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Microbial-Based Biosynthesis in Modern Medicine

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For many years, scientists have attempted to use microbial hosts to produce chemicals via a process known as microbial biosynthesis. Recent advances in synthetic biology have bolstered this field of research. In a recent study published in Nature, researchers successfully produced tropane alkaloids – medicines that have a wide variety of applications, including treating conditions as diverse as Parkinson's disease and motion sickness – in yeast. To achieve this, the scientists had to conduct over 30 genetic modifications in parallel. Their feat is the first successful study of its kind at this level of complexity.

Technology Networks
spoke with Dr Christina Smolke, lead author of the study and 
CEO of biotech startup Antheia, to learn more about microbial biosynthesis platforms and their utility in drug discovery and manufacturing.

Molly Campbell (MC): For our readers that are unfamiliar, please can you discuss the utility of tropane alkaloids in modern medicine? 

Christina Smolke (CS):
The tropane alkaloids, a class of plant-based anticholinergics, have activities as neuromuscular inhibitors. A number of tropane alkaloids are on the World Health Organization’s List of Essential Medicines and the recently published Food and Drug Administration List of Essential Medicines for their use in treating neuromuscular disorders such as Parkinson’s disease (PD), intestinal disorders and other issues caused by muscle spasms. For example, scopolamine is used to relieve motion sickness and post-operative nausea, and atropine is used to curb the drooling associated with PD or to help maintain cardiac function when intubating COVID-19 patients and placing them on ventilators. 

MC: How important are advances in synthetic biology to your field of research? 

Advances in synthetic biology have been very important for our work on microbial biosynthesis, especially in terms of advancing the complexity of cell systems that we can engineer. General approaches developed in synthetic biology (such as genome engineering, protein engineering and expression optimization) have been effective for addressing the biosynthesis of relatively simple molecules (i.e., those requiring a handful of enzymes to make), but run into a complexity threshold (which closes off a huge number of potential compounds/products). However, these general approaches alone don’t allow us to reconstruct the full complexity of nature’s chemistries; in order to build complicated medicinal products using a completely bottom up approach, we need not only three or five but sometimes 20 or more enzymes and genes to work together. In plants, these enzymes have often evolved to work together across different cells and tissue types to enable the plant to specialize chemistries for unique reactions and compounds. These natural strategies are typically lost in moving the pathway to a single-celled organism. We established a whole-cell engineering approach to really crack this problem.

MC: How is baker's yeast engineered to produce medicinal alkaloids? 

The full reconstruction of tropane alkaloid biosynthesis in baker’s yeast required the functional expression and integration of 26 genes from 10 different organisms (across four kingdoms) and eight gene deletions. The resulting whole-cell system expresses enzymes and transporters across every yeast organelle to truly re-envision the cell as a factory for efficiently assembling the most complex molecules known to humankind. 

MC: A huge issue in the synthesis of biopharmaceutical products is scale-up. Can you discuss this issue in relation to using microbial biosynthesis platforms?

Microbial fermentation of biopharmaceuticals has an advantage in scale-up, in that strategies, infrastructure and know-how for fermenting yeast at commercial scale are well established in the space. In addition, biopharmaceutical products are higher value and lower volume than other product classes, such as biofuels or commodity chemicals, and thus the fermentation processes themselves are generally more robust at commercial scale. One of the important variables for the field is downstream processing and being able to develop commercially viable recovery processes for the product from the fermentation broth at scale. In this regard, it is important to tackle the development of the yeast strain, fermentation process and recovery process – in parallel – from the R&D stage, to ensure all facets of the process will work together to reach the desired commercial metrics.

MC: When using microbial biosynthesis platform, how is the safety of the final product assessed? 

To date, in using a microbial fermentation process to produce an already approved active ingredient in a medicine, safety is primarily assessed by demonstrating equivalency of the purified product produced via microbial fermentation to the product produced via conventional approaches (e.g., extraction from the plant). Next, there are QA/QC requirements in meeting the USP pharmacopia standards for generic APIs, including impurities and stability requirements.

MC: Are there any challenges associated with mainstream use of microbial-based platforms for drug synthesis? 

From a manufacturing process perspective, there are not many challenges that are new to the industry. Specifically, a number of our active ingredients in drugs have been synthesized using microbial fermentation for decades, including many of our antibiotics, statins and even drugs such as recombinant insulin. With recent advances in synthetic biology, we can now use this manufacturing approach to produce more complicated medicinal products, including analgesics, sedatives, neuromuscular blockers and chemotherapeutics.

MC: In your opinion, how will microbial-based platforms for the synthesis of drugs evolve over the next ten years?

Microbial-based biosynthesis platforms set the foundation for a flexible and on-demand replacement for our fragmented and slow-moving drug supply chain. I believe microbial-based biosynthesis will become the main approach for the synthesis of complex natural product-like active ingredients. Rather than the months or years it takes to grow, harvest, and extract molecules from plants, this approach takes days. I also believe there are interesting opportunities when leveraging bioproduction via microbial fermentation to explore more distributed versus centralized production strategies, which will be increasingly important as we see our global supply chains face increasing pressure from pandemics, geopolitical events and environmental disasters.

Dr Christina Smolke was speaking to Molly Campbell, Science Writer, Technology Networks.