Like a scorned lover, the head of Amylin Pharmaceuticals Inc. (AMLN) felt blindsided and betrayed when longtime partner Eli Lilly & Co. (LLY) started a new diabetes-drug relationship with a European counterpart, recently released court documents show.

Amylin executives were further alarmed when they learned how Lilly planned to carry out its new partnership, which Amylin is now fighting in court. Lilly, for its part, professed indignation that Amylin would resort to a lawsuit that hampered Lilly's ability to market a new drug for a disease that is on the rise.

A rare behind-the-scenes glimpse of a pharmaceutical marketing alliance gone sour emerged from court documents that were confidential until a federal judge unsealed them late last week. Some language may amount to legal posturing--and the case may get settled amicably--but the documents show tension between the companies.

Amylin and Lilly co-promote the twice-daily injected drug Byetta, whose sales dropped 11% to $710 million for 2010 due to increased competition. The two partners have hit roadblocks bringing to market a once-weekly formulation of the same drug, to be branded Bydureon. They have been partners since 2002 and continue to work together, recently securing European regulatory approval of Bydureon and trying for U.S. approval.

Indianapolis-based Lilly, to jump-start its diabetes franchise, formed an alliance with Germany's Boehringer Ingelheim GmbH (BRI.YY) in January to co-develop and commercialize several drugs, including Tradjenta, cleared by U.S. regulators in May.

The problem is, Amylin argued, Tradjenta will compete with Byetta and Bydureon. Amylin claimed in a federal lawsuit filed in May that Lilly's implementation of the Boehringer deal is anticompetitive and undercuts the Lilly-Amylin alliance. A judge initially imposed restrictions on Lilly's marketing of Tradjenta but lifted them last month. Lilly wants a mediator to help resolve the dispute.

Months before the lawsuit, a communications breakdown signaled trouble between the partners. Amylin Chief Executive Daniel Bradbury said in a sworn declaration that he didn't learn about the Lilly-Boehringer deal until Jan. 10, the night before Lilly disclosed it at a health-care conference in San Francisco.

Bradbury, who helped to negotiate the original Amylin-Lilly alliance, said he met in San Francisco with Enrique Conterno, president of Lilly's diabetes unit. "Mr. Conterno did not comment on how Lilly would actually sell BI's products, much less seek any input from Amylin," Bradbury said in the court document.

Conterno did, however, tell Bradbury that Lilly remained committed to maximizing the value of the companies' partnership, according to Bradbury, a stance Lilly has maintained in its defense against Amylin's lawsuit.

Lilly said in a court document that it provided advance notice to Amylin, but it wasn't required to have Amylin involved in negotiating the Boehringer alliance.

Bradbury later was "surprised and disturbed" to hear Lilly executives say during a January conference call that Tradjenta didn't compete with Byetta and therefore Lilly planned to use the same sales force to promote both drugs, Bradbury said.

Lilly said there was no direct competition because of an "injection barrier" in care for people with type 2 diabetes--meaning most doctors first try oral drugs and then switch to injectables after oral options are exhausted.

Previously, Amylin argued, both companies viewed oral pills like Tradjenta as direct competitors to Byetta. Amylin said both companies' marketing plans and clinical studies of Byetta and Bydureon were designed to position them as alternatives to oral drugs, to be used as early as possible in a patient's care.

Lilly said in a court document that the "injection barrier" is a "well-recognized market reality driven by patient and physician preferences."

In a late February meeting, Bradbury told Conterno that he thought Lilly was creating an "antitrust issue" by selling "two directly competing products from its two competing alliances with the same sales force."

In a March meeting, according to an Amylin court document, Lilly executives said they planned to deploy more than 700 sales representatives who would promote Tradjenta, Lilly's Humalog and Byetta--in that order.

Lilly also said it planned to hire 325 new sales reps who would promote Humalog and Byetta ahead of Tradjenta, according to Amylin. Because these would be new sales reps, Amylin said, they would be at a disadvantage to the more-experienced reps promoting Tradjenta.

Lilly said it wouldn't enter collaborations expecting to disparage its products and partners. The company also said it couldn't make comparative claims between Byetta and Tradjenta, under U.S. Food and Drug Administration rules, because the clinical data don't exist.

In a sworn declaration, Lilly's Conterno said Lilly has no economic incentive to steer prescriptions toward Tradjenta, and that incentives for its sales reps reward increased prescriptions for Byetta.

Bradbury also cited what he perceived to be radio silence from Lilly about key developments. He said Lilly didn't tell Amylin the FDA's target date for a decision on Tradjenta, and that Amylin instead learned it "serendipitously from a report from the field." Similarly, he learned of the FDA's May 2 approval of Tradjenta only after the FDA issued a press release.

Eleven days later, Amylin filed its lawsuit. Now it was Lilly's turn to be indignant. Lilly said in a court document that Amylin chose not to invoke a dispute-resolution provision in the companies' contract.

"Instead," Lilly said, "Amylin filed an antitrust lawsuit and sought an [order] to prevent Lilly from disseminating accurate information to physicians about a new medicine...for the treatment of one of this country's most significant health crises, diabetes."

Amylin officials couldn't be reached. A Lilly spokesman declined immediate comment. Boehringer Ingelheim, the third party to the spat, couldn't immediately be reached for comment.

-By Peter Loftus, Dow Jones Newswires; 215-982-5581; peter.loftus@dowjones.com

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