It’s a big day for Aileron Therapeutics. The Cambridge, MA-based biotech firm announced this morning it has formed a partnership with Swiss drug and diagnostics giant Roche to discover, develop, and commercialize a new class of drugs known as “stapled peptides.”

Under the terms of the deal, Roche (OTCQX: RHHBY) will provide at least $25 million in technology access fees and R&D support to Aileron. What’s more, Aileron will be eligible to receive up to $1.1 billion in milestone payments if drug candidates are developed against five targets from Roche’s main therapeutic areas—oncology, virology, inflammation, metabolism, and the central nervous system. Aileron will also receive royalties on future sales for any marketed products resulting from the collaboration.

This is Aileron’s first major industry collaboration—and a big step forward for the company. My colleague Luke first wrote about Aileron back in November 2008, when the startup talked about its plan to develop peptide-based drug compounds that block interactions between proteins in the body that can’t be affected by conventional small-molecule chemical drugs or genetically engineered protein drugs. The peptides apparently work because they’ve been chemically “stapled” to resist unraveling under the influence of enzymes in the body that would render them useless.

Last year, Aileron closed a $40 million financing round led by the venture arm of GlaxoSmithKline and Boston-based Excel Medical Ventures, with participation from Novartis, Eli Lilly, Apple Tree Partners, and, yes, Roche. Aileron was founded in 2005 by the late Stanley Korsmeyer and Loren Walensky, a pair of biologists from Harvard Medical School and the Dana-Farber Cancer Institute, and Gregory Verdine, a Harvard University chemist.

It’s still very early for the company, in terms of any possible clinical impact. But last November, scientists at Harvard, Dana-Farber, and the Broad Institute of Harvard and MIT reported promising results from multiple disease models and animal tests, when they used a stapled peptide from Aileron to stop the production of a protein associated with uncontrolled growth of cancer cells. The hope is that stapled peptide drugs might be able to target previously “undruggable” protein targets inside cells, without the side effects of existing drugs.

In any case, the deal with one of the world’s biggest biotechs seems to support Aileron’s approach to date. “This alliance with Roche validates the broad potential for our Stapled Peptide platform across multiple therapeutic areas and classes of targets and also provides Aileron with capital to advance our platform and internal drug development pipeline” said Joe Yanchik, Aileron’s president and CEO, in a statement.

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Agios Pharmaceuticals is moving full steam ahead. The company has moved into a new 21,000-square-foot space in Cambridge, MA, that it says is the world’s largest lab devoted to studying how to throw a wrench into the overactive metabolism of cancer cells that normally allows them to grow and thrive. It has also recruited five new scientific advisers from top academic centers to help direct the work.

Agios (pronounced AHH-jee-oce) burst on the Boston biotech scene after the Fourth of July weekend, when it announced it had raised $33 million in an initial venture financing from Boston-based Third Rock Ventures, Flagship Ventures of Cambridge, and Seattle’s Arch Venture Partners. The company’s driving concept is that cancer cells become addicted to food. Basically, they have highly active metabolic enzymes, like those in fetal cells, that spur faster-than-normal growth. The key to stopping cancer cells in their tracks would therefore be to develop drugs that interrupt that rapid-fire metabolism. I got an update on the company’s progress in its first 100 days from interim CEO Kevin Starr, a partner with Third Rock.

The company’s founding lab is being set up at the University Park at MIT, a mixed-use development a short walk from Central Square. It has hired 10 employees there, who will work with 20 colleagues in China and India doing chemistry work, Starr says. Another 10 or 20 employees will be hired at the Cambridge site by the end of March, he says. Agios is identifying new targets to aim drugs at, and designing conventional small-molecule oral pills to block those pathways, he says. It’s also looking at whether existing metabolic drugs might be useful if designed differently for cancer. He wasn’t too specific about which tumor types the company is pursuing, but Agios has four different drug discovery programs moving ahead, and its first drug candidate could enter clinical trials by 2011, he says.

It sure sounded to me like Agios hasn’t eased up on the throttle much in the past 100 days, and isn’t too concerned about conserving its pennies in a worsening downturn. Starr said simply that the company’s strategy demands being nimble and making a big investment to seize this opportunity before someone else does.

“We believe that to build innovative, breakthrough companies it takes a boldness of vision and execution,” Starr says. “To make the strategy work, we need to invest in a big way.”

People, of course, are also key. Agios was founded by Lewis Cantley of Harvard Medical School, Tak Mak of the University of Toronto, and Craig Thompson of the University of Pennsylvania. Those folks all kept their day jobs at their academic institutions, and are being joined by another quintet of advisers from top research centers. They are: Chi Van Dang of Johns Hopkins University, Joshua Rabinowitz of Princeton University, Clary Clish of the Broad Institute, and Matthew Vander Heiden and James Bradner of the Dana-Farber Cancer Institute.

Agios’ ability to quickly rally all these players around the cancer metabolism work has already drawn interest from a half-dozen potential pharmaceutical partners, Starr says.

The company’s agenda for the next six months suggests it doesn’t intend to make cutbacks. It plans to hire more people, advance its four drug discovery programs toward identifying lead drug candidates, hire a permanent CEO and chief scientific officer, publish some of its work in top scientific journals, and sign a significant pharmaceutical industry partnership in 2009, Starr says. I interviewed Starr after a long week of interviews with biotech CEOs, and I’d say he was probably the most upbeat of any of them. “We’re excited. The more we get into this space, we see this is a breakthrough area in cancer. Getting key people involved is validation of it,” he says.

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Cambridge, MA-based Sirtris Pharmaceuticals (NASDAQ: SIRT) generated a flurry of media coverage, and a moderate stock gain, this week after announcing the first evidence that its formulation of resveratrol, a naturally occurring anti-aging substance found in red wine, helps to control symptoms of diabetes in humans. But it’s unclear that the study results—which were not reported in a peer-reviewed forum—will have much impact on the company’s future.

Sirtris reported at a JPMorgan health care conference in San Francisco yesterday that a preliminary “Phase 1b” safety trial, conducted on 98 Type 2 diabetes sufferers in India who had taken no previous drugs for diabetes, demonstrated that the company’s drug, called SRT501, had no serious side effects. After four weeks, the company said, patients who received the drug had an increased tolerance for glucose (that is, their bodies controlled glucose levels more effectively than before).

Phase 1 trials are not typically designed, however, to test how well a drug works. They’re usually conducted on healthy volunteers, and are merely intended to assess whether a drug is safe and well-tolerated at various doses, whether it accumulates in the bloodstream, and the like. Sirtris’s trial was somewhat unusual in that the participants were actual diabetes patients, but evidence of the drug’s effectiveness, at this stage, would have little effect on the drug’s chances for eventual regulatory approval—assuming that Sirtris intends to carry SRT501 through to commercialization, which it may not.

Sirtris designed SRT501 to be absorbed by the body more readily than pure resveratrol (which doesn’t show up at therapeutic levels in red wine, by the way, no matter how much you might attempt to drink). But as we reported in November, resveratrol derivatives are rapidly being overshadowed inside Sirtris by unrelated compounds with more power to activate SIRT1, the key gene that’s thought to be involved in the metabolic pathways that regulate aging and that seem to be out of whack in people with aging-related diseases such as diabetes and obesity. In a November Nature paper, Sirtris reported that three such compounds, called SRT1460, SRT1720, and SRT2183, are up to 1000 times as effective at activating SIRT1 as SRT501. CEO Christoph Westphal says the company plans to begin safety studies of the new compounds in the first half of this year.

Sirtris’s stock was hovering around $14.10 on the NASDAQ this morning, up roughly 7 percent over Monday’s price.

UPDATE 3:20 pm, 1/8/08: I spoke this afternoon with a Sirtris representative who emphasized that the company has never said that it will push aside testing and commercialization of SRT501. In fact, the company sees the compound as a potential treatment for MELAS (a rare mitochondrial disorder; the acronym stands for “mitochondrial myopathy, encephalopathy, lactic acidosis, stroke-like episodes”) and for Type 2 diabetes when used in combination with metformin, a popular anti-diabetes drug. The company plans to publish the results of the recent Phase Ib trial in a peer-reviewed publication this spring.

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