A multi-method and structure-based in silico vaccine designing against Echinococcus granulosus through investigating enolase protein

Pourseif, Mohammad M.; Yousefpour, Mitra; Aminianfar, Mohammad; Moghaddam, Gholamali; Nematollahi, Ahmad

doi:10.15171/bi.2019.18

Cited by 44 publications

(21 citation statements)

References 81 publications

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“…Historically, vaccination has proved to be an effective method of protecting large human population against viral diseases. Comparison to traditional vaccines like killed, attenuated or live vaccines, epitope based vaccines which contain specifically targeted immunogenic component of the pathogen responsible for causing diseases can be designed more rationally (Pourseif et al ., 2019).…”

Section: Discussionmentioning

confidence: 99%

In silicoapproach for designing of a multi-epitope based vaccine against novel Coronavirus (SARS-COV-2)

Saha¹,

Burra

2020

Preprint

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A novel Coronavirus (SARS-COV-2) has now become a global pandemic. Considering the severity of infection and the associated mortalities, there is an urgent need to develop an effective preventive measure against this virus. In this study, we have designed a novel vaccine construct using computational strategies. Spike (S) glycoprotein is the major antigenic component that trigger the host immune responses. Detailed investigation of S protein with various immunoinformatics tools enabled us to identify 5 MHC I and 5 MHC II B-cell derived T-cell epitopes with VaxiJen score > 1 and IC50 value < 100nM. These epitopes were joined with a suitable adjuvant and appropriate linkers to form a multi-epitope based vaccine construct. Further, in silico testing of the vaccine construct for its antigenicity, allergenicity, solubility, and other physicochemical properties showed it to be safe and immunogenic. Suitable tertiary structure of the vaccine protein was generated using 3Dpro of SCRATCH suite, refined with GalaxyRefine, and validated with ProSA, PROCHECK, and ERRAT server. Finally, molecular docking studies were performed to ensure a favorable binding affinity between the vaccine construct and TLR3 receptor. The designed multi-epitope vaccine showed potential to elicit specific immune responses against the SARS-COV-2. However, further wet lab validation is necessary to confirm the actual effectiveness, safety and immunogenic potency of the vaccine construct against derived in this study.

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Section: Discussionmentioning

confidence: 99%

In silicoapproach for designing of a multi-epitope based vaccine against novel Coronavirus (SARS-COV-2)

Saha¹,

Burra

2020

Preprint

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“…Two subpopulations of T cells (cytotoxic T lymphocytes and helper T lymphocytes) are involved in epitope recognition, and while CD8+ CTLs recognize antigens presented on MHC class I, CD4+ HTLs recognize antigens on MHC class II. Also, CD4+ HTLs play a vital role in coordinating both humoral and cell-mediated immune responses [ 39 – 41 ]. The two CTLs (C 2 and C 3 ) were selected due to their high antigenicity among the four identified epitopes.…”

Section: Discussionmentioning

confidence: 99%

Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In Silico Analysis

Chukwudozie

Chukwuanukwu

Iroanya

et al. 2020

Journal of Immunology Research

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The novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has previously never been identified with humans, thereby creating devastation in public health. The need for an effective vaccine to curb this pandemic cannot be overemphasized. In view of this, we designed a subcomponent antigenic peptide vaccine targeting the N-terminal (NT) and C-terminal (CT) RNA binding domains of the nucleocapsid protein that aid in viral replication. Promising antigenic B cell and T cell epitopes were predicted using computational pipelines. The peptides “RIRGGDGKMKDL” and “AFGRRGPEQTQGNFG” were the B cell linear epitopes with good antigenic index and nonallergenic property. Two CD8+ and Three CD4+ T cell epitopes were also selected considering their safe immunogenic profiling such as allergenicity, antigen level conservancy, antigenicity, peptide toxicity, and putative restrictions to a number of MHC-I and MHC-II alleles. With these selected epitopes, a nonallergenic chimeric peptide vaccine incapable of inducing a type II hypersensitivity reaction was constructed. The molecular interaction between the Toll-like receptor-5 (TLR5) which was triggered by the vaccine was analyzed by molecular docking and scrutinized using dynamics simulation. Finally, in silico cloning was performed to ensure the expression and translation efficiency of the vaccine, utilizing the pET-28a vector. This research, therefore, provides a guide for experimental investigation and validation.

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“…A preventive vaccine with heightened B-cell defense against SARS-CoV-2 infections should ideally have a high potential to induce neutralizing antibodies. In this regard, the prediction of B-cell epitopes through a multi-method analysis can provide a piece of authentic information about the B-cell immunodominant regions of such less-known infectious agent 17 . Here, we have created a consensus plot of spike glycoprotein amino acid sequence, which can understandably pro le the B-cell immunodominant regions and also potential B-cell epitope of spike glycoprotein of the virus.…”

Section: Pro Ling B-cell Immunodominant Regions Of Spike Glycoproteinmentioning

confidence: 99%

“…The potential B-cell epitopes (BCEs) were predicted by using the sequence-and structure-based tools. To predict linear and conformational BCEs with high accuracy, we implemented a multi-method approach based on the different currently available online BCE prediction web-servers 17 . We exploited the Table S8).…”

Section: Structure Re Nement Molecular Dynamics Simulation and Valimentioning

confidence: 99%

“…Conducting a rapid vaccine engineering approach during such a viral pandemic may need three important preliminary research steps, including (i) viral genome sequencing, (ii) bioinformatics and data analysis, and (iii) designing a gene-based vaccine construct. Under these circumstances, computational modeling and simulation methods can assist the vaccinologists to extrapolate close to real biological evidence for designing a promising recombinant vaccine with high accuracy, least cost, and minimal time17,30,31 . The in silico vaccinology, as a synergistic strategy is mainly based on (i) discovering of candidate vaccine…”

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confidence: 99%

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Prophylactic domain-based vaccine against SARS-CoV-2, causative agent of COVID-19 pandemic

Pourseif

Parvizpour

Jafari

et al. 2020

Preprint

Self Cite

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Coronavirus disease 2019 (COVID-19) is undoubtedly the most challenging pandemic in the current century with more than 253,381 deaths worldwide since its emergence in late 2019 (updated May 6th, 2020). COVID-19 is caused by a novel emerged coronavirus named as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Today, the world needs crucially to develop a prophylactic vaccine scheme for such emerged and emerging infectious pathogens. In this study, we have targeted spike (S) glycoprotein, as an important surface antigen of SARS-CoV-2, to identify its immunodominant B- and T-cell epitopes. We have conducted a multi-method B-cell epitope (BCE) prediction approach using different predictor algorithms to discover most potential BCEs. Besides, we sought among a pool of MHC class I and II-associated peptide binders provided by the IEDB server through the strict cut-off values. To design a broad-coverage vaccine, we carried out a population coverage analysis for a set of candidate T-cell epitopes and based on the HLA allele frequency in the top most-affected countries by COVID-19 (update 02 April 2020). The final determined B- and T-cell epitopes were mapped on the S glycoprotein sequence, and three potential hub regions covering the largest number of overlapping epitopes were identified for the vaccine designing (I531–N711; T717–C877; and V883–E973). Here, we have designed two domain-based constructs to be produced and delivered through the recombinant protein- and gene-based approaches, including (i) an adjuvanted domain-based protein vaccine construct (DPVC), and (ii) a self-amplifying mRNA vaccine (SAMV) construct. The safety, stability, and immunogenicity of the DPVC were validated using the integrated sequential (i.e. allergenicity, autoimmunity, and physicochemical features) and structural (i.e. molecular docking between the vaccine and human Toll-like receptors (TLRs) 4 and 5) analysis. The stability of the docked complexes was evaluated using the molecular dynamics (MD) simulations. These rigorous in silico validations supported the potential of the DPVC and SAMV to promote both innate and specific immune responses in the animal studies.

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A multi-method and structure-based in silico vaccine designing against Echinococcus granulosus through investigating enolase protein

Cited by 44 publications

References 81 publications

In silicoapproach for designing of a multi-epitope based vaccine against novel Coronavirus (SARS-COV-2)

In silicoapproach for designing of a multi-epitope based vaccine against novel Coronavirus (SARS-COV-2)

Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In Silico Analysis

Prophylactic domain-based vaccine against SARS-CoV-2, causative agent of COVID-19 pandemic

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