Considerations for Simplifying Downstream Processes

Published on: 
BioPharm International, BioPharm International, October 2022, Volume 35, Issue 10
Pages: 24–27

A simplified downstream process can save time and costs but requires enabling technologies.

Bioprocessing operations have been growing more complex in response to the emergence of increasingly complex biomolecules in development. The biopharma industry continues to strive in optimizing downstream purification processes. In talking with BioPharm International, Jungmin Oh, PhD, manager, new product development, Avantor, and Jonathan Hester, PhD, division scientist for 3M Separation and Purification Sciences Division discussed the industry’s efforts to simplify purification processes while keeping them just as effective. Their discussion further explored whether simplified downstream purification can be applied to newer complex biotherapeutics.

Emerging biomolecules

BioPharm: With the emergence of newer, more complex biomolecules moving through the clinical development pipeline, what have been the most challenging aspects of developing a downstream purification workflow?

Oh (Avantor): Many downstream processing steps for complex biomolecules iterate on steps for more established therapeutic products, such as monoclonal antibodies (mAbs)—steps whose capacity hasn’t kept up with advances in upstream production. These leave room for improvement, especially in chromatographic steps.

There are, however, innovative processing steps with unique challenges. For example, viral vectors used in cell and gene therapies can be difficult to purify thanks to the presence of empty or partial capsids that must be separated from full capsids before final formulation. This separation can be achieved through anion exchange chromatography, although process optimization is still needed.

Hester (3M): Newer modalities are posing challenges in the downstream purification workflow compared to protein products, such as mAbs, that have been the ‘bread and butter’ of the biologics industry up until now. For example, some of the most exciting cell and gene therapy therapeutics are based on viral vectors. In using therapeutics based on viruses, we must now answer the question, ‘How do you conduct viral clearance—removing potential impurity viruses—from a virus product?’ Instead of separating a virus from a protein as the industry had previously been conducting, we are now separating viruses from other viruses. This is a difficult fundamental challenge, but one we and many others are already working on, and one I am confident we can solve through innovative materials science.

Key enabling technologies

BioPharm: What technologies have so far been key at enabling optimization of downstream processing?

Hester (3M): The replacement of conventional, multi-use unit processes with single-use devices has been a huge driver enabling recent optimization of downstream processing. One example is conventional packed bed chromatography columns. A single column has conventionally been used over many cycles, requiring careful cleaning and validation procedures. These procedures use [a significant amount of] fluids in the form of buffers and cleaning fluids, are expensive, and require highly skilled operators to perform. A number of available single-use devices now enable replacement of multi-use columns, [such as] anion exchange columns, with a single-use capsule containing anion exchange filtration media that is operated much like a simple filter and replaced after each use. This eliminates all the wasteful, expensive, and time-consuming activities involved with cleaning and validating a multi-use column.

Additionally, the search for anion exchange filtration media with sufficient capacity to economically replace multi-use columns has resulted in exciting chemical innovations in ligand design. For example, new guanidinium and primary amine anion exchange ligands in these single-use devices often enable more robust operation of anion exchange polishing processes at fluid conditions under which conventional Q-functional anion exchange column resins fail to perform well. This can reduce the need to perform buffer exchange steps before polishing chromatography, leading to overall process simplification.

Oh (Avantor): One of the major issues biopharmaceutical manufacturers are facing at the moment is demand for speed. Optimizing buffers and buffer management has been helpful in alleviating that, as the use of single-use technology or hybrid approaches of outsourcing and in-house preparation allow buffer preparation to take place across a variety of scales. At the same time, improving buffer formulation with additives that increase binding capacity, stability, and separation dramatically can [significantly] increase the efficacy of chromatographic purification steps.

Quality support systems are also important in buffer optimization. Traditional sampling methods are destructive, risk contamination of buffer components, and waste time. With side sampling and non-destructive identification technologies such as Raman ID compatible packaging, however, there is no need for physical sampling. This not only decreases risk but enables heightened operational efficiency.

Tackling biomolecule complexity

BioPharm: How would simplifying downstream purification steps offer a better solution than ramping up the complexity of the process?


Oh (Avantor): Downstream processing is already complex, and its optimization is more difficult than that of upstream processing. Downstream production involves several steps, including multiple chromatography steps. Each step demands a different set of specialized resins, buffers, fluid transfer systems, and other technologies and materials. On top of that, ensuring quality and finding efficiencies require complicated analysis and optimization activities.

Because of all these steps, downstream processing can account for well over half the cost of drug production. Plus, the need for a variety of materials increases the amount of storage space needed and the probability of supply chain issues. Simplifying downstream processing would reduce the cost and time burdens in all these areas. Ultimately, this would also reduce the cost per gram of drug products, making them more accessible to patients.

Hester (3M): As long as excellent product quality is maintained, simplifying the downstream purification steps and reducing their number offer enormous benefits. Some product loss occurs at each step, and even small losses add up over a long process. Over a 15-step process, just a 5% loss at each step results in loss of over half the product. Additionally, complex downstream processes with many steps require extensive process development. This applies, not only to commercial products, but to any candidate we want to take into clinical studies or even toxicity studies, slowing the rate at which successful therapeutic candidates can be identified and brought to market.

There is a need to simplify the process into fewer steps to avoid expensive product losses, decrease costs, and get candidates into clinics at a faster rate. Additionally, there is a need for processes for a particular modality to be more standardized, requiring less expensive customization between drug products.

Simplified downstream processing

BioPharm: What (innovative) technologies are available to the industry to promote a simplified but still effective downstream purification process?

Hester (3M): A key feature of many new purification solutions is that the solutions themselves contain more complexity, which results in the process overall being less complex. [For instance,] we have learned to replace the conventional filters used in harvest to remove cell debris with hybrid chromatographic clarification filters that have ion exchange chromatography chemistry built right into the filtration media. They still remove cells and cell debris, but the chemistry on them also removes soluble contaminants.

Removal of these soluble contaminants helps the product reach a much higher point of purity earlier in the process and makes the clarified fluid more standardized from drug product to drug product. Additionally, and most importantly, those contaminants are, in many cases, the reason why the affinity column only achieves 97–98% purity instead of more than 99% purity. The contaminants create nonspecific binding events on the affinity column that enable some of the contaminants to pass through.

When we use these innovative chromatographic clarifying products upstream of the affinity column, we often see significant improvements of purity in the fluid coming off the affinity column. This in turn could potentially result in fewer or smaller polishing steps downstream. As we get more sophisticated in designing and building our process steps, including the very chemistries that go into them, we have an enormous opportunity to simplify the overall purification process.

Oh (Avantor): Emerging technologies that allow companies to monitor their processes and track raw material quality over time have significant potential to inform process efficiencies and supply chain decisions. While the use of data to refine process parameters is a comparatively simple process involving batch repetition, characterizing raw material variability involves the use of a variety of datasets. For example, the use of certificate of analysis data for all raw material lots manufactured, manufacturing in-process data, in-test actuals for conforming specs, and stability testing interval data can enable biopharma manufacturers not only to assess but also to predict the performance of raw materials and therefore choose the most impactful workflow interventions.

BioPharm: Are there specific biologic modalities for which a simplified downstream purification process will just not be sufficient (and that therefore require a complex process)?

Oh (Avantor): Many new modalities still require a complex process especially due to lack of targeted/specialized resins in the market. In many cases, the need for the complex process is not derived from the biologic itself but is more derived from having to work with existing resins that are developed for traditional biologics like mAb. Viral vectors still require ion exchange resins to separate empty from full capsid even though the charge difference is not sufficiently large enough. Furthermore, messenger RNA purification still relies on reverse phase for removing double stranded or fragments of RNA, even though such processes require flammable reagents such as acetonitrile. Without novel chromatography resins developed and targeted for those modalities, simplification of the process will always have limitations.

Hester (3M): I believe modalities that require a complex process, and therefore cannot be simplified, won’t be relevant to the industry. For example, a gene therapy drug that cures a disease in a single dose but costs one to two million dollars to produce isn’t a scalable, relevant treatment for very many patients. The processes that are being used to make those gene therapy products are going to have to get simpler.

It’s useful to think of an analogy between biologics production and petroleum production. Initial oil refining involved distilling crude oil to obtain a relatively small number of purified products—kerosene, to replace whale oil in lamps, as well as naphtha, a light oil used mainly as a solvent. Over time, the purification processes were simplified, in large part through the application of advanced materials science in the form of catalysts. This made possible the production of a greater number of separated and purified products from crude oil, such as modern gasoline. In addition to advancements in separation and purification technologies, these purified oil products resulted from an evolving understanding of what oil products were and were not useful and scalable.

Biologics purification will continue developing in a similar way, through an interplay between advancements in purification materials science and technology, and an increased understanding of what biological products have therapeutic value.

Article details

BioPharm International
Vol. 35, No. 10
October 2022
Pages: 24–27


When referring to this article, please cite it as F. Mirasol, “Considerations for Simplifying Downstream Processes,” BioPharm International 35 (10) 24–27 (2022).