Since the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019, it has evolved into different lineages, including Alpha, Beta, Delta, and Omicron. The development of broad-spectrum vaccines has become a necessity for preventing the highly mutated respiratory viruses. Traditional vaccine antigens, originating from prototype strains, cannot cover rapid mutations with these viruses, leading to breakthrough infections. With the development of synthetic biology, new technologies such as multivalent coupling of antigens, reconstructed dominate antigen modules, engineering design of conserved epitopes, epitope display, and computation-guided reconstruction have enabled redesigning antigens to achieve stronger immunogenicity with broader spectrum. The technology of synthetic biology is also applicable in the vaccine production process, such as antigen expression in nanoparticles, viral vectors, nucleic acids, and subunits. This article reviews the applications of synthetic biology technology in developing broad-spectrum vaccines in recent years, particularly for the broad-spectrum SARS-CoV-2 vaccines, and summarizes how to display common antigens and cross-antigenic sites by the reverse vaccinology for the activation of broad-spectrum immune responses against different mutant strains, achieving broad-spectrum vaccine protection effects through “remaining constant in response to ever-changing”. The article also provides a comprehensive comparison of the strengths and limitations of different broad-spectrum vaccine design strategies and discusses challenges to applying synthetic biology in the development of vaccines, offering valuable insights for universal against highly mutation viruses.

In recent years, bacterial infections have emerged as the second leading cause of death globally, posing a serious threat to public health and demanding prioritized intervention from the healthcare community worldwide. While antibiotics have conventionally been used as the primary strategy to combat bacterial infections, their efficacy is increasingly compromised due to the emergence of drug-resistant bacteria, especially multi-drug-resistant and even pan-drug-resistant superbacteria. Vaccines are thus considered as one of the most scientific, economical, safe, and effective means to prevent infectious diseases and improve public health, which are estimated to save 2 to 3 million lives annually, and can serve as a critical tool in the battle against antimicrobial resistance. However, the complexity of bacterial structure and pathogenic mechanism has hindered the development of vaccines. Challenges include screening and rationally design of effective antigens, ensuring compatibility of various antigen combinations, establishing animal models for preclinical evaluation, and defining reliable endpoints for clinical efficacy assessment. As a result, only a small number of bacteria vaccines have been successfully developed so far, and none of them has been licensed to combat the most prevalent drug-resistant infections, such as Staphylococcus aureus, Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae. Synthetic biology is a brand-new multidisciplinary focusing on repurposing natural biological systems and inventing innovative biological tools, technologies, devices, and systems for practical applications, and its concepts, principles and technologies have been extensively employed to facilitate vaccine development, including rational design, screening, and optimization of antigen, carrier, adjuvant and delivery system as well as the modulation of bacterial pathogenicity and immune responses. Herein, we outline the current status of the development of bacterial vaccines and the advancement of clinical trials for drug-resistant bacterial vaccines. Then, we summarize the application of synthetic biology technology in the development of major bacterial vaccines. Finally, we prospect the potential of synthetic biology in creating novel bacterial vaccines. Researchers have access to a greater variety of design possibilities for bacterial vaccines through synthetic biology. To maximize these benefits, we should employ synthetic biology and related technologies more efficiently in developing bacterial vaccines. Meanwhile, we should develop a scientific, reasonable, effective, and feasible management system, as well as regulatory measures, to expedite the development of efficient bacterial vaccines, therefore addressing the problem of antibiotic resistance to protect human health.

Glycoproteins with enveloped viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus, and human immunodeficiency virus (HIV), display a trimeric conformation. Different from the monomeric form, the trimeric proteins exhibit superior immunogenicity. Several trimerization motifs, such as Foldon derived from phage T4 fibritin, have been used to promote the formation of trimeric proteins with natural conformations. Although the Foldon-induced trimeric proteins are stable, their high immunogenicity limits applications in the development of vaccine antigens. In a previous study, we developed a recombinant human collagen type Ⅲ protein and determined its crystal structure, revealing a triple-helix conformation. However, the potential of this recombinant protein as a trimerization motif remained unknown. In this study, we demonstrated that the recombinant humanized type Ⅲ collagen (Rh3C) was able to act as a trimerization motif, facilitating the spontaneous trimer formation of the Rh3C-conjugated receptor-binding domain (RBD) within the spike (S) protein of SARS-CoV-2. This trimeric protein could induce a stronger SARS-CoV-2 RBD-specific IgG, IgG1, and IgG2a immune response, when compared with the monomeric RBD protein in the immunized mice. Notably, the Rh3C-RBD protein, when adjuvanted with the novel STING agonist CF501, also elicited significantly higher neutralizing antibody responses against both the pseudotyped SARS-CoV-2 (D614G) and its variant Omicron (BA.2.2) in the immunized mice. To showcase the broad applications of the Rh3C trimerization motif, we further demonstrated that the Rh3C-conjugated HA1 of the influenza virus could also elicit a stronger antibody response than free HA1. Considering the wide distribution of the Rh3C protein in human bodies, its use as a trimerization motif would not induce an immune response due to immune tolerance, thereby allowing the immune response to concentrate on targeted viral proteins. Therefore, this Rh3C-based trimerization motif holds great potential for the design and optimization of vaccines consisting of trimeric protein antigens.

The central dogma of biology, which delineates the flow of genetic information from DNA to RNA to protein, along with the principles of cellular immunology, provides a foundational understanding for harnessing the power of synthetic biology to combat cancer. The application of synthetic biology in the design and production of novel tumor vaccines marks a pivotal advance in the field of cancer immunotherapy. This study delves into the cutting-edge development in the creation of therapeutic tumor vaccines, with a particular focus on two critical components: antigen selection and vaccine design. The request for more precise and effective tumor vaccines has garnered the attention of researchers globally. These vaccines are designed to target tumor-specific antigens or those related to tumor growth and survival pathways. Traditional approaches to antigen selection have typically involved targeting specific genes with tumors. However, the advent of high-throughput sequencing and mass spectrometry has revolutionized this process by enabling the screening of novel antigens, thereby enhancing the precision and immunogenicity of vaccines. In recent years, the landscape of tumor vaccines has been significantly broadened by the engineering of vaccines through various platforms. These include DNA-based vaccines, mRNA vaccines, viral or bacterial vector vaccines, and cell-based vaccines. These innovative approaches offer a stark contrast to traditional peptide vaccines, significantly amplifying the immune response against a variety of tumor types. The versatility of synthetic biology allows for the customization of vaccines to target a wide array of tumor antigens, thereby potentiating a more robust and targeted immune reaction. The progress made in synthetic biology is not only refining existing vaccine strategies but also accelerating the pace of experimental research in tumor vaccines. This rapid advancement holds the promise of continually improving the clinical therapeutic effects of these vaccines. As researchers continue to unravel the complexities of tumor immunology and synthetic biology techniques become more efficient, the intersection of these fields is expected to yield a new generation of tumor vaccines that are not only more effective but also safer and more accessible to patients. In conclusion, the integration of biological knowledge and technological innovation in synthetic biology is transforming the development of tumor vaccines. The focus on optimizing antigen selection and vaccine design is driving the creation of more potent and tailored immunotherapies. It is anticipated that synthetic biology will play an even greater role in enhancing the efficacy of tumor vaccines, offering cancer patients with hope in the ongoing battle against this devastating disease.

Influenza viruses are highly variable and transmissible, and their infections can cause infectious respiratory diseases, such as seasonal influenza outbreaks around the world, one of the most serious public health problems at present, which can be prevented by influenza vaccination. The genome sequences, protein structures and functions of influenza viruses, as well as their packaging mechanisms are relatively clear. they are also important models, which can be used for developing conditional control genetic elements and the construction of intelligent responsive viruses. With the development of reverse genetics and synthetic biology technology, influenza viruses that are genetically engineered can better control virus replication to improve the safety of vaccines, and induce strong immune responses in human being, which have attracted wide attention in tumor immunotherapy. Several studies using simple or modified influenza viruses for treating liver cancer, melanoma, or lung cancer have found breakthroughs. In this paper, three novel strategies for attenuating influenza viruses, namely, proteolytic targeted chimeric virus, conditionally replicating influenza-attenuated live virus and highly interferon-sensitive virus, are described. The oncolytic effects of influenza viruses encoding premature stop codon chimeric antigen peptide, influenza viruses recombining with PD-L1 or CTLA4 immune checkpoint and influenza viruses expressing GM-CSF with truncated NS1 fragment on melanoma and hepatocellular carcinoma are reviewed, respectively, which suggest that the influenza viruses can be used as a live attenuated vaccine and a potential carrier for oncolytic viruses, and future researchers can be focused on constructing influenza viruses with more innovative strategies and different viruses to build a live attenuated vaccine and oncolytic viruses, in order to obtain high safety and more clinical curative treatment, improving the life quality of the patients.

The development of cancer vaccines is confronted with significant challenges. Synthetic biology emerges as a potent tool for addressing these challenges, due to its ability to modify and engineer microbes capable of adapting to and colonizing on tumor tissues to change the immunosuppressive tumor microenvironments, augment antigen presentations, and stimulate both innate and adaptive immune responses against tumors in situ. This review comments on several pivotal applications of synthetic biology in engineering bacterial and viral vectored cancer vaccines. We start with discussion on methods to mitigate the pathogenicity of bacterial or viral vectors, including the removal, deactivation, or modification of their virulent genes. Furthermore, we address strategies for enhancing their tropism and fitness within tumor tissues, such as the alteration of their cellular entry proteins or the implementation of environmentally controlled gene expression systems. Approaches to minimize their systemic toxicity are also described. To fully harness the potential of tumor microenvironment modifications induced by microbial replication, we underscore studies employing synthetic biology methods, which involve the introduction of foreign genes into the microbial genomes, thereby enabling the production of agents like cytokines, chemokines, or monoclonal antibodies to enhance the recruitment and activation of innate and adaptive cells, promote immunogenic cell death, and augment the presentation of tumor-associated antigens. We also delve into the applications of synthetic biology for the introduction of tumor antigens to the vectors, discussing various loading methods, locations, and releasing mechanisms to generate an optimized tumor-specific immune response. At the end, we highlight substantial challenges that arise in the development of microbial vectored cancer vaccines, including safety considerations, intricate interactions between anti-vector and anti-tumor immunity, and the inherent complexity of tumor biology, and propose strategies for addressing these obstacles. In conclusion, this review emphasizes the crucial role of synthetic biology in the engineering of microbes, which is instrumental in advancing the development of cancer vaccines.

Recent outbreaks of infectious diseases, such as the middle east respiratory syndrome, Zika infection, Ebola hemorrhagic fever, and Coronavirus disease (COVID-19) pose significant challenges on the rapid development of efficacious vaccines. Virus-vectored vaccines, as an important new vaccine, can be administrated noninvasively through aerosol inhalation or oral administration, which could stimulate humoral, cellular, and mucosal immune responses without the need for adjuvants, showing good immunogenicity and safety in clinical trials or in emergency use. With the deeper understanding of the viral genome and structural proteins, synthetic biology has enabled the design and modification of viruses to produce recombinant viral vector-based vaccines with high titer, safety, and immunogenicity, and such research has significant implications for the vaccine development. This review highlights major strategies employed in the construction of virus-vectored vaccines, including the construction method of replication-competent or replication-defective viral vectors, and the development of viral vectors commonly used in producing the recombinant vaccines. Among these viral vectors, replication-deficient adenovirus-based vectors with gene deletion in the E1 and E3 regions are most mature for use. Currently, adenoviral vectors that have been used in the approved recombinant vaccines include Ad5, Ad26 and ChAdOx1. Vesicular stomatitis virus and flavivirus with small genomes are negative-sense and positive-sense single-stranded RNA viruses, respectively, which are easy to prepare and more suitable for being used in developing recombinant vaccines with small antigen proteins. Poxviruses and herpesviruses have large genomes for high packing capacity, but they are most difficult to be modified with synthetic biology methods. Different viral vectors need to be prepared using different strategies, and consequently vaccines developed with these vectors have different immune effects. The construction strategies of different viral vector vaccines introduced in this review will provide valuable theoretical reference for the research and development of novel viral vector vaccines. In the future, virus-vectored vaccines will be iteratively developed for higher safety, stronger protection, better compliance and lower production cost.

Nanoparticle vaccines have been established firmly as a cornerstone of modern immunization strategies, with a compelling history that trace their pioneering use in human being back to 1981. Within the past four decades, these vaccines have not only demonstrated their efficacy, but have also been developed as powerful tools in fighting against a range of infectious diseases, most notably hepatitis B virus (HBV) and human papillomavirus (HPV). Their success can be attributed to their exceptional immunogenicity and impeccable safety as well, making them invaluable in curbing the spread of viruses and safeguarding the health and well-being of human being. The global outbreaks of the COVID-19 pandemic, driven by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has made vaccination into the forefront of public health priorities. This unprecedent challenge has accelerated the progress of various vaccine technologies, with nanoparticle vaccines attracting considerable attention. However, due to their relatively empirical design approaches and complicated manufacturing processes, progress in the clinical trials of SARS-CoV-2 nanoparticle vaccines has not been highlighted particularly. Therefore, the imperative for developing nanoparticle vaccines is to figure out their rational design, requiring groundbreaking advancement in novel technologies and theories. In this endeavor, synthetic biotechnology has emerged as an indispensable tool, driving the technological innovations of the production of nanoparticle vaccines. This article begins with an overview of technological advancements in the development of nanoparticle vaccines, encompassing progress from self-assembled nanoparticles to assist-assembled nanoparticles, and ultimately to antigen-display on formed nanoparticles. Furthermore, discoveries in understanding the unique roles of nanoparticle vaccines in enhancing antigen immunogenicity are updated, particularly in the function of nanoparticles with novel antigen presentation pathways. Finally, a comprehensive summary of the clinical trials of nanoparticle vaccines on fighting the COVID-19 pandemic is presented. In conclusion, we firmly believe that nanoparticle vaccines, bolstered by the scaffolding of synthetic biotechnology, are poised to emerge as steadfast guardians in the global battle against emerging and highly infectious diseases, and ongoing progress in this regard not only holds great promise, but also has potentials to revolutionize contagious disease prevention and control on a global scale.

The Diels-Alder reaction is a chemical process where a conjugated diene reacts with a dienophile to form cyclohexene. This reaction can generate up to four adjacent chiral centers and two carbon-carbon bonds simultaneously, making it an effective method to form C—C bonds. Therefore, it has attracted wide attention. Hetero-Diels-Alder (HDA) reactions, which involve heteroatoms, are an important tool for synthesizing natural heterocyclic rings. HAD reaction types are classified according to the heteroatoms involved, with the most common types being oxa Diels-Alder reaction and aza Diels-Alder reaction. At present, non-enzyme catalysts have been successfully applied to catalyze HDA reactions, which are catalyzed by chemical catalysts such as Lewis acids, metal ions, and organic molecules can do. However, compared to chemical catalysis, enzyme-catalyzed HDA reactions are favored due to their green, mild, efficient, and highly selective properties. With the discovery of enzyme-catalyzed HDA reactions in natural product biosynthetic pathways, uncovering the stereoselectivity and substrate specificity of HDA-related enzymes promotes our understandings of the relationship between sequences and functions. Additionally, it lays the foundation for further mining and modification of enzymes. However, there are several challenges need to be tackled. Firstly, although a few HDA enzymes have been studied, the vast majority are remained to be isolated and characterized. Secondly, the catalytic mechanisms of most reported HDA enzymes are not clear, and more information about their structures, key residues and catalytic processes remains to be uncovered. Thirdly, all reported cases present rather narrow substrate spectra, and the stereoselectivity is rather poor. Here, we summarize the currently known enzyme-catalyzed HDA reactions in heterocyclic natural product biosynthetic pathways, focusing mainly on those involved in the biosynthesis of pyridines and indole alkaloids. By summarizing and analyzing the entire biocatalytic pathways and catalytic mechanisms, we expect to guide further research and engineering of HAD enzymes to improve their activity and selectivity. We also hope to inspire the development of new biocatalysts for the synthesis of non-natural heterocyclic products.

Protein-protein interactions play a crucial role in biological processes such as cell signal transduction, gene expression and metabolic regulation, and thus their identification is essential for understanding these complex biological processes. Predicting protein-protein interactions is a hot topic of great significance, which can provide assistances in areas such as drug discovery and protein function research and design as well. In recent years, with the development of artificial intelligence, machine learning technologies have been applied gradually to the prediction of protein-protein interactions, which has shown good potentials. However, when processing a large amount of protein information, traditional machine learning methods are difficult to mine the intrinsic patterns and potential features, and deep learning techniques are needed. Compared with the three-dimensional structure of proteins, sequence information is easier to obtain, and the development of high-throughput sequencing technology provides abundant protein sequence information, which greatly facilitates the development of sequence-based deep learning technologies. Sequence-based deep learning models predict protein-protein interactions by learning intrinsic patterns and features from protein sequence information, which greatly improves prediction efficiency and accuracy. In this review, we focus on progress of deep learning in predicting sequence-based protein interactions, categorize, which is summarized according to the algorithmic framework and timeline, briefly describing the construction methods of datasets and the evaluation metrics of the models, discussing in detail the sequence encoding methods and common algorithmic architectures, and demonstrating the computational models based on various types of algorithms and their features and advantages. Finally, we analyze current challenges in predicting protein-protein interactions using deep learning methods, and discuss possible solutions. With the development of deep learning technology, the efficiency of predicting protein-protein interactions has increased dramatically. As a result, there is a need to develop models with stronger generalization and more robust prediction capabilities to aid the prediction of protein-protein interactions in the future.