Affinium Pharmaceuticals entered a three-year alliance with Pfizer Inc. for structure-based drug discovery in a deal valued at up to $30 million, excluding royalties.

Toronto-based Affinium, formerly known as Integrative Proteomics Inc., will use its functional, chemical and structural proteomics platform against New York-based Pfizer's targets.

"It's a drug discovery deal that is focused around structures of targets and target structures with bound active chemical matter," Affinium Chairman and CEO John Mendlein said. "Structure is important because it provides guidance at multiple steps in the drug discovery process."

Privately held Affinium will receive funding for research and development and database licenses, as well as potential discovery and clinical milestones, and royalties.

The goal of the alliance is to produce proteins for high-throughput screening, discover the physiologic relevance of the targets using protein-protein interactions, and discover the 3-dimensional structure of the target with and without active chemical matter that can be used for designing new drugs, Mendlein said.

To accomplish that, Affinium scientists will use their platform, which includes integrated mass spectrometry, nuclear magnetic resonance and X-ray systems. The alliance also will employ Affinium's ChemVision system and its internal chemistry capabilities against selected targets.

"By combining these technologies, we can integrate the right technology at the right point in the drug discovery process to open up the multiple bottlenecks," Mendlein said.

Pfizer will be providing the targets.

"Most of the targets that will be provided are in electronic format, and we turn them into a real target," Mendlein said. "We will go from the virtual of ones and zeros to the reality of drug discovery. This is a good way to take advantage of great genomics work."

Mendlein said Pfizer has sophisticated capabilities in structural drug discovery work through its acquisition of Warner-Lambert Co., of Morris Plains, N.J.

Structure-based drug discovery was popular during the 1980s, but fell out of favor when structure determination proved difficult, he said. Advances in technology since then have made it easier for companies to discover the structure of proteins.

Affinium was founded in 2000 by scientific co-founders Cheryl Arrowsmith, Aled Edwards and Jack Greenblatt, all of whom serve as scientific advisers to the company. The company has raised $33 million to date, Mendlein said.