Putative new combination vaccine candidates identified by reverse vaccinology and genomic approaches to control enteric pathogens.

OBJECTIVES: The pathogenic microorganisms that cause intestinal diseases can significantly jeopardize people's health. Currently, there are no authorized treatments or vaccinations available to combat the germs responsible for intestinal disease. METHODS: Using immunoinformatics, we developed a potent multi-epitope Combination (combo) vaccine versus Salmonella and enterohemorrhagic E. coli. The B and T cell epitopes were identified by performing a conservancy assessment, population coverage analysis, physicochemical attributes assessment, and secondary and tertiary structure assessment of the chosen antigenic polypeptide. The selection process for vaccine development included using several bioinformatics tools and approaches to finally choose two linear B-cell epitopes, five CTL epitopes, and two HTL epitopes. RESULTS: The vaccine had strong immunogenicity, cytokine production, immunological properties, non-toxicity, non-allergenicity, stability, and potential efficacy against infections. Disulfide bonding, codon modification, and computational cloning were also used to enhance the stability and efficacy of expression in the host E. coli. The vaccine's structure has a strong affinity for the TLR4 ligand and is very durable, as shown by molecular docking and molecular modeling. The results of the immunological simulation demonstrated that both B and T cells had a heightened response to the vaccination component. CONCLUSIONS: The comprehensive in silico analysis reveals that the proposed vaccine will likely elicit a robust immune response against pathogenic bacteria that cause intestinal diseases. Therefore, it is a promising option for further experimental testing.

COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.

Rational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general, computational vaccine design includes three major stages: (i) identification and annotation of experimentally verified gold standard protective antigens through literature mining, (ii) rational vaccine design using reverse vaccinology (RV) and structural vaccinology (SV) and (iii) post-licensure vaccine success and adverse event surveillance and its usage for vaccine design. Protegen is a database of experimentally verified protective antigens, which can be used as gold standard data for rational vaccine design. RV predicts protective antigen targets primarily from genome sequence analysis. SV refines antigens through structural engineering. Recently, RV and SV approaches, with the support of various machine learning methods, have been applied to COVID-19 vaccine design. The analysis of post-licensure vaccine adverse event report data also provides valuable results in terms of vaccine safety and how vaccines should be used or paused. Ontology standardizes and incorporates heterogeneous data and knowledge in a human- and computer-interpretable manner, further supporting machine learning and vaccine design. Future directions on rational vaccine design are discussed.

Reverse vaccinology-based multi-epitope vaccine design against Indian group A rotavirus targeting VP7, VP4, and VP6 proteins.

Rotavirus, a primary contributor to severe cases of infantile gastroenteritis on a global scale, results in significant morbidity and mortality in the under-five population, particularly in middle to low-income countries, including India. WHO-approved live-attenuated vaccines are linked to a heightened susceptibility to intussusception and exhibit low efficacy, primarily attributed to the high genetic diversity of rotavirus, varying over time and across different geographic regions. Herein, molecular data on Indian rotavirus A (RVA) has been reviewed through phylogenetic analysis, revealing G1P[8] to be the prevalent strain of RVA in India. The conserved capsid protein sequences of VP7, VP4 and VP6 were used to examine helper T lymphocyte, cytotoxic T lymphocyte and linear B-cell epitopes. Twenty epitopes were identified after evaluation of factors such as antigenicity, non-allergenicity, non-toxicity, and stability. These epitopes were then interconnected using suitable linkers and an N-terminal beta defensin adjuvant. The in silico designed vaccine exhibited structural stability and interactions with integrins (αvß3 and αIIbß3) and toll-like receptors (TLR2 and TLR4) indicated by docking and normal mode analyses. The immune simulation profile of the designed RVA multiepitope vaccine exhibited its potential to trigger humoral as well as cell-mediated immunity, indicating that it is a promising immunogen. These computational findings indicate potential efficacy of the designed vaccine against rotavirus infection.

Antibody-guided structure-based vaccines.

The vaccine field is pursuing diverse approaches to translate the molecular insights from analyses of effective antibodies and their targeted epitopes into immunogens capable of eliciting protective immune responses. Here we review current antibody-guided strategies including conformation-based, epitope-based, and lineage-based vaccine approaches, which are yielding promising vaccine candidates now being evaluated in clinical trials. We summarize directions being employed by the field, including the use of sequencing technologies to monitor and track developing immune responses for understanding and improving antibody-based immunity. We review opportunities and challenges to transform powerful new discoveries into safe and effective vaccines, which are encapsulated by vaccine efforts against a variety of pathogens including HIV-1, influenza A virus, malaria parasites, respiratory syncytial virus, and SARS-CoV-2. Overall, this review summarizes the extensive progress that has been made to realize antibody-guided structure-based vaccines, the considerable challenges faced, and the opportunities afforded by recently developed molecular approaches to vaccine development.

Transforming vaccine development.

The urgency to develop vaccines against Covid-19 is putting pressure on the long and expensive development timelines that are normally required for development of lifesaving vaccines. There is a unique opportunity to take advantage of new technologies, the smart and flexible design of clinical trials, and evolving regulatory science to speed up vaccine development against Covid-19 and transform vaccine development altogether.

The continued advance of vaccine adjuvants - 'we can work it out'.

In the last decade there have been some significant advances in vaccine adjuvants, particularly in relation to their inclusion in licensed products. This was proceeded by several decades in which such advances were very scarce, or entirely absent, but several novel adjuvants have now been included in licensed products, including in the US. These advances have relied upon several key technological insights that have emerged in this time period, which have finally allowed an in depth understanding of how adjuvants work. These advances include developments in systems biology approaches which allow the hypotheses first advanced in pre-clinical studies to be critically evaluated in human studies. This review highlights these recent advances, both in relation to the adjuvants themselves, but also the technologies that have enabled their successes. Moreover, we critically appraise what will come next, both in terms of new adjuvant molecules, and the technologies needed to allow them to succeed. We confidently predict that additional adjuvants will emerge in the coming years that will reach approval in licensed products, but that the components might differ significantly from those which are currently used. Gradually, the natural products that were originally used to build adjuvants, since they were readily available at the time of initial development, will come to be replaced by synthetic or biosynthetic materials, with more appealing attributes, including more reliable and robust supply, along with reduced heterogeneity. The recent advance in vaccine adjuvants is timely, given the need to create novel vaccines to deal with the COVID-19 pandemic. Although, we must ensure that the rigorous safety evaluations that allowed the current adjuvants to advance are not 'short-changed' in the push for new vaccines to meet the global challenge as quickly as possible, we must not jeopardize what we have achieved, by pushing less established technologies too quickly, if the data does not fully support it.

Vaccines for neglected, emerging and re-emerging diseases.

Efforts to produce vaccines against SARS and MERS were prematurely halted since their scope was perceived to be geographically restricted and they were subsequently categorized as neglected diseases. However, when a similar virus spread globally triggering the COVID-19 pandemic, we were harshly reminded that several other neglected diseases might also be waiting for the perfect opportunity to become mainstream. As climate change drives urbanization, natural selection of pathogens and their intermediate vectors and reservoirs, the risk of neglected diseases emerging within a larger susceptible pool becomes an even greater threat. Availability of a vaccine for COVID-19 is widely considered the only way to end this pandemic. Similarly, vaccines are also seen as the best tools available to control the spread of neglected (sometimes referred to as emerging or re-emerging) diseases, until the water, hygiene and sanitation infrastructure is improved in areas of their prevalence. Vaccine production is usually cost and labour intensive and thus minimal funding is directed towards controlling and eliminating neglected diseases (NDs). A customised but sustainable approach is needed to develop and deploy vaccines against NDs. While safety, efficacy and public trust are the three main success pillars for most vaccines, affordability is vital when formulating vaccines for neglected diseases.

The immunology of SARS-CoV-2 infections and vaccines.

SARS-CoV-2, the virus that causes COVID-19, emerged in late 2019, and was declared a global pandemic on March 11th 2020. With over 50 million cases and 1.2 million deaths around the world, to date, this pandemic represents the gravest global health crisis of our times. Thus, the race to develop a COVID-19 vaccine is an urgent global imperative. At the time of writing, there are over 165 vaccine candidates being developed, with 33 in various stages of clinical testing. In this review, we discuss emerging insights about the human immune response to SARS-CoV-2, and their implications for vaccine design. We then review emerging knowledge of the immunogenicity of the numerous vaccine candidates that are currently being tested in the clinic and discuss the range of immune defense mechanisms that can be harnessed to develop novel vaccines that confer durable protection against SARS-CoV-2. Finally, we conclude with a discussion of the potential role of a systems vaccinology approach in accelerating the clinical testing of vaccines, to meet the urgent needs posed by the pandemic.

Tumor-associated O-glycans of MUC1: Carriers of the glyco-code and targets for cancer vaccine design.

The transformation from normal to malignant phenotype in human cancers is associated with aberrant cell-surface glycosylation. It has frequently been reported that MUC1, the heavily glycosylated cell-surface mucin, is altered in both, expression and glycosylation pattern, in human carcinomas of the epithelium. The presence of incomplete or truncated glycan structures, often capped by sialic acid, commonly known as tumor-associated carbohydrate antigens (TACAs), play a key role in tumor initiation, progression, and metastasis. Accumulating evidence suggests that expression of TACAs is associated with tumor escape from immune defenses. In this report, we will give an overview of the oncogenic functions of MUC1 that are exerted through TACA interactions with endogenous carbohydrate-binding proteins (lectins). These interactions often lead to creation of a pro-tumor microenvironment, favoring tumor progression and metastasis, and tumor evasion. In addition, we will describe current efforts in the design of cancer vaccines with special emphasis on synthetic MUC1 glycopeptide vaccines. Analysis of the key factors that govern structure-based design of immunogenic MUC1 glycopeptide epitopes are described. The role of TACA type, position, and density on observed humoral and cellular immune responses is evaluated.

The 3Ds in virus-like particle based-vaccines: "Design, Delivery and Dynamics".

Vaccines need to be rationally designed in order be delivered to the immune system for maximizing induction of dynamic immune responses. Virus-like particles (VLPs) are ideal platforms for such 3D vaccines, as they allow the display of complex and native antigens in a highly repetitive form on their surface and can easily reach lymphoid organs in intact form for optimal activation of B and T cells. Adjusting size and zeta potential may allow investigators to further fine-tune delivery to lymphoid organs. An additional way to alter vaccine transfer to lymph nodes and spleen may be the formulation with micron-sized adjuvants that creates a local depot and results in a slow release of antigen and adjuvant. Ideally, the adjuvant in addition stimulates the innate immune system. The dynamics of the immune response may be further enhanced by inclusion of Toll-like receptor ligands, which many VLPs naturally package. Hence, considering the 3Ds in vaccine development may allow for enhancement of their attributes to tackle complex diseases, not usually amenable to conventional vaccine strategies.

Exploring future perspectives and pipeline progression in vaccine research and development.

Introduction: The COVID-19 pandemic had a profound impact on vaccines' Research and Development, on vaccines' market, and on immunization programmes and policies. The need to promptly respond to the health emergency boostered resources' al-location and innovation, while new technologies were made available. Regulatory procedures were revised and expedited, and global production and distribution capacities significantly increased. Aim of this review is to outline the trajectory of research in vaccinology and vaccines' pipeline, highlighting major challenges and opportunities, and projecting future perspectives in vaccine preventables diseases' prevention and control. Study Design: Narrative review. Methods: We comprehensively consulted key biomedical databases including "Medline" and "Embase", preprint platforms, including"MedRxiv" and "BioRxiv", clinical trial registries, selected grey literature sources and scientific reports. Further data and insights were collected from experts in the field. We first reflect on the impact that the COVID-19 had on vaccines' Research and Development, regulatory frameworks, and market, we then present updated figures of vaccines pipeline, by different technologies, comparatively highlighting advantages and disadvantages. We conclude summarizing future perspectives in vaccines' development and immunizations strategies, outlining key challenges, knowledge gaps and opportunities for prevention strategies. Results: COVID-19 vaccines' development has been largely supported by public funding. New technologies and expetited autho-rization and distribution processes allowed to control the pandemic, leading vaccines' market to grow exponentially. In the post-pandemic era investments in prevention are projected to decrease but advancements in technology offer great potential to future immunization strategies. As of 2023, the vaccine pipeline include almost 1,000 candidates, at different Research and Development phase, including innovative recombinant protein vaccines, nucleic acid vaccines and viral vector vaccines. Vaccines' technology platforms development varies by disease. Overall, vaccinology is progressing towards increasingly safe and effective products that are easily manufacturable and swiftly convertible. Conclusions: Vaccine research is rapidly evolving, emerging technologies and new immunization models offer public health new tools and large potential to fight vaccines preventables diseases, with promising new platforms and broadened target populations. Real-life data analysis and operational research is needed to evaluate how such potential is exploited in public health practice to improve population health.

Beyond the state of the art of reverse vaccinology: predicting vaccine efficacy with the universal immune system simulator for influenza.

When it was first introduced in 2000, reverse vaccinology was defined as an in silico approach that begins with the pathogen's genomic sequence. It concludes with a list of potential proteins with a possible, but not necessarily, list of peptide candidates that need to be experimentally confirmed for vaccine production. During the subsequent years, reverse vaccinology has dramatically changed: now it consists of a large number of bioinformatics tools and processes, namely subtractive proteomics, computational vaccinology, immunoinformatics, and in silico related procedures. However, the state of the art of reverse vaccinology still misses the ability to predict the efficacy of the proposed vaccine formulation. Here, we describe how to fill the gap by introducing an advanced immune system simulator that tests the efficacy of a vaccine formulation against the disease for which it has been designed. As a working example, we entirely apply this advanced reverse vaccinology approach to design and predict the efficacy of a potential vaccine formulation against influenza H5N1. Climate change and melting glaciers are critical due to reactivating frozen viruses and emerging new pandemics. H5N1 is one of the potential strains present in icy lakes that can raise a pandemic. Investigating structural antigen protein is the most profitable therapeutic pipeline to generate an effective vaccine against H5N1. In particular, we designed a multi-epitope vaccine based on predicted epitopes of hemagglutinin and neuraminidase proteins that potentially trigger B-cells, CD4, and CD8 T-cell immune responses. Antigenicity and toxicity of all predicted CTL, Helper T-lymphocytes, and B-cells epitopes were evaluated, and both antigenic and non-allergenic epitopes were selected. From the perspective of advanced reverse vaccinology, the Universal Immune System Simulator, an in silico trial computational framework, was applied to estimate vaccine efficacy using a cohort of 100 digital patients.

In silico discovery of epitopes of gag and env proteins for the development of a multi-epitope vaccine candidate against Maedi Visna Virus using reverse vaccinology approach.

Maedi Visna Virus (MVV) causes a chronic viral disease in sheep. Since there is no specific therapeutic drug that targets MVV, development of a vaccine against the MVV is inevitable. This study aimed to analyze the gag and env proteins as vaccine candidate proteins and to identify epitopes in these proteins. In addition, it was aimed to construct a multi-epitope vaccine candidate. According to the obtained results, the gag protein was detected to be more conserved and had a higher antigenicity value. Also, the number of alpha helix in the secondary structure was higher and transmembrane helices were not detected. Although many B cell and MHC-I/II epitopes were predicted, only 19 of them were detected to have the properties of antigenic, non-allergenic, non-toxic, soluble, and non-hemolytic. Of these epitopes, five were remarkable due to having the highest antigenicity value. However, the final multi-epitope vaccine was constructed with 19 epitopes. A strong affinity was shown between the final multi-epitope vaccine and TLR-2/4. In conclusion, the gag protein was a better antigen. However, both proteins had epitopes with high antigenicity value. Also, the final multi-epitope vaccine construct had a potential to be used as a peptide vaccine due to its immuno-informatics results.

Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning.

Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-based vaccine design program using reverse vaccinology with machine learning. Vaxign2 is a comprehensive web server for rational vaccine design, consisting of predictive and computational workflow components. The predictive part includes the original Vaxign filtering-based method and a new machine learning-based method, Vaxign-ML. The benchmarking results using a validation dataset showed that Vaxign-ML had superior prediction performance compared to other RV tools. Besides the prediction component, Vaxign2 implemented various post-prediction analyses to significantly enhance users' capability to refine the prediction results based on different vaccine design rationales and considerably reduce user time to analyze the Vaxign/Vaxign-ML prediction results. Users provide proteome sequences as input data, select candidates based on Vaxign outputs and Vaxign-ML scores, and perform post-prediction analysis. Vaxign2 also includes precomputed results from approximately 1 million proteins in 398 proteomes of 36 pathogens. As a demonstration, Vaxign2 was used to effectively analyse SARS-CoV-2, the coronavirus causing COVID-19. The comprehensive framework of Vaxign2 can support better and more rational vaccine design. Vaxign2 is publicly accessible at http://www.violinet.org/vaxign2.

Identification of novel putative immunogenic targets and construction of a multi-epitope vaccine against multidrug-resistant Corynebacterium jeikeium using reverse vaccinology approach.

The emergence of multidrug-resistant Corynebacterium jeikeium has limited treatment options and resulted in the inability to treat C. jeikeium infections, especially in immunocompromised patients. To our knowledge, no studies have been conducted to evaluate C. jeikeium antigens for vaccine development. Given the lack of effective treatments against C. jeikeium, this study aimed to identify potential immunogenic targets against C. jeikeium as a nosocomial pathogen using a reverse vaccinology approach. To achieve this goal, we performed several immuninformatics analyses, including antigenicity, allergenicity, PSI-BLAST to the human proteome, physiochemical properties, B-cell and T-cell epitopes, molecular docking, and immunosimulation. In addition, quartile scoring and prevalence assessment were used to select the most abundant immunogenic targets in different C. jeikeium strains. Finally, protein-protein interactions were performed and the multi-epitope vaccine was developed. Five putative immunogenic targets were presented as short-listed proteins in this study, including three enzymatic proteins (WP_011273969.1, WP_041626322.1, and WP_005292204.1), one protein with DUF3235 domain (WP_011273103.1), and one hypothetical protein (WP_005293648.1). Four linear B-cell epitopes of putative immunogenic targets, including WP_011273103.1 (LNSKPTPRNAAAKPKAK), WP_011273969.1 (GEGAQGSAAPADAQATANE), WP_005292204.1 (ASVSAAQKADGIAP), and WP_041626322.1 (YSKKVAEEMGVG) were selected and inserted into the mutant TbpB C-lobe protein. This platform can effectively present multiple epitopes to the immune system. However, experimental in vitro and in vivo analysis is required to confirm the safety, immunoreactivity, and efficacy of these putative immunogenic targets.

Towards specie-specific ensemble vaccine candidates against mammarenaviruses using optimized structural vaccinology pipeline and molecular modelling approaches.

Mammarena viruses are emerging pathogenic agents and cause hemorrhagic fevers in humans. These viruses accomplish host immune system evasion to replicate and spread in the host. There are only few available therapeutic options developed for Mammarena Virus (also called MMV). Currently, only a single candidate vaccine called Candid#1 is available against Junin virus. Similarly, the effective treatment Ribavirin is used only in Lassa fever treatments. Herein, immune-informatics pipeline has been used to annotate whole proteome of the seven human infecting Mammarena strains. The extensive immune based analysis reveals specie specific epitopes with a crucial role in immune response induction. This was achieved by construction of immunogenic epitopes (CTL "Cytotoxic T-Lymphocytes", HTL "Helper T-Lymphocytes", and B cell "B-Lymphocytes") based vaccine designs against seven different Mammarena virus species. Furthermore, validation of the vaccine constructs through exploring physiochemical properties was performed to confirm experimental feasibility. Additionally, in-silico cloning and receptor based immune simulation was performed to ensure induction of primary and secondary immune response. This was confirmed through expression of immune factors such as IL, cytokines, and antibodies. The current study provides with novel vaccine designs which needs further demonstrations through potential processing against MMVs. Future studies may be directed towards advanced evaluations to determine the efficacy and safety of the designed vaccines through further experimental procedures.

Design in biology and rational design in vaccinology: A conceptual analysis.

This review discusses the philosophical foundations of what used to be called "the scientific method" and is nowadays often known as the scientific attitude. It used to be believed that scientific theories and methods aimed at the truth especially in the case of physics, chemistry and astronomy because these sciences were able to develop numerous scientific laws that made it possible to understand and predict many physical phenomena. The situation is different in the case of the biological sciences which deal with highly complex living organisms made up of huge numbers of constituents that undergo continuous dynamic processes; this leads to novel emergent properties in organisms that cannot be predicted because they are not present in the constituents before they have interacted with each other. This is one of the reasons why there are no universal scientific laws in biology. Furthermore, all scientific theories can only achieve a restricted level of predictive success because they remain valid only under the limited range of conditions that were used for establishing the theory' in the first place. Many theories that used to be accepted were subsequently shown to be false, demonstrating that scientific theories always remain tentative and can never be proven beyond and doubt. It is ironical that as scientists have finally accepted that approximate truths are perfectly adequate and that absolute truth is an illusion, a new irrational sociological phenomenon called Post-Truth conveyed by social media, the Internet and fake news has developed in the Western world that is convincing millions of people that truth simply does not exist. Misleading information is circulated with the intention to deceive and science denialism is promoted by denying the remarkable achievements of science and technology during the last centuries. Although the concept of intentional design is widely used to describe the methods that biologists use to make discoveries and inventions, it will be argued that the term is not appropriate for explaining the appearance of life on our planet nor for describing the scientific creativity of scientific investigators. The term rational for describing the development of new vaccines is also unjustified. Because the analysis of the COVID-19 pandemic requires contributions from biomedical and psycho-socioeconomic sciences, one scientific method alone would be insufficient for combatting the pandemic.

mRNA vaccine for cancer immunotherapy.

mRNA vaccines have become a promising platform for cancer immunotherapy. During vaccination, naked or vehicle loaded mRNA vaccines efficiently express tumor antigens in antigen-presenting cells (APCs), facilitate APC activation and innate/adaptive immune stimulation. mRNA cancer vaccine precedes other conventional vaccine platforms due to high potency, safe administration, rapid development potentials, and cost-effective manufacturing. However, mRNA vaccine applications have been limited by instability, innate immunogenicity, and inefficient in vivo delivery. Appropriate mRNA structure modifications (i.e., codon optimizations, nucleotide modifications, self-amplifying mRNAs, etc.) and formulation methods (i.e., lipid nanoparticles (LNPs), polymers, peptides, etc.) have been investigated to overcome these issues. Tuning the administration routes and co-delivery of multiple mRNA vaccines with other immunotherapeutic agents (e.g., checkpoint inhibitors) have further boosted the host anti-tumor immunity and increased the likelihood of tumor cell eradication. With the recent U.S. Food and Drug Administration (FDA) approvals of LNP-loaded mRNA vaccines for the prevention of COVID-19 and the promising therapeutic outcomes of mRNA cancer vaccines achieved in several clinical trials against multiple aggressive solid tumors, we envision the rapid advancing of mRNA vaccines for cancer immunotherapy in the near future. This review provides a detailed overview of the recent progress and existing challenges of mRNA cancer vaccines and future considerations of applying mRNA vaccine for cancer immunotherapies.

New Approaches to Vaccinology Made Possible by Advances in Next Generation Sequencing, Bioinformatics and Protein modeling.

Vaccines can be powerful tools, but for some diseases, safe and effective vaccines have been elusive. New developments in nucleic acid sequencing, bioinformatics, and protein modeling are facilitating the discovery of previously unknown antigens through reverse vaccinology approaches. Sequencing the complementarity- determining region of antibodies and T cell receptors allows detailed assessment of the immune repertoire and identification of paratopes shared by many individuals, supporting the selection of antigens that may be broadly protective. Systems vaccinology approaches to asses the global host response to vaccination by evaluation of differentially expressed genes in blood, cellular or tissue transcriptomes can reveal previously unknown pathways and interactions related to protective immunity. While it is important to remember that discoveries made through reverse vaccinology and systems vaccinology must still be confirmed with traditional challenge models and clinical trials, these approaches can provide new perspectives that may help solve longstanding problems in veterinary vaccinology.