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With $1M in VC Cash, Ligon Discovery Gets Set to Commercialize Small-Molecule Microarrays

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By Justin Petrone

Ligon Discovery, a 6-month-old spinout from Harvard University, will spend a recently closed $1 million round of venture capital financing to help it launch its small-molecule microarray platform; continue ongoing internal drug-discovery programs; and invest in R&D, according to a company official.

CEO Patrick Kleyn told BioArray News this week that the Cambridge, Mass.-based startup is looking to partner with pharmaceutical and biotechnology companies that would like to use its small-molecule microarray, or SMMs, in their drug-discovery programs.

"We are looking for collaborations and want to get our name known to potential pharma, biotech, and academic customers," said Kleyn. "We have our platform up and running and we are ready to begin those relationships."

He added that Ligon is looking to hire "chemists, biologists, and some data-analysis specialists. Right now, we are a small operation, but we are looking in 2010 to do a series A financing round and will have a larger uptick in the number of individuals hired."

SMMs are manufactured by spotting unmodified compound collections at high density onto glass slides using Ligon's chemical attachment approach. Using the platform, hundreds of thousands of compounds on SMMs can be rapidly screened in parallel against hundreds of protein targets.

A centerpiece of the firm's technology is its surface chemistry, which was designed to allow the attachment of chemical collections — whether synthetic, natural, bioactive, or diversity-oriented. Since no special moiety is required for attachment, Ligon's SMMs are compatible with most existing chemical collections, the firm claims.

Kleyn said that Ligon's technology is similar to traditional DNA array technology in that it allows screening on a parallel scale, but that it has been harder to design a chemical array technology due to limitations with getting chemicals to bind to the same surface.

"When you are spotting a DNA molecule on array, you only have to solve that problem once because even as the sequence changes, it's still one chemical you put down," Kleyn said. "Think now about different scaffolds and functional groups and how you attach such a diversity of chemicals to a single surface with a single surface chemistry," he continued.

Kleyn said that, previously, those wishing to prepare chemical arrays would use a "bait-and-hook approach," combining chemicals of interest with complementary chemistry."But if you want to screen existing chemical sets, you don’t want to retrofit and redesign entire chemical libraries," he said.

Hoping to overcome this challenge, Ligon's founders developed a "promiscuous chemistry, which will attach about 75 percent of chemicals in a screening library and retain the signal-to-noise characteristics needed" for an array-based assay. The assay itself is a "standard Western blot" that includes incubating a slide with a protein and labeling it with antibody, Kleyn said.

"Conceptually, it’s a simple assay and its power is that it’s a microarray technology that you can do on parallel scale."

Using the assay, researchers can screen protein families, molecular pathways, and genome-wide targets in parallel to identify small molecules with optimal characteristics for drug development, according to Kleyn. He said that Ligon is using SMMs for two purposes: for the “discovery of novel inhibitors against high-value targets" and in collaborations with pharma companies, where targets can be screened against custom-designed chemical collections.

Kleyn said there is a third potential route for Ligon: selling products based on the SMM technology, such as "kits that would have known chemical libraries arrayed on SMMs that could be used by biological researchers who would be interested in doing a screen." He said that a move into the catalog array business is not being pursued at present but is a future possibility.

"Ligon is an early-stage drug-discovery company," Kleyn said. "We have a jewel business model where we enter into collaborations with pharma and biotech businesses, and we also have internal efforts where we have particular sets of targets where we have insights to their success and applicability and were looking for novel molecules."

Ligon sees its technology as competitive to other technologies, such as mass spectrometry, because of its ability to screen chemicals in a parallel way.

"The way SMM distinguishes itself is similar to the way that DNA array technology distinguishes itself from RNA analysis approaches, and that is the scale and minimal upfront assay development cost," said Kleyn.

"You might spend months or years developing an assay to do a high-throughput screen," he said." But this technology has minimal assay development requirements, so if you generate a list of 50 proteins you want to screen, you can look at the data in a couple weeks."

While Ligon is technically offering an array platform to study proteins, Kleyn said that current protein array platforms are complementary to what Ligon offers. He said that Ligon uses a Biacore surface plasmon resonance-based assay in its own screening programs.

"We have small molecules fixed on the surface and proteins floating," he said. "If we use Biacore, the protein is on the surface and the small molecule is in the solution. We are in a different space from protein arrays but, generally, large organizations would tend to use all available approaches."

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