(Adds details from court papers, comments from prosecutor, company)
BOSTON, Sept 22 (Reuters) - Aegerion Pharmaceuticals Inc will plead guilty to two misdemeanors and pay $40.1 million to resolve investigations into its marketing and sales of an expensive cholesterol drug, U.S. authorities said on Friday.
The settlements will resolve long-running investigations into Aegerion, a subsidiary of Canada's Novelion Therapeutics Inc, by the U.S. Justice Department and the U.S. Securities and Exchange Commission related to its drug Juxtapid.
Under the agreements, Aegerion will plead guilty to two misdemeanor drug misbranding violations of the Food, Drug and Cosmetic Act, pay $36 million to resolve cases by the Justice Department and another $4.1 million to resolve the SEC's case.
It also entered into a three-year deferred prosecution agreement to resolve a charge that it conspired to violate the Health Insurance Portability and Accountability Act.
The settlements finalized preliminary agreements Aegerion first disclosed in May 2016. The Cambridge, Massachusetts-based company in November merged with QLT Inc and became a subsidiary of the newly named Novelion Therapeutics.
"We are eager to get the problems that occurred with Aegerion under prior leadership behind us and we believe these agreements are in the best interest of shareholders," Aegerion said in a statement.
The U.S. Food and Drug Administration in December 2012 approved Juxtapid for treating a rare genetic condition that causes extremely high cholesterol.
The drug, which cost $250,000 to $300,000 annually per patient, featured a black box warning on its label that Juxtapid could cause liver toxicity and may cause adverse gastrointestinal reactions, prosecutors said.
But prosecutors said Aegerion, after gaining FDA approval, promoted Juxtapid for patients who had not been diagnosed with the condition.
Sales representatives also were trained to tell doctors and patients that Juxtapid would "take patients out of harm's way" and prevent "impending" heart attacks and strokes, despite the lack of data supporting those claims, prosecutors alleged.
Numerous patients had to discontinue using Juxtapid after suffering conditions including liver toxicity and gastrointestinal distress, prosecutors said.
The Justice Department in a civil lawsuit said Aegerion's promotion of Juxtapid for patients without the genetic condition led to false claims for payment to be submitted to government health care programs including Medicare.
"Aegerion put profits over patient safety and enriched itself at taxpayer expense," Acting U.S. Attorney William Weinreb in Boston said in a statement.
The SEC alleged Aegerion also misled investors by exaggerating how many new patients actually filled prescriptions for Juxtapid, its sole revenue source. (Reporting by Nate Raymond; editing by Jonathan Oatis)