Structural GenomiX Inc. entered into separate collaborations to use its genomics-driven, high-throughput, structure-based technology to facilitate drug discovery for Millennium Pharmaceuticals Inc. and Aventis Pharmaceuticals Inc.

Privately held Structural GenomiX, of San Diego, will identify lead compounds by solving the structures of up to 100 compounds for a designated drug target set for Aventis, of Bridgewater, N.J., the U.S. arm of Aventis Pharma AG, of Frankfurt, Germany.

Aventis will provide high-throughput screened compounds selected against the human drug target, and SGX will co-crystallize the compounds against the target set and provide Aventis with structural and compound-target binding information.

There will be an up-front payment and a series of milestone payments linked to specific stages of the “fairly short-term” collaboration, said Michael Grey, chief business officer for SGX, who noted the objective is to provide Aventis with data it can use to determine which compounds are suitable for clinical development.

“There is no commitment to do anything further [than the 100 compounds], but there are many different things that both parties could do, and that’s something we will continue to talk about as we go forward,” Grey said.

In the collaboration with Millennium, of Cambridge, Mass., SGX will use its technology to generate large-scale structural information for Millennium drug targets. It will focus on two areas of research. The first will use structural information from Millennium targets and co-crystallization with lead compounds, and the second will focus on using further structural analysis of a smaller number of certain target families to determine proteins that are closely related to the drug targets, allowing SGX to determine which proteins may, for instance, cause side effects.

The initial phase of the collaboration should be completed within a couple of years, Grey said.

“What the co-crystallization gives you is a picture of what is happening at the molecular level,” Grey said, with the result being that you can ultimately develop drugs that are more selective and more potent.

In return, Millennium will make an equity investment in privately held SGX that “is not a major stake,” he said.

Perhaps more importantly, both collaborations will give SGX “significant retained rights,” Grey said. With Millennium, SGX will choose a validated drug target from among Millennium’s targets that it can then use for its internal drug discovery program. That program focuses on protein kinases, nuclear hormone receptors and membrane proteins. All except the membrane protein program are in the lead identification stage and moving forward “quite rapidly,” Grey said.