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July 18, 2012

Aussie Supercomputer Simulates Common Cold’s Susceptibility to New Drug

Robert Gelber

The human rhinovirus, otherwise known as the common cold, is usually a fairly minor inconvenience for its human hosts. But the symptoms are far more serious for those suffering from asthma and chronic obstructive pulmonary disease (COPD).  Today roughly 70 percent of heightened asthma symptoms are linked to the common cold. Over 50 percent of those affected eventually require hospitalization. It is also responsible for sending more than 35 percent of COPD sufferers to hospitals each year.

To help the at-risk population, Biota Holdings Ltd., a Melbourne-based company is developing an antiviral drug. This has led members from St. Vincent’s Institute of Medical Research (SVI) and the University of Melbourne to research how the drug works against the rhinovirus.

In a press release describing the work, scientists are using supercomputing simulations as a basis for revealing the drug’s efficacy. Professor Michael Parker, who leads the research team, explained the basic mechanics behind the new compound. “Our recently published work with Biota shows that the drug binds to the shell that surrounds the virus, called the capsid. But that work doesn’t explain in precise detail how the drug and other similar acting compounds work,” he said.

Part of the team’s study involved creating a 3D model of the rhinovirus. It was simulated using the recently deployed Avoca supercomputer at Melbourne University. An IBM Blue Gene/Q machine, the system has 65,536, 1.6GHz power cores with 65 terabytes of memory. At 838 peak teraflops (690 teraflops Linpack), Avoca is the fastest computer in Australia and ranks 31st on the June 2012 TOP500 list.

Parker said that supercomputers like Avoca have enabled scientists to study how drugs function at a molecular level. The new system can now simulate the entire rhinovirus in useful time frames, which in turn can accelerate the discovery and development of new treatments. Prior to the Avoca’s installation, researchers only had the capability to run simulations on portions of the virus.

If the research proves successful, it could reduce the lethality of the common cold for at-risk populations while reducing associated medical costs.  Dr. John Wagner, the manager at IBM’s Research Collaboratory for Life Sciences in Melbourne, noted that simulations like this are going to drive life science research moving forward.  “This is the way we do biology in the 21st Century,” he said.

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