A novel computer program has identified thousands of new targets for existing drugs by comparing the molecular structures of drug compounds and chemicals that occur naturally in the body.

The technique could be used to uncover new applications or reveal potential side effects for drugs already on the market.

"It's a new approach, and it's a totally different from what everyone else has done. That's why it actually works," Nature quoted study author Bryan Roth, a pharmacologist at the University of North Carolina at Chapel Hill as saying.

The most common methods for predicting whether a small molecule binds to various drug targets involves either high-throughput laboratory screening or virtually simulating whether a particular compound fits together with proteins like a key in a lock.

However, the experimental approach is tedious and time consuming, while the computational method relies on the existence of high-resolution protein structures, which are hard to come by for many drug-sensitive proteins.

Last year, German scientists developed a new approach for finding novel drug targets for existing medications by showing that drugs with similar adverse side effects often share a common target protein, even when those drugs are chemically quite different.

In the new study, Roth and Brian Shoichet, a computational chemist at the University of California, San Francisco, have successfully identified new uses for marketed drugs by comparing existing drug compounds with different ligands - biologically active molecules that naturally bind proteins.