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The chief executive of Zafgen Inc. said Thursday the Boston biotechnology company will press forward with an experimental drug to treat an obesity-related disease despite the recent death of a patient in its late-stage clinical trial.

But the company is ending the main part of that trial, which was near completion, and studying the data that could enable it to file a new drug application with US regulators.

“We believe we have an adequate number of patients who’ve been through the trial without disruption so that we can analyze the data and assess the benefits,” chief executive Thomas Hughes said in an interview Thursday.

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Hughes said the patient, who has not been identified, died of respiratory failure from blood clots that collected in the lungs. But he said it could not be determined if Zafgen’s drug candidate beloranib, which treats a rare disorder called Prader-Willis Syndrome, was a factor.

“It’s an unfortunate and very sad thing,” Hughes said. “But blood-clotting is something that occurs commonly in this population. We have no basis to suggest that taking beloranib triggers clots. What we’re trying to assess is whether beloranib has the ability to amplify clotting.”

That is an aim of one part of Zafgen’s trial that is continuing, Hughes said. That extension is limited to those who completed the main part of the trial and elected to continue taking the drug. Unlike the discontinued main part of the trial, in which some patients were given placebos, all the patients in the extended trial will be given the drug.

Zafgen’s shares closed down 0.5 percent to $10.67, a loss of 5 cents on the Nasdaq Stock Market Thursday. Shares have dropped 65 percent since the start of the year.

Meanwhile, a lawsuit filed in US District Court in Boston on Wednesday by the law firm Block & Leviton LLP alleged that Zafgen and Hughes violated US securities laws by initially withholding disclosure of some “adverse events” experienced by patients in the company’s trial and of the fact that the patient who died had taken the drug rather than a placebo. The suit, which is seeking class-action status, was filed on behalf of shareholders. Only one, Aviad Bessler, was named.

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“Our investors believe they were misled by the company,” said Jeff Block, a partner in the law firm, which specializes in shareholder class-action suits.

Zafgen officials said it was company policy not to comment on lawsuits.

Hughes said Zafgen reached the decision to halt the main part of the trial and move ahead with the data analysis in consultation with the Food and Drug Administration.

The agency ordered a partial hold on the trial. That meant the company would have to reassess enrolled patients to make sure they were not at higher risk for the clotting before letting them resume taking the drug.

Hughes wouldn’t say how many patients had completed the trial, but he said the majority who had finished have chosen to continue in the extended study.

The company will report the results of its clinical study early next year before deciding whether to file an application for approval of beloranib, Hughes said.


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