Addressing challenging impurities in fusion proteins: A comprehensive review and cost-effective strategy for HCP and low molecular weight species control.

Fusion proteins represent a rapidly expanding class of biotherapeutics engineered by combining functional domains from different proteins to enhance therapeutic efficacy, stability, and pharmacokinetics. Their unique design enables extended half-life, reduced dosing frequency, and multi-targeting capabilities, making them highly versatile for diverse therapeutic indications. However, the manufacturing of fusion proteins presents significant challenges, particularly in managing complex product- and process-related impurities such as host cell proteins (HCPs), fragments, and low-molecular-weight (LMW) species. These impurities are difficult to eliminate due to their structural and physicochemical similarity to the target protein, complicating purification and scale-up. Part I of this paper provides a comprehensive review of published studies addressing impurity characterization and control strategies in fusion protein manufacturing. The review highlights critical impurity types, analytical tools for detection and quantification, and process strategies for effective removal while maintaining product integrity and regulatory compliance. Part II presents a case study from Kemwell Biopharma, illustrating a cost-effective platform purification strategy for complex fusion proteins. The approach is applicable to non-tagged, Fc-based, and multispecific fusion protein formats and demonstrates efficient removal of HCPs and LMW impurities while achieving high yield and purity. Together, the review and case study provide both a broad scientific understanding and a practical demonstration of scalable impurity control approaches, offering valuable insights for the development of robust and economically viable manufacturing processes for next-generation fusion protein therapeutics.