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Crossing the Digital Divide in Engineering Biology: Bringing Designs to Life with Cell-Free Protein Synthesis

March 22, 2024

In September 2022, our colleagues Eugene Chiu and Kevin O’Connell wrote about the potential engineering biology offers to solve the most significant issues facing the nation and our world today, promising new transformative capabilities in agriculture, health, industrial manufacturing, and more. Recognizing the strategic import of these capabilities, we are highlighting IQT activities and critical capabilities in this space. This post discusses cell-free protein synthesis, an emerging commercial platform allowing users to turn AI-based protein designs into physical reality.

The natural world contains an extraordinary diversity of biological molecules, many of which have been harvested as valuable nutrients, life-saving medicines, building materials, and more recently, even industrial catalysts. Historically, these compounds have been sourced from plants, animals, and microbes that have been painstakingly cultivated over generations. The increasing demand for new sustainable biological products with novel properties far outstrips the slow pace of natural product discovery and development. Engineering biology provides a powerful alternative to create these high-value compounds with exquisitely tailored features and functions by using synthetic biology to program cellular factories for their production. The recent explosion of artificial intelligence (AI) is profoundly changing the design landscape for biological products, producing more designs than can be easily built using conventional production methods. Cell-free protein synthesis is an emerging capability that is transforming engineering biology, reaching unprecedented speed and scales necessary to pull these innovative designs from digital space into physical reality.

Proteins are the most complex and versatile class of biological molecules. Biological molecules come in a multitude of shapes and sizes. Proteins, which are made from a standard palette of 20 amino acids, perform a dizzying array of functions: they block the development of cancer, catalyze chemical reactions, detect and process environmental signals, create electrical impulses, cause mechanical motion, and much more. All critical functions of engineered organisms come about because they contain new or engineered proteins. Engineered proteins are used in a broad range of applications from designer cancer therapies to synthetic meats to carbon-neutral cement.

Engineering biology couples synthetic biology and artificial intelligence to power cellular factories. The word “engineering” conjures blueprints with carefully drawn plans, construction equipment poised to transform concrete blocks and steel beams into towering buildings, and inspectors standing by to confirm all structures and systems are sound and ready for use. Engineering biology applies a similar “design-build-test” strategy for biological production of proteins. New protein designs are created based on design principles gleaned from vast stores of biological data, which are then encoded in synthetic genes by companies such as Twist Bioscience, Integrated DNA Technologies, Molecular Assemblies, Ansa Biotechnologies, and others. These designer genes are introduced to biological production chassis – commonly used microbes or mammalian cell lines – where they are read by cellular machinery and translated to proteins that can be harvested, purified, and packaged for a huge number of different applications. Few technologies have had the disruptive impact as AI on biological production. It is now far easier to use AI to computationally generate hundreds to thousands of novel protein designs than it is to engineer living cells to transform those designs into proteins.

The ability to design proteins has outpaced the means to produce them. Despite the importance of proteins across multiple facets of everyday life, conventional methods of protein production in chassis organisms are costly and slow. Standard laboratories are often outfitted to only accommodate small-scale protein production and can typically only synthesize a handful of proteins at one time. A single batch of cell-based protein synthesis may require weeks or months to perform given the time required to create cell lines carrying synthetic genes encoding the desired constructs, their expansion to relevant volumes for production, and potentially significant optimization to achieve necessary yields for downstream functional assays. In fact, some proteins cannot be produced by microbes at all because they interfere with the cell’s growth or because the chosen chassis does not possess the molecular equipment needed to process synthesized proteins for their intended use. Further, using living cells to transition from research scale production (microgram to milligram quantities of protein) to scales necessary for commercialization (gram to kilogram quantities of protein) is fraught with time-consuming technical challenges. Consequently, protein synthesis has become a hurdle to realizing the profound speed and scale AI can bring to engineering biology. 

Cell-free protein synthesis sidesteps biological production constraints. Unlike conventional cell-based biological production, cell-free protein synthesis is performed under carefully controlled conditions in a test tube, rather than the more complex and unwieldly environments within living cells.  Although derived from cells, cell-free protein synthesis extracts are highly engineered to have carefully balanced proportions of protein synthesis machinery relative to energy-providing substrates, synthetic DNA template, and additional cofactors that promote effective protein expression and folding. Several companies provide commercially available cell-free protein extracts that are customized to support production of specific protein targets at research scales (for example, New England Biolabs, ThermoFisher Scientific, Sino Biological, LenioBio, and Liberum Bio). Additionally, this method of protein synthesis can also facilitate rapid transition from research to commercial production cells since the complexities introduced by living cells and changing fermentation volumes are avoided.  Companies such as Resilience have adopted cell-free protein synthesis for commercial scale production of proteins including antiviral drugs. (In fact, they believe this capability is so important to have in-house that they purchased an entire company, SwiftScale Biologics.)

AI and automation are expanding the impact of cell-free protein synthesis. The simplified and scalable nature of cell-free protein synthesis makes it particularly well-suited for automation to synthesize hundreds to thousands of proteins in parallel. This capability is critical for screening of the vast numbers of AI-based designs that are now being generated, rather than forcing researchers to throttle this high-impact capability by testing only several “hand-made” protein designs at once. Additionally, data generated from large numbers of engineered proteins describing the functional impact of engineered modifications can in turn feed back into AI models and strengthen their performance. Tierra Biosciences, an IQT portfolio company, is leveraging automation and AI in a service-based cell-free protein synthesis platform that can produce hundreds of engineered proteins at one time, generating both protein products for their customers and a wealth of data describing synthesis performance to continually improve their platform.

More investment is needed to advance cell-free biological production capacity in the U.S.  The synthesis of custom proteins at speed and scale is a critical enabler for the broad adoption of AI-enabled biological design and realization of the next generation of biological medicines, foods, fuels, and materials that will change our lives and the world for the better. Limited domestic capacity for custom protein production has resulted in a gap increasingly filled by China-based GenScript, and Wuxi Biologics. Increasing capability and capacity to design, build and test proteins at speed and scale is key to accelerating U.S. leadership in engineering biology for these applications and many more.  Several publicly funded research and development programs in the U.S. have contributed to the growth of cell-free protein synthesis platforms; however, early commercial investment often prioritizes products over platforms. Patient capital is necessary to continue to advance synthesis capabilities, and incentives for early adopters of domestic capacity will provide these companies revenue to continue their growth and expand their impact. Continued growth of protein synthesis at speed and scale within the U.S. is essential to realize the promise of engineering biology.

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