perceive the product?

All good questions, to be sure. To answer them, the FDA asked 2,000 consumers to go online and watch an ad for a fake blood-pressure drug called Zintria. But the participants didn’t all see the same ad. Some heard the side effects cited while watching “mildly” positive images (rocks, chairs, metal arches), while others saw “strongly” positive images (babies, puppies, girls jumping with beach balls). Some viewers saw the side effects spelled out in superimposed text, while others didn’t.

Not surprisingly, those who watched cute babies and puppies while hearing about the side effects felt better overall about the product than those who watched the more boring images. Both groups, however, understood Zintria’s risks just fine—and they really got it when the side effects were displayed on the screen in clear text, too.

The FDA has published the study on the Web and re-opened the proposed rules to comments, which the public can submit up until February 27 (instructions below).

We here at Xconomy are plenty distracted by the plethora of peppiness in drug advertising. Here are our votes for … Next Page »

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Pfizer was where Pedro Lichtinger learned about pharmaceutical marketing from people who did some amazing things. For starters, New York-based Pfizer (NYSE: PFE) turned an old-school antifungal medicine into a $1.6 billion cash cow. Now as the CEO of San Diego-based Optimer Pharmaceuticals (NASDAQ: OPTR) Lichtinger is borrowing some ideas from that experience, looking to make the most of his company’s new antibiotic.

Optimer won FDA approval last May for its first marketed product, a twice-daily pill called fidaxomicin (Dificid). That drug is designed to fight a bug called C.difficile that causes diarrhea so severe it can kill patients, especially frail elderly people. It is a common problem in hospitals. The company got off to a respectable start, generating about $24 million in gross sales in its first six months. But the market for treating this pathogen, after it has been diagnosed in a hospital lab, isn’t huge. Optimer can expect to generate about $153 million in U.S. sales in 2015, according to analyst Eun Yang of Jefferies & Co.

So to get the biggest possible bang out of this new molecule, Optimer is thinking about not just treating “C.diff,” but preventing it. Like Pfizer did with fluconazole (Diflucan), Optimer sees a long-range future in which physicians will prescribe the product as part of a standard regimen as a preventive medicine for patients who are at high risk of getting C.diff and who are likely to face a lot of suffering and high-cost hospital interventions if they get the bug. The initial plan is to start with a clinical trial to prove the Optimer’s drug can help prevent that problematic result in patients undergoing bone-marrow transplants.

If this preventive strategy works, then Optimer’s new medicine could be used by up to 20,000 patients a year who undergo such transplants. Given that the drug is currently priced at $2,800 for a typical 10-day course, and it is likely to go up over time, so it could possibly add another $230 million to $380 million in annual sales by 2020, Lichtinger says.

“I came from Pfizer where this concept was applied to Diflucan, where years ago, it was the first major antifungal applied for prophylactic use,” Lichtinger says. “It’s still used today as a generic. I saw that drug go from a relatively small drug into a $1.6 billion drug as a result of this prophylactic approach.”

He was quick to add that he’s not forecasting Optimer’s drug will approach that rarefied sales figure, but he does add there is a wide variety of other patient groups that could benefit from getting preventive C.diff treatment, such as vulnerable patients undergoing heart or liver transplants, certain cancer patients, or those on ventilators in hospital intensive care units. “The opportunity is certainly even bigger than with the primary C.diff indication,” Lichtinger said during an interview earlier this month at the JP Morgan Healthcare Conference in San Francisco.

Bone marrow transplants seem like an obvious place … Next Page »

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Good morning from Mountain View, CA, and from the close of the 2012 Personalized Medicine World Conference, which brought together thought leaders of business, government, healthcare-delivery, research and technology. Four themes that emerged from this year’s program:

• Greater optimism, triggered by the 2011 approvals of two major oncologic agents paired with companion diagnostics: vemurafenib (Daiichi Sankyo and Roche / Genentech) for patients with metastatic melanoma with a mutant biological pathway known as BRAF V600E and crizotinib (Pfizer) for patients with non-small-cell lung cancer that overexpresses a protein called ALK. Walter Koch from Roche and Hakan Sakul from Pfizer proudly discussed their development processes and speedy approval timelines. Those approvals were also cited by several other talks as examples of major progress made in the quest to deliver the right drug to the right patient.

• Greater clarity from the FDA. Although the FDA was not able to meet its self-imposed deadline of year-end 2011 to finalize guidance to industry on the best practices for developing companion diagnostics, Elizabeth Mansfield reiterated Commissioner Hamburg’s commitment to personalized medicine and told the audience to expect final guidance before the end of June. Mansfield also said that the FDA would provide guidance on how to co-develop a drug & test in parallel, as well as how to “enrich” clinical trials through careful selection of patients, based on their genetics. Both of these important regulatory steps could happen in 2012. The most surprising revelation, though, was Mansfield’s staffing: her group has just four people to evaluate all personalized-medicine-related medical devices.

• More sequencing. Just a few weeks ago at the JP Morgan Healthcare Conference, 800-lb sequencing gorillas Illumina and Life Technologies / Ion Torrent announced that scientists can expect the $1,000 genome by the end of 2012. Piggybacking on that announcement, Mostafa Ronaghi, chief technology officer of Illumina, presented a thorough overview of his company’s progress to date, bragging that 90 percent of all sequences produced worldwide had been produced on an Illumina instrument. Among other projects, Ronaghi’s team is working on techniques to accurately cover the 8 percent of the genome that cannot be sequenced because of repetitive regions. (Ronaghi made his presentation just hours before news broke of Roche’s unsolicited $5.7 billion takeover bid for Illumina.)

• More translational bioinformatics. Given the implied data glut that whole genome sequencing will produce, last week’s conference revealed more accomplishments in the application of bioinformatics to the remedy of disease. One of the unsung heroes of this year’s conference was Elizabeth Worthey from the Medical College of Wisconsin, who walked the audience through a case study of a pediatric patient presenting with undefined inflammatory bowel disorder. Worthey’s whole exome sequencing and variant analysis of the patient revealed a key mutation in the XIAP gene. A cord blood transplant ultimately cured the child, who was eating, drinking and playing again within four months.

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Mark Twain used to toss around a saying about three kinds of lies. There are lies, damned lies, and statistics. This week in biotech, we saw some statistics that could lead some people to get a false impression that everything is just peachy in biotechland.

If you measure the state of life science innovation by the amount of money flowing in, things look swell. Venture capitalists poured $4.73 billion into 446 biotech companies last year, according to the MoneyTree report by the National Venture Capital Association and PricewaterhouseCoopers, based on data from Thomson Reuters. The venture industry association’s press release cheerily noted that overall venture funding jumped 22 percent last year. While software is still the No. 1 and faster-growing sector of the two, biotech held its own, with a solid 22 percent gain in dollars invested compared with a year earlier.

You have to dig deeper to see what’s really going on. There is still a good amount of money going toward late-stage development of drugs people started working on 10-15 years ago. But there is an alarming drop in support for today’s cutting-edge biotech startups. Last year, just 153 U.S. biotech and medical device startups got their first round of financing, the lowest amount of seed investment activity in 15 years, as reported by Ryan Flinn of Bloomberg News.

There’s something really wrong with this picture. Most any biologist will tell you we are living in a golden age of discovery, at a time when we will soon be sequencing entire human genomes for $1,000 in one day. We are able to ask questions about how life works that nobody could even imagine asking a few years ago. It ought to be the time to charge ahead with basic research, and early-stage R&D to test exciting new concepts in diseases like cancer, diabetes, Alzheimer’s, HIV, and more.

But everywhere you look, the story is about cuts, cuts, cuts. The National Institutes of Health, the primary government agency that supports basic biomedical research, used to write checks for one out of every three grant applications, but it’s now down to about one out of every six, NIH director Francis Collins said earlier this month at the JP Morgan Healthcare Conference. Pharma companies are cutting back on R&D, firing workers left and right, and leaning on cheaper outsourced vendors everywhere they can. As many as one-fourth to one-half of biotech venture capitalists are thought to be slowly going out of business, as they are unable to raise new investment funds. The same IPO investors that want to buy Facebook shares look at biotech stocks like a four-year-old looks at lima beans.

There are good reasons why we see all those things happening. Pharma companies have created enormous inefficiencies for themselves through mega-mergers, and now they need to spend years trying to get their houses in order. Biotech as an industry has overpromised and underdelivered, and many investors are tired of it. The FDA, stung by various drug safety scandals, has been cautious about approving new drugs (although there are signs that FDA leadership wants a more balanced approach). And of course, our society is still struggling to come to terms with healthcare reform, and the realization that it’s unsustainable to spend infinite amounts of money on healthcare.

John LaMattina

All that said, an entrepreneur or a bold Big Pharma executive is the kind of person who looks at that picture and believes he or she can overcome the hurdles, and form a plan to turn vision into reality. But there aren’t that many people out there with the can-do spirit, or guts, to put down real money behind really talented teams devoted to the discovery of new drugs. And because everybody’s talking about how to go from Phase I to Phase II with drugs people invented years ago, there’s a real possibility that once those projects run their course, we’ll all look around in 2020 and wonder where all the wonderful new drugs are going to come from.

“You can really get into a vicious cycle when you have to eat your own seed corn,” says John LaMattina, a senior partner with PureTech Ventures, and the former president of R&D at Pfizer.

There are exceptions, of course, with a few people trying creative new ways to plant seed corn. Third Rock Ventures and Atlas Venture are a couple of VC firms that have remained active, continuing to bet big on the edgiest stuff coming out of the labs. Most every Big Pharma company has set aside cash for corporate venture firms that are seeking to help fill the void being created by the shrinkage of traditional VC. Pfizer, Johnson & Johnson, Sanofi, Bayer, and deserve credit for working on creative new collaborations with top biomedical universities and research centers, which seek to minimize some of the problems with the fruitless alliances of the past. J&J made news this past week when it unveiled an incubator for 18-20 startups in San Diego which looks to fill up some lab space it had vacated through its own internal R&D cutbacks.

Right now, we are in an age of experimentation with new organizational structures for supporting biomedical R&D. The hope is that these new organizations can reduce the time, money, and high-risk profile that has made life sciences such a hit-or-miss investment over the years. Pharma companies know they don’t … Next Page »

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[Updated: Noon, 1/21/12] UCSF could end up being a much more independent institution if chancellor Susan Desmond-Hellmann gets her way.

That’s according to a story today in the San Francisco Chronicle, which reported on a proposal Desmond-Hellmann put forward this week to University of California regents, who were meeting at UC Riverside. The plan would be to make UCSF more like the Lawrence Livermore National Laboratory or Lawrence Berkeley National Laboratory. Those institutions contract with the UC for health and pension services, and are accountable to the regents, but essentially govern themselves with their own boards of directors, according to a report by the Chronicle’s Nanette Asimov.

If such a move were allowed, UCSF would be freed up from paying about $49 million a year to help support the rest of the cash-strapped UC system, the Chronicle said. The move is necessary, Desmond-Hellmann said, because costs of pensions and a new UCSF medical center are rising fast, meaning that even though UCSF’s research engine is growing, the institution will be losing money by 2015.

“What we have here is not sustainable,” Desmond-Hellmann said.

It’s a bold move from Desmond-Hellmann, the longtime Genentech executive who took over the top job at UCSF in August 2009. This week, UCSF released data showing it received $532 million in research funding from the National Institutes of Health in 2010, which was about $57 million more than the previous year, and the most of any public institution in the U.S. The university has also put together a string of high-profile collaborations with pharmaceutical and biotech companies under the new chancellor, including deals with Pfizer, Sanofi, and Bayer Healthcare. The UCSF vision, Desmond-Hellmann said in a campus address last October, is to become “the world’s pre-eminent health sciences innovator.”

You can check the full account from the Chronicle here. [Update with video link] You can also see a short video of Desmond-Hellmann’s presentation to the Regents by going to the UCSF site or watching it below.

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[[Correction: 11:20 am ET]] It’s never been easy to make a buck in biotech venture capital, but there used to be more predictability and logic to it, according to Clarus Ventures’ Nick Galakatos.

You’d invest a few million, or tens of millions, and push a new drug or device toward some scientific validation in a few years. The world would recognize the value, you’d cash out, and repeat the process.

But in the strange way the market has worked for biotech since the financial crisis of 2008, that’s not always how it is anymore.

“For any VC firm to be in business, you have to raise another fund, and to raise another fund, you have to have exits,” says Galakatos, the co-founder and managing director of Clarus. “When you think about exits, there are traditional ones, like IPOs and M&A. But the IPO market is not a healthy market, and the M&A market is idiosyncratic. And idiosyncratic is really the right word. You can’t predict the M&A market very well, you can’t probabilize that. Five years ago, you could say ‘I’ll create a company, and do X, and there will be five buyers.’ You can’t say that anymore.”

Galakatos, a 20-year veteran of biotech ventures, spoke philosophically at times about the state of biotech venture capital during an interview last week at the JP Morgan Healthcare Conference. Clarus, a firm with $1.2 billion under management in biopharmaceutical and medical technology companies, is feeling the same heat others have in this industry. Biotech VCs have all been pushed to show returns to their investors that justify their high-risk endeavors, especially when investors have plenty of other ways to put capital to work.

This will be an important year for Clarus, which will go a long way toward determining what its future looks like for the next five. The firm raised its last fund, worth a reported $660 million, in February 2008 just before the financial collapse. Clarus was “exceptionally fortunate” to raise the fund (now worth $700 million, Galakatos says) when it did. But now that four years have gone by, it will probably be just a few more months before Clarus hits the fundraising trail again, Galakatos says. “Probably in the latter part of this year, we’ll go out and raise a new fund,” he says.

[[Correction: the returns cited below are for current partners at Clarus, but their investments were made previously at MPM Capital, not Clarus.]] The partners at Clarus have had a strong run of returns. Before the financial crisis struck in 2008, the partners at Clarus were able to claim success when Rinat Neuroscience was bought by Pfizer for $500 million, Syrrx was acquired by Takeda Pharmaceuticals for $270 million, Tercica was bought by Ipsen for $373 million, and CoTherix was snapped up by Actelion for $420 million.

In the post-financial crisis era, Clarus has pulled out a few wins, but not as many. ESBAtech was sold … Next Page »

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Johnson & Johnson’s West Coast research leader, Diego Miralles, has met with a lot of biotech entrepreneurs who are curious about what J&J is doing to foster more startups at its facility in San Diego. At some point, a skeptical question usually comes up.

“What’s the catch?” Miralles says he’s sometimes asked.

He insists there isn’t any catch.

“We are genuinely trying to help the industry,” Miralles said last week in a meeting at the JP Morgan Healthcare Conference in San Francisco. “We think helping the biotech industry helps us. We strongly believe that a rising tide lifts all ships.”

J&J (NYSE: JNJ), which is based in New Brunswick, NJ, has been moving quickly the past few months on a new initiative to help biotech startups get up and running, through its new 30,000 square foot Janssen Labs startup space on the Torrey Pines Mesa. As Bruce first reported here in October, the idea is to create a space at J&J’s facility where 18-20 fledgling companies can get modern lab space, supplies, professional facilities management, and equipment that is supposed to free up the entrepreneurs to focus more on their science.

The life sciences industry has been buzzing about the concept since then, and Monday night more than 500 people turned out to see the new Janssen Labs in San Diego during an open house at J&J’s renamed Janssen Research & Development facility.

J&J insists that it won’t take equity stakes in the startups, or attempt to direct them, but that it hopes the industry, and eventually its shareholders, will benefit by “fertilizing the soil” for more innovation. At Monday night’s soiree, J&J publicly named the initial four startups settling into the space, selected from the first 100 applications that have rolled in from around the world since October.

Big Pharma companies have gotten some heat from entrepreneurs and VCs over the past couple of years for taking advantage of them, essentially by harvesting the best ideas at bargain rates as the startups struggle to raise more venture capital to keep going. But as biotech startups are now less able to fill up Big Pharma’s product pipeline, those same Big Pharma companies are experimenting with new ways to stir up more early-stage R&D. Sanofi CEO Chris Viehbacher has outlined a strategy to shift resources toward startups and academic collaborators, Pfizer has set up a network of academic collaborations around the country, and Bayer has sought to become a landlord to promising startups in San Francisco’s Mission Bay.

Here’s how the J&J startup space is supposed to work. Companies apply for space that can be configured to house one to three people, or as many as 25, Miralles says. Prescience International, the group that runs the San Jose BioCenter, will provide professional management of the space, and to handle … Next Page »

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Medivation’s long shot for Alzheimer’s came up short today. The San Francisco-based company (NASDAQ: MDVN) said today its Alzheimer’s drug candidate dimebon failed in a pivotal clinical trial. Medivation and its collaborator, Pfizer, said they plan to quit developing the drug.

The bad news came from a trial known as Concert, which enrolled more than 1,000 patients with mild to moderate symptoms of Alzheimer’s, the neurodegenerative disease that impairs the memory and cognition of millions of elderly people. The drug failed to show a statistically significant benefit on a common cognition score, or a measurement of activities of daily living and self-care.

“We are disappointed in the Concert results and the implications for Alzheimer’s disease patients and their caregivers,” said David Hung, Medivation’s CEO, in a statement.

The Medivation drug, original developed in Russia in the 1980s as an allergy treatment, showed some promise in a smaller study Medivation conducted including more than 180 patients with Alzheimer’s, which was published in 2008. But investors largely gave up on the drug when Medivation and Pfizer failed to reproduce the results in March 2010 in a pivotal trial of about 600 patients, known as Connection. Medivation suffered layoffs after that setback, but it has made a comeback on the strength of a prostate cancer drug called MDV3100, which showed last November that it was able to help men live longer. Details from that trial are expected to come out this year at a medical meeting.

“Given Dimebon’s poor precedence from its Phase III Connection trial in 2010, the failure of Concert should come as no surprise. Investor focus should remain on MDV3100 for prostate cancer,” said Biren Amin of Jefferies & Co., in a note to clients this morning. He notes that the full data from the pivotal study of MDV3100 is expected to be released at the American Society of Clinical Oncology’s Genitourinary symposium, scheduled for February 2-4.

Shares of Medivation fell 1.2 percent to $55.01 shortly after the opening bell.

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Like a lot of biotech executives focused on developing drugs, Martin Tolar has long been skeptical of the value of genomics in bringing about personalized medicine. But over the past few months of scoping out new opportunities, he’s become enough of a believer to jump into genomics with both feet, as the new CEO of Cambridge, MA-based Knome.

“You always hear about genomics and the revolution that never happened,” Tolar says. “There was Millennium and deCode, and others who raised lots of money. But I looked at this and said, ‘No, this is incredible, it’s really happening.’ All the pieces of equation are coming together.’”

Tolar, the former CEO of Wellesley, MA-based NormOxys, is joining Knome just as it has completed its fourth year in business, which was by far its best. The company is announcing today that it has won a new contract to analyze and compare 1,000 genomes for scientists at Johns Hopkins University, who are looking for genetic variants linked to asthma in African American and African Caribbean populations. It’s the latest addition to Knome’s roster of about 100 customers for its genomic-analysis software service, although the Hopkins project is by far the biggest. Knome isn’t disclosing the value of the new project, but the company expects to generate $20 million in revenue in 2012 from academic, biotech, and pharmaceutical industry customers, Tolar says.

Tolar joins Knome after his previous company—which raised $17.5 million in May 2010—discovered in clinical trials that its experimental drug worked in a different way than its scientists thought. The NormOxys drug was shown to alter the PI3 kinase pathway, instead of releasing controlled amounts of oxygen into cells. Tolar didn’t say much about the situation, other than that the NormOxys drug is still moving forward in clinical trials for a different use, and that he was more excited by the task in front of him at Knome.

Martin Tolar

Knome’s previous CEO, Jorge Conde, is staying with the company as chief strategy officer, and will focus on product development, Tolar says. The management team is being further filled out by Jonas Lee, a board member who will now join the company as chief marketing officer, while Marc Rubenfeld, formerly of Beckman Coulter, is joining as vice president of operations.

The timing is right for Knome to grow in 2012, Tolar says, because the torrid pace of innovation with faster/cheaper DNA sequencing hardware has created … Next Page »

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[Updated] Aveo Pharmaceuticals is starting the New Year with news that it has passed the most important clinical trial in company history, although it appears to have barely eked out the victory, which disappointed investors.

Cambridge, MA-based Aveo (NASDAQ: AVEO) said today that its lead experimental drug reached its goal in a pivotal clinical trial known as TIVO-1. The study showed Aveo’s drug was able to keep kidney tumors from spreading for a longer period of time than another drug in its class, sorafenib (Nexavar) from Bayer and Onyx Pharmaceuticals. The trial of 517 kidney cancer patients showed that Aveo’s tivozanib was able to keep tumors from spreading a median of 11.9 months, compared with 9.1 months for the existing drug. The study was designed to show the Aveo drug could keep tumors from spreading about an extra three months, so it barely passed.

Today’s statement didn’t say anything specific about the new therapy’s side effects, although CEO Tuan Ha-Ngoc said the study showed a “favorable safety profile” for the Aveo drug. More details on safety and effectiveness will be presented in June at the American Society of Clinical Oncology’s (ASCO) annual meeting, Aveo said in a statement. And importantly, Aveo and its partner, Japan-based Astellas Pharma, said they now plan to file applications for approval from regulators in the U.S. and Europe this year to start selling the new treatment.

Despite reaching the study’s main goal, Aveo shares fell today, possibly because investors were expecting to see the Aveo drug demonstrate a bigger advantage over the competition. Aveo stock fell $2.13, or about 12 percent, to $15.07 at 10:20 am Eastern.

[Update: 11:50 am Eastern] If there was one surprise in the results, it was that patients on the competing drug did a bit better than expected, Ha-Ngoc said by phone this morning. Patients on Onyx and Bayer’s sorafenib have typically been able to live for five to nine months without their tumors spreading, so today’s result of 9.1 months was on the high end of the expected range, creating a higher-than-expected hurdle for Aveo to clear. But Ha-Ngoc said the result definitively shows Aveo met its goal of demonstrating superiority over an active drug, unlike other experimental cancer treatments in this class, which have typically been tested against placebos. He added that Aveo’s drug was able to keep tumors from spreading for a median of 12.7 months for patients getting their first round of treatment, which is the largest benefit ever shown for patients in that group, he says.

“We are extremely happy today. It’s a fantastic way to start the year for us,” Ha-Ngoc says. Given the drug’s advantage in its safety profile, and its ability to delay tumor progression, tivozanib “should be in position to be the first-line treatment of choice,” Ha Ngoc says.

He added that the result is just the first time Aveo has passed a pivotal trial, and it is looking forward to additional studies of tivozanib as a treatment for other tumor types, and to help provide momentum for the rest of its pipeline. “We are here to build a real company,” he says.

The Aveo drug is an oral pill designed to cut off the blood supply that nourishes tumors, by specifically blocking three different forms of VEGF receptors that are on the surface of cancer cells. Aveo’s tivozanib is supposed to be a more selective blocker of VEGF than two currently marketed drugs that work in a similar way-Pfizer’s sunitinib (Sutent) and Bayer and Onyx’s sorafenib. Researchers hope that more selective VEGF receptor can more completely shut off blood flow to tumors, and also avoid blocking similar receptors on healthy cells-which can cause side effects.

The market for treating kidney cancer is significant. About 61,00 new cases of kidney cancer were diagnosed in the U.S. last year, and 13,000 people died from the disease, according to the American Cancer Society. Pfizer’s sunitinib, first approved in January 2006, generated $1.06 billion in sales in 2010. Bayer and Onyx’s sorafenib generated $934 million in sales the same year

Investors, and researchers, have had high hopes for the Aveo drug since it passed a mid-stage study of 272 patients, which was presented at the ASCO meeting in June 2009. The Aveo drug showed in that study it was able to keep tumors from spreading a median of 11.8 months, with mild side effects reported, including high blood pressure and hoarseness of voice.

So today’s TIVO-1 study essentially confirms what researchers had seen in the prior study.

Aveo didn’t provide detailed breakdowns of how the drug performed in various patient demographic groups, although it did suggest the drug’s advantage was more pronounced in patients getting their first round of therapy. The Aveo drug kept tumors in check for a median of 12.7 months compared with 9.1 months for those on the competing drug who were previously “treatment naive.” About 70 percent of the patients in the study fit this description, Aveo said.

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‘Tis the season to reflect on the past year and take a look at some of Xconomy Boston’s top stories.

As usual, these aren’t necessarily the highest-traffic stories (though in some cases they are). They are stories that exemplify what we are trying to deliver to our readers every day—narratives about the people, companies, and ideas that are shaping the future of technology, life sciences, and cleantech in our region, and across the country.

It was very hard to pick just 20 stories, like I usually do. I guess that’s a good thing. So I fudged it and actually picked slightly more—a dozen tech stories, and a dozen life sciences and cleantech stories.

In any case, our editor’s picks for 2011 span the fields of software, mobile, Internet, security, health IT, biotech, life sciences, energy, and hardware/materials.

They range in topic from people stories (Adriana Jenkins, Steve Jobs) to company strategies (Acme Packet, Vertex) to trends and analysis (big data, biotech risks); from universities (Harvard accelerator) to startups (MedicalRecords, Harvest Power) to big companies (IBM, Pfizer, Biogen Idec); from Q&As (Rob Day, Jim Baum) to company profiles (EnVivo, MC10) to news features (testing the nation’s first car collision-avoidance system); and from big community projects (Entrepreneur Walk of Fame) to cheeky area clusters (top 10 “boring” tech companies).

Here they are in their full glory, our top 20-ish stories of the year, sorted by sector:

Top 12 Tech Stories

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

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Geneticist Arthur Tinkelenberg has always been struck by the lack of strategy in scientific research. “Historically it’s been somewhat ad hoc,” he says. “For example, why do we study fruit flies? Because somewhere in the dim past, somebody did something interesting with a fruit fly, and now you have a whole field.”

So when Tinkelenberg was presented with the opportunity to lead New York-based biotech startup Enumeral Biomedical last spring, he jumped at the opportunity. Enumeral is based around technology invented by J. Christopher Love, an associate professor of chemical engineering at MIT who developed a way to measure how the human body responds to infection and disease. Enumeral’s technology, called “protein microengraving,” allows scientists to take cells from people who, say, have survived cancer, and then scrutinize those cells to identify antibodies involved in fighting the disease.

Enumeral’s startup team is marketing the technology as a completely new way to find ideas for innovative drugs—namely by studying real human cells, as opposed to fruit flies, bioengineered mice, or any of the other critters biotech researchers generally use. “We have to find better ways to validate drug candidates, and the way to do that is to start with human-based samples,” Tinkelenberg says.

Although it’s only been around about five months, Enumeral has already piqued the interest of venture capitalists and pharmaceutical companies. It has raised a total of $4.25 million from a group of investors led by Harris & Harris, a New York-based venture capital firm that invests in nanotechnology startups. And Tinkelenberg says the company is in ongoing discussions with potential pharmaceutical partners and hopes to have two to three deals locked up in the first quarter of 2012.

The quest to make drug discovery more human has been a major priority for Big Pharma in recent years. The industry has placed much of its hope in so-called humanized mice, which are rodents that have been engineered to possess fully human immune systems. Scientists expose the mice to human diseases and then extract … Next Page »

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San Diego-based Trius Therapeutics (NASDAQ: TSRX) got some long-awaited good news today for its lead antibiotic in development.

The company said today that its experimental drug, tedizolid phosphate, met the main goal of its pivotal clinical trial by showing it was roughly equal (non-inferior) to Pfizer’s linezolid (Zyvox) when treating acute skin and skin structure infections. The study enrolled 667 patients who were randomly assigned to get a once-daily form of the Trius drug for six days, or a twice-daily course of the Pfizer drug for 10 days. The Trius drug was effective for 79.5 percent of patients, while the Pfizer drug worked for 79.4 percent, Trius said in a statement.

“We are very pleased the trial demonstrated that a 6-day course of once daily oral tedizolid is as efficacious as a 10-day course of twice daily oral linezolid while showing an improved tolerability profile,” said Jeff Stein, Trius’s CEO, in a statement.

More details will be presented at a future scientific meeting, Trius said. But in today’s statement, the company said that 24 percent had adverse events in the study that were drug-related, compared with 31 percent on the existing Pfizer drug. The Pfizer product, approved by the FDA in 2000, generated $1.18 billion in worldwide sales last year. Both it and the Trius product are members of the class of antibiotics known as oxazolidinones. The Trius drug is designed to be a potent new option against some of the more dangerous bacterial infections out there, like MRSA.

Trius shares initially surged on the news, but then fell as the day continued, dropping 12 percent to $5.98 at 10:55 am Eastern time.

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Last week, Newton, MA-based AesRx announced that it has begun human trials of its lead drug, Aes-103, to treat sickle cell disease. To biotech observers, this may not have seemed like a big deal—sickle cell is a rare disease that affects only about 75,000 people in the U.S.—but for AesRx CEO Stephen Seiler, just getting this far is a major achievement. Seiler founded the company in 2008 and tried to raise $10 million in venture financing to advance the drug through “pre-clinical” (animal) trials. But he had to give up. “Everyone said, ‘This is sexy technology, but we don’t fund pre-clinical drugs anymore,’” Seiler says.

So Seiler, who bought the drug from a New Jersey company that had gone bankrupt, nurtured its early development with about $1.5 million in angel funding, money from his own pocket, and a $750,000 loan from the Massachusetts Life Sciences Center. Then, in November 2010, AesRx (pronounced ES-er-ex) formed a partnership with the National Institutes of Health, which committed an undisclosed amount of money to help advance the drug through pre-clinical studies and the first human trials. “It was a huge step towards getting us through the Valley of Death,” says Seiler, quoting terminology that CEOs often use to describe the chronic lack of venture funding for early-stage biotechs.

Seiler says Aes-103 is the only drug in development that targets the underlying cause of sickle cell disease. The condition, which is inherited, is caused by abnormal hemoglobin, the oxygen-carrying protein in red blood cells. The red blood cells become distorted into a sickle-like shape, causing pain, organ damage, infections, and other complications that can turn fatal. AesRx’s drug, called 5-hydroxymethyl-2-furfural (5HMF), is derived from sugar and designed to prevent blood cells from sickling.

There is one anti-sickling drug on the market already, but it has such harsh side effects it can’t be used in children—a huge proportion of the patient population. If Aes-103 proves safe in the healthy adult volunteers participating in the first trial, the company will design trials in children, Seiler says. “It’s important to get this into … Next Page »

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Alnylam Pharmaceuticals has been in the doghouse for a while now, as its technology of choice has fallen out of favor in the industry. But while many people have written it off, the Cambridge, MA-based company has started to show hints that it might—just might—be onto something that works against a rare and deadly disease.

The company (NASDAQ: ALNY) reported last month at a scientific meeting that one of its experimental RNA-interference drugs was able to shut down production of a protein that causes a disease called TTR amyloidosis. The findings, from an early-stage clinical trial of 31 patients, marked the first time that Alnylam has been able to show that an RNAi treatment can specifically block a disease-causing protein in human beings.

The potential of RNA interference has electrified scientists for years, because it offers the potential of blocking disease targets inside cells that can’t be effectively halted by conventional small-molecule or larger biotech drugs. But the excitement has faded the past couple years, as researchers have struggled to deliver these RNA-silencing molecules into cells, and major companies like Roche, Merck, and Novartis have cut back on their investments in the field. Through it all, Alnylam CEO John Maraganore has insisted that the only way to overcome the doubters is to deliver convincing proof from clinical trials, not just mouse or monkey experiments.

Alnylam has made some headway in the clinic the past couple years, and while it’s too early to say it has proved the skeptics wrong, it’s moving full steam ahead on this new flagship program, betting that it will prove that RNAi will someday live up to its promise.

“The level of confidence for us at Alnylam, and among our collaborators, has gone up enormously as a result of this data,” Maraganore says.

Based on the clinical findings (which I’ll get to in a minute), the company has raced ahead with a more potent-second generation delivery technology of its TTR drug, which it plans to move into its first clinical trial in early 2012. The plan is then to move ahead at breakneck speed by wrapping up that study before year’s end, starting a mid-stage study later in 2012, and then leaping all the way into the third and final phase of clinical trials normally required for FDA approval in 2013, Maraganore says.

There are scientific and business reasons why Alnylam has honed in on TTR to be its flagship program. The disease, transthyretin (TTR) amyloidosis, allows excessive amounts of amyloid proteins to build up in tissues throughout the body. Alnylam likes going after this disease partly because … Next Page »

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San Diego’s Lpath (OTC: LPTN), a biotech developing specialized monoclonal antibodies for cancer and other diseases, intends to raise about $10 million through a secondary offering of stock and warrants, according to a recent regulatory filing.

The company is working to advance two related drug candidates within an emerging field of medical science that targets bioactive signaling lipids, and could be used to treat a wide range of human diseases. One is a specialized formulation of the humanized monoclonal antibody sonepcizumab, which has shown promise in treating the wet form of age-related macular degeneration and other types of eye disease. The other drug candidate is a systemic formulation of sonepcizumab that Lpath was developing with Merck Serono as a potential late-stage cancer therapeutic. A third related drug candidate is in pre-clinical development.

Lpath and Merck ended their partnership in mid-2010, and Lpath says Merck has relinquished all rights to the drug. The biotech began working with Pfizer on the compound for diseases of the eye in early 2010, and Lpath later granted Pfizer a time-limited right of first refusal for its cancer drug candidate.

Lpath says it has financed its operations mostly through the private placement of equity and debt securities, and funding from corporate partners pursuant to research and development collaboration agreements. The company says it intends to use the net proceeds of the $10 million offering for general corporate purposes.

At the end of September, Lpath had an accumulated deficit of just over $36 million. The company says its costs for continuing research and development, including general operations, should be about $20 million to $30 million through the end of next year.

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In the news since the Thanksgiving holiday, we’ve had a fascinating bit of biomedical research from Internet guru Larry Smarr, a criminal conviction, and an extended Q&A with Eli Lilly CEO John Lechleiter. Your life sciences briefing begins now.

—Under fierce competition in the market for gene expression microarray tests, Santa Clara-based Affymetrix (NASDAQ: AFFX) agreed to pay $330 million to acquire San Diego-based eBioscience, a maker of flow cytometer instruments and chemical reagents used in biomedical diagnostics. Affymetrix said it plans to keep eBioscience’s management team and operations in San Diego.

—Pfizer (NYSE: PFE), the New York pharmaceutical giant, agreed to buy Excaliard Pharmaceuticals, a Carlsbad, CA-spinoff from Isis Pharmaceuticals (NASDAQ: ISIS). Isis said it’s getting $4.4 million upfront, and as much as $14 million over time for its stake in Excaliard, plus additional milestone and royalty payments. Excaliard was founded in 2006 to use Isis’ gene-silencing technology, known as antisense, to curb the activity of certain genes implicated in excessive skin scarring.

—A 23-page article offers an insightful glimpse into the converging future of personalized medicine, health IT, and wireless health. It is titled, “Quantified Health: Toward Digitally Enabled Genomic Medicine: A 10-Year Detective Story of Quantifying My Body.” I’m curious what other experts in these fields think about this bit of scientific research from Larry Smarr, founding director of the UC system’s California Institute for Telecommunications and Information Technology (CalIT2). I posted my question-and-answer session with Larry here.

—A San Diego jury convicted Kent Thomas Keigwin, a 61-year-old financial advisor, in the first-degree murder of John G. Watson, a retired life sciences CEO and local angel investor. Prosecutors argued that Keigwin killed Watson to steal millions of dollars from Watson’s accounts, by using Watson’s personal information to impersonate him. Keigwin is scheduled to be sentenced on Jan. 20.

—Amid the celebration of their success with Amira Biosciences (purchased earlier this year for $475 million by Bristol-Myers Squibb), Versant Ventures’ Brad Bolzon and Amira co-founder and CTO Peppi Prasit started a new company, Inception Sciences. Prasit and Bolzon plan to operate Inception Sciences as a holding company for spinning out individual drug development programs as separate corporate entities. I hope to get more details about the venture next week.

—In a ruling issued before Thanksgiving, a federal judge in San Diego declared that San Diego-based Histogen and its Histogen Aesthetics subsidiary are not infringing on a couple of key patents held by Carlsbad, CA-based SkinMedica. In a lawsuit filed in early 2009, SkinMedica alleged that Histogen was infringing on its proprietary “NouriCel” technology for culturing certain types of skin cells in growth media. Both companies use growth factors and other proteins derived from the cells to make skin care products.

—Luke devoted a two-part BioBeat column to his conversation with Eli Lilly CEO John Lechleiter about the pharma business generally, and Lilly (NYSE: LLY) in particular. In part 1, Luke talked mostly with Lechleiter about ways to get pharma out of its current rut. In part 2, Luke featured the Lilly CEO’s responses to questions that readers relayed to him via Twitter.

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The Michigan State University Bioeconomy Institute in Holland, MI announced earlier this month that, in an effort to establish a cluster of biotech businesses, it is the recipient of more than $1 million in grants: $580,000 from the U.S. Commerce Department’s Economic Development Administration and $500,000 from the Michigan Economic Development Corporation. The grants will go toward operating the institute’s Proof of Concept Center, a pilot plant that allows small startups developing novel, green chemical technologies to scale their products up to an industrial level.

“Scale-ups can pose a variety of technical, financial, and regulatory challenges,” says Paul Hunt, senior associate vice president for Research & Graduate Studies at MSU. ”With the Proof of Concept Center, the infrastructure is now available to small companies who would not normally have access to a pilot plant. Ultimately, the goal is to advance Michigan’s economy by encouraging the production of bio-based chemicals for use in the auto, furniture, and fuel industries.”

The MSU Bioeconomy Institute will provide firms with access to more than 7,000 gallons of stainless steel, glass-lined, and Hastelloy chemical reactors, as well as centrifuges, dryers, filters, and related ancillary equipment. In addition to providing access to capital equipment for scale-up production, MSU will also provide research and chemical manufacturing expertise and regulatory compliance assistance.

West Michigan’s regional economic development organization, Lakeshore Advantage, will also manage a laboratory-based incubator for green entrepreneurial ventures, offering advice on business planning, market development, and business proposals. The Prima Civitas Foundation will coordinate statewide recruitment of client firms for the Proof of Concept Center, as well as facilitate firms’ contacts with venture funds and angel networks, beginning with North Coast Technology Investors. In addition, the … Next Page »

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Pfizer is making a new bet on a new drug to fight excessive scarring, by acquiring a former skunkworks project from Isis Pharmaceuticals (NASDAQ: ISIS).

New York-based Pfizer (NYSE: PFE) said today it has reached an agreement to acquire Carlsbad, CA-based Excaliard Pharmaceuticals, a spinoff from Isis. Terms of the deal aren’t being disclosed, but Isis said today it is getting $4.4 million upfront, and as much as $14 million over time for its equity stake, plus further milestones and royalty payments. Excaliard was founded in 2006 with technology from Isis, and the company received a $15.5 million Series A investment the following year from Alta Partners, ProQuest Investments, and RiverVest Ventures.

Excaliard was started to use Isis’ gene-silencing technology, known as antisense, to curb the activity of certain genes implicated in excessive skin scarring. As I described in a feature story in these pages two years ago, Excaliard’s hope is to make scars less visible and bumpy, like those from the 1 million Caesarian section births performed each year, knee surgeries, and reconstructive plastic surgeries. It could also be used for some rarer dermatology conditions like hypertrophic scars that are red, raised, itchy and swollen, or keloids, that are large and raised above the skin like a benign tumor.

If Excaliard can demonstrate this approach works in clinical trials, it could have a wide-open market opportunity, since there are no other FDA approved drugs that it can consider direct competitors. The company said in a statement that it has completed three mid-stage clinical trials, although it didn’t describe the results.

“The acquisition of Excaliard is part of our corporate research and development strategy to actively complement our robust internal project pipeline with innovative and differentiated drugs from biotech partners,” said Mikael Dolsten, Pfizer’s president of worldwide R&D, in a statement.

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The price of shares at San Diego’s Gen-Probe, Amylin Pharmaceuticals, and Optimer were clipped for various reasons over the past week, but several local startups successfully raised capital. Our good news, bad news briefing begins here.

—Rempex Pharmaceuticals, a San Diego biopharmaceutical startup developing a new approach to antibiotics resistance, said it raised $67.5 million in Series B venture funding—bringing total funding for the company to $76 million since its founding less than five months ago. The startup is on a fast track, and plans to use the capital to accelerate the commercialization of its therapies for treating gram-negative bacterial infections. Rempex said it plans to file a new drug application for its first drug candidate in the second half of 2012. New investors Frazier Healthcare Ventures and Vivo Ventures joined existing investors SV Life Sciences, OrbiMed Advisors, and Adams Street Partners in the latest round.

—Cambridge, MA-based Vertex (NASDAQ: VRTX) has held the high ground in hepatitis C therapies since the FDA approved its protease inhibitor drug telaprevir (Incivek) last year. But two rivals are gaining ground. The price of Vertex shares have fallen with the rise of Alpharetta, GA-based Inhibitex (NASDAQ: INHX) and Princeton, NJ-based Pharmasset (NASDAQ: VRUS). Vertex, which has operations in San Diego, hit a 52-week high of $58.87 on May 12, but it has been trading around $31 in recent days.

—Adding to the competition in hepatitis C drugs, San Diego-based iTherX Pharmaceuticals raised almost $3.2 million to advance its development of a prophylactic treatment for Hepatitis C, according to a regulatory filing earlier this week. The startup said in March that its drug candidate TX-5061 appears to prevent the hepatitis C virus from entering liver cells, and has shown “potent preclinical antiviral activity against all HCV genotypes.” Former UCSD virologist Flossie Wong-Staal is a co-founder and chief scientific officer. The company raised $2.8M in 2010.

—San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) agreed to pay Eli Lilly more than $1.5 billion as it gradually reassumes responsibility for global commercialization of its best-selling diabetes drug in a deal that ends its 10-year partnership with Lilly. Under their agreement, which also ends litigation with Lilly, Amylin will take over sales of exenatide (Byetta) in the U.S. by the end of this month—and global sales of both Byetta and an experimental, extended release version (Bydureon) over the next two years. Amylin shares, which hit a 52-week high of $16.65 on Jan. 27, have been trading around $10 a share over the past few weeks.

—Xconomy east coast biotechnology editor Arlene Weintraub profiled PharmaSecure, a four-year-old startup in Lebanon, NH, with operations in San Diego, Michigan, and India. The company provides machines to drug-makers that print unique bar codes and serial numbers on drug packaging. PharmaSecure raised $3.9 million last month from Innovation Endeavors, Gray Ghost Ventures, Healthtech Capital, and angel investors. The Tech Coast Angels (TCA) participated in … Next Page »

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