Computers select personal medicine

BBC health news reports UK-US scientists have given one glimpse of the future of personalised medicine. Using supercomputers, they simulated the shape of a key protein involved in HIV infection in an individual patient and then ranked the drug molecules most likely to block the activity. The research was reported at the annual meeting of the American Association for the Advancement of Science (AAAS).

In the future, it is expected that patient-specific drug selection will become routine. Researchers now recognise that pharmaceutical products do not have the same effects in all people. Subtle genetic differences between individuals will lead to a range of outcomes. Prof Peter Coveney and colleagues from University College London and Rutgers University have demonstrated how you might tackle this problem using the latest genetic sequencing techniques and big computation.

They took as their target the HIV protease molecule, which is critical in helping to build the viral particle, or virion, in a cell that will eventually break out to infect the next cell. The protease has a slightly different shape in each individual, in particular in the protein’s active zone where it slices the components that will form the next virion. This is a consequence of the very specific genetic sequence of the virus in that person, but unless that shape is known, there is uncertainty as to which particular drug will bind to the protease and stop it in its tracks. The UCL team showed how one could take the specific viral sequence, infer the shape and then work out the most appropriate drug. “We show that it’s possible to take a genomic sequence from a patient; use that to build the accurate, patient-specific, three-dimensional structure of the patient’s protein; and then match that protein to the best drug available from a set. In other words, to rank those drugs – to be able to say to a doctor ‘this drug is the one that’s going to bind most efficiently to that site. The other ones, less so’.”

As well as reporting this work at the AAAS meeting, Prof Coveney’s UCL-Rutgers team has also written up the research in the Journal of Chemical Theory and Computation.

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