T-cell epitope-based vaccine designing against Orthohantavirus: a causative agent of deadly cardio-pulmonary disease

Joshi, Amit; Ray, Nillohit Mitra; Singh, Joginder; Upadhyay, Atul Kumar; Kaushik, Vikas

doi:10.1007/s13721-021-00339-x

Cited by 20 publications

(12 citation statements)

References 48 publications

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“…This examination not just give experiences about characteristic and mutational determination pressures acting at genomic levels of T. whipplei yet besides offer a superior cognizance of transformative improvements in this host-versatile bacterium. This computational examination uncovered the data concerning profoundly translated proteins and enzymes of this bacterium, and the conceivable amino acids that can be considered in epitope-based prophylaxis plan to get the inhibitory effect on bacterial action on its host or to create a better conceivable treatment like in immunoinformatics-based recent studies [ 14 , 15 ]. Ribosomal RNA (16S and 23S) codon usage patterns were analyzed here to determine the changes associated with evolutionary or phylogenetic patterns of the bacterium.…”

Section: Introductionmentioning

confidence: 99%

Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei

Joshi

Krishnan

Kaushik

2022

Journal of Genetic Engineering and Biotechnology

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Background The Tropheryma whipplei causes acute gastroenteritis to neuronal damages in Homo sapiens. Genomics and codon adaptation studies would be helpful advancements of disease evolution prediction, prevention, and treatment of disease. The codon usage data and codon usage measurement tools were deployed to detect the rare, very rare codons, and also synonymous codons usage. The higher effective number of codon usage values indicates the low codon usage bias in T. whipplei and also in the 23S and 16S ribosomal RNA genes. Results In T. whipplei, it was found to hold low codon biasness in genomic sets. The synonymous codons possess the base content in 3rd position that was calculated as A3S% (24.47 and 22.88), C3S% (20.99 and 22.88), T3S% (21.47 and 19.53), and G3S% (33.08 and 34.71) for 23s and 16s rRNA, respectively. Conclusion Amino acids like valine, aspartate, leucine, and phenylalanine hold high codon usage frequency and also found to be present in epitopes KPSYLSALSAHLNDK and FKSFNYNVAIGVRQP that were screened from proteins excinuclease ABC subunit UvrC and 3-oxoacyl-ACP reductase FabG, respectively. This method opens novel ways to determine epitope-based peptide vaccines against different pathogenic organisms.

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Section: Introductionmentioning

confidence: 99%

Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei

Joshi

Krishnan

Kaushik

2022

Journal of Genetic Engineering and Biotechnology

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“…Joshi et al [51] developed in silico studies using numerous tools, including AllergenFP, NETMHCII 3.2, VaxiJen, ToxinPred, PEPFOLD 3.5, DINC, IEDB-Population coverage, MHCPred, and JCat server, in their extensive study by harnessing statistical algorithms like HMM, ANN, ML, etc., that helped generate more accurate predictions of potential candidates for vaccine development. This novel methodology is simple, affordable, and quick, which will aid computational biologists to develop a vaccine to ward off this virus [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

Fasciola gigantica vaccine construct: an in silico approach towards identification and design of a multi-epitope subunit vaccine using calcium binding EF-hand proteins

2023

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Continuous attempts have been made to pinpoint candidate vaccine molecules and evaluate their effectiveness in order to commercialise such vaccines for the treatment of tropical fascioliasis in livestock. The pathophysiology of fascioliasis can be related to liver damage brought on by immature flukes that migrate and feed, as well as immunological reactions to chemicals produced by the parasites and alarm signals brought on by tissue damage. Future research should, in our opinion, concentrate on the biology of invasive parasites and the resulting immune responses, particularly in the early stages of infection. The goal of the current study was to use the calcium-binding proteins from F. gigantica to create a multi-epitope subunit vaccine. The adjuvant, B-cell epitopes, CTL epitopes, and HTL epitopes that make up the vaccine construct are all connected by certain linkers. The antigenicity, allergenicity, and physiochemical properties of the vaccine construct were examined. The vaccine construct was docked with toll-like receptor 2, and simulations of the molecular dynamics of the complex's stability, interaction, and dynamics were run. After performing in silico cloning and immunosimulation, it was discovered that the construct was suitable for further investigation. New vaccination technologies and adjuvant development are advancing our food safety procedures since vaccines are seen as safe and are accepted by the user community. This research is also applicable to the F. hepatica system.

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“…In the current study, we have predicted linear as well as conformational B-cell epitopes on envelope protein using immunoinformatics tools. In recent years, several researchers have employed immunoinformatics methods to develop epitope-based vaccines for Dengue virus (Krishnan G et al 2020 ), Orthohantavirus (Joshi et al 2022 ), and SARS-CoV-2 (Sarkar et al 2020 ; Rahman et al 2020 ). By targeting sandfly saliva and parasite-derived membrane and secretory antigens, Ojha et al developed a multi-epitope vaccination for Visceral leishmaniasis (Ojha et al 2020 ).They predicted immunogenic B-cell, HTL, and CTL epitopes from all of the identified protein sequences.…”

Section: Discussionmentioning

confidence: 99%

Prediction of Conformational and Linear B-Cell Epitopes on Envelop Protein of Zika Virus Using Immunoinformatics Approach

Srivastava

2023

Int J Pept Res Ther

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The current spread of Zika virus infection in India has become a public health issue due to the virus’s possible link to birth abnormalities and neurological disorders. There is a need for enhanced vaccines or drugs as a result of its epidemic outbreak and the lack of potential medication. B-cell mediated adaptive immunity is capable of developing pathogen-specific memory that confers immunological protection. Therefore, in this study, the envelope protein of the Zika virus was retrieved from the NCBI protein database. The ABCpred and BepiPred software were used to discover linear B-cell epitopes on envelope protein. Conformational B-cell epitopes on envelope protein were identified using SEPPA 3.0 and Ellipro tools. Predicted B-cell epitopes were evaluated for allergenicity, toxicity, and antigenicity. Two consensus linear B-cell epitopes, envelope 165−180 (AKVEITPNSPRAEATL) and envelope 224−238 (PWHAGADTGTPHWNN) were identified using ABCpred and BepiPredtools. SEPPA 3.0 and Elliprotools predicted consensus conformational envelope 98−110 (DRGWGNGCGLFGK) and envelope 248−251 (AHAK) epitopes and one residue ( 75 PRO) within envelope protein as a component of B-cell epitopes. These predicted linear and conformational B-cell epitopes will help in designing peptide vaccines that will activate the humoral response. However, in-vitro and in-vivo laboratory experimental confirmations are still needed to prove the application’s feasibility.

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T-cell epitope-based vaccine designing against Orthohantavirus: a causative agent of deadly cardio-pulmonary disease

Cited by 20 publications

References 48 publications

Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei

Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei

Fasciola gigantica vaccine construct: an in silico approach towards identification and design of a multi-epitope subunit vaccine using calcium binding EF-hand proteins

Prediction of Conformational and Linear B-Cell Epitopes on Envelop Protein of Zika Virus Using Immunoinformatics Approach

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