This MIT Technology Review article is rather interesting:
A biotech company called CombinatoRx has found that at the right doses, thousands of counterintuitive drug pairs are synergistic. The Cambridge, MA, company has eight drug combinations in clinical trials and several more in preclinical development. In a few years, diabetics, instead of injecting insulin, might be prescribed a cholesterol drug and a pain medication to help control their blood sugar. People suffering from chronic pain might find relief through a combination of a steroid and an antidepressant, with fewer side effects than they experience with current therapies.
Their process is experimental
The company has a library of thousands of compounds–drugs approved in the United States and other countries, food additives, natural products, drugs under development by partner companies–that can be combined in millions of ways. Add to that the need to test multiple doses, and there are tens of millions of experiments to perform, says Borisy.
For each pair of compounds, CombinatoRx tests 36 dosages on several cell types. To test whether a combination has potential as a therapy for inflammatory diseases like arthritis, for example, researchers try the combination on white blood cells. They first stimulate the cells to mimic inflammatory disease, then administer the different dosages to the cells, and finally test for indicators of inflammation (such as signaling molecules that keep the immune system on alert). Data from these experiments are fed into a computer featuring software that determines whether the drugs have synergy and, if so, at which doses. If a combination shows promise, the company tests it in animals and then starts clinical trials.
Someday a proportion of these experiments may be done by computational biology — i.e., to elminate unlikely pairings. I couldn’t guess how that will develop, but am encouraged by the high rate of investment in computational molecular biology startups.

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