Using MIT-Harvard Technology, Ligon Discovery Speeds Up Search for New Drugs

Xconomy Boston — 

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 make any number of drug-screening assays. Angela Koehler, a chemist at the Broad Institute and co-founder of Ligon, discovered several years ago that an isocyanate chemistry could be used to bind a majority of small molecules to glass slides used to find drug candidates, without requiring time-consuming chemical modifications that are typically required to develop such tests.

The startup can use the chemistry to attach thousands of small molecules onto slides, which are used to identify molecules that bind to disease proteins in a high-speed screening process. The chemistry enables Ligon to link more than 75 percent of the small molecules in a typical compound collection to the glass slides, providing them the ability to screen hundreds of thousands of molecules against dozens of protein targets at the same time, according to Ligon. Koehler (who made the company’s key discovery with colleagues in the standout chemist Stuart Schreiber’s lab at Harvard) has in recent years published numerous research papers that demonstrate its use in identifying drug candidates against transcription factors and other proteins that have historically proved very challenging for drug discovery.

Ligon has a two-pronged business strategy to exploit Koehler’s discovery, according to Kleyn. First, the company is seeking partnerships with drug companies that would pay to use the startup’s technology as well as provide future payments based on the success of drugs it discovers with the technology. Thus far, the startup has formed such a partnership with the Cambridge, MA-based biotech Lycera, which plans to use Ligon’s technology to discover small molecule drugs for immune disorders. (Last week Lycera, which is covered by Xconomy’s new Detroit site because it has a key R&D site in Plymouth, MI, raised $11 million from investors.) The second prong of Ligon’s strategy is to use its technology to discover its own drugs against difficult-to-drug targets like protein-protein interactions. Ligon has completed initial screens against over 50 such targets and is now moving ahead with its first drug candidates in cancer, inflammation, and metabolic disease.

Kleyn says that his firm is in talks with multiple potential partners, the names of which he was unable to disclose because of confidentiality concerns. However, it came to light during the Boston Biotech Business Development Conference in April that Ligon had met with executives at the London-based drug giant GlaxoSmithKline’s Center of Excellence for External Drug Discovery (CEEDD), which does option-based deals with biotechs to enhance Glaxo’s pipeline of potential drugs. Michelle Dipp, the head of the CEEDD, mentioned her outfit’s interaction with Ligon during the conference but did not disclose the nature of talks between her group and the startup.

Nevertheless, the buzz about Ligon bodes well for its future. Kleyn says that his firm, which raised $1 million in seed money from the investment firm IncTank Ventures last year, wants to raise between $3 million and $5 million in a Series A round of venture capital. The money would help fund its internal drug-discovery efforts and support its search for new partners. The Ligon crew knows how to raise cash for biotech startups. Kleyn was chief scientific officer for Gemini Genomics (now part of San Diego-based Sequenom), where he took part in the firm’s $96 million initial public offering. Ligon has also recruited Errol De Souza, the former CEO of Cambridge-based Archemix, as its chairman.

Now that Ligon’s been discovered, the startup faces the even bigger challenge of finding a drug that can go the distance in human clinical trials. We’ll see how they handle this hurdle in the coming years.

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