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Chemalytics Wins $1.4M SBIR Grant to Develop Cloud-based Drug Screening Platform

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The National Institutes of Health has awarded a $1.4 million Phase II Small Business Innovation Research grant to Chemalytics, the informatics arm of Philadelphia-based bioinformatics consulting firm B-Tech, to develop and bring to market the Chemalytics Virtual Screening Platform, its cloud-based screening platform for drug discovery.

Previously, the four-year-old company received just over $170,000 from the NIH's National Institute of General Medical Sciences, which it used to build and implement a prototype of its system on the Amazon EC2 cloud computing environment. According to the abstract that was submitted as part of that application, those funds, which were disbursed in 2011, were to support the "development of the software infrastructure required for computational cluster virtualization and management; development of a basic user interface for submission and management of virtual screening requests and evaluation of results; [and for] validation of this approach through analysis of screening results."

After a pilot study where the company demonstrated that it cost about $30 to screen roughly 10,000 compounds using off-the-shelf software and cloud resources, Chemalytics' next step was to show that it was feasible to use those same resources to screen libraries containing millions of compounds against therapeutic targets, Brian Moldover, the founder of B-Tech and Chemalytics, explained to BioInform — the pilot helped the company secure the NIH funding it needed for the proof-of-concept.

Such a system would be a cheaper alternative to large and often expensive computer clusters and would remove the need for dedicated IT and computational chemistry staff, he said. It would also be an alternative to software solutions sold by companies such as Mcule, Schrödinger, and Accelrys, for scientists whose primary research focus isn't drug discovery and who require only sporadic access to associated infrastructure, he added.

Chemalytics successfully met the product development and validation goals it set for itself during phase I working in collaboration with researchers at the University of Missouri — in Kansas City and St Louis — and Temple University, according to Moldover. He said that the company has put together a pipeline that uses a combination of proprietary and publically available software such as AutoDock that helps users match compounds to receptors "quickly and inexpensively." Since it runs on the cloud, "[we can] adapt the size of the computational infrastructure based on the size of the job. If it’s a little job, we can run it on one machine [and] if it’s a big job, we can run it on thousands of machines," he said. As an example, Chemalytics was able to use the platform to screen a 6-million-compound chemical library using about 1,700 Amazon machines.

Chemalytics is making the early version of its pipeline available in a limited fashion for biologists, chemists, and medicinal chemists in academia and the biotechnology industry who are interested in trying it out ahead of the commercial release planned for this summer — these users would only be able to screen the roughly 1,600 compounds in the NCI Diversity Set III. Chemalytics will offer two pricing schemes: a pay-as-you-go option where customers are charged based on the size of the library they would like to screen; and an annual site license where customers pay a $5,000 base licensing fee which covers consulting and computational time. Later on, Chemalytics will offer a service where it will run the screening and return a list of potential drugs to customers who prefer not to use the software themselves.

But there is still work to be done before the platform goes on sale. Although it is functional — it has been used, for example, to identify two new potential drugs for acute chronic myeloid leukemia that have been through pharmacokinetics testing and are now in animal testing — there are still improvements to be made on front end that would make it simpler for customers to use, Moldover said. Chemalytics' plans on that front include integrating new data analysis and visualization tools, according to abstract of the current NIGMS grant.

The funds will also support the "integration of additional chemical libraries and library filtering tools to focus search space prior to docking [and] validation of this approach through analysis of screening results with our collaborators and commercial partners," the abstract states. During Phase II, Chemalytics will also continue working with its partners at the University of Missouri and Temple University — the latter is also providing a new office space and business services for the four-person company.

As part of these efforts, Chemalytics has signed an agreement with the Hungarian cheminformatics company ChemAxon that allows the former to license and integrate the latter's applications, software, and database structures with the virtual screening platform, as well as to hire two ChemAxon employees as contractors. Chemalytics will continue to collaborate with its existing partners at Temple and UM on the ongoing AML drug discovery project as well as on projects focused on new antibacterials and antifungals. It will also continue its collaborations with industry including an existing arrangement with Haro Pharmaceutical, a local partner with whom Chemalytics has identified and patented a number of kinase inhibitors.

The company is also hoping to hire scientific software developers and a computational chemist to support its development efforts — it intends to raise its headcount to seven employees.

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