In-silico design of envelope based multi-epitope vaccine candidate against Kyasanur forest disease virus

Arumugam, Sathishkumar; Prasad, Varamballi

doi:10.1038/s41598-021-94488-8

Cited by 22 publications

(13 citation statements)

References 81 publications

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“…Simultaneously, it was observed that as antigen levels decreased, immunoglobulin levels increased. These outcomes confirm the effectiveness of the developed vaccine (Arumugam and Varamballi, 2021). The current spike protein-based multi-epitope subunit vaccine development showed promising results when analyzed through viroinformatics tools.…”

Section: Discussionsupporting

confidence: 67%

Development of a multi-epitope spike glycoprotein vaccine to combat SARS-CoV-2 using the bioinformatics approach

Shehzad¹,

Sumartono²,

Nugraha³

et al. 2022

J Pharm Pharmacogn Res

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Context: The current COVID-19 pandemic has significantly impacted health and socio-economic status worldwide. The only way to combat this situation is to develop an effective vaccine and immunize people around the globe. Aims: To construct a multi-epitope spike glycoprotein-based vaccine from the SARS-CoV-2 Surabaya isolate using a bioinformatics approach. Methods: The spike protein was submitted to IEDB, VaxiJen, AllerTOP, and ToxinPred webservers to predict antigenic, non-allergic, non-toxic, B- and T-cell epitopes. To develop a multi-epitope vaccine, an adjuvant cholera toxin B subunit was linked to B-cell and B-cell with T-cell through EAAAK and GPGPG linkers, respectively. The designed vaccine 3D structure development, refinement, and validation were done through PHYRE2, Galaxy Refine, and RAMPAGE webservers. Moreover, the Cluspro-2.0 webserver was used for the molecular docking of the vaccine designed with TLR3. The vaccine+TLR3 complex was docked with Surfactant protein A as a control to validate the docking results. Finally, immune-simulation and in silico cloning of the vaccine were carried out by C-ImmSim webserver and SnapGene software, respectively. Results: A multi-epitopic vaccine containing B and T-cell was developed using 392 amino acids with a molecular weight of 40825.59 Da. The docking and immunogenicity results of the vaccine met all established parameters for constructing a quality vaccine. Furthermore, the optimized sequence of the vaccine was successfully cloned in expression vector pET 28 a (+) that yielded a colon of 2724 bp. Conclusions: The vaccine’s immunogenicity demonstrates its effectiveness against SARS-CoV-2 infection. Further confirmatory testing may therefore be performed as soon as possible in the public interest.

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Section: Discussionsupporting

confidence: 67%

Development of a multi-epitope spike glycoprotein vaccine to combat SARS-CoV-2 using the bioinformatics approach

Shehzad¹,

Sumartono²,

Nugraha³

et al. 2022

J Pharm Pharmacogn Res

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“…The multi-epitope vaccine's DNA sequence was generated and transformed to Escherichia coli expression system utilizing the Java Codon Adaptation Tool (JCat) platform. The vaccine expression in E. coli was measured through the codon adaptation index (CAI) and the vaccine's GC percentage 46 .…”

Section: Methodsmentioning

confidence: 99%

“…The vaccine construct was docked with a variety of immune cell receptors in order to determine how effective it will be in generating an immune response 47 . The vaccine's binding affinity was predicted in a blind docking study for TLR-4 (4G8A), MHC-I (1I1Y), and MHC-II (1KG0) receptors 46 . Using PatchDock 48 docking investigation was accomplished followed by FireDock server to refine the docked complexes 49 .…”

Section: Methodsmentioning

confidence: 99%

Identification and construction of a multi-epitopes vaccine design against Klebsiella aerogenes: molecular modeling study

Alzarea

2022

Sci Rep

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A rapid rise in antibiotic resistance by bacterial pathogens is due to these pathogens adaptation to the changing environmental conditions. Antibiotic resistance infections can be reduced by a number of ways such as development of safe and effective vaccine. Klebsiella aerogene is a gram-negative, rod-shaped bacterium resistant to a variety of antibiotics and no commercial vaccine is available against the pathogen. Identifying antigens that can be easily evaluated experimentally would be crucial to successfully vaccine development. Reverse vaccinology (RV) was used to identify vaccine candidates based on complete pathogen proteomic information. The fully sequenced proteomes include 44,115 total proteins of which 43,316 are redundant and 799 are non-redundant. Subcellular localization showed that only 1 protein in extracellular matrix, 7 were found in outer-membrane proteins, and 27 in the periplasm space. A total of 3 proteins were found virulent. Next in the B-cell-derived T-cell epitopes mapping phase, the 3 proteins (Fe2+− enterobactin, ABC transporter substrate-binding protein, and fimbriae biogenesis outer membrane usher protein) were tested positive for antigenicity, toxicity, and solubility. GPGPG linkers were used to prepare a vaccine construct composed of 7 epitopes and an adjuvant of toxin B subunit (CTBS). Molecular docking of vaccine construct with major histocompatibility-I (MHC-I), major histocompatibility-II (MHC-II), and Toll-like receptor 4 (TLR4) revealed vaccine robust interactions and stable binding pose to the receptors. By using molecular dynamics simulations, the vaccine-receptors complexes unveiled stable dynamics and uniform root mean square deviation (rmsd). Further, binding energies of complex were computed that again depicted strong intermolecular bindings and formation of stable conformation.

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“…The server delivers the codon adaptation index (CAI) (>0.8–1.0) and the GC content (30–70% in the output files to verify the transcription and translation efficiency of the planned vaccine construct [ 79 ]. Two restriction sites, EcoRI and BamHI, were inserted into the C and N terminals of the sequence, and SnapGene v5.0.8 software was employed to clone the modified sequence with the restriction site into pET-28a (+) plasmid obtained from SnapGene “ (accessed on 21 July 2022)” [ 80 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of a Potential Vaccine against Treponema pallidum Using Subtractive Proteomics and Reverse-Vaccinology Approaches

et al. 2022

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Syphilis, a sexually transmitted infection, is a deadly disease caused by Treponema pallidum. It is a Gram-negative spirochete that can infect nearly every organ of the human body. It can be transmitted both sexually and perinatally. Since syphilis is the second most fatal sexually transmitted disease after AIDS, an efficient vaccine candidate is needed to establish long-term protection against infections by T. pallidum. This study used reverse-vaccinology-based immunoinformatic pathway subtractive proteomics to find the best antigenic proteins for multi-epitope vaccine production. Six essential virulent and antigenic proteins were identified, including the membrane lipoprotein TpN32 (UniProt ID: O07950), DNA translocase FtsK (UniProt ID: O83964), Protein Soj homolog (UniProt ID: O83296), site-determining protein (UniProt ID: F7IVD2), ABC transporter, ATP-binding protein (UniProt ID: O83930), and Sugar ABC superfamily ATP-binding cassette transporter, ABC protein (UniProt ID: O83782). We found that the multiepitope subunit vaccine consisting of 4 CTL, 4 HTL, and 11 B-cell epitopes mixed with the adjuvant TLR-2 agonist ESAT6 has potent antigenic characteristics and does not induce an allergic response. Before being docked at Toll-like receptors 2 and 4, the developed vaccine was modeled, improved, and validated. Docking studies revealed significant binding interactions, whereas molecular dynamics simulations demonstrated its stability. Furthermore, the immune system simulation indicated significant and long-lasting immunological responses. The vaccine was then reverse-transcribed into a DNA sequence and cloned into the pET28a (+) vector to validate translational activity as well as the microbial production process. The vaccine developed in this study requires further scientific consensus before it can be used against T. pallidum to confirm its safety and efficacy.

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In-silico design of envelope based multi-epitope vaccine candidate against Kyasanur forest disease virus

Cited by 22 publications

References 81 publications

Development of a multi-epitope spike glycoprotein vaccine to combat SARS-CoV-2 using the bioinformatics approach

Development of a multi-epitope spike glycoprotein vaccine to combat SARS-CoV-2 using the bioinformatics approach

Identification and construction of a multi-epitopes vaccine design against Klebsiella aerogenes: molecular modeling study

Identification of a Potential Vaccine against Treponema pallidum Using Subtractive Proteomics and Reverse-Vaccinology Approaches

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