Software tools for simultaneous data visualization and T cell epitopes and disorder prediction in proteins

Jandrlić, Davorka R.; Lazić, Goran M.; Mitić, Nenad S.; Pavlović, Mirjana

doi:10.1016/j.jbi.2016.01.016

Cited by 11 publications

(9 citation statements)

References 64 publications

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“…The database of epitopes consists of a collection of epitopes from pathogens such as virus, bacteria, protozoa, and fungus. 29 These databases have become a commonly used information source in the search of antigen for the vaccines, diagnosis, and as immunotherapies. 52 However, the search needs to be totally directed to the type of immunologic response focused.…”

Section: Discussionmentioning

confidence: 99%

“…This increase is due to the bioinformatic tools which have helped many researchers in several areas 24 , 25 – 29 especially in the identification of adequate vaccine candidates, immunologic information, and presenting important and satisfying analysis. 30 The peptide vaccine design based on immunogenic information enables another important aspect of the reverse vaccinology, being considered an evolving technology, as they reduce the vaccine development time, which lowers their financial cost and eases its projection.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against Corynebacterium pseudotuberculosis

Droppa-Almeida

Franceschi

Padilha

2018

Bioinform Biol Insights

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Caseous lymphadenitis (CLA) is a disease caused by Corynebacterium pseudotuberculosis bacteria that affects sheep and goats. The absence of a serologic diagnose is a factor that contributes for the disease dissemination, and due to the formation of granuloma, the treatment is very expensive. Therefore, prophylaxis is the approach with best cost-benefit relation; however, it still lacks an effective vaccine. In this sense, this work seeks to apply bioinformatic tools to design an effective vaccine against CLA, using CP40 protein as standard for the design of immunodominant epitopes, from which a total of 6 sequences were obtained, varying from 10 to 16 amino acid residues. The evaluation of different properties of the vaccines showed that the vaccine is a potent and nonallergenic antigen remaining stable in a wide range of temperatures. The initial tertiary structure of the vaccine was then predicted and a model selected. Later, the process of CP40 protein and TLR2 receptor binding was performed, presenting interaction with this receptor, which plays an important role in the activation of the immune response.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against Corynebacterium pseudotuberculosis

Droppa-Almeida

Franceschi

Padilha

2018

Bioinform Biol Insights

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“…In theory, a humanized antibody, free of antigenic properties, should not be immunogenic. In reality, the immense variance of CD4+ T cell epitopes and MHC haplotypes allows for fully humanized antibodies to remain immunogenic in some patients [83, 84]. To mitigate this, deimmunization strategies can be used when designing protein therapeutics.…”

Section: Strategies For Overcoming the Pitfalls Of Immunogenicitymentioning

confidence: 99%

Unraveling the Effect of Immunogenicity on the PK/PD, Efficacy, and Safety of Therapeutic Proteins

Smith

Manoli

Jaw

et al. 2016

Journal of Immunology Research

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Biologics have emerged as a powerful and diverse class of molecular and cell-based therapies that are capable of replacing enzymes, editing genomes, targeting tumors, and more. As this complex array of tools arises a distinct set of challenges is rarely encountered in the development of small molecule therapies. Biotherapeutics tend to be big, bulky, polar molecules comprised of protein and/or nucleic acids. Compared to their small molecule counterparts, they are fragile, labile, and heterogeneous. Their biodistribution is often limited by hydrophobic barriers which often restrict their administration to either intravenous or subcutaneous entry routes. Additionally, their potential for immunogenicity has proven to be a challenge to developing safe and reliably efficacious drugs. Our discussion will emphasize immunogenicity in the context of therapeutic proteins, a well-known class of biologics. We set out to describe what is known and unknown about the mechanisms underlying the interplay between antigenicity and immune response and their effect on the safety, efficacy, pharmacokinetics, and pharmacodynamics of these therapeutic agents.

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“…T‐cell epitope prediction methods can be classified into two categories: sequence‐based and structure based . Very few techniques have been explored for structure‐based approach due to the higher complexity involved and the longer computational times required compared to sequence‐based approaches …”

Section: T‐cell Epitope Prediction Methodsmentioning

confidence: 99%

Current methods for the prediction of T‐cell epitopes

et al. 2018

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T-cell epitopes are specific peptide sequences derived from foreign or own proteins that can initiate an immune response and which are recognized by specific T-cells when displayed on the surface of other cells. The prediction of T-cell epitopes is of particular interest in vaccine design, disease prevention and the development of immunotherapeutics. There are two principal categories of predictive methods: peptide-sequence based and peptide-structure-based. Sequence-based methods make use of various approaches to identify likely immunogenic amino acid sequences, such as sequence motifs, decision trees, partial least squares (PLS), quantitative matrices (QM), artificial neural networks (ANN), hidden Markov models (HMM), and support vector machines (SVM).Structure-based methods are more diverse in nature and involve approaches such as quantitative structure-activity relationships (QSAR), molecular modelling, molecular docking and molecular dynamics simulations (MD). This review highlights the key features of all of these approaches, provides some key examples of their application, and compares and contrasts the most important methods currently in use.

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Software tools for simultaneous data visualization and T cell epitopes and disorder prediction in proteins

Cited by 11 publications

References 64 publications

Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against Corynebacterium pseudotuberculosis

Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against Corynebacterium pseudotuberculosis

Unraveling the Effect of Immunogenicity on the PK/PD, Efficacy, and Safety of Therapeutic Proteins

Current methods for the prediction of T‐cell epitopes

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