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Computers spot drug's deadly side effects
[December 07, 2007]

Computers spot drug's deadly side effects

(New Scientist Via Thomson Dialog NewsEdge) CAN the pharmaceutical industry avoid another Vioxx? The painkiller was pulled from the market in 2004 when it became clear that it increased the risk of heart attacks and strokes. Tens of thousands of people sued, forcing its manufacturer, Merck, to pay $4.85 billion to settle the cases. If there were a way of spotting side effects missed by clinical trials it would save lives and money.

Now computing experts say they have one. Though not foolproof, it provides a relatively quick and easy method for zeroing in on some of the side effects that existing tests miss.

The inspiration comes from the methods used to test candidate drugs. If a disease is related to a specific molecule in the body, drug companies can run simulations to gauge what compounds might bind to that molecule and affect it. This helps to eliminate compounds that will not work and fine-tune the development of those that do.

Philip Bourne and his colleagues at the University of California, San Diego, have co-opted this process in a bid to spot side effects. As a proof of concept, they studied a class of drug that has already been approved. Selective oestrogen receptor modulators, which include Tamoxifen, are used to treat breast cancer and other diseases. To look for possible side effects of such drugs, Bourne and colleagues searched around 800 human proteins for sites that the drug might bind to.

The simulation yielded one direct hit: a protein that helps control the movement of calcium in and out of cells (PLoS Computational Biology

, DOI: 10.137/journal.pcbi.0030217). The result suggests the approach may work, since the problems associated with Tamoxifen can be explained by a disruption in calcium levels. Heart problems are one side effect and cardiac muscle cells are sensitive to changes in internal calcium levels.

"There is a lot of potential for this process," says Bourne. Using current techniques, he adds, side effects are discovered by animal tests, at least under the best-case scenario. "In the worst cases, it's not until the drug is on the market and killing people."

While Bourne's paper is one of the first to discuss the technique, some pharmaceutical firms are already using similar approaches. Laszlo Urban, head of safety profiling at the Novartis Institutes for BioMedical Research in Cambridge, Massachusetts, says his firm used a related method last year. He declined to reveal the candidate drug involved, but says that the approach identified a possible side effect that was severe enough for development to be scrapped.

Urban also notes one of the technique's limitations. Around 25,000 proteins have been identified from the sequence of the human genome, but not all have been studied in detail - and you need to know a lot of detail about a particular protein's binding sites before computer simulations can be used to check for side effects.

Copyright 2007 Reed Business Information - UK. All Rights Reserved.

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