CAMBRIDGE — When you take over one of the Boston area’s largest biopharmaceutical companies after the longtime chief executive has quit abruptly — and as its parent company is shrinking research and development globally — you will be peppered with inquiries.
“There’s a lot of questions about what’s happening at Millennium,” Anna Protopapas, the new president of Millennium Pharmaceuticals, acknowledged in an interview Monday.
For now, though, when nervous Millennium scientists and confused industry officials approach Protopapas about their concerns and the uncertainty hanging over the company, the 48-year-old Millennium veteran is better able to offer reassurance than clear answers.
Millennium’s corporate parent, Japan’s Takeda Pharmaceutical Co., is “working through the process” of restructuring its worldwide research operations, Protopapas said. That probably means some people will be out of work.
“We’ll have that information by the end of the summer, and the people affected [by job cuts] will be notified,” she said. “Takeda is trying to eliminate some duplication. There is no change in the commitment to oncology research. Takeda recognizes that this area is a center of innovation in life sciences, and it is committed to having a significant presence here.”
‘It seems clear the major decisions are going to be made by the mother ship.’
The questions are fueled by last month’s departure of Deborah Dunsire, 50, one of the best-known women in the biomedical industry, who had led Millennium since 2005 and negotiated its $8.8 billion sale to Takeda in 2008. Since then, Takeda has often been cited by local biotech officials as an example of how benevolent, hands-off global pharmaceutical giants continue to invest in and expand the Massachusetts companies they acquire.
But Dunsire’s resignation was prompted by a Takeda decision to merge Millennium’s Cambridge-based cancer research unit into corporate research and development, which is being streamlined because earnings are weaker than expected. While Takeda initially had consolidated its cancer research under Millennium, the Cambridge research unit and its 900 employees will now report to Tachi Yamada, the new Takeda chief medical and scientific officer, based in Deerfield, Ill.
“The situation with Takeda and Millennium has been the exception rather than the norm, especially for a Japanese company,” said Chris Leo, senior vice president at the Boston consulting firm Back Bay Life Science Advisors. “Takeda really left Millennium alone for the past five years. But everyone in big pharma has been restructuring and streamlining research in order to drive efficiency and cut some costs out of the equation. Takeda is just falling in line.”
If there are layoffs at Millennium, which has nearly 1,400 employees, including commercial and administrative staffers, the real question is whether it can retain local talent, particularly in research, Leo said.
“Millennium was always one of the best places to work, not only in biopharma but in any industry,” he said. “They’re still going to be a presence in R&D here, and I’m sure they’ll have some autonomy, but it seems clear the major decisions are going to be made by the mother ship.”
One consequence of the restructuring already happening is an organizational split in what had been an integrated division. Dunsire oversaw both the research and commercial sides of Millennium. Her successor, Protopapas, heads the commercial operation and retains oversight of global business development, including the effort to expand Takeda’s presence in Europe and the developing world through acquisitions and alliances.
But the research operation reports to Yamada, hired by Takeda last year after leading global health programs at the Bill and Melinda Gates Foundation. In a sign that he remains committed to the Boston area, Protopapas said, Yamada is weighing the establishment of a “translational research” lab at Millennium’s new research and lab complex at 300 Massachusetts Ave. to extend its cutting-edge cancer research techniques to other areas.
Efforts to reach Yamada to discuss his plans for Millennium were unsuccessful Monday.
Protopapas sought to downplay the significance of Millennium’s split structure. She noted the company continues to deploy cross-functional product teams, including research and commercial representatives, for three experimental drugs: a pill for multiple myeloma and therapies to treat prostate cancer and peripheral T-cell lymphoma. All three medicines are in late-stage clinical trials. If those drugs are approved in the US market in the next two years, she said, the commercial force will grow.
“Reporting lines don’t necessarily determine how people interact with one another,” Protopapas said. “People here have worked together for years. We have our hands full with these three drugs over the next few years.”
Protopapas, a Greek native of Cyprus who is now a US citizen, embodies the international character of Takeda. Even before taking the Millennium reins from the Zimbabwe-born Dunsire, Protopapas, who has worked at the company for 16 years, made her mark by engineering a series of acquisitions to extend Takeda’s footprint worldwide. Those deals included the $13.5 billion takeover of Zurich-based Nycomed Pharma GmbH in 2011. That purchase gave the company a strong presence throughout Europe as well as in emerging nations like Russia and Brazil.
Other drug giants with revamped research and development have moved drug-discovery programs to the Boston area. For instance, Pfizer Inc. shifted some work here from Connecticut, while Sanofi SA transferred programs from New Jersey. It’s unclear whether Takeda might follow this model. But even if Millennium’s research labs take a hit, it is possible they could expand again down the road, Protopapas suggested.
“There’s a very strong recognition by Takeda leadership that Boston is a great place to access expertise and talent,” she said.