The first half of this year, Amylin Pharmaceuticals CEO Dan Bradbury was absorbed in the closest thing corporate America has to political warfare—a boardroom challenge from billionaire Carl Icahn and another unhappy shareholder, Eastbourne Capital. The second half has been more about doing the basics Amylin (NASDAQ: AMLN) must do if the San Diego diabetes specialist is ever going to enter the top tier of big, profitable biotech companies.

Now that the dust appears to finally have settled on the proxy fight—new director Paulo Costa was elected the chairman last month—Bradbury has been back hammering away at the company’s need to make sure it nails the potential blockbuster diabetes drug in its pipeline. Yesterday, he was happy to talk about it by phone while he visited Amylin’s new biotech drug factory in West Chester, OH.

The importance of Amylin’s new factory to its future is hard to overstate, so there’s good reason for the CEO to drop in and make sure the troops keep their collective eye on the ball. Amylin and its partner Eli Lilly have made a $500 million investment in the factory, dating back to December 2005, in order to meet market demand for what they hope will be the next big thing for diabetes, exenatide once-weekly. This plant, which now has 250 employees, is getting ready to undergo an FDA inspection in the next six months as Amylin and Lilly seek clearance to start selling the drug in the U.S. It’s the only place in the world with the expertise, and capacity, to meet the first three years of market demand for exenatide once-weekly, which will seek to grab big market share among the 25 million people in the U.S. with diabetes.

To hear Bradbury tell the story, this is the time to execute on the fundamental game plan with things like manufacturing, and not for Monday morning quarterbacking about whether the coach is calling the right plays.

Dan Bradbury

“Certainly in the first half of the year there were a lot of distractions for me. I have more time now to focus on actually running the business as opposed to board issues,” Bradbury says, during a break from meetings with Amylin’s Ohio staff. “It’s all about execution at the moment.” He adds,”We need to make sure everyone is fully on board with where we are as a company. The launch of exenatide once-weekly next year is critical to the future of the company.”

Why does getting this new drug right matter so much? Amylin generates almost 90 percent of its revenue from exenatide (Byetta), a novel peptide drug that was first approved by the FDA in April 2005 for patients who weren’t able to control their blood sugar with existing meds. The drug has gone on to become a commercial success, generating $678.5 million in sales last year, just its third full year on the market.

But the existing product has its limits, partly because it must be injected twice-daily. So Amylin and Lilly have sought to make this drug a lot more appealing to millions of patients by obtaining a license to drug delivery technology from Cambridge, MA-based Alkermes (NASDAQ: ALKS). That technology encapsulates the same peptide in a polymer microsphere that slowly dissolves in the bloodstream, so patients only need to get stuck with a needle once a week, not twice a day.

This new-and-improved drug has generated clinical trial data so far that Bradbury says are good enough to beat the biggest selling drugs in the diabetes market—Merck’s …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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San Diego-based Amylin Pharmaceuticals has witnessed an extraordinary struggle for control of its board of directors in which a key turning point came when founding CEO Howard “Ted” Greene publicly switched sides and urged shareholders to vote for the dissidents’ nominees.

So what does Greene have to say about the results of the shareholder vote that Luke reported this morning? I caught up with Greene this afternoon by telephone in northern Michigan, where he’s on vacation. He says the changes give the San Diego diabetes drug developer a fresh opportunity.

Greene sounds generally upbeat about the results, in which four new directors are joining Amylin’s 12-member board—two dissident nominees, and two new company nominees. From the dissidents’ camp, shareholders elected Alex Denner, a fund manager for billionaire investor Carl Icahn, and Kathleen Behrens, a consultant nominated by Eastbourne Capital Management. From the company’s own slate of candidates, shareholders elected two new independent directors, former Icos chairman and CEO Paul N. Clark and former Novartis CEO Paulo F. Costa.

“One-third of the board has turned over,” Greene says. “So the new board is going to take a hard look at the company’s performance and the way they do some of the marketing and sales.”

One of the extraordinary aspects to the outcome of the board election is not merely that the dissident faction gained two board seats in the May 27 shareholder vote. It’s that they dethroned the two most prominent incumbents—Amylin chairman Joseph Cook and lead independent director James Wilson—in an election that was a pure popularity contest. The 12 nominees elected to Amylin’s board are the ones who received the most shareholder votes. Cook and Wilson, who were the public faces of the company’s defensive reaction to the shareholder activists, were the ones who became least popular in the end.

Icahn and Eastbourne, which together hold about a 22.5 percent stake in Amylin, were targeting Cook and Wilson in their call for a board shakeup and improved performance at Amylin. But Greene, who is Amylin’s biggest individual shareholder and a leading figure in San Diego’s biotech community, clearly helped tip the balance.

When Greene was asked to resign from Amylin’s board in April, he groused in an open letter filed with the SEC that “the obvious and appropriate choice to not …Next Page »

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Although the financial meltdown has hit San Diego’s venture community pretty hard, Lux Capital’s Larry Bock says he made his most-successful investments during the biotech nuclear winter of the early 1990s. So what areas of venture innovation seem promising today? That’s what Xconomy is here for, my friends. Read on.

— Serial healthcare entrepreneur James Sweeney sees a wave of innovation coming in the field of wireless healthcare, and it might be worth listening to what he has to say. As Xconomy’s Juha-Pekka Tikka reported, one of the eight healthcare companies he founded was CardioNet, which is now regarded as the first commercially successful wireless health company in the United States. Sweeney will discuss his vision for wireless healthcare this Thursday morning at the Convergence Summit organized by San Diego’s Wireless Life Sciences Alliance at the Estancia La Jolla Hotel & Spa.

—For a company locked in a proxy fight, San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN) did a good job last week of showing it doesn’t need billionaire investor Carl Icahn to cut its costs or to advance new drug products. Amylin said Monday it plans to lay off 200 sales reps, or 11 percent of its global workforce, as part of a sales reorganization. On Tuesday, the diabetes drug developer said it had submitted a new drug application to the U.S. Food and Drug Administration for exenatide, its once weekly drug for type 2 diabetes.

—The price of shares in Acadia Pharmaceuticals (NASDAQ: ACAD) more than doubled on Monday, when the San Diego biotech said it stands to get as much as $395 million in milestone payments from Biovail, Canada’s largest publicly traded pharmaceutical. Acadia’s stock lost some of its altitude through the week, closing at $1.81 a share on Friday, after trading above $2.60 a share Monday. Acadia has scheduled a conference call this afternoon to discuss its Q1 financial results and drug development programs.

—San Diego’s Vical (NASDAQ: VICL) said it is nearly ready to begin producing a prototype vaccine for the H1N1 influenza, aka swine flu . In a Q1 conference call Thursday, Vical CEO Vijay Samant said the company should be ready to start making vaccines this week that are suitable for clinical trials. “We are talking of production time of six to nine weeks rather than six to nine months with conventional vaccines,” Samant said.

—Spectrum San Diego is ready to introduce its CarScan technology next week at the Force Protection Equipment Demonstration conference in Stafford, VA. Spectrum’s founding CEO Steven W. Smith, who is an expert in digital signal processing and ultra-low level X-ray emissions, told me the car-scanning technology he developed produces clearer images of interior compartments by combining two different types of ultra-low level X-ray emissions. Motorists can remain in the car while it’s being scanned.

—Reva Medical, which got $42 million in venture capital in 2007 after clawing its way back from near death when the market for its metal stent collapsed, is preparing to move to human studies of its fully dissolvable cardiac stent. CEO Robert Shultz told Xconomy’s Denise Gellene the clinical trial will likely include 300 to 500 patients and take two …Next Page »

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Amylin Pharmaceuticals (NASDAQ: AMLN), which is engaged in a proxy fight, has submitted a new drug application to the U.S. Food and Drug Administration for exenatide, its once weekly drug for type 2 diabetes. The San Diego biotech made the announcement today with Eli Lilly (NYSE: LLY), its marketing partner, and Cambridge, MA-based drug developing company Alkermes (NASDAQ: ALKS).

Amylin, Lilly, and Alkermes have been working to develop a new version of Byetta, the diabetes drug developed by Amylin, as a once-a-week injection based on Alkermes’ proprietary technology for long-acting medications.

“The clinical data supporting this submission highlight the potential of exenatide once weekly to significantly advance the treatment of type 2 diabetes,” says Amylin’s president and CEO Daniel Bradbury, according to the companies’ joint statement. “If approved, exenatide once weekly would be the first and only once-a-week therapy for the treatment of type 2 diabetes,” says David Vondle, Lilly’s global brand development leader.

Billionaire investor Carl Icahn and Eastbourne Capital Management, who together hold a 22 percent stake in Amylin, have targeted the San Diego biotech’s financial performance (and lagging Byetta sales) in their quest to gain more control on the company’s board. Amylin said yesterday it plans to lay off 200 employees in a restructuring of its sales force.

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Amylin Pharmaceuticals (NASDAQ: AMLN) became one of San Diego’s Cinderella success stories in 2005, when the U.S. Food and Drug Administration approved two of its diabetes drugs—some 18 years after the biotech was founded. But the company has been buffeted by some unusual challenges in recent months.

Demand for exenatide, Amylin’s lead diabetes drug, has slumped since last summer, when the FDA reported that six patients using the drug marketed as Byetta had developed pancreatitis, an inflammation of the pancreas that in some cases can be fatal. The agency didn’t link those cases to exenatide, in fact, diabetic patients are at greater risk for such infections. But the warning put a big question mark over Amylin, which gets almost 90 percent of its product revenue from this drug. The price of Amylin shares have tumbled by two thirds since Aug. 18, when the FDA issued its warning .

Since then, a more significant question has arisen, which is whether the pancreatitis issue will affect Amylin’s request for FDA approval of a longer-lasting version of exenatide that requires injections only once-a-week, instead of twice daily. The company has been working on winning FDA approval with Eli Lilly(NYSE: LLY), which also markets Byetta in a partnership with Amylin. The progress of their application once seemed assured, but now the course is much more uncertain. After a setback with the FDA in November, when the price of Amylin shares fell to a seven year low, the company cut 340 employees, or 16 percent of its workforce. Amylin said the move was intended to save about $100 million and put the company in a stronger financial position for 2010.

In the meantime, the decline in Amylin’s stock price also stoked trouble on a different front with a couple of dissident shareholder groups, including one headed by Carl Icahn, the billionaire investor and corporate raider. Icahn began to significantly increase his stake after Amylin’s plunge last August, and now owns a 9.4 percent stake in the company.

In January, Icahn disclosed plans to nominate five directors to Amylin’s board. That was a sign to some analysts that Icahn wants to shake up Amylin and possibly even push …Next Page »

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Amylin Pharmaceuticals stock shot up this morning after the company said it had some good fortune in dealings with the FDA. The San Diego biotech said it will be able file an application to market its diabetes drug, the once-weekly version of exenatide, in the first half of 2009 after all. That’s despite a warning the company issued last month that said it might take a lot longer.

Amylin (NASDAQ: AMLN) shares climbed 26 percent to $10.75 at 10:17 am Eastern time after the news was released. Amylin’s technology partner, Cambridge, MA-based Alkermes, got a milder boost, rising 4.4 percent to $9.08.

The FDA came around to Amylin’s idea that an extension study of a trial called Duration-1 would offer enough proof to show that the version of once-weekly exenatide used in clinical trials is equivalent to the stuff it plans to make in a large-scale commercial plant in Ohio. This is critical for Amylin, which is counting on the once-weekly exenatide to drive much of its future growth. The current version of exenatide (Byetta) is Amylin’s biggest moneymaker, generating $636 million in sales in 2007 for Amylin and its marketing partner, Eli Lilly. Even so, it can be a drag for patients because it must be taken in twice-daily injections. And more recently, demand has been dropping because since the FDA warned physicians about cases of pancreatitis that occurred in patients taking the medicine.

The once-weekly exenatide uses polymer technology to help make the drug last longer in the body, requiring fewer injections. That should make patients more willing to keep them taking the drug to control their blood sugar.

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These are grim times for many industries, and the life sciences are no exception. Most of these enterprises depend on the ability to raise fresh investment capital on a regular basis, so when investors turn cautious, things can get ugly fast.

To get a sense of just how big of a bruising San Diego biotechs are heading for, I combed through the balance sheets of 23 publicly-traded companies. My main questions are the most vital ones to any biotech company—how much cash does the operation have, and how fast is it burning through it?

This, of course, is a national story that will reverberate locally. Profitable industry powerhouses like Amgen and Genentech aren’t in trouble, but about half of the 248 unprofitable biotechs that are publicly traded have less than a year’s worth of cash on hand, according to an October report by Eun Yang, an analyst with Jeffries & Co. Of the 23 publicly traded companies I analyzed in San Diego just three are what could be called consistently profitable: Invitrogen, Illumina and Genoptix. Of the 23 sampled, just 10 have more than $100 million of cash and investments socked away in the bank.

If the markets don’t turn around by the middle to late 2009, it’s clear that a lot of these companies will be suffering. “A considerable amount of companies will have to consider drastic measures or go out of business. It is indeed not pretty,” says Kleanthis Xanthopoulus, CEO of Regulus Therapeutics, in an email. (Xanthopoulus, an Xconomist, runs a private company that spun off two relatively healthy companies. Both have more than $500 million in available cash: Carlsbad, CA-based Isis Pharmaceuticals and Cambridge, MA-based Alnylam Pharmaceuticals.

This isn’t a comprehensive list, and it’s in no particular order. My hope is this covers most of the major publicly traded players in the region. If you have any suggestions for companies to add, please send me a note at editors@xconomy.com. (For the real masochists out there, I did a similar analysis in Seattle last week, so you can see which region is worse off.)

—Amylin Pharmaceuticals (NASDAQ: AMLN). This San Diego-based company made headlines when it cut 340 jobs at its local headquarters. The move was made to cope with a double whammy of declining demand for its best-selling product, exenatide, (Byetta) and an FDA delay in approval of a more convenient once-weekly form of the medicine. The company had $806 million in cash at the end of September, and says the cuts should enable it to preserve $80 million in 2009 and turn cash flow positive by the end of 2010.

—Somaxon Pharmaceuticals (NASDAQ: SOMX). This San Diego company has an important FDA deadline coming up on Dec. 1 for the review of an insomnia medicine. Any delays, which have become common at the overworked agency, could spell trouble. Somaxon had $22.6 million in cash and investments at the end of September, and ran up a net loss of $10.3 million in third quarter.

—Arena Pharmaceuticals (NASDAQ: ARNA). This San Diego drug developer, working on medicines for obesity and diabetes, has more cash than most. It expects to end the year with $115 million in cash on hand after paying off some debt. It reported a net loss of $56.2 million in the third quarter. One worrisome stat: Arena started the year with $398 million in cash and investments. Let’s hope for shareholders’ sake the company has turned off that gusher in spending. …Next Page »

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If Aileron Therapeutics is on the right track, it will turn “stapled peptides” into a biotech industry buzzword along the lines of RNA interference. The Cambridge, MA-based company says its technology, like RNAi, is starting to show in animal tests that it can work against diseases where conventional drugs don’t.

This company, whose name is inspired by the hinged wing flaps that stabilize an aircraft, got its start in 2005. It began with technology from the late Stanley Korsmeyer and Loren Walensky, a pair of biologists from Harvard Medical School and the Dana-Farber Cancer Institute, combined with chemistry contributions from Gregory Verdine of Harvard University. Aileron has raised $20 million since inception from the venture investing arm of Novartis and Apple Tree Ventures. Aileron’s aim is to develop what it calls “stapled peptides” as a new class of drugs that block all sorts of interactions between proteins in the body that can’t be affected by conventional small-molecule chemicals or genetically engineered protein drugs.

“If you look at the pharmaceutical industry today, there are about 10,000 diseases, and 500 to 600 targets that are druggable with conventional small molecules,” says Aileron CEO Joe Yanchik. “We believe we can open up opportunities for thousands of new targets.”

Conventional small-molecule chemical drugs, like Pfizer’s atorvastatin (Lipitor) usually need “a nice deep pocket” on the targeted protein for the compound to settle into, Yanchik says. The problem is that only about one-tenth of proteins have this kind of pocket, while many more have long, flatter pockets inside that are “like a hot dog bun, for lack of a better term,” Yanchik says.

Engineering peptides, which are small protein fragments, to have better properties than other drugs is not a new idea—they are critical players inside cells, and have been studied for decades. A few peptide drugs are already on the market, such as Amylin Pharmaceuticals’ and Eli Lilly’s exenatide (Byetta) for diabetes. But most peptides have no chance as drugs, because once they get absorbed, they get chewed up by enzymes in the body that render them useless within minutes, Yanchik says.

Aileron’s insight is that the body’s enzymes can only do this when peptides—which are folded-up chain-like molecules—become unraveled. So it is designing ways to chemically “staple” the peptides into the proper folded shape. The end product, Yanchik says, will resist being chewed up by enzymes, will be efficient at penetrating cells, and will bind tightly and long enough to its target to have the intended effect.

The work is still in very early stages. Aileron hopes to bring forward its first drug candidate—likely a leukemia or lymphoma treatment—into clinical trials within one year, Yanchik says.(Indeed, Aileron recently got a paper published in Nature which showed it could identify a new target on cells to trigger apoptosis, or programmed cell death—a mechanism that firms like Genentech (NYSE: DNA) and Amgen (NASDAQ: AMGN), have been working on for years as a means of treating cancer.)

Unlike the compounds that many other companies are developing, Aileron’s drugs have the ability to hit a wide variety of targets on cells, which might make them potentially more effective than compounds that only hit one specific target Yanchik says. The trade-off, though, is that in theory Aileron’s drugs could have unforeseen side effects by affecting healthy cells. Company scientists haven’t seen those effects in animal studies, he says.

So far, Yanchik says he’s seen enough evidence that the drugs are potent and stable in animals to move ahead with an expansion plan. The company has been on a pace of hiring a new person once every three weeks this year, and now has a staff of 21. Yanchik is looking to raise more capital to expand the company, and is talking with pharmaceutical companies that might be interested in becoming partners. Drug companies are aware of the Aileron work, and likely trying to mimic some of it in their own labs, Yanchik says. “We believe we’re on the edge of something important here,” he says.

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San Diego-based Amylin Pharmaceuticals and its partner, Cambridge, MA-based Alkermes, both took a dive in the stock market today after they said they might face regulatory delays in developing a new diabetes drug. The companies said the FDA might ask them to run another clinical study before they can receive approval of a once-weekly form of the diabetes drug exenatide.

Amylin (NASDAQ: AMLN) fell 21 percent to $8.46 at 1:30 pm Eastern time, while Alkermes (NASDAQ: ALKS) dropped 9 percent to $9.21. Amylin has been in talks with the FDA about what it needs to do to demonstrate that the once-weekly exenatide used in clinical trials is equivalent to the drug it plans to manufacture at large scale in an Ohio factory.

Investors reacted to this line disclosed in a regulatory filing by Alkermes with the Securities and Exchange Commission: “Amylin has recently received feedback from the FDA that these data have not met their requirements to demonstrate comparability.” Amylin said it still hopes to submit its new drug application by the end of the first half of 2009 for the more convenient form of exenatide, currently marketed as a twice-daily injection called Byetta. If the FDA demands a new study, that application will be delayed, Amylin said.

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Activist shareholders are circling Amylin Pharmaceuticals. Eastbourne Capital, which owns a 12.5 percent stake in the San Diego-based biotech company, said on Monday that it is looking at ways to boost the stock price, including possibly selling the company, according to this Reuters report.

Much has been made about declining demand for exenatide (Byetta), the company’s top product for diabetes. Amylin (NASDAQ: AMLN) has seen its stock price plummet even worse than most biotechs this year, by some 68 percent. The selling was sparked partly by an FDA warning in August of six new cases of pancreatitis, including two deaths, among patients taking Byetta. The agency is currently considering an updated warning to the drug’s prescribing information. Amylin insists the drug’s benefits outweigh its risks, and it’s continuing to invest loads of cash in a once-weekly version of exenatide.

Eastbourne isn’t the only activist that sees opportunity in Amylin. Billionaire investor Carl Icahn said in mid-September that he had raised his stake in Amylin to 7.3 percent. Officials at Amylin didn’t immediately respond to Reuters’ request for comment.

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Amylin Pharmaceuticals said today it has scored a $125 million cash payment from Eli Lilly to manufacture a once-weekly injectable version of exenatide for diabetes. The San Diego-based biotech company will also get a $165 million line of credit from Lilly, which it can draw upon starting in the fourth quarter of 2009 through the second quarter of 2011, Amylin said.

Amylin (NASDAQ: AMLN) and Eli Lilly have long been partners on the original exenatide, a twice-daily injection marketed as Byetta. It’s Amylin’s main cash cow, generating $180 million in sales in the quarter ending September 30, Amylin said today in a statement. Now the companies are betting big that a once-weekly injection will be able to pass muster with the FDA, and ultimately be even more of a hit with patients. The companies have together invested more than $500 million in a West Chester, OH, factory to keep up with the anticipated demand. Under the deal, Amylin will supply the drug for the U.S. market, and provide it to Lilly for sales outside the U.S.

The supply agreement between the two companies comes at a time when they have been under scrutiny over cases of pancreatitis that have been reported in patients taking the currently marketed version of exenatide, including two deaths. It hasn’t crushed product sales, though; in fact, net sales grew 14 percent in the third quarter, Amylin said. Amylin had about $805 million in cash and investments at the end of September, and the new infusion from Lilly will be added on top of that.

“This agreement strengthens our balance sheet and provides us with financial flexibility in the future, while moving us closer to our goal of bringing exenatide once weekly to patients as quickly as possible,” said Amylin CEO Daniel Bradbury, in a statement.

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