Beyond mAbs: Bringing Platform Approaches to Complex Biologics Purification

Kenneth Holbourn suggested that standardizing more of downstream purification could reduce process development complexity and support a faster transition into clinical manufacturing.

Monoclonal antibodies (mAbs) have benefited from decades of manufacturing experience and increasingly standardized production processes. But biologics pipelines are also becoming more diverse, encompassing antibody fragments, fusion proteins, enzymes, cytokines and other recombinant proteins that do not always fit established mAb manufacturing platforms.

For many non-mAb proteins, the challenge is building a purification process around the specific characteristics of the molecule. Kenneth Holbourn, Process Development Technical Lead at FUJIFILM Biotechnologies, described downstream development as “process intensive,” with differences in solubility, expression and purification needs affecting the number and type of steps required before manufacturing.

In this Xtalks Spotlight, Kenneth draws on more than 15 years at the company and his background in structural biology to discuss the continuing role of microbial expression systems, why downstream purification can require more customization outside conventional mAb formats and how platform approaches could shorten the path from development to clinical manufacturing.

Microbial Systems Remain Relevant as Biologics Diversify

While mAbs continue to dominate mammalian biologics production, the molecules being developed around them are becoming more complex.

Bispecific antibodies, antibody fragments and increasingly elaborate fusion proteins are broadening the range of therapeutic formats entering development. Some of these molecules can be produced effectively in microbial systems, alongside established categories such as enzymes, cytokines and other recombinant proteins.

Kenneth noted that microbial manufacturing continues to offer advantages in speed, cost and production efficiency. As he explained, “when you start to move towards antibody fragments, that actually is still dominated heavily by the microbial space.”

Kenneth said the microbial sector is estimated to be growing at approximately 10% annually. As therapeutic developers explore smaller antibody-derived formats and proteins linked to other functional components, he expects microbial expression to remain an important part of the manufacturing landscape.

Why Complex Biologics Resist Standardized Purification

Established platform processes simplify parts of conventional mAb manufacturing.

For antibodies containing an Fc domain, Protein A affinity chromatography can provide a relatively consistent first capture step. Subsequent purification can then follow workflows that manufacturers have already developed and repeated across multiple products.

Unlike established mAb workflows, many complex non-mAb proteins lack a common purification scaffold, limiting how much of downstream processing can be standardized across programs.

Kenneth described this as a return to more molecule-specific process development: “For the more complicated ones, especially the microbial ones where you don’t have the advantage of that similar scaffold, it is leaning back into traditional science. So, this is a lot of process development, and this leads to a lot of variation downstream.”

A microbial protein may be soluble or insoluble. A protein expressed in yeast may be secreted. Other molecules can require solubilization, refolding, additional chromatography columns or ultrafiltration and diafiltration steps at different points in the process.

Each variable affects how the downstream process must be developed and later transferred into manufacturing.

Facilities must also accommodate different equipment configurations and unit operations, while manufacturing teams may have to learn a substantially different process for each molecule. This variation can limit how much of the manufacturing process CDMOs can replicate from one project to the next.

Partial Platforming Can Standardize More of the Purification Process

FUJIFILM Biotechnologies has taken an affinity-tag approach to standardizing more of the purification process.

This strategy combines an affinity tag with a specific protease. The tag is added to the target protein to enable common affinity-based purification steps and is subsequently removed by the protease.

The approach standardizes part of downstream purification while leaving molecule-specific steps for further development.

Kenneth explained, “By putting a tag on the front of the molecule, we can use mostly the same separations. We can do the same downstream steps for two-thirds of the process.”

He said the company’s existing microbial expression platform can allow fermentation to follow an established workflow, while the purification strategy standardizes more of the downstream process. Once the affinity tag has served its purpose, the protease removes it, leaving the target protein without additional residues.

Kenneth called this a form of “partial platforming,” with some steps standardized and others remaining molecule-specific.

More Repeatable Processes Could Ease Clinical Manufacturing

“If we only have to develop one step rather than say six steps, it’s fast for us to develop that,” Kenneth explained. Fewer molecule-specific steps could also simplify the transition into clinical manufacturing.

Established raw materials, consumables, batch records and equipment requirements can reduce the amount of work that must be recreated for every new process. In addition, established workflows can reduce the need to rewrite manufacturing documents, requalify methods or source less common materials for each new program.

Operators may not have to train on an entirely new workflow for each molecule, while equipment scheduling, maintenance and monitoring can become more predictable. As Kenneth put it, “If two-thirds of my equipment is going to be the same every time, it’s easy for scheduling maintenance and equipment monitoring. It’s easy for the staff because they’re running the same steps time and time again.”

He suggested that the same purification strategy could also be applied to challenging Chinese hamster ovary (CHO)-expressed proteins where “expression levels vary, and it can be hard to purify these away from a lot of the sort of endogenous whole cell proteins in a CHO cell.” This could involve adding a tag for purification and then removing it from the target protein.

“We’re mainly focused in the microbial space, but we are already exploring using this in the CHO space,” Kenneth concluded.

This article was created in collaboration with the sponsoring company and the Xtalks Editorial team.