Some San Diego life sciences companies reported a burst of new financing, while embattled Sequenom told investors it’s trying to conserve its available cash. Here’s our rundown of the latest highlights:

—San Diego’s Trius Therapeutics, a venture-backed biotech developing a new antibiotic for treating acute and life-threatening bacterial infections, disclosed plans to raise as much as $86 million in an initial public stock offering. With additional funding, the company will proceed to Phase 3 clinical trials of torezolid, which Trius describes as a second-generation successor to linezolid, the Pfizer antibiotic known as Zyvox.

—Life Technologies (NASDAQ: [[ticker: LIFE]]), the Carlsbad, CA-based provider of biotech instruments and lab supplies, agreed to acquire Woburn, MA-based BioTrove, which has developed a high throughput gene expression and genotyping analysis system.

— SpectraScience, the San Diego medical device maker, has raised more than $4.3 million through a private placement that combines preferred shares and warrants. SpectraScience (OTCBB: [[ticker: SCIE]]) CEO Jim Hitchin told Bruce the offering closes a $5 million round the company began earlier this year.

—PaxVax, a San Diego startup backed by Seattle’s Ignition Capital, has raised $2 million of a planned $6 million investment round. The biotech founded in early 2007 is developing a new type of vaccine that is administered as oral tablets and avoids much of the requirements that conventional vaccines require.

—Sequenom, San Diego’s embattled diagnostics company, said it expects to end the year with $39 million in cash—but that’s not enough to get through 2010 without raising funds or slowing spending. In April, Sequenom (NASDAQ: [[ticker: SQNM]]) disclosed that it had “mishandled data” from a prenatal Down syndrome diagnostic test, indefinitely postponing that product launch.

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Rib-X Pharmaceuticals, the New Haven, CT-based developer of novel antibiotics, is announcing today that one of its experimental treatments passed a mid-stage clinical trial for patients with a common form of pneumonia. It’s looking to deal with a Big Pharma company with the money and resources to take the drug through the next steps needed for FDA approval.

The study looked at 160 patients with mild to moderate community-acquired pneumonia, who were randomly assigned to get one of three different doses of Rib-X’s oral pill version of radezolid (pronounced ruh-DAY-zo-lid). Researchers found that 78 to 92 percent of patients were considered clinically cured, while the most common side effect was a mild irritation in the intestines.

The Rib-X antibiotic was designed with the help of a proprietary computer system that identified points of vulnerability in bacteria, and ways in which they develop resistance to existing drugs, as Ryan reported in October. The company’s goal is to create two versions of radezolid, an oral and intravenous form, so that physicians can use them to treat a wide-range of bacterial invaders, both among hospitalized patients and those who can take an oral pill at home. If Rib-X can navigate the final stage of clinical trials to prove both of these versions are effective, it will be in position to compete with one of Pfizer’s fast-growing products, linezolid (Zyvox), which generated $1.1 billion in sales last year.

“We feel this is very promising data,” says Susan Froshauer, Rib-X’s CEO. “We’re not seeing the kind of bone marrow suppression that you see with other treatments in the class.”

Still, the data is from a mid-stage study, so it’s too early to conclude that this drug will be a winner. The point was to assess the lowest possible dose at which Rib-X could see an anti-bacterial effect, Froshauer says. Researchers saw comparable effectiveness at all three doses tested, …Next Page »

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We all look for milestones in life, but several San Diego biotechs are approaching important junctures where they’re expected to report positive results from their drug development studies. Read on to find out which ones, and to catch up on the rest of San Diego’s life sciences news.

—San Diego’s Ardea Biosciences (NASDAQ: RDEA) reported some encouraging results last week for the drug it is developing to treat gout. A small number of patients found the drug lowered the amount of uric acid in their blood to acceptable levels within eight days. Still, Ardea is facing increasing competition, since the FDA approved Takeda Pharmaceutical’s gout drug in February and an FDA advisory panel recommended Savient Pharmaceutical’s gout treatment earlier this week.

—Trius Therapeutics CEO Jeff Stein told Luke the company plans to present full results from its recent clinical trial of a new antibiotic for treating MRSA at a conference in September. The startup also is working on a pivotal clinical trial strategy, and it is searching for a potential partner.

—San Diego’s Biocom, the life sciences industry trade group, hosted the CalAsia conference for the first time this week, and more than 300 representatives of the international biotech community attended. In a Q&A with Xconomy, Dr. Hui Cai of Inflexion BioPartners discussed the concerns that U.S. companies have about doing business in China—and China’s concerns about doing business with U.S. companies. In an e-mail yesterday, she adds, “A consensus out of CalAsia is [that] the line between U.S. and Asia certainly is becoming fuzzy. Gaps we see today in knowledge, processes, and other aspects will eventually disappear, and global standards will be established.”

—San Diego’s Lpath is nearing a make-or-break milestone in its development of sonepcizumab, an experimental cancer drug. The biotech stands to receive up to $8 million from Merck Serono for achieving performance targets related to the clinical trial Lpath is wrapping up, and an additional $31 million if the Swiss pharmaceutical company exercises an option to develop the drug.

—San Diego-based aFraxis, which is focused on developing treatments for Fragile X syndrome and autism, has raised $750,000 in early stage funding, according to a recent SEC filing. The startup is backed by San Diego’s Avalon Ventures, and Avalon’s Jay Lichter is listed as chief executive and director.

—Illumina, the San Diego biotech that provides DNA research tools for scientists, plans to offer a service that will enable consumers to get their DNA sequenced—at a cost of $48,000. As expensive as that may sound, it is half as much as the DNA sequencing service offered by Cambridge, MA-based Knome. The idea is to give patients access to comprehensive, personalized information about their vulnerability to disease.

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San Diego-based Trius Therapeutics saw what it wanted from a clinical trial of its new antibiotic against deadly MRSA infections, and now it’s gearing up this summer to take its game to a higher level.

Trius reported earlier this week some impressive results from a trial of 188 patients with complicated skin infections who took low, medium, or high doses of its drug, torezolid (TR-701). The treatment caused 98 percent of patients on the lowest dose to be clinically cured, with no side effects serious enough to make patients drop out of the study. While this is medically intriguing, and enough for Trius to pick the right dose, it’s not enough proof for FDA approval. So I followed up with Trius CEO Jeff Stein to find out what’s coming next.

Before getting too far into that, it’s worth a reminder of what Trius is trying to accomplish. The company’s experimental antibiotic is from the same class of treatment as Pfizer’s linezolid (Zyvox). The Pfizer drug generated $1.12 billion in sales last year, so a lot of people think it’s a worthwhile advance in the fight against dangerous infections, like MRSA bacterium that people tend to pick up in hospitals. Trius hopes to offer a better alternative—a pill that can be taken at a lower dose, over a shorter period of time, and be given once a day instead of twice. That’s important, because greater convenience means patients are more likely to follow doctors’ orders—taking an antibiotic as prescribed is critical to wiping out the bug, and reducing the chances of drug resistance.

The full clinical trial results are expected to be presented at the Interscience Conference on Antimicrobial Agents and Chemotherapy in September, but Stein said there’s nothing in the data that’s disappointing. The Trius group, with about 35 employees, is working on a pivotal clinical trial strategy that will enroll about 1,200 patients in a pair of studies required by the FDA. They are also putting some resources into an intravenous formulation of the drug. And they’re talking with potential partners with the money and manpower to take this drug the rest of the way.

“I’m not aware of results from other companies with an oral drug that’s this effective, in a once-daily pill given over a short course of treatment,” Stein says. “That’s our difference.”

The first big trial—still in a draft form—sounds like it ought to generate the kind of unequivocal answer that the FDA and doctors want to see about a new drug. It will randomly assign patients …Next Page »

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There was a lot of life sciences news over the past week in San Diego, with much of it coming out of the American Diabetes Association annual meeting in New Orleans.

—At a time when San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN) doesn’t need more challenges, Denmark’s Novo Nordisk announced that liraglutide, its once-daily diabetes drug, is substantially better at controlling blood sugar in type 2 diabetes than Amylin’s exenatide, which is injected twice-daily.

—If Amylin Pharmaceuticals’ rivals are targeting the diabetes specialist, at least the San Diego biotech is a moving target. Amylin says the latest clinical data for the new formulation of its exenatide diabetes drug (which only has to be injected once weekly instead of twice daily) shows patients were able to maintain control over blood sugar for two years, helped them lose weight, and lowered their blood pressure.

—San Diego’s Orexigen Therapeutics (NASDAQ: OREX) posted new results of its late-stage drug for treating obesity, showing that 41.5 percent of patients on the drug lost 10 percent of their body weight. That compared with 20.2 percent who did as well taking a placebo.

—Another San Diego drug developer, Arena Pharmaceuticals, (NASDAQ: ARNA) says patients on its lorcaserin treatment for a year generally had reduced their risk of heart attacks.

—San Diego’s Anadys Pharmaceuticals (NASDAQ: ANDS) is cutting its workforce by 40 percent and focusing its remaining resources on its lead drug candidate for treating the hepatitis C virus. The company also says it’s raising $17.5 million.

—Trius Therapeutics, a San Diego biotech developing a new antibiotic against deadly MRSA bacterial infections, said a study showed 98 percent of patients on the lowest dose of its new compound achieved a clinical cure. 

—Raj Krishnan, a bioengineering Ph.D candidate at UC San Diego, began entering student entrepreneur and business contests as a way to raise money for Biological Dynamics, the cancer diagnostics company he co-founded. It worked. He has now won 13 awards, and his most recent win included a check for $40,000. Krishnan, 27, says his research is focused on technology to identify a key biomarker for almost every type of cancer.

—After getting a $20 million infusion from investors last month, San Diego’s Vical (NASDAQ: VICL) says it has enough resources to continue operating through the end of 2011, which should be enough time to complete its clinical study of an immune-stimulating therapy for metastatic melanoma. Vical also is developing a vaccine to prevent life-threatening cytomegalovirus infections in bone marrow transplant patients.

—Bothell, WA-based Sonosite (NASDAQ: SONO) says it’s acquiring San Diego’s CardioDynamics International (NASDAQ: CDIC) in a deal valued at about $10 million. Sonosite makes portable ultrasound machines and CardioDynamics makes noninvasive medical diagnostic tools for cardiovascular disease.

—San Diego-based Tocagen, which is developing gene therapy treatments for terminally ill cancer patients, was among three biotechs that raised cash recently. Tocagen has raised $10.8 million in an $11.2 million equity offering that began in September. The startup was founded in 2007 by Harry Gruber, who previously founded Gensia Pharmaceuticals, Viagene, Aramed, and Metabasis, among others.

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Trius Therapeutics, the San Diego-based biotech company, has passed an important milestone in its quest to develop a more convenient, more effective antibiotic against deadly MRSA bacterial infections that people tend to get in the hospital.

Trius released results today from a study in which 188 patients with severe skin infections were randomly assigned to get a low, mid-range, or high dose of its experimental antibiotic, torezolid (TR-701). The study found the once-daily pill, given for five to seven days, helped 98 percent of patients on the lowest dose achieve what’s considered a clinical cure. There were no clinical relapses at follow-up visits three to four weeks after treatment.

“The nature of such infections usually warrants use of an IV antibiotic, but the trial results indicate that oral torezolid successfully treated these severe infections quickly and effectively,” said Joseph Surber, chief medical officer of Southwest Regional Research Group, and a clinical investigator on the study, in a company statement.

Biotech and pharmaceutical companies have been pushing hard for several years—without much success—to develop new antibiotics that can kill tough bugs like the MRSA pathogen that are becoming increasingly resistant to standard treatments. An estimated 19,000 people in the U.S. die from bacterial infections each year, more than die from HIV, Trius CEO Jeff Stein told me back in October. Two other companies trying to crack this market—South San Francisco-based Theravance, and Cambridge, MA-based Targanta Therapeutics—ran into various roadblocks and delays after applying to the FDA for market approval.

Trius’s goal is to develop a drug from the same chemical family, but with a superior profile compared to Pfizer’s linezolid (Zyvox), one of the fastest-growing antibiotics.

Antibiotics in this class are potent killers of drug-resistant bacteria, like MRSA. The Trius candidate appears to be more potent in animal tests than linezolid, meaning it can be taken at a much lower dose—which could offer fewer side effects and lower manufacturing costs. It also could be given once a day instead of twice a day, Stein has said. Both Pfizer’s drug and Trius’s can be taken as oral pills, but the added convenience of less-frequent dosing could be important, because antibiotic resistance thrives when patients fail to take all their required meds. Giving them a once-daily pill option may increase the odds that patients will stay in compliance with doctors’ orders.

The Trius therapy was considered well-tolerated, and 92 percent of the side effects considered possibly drug-related were graded as mild, researchers said. No patients dropped out because of adverse events. The least number of side effects were reported on the lowest dose, of 200 milligrams, Trius said.

The trial results have given Trius enough information to pick the lowest dose, 200 milligrams once a day, for the next step in development, a Phase III pivotal clinical trial in patients with severe skin infections. The company plans to complete an early-stage trial of an intravenous form of the drug later this year, and to merge the IV and oral development programs in Phase III trials early next year, Trius said in a statement.

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Biotech investing can sometimes be a downright confusing game, even for people who are supposed to know what they are talking about. Ask the folks at San Diego-based Optimer Pharmaceuticals (NASDAQ: OPTR).

Optimer has been one of a few bright spots in biotech over the past year. Back in November, its lead drug candidate, an antibiotic for C.difficile bacterial infections that cause horrific and potentially fatal cases of diarrhea, reached its main goal in a clinical trial of 600 patients. It was slightly better than the standard vancomycin antibiotic at curing patients, and was significantly better at preserving healthy bacteria in the gut that protect people suffering a relapse. It’s the first new treatment against this pathogen in decades, and it’s about to hit the market right when public health officials are freaking out about fast-rising incidence of “C. diff” in U.S. hospitals. The statistical analyses left no doubt that this drug was working.

Optimer discussed this data in significant detail six months ago, but more complete data were presented on Sunday, May 17, at a medical meeting in Helsinki, Finland. Not much was really new, except for one tidbit about a subpopulation of patients with an especially virulent form of “C.diff” infection known as BI or NAP1/027. The Optimer drug, fidaxomycin, was no better than standard vancomycin at preventing recurrences. About one-third of all patients who get “C.diff” have this especially aggressive form.

So how did the market react to this news? It shot first and asked questions later.

Shares of Optimer closed at $11.60 the last day of trading before the Helsinki presentation. The next day of trading, analysts from Needham & Co., JMP Securities, and Ladenburg Thalmann all downgraded their ratings on the stock. Shares plummeted as much as 18 percent during the day, to as low as $9.54 on heavy volume, as investors followed their interpretation of the bad news.

Then things got weird. Two days later, Ladenburg Thalmann changed its mind, and upgraded the stock again to “Buy.” All those investors who ran for the exits in fear suddenly looked kind of foolish, as the stock regained all those losses and more, closing at $12.28. Since then, Optimer has done nothing but climb even higher, closing yesterday at $13.84—a whopping 19 percent gain since the supposedly negative results came out in Helsinki. Not bad for an obscure stock that was trading for less than $5 back in early November.

What’s going on here? That was the gist of my questioning a couple weeks ago when I spoke to Optimer’s chief financial officer, John Prunty, and chief commercial officer Kevin Poulos.

A lot of people were essentially confused …Next Page »

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Most biotech stories in 2009 are about companies hunkering down or otherwise playing it safe with incremental advances, not people just getting started with an audacious dream. Malcolm Kendall has one of those dreams. He’s starting a company that aims to identify new targets on cells that haven’t been proven before, and create antibiotics to hit those targets. It’s all in the name of coming up with a creative way to fight dangerous pathogens that infect people in the hospital.

The new company, Indel Therapeutics, is based in Vancouver, BC, not far from where its intellectual property originated at the University of British Columbia. Kendall, a former venture capitalist with Durham, NC-based Intersouth Partners, is the CEO, and he told me the story a couple weeks back while he was fundraising in Seattle at Invest Northwest with chairman Mike Abrams, the former CEO of Vancouver, BC-based AnorMed.

Indel is trying to solve one of the problems that freaks out U.S. hospital administrators. There is growing incidence each year of nasty and sometimes deadly bacteria like MRSA or “C.Diff” plaguing U.S. hospitals. Every year, about 1.7 million people in the U.S. get hospital-acquired infections, which kill about 99,000 people a year. It costs the U.S. health system $27.5 billion annually—which is about the same amount the country spends on its entire biomedical research budget. Many of these bugs are becoming increasingly resistant to traditional antibiotics, and pharmaceutical companies have struggled to come up with anything good enough to pass muster with the FDA (see recent stumbles with new antibiotics from Theravance and Targanta Therapeutics). So Indel sees this as a pharmaceutical market that’s ready for new ideas.

“If this works, this is big,” Kendall says. “There’s a screaming need for new targets and novel compounds.”

The idea, from UBC scientist Neil Reiner (who is chair of the Indel scientific advisory board), is to look for subtle differences …Next Page »

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MRSA is the headline-grabbing boogeyman of the day when it comes to the type of deadly infections that people can pick up in the hospital. But there are all sorts of other nasty bugs crawling around your healthcare facility, and San Diego-based Calixa Therapeutics says it is on its way to creating a new drug to fight one of them.

Calixa, which has remained stealthy for its first couple years in business, is announcing today that it has passed a Phase I clinical trial of 64 healthy volunteers, which shows its antibiotic for pseudomonal infections appears safe. The drug appears to have a good enough profile to move into the next phase during the second quarter, with a study of about 100 patients that will provide a measure of its effectiveness.

Calixa got its start when it raised a hefty $30 million in a Series A venture financing in November 2007 from some big-name venture firms, Domain Associates, Frazier Healthcare Ventures, and Canaan Partners. The investors are betting on Calixa’s ability to develop CXA-101, a new type of cephalosporin antibiotic, which is used against pseudomonas infections. This bug infects about four people out of every 1,000 discharged from the hospital, accounting for roughly one-tenth of all hospital-acquired infections, according to the Centers for Disease Control and Prevention. Like other better-known bugs like MRSA or “C.Diff”, it is developing resistance to many common antibiotics, and can kill people.

The basic premise behind Calixa is to give doctors more weapons to knock down the invader. This type of infection made headlines back in January when Mariana Bridi da Costa, a 20-year-old model, died after picking up pseudomonas through a urinary tract infection.

“This is a nasty bug, and there’s an unmet medical need,” says James Ge, the company’s chief scientific officer.

Calixa is led by CEO Eckard Weber, …Next Page »

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Gilead Sciences, the Foster City, CA-based biotech company that has a research center in Seattle, said a scientific committee of the European Union adopted a negative opinion of its aztreonam lysine drug. The treatment, an inhalable antibiotic for cystic fibrosis developed by Seattle-based Corus Pharma, was turned down by the FDA last fall. EU regulators said Gilead needs more evidence about long-term benefits, repeated treatments in different age groups, and risk of bacterial resistance, said Thomas Russo, an analyst with Robert W. Baird.

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Optimer Pharmaceuticals has seen its stock almost triple from its low point in the past year, and yesterday it took advantage of the rising tide. The San Diego biotech company (NASDAQ: OPTR) received commitments from investors to buy new shares and warrants that add up to a cash infusion worth $32.9 million.

The company agreed to sell about 2.8 million new shares at $10 apiece to investors, as well as some new units for a higher price of $10.93 that includes one share plus a warrant to buy a partial share in the future. Optimer didn’t say much about what it will do with the money, other than fuel its ongoing drug development programs.

The company was in a position to raise that kind of cash—without selling huge numbers of shares that might greatly dilute the value of existing ones—because it has had a string of successes in clinical trials the past six months. Optimer reported results in November from a 629-patient trial from its experimental drug for the dreaded “C. Diff” bacteria that people get in hospitals, and that causes horrific, and sometimes fatal diarrhea. The Optimer drug produced a higher rate of cures than the standard antibiotic, and was better at preventing relapses that often forces people to be re-hospitalized with tougher cases. Then last month the company followed that up with another clinical trial success for its second drug in the pipeline, a candidate for traveler’s diarrhea.

Optimer, which currently has no products on the market, had $46.5 million in cash and investments the last time it reported financials at the end of September, and it is spending $8 million to $9 million a quarter, said analyst Thomas Russo of Robert W. Baird, in a note to clients today. He expects the company will raise more money again before the end of June, and sign a partnership to help with marketing fidaxomicin (OPT-80), the drug for “C.Diff.”

“We view this transaction positively, as cash runway trumps dilution for pre-commercial stage biotechs in this environment,” Russo wrote.

Optimer shares rose 1 cent after the deal was announced, to $10.94.

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A group of biotech veterans and up-and-comers in the Boston area are forming a startup called Novophage to make engineered viruses that may help combat the growing problem of resistance to antibiotics.

It’s early days for Novophage. The firm has no office or venture backers to speak of, but it has formed an impressive roster of scientific co-founders that includes MIT’s prolific biotech inventor Bob Langer, Boston University bioengineering professor James Collins, and MIT chemical engineering professor Gregory Stephanopoulos. Research related to the firm’s science—led by co-founder Timothy Lu, a student at Harvard Medical School—was due to be published this week in the online version of the Proceedings of the National Academy of Sciences. I got the inside scoop on this company’s strategy from Lu and Collins yesterday.

Novophage’s engineered viruses have shown the potential to be used in combination with traditional antibiotics, offering what could be a new way kill bugs that have developed resistance, Lu says. This combination strategy offers an alternative to developing new stand-alone antibiotics, which have been slow to reach the market the past couple of years. For example, the FDA late last year shot down Cambridge, MA-based biotech firm Targanta Therapeutics’ bid to garner approval of an antibiotic called oritavancin for complex skin and skin-related infections caused by antibiotic-resistant bacteria. Another contender, South San Francisco-based Theravance, has also been delayed by regulatory hang-ups.

“We wouldn’t have to worry about antibiotic resistant bacteria if there were a lot of new antibiotics coming out from the pharmaceutical industry,” Lu says. “Our technology provides the ability to extend the useful lifetime of antibiotics and to solve the growing antibiotic-resistance problem.”

Lu and his fellow researchers have engineered bacterial viruses, called bacteriophages or phages, to strike at the natural DNA repair mechanism in bacteria that helps them resist antibiotics. To accomplish this, BU’s Collins explained to me, the phages serve as Trojan …Next Page »

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San Diego-based Optimer Pharmaceuticals said today it is preparing to apply for approval to sell fidaxomicin (OPT-80) in the European Union on the basis of one successful Phase III trial. The company reported positive results of the new antibiotic in November from the first of two pivotal studies for patients suffering from “C. Diff” bacterial infections. The company says it still intends to complete the second study before it will seek approval for marketing from the U.S. Food and Drug Administration.

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Oscient Pharmaceuticals, a Waltham, MA-based drug maker, says it is laying off 32 percent of its total workforce, or about 100 jobs, to conserve cash. The company—which markets fenofibrate (Antara) for high cholesterol and antibiotic gemifloxacin mesylate (Factive) for bronchitis—expects a charge of $2 million in this fiscal quarter related to the layoffs. The cuts, however, are projected to save the firm $8 million annually. Here’s a link to our Boston Layoff Tracker.

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Mpex Pharmaceuticals has reeled in $27.5 million in the first closing of a Series D round of financing as the firm advances its inhaled antibiotic for chronic respiratory ailments through clinical trials, according to the company.

The San Diego-based drug developer says that its fourth round of financing was led by Investor Growth Capital and included investments from SV Life Sciences, HBM BioVentures, Aberdare Ventures, and Adams Street Partners. Mpex notes that its backers have committed to invest up to $40 million in the Series D round.

Mpex CEO Daniel Burgess says in a prepared statement that this latest round of financing is enough to fund the company through its Phase 2 trials of an inhaled version of approved antibiotic levofloxacin to prevent lung infections in patients with cystic fibrosis as well as chronic obstructive pulmonary disease. The company also plans to use the financing to prepare for late-stage clinical trials needed to get marketing approval for the drug.

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Ryan McBride wrote:

Forma Therapeutics came out of stealth mode early this month to reveal its plans to discover drugs for difficult-to-treat cancers—and today the Cambridge, MA-based biotech startup is announcing a deal with antibiotics maker Cubist Pharmaceuticals aimed at applying the startup’s nascent technology to discover antibacterial compounds, according to a press release.

Lexington, MA-based Cubist (NASDAQ:CBST) has agreed to pay Forma up to $14 million over the next three years—including upfront fees, research funding, and an equity investment—to discover potential antibiotics for bugs such as MRSA and gram-negative bacteria with resistance to existing treatments. The deal also makes Forma eligible for up to $54 million in payments related to the development of drugs discovered in the partnership.

This latest partnership follows Forma’s news two weeks ago about the firm’s agreement with Novartis that gives the Swiss drug giant the option to license cancer treatments discovered by the startup. Forma—which was founded by scientists at the Broad Institute of Harvard and MIT and biotech industry veterans such as its CEO, Steven Tregay—combines cell-based screening methods with computer modeling and chemistry techniques to discover drugs, according to the company.

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Ryan McBride wrote:

Rib-X Pharmaceuticals has raked in $25 million in a debt financing to develop its pipeline of antibiotics for drug-resistant infections. The New Haven, CT-based biotech firm is expected this morning to reveal details of the financing and final results of a mid-stage clinical trial of its antibiotic delafloxacin.

Last time I spoke with Rib-X CEO Susan Froshauer, in September, she was on the hunt for a commercial partner to help fund further development of the firm’s lead antibiotics. The company has yet to land such a partner, but Froshauer was pleased that some previous equity backers—Warburg Pincus, ABS Ventures, Axiom Ventures, EuclidSR Partners, MedImmune Ventures, Oxford Bioscience Partners, SR  One, and Vox Equity Partners—opted to support her company in the debt round. Rib-X, founded in 2001, had previously raised $123 million in equity financing.

Rib-X says that delafloxacin showed positive results in the recent mid-stage clinical trial as a treatment for certain skin and tissue infections caused by bacteria such as the infamous antibiotic-resistant strain MRSA as well as bugs resistant to quinolone antibiotics. The 150-patient study showed that delafloxacin had efficacy comparable to that of the antibiotic tigecycline (Tygacil), marketed by Madison, NJ-based drug firm Wyeth, and better tolerability than the already-approved drug, according to Rib-X.

Rib-X has developed delafloxacin to treat the same types of bugs as South San Francisco-based Theravance’s (NASDAQ:THRX) telavancin and Cambridge, MA-based Targanta Therapeutics’ (NASDAQ:TARG) oritavancin. The FDA shot down Targanta’s bid to gain approval of oritavancin in late 2008, indicating that the company didn’t have enough data, particularly on the ability of oritavancin to treat MRSA. Froshauer notes that her firm’s recent delafloxacin study was completed last year with a higher percentage of MRSA patients than the oritavancin studies. She adds that delafloxacin is available in both intravenous infusions and oral pills, which enable patients to easily continue treatment after they leave the hospital. Oritavancin and other competing antibiotics are available in IV form only.

“We think of course that we’re in really good shape because we can look to those experiences and have a lot of take-home messages [from the FDA],” Froshauer says.

Still, Rib-X is considering additional uses of delafloxacin. Froshauer says that the company may decide to develop the antibiotic as a prophylactic treatment given to patients before surgeries to prevent infections. But the company is going to let its hoped-for development partner to weigh in on whether to develop delafloxacin for pre-surgical prophylaxis, she says, adding that its partner would also impact the design and timing of its next clinical trial of the drug.

Rib-X—which has a pipeline of other antibiotics discovered internally—licensed delafloxacin in 2006 from Japanese drug-maker Wakunaga Pharmaceutical Company. Froshauer says that health-care products giant Abbott Laboratories had previously developed delafloxacin in pill form for bronchitis and pneumonia, but opted to drop the program after two successful trials due to a change in strategy at the Abbott Park, IL-based firm. Rib-X developed the IV form of the antibiotic.

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San Diego’s Optimer Pharmaceuticals had its breakout moment in November, when it showed its experimental drug could wipe out the dreaded C. Diff bacteria, a horrific, sometimes fatal form of diarrhea that people sometimes pick up in the hospital. What fewer people realize is Optimer (NASDAQ: OPTR) has another anti-diarrhea drug in the works that’s designed to stop the milder forms of diarrhea that Americans tend to get when they travel to developing countries.

Optimer’s second drug candidate is called prulifloxacin. It’s part of a class of antibiotics known as fluoroquinolones, and it is commercially available in Japan and Korea in an intravenous form. Optimer’s trick is to make it into an oral form, taken once-a-day for three straight days, which ought to stop a variety of different bugs from making people get so sick that it ruins their vacation.

People currently take Bayer’s ciprofloxacin (Cipro) for traveler’s diarrhea, but Optimer’s drug is more potent and hopes to grab much of the market share, says Optimer CEO Michael Chang. The Bayer drug is in the same class, but has to be taken twice a day for five days, which means patients find it hard to comply with the schedule, says Optimer chief commercial officer Kevin Poulos. It’s also not well-tolerated when people spend time in the sun, which can really sap the fun out of your vacation. This isn’t a huge market—about $200 million are up for grabs—but Optimer thinks it can carve out a strong niche to diversify its sources of revenue in the future, Poulos says.

“This will be the most convenient, and most potent antibiotic for infectious diarrhea approved by FDA, if it’s approved,” Poulos says. “It’s a small market compared to other indications, but the beauty of it is that it’s a market that hasn’t had a lot of attention paid to it. We consider that as an advantage. I’d rather enter a market where we have a unique advantage, instead of a market that’s crowded, like respiratory antibiotics. We feel we can get a large share in a small market, versus a small share in a bigger market.”

The drug has already passed one clinical trial it needs to include in an application for FDA approval, and it expects to get results from a second required trial before the end of March, Chang says. If that goes well, the company will file for FDA approval of prulifloxacin before the end of the year.

This drug isn’t meant to be taken as a preventive treatment; instead patients would wait until they feel a touch of diarrhea coming on, and then take the pill, Chang says. It’s supposed to work fast, so a patient could take it and have their diarrhea go away within 24 hours, he says. About 80 percent got relief from their diarrhea, compared with 40 percent who took placebo. If patients didn’t have their diarrhea improve within the first day, they were able to get a standard treatment to take care of it, Chang says.

The first trial tested the Optimer drug in Mexico and Peru, where it was largely up against E. Coli. The second trial was in India, Guatemala, and Mexico, where the drug mainly had to fight shigella, Chang says. “That way we can cover more people traveling to different parts of the world,” Chang says.

If all goes according to plan, this drug will arrive on the market about the same time in 2010 as Optimer’s other drug, OPT-80, for “C. Diff” bacteria. That drug, which still needs to pass one more clinical trial this year, was recently given the generic name of fidaxomicin. One big event on Optimer’s to-do list this year will be forming a partnership outside the U.S. to help with marketing fidaxomicin, while keeping control of it in the U.S.

“The value driver for Optimer is fidaxomicin, the ratio is about 80/20,” Chang says. “But this second drug (prulifloxacin) is going to be the best-in-class, we think, and has reasonable potential to be a good earnings contributor.”

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Targanta Therapeutics (NASDAQ:TARG), the Cambridge, MA-based biotech firm that saw its value sink last month after the FDA decided not to approve its lead antibiotic oritavancin as a treatment for MRSA and other infections, has agreed to be acquired by drug maker The Medicines Company, the proposed buyer says.

The Medicines Company (NASDAQ:MDCO) said yesterday that it would acquire 100 percent of Targanta’s common stock for $2 per share or $42 million in cash, plus additional cash payments contingent on regulatory approvals of oritavancin and sales milestones. Oritavancin, which must undergo more late-stage clinical trials before the FDA will consider its approval again, could help address the growing demand for drugs to combat antibiotic-resistant infections, a market that reached $1.1 billion in 2007, said Clive Meanwell, chairman and CEO of Parsippany, NJ-based The Medicines Company, in a statement.

Both companies’ boards of directors have approved the buyout deal, but Targanta shareholders must approve the deal, The Medicines Company says.

The buyout could expedite what has already been a rapid evolution of Targanta. The company, originally based in Montreal, was formed in 2005 when it licensed oritavancin from California biotech firm InterMune. The company tapped Boston-area biotech veteran Mark Leuchtenberger to be its CEO in 2006, and he promptly moved the firm’s headquarters to Cambridge and led it through its $57.5 million initial public offering the following year.

Targanta’s fortunes changed late last year when an FDA panel decided not to recommend oritavancin for approval as a treatment for certain skin and tissue infections. And last month the FDA took the panel’s advice and declined to approve the antibiotic, telling the company that it needed to do further patient studies to prove its effectiveness and safety.

The company cut 75 percent of its staff, or about 60 workers, last month to conserve cash and realign its focus from its anticipated commercial launch of oritavancin this year to conducting more clinical trials for the drug.

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Cambridge, MA-based Targanta Therapeutics (NASDAQ: TARG) received a harsh blow last week as the FDA declined to approve it sole drug candidate, an antibiotic called oritavancin intended to treat antibiotic-resistant infections like MRSA. Today Targanta announced staff cutbacks intended to help the company conserve capital while it seeks approval for oritavancin in Europe and tries to get the drug back on track for approval in the United States. The company will reduce its workforce by 86 people, or about 75 percent, leaving it with only 27 employees. We have updated Xconomy’s Boston Tech Layoff Tracker with the latest numbers.

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