Opening the door to data flow

BURLINGAME,Calif.—Seeking a way to move data-rich and complex information back andforth between collaborating parties—a major challenge for researchteams whose members operate in multiple locations—Collaborative Drug Discovery Inc. (CDD) has made 10 of ChemBridge Corp.'s most popular screening libraries available to researchers via CDD's Public Access database.

The collaboration, announced in September, adds several ofChemBridge's screening libraries to CDD's database of more than 1million contributed compounds, giving researchers access to a growingbody of public data from leading vendors, researchers, scientificliterature and patent resources. In addition, researchers who subscribeto CDD's Vault database, the commercial version of the public database,can access data directly from their private groups, mining thelibraries using their own private data to more effectively identifycompounds of interest within the ChemBridge datasets. Financial termsof the partnership were not disclosed.

Dr. Barry Bunin, CEO of CDD, says both the company's public andprivate users will benefit from the valuable new molecules and datathat have been added to its database.

"It is a new way of simultaneously interacting with lots of datafrom lots of collaborations," Bunin says. "Our database is a greatsolution for academics, new start-ups that are looking for data on anew target and even large pharmas that screen millions of compounds viapartnerships all over the world. All of these parties use us for leadidentification and optimization. Now we have some of the largest setsof data uploaded from one of the better-known vendors. This partnershipis a real coming-of-age for us."

Based in San Diego, ChemBridge is a globaldiscovery chemistry company providing custom chemistry services,small-molecule screening compound libraries and specialty buildingblocks for organic synthesis. According to the company, more than 500major and mid-size pharmaceutical companies, biotechs and use itsportfolio of products, including its library of 10,000 specialtybuilding blocks and 800,000 drug-like and lead-like small-moleculescreening compounds.

Among the ChemBridge libraries being offered in CDD's database areDIVERSet, a 50,000 small-molecule dataset covering a broad range ofpharmacophore space; CNS-Set, which contains 56,000 molecules with anincreased probability of blood brain barrier penetration; MicroFormat,a ready-to-screen collection of 100,000 to 200,000 small molecules,pre-plated in DMSO in 0.25 umol and higher amounts and 0.1mg to 5mgamounts; KINASet, a kinase library of 11,000 compounds which werecollected using a ligand-based pharmacophore selection method;NOVACore, a newly synthesized chemical library consisting oflow-molecular weight screening compounds and more than 100,000compounds based on more than 100 templates; PHARMACophore, a chemicallydiverse screening library containing 67 synthetically complex and novelcore scaffolds; and GPCR, a targeted library representing 14,000compounds based on nine templates.

In total, the integration will enable researchers to access about600,000 lead-like, quality small molecules at the touch of a button. Inaddition, ChemBridge has generated hit-to-biological target dataamassed from years of publication results from library screens, whichare tracked and annotated.

The data is not only easily searchable by keyword or chemicalstructure, but it also exists in a flexible format, allowing freeaccess to the public domain site along with private users, saysJennifer Milanovich, associate director of sales and marketing atChemBridge.

"The biologically relevant information also gets linked to thescreening compound hits, giving extra data and allowing users to drilldown to deeper levels or easily access an overview of criticalinformation," Milanovich says. "These days, it's all about datamanagement and how to process through this in a sane and usable formatto get to the information that matters. In this sense, CDD provides acomprehensive platform that can take a researcher from biologicalresults to chemical structure to the commercial source for structuresof interest. I believe that CDD has done a very good job of addressingthis need, offering low-cost solutions for smaller labs on a budget,while still addressing sophisticated software data management needs forprivate users with specific requests."

Anyone can register for free, read-only access to these new and allpublic data sets on CDD's Web site. Read-and-write access, includingthe ability to archive, mine and collaborate around private data and toimport and export both private and public data, can be accessedfollowing a free trial with full commercial access to Vault. Thecompounds are available for testing hypotheses from ChemBridge.Additional molecules not in the public site can be ordered, and thecorresponding structures can also be archived in private sites andlinked to biological activity data.

"If you need to find a library suited to your target, or if you'rean experimentalist who wants to track all of your experiments and buildon what you have done previously, or if you are a computationalscientist who wants to interact with experimentalists to testhyptotheses—we have a solution for you," Bunin says. "If you are aprivate user, you have a dashboard that shows up-to-the-minute changesand updates. You can be a Big Pharma company with five CROs and giveeach one access to only one-fourth of the data, and be able to switchback and forth between the five groups. It's very flexible and easy touse."

The integration removes challenges when a large amount of complexinformation needs to flow readily back and forth between collaboratingparties, Milanovich says.

"Anytimeyou have an easy to use software platform that can be accessed by bothpublic and private parties, then you open up the doors to data flowwithout having to reinvent the wheel or input a large capitalinvestment upfront," she says. "Anyone can access the site and see theformatted data and build awareness via links and further drilling downinto assay and screening details on both a biological and chemicalfront. From this standpoint, the standardization helps to transmit theinformation quickly, with ease and in an almost intuitive manner."