How to scale the manufacturing of RNA therapeutics

RNA-based therapies have rapidly emerged as one of the most transformative advancements in modern medicine. These innovative treatments use the power of RNA to target and modify cellular processes with precision, holding great promise for addressing a wide range of diseases. From the intricacies of rare genetic disorders to widespread health challenges like cardiovascular disease, RNA therapeutics are set to revolutionize patient care. A prominent example, RNA interference (RNAi), including siRNA therapies, showcases this potential by utilizing small RNA molecules to silence specific genes, effectively halting the production of disease-causing proteins.

The surge in RNA therapies is reflected in the market’s rapid growth. Projected to reach a remarkable $18 billion by 2030, with a compound annual growth rate of 5.6% from 2023, this expansion is driven by the increasing prevalence of chronic diseases and significant R&D investments [1]. As RNA-based drug modalities target a broader range of therapeutic areas — including those where traditional small-molecule drugs have proven less effective — the applications are expanding to encompass large patient populations [2]. This includes critical areas such as cardiovascular drugs, which will require manufacturing capabilities in the multi-metric ton range, such as inclisiran, a siRNA therapy.
This escalating demand presents a fundamental challenge: the need for highly efficient, cost-effective and, most crucially, scalable manufacturing processes. Without the ability to produce these life-changing therapies at the required volumes, the full potential of RNA medicines cannot be realized for the millions who stand to benefit from them. This is why the industry has to overcome existing manufacturing obstacles and achieve scale, purity and sustainability to produce RNA therapeutics successfully.

Limitations of traditional RNA manufacturing

For decades, phosphoramidite chemistry (PAC) has served as the foundational method for oligonucleotide synthesis, widely used across early- and clinical-stage RNA production. This solid-phase oligonucleotide synthesis (SPOS) process assembles RNA sequences one nucleotide at a time through a series of stepwise chemical coupling reactions. Although reliable for constructing a wide range of RNA sequences, PAC was not designed to meet the multi-metric ton demands now facing the RNA therapeutics industry, which are required for duplexed or chemically modified RNA constructs, such as siRNAs.
Despite its utility, PAC struggles significantly to efficiently deliver commercial-scale RNA manufacturing, particularly for considerable indications, due to several inherent constraints, including:

Limited synthesis scalability
Low yield with increasing length
High infrastructure burden
Capital-intensive scale-up
Sustainability shortfalls
Chemical complexity and impurities

While incremental innovations, such as liquid-phase synthesis (LPOS) and solvent recycling, have been introduced to improve PAC’s attractiveness, they do not fully address these core limitations. As the RNA therapeutics industry evolves toward broader indications and larger-volume production, these challenges have become a primary driver for the urgent exploration and adoption of alternative approaches that promise greater scalability, flexibility and sustainability.

Enzymatic synthesis for scalable RNA production

The limitations of traditional PAC methods have catalyzed an industry-wide focus on enzymatic manufacturing approaches as a next-generation solution for RNA therapeutics. This alternative solution leverages engineered enzymes to construct oligonucleotides, offering a scalable, aqueous and modular alternative to traditional synthesis. This enzymatic approach represents a radical shift for scalability, offering several key advantages:

Mild, aqueous conditions
Unlike PAC’s reliance on harsh reagents and protecting group chemistry, enzymatic RNA synthesis operates under mild, aqueous conditions. This stark contrast simplifies process design immensely, eliminating many chemical complexities that typically contribute to yield loss, impurity formation and significant solvent waste. The gentler conditions enhance the flexibility of scale-up, making it easier to expand production without encountering the severe operational challenges associated with hazardous chemicals.
Fewer steps, solution-phase format
Enzymatic workflows are characterized by fewer overall steps and a solution-phase format, as opposed to the solid-phase, multi-step nature of traditional methods, such as PAC. This streamlined process inherently supports more modular and scalable manufacturing. The solution-phase format enables more homogeneous reactions and facilitates the handling of larger volumes, accommodating both short and long RNA constructs with greater efficiency. This modularity means that scaling up can involve simply increasing reactor size or adding parallel lines with greater ease, rather than replicating complex, solvent-intensive solid-phase systems.
Reduced chemical complexity
By eliminating the need for many harsh reagents and protecting groups, enzymatic synthesis significantly reduces chemical complexity. This directly translates into fewer side reactions and a cleaner product profile, leading to less yield loss and reduced waste generation. A less complex chemical environment not only improves the overall efficiency of the manufacturing process but also makes it more manageable and scalable, as the challenges of impurity identification, quantification and removal are substantially mitigated. This inherent simplicity is a powerful enabler for reaching commercial-scale production efficiently and cost-effectively.

A strategic approach to industrial scalability

To meet the escalating demand for RNA therapeutics and overcome the persistent limitations of traditional PAC methods, Codexis has used its expertise in enzyme engineering to bring RNA manufacturing to the forefront. The result is the ECO Synthesis™ manufacturing platform — a flexible, enzyme-enabled system designed to address the challenges of large-scale RNA production. This platform utilizes highly engineered enzymes for both the sequential synthesis of RNA therapeutics and enzymatic ligation, supporting the truly scalable and modular production of full-length RNA therapeutics.

Built on the company’s deep expertise in protein engineering and process development, ECO Synthesis offers two distinct, yet complementary, approaches to RNA synthesis, which can be used independently or in combination depending on the therapeutic format and specific manufacturing needs, each contributing to enhanced scalability:

Fully sequential enzymatic synthesis: This approach employs a cyclic, enzymatic process to construct RNA strands one nucleotide at a time, but in a highly controlled and inherently more scalable manner than PAC.
Ligation-based assembly: For more complex constructs, such as siRNA or duplexed RNA, the ECO Synthesis platform enables high-efficiency ligation-based assembly of multiple shorter single-stranded RNA fragments into the desired final therapeutic. These shorter fragments can be produced via sequential enzymatic synthesis or even traditional PAC, and are then precisely joined using engineered dsRNA ligases.

Both of these powerful workflows are underpinned and enabled by Codexis’ proprietary CodeEvolver® enzyme engineering platform. This platform serves as the foundation of scalability by developing highly optimized enzymes that deliver exceptional substrate specificity, robust catalytic performance across a broad range of process conditions and crucial tolerance for chemically modified bases and high-concentration substrates. These enzymes are developed using the CodeEvolver platform, enabling fit-for-purpose design for performance with 2′-OMe, 2′-F, phosphorothioates, and other modifications common in RNAi therapeutics. Their properties enable manufacturers to achieve scalable, GMP-compliant production with consistent quality. The ability of these enzymes to perform effectively with high substrate concentrations is a key factor in achieving significantly higher yields per batch, directly impacting the overall economic viability and industrial scalability of the process.

The ECO Synthesis platform delivers a range of significant advantages, all grounded in enzyme-enabled efficiency, process adaptability and, most critically, commercial scalability. By integrating Codexis’ deep enzyme engineering expertise with platform-ready manufacturing workflows, ECO Synthesis supports both performance optimization and long-term operational value across a diverse array of RNA constructs.

Advancing RNA therapeutics at scale

The landscape for RNA therapeutics is evolving rapidly, marked by expanding modalities, rising demand and increasingly complex design challenges. As RNA programs mature and move toward broader clinical applications, the urgent need for scalable, high-quality and environmentally sustainable manufacturing is more critical than ever. The ability to produce RNA medicines efficiently and at the volumes required for large patient populations will determine their ultimate impact on global health.
Codexis is actively meeting this crucial moment with its fit-for-purpose enzymatic solutions and a deep commitment to collaboration. With a platform like ECO Synthesis, which offers both fully sequential synthesis and ligation-based assembly, Codexis provides the precise tools and dedicated support that RNA developers need to overcome existing manufacturing limitations. This collaborative approach empowers partners to advance confidently toward commercial readiness, ensuring that groundbreaking RNA therapies can reach the patients who need them.

Recognizing the benefits of RNA therapies in transforming disease treatment requires the industry to continue embracing innovation and leveraging cutting-edge technologies. To this end, leaders and innovators in the biopharmaceutical space should explore the latest advancements in RNA manufacturing and consider working with experienced technology partners.

To learn more about scaling RNA production, read the latest eBook from Codexis, and contact our expert team to discuss your manufacturing goals.
Together, we can accelerate the development of RNA therapies and shape a more accessible, sustainable and healthier future of medicine.

References

1. MarketsandMarkets. RNA Therapeutics Market – Global Forecast to 2028. Available at: https://www.marketsandmarkets.com/ResearchInsight/rna-therapeutics-market-size-and-share.asp.
2. Wang, Y., Zhang, Y., Wang, J., et al. (2021). Enzymatic Synthesis of Oligonucleotides: Opportunities for Biomanufacturing. Frontiers in Bioengineering and Biotechnology, 9, 628137. https://doi.org/10.3389/fbioe.2021.628137