When you hear about personalized medicine, you might think first of the applications for cancer treatment, or maybe cystic fibrosis. But Dave Martin, the former head of R&D at Genentech, is thinking about personalized medicine in a whole new context—for antibiotics.

This concept, at South San Francisco-based AvidBiotics, is still at its earliest stages of development, and the company’s most promising antibiotic candidate probably won’t enter clinical trials until 2013, Martin says. But the program has potential to become a fascinating case study that nudges the healthcare system away from the reactionary, “one-size-fits-all” antibiotic prescribing habit that has led to problems with drug-resistant superbugs.

Here’s how AvidBiotics is thinking about taking on a dangerous bacteria called Clostridium difficile, or “C. diff.” About 3 percent of U.S. adults have C. diff in their guts already, and it usually co-exists just fine with all the other bacteria, causing no problems. But C. diff can become a problem if a patient comes to the hospital in a high-risk situation to get a certain form of surgery, cancer care, or maybe to spend time on a ventilator in the intensive-care unit. Knowing there’s a high risk these patients will get a virulent form of C. diff, the hospital can run a 45-minute diagnostic test from Sunnyvale, CA-based Cepheid to see if the patient is a carrier.

If so, the doctor could someday prescribe a targeted “narrow-spectrum” antibiotic from AvidBiotics that’s designed to kill the C. diff bug, and spare virtually all the normal, healthy bacteria in the gut. By using the drug in a preventive setting, doctors hope to stop the bug before it causes the nasty diarrhea that hospitals dread. An estimated 700,000 people a year are affected by C. diff, and the death rate is estimated at about 6 percent. By attempting to prevent the worst symptoms before they appear, a drug/diagnostic combo has potential to greatly reduce the number of long-term hospitalizations, which can easily cost the healthcare system more than $100,000 per episode.

“An ounce of prevention is really valuable in this disease. If we can prevent this disease in high-risk patients, rather than waiting until patients are very sick, then everybody wins,” Martin says.

This would represent an unusual approach to antibiotics. These drugs today are often prescribed after a patient gets sick. The doctor doesn’t know right away what bug caused it, and he or she has to wait a day or two for a lab culture to provide the answer. Rather than wait around for symptoms to get worse, the doctor often has to act quickly, prescribing a carpet bomb “broad spectrum” antibiotic that kills all kinds of bacteria, both bad and good. Researchers know that this indiscriminate killing of bugs in the gut interferes with the natural equilibrium, and creates problems for people’s immune systems, and nutrient absorption, that can linger for months, Martin says.

AvidBiotics isn’t the only company thinking about a prevention strategy with a narrow-spectrum antibiotic—San Diego-based Optimer Pharmaceuticals (NASDAQ: OPTR) is pursuing a similar strategy with its newly marketed product, fidaxomicin (Dificid). That company, which I reported on earlier this week, is studying its new FDA-approved antibiotic as a way to prevent C. diff infection in patients undergoing bone marrow transplants, where C. diff infections are known to increase the death rate, and cost an average of $130,000 per patient to treat. (Martin says the Optimer drug is an important advance, but he believes his company’s experimental drug is designed to more narrowly hit C. diff, while sparing other forms of bacteria.)

AvidBiotics, which I profiled here in September 2010, is using technology platform it licensed from UCLA to make engineered proteins that hit specific molecular targets on the surface of bacterial cells. These molecules, which the company calls Avidocins, are supposed to … 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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South San Francisco-based Theravance said today that Astellas Pharma, its longtime partner in marketing a new antibiotic, has decided to walk away from its collaboration.

Theravance (NASDAQ: THRX) said Japan-based Astellas has exercised its right to terminate its worldwide license agreement to co-market telavancin (Vibativ) as a once-daily injectable drug for bacterial infections. Astellas has stopped promoting the product, it doesn’t owe a termination payment, and it is still entitled to collect a 2 percent royalty on net sales of the drug over the next 10 years, Theravance said in a statement. Astellas plans to transfer inventory of the drug to Theravance and finish up various clinical, regulatory and medical tasks by March 31.

The drug rights now revert to Theravance, which will consider options on what to do next, including possibly finding another partner, the company said in a statement. The product—Theravance’s only one on the market—won FDA approval in September 2009, and was cleared for sale in Europe in September, but it has never gotten much traction in the antibiotic marketplace. The drug—which is currently hemmed in by manufacturing shortages—generated just $800,000 in royalties from $4.5 million in net sales in the most recent quarter ended Sept. 30. While telavancin was once a big part of the Theravance story, most of its value is now tied up in experimental drugs for chronic obstructive pulmonary disease and other conditions.

Theravance got $65 million in an upfront payment as part of its collaboration with Astellas in 2005, and was eligible for $156 million more in payments for reaching certain clinical and regulatory milestones. The deal allowed Theravance to collect a “high-teens to upper 20s” percentage royalty on sales of the product.

Theravance noted in a regulatory filing today that the manufacturing supply issue for telavancin could be significant. “If these issues at the manufacturer are not promptly resolved, obtaining supply would require identifying and qualifying an alternative manufacturer, which could take 12 to 24 months,” the company said.

“We believe that Vibativ is an important, life-saving medicine, and we appreciate Astellas’ commitment to a smooth transition. We will continue the focus on re-establishing consistent Vibativ product supply. We will assess strategic alternatives for Vibativ, including repartnering, and will provide updates later this year,” Rick Winningham, Theravance’s CEO, said in a statement.

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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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Optimer Pharmaceuticals got approval in the U.S. for its new antibiotic just in time for the Memorial Day weekend, and now it has closed out the year by getting clearance for the drug in Europe.

The San Diego-based biotech company (NASDAQ: OPTR) said today it has gotten clearance from the European Commission to start selling fidaxomicin (Dificlir) as a new treatment for C.difficile infections. Japan-based Astellas Pharma has the rights to market the drug in Europe, through a partnership agreement that paid Optimer $68 million upfront back in February.

Optimer and Astellas are hoping to capitalize on the opportunity to fight C. difficile, a hardy bug that causes diarrhea so severe it can be fatal. Optimer’s drug is designed to specifically kill this bug, while sparing most of the healthy bacteria in the gut. Optimer showed in clinical trials that its treatment cures patients about 90 percent of the time, offering a slight advantage over standard vancomycin. The trials, which followed patients for 30 days, showed that about half as many patients on the Optimer drug had a recurrence, when compared with those who got vancomycin. The drug generated $10.6 million in sales in its first quarter on the U.S. market.

“The European approval is a key step in making fidaxomicin more widely available to patients across the globe to treat this very serious disease,” said Pedro Lichtinger, Optimer’s CEO, in a statement.

The drug is marketed in the U.S. under the name Dificid.

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

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

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

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

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

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

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

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New Haven, CT-based Rib-X Pharmaceuticals announced today that it has filed a registration statement with the SEC for an initial public offering. The company, which is developing antibiotics, has yet to determine the number of shares it will offer or the price range. Deutsche Bank Securities will manage the offering, with assistance from William Blair & Company, Lazard Capital Markets, and Needham & Company.

Rib-X developed a drug-discovery platform based around an atomic, three-dimensional picture of the interactions between drug candidates and the bacteria they are targeting. The company has two antibiotics in clinical trials, one to treat skin infections and the other to treat drug-resistant infections. It has also partnered with French drug giant Sanofi to develop a new class of antibiotics—a deal that could be worth as much as $772 million to Rib-X.

Since its inception in October 2000, Rib-X has raised a total of $208.4 million in private funding. Its investors include Warburg Pincus, MedImmune Ventures, and Oxford Bioscience Partners.

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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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San Diego-based Optimer Pharmaceuticals is new to this idea of being a commercial enterprise, but it did OK in its first quarter with an actual product to sell.

Optimer (NASDAQ: OPTR) said today it generated $10.6 million in net sales of fidaxomicin (Dificid) in the quarter that ended on Sept. 30. The drug, a treatment for dangerous “C.difficile” infections that people get in hospitals, was cleared for sale by the FDA on May 27, but Optimer didn’t actually begin selling the product until July 19. Through the end of September, Optimer said 535 hospitals ordered the product, and its sales reflect 4,335 treatments.

The company spent about $27 million on sales, general and administrative expenses during this product launch period, way above the $4.8 million in SG&A spending it recorded a year earlier, when it was still strictly an R&D operation. Optimer reported a net loss of $26.8 million in the quarter, or about 57 cents a share, which was about 6 cents more than analysts were expecting, according to briefing.com. Shares of Optimer fell 11 percent in after-hours trading.

But the trajectory of demand for the new antibiotic does look encouraging, and the early sales spike can’t be explained entirely by wholesalers stocking up inventory, which they commonly do for new products. Wholesalers shipped 884 treatments to pharmacies and long-term care facilities in August, and 1,400 treatments in September, Optimer said.

Optimer showed in clinical trials that its treatment cures patients about 90 percent of the time, offering a slight advantage over standard vancomycin. The trials, which followed patients for 30 days, showed that about half as many patients on the Optimer drug had a recurrence, when compared with those who got vancomycin.

Optimer has told analysts that it expects to turn profitable after about three years on the market, according to a Sept. 19 report by analyst Eun Yang of Jefferies & Co. Yang forecasted prior to the FDA approval that Optimer could reach $158 million in sales in 2015.

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Connect, the San Diego nonprofit group for innovation and entrepreneurship, says it has selected three finalists in eight categories for the region’s 24th annual Most Innovative New Product (MIP) Awards competition. The 24 finalists were culled from more than 140 nominations submitted, according to a statement from Connect. The finalists in each category are evaluated by San Diego experts and business executives in that category. Winners will be announced at an awards luncheon, set for Dec. 9 at the Hilton La Jolla Torrey Pines.

The finalists in each category are:

Clean Technology

Genomatica, for Process that produces high-volume industrial chemicals from renewable feedstocks.

Noble Environmental Technologies, for proprietary ECOR process to produce environmentally friendly building materials.

Wildcat Discovery Technologies, for electrolytic process that makes environmentally friendly materials.

Communications and IT

Ethertronics, for its Ether 1.2.1 technology for embedded antennas in mobile devices.

Kyocera Communications for Kyocera Echo, a dual-touchscreen smartphone.

Swarmology for Swarm.it, real-time contextual search and marketing technology.

Life Science – Diagnostics and Research Tools

Biocept, for OncoCEE-BR diagnostic screening technology to detect circulating tumor cells.

Life Technologies, for Ion Personal Genome Machine, technology for semiconductor-based DNA sequencing.

Targeson, for ultrasound contrast imaging of VEGFR2 receptor on lining of blood vessels.

Life Science – Medical Products

Hypnoz Therapeutic Devices, for Jaw Elevation Device used to maintain open airway during medical procedures.

IOS Technologies, for technology that enables dental professionals to create digital impressions and 3-D models.

Optimer Pharmaceuticals, for fidaxomicin (DIFICID), a new antibiotic treatment for C. difficile.

Software

FICO, for Falcon Fraud Manager 6 Analytics, used to detect payment card fraud.

MOGL for MOGL, online restaurant mobile rewards program.

SwoopThat, for online technology that helps college students find cheapest online price for every book they need to buy.

Hardware and General Technology

Aculon, for Aculon AL-X and Aculon H1-X products, nano-scale films and coatings for a variety of survaces.

LifeProof, for LifeProof case for the iPhone 4.

Memjet, for high-speed inkjet printing technology.

Action and Sport Technologies

Hydroflex, for flexing surfboard design.

KVA Stainless, for technology to produce seamless stainless steel tubing, pipes, stamping, and forming.

TaylorMade Golf, for R11 Driver with movable weight than enables golfers to customize to their swings more precisely.

Aerospace and Security Technologies

Geodetics, for positioning and navigation technology for dynamic platforms offering a variety of processing, global positioning system (GPS) and inertial measurement unit (IMU) options that can be configured to cover a broad performance spectrum.

Langford & Carmichael, for ScenGen, a software program that generates all possible scenarios for a given situation at a very high speed.

MicroPower Technologies, for MPT2500 Rugged-i, solar-powered wireless video surveilance camera technology.

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This week in New England we’ve seen financings and data updates from drug developers, as well as an acquisition in the life sciences tools space.

—An SEC filing revealed that New Haven, CT-based BioRelix has brought in $3.6 million in new funding, as part of a round that could hit $5.3 million. The company is developing antibiotics against RNA drug targets known as RiboSwitches.

—Waltham, MA-based Syndax Pharmaceuticals has reported that its lead drug had performed well in a Phase 2 breast cancer trial. Syndax had previously reported positive data of the drug, entinostat, in a lung cancer trial two months ago, and reported the breast cancer data at the American Society of Clinical Oncology (ASCO) Breast Cancer Symposium this week.

—Cambridge, MA-based Aura Biosciences raised $4.5 million in financing, bringing the company’s total funding pot to $10 million in two years of operating. The startup, which develops tiny protein cells for delivering cancer drugs directly into tumors, has not named the specific investors in the round, but noted they are individuals who are pharmaceutical industry CEOs or entrepreneurs. The nano-particles look like viruses but are engineered to prevent the triggering of dangerous immune reactions.

—Caliper Life Sciences (NASDAQ: CALP) of Hopkinton, MA, will be bought by Waltham-based PerkinElmer for $600 million in cash, at $10.50 per share. Caliper makes imaging and detection technology.

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San Diego-based Trius Therapeutics, the developer of a new antibiotic, said today it has secured its first big commercial partnership to market the experimental drug around the world.

Trius (NASDAQ: TSRX) said today that it has provided an exclusive license to Germany-based Bayer to develop and market torezolid phosphate in China, Japan, Africa, Latin America, the Middle East, and all other countries in Asia except North and South Korea. Bayer agreed to pay $25 million in upfront cash, pay one-fourth of the development expenses to secure regulatory approvals, provide $69 million in future milestone payments, and deliver Trius a double-digit percentage royalty on sales. Trius retains 100 percent ownership of the drug in the U.S., Canada, and Europe.

Bayer Healthcare’s chairman, Jorg Reinhardt, played up the China angle in his prepared statement. “Bacterial infectious diseases represent one of the largest therapeutic areas in China and continue to grow rapidly there and in other emerging markets,” he said.

The Trius drug is designed to be given as either an intravenous injection in the hospital, or as an oral pill, to fight acute skin infections and pneumonia. The treatment is in the third and final stage of clinical trials usually required for FDA approval. If it goes on to win regulatory approval, the Trius drug would be a new member of the class of oxazolidinones, which includes Pfizer’s billion-dollar hit, linezolid (Zyvox).

Shares of Trius climbed 3.3 percent to $8.05 at Noon Eastern today on news of the Bayer deal.

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

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

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

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

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

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

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New Haven, CT-based Rib-X Pharmaceuticals announced today that it could receive about $772 million from Sanofi (NYSE: SNY) under a new research collaboration and option for Sanofi to license novel classes of antibiotics from Rib-X’s RX-04 program for the treatment of resistant Gram-negative and resistant Gram-positive infections. Sanofi paid $10 million upfront and could pay up to $9 million in near-term research milestones, as well as other clinical and commercialization milestones and royalties. Rib-X could also receive $86 million in development and regulatory milestones and $100 million in commercial milestones for each product identified in the collaboration—Sanofi is targeting four for now, but there is no upper limit, the companies said.

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Turns out that Optimer Pharmaceuticals won’t have to spend the holiday weekend on pins and needles. The San Diego-based biotech company got its wish today, as the FDA approved Optimer’s first new product for sale in the U.S.

The FDA cleared fidaxomicin (Dificid) as a new treatment for C. difficile, a hardy bacterial infection that hangs out in the nooks and crannies of hospitals, and causes diarrhea so severe it can be fatal. Optimer’s drug is designed to specifically kill this bug, while sparing most of the healthy bacteria in the gut. Optimer showed in clinical trials that its treatment cures patients about 90 percent of the time, offering a slight advantage over standard vancomycin. The trials, which followed patients for 30 days, showed that about half as many patients on the Optimer drug had a recurrence, when compared with those who got vancomycin.

Hard data on how many people are affected by “C.diff” is hard to obtain, partly because it’s hard to diagnose, and partly because hospitals don’t really like to advertise the fact that so many people get these dangerous infections in their buildings. Health officials estimate “C.diff” kills between 15,000 and 30,000 people in the U.S. each year, many of them elderly. One analyst who follows Optimer, Eun Yang of Jefferies & Co., has estimated the product could generate $158 million in sales in 2015.

The FDA issued a just-the-facts press release on its approval, just before knocking off for the holiday weekend. You can read the full prescribing information, which describes how the Optimer drug is superior to vancomycin.

“In recent years, many in the infectious disease community have seen an increase in the number of cases of people with a C. difficile infection,” said Edward Cox, director of the office of antimicrobial products in the FDA’s Center for Drug Evaluation and Research, in a statement. “Dificid is an effective new treatment option for patients who develop Clostridium difficile-associated diarrhea.”

Optimer hasn’t yet issued its own statement, and investors will surely want to comb carefully through the detailed prescribing information approved by the FDA, which doctors and insurers will rely on for guidance on how to use the drug. Optimer has said it plans to discuss the price of the product with investors next week.

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At least a few people in San Diego are sitting tight today at work, unable to get a jump on the holiday weekend.

That’s the case at San Diego-based Optimer Pharmaceuticals (NASDAQ: OPTR), which is awaiting word from the FDA on whether its first drug can be cleared for sale in the U.S. The agency’s deadline to complete its review of Optimer’s fidaxomicin (Dificid) is Memorial Day, Monday May 30, but since that’s a federal holiday, it’s possible the good folks in Rockville, MD will deliver their verdict before the holiday weekend kicks off today.

This is a big moment for Optimer, although not a very suspenseful one. The company won a 13-0 endorsement from an FDA advisory panel last month, which recommended its new antibiotic be approved for treating C. difficile, a sometimes deadly bacterial infection people get in hospitals. If approved, this will be Optimer’s first approved product after spending 13 years and more than $175 million on R&D.

The company, which has about 100 employees now, plans to double in size this year as it seeks to commercialize a product with potential to generate $158 million in sales in 2015, according to analyst Eun Yang of Jefferies & Co.

“For us, it’s a dream come true. There are hundreds or even thousands of biotech companies that never see their product all the way through to the market,” says Optimer CEO Pedro Lichtinger. “For us to get the product to this stage and carry it to the commercial stage, it’s fantastic.”

Pedro Lichtinger

C.diff, a hardy bug that lurks in hard-to-reach surfaces at hospitals and nursing homes, is estimated to kill between 15,000 and 30,000 people in the U.S. each year, many of them elderly. The disease, which is hard to diagnose properly, is currently treated with a common generic drug called metronidazole or an oral form of vancomycin (Vancocin) from Exton, PA-based Viropharma (NASDAQ: VPHM).

Optimer’s drug is designed to specifically kill the C.diff bug, while mostly sparing healthy bacteria in the gut. Optimer showed that its antibiotic can cure patients a little more than 90 percent of the time, which was slightly better than the standard vancomycin. The trials, which followed patients for 30 days, showed that about half as many patients on the Optimer drug had a single recurrence, when compared with those who got vancomycin.

If the FDA delivers a positive verdict today, or sometime early next week, the big questions will be about the drug’s label, and its price. The FDA advisory panel last month had some debate about the meaning of the word recurrence, and shortly after the panel, Lichtinger said Optimer would have to work carefully with the FDA on language to describe the drug’s benefit fairly and precisely, based on clinical studies. Optimer is hopeful that the prescribing label, which doctors and insurers depend on for guidance, will say something about how the new drug offers a “superior and sustained clinical response,” Lichtinger says.

Once approved, Optimer plans to announce the price … Next Page »

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We’ve been seeing some big life sciences deals in recent weeks, the latest being Nestlé’s acquisition of San Diego’s Prometheus Labs. Here’s our wrap-up of the past week.

—Switzerland’s Nestlé Health Science agreed to acquire San Diego’s Prometheus Laboratories in what one analyst estimated as a $1.1 billion deal. The Nestlé subsidiary has been on a buying spree, acquiring CM&D Pharma, which is focused on cancer and inflammatory bowel diseases, in February; and Vitaflo, which develops treatments of inherited metabolic diseases, last August. San Diego’s Prometheus, which has been in registration for an IPO since late 2007, also is a specialty pharma and diagnostics company focused on cancer and gastrointestinal disorders.

—San Diego-based Trius Therapeutics (NASDAQ: TSRX), which is developing a new generation of antibiotics for treating multi-drug resistant infections, surprised me yesterday by disclosing plans to raise $30.2 million through a private stock placement. I recently talked with Trius CEO Jeff Stein about the company’s travails in raising capital through an IPO last year, and how government R&D contracts are supporting the biotech’s early stage drug development.

—La Jolla Pharmaceutical has been an icon of San Diego’s biotech community, but preliminary data from a preclinical study of a compound the company has been studying for repairing scar tissue could spell the end of the company’s 21-year run. In a statement Monday, the biotech says its LJP1485 compound will not show a statistically significant improvement compared to a placebo. CEO Dierdre Gillespie told me in an e-mail yesterday that it will still be a few days before another update is available. The biotech has raised $428.1 million without producing any commercial therapies, according to The San Diego Union-Tribune.

—San Diego-based ResMed ( NYSE: RMD), which provides technology for treating … Next Page »

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San Diego’s Trius Therapeutics, like Zogenix and Pacira Pharmaceuticals, was among the local IPOs that got caught in the jaws of the amazing life sciences valuation-shrinking machine of 2010.

Trius initially filed its IPO in late 2009 to raise as much as $86 million by March 2010, so the company could price its shares in time to fund its planned Phase 3 clinical trials of torezolid phosphate, a promising antibiotic for treating acute, methicillin-resistant skin infections. Torezolid is the company’s lead drug candidate, and as Trius CEO Jeff Stein told me recently, the company was working on its IPO and finalizing the protocols for its late-stage clinical trials at roughly the same time.

As fate would have it, though, the FDA decided in late February to change its guidelines for such studies—necessitating a substantial overhaul of the company’s application for a special protocol assessment (SPA). The SPA process is designed to serve as a kind of roadmap for both the company and federal drug regulators, and sets out how data from the trial can be used as the primary basis for a new drug application.

Jeff Stein

Reaching an agreement on the revised protocols took until mid-June, forcing the company to delay its IPO into what Stein called the summer doldrums. Stein says Trius didn’t want to postpone the IPO any further, as the company needed the capital to fund the planned clinical trials. Trius also is on a tight timeline for launching the new drug, which was tied to other steps in the company’s overall strategy.

“We made the right decision,” Stein said. “The fact that we got it done at all is a testament to the strength of the [torezolid] story, the quality of our management team, and everything else.”

The company paid a price, though, when underwriters chopped the price and increased the number of Trius shares, leading the company to generate about $30 million less than expected in its IPO. Instead of generating close to $80 million, Trius raised … Next Page »

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We had a grab bag of life sciences-related coverage this week, with a big device company acquisition, some wild ideas for global health, and a whole lot of focus on biofuels.

—Kleiner Perkins Caufield & Byers never has done much investing in the Northwest from what I can tell, but this week I came across a quiet company in South Lake Union that the fabled VC firm built to help convert organic waste into clean-burning natural gas. The big idea at this company, called Harvest Power, is to develop what you could call a giant concrete stomach.

—While biofuel entrepreneurs are brimming with enthusiasm about weaning the world off fossil fuels, I thought it would be helpful to get a bit of a reality check from a top local scientist who’s been thinking hard about this problem—Nitin Baliga of the Institute for Systems Biology. Baliga will also provide some brief welcoming remarks at the next Xconomy Seattle event on May 19, titled “Separating Hype from Reality in Alternative Fuels.”

—This week, I spent a fair bit of time recruiting new speakers to flesh out the agenda for the event mentioned above. The new additions, who will each provide 4-minute “burst” talks about their approach to alternative fuels, are Kelly Ogilvie of Blue Marble Energy, Hoby Douglass of General Biodiesel, and Jeff Surma of S4 Energy Solutions.

—Seattle-based Dendreon (NASDAQ: DNDN) came out with its first-quarter earnings report, and there were no big surprises. The company hit its forecast for sales in the first three months, has started scaling up sales in April now that it has more available manufacturing capacity, and reiterated that it plans to sell $350 million to $400 million worth of sipuleucel-T (Provenge) for prostate cancer patients in 2011.

—One of the big dreams in biofuels is that someday we’ll have open ponds in the desert, full of fast-dividing algae that are genetically modified to spit out the maximal amount of oil. Ned David of Arch Venture Partners has pushed that idea forward as a co-founder of Sapphire Energy, but a couple years into that endeavor, he realized he needed to capture a whole heck of a lot of carbon dioxide from the air in order to feed the algae at companies like Sapphire. The result is his latest startup, Kilimanjaro Energy, which I profiled this week.

—Seattle Genetics (NASDAQ: SGEN) got a big date to circle on the calendar—August 30. That’s when the FDA has agreed to complete its review of the company’s application to start marketing brentuximab vedotin (SGN-35) in the U.S. The agency agreed to a faster-than-usual six-month review schedule for this drug because of its groundbreaking potential against a couple deadly forms of cancer.

—The Bill & Melinda Gates Foundation has taken some flack for its approach to funding big science ideas in the past, which some contended was too heavily weighted toward big-money, long-term projects. The foundation has sought ways to make a bigger impact by tilting more of its research portfolio to really early-stage, out-of-the-box proposals that get $100,000 to sink or swim, which discovery director Chris Wilson explained in our interview.

—Considering a career in biotech? I’m not so sure it’s a good idea to encourage young people to dive in, as you can see in this week’s BioBeat. The action is clearly in computer science, and unless something pretty dramatic happens in government research funding, or pharma/biotech business models, it looks like it will stay that way for quite some time.

—Seattle-based Oncothyreon (NASDAQ: ONTY) pulled in more than $40 million in a new stock financing. This will provide a lot more fuel for the company to pursue development of the cancer drugs in its pipeline other than Stimuvax, the immune-booster that is being developed in partnership with Merck KGaA.

—GE Healthcare made a pretty sizable acquisition last week when it took over Issaquah, WA-based Applied Precision. The local operation, which has 130 employees, makes super high resolution microscopes with software and data visualization tools for biomedical researchers.

—Lastly, Vancouver, BC-based Indel Therapeutics reported that it raised $1.4 million in a Series B financing to support its development of new antibiotics. Things have been pretty quiet lately on the financing front—makes me wonder if there are some big ones in the works.

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Optimer Pharmaceuticals spokeswoman Christina Donaghy was killed in a car crash Sunday in Cardiff-by-the-Sea, CA, a suburban coastal community about 25 miles north of San Diego, according to a report today in The San Diego Union-Tribune. Donaghy, 43, was in the back seat of a 1974 Porche Targa when the driver lost control on Manchester Avenue and collided with a Chevy S-10 pickup. A man believed to be the driver was seriously injured and another man in the Porche also was killed. Two people in the pickup also were injured. Optimer is awaiting an FDA ruling on its new drug application for fidaxomicin, an antibiotic for treating C. difficile infections.

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