In silico designing of peptide based vaccine for Hepatitis viruses using reverse vaccinology approach

Chaudhuri, Dwaipayan; Datta, Joyeeta; Majumder, Satyabrata; Giri, Kalyan

doi:10.1016/j.meegid.2020.104388

Cited by 13 publications

(9 citation statements)

References 68 publications

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“…J-CAT server (Grote et al 2005 ) was used to determine coding sequence of predicted vaccine, along with codon adaptive index. It was further use to design recombinant plasmid by deploying SnapGene tool (from GLS Biotech, available at snapgene.com), that can be used for cloning and producing vaccine and develops more practical insights of epitope-based peptide vaccine (Chaudhuri et al 2020 ).…”

Section: Methodsmentioning

confidence: 99%

In-silico designing of epitope-based vaccine against the seven banded grouper nervous necrosis virus affecting fish species

Joshi

Pathak

Mannan

et al. 2021

Netw Model Anal Health Inform Bioinforma

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Neural necrosis virus (NNV) of family Nodaviridae affect wide range of fish species with viral encephalopathy and retinopathy causing mass mortality up to 100%. Currently there is no effective treatment and depopulation is only suggested recommendation. New avenues and approach are required to control this harmful malady. In this study we developed an epitope-based vaccine (EBV), against NNV using computation approach. We have selected two conserved proteins RNA-dependent RNA polymerase (RdRP) and capsid proteins. Based on more than ~ 1000 epitopes we selected six antigenic epitopes. These were conjugated to adjuvant and linker peptides to generate a full-length vaccine candidate. Biochemical structural properties were analyzed by Phyre2 server. ProtParam, Molprobity. Ramachandran plot results indicate that 98.7% residues are in a favorable region and 93.4% residues in the favored region. The engineered EBV binds to toll like receptor-5 (TLR5) an important elicitor of immune response. Further molecular docking by PatchDock server reveals the atomic contact energy (i.e. − 267.08) for the best docked model of EBV and TLR5 receptor. The molecular simulation results suggest a stable interaction; the RMSD and RMSF values are 1–4 Ǻ and 1–12Ǻ, respectively. Further we have suggested the best possible codon optimized sequence for its cloning and subsequent purification of the protein. Overall, this is a first report to suggest an in-silico method for generation of an EBV candidate against NNV. We surmise that the method and approach suggested could be used as a promising cure for NNVs.

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Section: Methodsmentioning

confidence: 99%

In-silico designing of epitope-based vaccine against the seven banded grouper nervous necrosis virus affecting fish species

Joshi

Pathak

Mannan

et al. 2021

Netw Model Anal Health Inform Bioinforma

View full text Add to dashboard Cite

show abstract

“…no Researcher group Country of origin Human pathogen Target protein Remarks Reference 1 Chaudhuri D, et al. 2020 India Hepatitis B virus, and Hepatitis C virus Viral protease, core, and membrane protein Identified T cell, B cell epitopes and designing a common peptide-based vaccine ( 77 ) 2 Saha CK, et al. 2017 Bangladesh Hendra virus, Nipah virus.…”

Section: Introductionmentioning

confidence: 99%

Immunoinformatics Approach for the Identification and Characterization of T Cell and B Cell Epitopes towards the Peptide-Based Vaccine against SARS-CoV-2

Chakraborty

Sharma

Bhattacharya

et al. 2021

Archives of Medical Research

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“…The simulation steps allowed are 1100 and volume to 110. C-ImmSim server has been successfully applied in several studies to understand host immune system dynamics in response to an antigen [ [49] , [50] , [51] , [52] , [53] ].…”

Section: Methodsmentioning

confidence: 99%

A computational study to disclose potential drugs and vaccine ensemble for COVID-19 conundrum

Ahmad

Waheed

Ismail

et al. 2021

Journal of Molecular Liquids

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In silico designing of peptide based vaccine for Hepatitis viruses using reverse vaccinology approach

Cited by 13 publications

References 68 publications

In-silico designing of epitope-based vaccine against the seven banded grouper nervous necrosis virus affecting fish species

In-silico designing of epitope-based vaccine against the seven banded grouper nervous necrosis virus affecting fish species

Immunoinformatics Approach for the Identification and Characterization of T Cell and B Cell Epitopes towards the Peptide-Based Vaccine against SARS-CoV-2

A computational study to disclose potential drugs and vaccine ensemble for COVID-19 conundrum

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