After weeks of anticipation, the Food and Drug Administration rejected a drug that BioMarin Pharmaceutical (BMRN) hoped to sell to treat Duchenne muscular dystrophy, a rare disease that causes muscles in boys to stop working and eventually results in death because they can no longer breathe. About 20,000 new cases are diagnosed each year.

In a brief statement, the drug maker said the FDA sent a so-called complete response letter to say agency officials “concluded that the standard of substantial evidence of effectiveness has not been met.” A BioMarin spokeswoman told us the FDA wants to see results from a new late-stage study trial for its drug, which is known as drisapersen, but that ongoing clinical trials will continue. A decision to run such a trial will not be made until after meetings are held with the FDA and after European regulators decide in June whether to approve the drug.

The rejection is not surprising. Two months ago, the FDA took the unusual step of not asking its advisory panel for an official up-and-down vote on whether to recommend marketing approval. But 15 of the 17 experts did signal that approval might be an uphill battle after voting that a lack of statistical significance in a late-stage study of 186 patients weakened positive outcomes seen in two smaller and earlier studies.

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Wall Street “expectations for approval had come down after the [advisory committee],” wrote Evercore ISI analyst Mark Schoenebaum in a research note this morning. “Our most recent [investor] survey suggested that [only] a minority of investors — 28 percent — expected the drug to be approved.” He added that he spoke with the company and was told the FDA wants to see data from another late-stage trial.

The decision is a setback for the many parents who have aggressively lobbied Congress and the FDA over the past decade to approve DMD drugs and speed approval of experimental medicines, in general. The effort to win approval of DMD medications, in particular, has been a closely watched litmus test of the extent to which the FDA is more willing to balance patient demands with data-driven reviews.

“This is a very sad day for the Duchenne community,” said Debra Miller, the founder and director of CureDuchenne, an advocacy group that also raises money to invest in drug companies that are developing products to combat the disease. The organization also runs a venture philanthropy arm that has small holdings in BioMarin and has donated money to Sarepta Therapeutics (SRPT).

“I am deeply disappointed in the FDA’s decision,” she said. “The FDA did not consider the strong patient voice in favor of this drug. The boys who have been on drisapersen and their parents wanted to see drisapersen approved. The top Duchenne specialists supported the approval of drisapersen. As a mother of a boy with Duchenne and as the leader of an advocacy organization, I feel strongly that drisapersen has substantial benefit to boys with Duchenne.”

Of course, the decision is also a setback for BioMarin. The drug maker made a big bet in 2014 after agreeing to pay $680 million to buy Prosensa, which, along with GlaxoSmithKline (GSK), had originally begun testing the medicine. That deal was reached about a year after the companies revealed that their late-stage study of 186 patients had failed.

But as noted previously, after Glaxo walked away, Prosensa mined its study data and found the drug appeared to be effective in younger patients if given over a longer period of time. BioMarin, which specializes in rare diseases, believed it could convince the FDA to review the drug on the basis of this subgroup analysis. If the drug is ever approved, BioMarin would have to pay another $160 million to Prosensa shareholders. However, half of that money would not be owed if FDA approval occurs after May 15.

Meanwhile, attention will turn to another FDA advisory meeting to be held on Jan. 22, when an agency panel will review a DMD drug being developed by Sarepta. The prospects for this drug, however, are also uncertain. The company hopes the agency will look favorably on a mid-stage study that relied on a very small group of patients.

Both drugs, however, target just 13 percent of the DMD patient population who have the gene mutation that causes the disease. A drug that targets a different segment of patients and that is being developed by PTC Therapeutics (PTCT) may be approved by the FDA this summer.

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