The shake-up, which ProStrakan said is due to its successful integration into KHK over the last two years, will see Dr Allen, who has been a director since 2005, and fellow non-executive Michael Asbury leave on December 31.
Tom Stratford, chief executive of ProStrakan, said: "Peter and Mike have each been long-standing members of the ProStrakan board and, during their time with us, ProStrakan has grown significantly and transitioned from being a small independent company into an important part of Kyowa Hakko Kirin."
Dr Brown is chairman of Dundee University spin-out CXR Biosciences and London-based Cell Therapy Catapult as well as senior non-executive director of lung specialist Vectura.
He used to chair commercialisation company BTG. He was chairman of Scottish-Norwegian diagnostics company Axis-Shield when it fell to US company Alere.
Previously, as chief executive he oversaw the turnaround of smallpox vaccine firm Acambis, although his £1.8 million severance package when he left in 2004 raised eyebrows.
Dr Brown co-chairs the Scottish Government's life sciences industry advisory board and is chairman of the Roslin Foundation, which supports Edinburgh University's Roslin Institute.