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The clock on marketing exclusivity can run even while a drug maker is awaiting clearance to sell a controlled substance, according to court ruling. And the decision is a setback to Eisai, which claimed it unfairly lost valuable marketing time due to regulatory procedures, although a new bill winding its way through Congress could override the decision.

Here’s the back story: In 2012, Eisai won FDA approval for two new drugs – the Belviq diet pill and the Fycompa epilepsy treatment – which triggered the beginning of a five-year marketing exclusivity period. This meant generic rivals could not sell lower-cost versions of either medication.

But Eisai encountered delays launching its drugs because both are controlled substances – medicines that have some potential for abuse or dependence. This meant the drugs could not be marketed until the US Drug Enforcement Agency placed them on special lists for which distribution is restricted.

Belviq, for instance, was approved by the FDA in June 2012, but not listed by the DEA until June 2013. And Fycompa was approved in October 2012, but not listed by the DEA until January 2013, although final scheduling did not occur for another year.

This delayed Eisai from selling either drug, since FDA approvals stipulate DEA listings must be completed first. So Eisai filed a “citizen’s petition” asking the agency to extend the exclusive marketing period for the drugs to make up for the lost time. The FDA, however, bounced the request.

That brings us to last year when Eisai filed its lawsuit, arguing it was unfairly penalized. The drug maker charged it was prevented from marketing the medicines on a timely basis because both agencies bungled the process. Specifically, Eisai claimed the FDA mishandled the process for notifying the DEA of the approvals and then DEA scheduling was tardy and wasted valuable marketing time

As far as Eisai was concerned, other drug makers whose medicines do not require DEA listings receive full five-year exclusivity periods. Eisai also claimed FDA has treated drug makers inconsistently by not devising a uniform timetable for sending recommendations about drugs that are controlled substances to the DEA.

But in a 32-page opinion, US District Court Judge Randolph Moss disagreed with the drug maker. He explained that all drugs listed as controlled substances are treated alike in that none are given deferred approval dates while the DEA completes its scheduling process.

“This case illustrates that the date on which the FDA approves a drug is not always the date on which the drug may be marketed,” Moss wrote in his decision. “Although this disparity may reflect a flaw either in the FDA’s regulation or in the statute, it does not reflect any deficiency in the agency’s interpretation of its regulation.”

AnEisai spokeswoman wrote us to say that the drug maker is disappointed and considering whether to file an appeal. “We believe [the ruling] undermines the incentives for innovation that Congress intended to grant those companies, such as Eisai, who bring novel and important medicines to market,” she wrote in an e-mail.

Meanwhile, there is a bill moving through Congress that would delay approval dates for drugs the FDA recommends to the DEA for listing as a controlled substance. This would, in turn, delay the start of an exclusive marketing period, which is what Eisai had sought. The bill earlier this year passed out of the House to the Senate Health, Education, Labor and Pensions committee.

Whether a bill becomes law remains to be seen, of course. If not, the ruling may make it more difficult for drug makers to bank on the full exclusivity period in which to market any medicine that is listed as a controlled substance.

Hat tip to FDA Law blog