Acquisition news was big this week for New England-area tech and life sciences companies, but we also saw a few startup financings.

—Cambridge-based Genzyme (NASDAQ: GENZ) sold its diagnostics products unit to Japanese firm Sekisui Chemical for $265 million in cash. The deal comes as part of Genzyme’s plan to sell off three of its businesses in order to boost shareholder value, announced in May. It sold its genetic testing unit in September to Burlington, NC-based Laboratory Corporation of America (NYSE:LH) for $925 million.

—Natick, MA-based medical devices firm Boston Scientific (NYSE: BSX) paid $193 million to acquire the remainder of Los Gatos, CA-based Sadra Medical, a maker of technology for percutaneous aortic valve repair. Boston Scientific already owned 14 percent of the company, and could also pay an additional $193 million if Sadra hits regulatory and sales targets through 2016.

—Novell, a Waltham, MA-based maker of networking and workload management software, announced it had agreed to be acquired by Seattle-based Attachmate for $2.2 billion in cash, or $6.10 per share. Novell (NASDAQ: NOVL) also said it was selling select IP assets to Microsoft-organized tech consortium CPTN Holdings for $450 million.

—Cambridge biotech Archemix sold its intellectual property assets in the hemophilia drugs space to Baxter (NYSE: BAX) for $30 million upfront and potentially another $285 million in milestone payments. The deal, expected to close this year, gives Baxter an exclusive license to Archemix’s ARC19499, a hemophilia treatment in a Phase 1 clinical trial in the U.K., among other assets.

—SunBorne Energy Technologies, a Cambridge-based startup developing a method for generating low cost solar electricity for use in India, brought in $3.1 million in equity- and rights-based funding. The startup is backed by Highland Capital Partners and previously raised a $5.1 million equity round in December 2009.

—Boston-based mobile app developer AisleBuyer raised $4 million in an equity and debt offering. The startup is putting the money toward new hires and expanding the stores that use its app, which enables consumers to scan and pay for an item in a store straight from their phones, without having to wait in line. The funding round included a line of credit from Silicon Valley Bank and an equity investment from Richard Heise, Jr, the founding investor of InnerWorkings, Echo Global Logistics, Mediabank, Forseva, and Groupon.

—Gotuit, a Woburn, MA-based provider of technology for ascribing metadata to online video content, was bought by Digitalsmiths of Research Triangle Park, NC, for an undisclosed sum. Gotuit’s backers include Atlas Venture, Highland Capital Partners, and the Kraft Group.

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Archemix, a Cambridge, MA-based biotech developing aptamer drugs for the treatment of chronic and acute diseases, has sold its assets in the hemophilia space to Baxter International, according to an announcement today. Baxter (NYSE: BAX) will pay Archemix $30 million upfront and up to $285 million in milestone payments in an exclusive license agreement for the assets, which include ARC19499, a hemophilia treatment in a Phase 1 clinical trial in the U.K. The deal is expected to close this year.

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Ligon Discovery has been discovered, and I could argue that I was there the moment it happened. Patrick Kleyn, co-founder and CEO of Ligon, was sitting in the back of a crowded conference for drug industry dealmakers in Harvard Square last month when a senior pharmaceutical executive on an industry panel noted Kleyn’s fledgling firm as one of the promising young life sciences companies in the Boston area. Kleyn was seated next to me, and I saw him beaming after receiving the shout-out.

There are a few ways to get discovered as a new biotech startup: exciting science, big-name founders, success in raising venture capital, or any combination of these. Ligon falls into the “exciting science” category, because its small-molecule microarray technology could revolutionize the way researchers go from identifying a potential disease protein or target to finding a drug that can home in on that target. It’s been just a year since Cambridge, MA-based Ligon spun off from the Broad Institute of MIT and Harvard, and the firm is already generating some positive buzz at venues like the Boston Biotech Business Development Conference in Harvard Square last month.

Ligon might have the right technology at the right time. Genetic research has uncovered a plethora of proteins in recent years that play key roles in human diseases. Yet it can take several months or more than a year to design a test or assay that can be used to screen libraries of small molecules for ones that can bind to the newly uncovered disease proteins. Ligon’s technology is designed to greatly reduce those long turnaround times in drug discovery.

“One of the key benefits for a [pharmaceutical] company, when you talk about time to market, is the ability to go from an idea of screening certain targets to looking at structures or hits from a screen within weeks,” Kleyn says. “Whereas, a very typical turnaround time for that [process] in a large pharmaceutical company would be a year plus.”

Ligon’s technology borrows a concept from open-source software development for designing tests for drug discovery, says Kleyn, the former director of scientific planning for the Broad Institute. While open source gives programmers common codes for developing software, Ligon has a single form of chemistry that can be used to … Next Page »

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New England’s life sciences companies gave us a number of cool new technologies and interesting deals to talk about this week.

—Cambridge, MA-based Genzyme (NASDAQ: GENZ) finished cleaning up its Allston, MA-based plant after a viral contamination which caused 6-to-8 week supply shortages of two of its best-selling drugs.

–-Archemix, also of Cambridge, forged an alliance with Boulder, CO-based miRagen Therapeutics to develop drugs that combine the Massachusetts firm’s “aptamer” technology with the Colorado company’s microRNA technology. Specific financial terms of the arrangement weren’t disclosed.

—Waltham, MA-based medical device company Augmenix revealed in an SEC filing that it had collected $4.7 million out of an equity round potentially worth $7.5 million. Augmenix is developing a synthetic material to protect healthy tissue during radiation treatments for prostate cancer.

—Joule Biotechnologies, a heretofore stealthy startup in Cambridge stepped into the sunlight to show off its technology, which aims to produce fuels and chemicals using engineered microbes capable of photosynthesis—no plant material or algae required. Founded in 2007 by partners at Flagship Ventures, Joule believes its technology is capable of producing more than 20,000 gallons of ethanol or hydrocarbons per acre on an annual basis, and yielding transportation fuels at prices that rival those of petroleum-based fuels.

—Waltham-based Avila Therapeutics raised $30 million in a Series B financing round led by the Novartis Option Fund and joined by return investors Abingworth, Advent Venture Partners, Atlas Venture, and Polaris Venture Partners. Avila and Novartis Option Fund also reached an agreement worth as much as $200 million in upfront and future milestone payments to co-develop Avila’s drugs, which are designed to bind more tightly to their targets that traditional drugs.

—Clinical trials management software maker Phase Forward (NASDAQ: PFWD), also of Waltham, shelled out $11 million to acquire Indianapolis, IN-based Maaguzi. The Indiana firm runs an online service for collecting data from patients.

—Cerulean Pharma of Cambridge raised $10 million in a Series B financing round from return investors Polaris Venture Partners, Venrock Associates, Lux Capital, and Bessemer Venture Partners. The startup is developing nanoparticle-based treatments and plants to use some of the new funding to push it’s lead drug candidate, a cancer drug, through clinical trials.

—Shares of Cambridge-based Ariad Pharmaceuticals (NASDAQ: ARIA) surged after the company released promising preliminary data from a mid-stage trial of its lead drug candidate, ridaforolimus, as a treatment for breast cancer. More complete data on the drug should be available later this year.

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I’ve got a nice variety of deals—particularly venture financings—to tell you about this week.

—Swiss drug giant Novartis opted to extend a collaboration with Alnylam Pharmaceuticals (NASDAQ:ALNY) of Cambridge, MA, for a fifth year. Under the extension, Novartis will continue to fund certain RNA interference research and development efforts at Alnylam through October 2010.

—Software maker Ibrix agreed to be acquired by Hewlett-Packard for an undisclosed sum. The Billerica, MA-based firm’s technology allows large enterprises to manage network file servers holding petabytes of data.

—Andover, MA-based Acquia raised $8 million in a second financing round. North Bridge Venture Partners and Sigma Partners participated in the deal, as well as the 2007 first round of financing for Acquia, which sells a commercial version of the open-source content-management platform Drupal.

—Cambridge-based Archemix teamed with Watertown, MA-based Dicerna Pharmaceuticals to make new drugs that combine the former’s “aptamer” technology with the latter’s RNA interference technology. Specific financial terms were not revealed, but Dicerna has an option to get exclusive rights to take the new drugs through development.

—Aveo Pharmaceuticals, also of Cambridge, cut a deal worth $20 million—including $5 million in cash and $15 million in investment—to extend a partnership with Melville, NY-based OSI Pharmaceuticals (NASDAQ: OSIP). The deal, which also includes two years of research funding, will give OSI expanded access to Aveo’s mouse model of cancer.

—Boston-based virtualization company … Next Page »

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Cambridge, MA-based Archemix, the developer of a new class of drug called aptamers, said today it has formed an R&D collaboration with Boulder, CO-based miRagen Therapeutics, a developer of microRNA treatments. The two companies will plan to attach aptamer drugs to microRNA molecules with a goal of delivering the compounds inside cells. Both companies will contribute resources to the collaboration, and miRagen is getting options to do exclusive development of drugs that emerge from the partnership, although detailed financial terms weren’t disclosed.

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A mixture of good news and bad for New England life sciences this week with a couple of companies closing their doors while others forged new partnerships and made acquisitions. Health IT was a particularly busy area.

—Waltham, MA-based Phase Forward (NASDAQ:PFWD) acquired the interactive voice and Web-response services business of Princeton, NJ-based contract research company Covance (NYSE:CVD) for $10 million. As part of the deal, Phase Forward will supply its clinical trials data management software to Covance’s customers.

—Also in Waltham, MedVentive—a developer business intelligence software for health plans, medical centers, and pharmacies—completed a $7.25 million Series C round of venture capital. Backers included Excel Venture Management whose managing director, Enrico Petrillo, has joined MedVentive’s board of directors.

—On the same day, iMedX of Sheldon, CT, raised $13.3 million in financing. The company provides software for outsourced transcription services for doctors and also operates in India.

—Luke reported that Cambridge, MA-based Biogen Idec is developing 12 different possible cancer drugs in a bid to expand its share of the cancer drug market. Biogen Idec (NASDAQ: BIIB) is currently the world’s largest manufacturer of drugs to treat multiple sclerosis but is going for a bigger piece of the expected $84 billion in sales of cancer drugs in 2012.

—That’s not the only recent change at Biogen Idec. Co-founder Phillip Sharp retired from Biogen’s board of directors Thursday after 31 years. Sharp is one of biotech’s pioneers and a Nobel Laureate. Now Biogen’s board must decide whether or not to replace him, since there is no requirement to do so.

—Cambridge, MA-based Biopure (NASDAQ:BPUR) filed for Chapter 11 bankruptcy after years of trying to get its blood substitute approved by government regulators in America and Europe. The company’s assets will be sold to OPK Biotech, as well as sold in a bankruptcy court auction.

—Alnylam Pharmaceuticals (NASDAQ:ALNY) of Cambridge, MA, announced that major Swiss drug company Novartis is extending the companies’ research collaboration in RNA interference treatments for a fifth year. Novartis will continue to fund research and development efforts at Alnylam through October 2010.

—Speaking of RNA interference, Watertown, MA-based Dicerna is teaming up with Cambridge, MA-based Archemix to create drugs that combine Dicerna’s RNAi technology with Archemix’s proprietary “apatmer” technology. Financial specifics of the deal were not disclosed.

—Cambridge, MA-based Aveo Pharmaceuticals took in $20 million in a deal that extended a partnership with Melville, NY-based OSI Pharmaceuticals (NASDAQ: OSIP). Aveo has worked with OSI since 2007 and in the new deal will provide its partner with expanded access to its mouse model for cancer. The two companies may share revenue if any drugs come out of the collaboration.

—Lexington, MA-based Epix Pharmaceuticals announced that it will liquidate its assets and shut down in August after running out of cash. The company developed a still-experimental drug to treat Azheimer’s disease.

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Dicerna Pharmaceuticals has set its sights on silencing problematic genes using what it calls the “second doorway” of RNA interference—an approach to the burgeoning field that other RNAi companies aren’t pursuing. But to get its drugs over the transom and where they need to go in the body, the Watertown, MA-based company will need a little help, and for that it has turned to Cambridge, MA-based Archemix.

The two firms have partnered up to develop combination treatments that will merge Archemix’s proprietary “aptamer” treatments with Dicerna’s gene-silencing drugs. Both companies hope the alliance will yield drugs that can precisely—and potently–home in on the molecular roots of disease. Specific financial terms of the deal aren’t being disclosed, although Dicerna and Archemix will split the early development costs, and Dicerna has an option to get exclusive rights to take the new drugs through development, leaving the usual milestone payments and product royalties to Archemix if the collaboration bears fruit.

The idea behind RNAi-based drug development is to create specially engineered RNA molecules that selectively turn off disease-causing genes. Entrants to the field typically have to pay some sort of toll to Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ: ALNY), which has an extensive RNAi IP estate, but Dicerna insists it has found a “second doorway.” Simply put, it’s designing drugs that are a little longer than so-called small interfering RNA molecules being developed by Alnylam and others—and which are therefore not covered by Alnylam’s patents. Dicerna says its drugs may have the added advantage of being more potent that other RNAi-based treatments.

Importantly, these slightly longer RNAi drugs can be made with a handle on them that allows them to be welded together with other drug compounds that could give them extra kick. … Next Page »

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Agios Pharmaceuticals has landed a big fish in the world of cancer drug development. The Cambridge, MA-based company has hired David Schenkein, the senior vice president in charge of cancer drug development at Genentech, to be its first permanent CEO, starting in August. He will replace Kevin Starr, a partner with Third Rock Ventures, who has been serving as its interim CEO in the company’s early days.

It’s a coup for Agios, which debuted with a $33 million initial round of venture capital last Fourth of July weekend. Schenkein will join Duncan Higgons, formerly the president and chief operating officer of Cambridge, MA-based Archemix, who has recently signed on as the chief operating officer at Agios. As I explained in earlier stories about the company last July and November, the idea at Agios is to throw a wrench into the overactive metabolic enzymes that allow cancer cells to grow and thrive. Essentially, the startup hopes to starve cancer cells to death.

Schenkein, 52, has been responsible for clinical development and regulatory work on numerous cancer therapies at South San Francisco-based Genentech over the past three years, as it asserted itself as the largest U.S. maker of cancer drugs. He has worked on efforts to expand usage of top-selling antibody drugs like bevacizumab (Avastin), rituximab (Rituxan), and trastuzumab (Herceptin). Schenkein also has roots in Boston. He played a key role at Millennium Pharmaceuticals in the development of bortezomib (Velcade), and prior to that was the director of the cancer center at Tufts Medical Center.

“David is one of the most sought after executives in the biotech/pharma industry. This speaks volumes about the science and vision of Agios,” Starr says.

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Archemix, a Cambridge, MA-based biotech startup developing aptamer drugs, reports that Kenneth Bate will replace Duncan Higgons as CEO of the company. Higgons, who had become chief executive of the firm in January, is taking a job with another private biotech firm, according to Archemix. Bate was most recently president and CEO of Lexington, MA-based drug developer NitroMed, which walked away from a proposed merger with Archemix early this year.

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Plenty of deals to discuss from all areas of technology and life sciences this week—including a couple of M&A switcheroos.

—Diagnostics maker Exact Sciences (NASDAQ:EXAS) of Marlborough, MA, sold its assets related to prenatal and reproductive health to Cambridge, MA-based Genzyme (NASDAQ:GENZ) for $24.5 million. In response, San Diego-based Sequenom (NASDAQ:SQNM) ended its attempted takeover of Exact—an all-stock deal valued at $41 million.

—CloudSwitch of Waltham, MA, raised $7.4 million in a Series A financing round. Atlas Venture and Matrix Partners co-led the deal for the cloud-computing startup, which was co-founded by CEO Ellen Rubin and John Considine.

—New Haven, CT-based antibiotic developer Rib-X Pharmaceuticals raised $25 million in a debt financing. Previous investors Warburg Pincus, ABS Ventures, Axiom Ventures, EuclidSR Partners, MedImmune Ventures, Oxford Bioscience Partners, SR One, and Vox Equity Partners participated in the deal.

—Virtual Computer, a PC virtualization startup in Westford, MA, raised $15 million in a Series B funding round led by return investors Highland Capital Partners and Flybridge Capital Partners and joined by strategic investor Citrix Systems of Fort Lauderdale, FL.

—IT security consulting firm GlassHouse Technologies of Framingham, MA, acquired Chicago-based CSSG, a fledgling security consulting firm, for an undisclosed sum. Wade explains the strategy behind the deal and a bit about its history.

—Software maker Centive of Lowell, MA, was acquired by San Jose, CA-based Xactly for an undisclosed sum. Centive offers an on-demand version … Next Page »

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There were some interesting M&A developments this past week involving or potentially affecting Massachusetts life sciences firms. Those, and the rest of the week’s news, below.

—Regulus Therapeutics, a joint venture of Cambridge, MA-based Alnylam (NASDAQ: ALNY) and Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISISI), unveiled plans to raise “a very respectable amount” of capital from private investors and reorganize as an independent corporation. The company was formed about a year and a half ago to develop drugs based on microRNA, tiny RNA fragments that affect the behavior of gene networks and which could be useful in treating diabetes, heart failure, and other complex diseases.

—Antiviral drug developer Panacos Pharmaceuticals (NASDAQ:PANC) of Watertown, MA, sold its HIV drug candidate, bevirimat, to Salt Lake City, UT-based Myriad Pharmaceuticals for $7 million.

—Boston’s Enlight Biosciences added healthcare giant Johnson & Johnson (NYSE:JNJ) to the roster of partners who back its efforts to advancing new technologies for use in the discovery and development of drugs. J&J agreed to invest up to $13 million in Enlight’s programs.

—Cambridge, MA-based Stromedix won patent protection for its technology for blocking fibrosis, an underlying process in different types of organ failure. The startup acquired the anti-fibrosis technology from Cambridge, MA-based Biogen Idec (NASDAQ: BIIB).

—Omni Life Science of Raynham, MA, joined with Enztec of Christchurch, New Zealand, to form a new company, called Orthopaedic Synergy, of which Omni and Enztec will both be wholly owed subsidiaries. The new firm also raised $4.8 million of a Series A financing from Pioneer Capital Partners of Auckland, New Zealand, and its limited partners, and plans to bring the round up to $6 million with an additional contribution from Birnie Capital Partners, also of Auckland, in March.

—New Haven, CT-based antibiotic developer Rib-X Pharmaceuticals raised $25 million in a debt financing from Warburg Pincus, ABS Ventures, Axiom Ventures, EuclidSR Partners, MedImmune Ventures, Oxford Bioscience Partners, SR One, and Vox Equity Partners. Ryan talked with Rib-X CEO Susan Froshauer about the prospects for … Next Page »

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NitroMed (NASDAQ:NTMD), the Lexington, MA-based drug developer that struggled to market a heart failure drug for African-Americans, says it has agreed to be acquired for 80 cents per share in cash by investment firm Deerfield Management. This means NitroMed bailed out of previous agreements to sell BiDil to specialty drugmaker JHP Pharmaceuticals and to merge with Cambridge, MA-based biotech firm Archemix.

Archemix issued a separate statement confirming the terminated deal with NitroMed, and the associated fallout. Now that it’s planning to be independent again, Archemix said CEO Errol De Souza, who negotiated the deal with NitroMed, is resigning from the top job and will remain on the board of directors. Duncan Higgons, who was previously executive vice president of business operations, is replacing him as interim president and CEO of Archemix. De Souza had planned to step down after the merger with NitroMed.

Deerfield’s buyout offer, which is subject to NitroMed shareholder approval and other conditions, came last month after NitroMed announced the previous month that it agreed to an all-stock merger with privately held Archemix. The offer represents a 25 percent premium above NitroMed’s closing stock price yesterday of 64 cents. The Deerfield bid puts NitroMed’s value at about $36.8 million.

In October, before Deerfield made its bid, NitroMed said it would sell all assets related to BiDil (isosorbide dinitrate/hydralazine hydrochloride), its heart failure drug approved by the FDA for self-identified African Americans in 2005, for about $26 million. Now Deerfield’s acquisition of NitroMed is expected to close in April.

Archemix’s and JHP’s breakup fees with NitroMed provide some degree of a silver lining. As part of the firms’ agreements with NitroMed, Archemix is due to get a $1.5 million termination fee from NitroMed and JHP is expected to receive $900,000.

Archemix continues to land lucrative deals related to its drugs called aptamers, which use short pieces of DNA or RNA to bind with disease-related proteins. Last month Archemix received $27.5 million in upfront money in a deal to develop aptamer treatments for London-based drug giant GlaxoSmithKline. Two months before landing the GSK deal, former Archemix CEO De Souza told me that his firm had enough cash to support operations through the middle of 2010.

Also, Archemix says that it has just started mid-stage clinical trials of its lead aptamer drug for treating a rare blood disorder known as thrombotic microangiopathiesement.

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NitroMed (NASDAQ:NTMD) says that its board of directors has opted to delay a shareholder vote from today until January 20 on the company’s proposed sale of all assets related to its heart drug for African Americans, isosorbide dinitrate/hydralazine hydrochloride (BiDil), to JHP Pharmaceuticals for about $26 million. The Lexington, MA-based firm says it has delayed the vote as it considers an unsolicited buyout offer made by investment firm and major NitroMed shareholder Deerfield Management, which has told the company its offer is worth 75 cents per share, up from its initial offer of 50 cents per share last month. NitroMed last year agreed to an all-stock merger with Cambridge, MA-based biotech firm Archemix, which must also be approved by shareholders.

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New England tech and life sciences firms have cut many a deal since last we rounded up. Here are some of the most interesting ones.

—Cambridge, MA-based Semprus Biosciences, a spinoff from the famed Langer Lab at MIT, closed an $8 million Series A round of venture capital co-led by 5AM Venture and Pangaea Ventures. Semprus is working on long-lasting polymer surfaces to help combat the microbes that like to grow on medical devices.

—Y Combinator startup Posterous, a developer of tools for “dead simple blogging” raised $750,000 from Zimbra CEO Satish Dharmaraj, former Netscape CTO Eric Hahnof, Guy Kawasaki, Mitch Kapor, and other high-profile investors.

—Archemix of Cambridge, MA, inked a deal with pharma giant GlaxoSmithKline worth $27.5 million upfront and potentially another $200 million in milestone payments for each of the seven of Archemix’s “aptamer” drugs covered by the agreement. The deal will not affect a planned reverse merger with Lexington, MA-based NitroMed (NASDAQ: NTMD), according to Archemix’s CFO.

—EMC (NYSE: EMC) acquired some of the assets and personnel of Seattle’s SourceLabs. The Hopkinton, MA-based firm plans to integrate the new assets and staff into its cloud computing business.

—Lexington, MA-based Indevus Pharmaceuticals (NASDAQ: IDEV), which is developing several drugs for hormonal disorders, said it will be acquired by Endo Pharmaceuticals (NASDAQ: ENDP) for $370 million, with another $267 million on the table if regulatory and sales goals are met.

—Forma Therapeutics, a Cambridge, MA-based startup co-founded by scientists at the Broad Institute of Harvard and MIT, raised $25 million from the Novartis Option Fund, Bio*One Capital, and others. Forma aims to turn new knowledge about the genetic underpinnings of cancer into new treatments for the disease.

—Needham, MA-based ClickSquared, a provider of a software-as-a-service system for direct marketing, raised an $11 million Series B round led by JMI Equity, ABS Venture, and Flybridge Capital Partners. The round brings ClickSquared’s total raised to $46 million.

—RatePoint, ClickSquared’s Needham neighbor, also completed a Series B round, this one worth $10 million. Castile Ventures led the deal, and .406 Ventures and Prism VentureWorks joined in backing the developer of online surveys and widgets.

—Satori raised $22 million in venture capital from InterWest Partners, Prospect Venture Partners, New Enterprise Associates, and others. The Cambridge, MA-based startup, founded by Boston-based PureTech Ventures, which also joined the funding round, is aiming to develop small-molecule drugs that can be safely taken on a chronic basis to block the production of toxic proteins that cause Alzheimer’s disease–hopefully halting it in its early stages.

—Waltham’s Polaris Venture Partners participated in a $7.5 million Series C round for JibJab, the online parody maker that has recently begun making e-cards. Overbrook Entertainment and Sony Pictures Entertainment led the deal.

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There was quite a bit of news this week relating to RNA-interference drugs, and to FDA approval (or non-approval, as the case may be) of drugs under development by local biotechs. Without further ado:

—It was sports week for Ryan. First, he interviewed biotech hedge fund founder Rich Aldrich, part of the group that owns the Boston Celtics, who said why he’s excited about Alnylam, Alnara, and the future of his fund. Then he talked with David Lucchino, CEO of Cambridge, MA-based Semprus Biosciences and nephew of Red Sox CEO Larry Lucchino, about Semprus’s $8 million Series A round and its plans to develop longer-lasting polymer-based surface materials for plastic and metal medical implants.

—Yet another new pharmaceutical company focusing on RNA-interference, Norwood, MA-based AiRNA, emerged from stealth mode, with a focus on so-called asymmetrical interfering RNA molecules 15 base pairs in length, which are shorter (and may therefore have fewer side effects) than the RNAi molecules being developed by Alnylam and others. Alnylam, meanwhile, announced it has filed an application with the FDA to start the first clinical trials of its systemic RNAi anti-cancer drug, ALN-VSP.

—In Waltham, MA, Entra Pharmaceuticals collected the first $4.2 million of what could end up being a $12.5 million Series A venture round, with Flybridge Capital Partners and North Bridge Venture Partners participating.

—BioTrove of Woburn, MA, changed its mind about going public in the current market, canceling the planned $75 million IPO for which it first filed eight months ago.

—Weeks after news that the FDA had declined to approve its lead drug candidate, an antibiotic intended to treat the MRSA infection, Cambridge, MA-based Targanta Therapeutics laid off 86 employees, about three-quarters of its staff.

—In a private offering of its stock, genetic analysis tools maker Helicos Biosciences … Next Page »

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(Update: The first paragraph includes information that seven drugs are subject to the partnership, and the final paragraph includes comment from Archemix about this deal’s impact on its proposed merger.)

Archemix scored one of the biggest biotech deals of the year just in time for Christmas. The privately held Cambridge, MA-based drug developer secured a partnership with GlaxoSmithKline, the world’s second-biggest drugmaker, that will bring in $27.5 million in upfront cash and potentially another $200 million in milestone payments for each of the seven drugs included in the alliance.

Under the deal, Glaxo will get access to Archemix’s proprietary “aptamer” technology, which employs short strings of DNA or RNA designed to bind tightly and specifically with disease-related proteins. The goal will be to develop treatments for inflammatory diseases like rheumatoid arthritis and inflammatory bowel disease. In return, Archemix will get $27.5 million in cash upfront, including a $6.5 million equity investment from Glaxo. Another $200 million in milestone payments for each drug could go to Archemix if these drugs reach certain milestones in development, the companies said in a statement. If the drugs ever become marketed products, Archemix could stand to get a “double-digit” percentage royalty on sales.

“We are very excited about this collaboration with GSK. GSK is an outstanding partner with leadership and expertise in inflammation, and we look forward to expanding our efforts in inflammation where aptamers could offer novel options to treat disease,” said Errol DeSouza, Archemix’s CEO in a statement.

Archemix didn’t have much to say in the statement about how this alliance affects its most important corporate strategy of the moment—its planned merger with Lexington, MA-based NitroMed (NASDAQ: NTMD). That deal, announced Nov. 18, would provide a lifeline to NitroMed shareholders by giving them access to Archemix’s technology and cash, while allowing Archemix the access to public investors it wants by giving it a spot on the NASDAQ, which wouldn’t be possible now through an IPO.

Of course, the terms of the merger, which still needs to be approved by shareholders of both companies, were negotiated before Archemix secured this stabilizing deal with Glaxo. Obviously, Archemix has a little more security now than it did a month ago, and its value probably just went up by quite a bit. Because of the upfront payment from the Glaxo deal, Archemix now expects it will have $78 million to $88 million in cash if the combination with NitroMed is finalized.

But this isn’t a done deal. To complicate matters further, NitroMed has gotten an unsolicited takeover bid from Deerfield Management, the huge biotech hedge fund, which already owns 12 percent of NitroMed and wants to buy the rest of its shares for 50 cents a share. We’ll be watching to see how this story unfolds, whether NitroMed and Archemix get hitched, or end up going their separate ways.

Archemix says the merger is still proceeding as planned, even after signing the Glaxo deal. ”This GSK collaboration is part of Archemix’s ongoing strategy to establish partnerships for aptamer therapeutics in key disease areas, and this changes nothing about the proposed Nitromed merger. We are continuing to be on track with progress toward closing the Nitromed deal, including an S-4 filing that was made last week with the SEC,” said Gregg Beloff, Archemix’s chief financial officer.

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Boston-area life sciences firms made a good showing at two important meetings this week. Luke and Ryan gave the rundown on those, and took a look at a couple very interesting startups.

—Ryan checked in with Frank Reynolds, spinal-cord-injury survivor and CEO of InVivo Therapeutics, about the progress of his company’s Cambridge, MA-based effort to develop an implant that could prevent some cases of paralysis. With $3 million from family and friends (so far) and technology initially developed in the famous Langer lab at MIT, InVivo could get FDA clearance to begin human testing of its polymer-based device next year.

—Cambridge, MA-based Ascent Therapeutics inked a deal worth as much as $200 million with Novartis; the agreement would give the drug giant rights to co-develop Ascent’s new class of treatments, called “pepducins.”

—Xconomist David Resnick shared his hope that the Obama administration will breathe new life into two areas of life sciences: embryonic stem cell research and personalized medicine.

—Sirtris CEO Christoph Westphal was tapped to help lead GlaxoSmithKline’s Center of Excellence for External Drug Discovery and help GSK form alliances that will strengthen its pipeline. Westphal will also continue to run Cambridge, MA-based Sirtris, which GSK acquired in June for $720 million.

—We dispatched Ryan to the Massachusetts Biotechnology Council’s annual MassBio Investors Forum, a sort of a mixer for local biotechs and the various investors, partners, and other backers who (hopefully) keep them going. With traditional sources of cash scarce this year, the MBC put more emphasis on funding from disease foundations such as the Cystic Fibrosis Foundation and Michael J. Fox Foundation for Parkinson’s Research.

—The FDA declined to approve an application … Next Page »

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Lexington, MA-based drug maker NitroMed (NASDAQ:NTMD) says it has received an unsolicited bid from investment group Deerfield Management—which already owns about 12 percent of NitroMed’s stock—to acquire NitroMed for 50 cents per share in cash, a 40-percent premium on its closing price today of 30 cents per share. The company says it’s evaluating the offer. The unsolicited bid follows the November 18 announcement of a proposed all-stock merger between NitroMed and Cambridge, MA-based biotech firm Archemix, which is pending approval from both firms’ shareholders and the sale of NitroMed’s heart failure drug BiDil (hydralazine and isosorbide dinitrate) to JHP Pharmaceuticals.

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Half a dozen Boston-area tech and life sciences startups have something to be thankful for heading into this week’s holiday, all of them having managed to close venture deals in a very tricky environment. A few public companies cut some interesting deals as well.

—ReGen Power Systems, a Salem, MA-based firm developing a power-producing external combustion engine, raised $5 million from 21Ventures and Quercus Trust. ReGen plans to use the money to build two prototypes of its engine for evaluation and field testing.

—RFID systems maker ThingMagic of Cambridge, MA, inked a strategic investment and technology development deal with CIA-founded venture firm In-Q-Tel. The terms of the deal were not disclosed.

—In-Q-Tel also made an unspecified investment in Febit, a German maker of DNA- and RNA-sequencing devices with laboratories in Lexington, MA.

—Nashua, NH-based virtualization software maker AutoVirt added $4 million to its Series A round from return investors Kepha Partners and Sigma Partners, bringing its total raised to $8.5 million.

—Hadley, MA-based SunEthanol, a developer of cellulosic ethanol technology, raised $25 million in a Series B round of financing led by Venrock and Battery Ventures and joined by BP, Soros Fund Management, Camros Capital, and Long River Ventures. The firm also … Next Page »

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