UCL in the News: Treating the Patient, Not the Illness

Aaron Dubrow, Texas Advanced Computing Center In biomedicine, the Holy Grail is patient-specific medical treatment, says Peter Coveney, Professor of Physical Chemistry at UCL and Director of the Centre for Computational Science there.

Instead of a generalized approach to illness, personalized medicine promises treatments developed just for you and sophisticated diagnostic tools to differentiate your genetic disposition and strain of illness from your neighbor's. …

His simulations of drug-resistant HIV protease proteins, performed with the resources of the Texas Advanced Computing Center (TACC), push the limits of biomedical research and test methods for the fast and accurate treatment of unique illnesses. …

"Given that we know so much now about the genetic makeup of individuals and are able to collect data on them as individuals, not just as a 'generic patient', the obvious challenge is to develop treatments that address the particular patient and the ailments that they may have," Coveney explained. …

"Many of these infectious diseases are clever enough to develop strategies to resist the drugs over time," Coveney said. "The HIV virus is very good at doing this because of the way it copies itself. The error rate in reproduction is so great that its mutations allow it to outwit drugs." Though Coveney's research has dealt mainly with HIV, his computational approach could apply equally well to the flu, hepatitis and other mutating diseases. …

Coveney and his colleagues first developed fine-detailed molecular representations for HIV protease and saquinavir, the first HIV drug to be discovered that inhibits the replication of HIV by binding to the protease molecule. They then used molecular dynamics codes that fully exploit the massively parallel power of TACC's supercomputers to determine how well the drug binds to the "wild-type" HIV protease and to three drug-resistant mutant strains. …

Identifying the cause of HIV drug-resistance is important, but Coveney's ultimate goal is to create a system that can recognize mutations quickly and administer the proper preventive drug in a suitable timescale. "Can we do computations sufficiently rapidly and accurately and rank the different drugs that might be used as treatments in terms of which will be most favoured versus which will be most resisted by the patient? In the long run, these sorts of scenarios in biomedicine may end up being life or death decisions, and will use computational methods," Coveney said. "Our research is putting some of the pegs in the ground for whether that's viable or not." …

To date, Coveney has focused his biomedical research mainly on the HIV protein, protease. However, his future studies will model and predict the binding energies of reverse transcriptase, another molecule involved in HIV replication that is significantly larger than protease. …

At present, the realistic application of patient-specific medicine remains quite a few years away. But by harnessing the power of supercomputers, Coveney is blazing a path to rapid advances in computationally-assisted diagnosis and drug prescription.

"To be able to tailor medical treatment to a person and their ailments, instead of giving them some average course of treatment - we're only going to get to that level of patient specificity if we use computational science and high performance computing, of that there can be no doubt," Coveney said. "Computational science is not going away, it's just going to become increasingly pervasive as time goes on."