EpiJen: a server for multistep T cell epitope prediction

Doytchinova, Irini; Guan, Peipei; Flower, Darren R.

doi:10.1186/1471-2105-7-131

Cited by 157 publications

(78 citation statements)

References 86 publications

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“…2.2. CTL epitope prediction and modeling CTL-specific epitope prediction was performed using NetCTL 1.2 (Larsen et al, 2007), EpiJen (Doytchinova et al, 2006), and NHLApred (Bhasin and Raghava, 2007). NHLApred and EpiJen expanded the MHC class I binding prediction to different MHC alleles, making it possible to specify a favored MHC allele from the existing list of HLA alleles.…”

Section: Retrieval Of Target Amino Acid Sequencementioning

confidence: 99%

“…NetCTL 1.2 also makes predictions about TAP transport efficiency via a weight matrix method proposed by Peters et al (2003). In NHLApred, the CTL epitopes are predicted with a combinatorial approach consisting of ANNs and quantitative matrices (QMs) (Bhasin and Raghava, 2007), and the EpiJen server implements a QM method to predict CTL epitopes (Doytchinova et al, 2006). Six T-cell epitopes were identified by these prediction algorithms and are shown in Table 1.…”

Section: Ctl Epitope Prediction and Modelingmentioning

confidence: 99%

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Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach

Poorinmohammad¹,

Mohabatkar²

2014

Turk J Biol

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A novel SARS-like illness called Middle East respiratory syndrome coronavirus (MERS-CoV), caused by an emerging coronavirus, has been a recent cause for concern due to its fatality and pandemic potential. Developing a peptide-based vaccine could be helpful in fighting against the virus. Since the experimental procedure is time-consuming and expensive, computational analysis can play an important role in accelerating the process. Therefore, the aim of this study was to computationally identify cytotoxic T-lymphocyte epitopes presented by the human leukocyte antigen (HLA)-A*0201, as this is the most frequent HLA class I allele among Middle Eastern populations. The receptor-binding domain of the spike glycoprotein of MERS-CoV, by which the virus binds to its entry receptor to further infect host cells, is a potential candidate used here for running our in silico epitope identification process. The results include predicted epitopes together with their interaction properties with major histocompatibility complex (MHC) molecules and also the binding behavior of MHC-epitope complexes to human T-cell receptor. Predicted epitopes with the most preferable binding properties are beneficial for vaccine development. Therefore, the huge experimental workload for epitope-based vaccine design will be minimized.

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Section: Retrieval Of Target Amino Acid Sequencementioning

confidence: 99%

Section: Ctl Epitope Prediction and Modelingmentioning

confidence: 99%

Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach

Poorinmohammad¹,

Mohabatkar²

2014

Turk J Biol

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“…T-cell epitope prediction T-cell epitopes of the CHIKV structural proteins were predicted using the EpiJen online server [24]. The entire structural polyprotein sequence of CHIKV was used as input to EpiJen and the server was run in the default mode.…”

Section: Mapping Of Mutationsmentioning

confidence: 99%

Genetic characterization of 2006–2008 isolates of Chikungunya virus from Kerala, South India, by whole genome sequence analysis

et al. 2009

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Chikungunya virus (CHIKV), a positive-stranded alphavirus, causes epidemic febrile infections characterized by severe and prolonged arthralgia. In the present study, six CHIKV isolates (2006 RGCB03, RGCB05; 2007 RGCB80, RGCB120; 2008 RGCB355, RGCB356) from three consecutive Chikungunya outbreaks in Kerala, South India, were analyzed for genetic variations by sequencing the 11798 bp whole genome of the virus. A total of 37 novel mutations were identified and they were predominant in the 2007 and 2008 isolates among the six isolates studied. The previously identified E1 A226V critical mutation, which enhances mosquito adaptability, was present in the 2007 and 2008 samples. An important observation was the presence of two coding region substitutions, leading to nsP2 L539S and E2 K252Q change. These were identified in three isolates (2007 RGCB80 and RGCB120; 2008 RGCB355) by full-genome analysis, and also in 13 of the 31 additional samples (42%), obtained from various parts of the state, by sequencing the corresponding genomic regions. These mutations showed 100% co-occurrence in all these samples. In phylogenetic analysis, formation of a new genetic clade by these isolates within the East, Central and South African (ECSA) genotypes was observed. Homology modeling followed by mapping revealed that at least 20 of the identified mutations fall into functionally significant domains of the viral proteins and are predicted to affect protein structure. Eighteen of the identified mutations in structural proteins, including the E2 K252Q change, are predicted to disrupt T-cell epitope immunogenicity. Our study reveals that CHIK virus with novel genetic changes were present in the severe Chikungunya outbreaks in 2007 and 2008 in South India.

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“…HLA A*0201-restricted epitopes derived from the L. infantum proteins and included in the chimeric peptides were predicted using the online available algorithms SYFPEITHI (30) and EpiJen (31) with a cutoff score adjusted to ≥18 and <50 nM, respectively (Table 2). SYFPEITHI was also used for the in silico prediction of potent H2-Kb- or H2-Db-restricted epitopes (Table 2).…”

Section: Methodsmentioning

confidence: 99%

A Poly(Lactic-co-Glycolic) Acid Nanovaccine Based on Chimeric Peptides from Different Leishmania infantum Proteins Induces Dendritic Cells Maturation and Promotes Peptide-Specific IFNγ-Producing CD8+ T Cells Essential for the Protection against Experimental Visceral Leishmaniasis

et al. 2017

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Visceral leishmaniasis, caused by Leishmania (L.) donovani and L. infantum protozoan parasites, can provoke overwhelming and protracted epidemics, with high case-fatality rates. An effective vaccine against the disease must rely on the generation of a strong and long-lasting T cell immunity, mediated by CD4+ TH1 and CD8+ T cells. Multi-epitope peptide-based vaccine development is manifesting as the new era of vaccination strategies against Leishmania infection. In this study, we designed chimeric peptides containing HLA-restricted epitopes from three immunogenic L. infantum proteins (cysteine peptidase A, histone H1, and kinetoplastid membrane protein 11), in order to be encapsulated in poly(lactic-co-glycolic) acid nanoparticles with or without the adjuvant monophosphoryl lipid A (MPLA) or surface modification with an octapeptide targeting the tumor necrosis factor receptor II. We aimed to construct differentially functionalized peptide-based nanovaccine candidates and investigate their capacity to stimulate the immunomodulatory properties of dendritic cells (DCs), which are critical regulators of adaptive immunity generated upon vaccination. According to our results, DCs stimulation with the peptide-based nanovaccine candidates with MPLA incorporation or surface modification induced an enhanced maturation profile with prominent IL-12 production, promoting allogeneic T cell proliferation and intracellular production of IFNγ by CD4+ and CD8+ T cell subsets. In addition, DCs stimulated with the peptide-based nanovaccine candidate with MPLA incorporation exhibited a robust transcriptional activation, characterized by upregulated genes indicative of vaccine-driven DCs differentiation toward type 1 phenotype. Immunization of HLA A2.1 transgenic mice with this peptide-based nanovaccine candidate induced peptide-specific IFNγ-producing CD8+ T cells and conferred significant protection against L. infantum infection. Concluding, our findings supported that encapsulation of more than one chimeric multi-epitope peptides from different immunogenic L. infantum proteins in a proper biocompatible delivery system with the right adjuvant is considered as an improved promising approach for the development of a vaccine against VL.

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EpiJen: a server for multistep T cell epitope prediction

Cited by 157 publications

References 86 publications

Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach

Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach

Genetic characterization of 2006–2008 isolates of Chikungunya virus from Kerala, South India, by whole genome sequence analysis

A Poly(Lactic-co-Glycolic) Acid Nanovaccine Based on Chimeric Peptides from Different Leishmania infantum Proteins Induces Dendritic Cells Maturation and Promotes Peptide-Specific IFNγ-Producing CD8+ T Cells Essential for the Protection against Experimental Visceral Leishmaniasis

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