Drug efficacy simulation on virtual human pioneers tailored HIV treatment

University College London scientists have used the combined processing power of the US and UK supercomputer Grids to simulate the efficacy of an HIV drug in blocking a key protein used by the virus

Using The EU-funded Virtual Physiological Human (VPH) initiative, the method could ultimately be used to tailor personal drug treatments: for example, for HIV patients developing resistance to their drugs.

The study by Professor Peter Coveney and colleagues at UCL Department of Chemistry involved a sequence of simulation steps, performed across multiple supercomputers on the UK's National Grid Service and the US TeraGrid.

A large number of simulations were run to predict how strongly the drug Saquinavir - an HIV-inhibitor - would bind to three resistant mutants of HIV-1 protease - a protein produced by the virus to propagate itself. These protease mutations are associated with the disease's resistance to Saquinavir.

Nine drugs are currently available to inhibit HIV-1 protease, but doctors have no way of matching a drug to the unique profile of the virus as it mutates in each patient, and have to rely on trial-and-error methods to find the best match to a patient's genotype.

VPH links global networks of computers to simulate the human body's internal workings, allowing scientists to simulate the effects of given drugs, and track what is happening at the organ, tissue, cell and molecular level. The VPH project aims to boost collaboration between clinicians and scientists to explore the scope for patient-specific medical treatments based on modern modelling and simulation methods.

The study represents a first step towards the ultimate goal of 'on-demand' medical computing, says Professor Coveney, where doctors could "borrow supercomputing time" from Grids to make critical decisions on life-saving treatments.

"For it to be clinically relevant you have to have a very fast results turnaround ̵1; two weeks, typically," Coveney explains. "Such simulations at present require a substantial amount of computing power [and] might prove costly for the National Health Service, but technological advances and those in the economics of computing would bring costs down."

Image: UCL researchers needed to predict how strongly the drug Saquinavir - an HIV-inhibitor - would bind to three resistant mutants of HIV-1 protease, a protein produced by the virus to propagate itself

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