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"We are pleased Lilly must turn over misappropriated intellectual property," Emisphere said in its statement.
A Lilly spokesman said the company plans to appeal the order, which he characterized as a clarification of the January decision. The appeal, which must be submitted by May 3, would trigger a stay of the order, the spokesman said, adding that the patent would remain with Lilly until the Court of Appeals for the Federal Circuit in Washington rules.
Emisphere, whose business is based on developing oral formulations of drugs that can otherwise be delivered only by injection, said the patent covers a particular drug-delivery agent using GLP-1, or glucagon-like peptide-1, molecules, which stimulate the body's ability to produce insulin.
Emisphere ended the cooperation, which included development of an oral formulation of a drug to treat osteoporosis, in 2004. Lilly filed suit to keep Emisphere from ending the agreement, but the January court decision found Emisphere properly terminated it.