In silico prediction of potential vaccine candidates on capsid protein of human bocavirus 1

Kalyanaraman, Narayanan

doi:10.1016/j.molimm.2017.11.024

Cited by 16 publications

(10 citation statements)

References 58 publications

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“…13,680 HLA I and 5091 HLA II alleles belonging to different populations of the world have been reported in IPD-IMGT/HLA Database (release version 3.33, July 2018) [68,69]. Peptide selection in the current study was done by accounting for multiple epitopes which provide opportunity to include large number of HLA alleles belonging to HLA-A, HLA-B, HLA-DP, HLA-DQ and HLA-DR. Further, docking studies have been carried out previously to ascertain the same in case of influenza virus and human baculo virus [18,70]. Docking analysis was also carried out for EBOV epitopes with only HLA A0201 allele earlier [51].…”

Section: Discussionmentioning

confidence: 99%

Conserved peptide vaccine candidates containing multiple Ebola nucleoprotein epitopes display interactions with diverse HLA molecules

Jain

Baranwal

2019

Med Microbiol Immunol

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Immunoinformatics has come by leaps and bounds to finding potent vaccine candidates against various pathogens. In the current study, a combination of different T (CD4 + and CD8 +) and B cell epitope prediction tools was applied to find peptides containing multiple epitopes against Ebola nucleoprotein (NP) and the presentation of peptides to human leukocyte antigen (HLA) molecules was analyzed by prediction, docking and population coverage tools. Further, potential peptides were analyzed by ELISA for peptide induced IFN-γ secretion in peripheral blood mononuclear cells isolated from healthy volunteers. Six peptides were obtained after merging the overlapping multiple HLA I (CD8 +) and II (CD4 +) restricted T cell epitopes as well as B cell epitopes and eliminating the peptides liable to generate autoimmune and allergic response. All peptides displayed 100% conservancy in Zaire ebolavirus. In other Ebola virus species (Sudan, Bundibugyo and Taï forest) and Filoviridae members (Lloviuvirus and Margburgvirus), some peptides were found to be conserved with minor variations. Prediction tools confirmed the ability of predicted peptides to bind with diverse HLA (HLA-A, HLA-B, HLA-DP, HLA-DQ and HLA-DR) alleles. CABS-dock results displayed that the average root mean square deviation (RMSD) value was less than three in majority of cases representing strong binding affinity with HLA alleles. Population coverage analysis predicted high coverage (> 85%) for expected immune response in four continents (Africa, America, Asia and Europe). Nine out of ten blood samples exhibited enhanced IFN-γ secretion for two peptides (P2 and P3). Thus, the identified NP peptides can be considered as potential synthetic vaccine candidates against Ebola virus.

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Section: Discussionmentioning

confidence: 99%

Conserved peptide vaccine candidates containing multiple Ebola nucleoprotein epitopes display interactions with diverse HLA molecules

Jain

Baranwal

2019

Med Microbiol Immunol

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“…The first step involved hypothetical confirmation for occurrence of surface protein and antigenic features assessed from protein primary sequences employing well-known tools: SignalP4.0, PredGPI, MAAP, VaxiJen and TMHMM in sequential manner to identify probable antigens [19,20]. The proteins of P. falciparum were reflected as high-grade antigen candidates if they have forecasted features of a surface protein, i.e., a signal peptide, a glycophosphatidylinositol (GPI) anchor and transmembrane domain(s).…”

Section: Prediction Of Antigens and Physico-chemical Characterizationmentioning

confidence: 99%

“…Finally, the PPC of 5 GDPAA minimal epitope set and epitope ensemble were executed for the selected malaria endemic regions in the present study (India, South America, South-east Asia, Central Africa, East Africa, North Africa, South Africa and West Africa). So as to compare the predictive efficiency of PPC analysis for GDPAA epitope ensemble selection, the same protocol was also applied to predict epitope ensemble of 5 RSKMA and 151 EKE of P. falciparum [19,36].…”

Section: Population Coverage Analysis Of Predicted T Cell Epitope Ensmentioning

confidence: 99%

Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum

et al. 2019

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Background: In the current scenario, designing of world-wide effective malaria vaccine against Plasmodium falciparum remain challenging despite the significant progress has been made in last few decades. Conventional vaccinology (isolate, inactivate and inject) approaches are time consuming, laborious and expensive; therefore, the use of computational vaccinology tools are imperative, which can facilitate the design of new and promising vaccine candidates. Results: In current investigation, initially 5548 proteins of P. falciparum genome were carefully chosen for the incidence of signal peptide/ anchor using SignalP4.0 tool that resulted into 640 surface linked proteins (SLP). Out of these SLP, only 17 were predicted to contain GPI-anchors using PredGPI tool in which further 5 proteins were considered as malarial antigenic adhesins by MAAP and VaxiJen programs, respectively. In the subsequent step, T cell epitopes of 5 genome derived predicted antigenic adhesins (GDPAA) and 5 randomly selected known malarial adhesins (RSKMA) were analysed employing MHC class I and II tools of IEDB analysis resource. Finally, VaxiJen scored T cell epitopes from each antigen were considered for prediction of population coverage (PPC) analysis in the world-wide population including malaria endemic regions. The validation of the present in silico strategy was carried out by comparing the PPC of combined (MHC class I and II) predicted epitope ensemble among GDPAA (99.97%), RSKMA (99.90%) and experimentally known epitopes (EKE) of P. falciparum (97.72%) pertaining to world-wide human population. Conclusions:The present study systematically screened 5 potential protective antigens from P. falciparum genome using bioinformatics tools. Interestingly, these GDPAA, RSKMA and EKE of P. falciparum epitope ensembles forecasted to contain highly promiscuous T cell epitopes, which are potentially effective for most of the world-wide human population with malaria endemic regions. Therefore, these epitope ensembles could be considered in near future for novel and significantly effective vaccine candidate against malaria.

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“…schematically in Figure 1. The same tools can also be used to predict the antigenicity of the protein directed to vaccine design of emerging pathogens (Bazmara et al, 2017;Hajighahramani et al, 2017;Kalyanaraman, 2018;Negahdaripour et al, 2017;Nezafat et al, 2016;Pahil, Taneja, Ansari, & Raghava, 2017;Shi et al, 2015;Yasmin et al, 2016). Conserved region determined by entropy method (Supplementary data 1) usually contributed to the structural and functional properties.…”

Section: B-cell Epitopes Predictionmentioning

confidence: 99%

In silico mutagenesis: decreasing the immunogenicity of botulinum toxin type A

Tjoa

Vianney

Putra

2019

Journal of Biomolecular Structure and Dynamics

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Botulinum toxin serotype A is a prominent therapeutic enzyme, for both clinical and cosmetic uses. Since this protein is produced by bacteria, it exhibits an allergenic effect when subjected to human therapy. Protein mutagenesis is one method to improve the characteristics of protein. However, in silico study is needed to give suggestion of which amino acid should be mutated. Hence, a lot of money and time can be saved. This study initially screened which residue of the Botulinum toxin serotype A is B-cell epitopes both linearly and conformationally. By overlapping the B-cell epitopes with the excluded conserve sequence, seven residues were allowed to be mutated. There were two proposed muteins showing a reduction in the antigenicity probability: DE147, E510F, T1062F, DE1080, N1089M and DQ1090; and DE147, E510F, T1062F, E1080W, N1089M and DQ1090. Molecular dynamics simulation of the 3D proposed muteins indicated an increase of flexibility in both muteins compared to that in the native protein. Both muteins have lower antigenicity. In addition, they are similar in structure, stability and functionality compared to the native protein.

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In silico prediction of potential vaccine candidates on capsid protein of human bocavirus 1

Cited by 16 publications

References 58 publications

Conserved peptide vaccine candidates containing multiple Ebola nucleoprotein epitopes display interactions with diverse HLA molecules

Conserved peptide vaccine candidates containing multiple Ebola nucleoprotein epitopes display interactions with diverse HLA molecules

Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum

In silico mutagenesis: decreasing the immunogenicity of botulinum toxin type A

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