Vaxjo: A Web-Based Vaccine Adjuvant Database and Its Application for Analysis of Vaccine Adjuvants and Their Uses in Vaccine Development

Sayers, Samantha; Ulysse, Guerlain; Xiang, Zuoshuang; He, Yongqun

doi:10.1155/2012/831486

Cited by 49 publications

(37 citation statements)

References 49 publications

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“…In addition to the prediction of antigens, it is often challenging to rationalize the selection and usage of other vaccine components, for example, vaccine adjuvants [15] and DNA vaccine plasmids [16]. Bioinformatics programs are also needed to support the rational design of these individual vaccine components.…”

Section: Progresses and Challengesmentioning

confidence: 99%

“…The VirmugenDB database has collected >200 virmugens and associated live attenuated vaccines [46]. (3) The Vaxjo vaccine adjuvant database [15]. Vaxjo has collected 93 vaccine adjuvants that have been used in 379 vaccines stored in VIOLIN.…”

Section: Progresses and Challengesmentioning

confidence: 99%

“…VO has been used in the VIOLIN system as a way to more logically represent, share, and link vaccine data stored in VIOLIN [15,16,46,47]. For example, the information of virmugens and related vaccines stored in VirmugenDB has been represented in the Vaccine Ontology (VO) [57,64].…”

Section: A Promising Solution: Ontology-based Data Miningmentioning

confidence: 99%

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Ontology-supported research on vaccine efficacy, safety and integrative biological networks

2014

Expert Review of Vaccines

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Summary While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including the Vaccine Ontology, Ontology of Adverse Events, and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network (“OneNet”) Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

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Section: Progresses and Challengesmentioning

confidence: 99%

Section: Progresses and Challengesmentioning

confidence: 99%

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Ontology-supported research on vaccine efficacy, safety and integrative biological networks

2014

Expert Review of Vaccines

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“…The various adjuants used are aluminum salts, Freund's complete adjuvant (FCA) which an emulsion of water and mineral oil containing killed mycobacteria, Freund's incomplete adjuvant (FIA) which does not have mycobacteria and is less toxic, lipopolysaccharides (LPSs) from Gram-negative bacteria, and muramyldipeptide (MDP). Currently, several hundred natural and synthetic compounds are known to have adjuvant activity (Petrovsky and Aguilar 2004;Sayers et al 2012). However, in the USA, alum salts and AS04 (composed of aluminum salt and MPL) are only licensed for use in humans (Giannini et al 2006).…”

Section: Computational Vaccine Adjuvant Designingmentioning

confidence: 99%

Overview of computational vaccinology: vaccine development through information technology

et al. 2014

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Pathogenic organisms, causes of various infectious diseases, possess a rich repository of antigenic proteins that engender an immune response in a host. These types of diseases are usually treated with the use of pharmaceuticals; unfortunately, many of these also have a potential to induce fatal side effects, especially allergic responses in the diseased host. In addition, many pathogens evolve (by selective survival) single or multi-drug resistance (MDR). Therefore, a means to prevent the host from becoming susceptible to the pathogen from the onset, rather than trying to devise pharmacologic protocols to treat an ongoing infection, are increasingly seen as desirable to reduce the incidence of infectious diseases altogether. To this end, cost-effective development and use of "safe" vaccines is key. This paper provides an overview on the new and expanding area of computational vaccinology and a brief background on pathogen antigenicity, identification of pathogen-specific antigens, and screening of candidate antigens using various tools and databases developed in the recent past.

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“…A web-based vaccine adjuvant base, Vaxjo, curates, stores, and analyses vaccine adjuvants and their usages in vaccine developments [200]. Table 3 Mechanisms of adjuvants in eliciting an immune response [198].…”

Section: General Aspectsmentioning

confidence: 99%

Applications of immunochemistry in human health: advances in vaccinology and antibody design (IUPAC Technical Report)

Klein

Templeton

Schwenk

2014

Pure and Applied Chemistry

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This report discusses the history and mechanisms of vaccination of humans as well as the engineering of therapeutic antibodies. Deeper understanding of the molecular interactions involved in both acquired and innate immunity is allowing sophistication in design of modified and even synthetic vaccines. Recombinant DNA technologies are facilitating development of DNA-based vaccines, for example, with the recognition that unmethylated CpG sequences in plasmid DNA will target Toll-like receptors on antigen-presenting cells. Formulations of DNA vaccines with increased immunogenicity include engineering into plasmids with "genetic adjuvant" capability, incorporation into polymeric or magnetic nanoparticles, and formulation with cationic polymers and other polymeric and non-polymeric coatings. Newer methods of delivery, such as particle bombardment, DNA tattooing, electroporation, and magnetic delivery, are also improving the effectiveness of DNA vaccines. RNA-based vaccines and reverse vaccinology based on gene sequencing and bioinformatic approaches are also considered. Structural vaccinology is an approach in which the detailed molecular structure of viral epitopes is used to design synthetic antigenic peptides. Virus-like particles are being designed for vaccine deliveries that are based on structures of viral capsid proteins and other synthetic lipopeptide building blocks. A new generation of adjuvants is being developed to further enhance immunogenicity, based on squalene and other oil-water emulsions, saponins, muramyl dipeptide, immunostimulatory oligonucleotides, Toll-like receptor ligands, and lymphotoxins. Finally, current trends in engineering of therapeutic antibodies including improvements of antigen-binding properties, pharmacokinetic and pharmaceutical properties, and reduction of immunogenicity are discussed. Taken together, understanding the chemistry of vaccine design, delivery and immunostimulation, and knowledge of the techniques of antibody design are allowing targeted development for the treatment of chronic disorders characterized by continuing activation of the immune system, such as autoimmune disorders, cancer, or allergies that have long been refractory to conventional approaches.

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Vaxjo: A Web-Based Vaccine Adjuvant Database and Its Application for Analysis of Vaccine Adjuvants and Their Uses in Vaccine Development

Cited by 49 publications

References 49 publications

Ontology-supported research on vaccine efficacy, safety and integrative biological networks

Ontology-supported research on vaccine efficacy, safety and integrative biological networks

Overview of computational vaccinology: vaccine development through information technology

Applications of immunochemistry in human health: advances in vaccinology and antibody design (IUPAC Technical Report)

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