By Mary Welch

3-Dimensional Pharmaceuticals Inc. signed a deal worth at least $9 million with DuPont Pharmaceuticals Co. to help it discover drugs for specific targets, and separately DuPont obtained a non-exclusive license to 3-D's DirectedDiversity technology.

Exton, Pa.-based 3-Dimensional (3DP) will receive payments of up to $9 million, including an up-front technology access fee, research and development funding and milestone payments. No equity is involved. In addition, 3DP will receive royalties on sales of resulting products and will be eligible for additional payments if more than one target is selected.

"The initial contract is for one target but it can be expanded," said Scott Horvitz, 3DP's vice president for finance and administration. "There is a separate agreement with additional financial terms if another target is selected but DuPont does not want that information disclosed. We also cannot say what disease area or areas are involved."

A private company, 3DP will use its proprietary DirectedDiversity technology to generate custom combinatorial chemistry libraries based on molecules and information provided by DuPont and optimize those molecules into preclinical drug candidates. DuPont, based in Wilmington, Del., will then be responsible for preclinical and clinical development, marketing and sales of any products.

"We can discover and refine drugs against a wide range of molecular targets more quickly than conventional approaches," Horvitz said. "We think it's significant to have a major pharmaceutical company seeking to leverage its discovery resources - and DuPont is very strong in chemistry and basic research - with 3-D to help accelerate its mainstream drug discovery process."

DuPont's non-exclusive license of 3DP's DirectedDiversity drug discovery patents will be used to support DuPont's internal research programs. DuPont will pay an annual site license fee for each DuPont facility using the technology.

"This is a different deal with additional financial terms to it," said Ray Salemme, 3DP's president and chief scientific officer, and a founder. "This is the first time that a major pharmaceutical company has recognized 3DP's intellectual property position and is in a licensing agreement for the rights to those patents. There is no other technology transfer."

The DirectedDiversity technology integrates computer-controlled rational drug design with combinatorial chemistry. It controls and manages the overall information flow for combinatorial drug discovery and provides the computational tools needed to optimize drug properties rapidly using parallel automated chemical synthesis, the company said.

A key element of DirectedDiversity is that after the best virtual drug candidates are biologically evaluated in the laboratory, detailed information about their structural activity relationships with the genetic target are retained and fed back into the computer for the next iterative generation of compounds for assessment. Normally, information about activity against a target is lost if the compounds are not hits, the company said.