A cutting-edge immunoinformatics approach for design of multi-epitope oral vaccine against dreadful human malaria

Pritam, Manisha; Singh, Garima; Swaroop, Suchit; Singh, Akhilesh Kumar; Pandey, Brijesh; Singh, Satarudra Prakash

doi:10.1016/j.ijbiomac.2020.04.191

Cited by 29 publications

(15 citation statements)

References 154 publications

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“…Molecular dynamics of the top ranked complex of the vaccine construct and TLR8 was completed through iMODS web server to elucidate the typical protein motion within the internal coordinates through normal mode analysis (NMA) (López-Blanco et al 2014 ). The iMODS server calculates the dihedral coordinates of Cα atoms of docked complexes to measure the actual mobility of the proteins based on elastic network model (ENM) (Pritam et al 2020 ). Furthermore, it calculates B-factor plot with structure deformation, covariance, mode variance, as well as calculates the eigenvalue.…”

Section: Methodsmentioning

confidence: 99%

Designing a next generation multi-epitope based peptide vaccine candidate against SARS-CoV-2 using computational approaches

Saha¹,

Ghosh

Burra³

2021

3 Biotech

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COVID-19 caused by SARS-CoV-2 was declared a global pandemic by WHO (World Health Organization) in March, 2020. Within 6 months, nearly 750,000 deaths are claimed by COVID-19 across the globe. This called for immediate social, scientific, technological, public and community interventions. Considering the severity of infection and the associated mortalities, global efforts are underway to develop preventive measures against SARS-CoV-2. Among the SARS-CoV-2 target proteins, Spike (S) glycoprotein (a.k.a S Protein) is the most studied target known to trigger strong host immune response. A detailed analysis of S protein-based epitopes enabled us to design a novel B-cell-derived T-cell Multi-epitope-based peptide (MEBP) vaccine candidate. This involved a systematic and comprehensive computational protocol consisting of prediction of dual-purpose epitopes and designing an MEBP vaccine construct. This was followed by 3D structure validation, MEBP complex interaction studies, in silico cloning and vaccine dose-based immune response simulation to evaluate the immunogenic potency of the vaccine construct. The dual-purpose epitope prediction protocol was designed such that the same epitope elicits both humoral and cellular immune response unlike the earlier designs. Further, the epitopes predicted were screened against stringent criteria to ensure selection of a potent candidate with maximum antigen coverage and best immune response. The vaccine dose-based immune response simulation studies revealed a rapid antigen clearance through antibody generation and elevated levels of cell-mediated immunity during repeated exposure of the vaccine. The favourable results of the analysis strongly indicate that the vaccine construct is indeed a potent vaccine candidate and ready to proceed to the next steps of experimental validation and efficacy studies.

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Section: Methodsmentioning

confidence: 99%

Designing a next generation multi-epitope based peptide vaccine candidate against SARS-CoV-2 using computational approaches

Saha¹,

Ghosh

Burra³

2021

3 Biotech

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“…There is no standard approach in the design of multi‐epitope vaccines (MEVs). Different approaches are employed where the chimeric protein can be composed of fused B cell and Major Histocompatibility class I and II [cytotoxic T‐lymphocyte (CTL) and Helper T‐lymphocyte (HTL)] epitopes (Kalita et al., 2019; Pritam et al., 2020), or CTL and HTL epitope fused together (Rahmani et al., 2019; Vakili et al., 2018) or B‐cell epitopes alone (Wu et al., 2020).…”

Section: Discussionmentioning

confidence: 99%

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

Machimbirike

Pornputtapong

Senapin

et al. 2021

Journal of Fish Diseases

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Edwardsiella ictaluri infects several fish species and protection of the all the susceptible fish hosts from the pathogen using a monovalent vaccine is impossible because the species is composed of host-based genotypes that are genetic, serological and antigenic heterogenous. Here, immunoinformatic approach was employed to design a cross-immunogenic chimeric EiCh protein containing multi-epitopes. The chimeric EiCh protein is composed of 11 B-cell epitopes and 7 major histocompatibility complex class II epitopes identified from E. ictaluri immunogenic proteins previously reported.The 49.32 kDa recombinant EiCh protein was expressed in vitro in Escherichia coli BL-21 (DE3) after which inclusion bodies were successfully solubilized and refolded.Ab initio protein modelling revealed secondary and tertiary structures. Secondary structure was confirmed by circular dichroism spectroscopy. Antigenicity of the chimeric EiCh protein was exhibited by strong reactivity with serum from striped catfish and Nile tilapia experimentally infected with E. ictaluri. Furthermore, immunogenicity of the chimeric EiCh protein was investigated in vivo in Nile tilapia juveniles and it was found that the protein could strongly induce production of specific antibodies conferring agglutination activity and partially protected Nile tilapia juveniles with a relative survival percentage (RPS) of 42%. This study explored immunoinformatics as reverse vaccinology approach in vaccine design for aquaculture to manage E. ictaluri infections.

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“…The C-IMMSIM server predicts the peptide interactions with the immune system employing position-specific scoring matrices (PSSM). The C-ImmSim server is routinely employed in immunoinformatics studies and gives reliable results with regard to the vaccination strategy employed [ 66 , 67 , 68 ]. The simulation was conducted in 1000 steps, with two doses given over a four-week interval.…”

Section: Methodsmentioning

confidence: 99%

Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis

et al. 2021

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Schistosomiasis is a parasitic infection that causes considerable morbidity and mortality in the world. Infections of parasitic blood flukes, known as schistosomes, cause the disease. No vaccine is available yet and thus there is a need to design an effective vaccine against schistosomiasis. Schistosoma japonicum, Schistosoma mansoni, and Schistosoma haematobium are the main pathogenic species that infect humans. In this research, core proteomics was combined with a subtractive proteomics pipeline to identify suitable antigenic proteins for the construction of a multi-epitope vaccine (MEV) against human-infecting Schistosoma species. The pipeline revealed two antigenic proteins—calcium binding and mycosubtilin synthase subunit C—as promising vaccine targets. T and B cell epitopes from the targeted proteins were predicted using multiple bioinformatics and immunoinformatics databases. Seven cytotoxic T cell lymphocytes (CTL), three helper T cell lymphocytes (HTL), and four linear B cell lymphocytes (LBL) epitopes were fused with a suitable adjuvant and linkers to design a 217 amino-acid-long MEV. The vaccine was coupled with a TLR-4 agonist (RS-09; Sequence: APPHALS) adjuvant to enhance the immune responses. The designed MEV was stable, highly antigenic, and non-allergenic to human use. Molecular docking, molecular dynamics (MD) simulations, and molecular mechanics/generalized Born surface area (MMGBSA) analysis were performed to study the binding affinity and molecular interactions of the MEV with human immune receptors (TLR2 and TLR4) and MHC molecules (MHC I and MHC II). The MEV expression capability was tested in an Escherichia coli (strain-K12) plasmid vector pET-28a(+). Findings of these computer assays proved the MEV as highly promising in establishing protective immunity against the pathogens; nevertheless, additional validation by in vivo and in vitro experiments is required to discuss its real immune-protective efficacy.

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A cutting-edge immunoinformatics approach for design of multi-epitope oral vaccine against dreadful human malaria

Cited by 29 publications

References 154 publications

Designing a next generation multi-epitope based peptide vaccine candidate against SARS-CoV-2 using computational approaches

Designing a next generation multi-epitope based peptide vaccine candidate against SARS-CoV-2 using computational approaches

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis

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