Innovative processes transforming oligonucleotide manufacturing

Published: 19-Oct-2022

Bachem, the Swiss pharmaceutical company, has invested in a capacity expansion for the large-scale production of oligonucleotide active pharmaceutical ingredients (APIs)

Each step within the company’s oligonucleotide manufacturing process uses unique, innovative equipment to deliver the highest-quality products and to increase sustainability.

Tailor-made oligonucleotide synthesisers
To ensure only the highest-quality oligonucleotide is supplied to customers, Bachem designed a large-scale oligonucleotide synthesiser. This synthesiser optimises the process of oligonucleotide synthesis and has been qualified for GMP batches from a 0.2 mol to 2.0 mol scale.

One of the engineering solutions used for the innovative synthesiser is in-line mixing of dichloroacetic acid (DCA) and toluene. This solution is used as the initial step for all coupling cycles of oligonucleotide synthesis, deprotecting the 5’-dimethoxytrityl (DMT) group and releasing the 5’-hydroxy group to ensure the coupling reaction takes place. 

For the majority of synthesisers, the percentage of DCA in toluene is fixed, whereas Bachem’s new skid has a possibility to change the ratio of DCA (usually between 3–10%). This ability to change the concentration is highly beneficial as using too much DCA can cause undesired side-reactions and decrease API quality.

In addition, Bachem has also introduced further innovative customisations to optimise oligonucleotide synthesis. These new customisations aim to provide a more efficient process that will consistently produce high-quality crude API.

First, a heat exchanger has been added to enable full temperature control, maintaining the optimal conditions for deprotection and coupling. The synthesiser also features dynamic axial columns (DACs) that contain a piston that moves throughout each synthesis cycle of the process. This piston allows full control of the column’s volume, avoiding dead volume and optimising the amount of solvent required. 

Automated C&D equipment
After synthesis has taken place, an oligonucleotide has to undergo a process of cleaving and deprotection (C&D). To improve efficiency, Bachem has equipped its oligonucleotide production line with an automated, large-scale C&D system that uses a two-step process.

Once the synthesis is complete and the same column has been installed onto the C&D skid, the first step is to deprotect the cyanoethyl groups before the cleavage of the oligonucleotide from its solid support.

Importantly, a solution of room temperature ammonia is able to circulate throughout the column of a given volume. This solution carries the released oligonucleotide to the collector vessel, which is made from Hastelloy, providing resistance against highly corrosive solutions. 

The second step of the process is the deprotection of the protecting groups from the oligonucleotide. Once the ammonia solution has recirculated several times between the vessel and the column, all the oligonucleotide is cleaved from its support before it’s collected in the vessel.

The vessel is then closed and heated under pressure with the ammonia solution using a unique automated temperature feature. And if other deprotection solutions are required, Bachem’s C&D machine is also equipped with a multiport inlet.  

After the C&D step has been completed, the oligonucleotide is free from the support and protecting groups, meaning the crude API is ready for ultrafiltration.

Continuous chromatography for oligonucleotide purification
To further optimise the process of oligonucleotide manufacturing, Bachem has set up the first continuous chromatography equipment for use at an industrial scale. 

By enabling the continuous recycling of side-cuts (mixed fractions of impurities and API), solvent consumption can be decreased by more than 30% compared with single-column batch purification. This innovative Multicolumn Countercurrent Solvent Gradient Purification (MCSGP) technology therefore improves sustainability during this important step.  

In addition, this technology is also cost-effective and substantially reduces waste. MCSGP runs continuously, providing high product yield without negatively impacting purity, whilst allowing room for additional savings in cycle time. These savings in cycle time can reach up to 70% compared with other batch chromatography methods. 

The unique, custom-built synthesiser, C&D system and MCSGP equipment will all enhance the quality, sustainability and cost-effectiveness of oligonucleotide API production. 

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