Managing Manufacturing Requirements for Live Biotherapeutics

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In 2018, Synlogic explored options for producing clinical-trial material for its lead programs, including a candidate therapy for the rare metabolic disease phenylketonuria (PKU). Like other emerging drug developers, the company evaluated the merits of outsourcing manufacturing to third parties. However, Synlogic leverages synthetic biology tools to design and develop therapeutics based on genetically engineered microbes. Thus, it also needed to consider requirements specific to live biotherapeutics. Late in 2018, Synlogic announced plans to establish its own current good manufacturing practice (CGMP)-compliant infrastructure for internal production of therapeutic candidates.

Despite obstacles raised by the COVID-19 pandemic, Synlogic has expanded its capabilities and advanced clinical candidates. In April 2022, I corresponded with Tony Awad, the company’s chief operating officer, to learn about manufacturing requirements for live biotherapeutics and considerations for developing internal capabilities.

Our Conversation
How would you describe your company’s products? Synthetic biotics are candidate therapeutics enabled by a proprietary, reproducible, target-specific drug design based on the principles of synthetic biology. We use programmable, precision genetic engineering of well-characterized probiotics to exert localized activity for therapeutic benefit, with a focus on metabolic and immunologic diseases. All of our programs to date have used the same “starter strain” or chassis, a well-studied probiotic called Escherichia coli Nissle (EcN).

Because our therapies consist of living cells, they must be grown using fermentation processes. Once cells have been cultured, we proceed to diafiltration and buffer exchange using tangential-flow filtration (TFF). The TFF step formulates our cells and prepares them for lyophilization, which forms a powder designed for oral resuspension. Lyophilization increases the shelf life of our investigative therapeutics and enables us to produce a patient-friendly presentation.

How would you describe your facility and its core capabilities? Synlogic has established a multiproduct, multipurpose manufacturing facility equipped for low-bioburden bulk drug product (BDP) and drug product (DP) manufacturing. The fully integrated manufacturing organization includes quality control (QC) laboratories that support incoming raw material sampling/testing and release testing. Building our own CGMP-compliant facility enabled us to move production in house from a contract manufacturing organization (CMO). We’ve gained speed and control, and we are realizing higher levels of quality and cost-efficiency.

One key feature is that we have implemented single-use technologies throughout our processes. Disposables help us to switch between programs faster and more effectively by minimizing required cleaning and risks for cross-contamination. Such equipment also reduces the required facility footprint, thus reducing up-front capital investments.

Why does Synlogic colocate spaces for fermentation, lyophilization, and QC testing? When fermenting bacteria that are used for protein expression and extraction, maintaining high cell viability at the time of harvest is not essential. We require colocation of fermentation, downstream processing, and lyophilization because our therapeutic is based on living organisms. “The bugs are the drugs,” so viability is one of our critical quality attributes (CQAs). Maintaining healthy cells helps to ensure high viability, and that yields an active drug.

Because our drug-product cells are metabolically active, they will die over time unless they are dried to a stable form in powder. We minimize the duration of processing time by colocating fermentation and lyophilization, thus minimizing cell death and maintaining high viability.

You mentioned Synlogic’s transition to in-house manufacturing. What activities do you perform internally? Over the past three to four years, we have invested significantly in our own manufacturing capabilities. I like to describe us as a fully integrated manufacturing organization: We can do everything from handing off a finalized strain to delivering a drug product and packaging it for transport to a patient’s home. Our capabilities span process development, analytical development, formulation, CGMP production, packaging/labeling, QC, and quality assurance (QA).

We have redundancy established for QC, with an external contract research organization (CRO) available to outsource a couple of tests and assays as needed. This combination of in-house capability and external assistance enables us to be flexible and provides us with more capacity to perform required release testing on multiple strains and products.

My impression is that CMOs often do not work with live biotherapeutics. Why? Identifying a CMO that could meet the needs of our pipeline programs was difficult. Many contract partners will not work with live bacteria, and the few that do can have long lead times and high costs, especially because of the COVID-19 pandemic. CMOs that have experience with live bacteria sometimes lack mature quality infrastructure because their bacterial production is geared more toward industrial applications than for manufacturing biotherapeutics. We require colocation of fermentation, downstream processing, and lyophilization, but many CMOs do not have fermentation and lyophilization under one roof. The few that do have limited lyophilization capacity, which does not match our needs for fermentation scaling. And although fermenting bacteria for protein production is a common process, expertise in maintaining high viability is uncommon — and that aspect is critical to our work.

What capabilities are easy and difficult for small biotech companies to develop? Such companies generally find it easy to establish capabilities for phase 1–2 clinical trials because the material demands are much more modest than they are for phase 3 trials. Companies can support clinical demands with low-scale production while being cost effective. When operating at small scales, developers might have more options, and compliance requirements are not as stringent.

I recommend that companies in good financial standing establish research and process sciences/manufacturing under the same roof. Having an iterative process between those groups strengthens and facilitates the exchange of technical expertise.

We have found fermentation capabilities to be easier to establish than those for lyophilization. Although freeze-drying is a common process in the pharmaceutical industry, lyophilizing a live biotherapeutic is not a trivial process because we are trying to maintain high cell viability.

How important is automation to your facility? We use it extensively to operate fermentors, lyophilizers, and even analytical instruments in QC settings. A fermentor will run 16–22 hours during an EcN process. Without automation, we would need operators to work around the clock.

I highly recommend that small biotech companies implement automation wherever possible because it reduces manual operations and manipulations, helping to minimize overall production costs. Cost efficiencies and burn-rate reduction are always valuable for small companies.

What lessons are you learning as Synlogic scales up? We are ahead of the game because we have established process-sciences groups with internal expertise. That will help us to remediate technical challenges. One difficulty that comes to mind is getting buy-in from regulatory agencies to support smooth developmental progression. It is critical to build strong relations and correspondence with regulators from early development stages. That facilitates transitions through manufacturing processes for different clinical phases.

Scale-up requires larger equipment, more raw material, and more consumables — all of which take long lead times to procure. The pandemic has not been kind to supply chains. Items that usually had lead times of six to eight weeks now require six to eight months, if not longer. Such delays mean that more planning and less reacting are necessary; otherwise, manufacturing will become a bottleneck for late-stage clinical and commercial production.

Brian Gazaille is associate editor of BioProcess International, part of Informa Connect; Learn more about the Synlogic facility at