LONDON - The bioinformatics company Inpharmatica Ltd. signed its first license agreement, with Parke-Davis Pharmaceutical Research, for Biopendium, a database linking gene sequences with protein structure and ligand binding.

The value of the deal was not disclosed but Chris Ashton, commercial director, told BioWorld International it exceeded the total investment in the company to date. "This deal could bring us to profitability, but we also have a significant investment program."

London-based Inpharmatica, founded in 1998 by University College London and the Wolfson Institute for Biomedical Research in London, had raised about #3.75 million (US$6.1 million) to date.

The deal is for three years with an option to expand the collaboration and also to extend it for another three years. Biopendium is based on sequence and structure information from public databases, and as part of the deal Inpharmatica will now customize it by incorporating Parke-Davis' proprietary data.

"Since we launched Biopendium in October 1999, everyone we have shown it to has asked the same question: How can we build our proprietary sequences into the database?" Ashton said.

"I think this is where we have an edge over non-exclusive databases," he said. "Biopendium starts off the same but it then diversifies as clients factor in their proprietary information. In other words, everyone can turn it into a proprietary database."

Carrying out this work increases the contract value to Inpharmatica. The contract is also designed to measure the contribution of Biopendium to the R&D effort, and this will be reflected in milestone payments.

The deal with Parke-Davis, a division of Warner-Lambert Co., of Morris Plains, N.J., covers all R&D activity worldwide. Christine Humblet, senior director of biomolecular structure and drug design at Parke-Davis, said in-house developments, data and expertise will be integrated with Biopendium, providing "a corporate-wide, global solution to structural biology."

Biopendium currently contains precalculated analyses on more than 500,000 sequences, revealing approximately 200 million protein structure annotations. By comparing each protein sequence to all others, this database reveals relationships between individual proteins, simplifying the search for drug targets and making it possible to select proteins that are less likely to cause side effects. Biopendium is updated each quarter as new data are added to public databases.

Inpharmatica is now moving into the next stage of development in which it intends to integrate bioinformatics with cheminformatics. "We are bringing serious investment to developing a system for relating small molecules to protein targets," Ashton said. "This will make it possible to preselect molecules that are likely to interact, meaning screening will no longer be just a numbers game."