3-Dimensional Pharmaceuticals Inc. entered an alliance with Johnson & Johnson Pharmaceutical Research & Development LLC to discover and optimize small-molecule leads directed at genomics targets.

Johnson & Johnson will provide an undisclosed number of targets for undisclosed indications.

3DP, of Yardley, Pa., will receive an up-front technology access fee for its DiscoverWorks technology and research funding during the research collaboration. 3DP also is scheduled to receive milestone payments and royalties on sales of any products resulting from the collaboration.

DiscoverWorks entails a combination of automated chemical synthesis, advanced computational tools for compound selection, and software for overall process control.

“This is a program where the targets are being supplied by J&J, and we’re using our technology to find hits and leads for their targets, which is different from licensing out [our compounds], where we would have higher royalties,” said Scott Horvitz, vice president of finance and administration for 3DP.

Money received from J&J will be funneled into 3DP’s internal drug discovery efforts, which focus on oncology and metabolic diseases, he said. Originally, the company focused on oncology and cardiovascular diseases.

“We will consider looking at partners at certain phases of clinical development or taking products through the clinic,” he said.

Horvitz said the company has about $100 million in cash, but how far it takes it depends on how far 3DP takes its internal programs.

“It is fair to say that it covers our needs for at least the next couple of years,” Horvitz said.

This is the second deal that 3DP has with a J&J company. In January 2001, 3DP sold the worldwide rights to its orally active direct thrombin inhibitor program, 3DP-4815, to Centocor Inc., of Malvern, Pa., a wholly owned J&J subsidiary. (See BioWorld Today, Jan. 3, 2001.)

That program is now in Phase I trials. In October, 3DP announced a $4 million milestone payment from Centocor, but the triggering event was not disclosed.

Another oncology product is an orally active urokinase inhibitor designed to inhibit the supply of blood to, and growth of, tumors. This program is licensed to a subsidiary of Schering AG, of Frankfurt, Germany.

“We have a number of other oncology-focused programs that have not been licensed and that we are developing internally,” Horvitz said.

Horvitz said the company has a two-pronged business model. One aspect is to generate revenue by partnering its technology with pharmaceutical companies.

The second prong of 3DP’s business strategy is to use its technology on its internal programs for drug discovery, which Horvitz said 3DP expects will create more long-term value for its shareholders.

3DP’s stock (NASDAQ:DDDP) rose 27.5 cents on Friday to close at $8.76.