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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—After naming former Boston Scientific executive Fred Colen as CEO last month, San Diego’s BeneChill raised nearly $15 million in a round that’s targeting a total of $25.6 million, according to a recent regulatory filing. BeneChill, founded in 2004, has been developing therapeutic hypothermia medical products. The company’s European headquarters is in Lausanne, Switzerland, and BeneChill has European approval to sell its intra-nasal cooling system—which induces therapeutic hypothermia immediately following cardiac arrest.

—San Diego’s Sotera Wireless has been busy getting its ducks in a row. After applying for FDA approval of its vital signs wireless patient care monitoring technology in August, Sotera raised $12.2 million last week in Series D financing. Sotera said it also signed a commercial partnership agreement with Kansas City, MO-based Cerner, the giant health IT systems provider. If all goes as planned, funding from the current financing round will be used to support the launch of Sotera’s “ViSi Mobile System” in early 2012.

—Melinda Richter, the founder and CEO of San Francisco-based Prescience International sat down with me to discuss her plans for the life sciences incubator going in at Johnson & Johnson’s pharmaceutical R&D facility in San Diego. The J&J facility, known as the Janssen Labs at San Diego, will host 18 to 20 early stage startups. Richter, who will manage the facility under a contract with Janssen, said she wants to dramatically lower the costs for starting a life sciences company.

—Optimer Pharmaceuticals (NASDAQ: OPTR) said it won approval to start selling its new antibiotic, fidaxomicin (Dificlir) in Europe as a new treatment for C. difficile infections of the gut. Japan’s Astellas Pharmaceuticals has the rights to … Next Page »

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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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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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The long Memorial Day weekend made for a short roundup of life sciences news this week. So we’ll be brief.

—The FDA approved Optimer Pharmaceuticals‘ drug application for fidaxomicin (Dificid) as a new treatment for the nasty intestinal infection caused by the Clostridium difficile bacterium. Optimer says its treatment cures patients about 90 percent of the time, and fewer patients return with problems than patients who get vancomycin, the standard antibiotic.

—Optimer officials said, though, that fidaxomicin will cost $2,800 for a 10-day course of capsules to treat potentially deadly cases of C. difficile. That’s about twice as much as vancomycin, the only other government-approved therapy for the infection, according to The San Diego Union-Tribune.

—A federal judge in San Diego issued a temporary restraining order against Indiana’s Eli Lilly (NYSE: LLY) that was sought by San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN). Amylin sued Lilly for violating their marketing agreement for Amylin’s diabetes drug exenatide after Lilly signed a similar marketing deal with Germany’s Boehringer Ingelheim for a rival diabetes drug. A Lilly executive called the TRO “disappointing” in a statement and said, “Amylin’s allegations against Lilly are entirely without merit and we fully expect to prevail in this litigation.”

—San Diego’s Orexigen Therapeutics (NASDAQ: OREX), said it will hold a live webcast and conference call early Friday to provide an update on its requested regulatory approval for its weight loss drug, a combination of naltrexone and buproprion (Contrave). The announcement prompted a buying spree on Wall Street that pushed Orexigen shares up 18 percent, or 51 cents, to $3.34. The U.S. Food and Drug Administration turned back Orexigen’s new drug application in February, saying Orexigen and its Big Pharma partner, Japan’s Takeda Pharmaceutical, need to do some more clinical studies of the drug’s effects on heart function.

—San Diego’s Somaxon Pharmaceuticals is fighting efforts by four generic drug-makers to invalidate Somaxon patents that are supposed to protect its sleeping pill doxepin (Silenor) through 2027. The four companies want to sell lower-cost generic versions of doxepin.

—Polaris Venture Partners, which counts San Diego’s Fate Therapeutics and MedVantx among the life science startups in its portfolio, is opening an office in Palo Alto, CA—after closing its shop in Seattle. Dave Barrett, a general partner at the Boston-based VC firm, told Bob it became more and more important for Polaris to have a strong base of operations in the Bay Area.

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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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The past week was big for life sciences news in San Diego, with acquisitions, funding deals, and important advances in new antibiotics grabbing much of the attention. We’ve got it rounded up for you here.

—An FDA advisory panel voted 13-0 in favor of recommending approval of a new antibiotic that San Diego’s Optimer Pharmaceuticals (NASDAQ: OPTR) developed to combat C. difficile, a dangerous bacterial infection people usually get in hospitals. The panel’s recommendation means Optimer’s drug, fidaxomicin, will likely be approved by the FDA, though the agency is not required to follow the recommendation. The company has spent nearly $200 million developing the drug over the past decade.

—The day after the panel vote, Optimer announced an agreement with Lexington, MA-based Cubist to co-promote fidaxomicin, sales of which could reach $250 million a year, according to some analysts. Optimer could pay Cubist as much as $47.5 million over the two-year period covered by the agreement. After the deal was announced Optimer shares fell by 81 cents, or almost 6 percent, to close at $12.99 a share.

—Orexigen Therapeutics reported Monday that its experimental diet pill, naltrexone SR/bupropion SR (Contrave), didn’t affect the blood pressure of people who took the drug as part of a late-stage study. Orexigen presented its data at the American College of Cardiology conference in New Orleans, saying normal 24-hour blood pressure patterns were seen in 182 obese people who took the drug. The results were important because the drug failed to win FDA approval in February, and the agency said Orexigen needed to do more studies of the drug’s effects on heart function.

—While there is no shortage of ideas for new ways to fight dangerous bacterial infections, Luke wrote in his BioBeat column that the lack of innovation in the antibiotics field is worrisome. By coincidence, several San Diego leaders in antibiotics R&D are holding a news conference this afternoon at the Sanford-Burnham Medical Research Institute on antimicrobial resistance to … Next Page »

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San Diego-based Optimer Pharmaceuticals (NASDAQ: OPTR) won the blessing of an FDA advisory panel today for its novel antibiotic, but now the big issue will likely be how the benefit of the drug will be communicated to doctors and patients.

Advisors to the FDA at a meeting in Silver Spring, MD voted 13-0 in favor of Optimer’s fidaxomicin, saying it has demonstrated it is safe and effective against a dangerous bacterial infection people get in hospitals known as C. difficile. But the panel was much less certain on a second question posed by the FDA, on whether Optimer’s antibiotic has proven a benefit against recurrences of the dangerous bug. The panel voted 7-6 against Optimer on that question, after having a discussion about how to properly define recurrences.

The FDA usually follows the advice of its expert panels, although it isn’t required to do. The agency’s deadline to complete its review of the Optimer drug is May 30.

Optimer CEO Pedro Lichtinger, reached by cell phone after the advisory panel’s vote, was quite upbeat. If the FDA clears the new antibiotic for sale, it will be Optimer’s first approved product in the U.S.

“This is an outstanding day for patients, healthcare providers and of course for Optimer,” Lichtinger says. “This drug is going to get approved.”

Optimer had argued that its antibiotic offered an advantage in terms of preventing recurrences of “C.diff,” which often lead to complex, costly, and risky cases of hospitalization. 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.

Pedro Lichtinger

The Optimer trials weren’t designed to ask how patients fared in cases of more than one recurrence, which prompted much discussion on the panel about whether the company can actually say it has shown a benefit against recurrence, Lichtinger says. This means that the company and the FDA are going to spend some time working on the best terminology to accurately describe the benefit seen from the Optimer drug, he says.

“There’s no question this is a superior product at 30 days post-treatment,” Lichtinger says. “We’ll engage with FDA on the right language so the superiority can be properly communicated.” He added: “Using the word recurrence to describe its benefit was confusing” to some of the panel members.

Optimer’s drug has some other features that will help it differentiate itself in the market. The drug, an oral pill, is designed to be quite different than the standard vancomycin. The Optimer drug is a “narrow-spectrum” antibiotic, meaning it is specifically designed to kill “C.diff” without wiping out all kinds of other so-called “good” bacteria in the gut. The drug also stays in the gastrointestinal tract where it needs to be active, and doesn’t get absorbed, where it can cause side effects.

Stock trading in Optimer was halted today, which the NASDAQ sometimes does for development-stage biotech companies facing such critical moments at FDA public hearings. The stock closed yesterday at $13.80 a share, heading into the FDA committee meeting.

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There are lots of exceptions to the rules in the biotech business, and a big one jumped out me this past week, related to antibiotics.

One day, Reuters ran a story about the overall abysmal state of the world’s pipeline of new antibiotics. Next day, there were reports about how San Diego-based Optimer Pharmaceuticals appears poised to sail through a meeting scheduled for tomorrow of an FDA advisory panel that will size up the merits of its new antibiotic.

Having followed a number of antibiotics developers for the past few years, it strikes me there is no shortage of ideas for fighting dangerous bacterial infections. There are interesting companies all over the map: South San Francisco companies like Achaogen and Theravance (NASDAQ: THRX); Watertown, MA-based Tetraphase Pharmaceuticals and Lexington, MA-based Cubist Pharmaceuticals (NASDAQ: CBST); New Haven, CT-based Rib-X Pharmaceuticals; and a pair of San Diego companies, Trius Therapeutics (NASDAQ: TSRX) and Optimer (NASDAQ: OPTR).

There is government funding available to support this work—Achaogen alone has raked in $155 million in support from government and philanthropic support, not to mention $95 million from venture capitalists. The drugs themselves often perform relatively consistently from early-stage to late-stage studies. And when they work, they can make sizable amounts of money—see Pfizer’s linezolid (Zyvox), which generated $1.18 billion in worldwide sales last year.

Yes, there has been some shifting of regulatory standards at the FDA, which put a crimp in many antibiotic business plans over the past year. But given all the forces properly aligned to support antibiotics, this shouldn’t be a classic case of market failure. And yet here we are, with only five new antibiotics approved by the FDA from 2003 through 2007, as Andy Pollack reported in the New York Times in November. FDA commissioner Margaret Hamburg has said the number of new antibiotics in development is “distressingly low.” Only five of the 13 biggest Big Pharma companies work on antibiotics now, which partly reflects their enduring fixation on blockbusters that can move the financial needle at their overly bloated organizations (but that’s another story, covered here last week.)

The lack of innovation in the antibiotics field is worrisome. Public health officials fret that because of the overuse of the antibiotics on the market today, we are encouraging the rise of more drug-resistant “superbugs” like the sometimes deadly MRSA and C.difficile. More, undoubtedly, will evolve in the future.

This is really just a hunch, but I would argue that a big part of the problem here is an overall lack of will in the biotech industry to create new antibiotics. While everybody talks about the hot new breast cancer drugs or the new thing for diabetes—which are sort of like biotech’s versions of the iPad and iPhone in terms of glamour—the only people who seem really interested in antibiotics are the people at those companies mentioned above. There have been some painful regulatory … Next Page »

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There was good news and bad news from San Diego’s life sciences community over the past week. Here’s our recap for you.

—San Diego-based Illumina (NASDAQ: ILMN) said it shipped a record number of DNA mapping systems during the fourth quarter that ended Jan. 2. With demand for its genetic equipment soaring, Illumina said its profit was three times the same quarter last year. Illumina also disclosed plans to relocate its 1,100 San Diego employees to the San Diego campus of Biogen Idec, the Cambridge, MA-based company that is pulling up stakes in San Diego.

—IntegenX of Pleasanton, CA, acquired Carlsbad, CA-based GenVault for an undisclosed amount, and raised $15.6 million in new capital in a round led by existing investor Domain Associates. IntegenX makes automated sample preparation systems for genetics laboratories. GenVault produces bio-sample storage systems that do not depend on refrigeration.

—Orexigen Therapeutics (NASDAQ: OREX) eliminated 23 jobs, or about 40 percent of its workforce, after the FDA rejected the company’s request to sell the obesity drug Contrave in the United States. Orexigen said it expects the cuts will save $5 million a year.

—San Diego-based Leading Ventures‘ co-founder and senior managing director John Rodenrys took me to the living tissue laboratory of UC San Diego bioengineering professor Geert Schmid-Schönbein to better explain the firm’s venture funding strategy. Leading Ventures is providing funding for two startups based on technologies developed in Schmid-Schönbein’s lab.

—San Diego-based Optimer Pharmaceuticals (NASDAQ: OPTR) disclosed a deal with Japan’s Astellas Pharma that gives Astellas exclusive rights to market its treatment for C. difficile infections in Europe, and certain countries in the Middle East, Africa, and the Commonwealth of Independent States. Optimer filed for FDA approval of the drug fidaxomicin in late November.

—Physio-Control of Redmond, WA, and BeneChill of San Diego formed a strategic partnership to sell a portable system that BeneChill developed for use by emergency medical technicians that chills the brains of people who have suffered a stroke, heart attack, or traumatic brain injury. The new partners plan to start marketing the RhinoChill System in Europe this quarter.

—San Diego-based Altair Therapeutics shut down after the startup’s lone drug candidate for asthma failed in a mid-stage clinical trial. Altair was a spinoff from Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS), which has re-acquired Altair’s assets, blocked further clinical development, and dissolved Altair.

—San Diego’s Genomatica, which is developing sustainable chemicals technology, signed a strategic agreement with Houston’s Waste Management to develop ways of making basic chemicals from landfill gas and other sources.

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San Diego-based Optimer Pharmaceuticals has found a partner to help market its most important drug candidate outside the U.S.

Optimer (NASDAQ: OPTR) is announcing today it has struck a deal with Japan-based Astellas Pharma in which Astellas gets exclusive rights to market fidaxomicin in Europe, plus parts of the Middle East, Africa, and the Commonwealth of Independent States. Astellas agreed to pay $68 million upfront, another $156 million in milestone payments, plus a tiered double-digit percentage royalty on sales in the territory. Astellas will pay all the development expenses in its territory, and handle the fidaxomicin application for approval with European regulators.

The deal is the latest boon for Optimer, which has had some wind in its sails lately. The company filed for FDA approval of fidaxomicin in late November, asking U.S. regulators to clear its drug as a new option for treating potentially deadly infections with “C.difficile” bacteria. The company sought, and the FDA has granted, a faster than usual six-month regulatory review, which the agency sometimes offers to treatments with lifesaving potential. Last week, Optimer got the attention of a key physician audience, when results from one of its pivotal clinical trials for fidaxomicin were published in the New England Journal of Medicine. Since “C.diff” doesn’t often make headlines, getting that attention was critical for Optimer, as it lays the groundwork to market the drug on its own in the U.S.

If the drug wins regulatory clearance, it will be Optimer’s first marketed product.

“We expect the Astellas collaboration will help Optimer realize the full potential of fidaxomicin,” said Lichtinger said in a statement.

The next big step for Optimer comes on April 5, as it is scheduled to appear before an FDA advisory panel, to make its case in favor of the new antibiotic. The FDA then has a deadline of May 30 to complete its review, and determine whether to allow the product on the U.S. market.

Optimer plans to hold a webcast conference call at 9 am Eastern/6 am Pacific to discuss the new Astellas collaboration.

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The Thanksgiving holiday helped to keep activity in San Diego’s life science companies at minimum levels over the past week. Still, what we picked up was interesting reading. Judge for yourself.

—San Diego’s Optimer Pharmaceuticals (NASDAQ: OPTR) filed a new drug application with the FDA for fidaxomicin, the drug it developed to treat patients with Clostridium difficile infection, the most common cause of diarrhea in hospitals. Optimer also asked for a priority review that takes six months instead of the usual 10. If granted, the FDA could issue a decision as early as the second quarter of 2011.

—San Diego’s Histogen said it has raised $10 million in Series A funding, which has enabled the life sciences startup to mount some mid-stage clinical trials of its regenerative medical treatements. The funding represents a comeback of sorts for Histogen, which was forced to lay off all 36 employees last year after rival SkinMedica of Carlsbad, CA, filed a patent infringement lawsuit against the startup.

—A life sciences industry survey by San Diego’s Biocom, Pricewaterhouse Coopers, and MassBio found that U.S. Food and Drug Administration officials are becoming more likely to change their position during the latter stage of the product review process. Sixty-three percent of the 50 companies participating in the study said the FDA had changed its position during at least one review, compared to 40 percent who made similar comments in a previous survey conducted in 2006.

—Aileron Therapeutics of Cambridge, MA, got exclusive rights to “click” chemistry technology that Nobel laureate K. Barry Sharpless developed at The Scripps Research Institute in San Diego. Click chemistry generates substances quickly and reliably by joining small reactive molecular building blocks together selectively to form extremely tight bonds. Financial terms were not disclosed.

—Roche terminated its collaboration and licensing agreement to develop a new treatment for hepatitis C with San Diego’s Ligand Pharmaceuticals (NASDAQ: LGNDD). Ligand and the Swiss pharmaceutical giant signed the deal two years ago.

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San Diego-based Optimer Pharmaceuticals has spent more than $200 million and a dozen years of effort to get to the point where it can ask the FDA to clear its first product for sale on the U.S. market. And that’s the position Optimer finds itself in now.

Optimer (NASDAQ: OPTR) is announcing today that it has completed its new drug application filed with the FDA, which asks regulators to approve fidaxomicin as a new treatment for a dangerous bacterial infection known as Clostridium difficile, or “C.diff” for short. This particularly nasty bug causes awful diarrhea, the kind that can lead to severe dehydration, inflammation of the colon, hospitalization, and even death. The company is seeking a faster-than-usual six-month regulatory review, instead of the usual 10-month period, which the FDA sometimes provides for potentially lifesaving new therapies.

If the FDA clears this new therapy for sale, it would become Optimer’s first marketed product and the first new therapy for this dangerous hospital-based infection in about 25 years. 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 application to the FDA is based on clinical trials that show it is about equal to vancomycin at killing the bug initially, but that its real advantage is in reducing the rate of recurrences, particularly in vulnerable subpopulations like the elderly, those taking other antibiotics, and in patients with weakened immune systems.

Pedro Lichtinger

“When I was getting started at Pfizer, all the managers who joined when they were younger had a dream to bring to the market highly effective products that will benefit patients. That dream has stayed with me,” says Pedro Lichtinger, Optimer’s CEO. “When I retired from Pfizer, what I saw in Optimer was an opportunity to make a major advancement in medicine, that was at the same time cost-effective and would do a lot of good for thousands of patients.”

Partly because this disease doesn’t generate many scary headlines, Optimer tends to keep a pretty low profile. But the data to support its application looks like a pretty solid bet. It reached its primary goal in a pivotal clinical trial of about 600 patients in November 2008, and then confirmed … Next Page »

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Optimer Pharmaceuticals has some bad news out today. The San Diego-based developer of antibiotics said it has halted a study of an experimental antibiotic for traveler’s diarrhea after a higher than expected rate of skin rashes. Shares of Optimer (NASDAQ: OPTR) fell more than 15 percent after the news broke.

The company made the disclosure today in an 8-K filing with the Securities and Exchange Commission. Optimer said it informed the FDA yesterday that it was halting a study that looked at interactions between prulifloxacin (Pruvel) and antacids. The rashes were “mild in severity, and required little or no treatment and all resolved completely,” the company said in the filing. Optimer is now going to investigate the cause of the rashes, and said it can’t estimate how long it might delay its new drug application for the product, which has already passed a pair of pivotal Phase III trials which didn’t show any increased rates of rashes.

This is certainly an unhappy surprise for Optimer, but it would be a stretch to call it devastating because this isn’t the company’s primary asset in development. Most of Optimer’s value is based on its lead antibiotic, fidaxomicin, for deadly “C.diff” infections that people get in the hospital. Optimer’s strategy with its second drug, which then-CEO Michael Chang explained to me in January 2009 feature story, was to create a more potent alternative to Bayer’s ciprofloxacin (Cipro). The total market up for grabs isn’t huge—an estimated $200 million. Optimer hoped to capture some of that to provide a secondary revenue stream, the company said at the time.

Both the Bayer drug and Optimer’s candidate are members of the antibiotic class known as fluoroquinolones, which are known to sometimes cause rashes, Optimer said in its statement today. You can read more about this compound’s past clinical trial results by checking a summary on the Optimer website.

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Either I have too much time on my hands, or the first half of today’s headline is pretty close to a Haiku in English. Don’t grade me. Let’s just move on with the roundup of life sciences news.

—We briefly noted that San Diego’s Conatus Pharmaceuticals acquired Idun Pharmaceuticals for an undisclosed sum from Pfizer, which has been operating the San Diego-based subsidiary since 2005. But PE Hub’s Dan Primack cogently unraveled how Conatus, which was formed by executives who left Idun, likely paid less than 10 percent of what Pfizer paid to acquire Idun just five years ago.

—Plans by Complete Genomics to raise as much as $86 million through an IPO could lead to a payout for San Diego’s Enterprise Partners Venture Capital, which is among several VCs that invested in the Mountain View, CA, company. Complete Genomics has been developing its own methodology for inexpensive gene sequencing.

—Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) and Cambridge, MA-based Genzyme (NASDAQ: GENZ) said their drug for people with severely high cholesterol passed a pair of key clinical trials. The companies are preparing to seek clearance from regulators next year to begin selling the drug in the U.S. and Europe.

—Ryan talked with two former Vertex Pharmaceuticals (NASDAQ: VRTX) executives, Roger Tung and Rich Aldrich, to unravel how Eli Lilly walked away from nearly its entire stake in the drug telaprevir, the hepatitis C treatment that is nearing approval as a treatment for the chronic liver disease. Today, telaprevir represents a potential multibillion-dollar molecule for Cambridge, MA-based Vertex, which has significant operations in San Diego.

—OK, the Trius Therapeutics IPO was ugly—but the important thing is it got done. The San Diego biotech, which is developing technology to create a class of new antibiotic compounds, raised about $49 million instead of $78 million it had hoped to rake in through its IPO. After postponing its IPO for months earlier this year, Trius (NASDAQ: TSRX) cut its share price and increased the number of shares shortly before the offering.

—San Diego’s Optimer Pharmaceuticals (NASDAQ: OPTR) filed an application to start marketing fidaxomicin in the European Union as a treatment for C.difficile bacterial infections. Optimer plans to seek FDA approval later this year.

—San Diego’s BrainCells Inc. agreed to pay as much as $51 million to acquire a drug, sabcomeline, from London-based Proximagen that could have potential against various psychiatric diseases.

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San Diego-based Optimer Pharmaceuticals (NASDAQ: OPTR) has named Pedro Lichtinger as its new chief executive officer. Lichtinger will replace Michael Chang, who will continue at Optimer as chairman of the board and as a consultant, the company said in a statement. Lichtinger is a former executive from Pfizer, and was most recently the president of that company’s primary care business. Optimer is in the final stages of development with antibiotics for C.difficile bacterial infections that people get in hospitals, and another for traveler’s diarrhea.

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San Diego-based Optimer Pharmaceuticals, the developer of an antibiotic for a dangerous hospital infection, said today it has raised $51.5 million through a secondary stock offering after deducting expenses. The company (NASDAQ: OPTR) sold about 4.9 million shares of common stock at $11 a share. Jefferies & Co. was the sole book-running manager in the offering. Last month, Optimer said its fidaxomicin drug candidate passed its second pivotal test against C.difficile bacterial infections, and that it plans to apply for FDA approval of the drug in the second half of 2010.

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One of the buzzwords I keep hearing is that biotech investors want companies that are “de-risked.” This is kind of amusing, because the complex nature of biology makes biotech drug development one of the riskiest investments of all. But this craving for security is positive, at least for a while, if you are San Diego-based Optimer Pharmaceuticals.

Optimer (NASDAQ:OPTR) removed a lot (if not all) of the risk from its profile Thursday when its lead drug candidate passed a second pivotal clinical trial. The company showed its antibiotic for “C.difficile” bacterial infections, in 535 patients, was roughly equal to the gold standard antibiotic at curing people, and twice as good at preventing dangerous recurrences. That finding was consistent with another study of 629 patients reported in November 2008.

Not surprisingly, Optimer’s stock climbed as much as 15 percent Friday morning , before settling down to a modest 6 percent gain, closing at $12.54 a share.

The success of this pivotal clinical study means that Optimer is racing to send in an application to the FDA for clearance to start selling its first product, fidaxomicin. Optimer plans to file the FDA application by this summer, and it hopes to get a 6-month expedited review, which should make the drug available in early 2011, CEO Michael Chang says. Another application is being prepared for Europe.

If Optimer can get through the regulatory agencies, it will be in a unique position. There is no other antibiotic in development specifically for “C.diff” infections that’s within five years of reaching the market, Chang says, while incidence of this potentially deadly bug is growing. This is sure to spark plenty of speculation about who might form a partnership with Optimer to market this drug overseas, or who might want to buy the company altogether.

Michael Chang

“We expect shares likely will continue to move higher ahead of potential lucrative partnership opportunity/take-out possibility,” said Eun Yang, an analyst with Jeffries & Co. in New York, in a note to clients on Friday. “We view regulatory risks as very low.”

When I met Chang a few weeks ago at the JP Morgan Healthcare Conference in San Francisco, he tried to pooh-pooh any speculation of an imminent partnership, or takeover. I asked him why pharma hadn’t yet written a big partnership check already, given that fidaxomicin had passed a major Phase 3 study in November 2008.

“Pharma thinks that small startup companies are desperate. So they are playing … Next Page »

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San Diego-based Optimer Pharmaceuticals has nailed the second big trial designed to prove it has a new antibiotic for a deadly infection people can get in hospitals.

Optimer (NASDAQ: OPTR) said today that it reached its main goal of showing its experimental antibiotic, fidaxomicin, was roughly equivalent to the gold standard vancomycin drug when attempting to cure patients infected with “C.difficile” bacteria. The Optimer drug was about twice as good as vancomycin at preventing dangerous recurrences.

The findings, from a trial of 535 patients in North America and Europe, confirm what Optimer found from a previous trial of 600 patients, which was reported back in November 2008. Now that both pivotal studies are complete, Optimer plans to ship off a new drug application to the FDA by the second half of this year. If approved, fidaxomicin would be Optimer’s first marketed product, and it could represent the first new effective treatment for “C.diff” in decades. This particularly nasty bug causes severe diarrhea, the kind that can lead to severe dehydration, inflammation of the colon, hospitalization, and death.

Hospitals aren’t exactly too keen on reporting how often their patients suffer this infection, but about 30 to 40 cases were reported per 100,000 people discharged from these institutions in 2001, and that figure has climbed to about 100 cases per 100,000 discharges in 2005, according to data from the Centers for Disease Control and Prevention.

“The growing incidence of C.difficile in hospitals, long-term care facilities, and in the community, which we believe is caused in part by the use of broad-spectrum antibiotics and an aging population, create a need for new therapies,” said Sherwood Gorbach, Optimer’s chief medical officer, in a statement.

The latest trial found that 91.7 percent of patients on the Optimer drug had a clinical cure, compared with 90.6 percent on standard vancomycin. About 12.8 percent of patients on the Optimer drug had a recurrence, compared with 25.3 percent in the control group. The new drug was considered well-tolerated, Optimer said.

Shares of Optimer climbed 20 percent in after-hours trading following the announcement. Optimer plans to discuss the results in more detail with investors on a conference call at 5 pm Eastern/2 pm Pacific time.

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