The committee voted 6 to 4 against the oral drug, AMX0035, saying the company's clinical study data failed to establish it was effective.
Amylyx's FDA submission was based on a 24-week placebo-controlled study of 137 participants with ALS.
Amylyx, in response to FDA's decision, said it is confident in the trial data and the benefits of the drug as a treatment option for ALS.
ALS, whose cause is largely unknown, leads nerve cells in the brain and spinal cord to break down, affecting physical function and resulting in severe disability and death.
The FDA's decision on the drug is expected by June 29. The agency typically follows the panel's recommendations, though it is not obligated to do so.
The panel's decision was in line with briefing documents released on Monday, where the FDA staff reviewers raised concerns over the drug's trial data and efficacy.
"We were asked to look for substantial evidence with persuasiveness and robustness, and I think this one trial doesn't quite meet that bar," said Kenneth Fischbeck, one of the panel members. Fischbeck is an investigator with the National Institutes of Health.
The close vote against the drug was in contrast to strong support from patients during the "open public hearing".
Patient representative Mark Weston, who voted for the drug, said both Amylyx and the FDA agree it "causes no material harm".
Amylyx recently initiated a larger trial in about 600 patients globally, but completion is not expected until 2024.
By Leroy Leo
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