Computers Crack Down on Drug Side Effects

09 December 2007
Posted by Chris Smith.

At one time the only way to find out whether a potential drug might be safe was to test it on animals and then on humans.  And it was often only after it had been licensed and begun to fly off doctors' prescriptions pads that rare, and sometimes deadly side effects were uncovered.

Now scientists have developed a computer programme that can screen potential drug molecules for potential side effects before they've even left the test tube, a move which could save pharma companies a fortune. The work is the brain child of UC San Diego computer scientist Philip Bourne. He and his colleagues have based their approach on a technique already employed by drug companies to first identify chemicals that might have therapeutic effects. Pharmaceutical developers run simulations comparing structures of molecules that might be linked to certain diseases in the body with chemical compounds they have made. They're looking for signs that their compound might be able to affect their chosen molecular "target". So what the San Diego team have done is to develop a system that compares drug molecules against the stuctures of large numbers of human proteins - 800 in the present study - looking for interactions.

As a proof of concept they tested their approach on the breast cancer drug tamoxifen and identified a hit. The system predicted an effect on a protein that pumps calcium into and out of cells. And this fits perfectly because Tamoxifen is known to cause heart problems in some patients, and heart cells rely on calcium to contract. But the approach, published in PLoS Computational Biology, still has some way to go. The human genome encodes at least 25,000 different proteins, many of which have not yet been fully or even partially characterised. However, it's early days and an encouraging start. And as Bourne points out "there is a lot of potential for this process".

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