SAN FRANCISCO — Genzyme, the Cambridge-based biotechnology company that has built a franchise around developing drugs to treat rare genetic disorders, is disclosing Monday that it will pay $700 million to buy a chunk of Alnylam Pharmaceuticals Inc. and tap its pipeline of rare- disease drug candidates.
The announcement, coming as the annual J.P. Morgan Healthcare Conference gets underway in San Francisco, underscores the commitment of Genzyme’s corporate parent, the French drug maker Sanofi SA, to build a more formidable portfolio of experimental treatments for rare genetic disorders just weeks after Genzyme suffered a major setback when the Food and Drug Administration rejected its much-anticipated multiple sclerosis therapy.
“We’ve had some challenging times,” said Genzyme’s chief executive, David Meeker. “This sends a strong message that we’re back trying to build a pipeline in rare genetic diseases, working with Alnylam.”
Alnylam, another Cambridge company, has emerged as a leader in the field of RNA interference therapeutics, or RNAi, which fights diseases by silencing genes that cause the unwanted overproduction of proteins in cells.
Genzyme in 2012 struck an alliance that gave it the rights to market Alnylam’s lead product, patisiran, in Japan and other Asian Pacific countries. Patisiran, which is in late-stage clinical trials, treats transthyretin-familial amyloid polyneuropathy, a rare life-threatening disease that damages the nervous system.
John Maraganore, chief executive of Alnylam, called the expanded deal with Genzyme “transformational,” giving his company the capital to accelerate its development of more than a half-dozen drugs and putting the worldwide marketing muscle of Genzyme and Sanofi to work on Alnylam’s behalf.
Maraganore and Sanofi’s chief executive, Christopher A. Viehbacher, will be briefing investors on their agreement Monday morning.
The deal will give Genzyme a 12 percent stake in Alnylam with an option to buy as much as 30 percent of the company at some point in the future.
It will also give Genzyme broad marketing rights to Alnylam’s portfolio of clinical and preclinical drugs deploying RNAi technology. Meeker said Alynylam is “right on track” with its “5 by 2015” goal of advancing five therapies by next year.
Under the agreement, Genzyme will also gain the rights to commercialize patisiran in Eastern Europe, the Middle East, Africa, and Latin America, as well as Asia. Alnylam will retain the rights to market the drug in North America and Western Europe.
Each company will book revenues from sales in its territories, though Genzyme will pay Alnylam royalties from its sales of patisiran.
In addition, Genzyme will have the rights to exclusively market globally — or co-market with Alnylam — three other drugs from its pipeline. And it will have the option through 2020, with a possible one-year extension, to commercialize any Alnylam drug it chooses outside the United States and Western Europe.
Alnylam, for its part, gains a deep-pocketed partner as it ramps up development of drugs to treat rare genetic disorders, ranging from hemophilia to porphyria, while remaining an independent company.
“The deal with Genzyme really positions us to expand our pipeline and accelerate the progress of RNAi therapeutics to the market,” said Barry Greene, Alnylam’s president and chief operating officer.
Genzyme’s agreement with Alnylam has been approved by the boards of both companies, but it remains subject to regulatory approval.