The pharmaceutical industry rarely uses free energy perturbation-based methods in computer-aided drug design because these methods have low throughput, require a high level of user expertise and do not always produce results of the desired accuracy. Last week in the Journal of the American Chemical Society, Metabasis Therapeutics Inc. described a new approach to free energy perturbation that it says is extendable to any therapeutic area and ultimately could replace existing methods when the software becomes commercially available.

The company has used the technique to discover two compounds against a heretofore intractable target for Type II diabetes, with one now in Phase II studies.