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Federal regulators have ordered Zafgen Inc. to halt its clinical trial of an experimental drug to treat an obesity-related condition after two patients who had taken the drug died.

Boston-based Zafgen said it was notified by the Food and Drug Administration that it had put a “complete clinical hold” on the company’s late-stage clinical study for beloranib. The drug was developed for patients with a rare genetic disorder known as Prader-Willi Syndrome, which causes unrelenting hunger and severe and life-threatening obesity.

The main part of the study, which enrolled 108 patients, had already been shut down on orders from the FDA in October after Zafgen disclosed the first death of a patient who had taken beloranib.

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Zafgen said it learned of the second death Tuesday. That patient was one of 55 who had completed the first part of the study, volunteered to continue taking the drug, and were cleared to take part in an extended part of the study.

Both patients died from blood clotting in the lungs, but the company said it didn’t have enough data to know whether the drug had triggered the clotting.

“We are working diligently to assemble and analyze the data from our ... clinical trial to be able to provide a clear view of the safety and efficacy of beloranib in the Prader-Willi Syndrome population,” Zafgen chief executive Thomas Hughes said in a company statement.

Shares of Zafgen closed down nearly 6 percent Thursday, after losing more than 60 percent of their value Wednesday. The stock fell 32 cents to $5.06 on the Nasdaq Stock Market. It had traded as high as $55.26 back in March.

The company’s statement said Zafgen remains committed “to advancing beloranib as a potential new therapy for this underserved patient population” and would report the findings from its nearly completed clinical study in the first quarter of next year.

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Representatives of Zafgen and the FDA declined to discuss the trial’s halt.


Robert Weisman can be reached at robert.weisman@globe.com. Follow him on Twitter @GlobeRobW.