Structural Bioinformatics Inc., which devised a method for accelerating small molecule drug design based on detailed 3-D structures of targeted proteins, signed its first major collaboration with BioChem Pharma Inc. for compounds to treat hepatitis C and cancer.

Financial terms of the agreement were not disclosed. Susan Burgess, vice president of corporate development for Structural Bioinformatics, said her San Diego-based company will receive an up-front fee, research funding and milestone payments from BioChem Pharma, of Laval, Quebec.

The compounds for hepatitis C will be designed to block an essential viral protein, which was not identified. In the cancer treatment, Structural Bioinformatics will target a protein-to-protein interaction in a signaling pathway, which if blocked would trigger apoptosis, or cell death.

In both hepatitis C and cancer, Structural Bioinformatics already knows the 3-D construction of the targeted proteins. The company will use its technology to refine details of the structure and pinpoint the active sites, which determine the design of template compounds that interact with or mimic the proteins. Those templates then are used to search computer-based virtual chemical libraries or real libraries for drug candidates.

By the time BioChem Pharma begins screening the compounds in its cellular assays for hepatitis C and cancer, the company will be looking for those with the most activity against the targets. Burgess said Structural Bioinformatics will be able to identify potential lead drug candidates within several months. — Charles Craig