Harnessing synthetic biology for advancing RNA therapeutics and vaccine design

Traditional drug development, relying heavily on synthetic chemistry, often faces limitations in addressing complex or genetically rooted diseases. The high cost and lengthy development timelines are particularly problematic for emerging diseases. Synthetic biology, already impacting agriculture, environment, and biofuels, presents an attractive alternative. It involves engineering organisms or biomolecular parts for new functionalities, encompassing enzyme engineering, chemical production, genetic part assembly, and cell therapies. While a relatively new field, its roots trace back to genetic engineering techniques developed since the 1970s, building upon advancements like PCR and genomics. This review focuses on how synthetic biology can leverage the unique attributes of RNA molecules—beyond their messenger role—to improve the development of RNA-based therapies and vaccines.

The review extensively cites existing literature on various aspects of synthetic biology and RNA therapeutics. It covers the history and development of synthetic biology, including key milestones like the creation of the first synthetic biological system. The literature review also explores the use of DNA in synthetic systems and the shift towards RNA-based systems due to their safety and rapid action. Specific applications of RNA devices and circuits, such as in diagnostics and cell therapies (e.g., CAR T-cell therapy), are reviewed, referencing studies on their effectiveness and limitations. The role of RNA therapeutics, including ASOs, siRNAs, and CRISPR-Cas systems, is also discussed, citing FDA-approved drugs and ongoing research.

This is a review article, not an experimental study. The methodology involves a comprehensive literature search and synthesis of existing research on synthetic biology and its applications to RNA therapeutics and vaccines. The authors systematically analyze how synthetic biology principles can be applied to improve different aspects of RNA-based technologies, including codon optimization, chimeric protein design, RNA construct modifications (modRNA, saRNA, circRNA), and delivery systems (viral vectors, bacterial vectors, liposomes). The review organizes information into sections focusing on biomedical applications of RNA in synthetic biology, covering diagnostics, living therapeutics, RNA therapeutics and vaccines, and specifically using synthetic biology to advance RNA vaccines. Each section presents a detailed overview of current approaches, challenges, and opportunities for advancement.

The review identifies several key ways synthetic biology enhances RNA therapeutics and vaccines: 1. **Codon Optimization:** Optimizing codons within RNA constructs improves translation efficiency and antigen production in the target cells, although potential risks like misfolded proteins need consideration. 2. **Chimeric Proteins & Multi-Antigen Delivery:** Encoding chimeric proteins or using IRESs and self-cleaving 2A peptides allows the expression of multiple antigens from a single RNA construct, addressing size limitations and improving vaccine efficacy against complex pathogens. 3. **Modified RNA Constructs:** Modifications such as modRNA, saRNA, and circRNA enhance mRNA stability and lifespan, potentially leading to more potent and prolonged immune responses and facilitating easier distribution. CircRNA vaccines show particular promise due to their heat stability. 4. **Advanced Delivery Systems:** Synthetic biology tools can modify biological delivery vectors (viral, bacterial) to enhance targeting and reduce unwanted immune reactions. Minimalized synthetic bacterial genomes could provide safer and more specific delivery systems. Liposomes, already used in mRNA vaccines, can be further engineered for targeted delivery. 5. **AI and Machine Learning:** The authors foresee a significant role for AI and machine learning in improving RNA therapeutics and vaccines by optimizing RNA sequences, identifying new targets, designing specialized RNA components, and overcoming limitations in expressing complex antigens.

The review successfully demonstrates the powerful synergy between synthetic biology and RNA technology in advancing therapeutic and vaccine development. The findings highlight significant advancements in overcoming limitations of traditional RNA-based approaches. The discussion of AI's potential impact underscores the future direction of the field, suggesting novel approaches to tackle current challenges like expressing multi-domain and polysaccharide antigens. The integration of synthetic biology with AI holds immense potential for creating more effective, safe, and easily deployable RNA-based medical products, addressing a wide range of diseases.

Synthetic biology provides a versatile platform for developing highly effective RNA therapeutics and vaccines. Addressing current limitations through codon optimization, multi-antigen design, modified RNA constructs, and advanced delivery systems, along with the integration of AI-driven design, will lead to transformational progress in healthcare. Future research should focus on refining these techniques, exploring novel applications, and mitigating potential risks to fully realize the potential of this powerful combination.

As a review article, this paper is limited by the scope of existing literature. While it provides a comprehensive overview of current advancements, it cannot predict the precise outcomes of future research and development. The clinical translation of some of the discussed technologies still requires extensive testing and validation before widespread use. The complexities involved in optimizing codon usage and the potential for off-target effects are also acknowledged.