scholarly journals Design an efficient multi-epitope peptide vaccine candidate against SARS-CoV-2: An in silico analysis

2020 ◽  
Author(s):  
Zahra Yazdani ◽  
Alireza Rafiei ◽  
Mohammadreza Yazdani ◽  
Reza Valadan
Keyword(s):  
Escherichia Coli ◽  
In Silico ◽  
Tertiary Structure ◽  
Peptide Vaccine ◽  
High Mobility ◽  
In Silico Analysis ◽  
Epitope Peptide ◽  
Cellular And Humoral Immunity ◽  
Cellular Immune ◽  
Immunodominant Epitopes

AbstractBackgroundTo date, no specific vaccine or drug has been proven to be effective for SARS-CoV-2 infection. Therefore, we implemented immunoinformatics approach to design an efficient multi-epitopes vaccine against SARS-CoV-2.ResultsThe designed vaccine construct has several immunodominant epitopes from structural proteins of Spike, Nucleocapsid, Membrane and Envelope. These peptides promote cellular and humoral immunity and Interferon gamma responses. In addition, these epitopes have antigenicity ability and no allergenicity probability. To enhance the vaccine immunogenicity, we used three potent adjuvants; Flagellin, a driven peptide from high mobility group box 1 as HP-91 and human beta defensin 3 protein. The physicochemical and immunological properties of the vaccine structure were evaluated. Tertiary structure of the vaccine protein was predicted and refined by I-Tasser and galaxi refine and validated using Rampage and ERRAT. Results of Ellipro showed 242 residues from vaccine might be conformational B cell epitopes. Docking of vaccine with Toll-Like Receptors 3, 5 and 8 proved an appropriate interaction between the vaccine and receptor proteins. In silico cloning demonstrated that the vaccine can be efficiently expressed in Escherichia coli.ConclusionsThe designed multi epitope vaccine is potentially antigenic in nature and has the ability to induce humoral and cellular immune responses against SARS-CoV-2. This vaccine can interact appropriately with the TLR3, 5, and 8. Also, this vaccine has high quality structure and suitable characteristics such as high stability and potential for expression in Escherichia coli.

scholarly journals Design an Efficient Multi-Epitope Peptide Vaccine Candidate Against SARS-CoV-2: An in silico Analysis

2020 ◽  
Vol Volume 13 ◽  
pp. 3007-3022 ◽  
Author(s):  
Zahra Yazdani ◽  
Alireza Rafiei ◽  
Mohammadreza Yazdani ◽  
Reza Valadan
Keyword(s):  
In Silico ◽  
Vaccine Candidate ◽  
Peptide Vaccine ◽  
In Silico Analysis ◽  
Epitope Peptide ◽  
Silico Analysis

In Silico Study of Potential Cross-Kingdom Plant MicroRNA Based Regulation in Chronic Myeloid Leukemia

2020 ◽  
Vol 17 (2) ◽  
pp. 125-132
Author(s):  
Marjanu Hikmah Elias ◽  
Noraziah Nordin ◽  
Nazefah Abdul Hamid
Keyword(s):  
Targeted Therapy ◽  
In Silico ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Target Prediction ◽  
In Silico Analysis ◽  
Microrna Target ◽  
Good Target

Background: Chronic Myeloid Leukaemia (CML) is associated with the BCRABL1 gene, which plays a central role in the pathogenesis of CML. Thus, it is crucial to suppress the expression of BCR-ABL1 in the treatment of CML. MicroRNA is known to be a gene expression regulator and is thus a good candidate for molecularly targeted therapy for CML. Objective: This study aims to identify the microRNAs from edible plants targeting the 3’ Untranslated Region (3’UTR) of BCR-ABL1. Methods: In this in silico analysis, the sequence of 3’UTR of BCR-ABL1 was obtained from Ensembl Genome Browser. PsRNATarget Analysis Server and MicroRNA Target Prediction (miRTar) Server were used to identify miRNAs that have binding conformity with 3’UTR of BCR-ABL1. The MiRBase database was used to validate the species of plants expressing the miRNAs. The RNAfold web server and RNA COMPOSER were used for secondary and tertiary structure prediction, respectively. Results: In silico analyses revealed that cpa-miR8154, csi-miR3952, gma-miR4414-5p, mdm-miR482c, osa-miR1858a and osa-miR1858b show binding conformity with strong molecular interaction towards 3’UTR region of BCR-ABL1. However, only cpa-miR- 8154, osa-miR-1858a and osa-miR-1858b showed good target site accessibility. Conclusion: It is predicted that these microRNAs post-transcriptionally inhibit the BCRABL1 gene and thus could be a potential molecular targeted therapy for CML. However, further studies involving in vitro, in vivo and functional analyses need to be carried out to determine the ability of these miRNAs to form the basis for targeted therapy for CML.

A structural in silico analysis of the immunogenicity of l-asparaginase from Escherichia coli and Erwinia carotovora

Biologicals ◽  
2019 ◽  
Vol 59 ◽  
pp. 47-55 ◽  
Author(s):  
Lisandra Herrera Belén ◽  
Jorge Beltrán Lissabet ◽  
Carlota de Oliveira Rangel-Yagui ◽  
Brian Effer ◽  
Gisele Monteiro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
In Silico ◽  
In Silico Analysis ◽  
Erwinia Carotovora ◽  
Silico Analysis

In Silico Analysis for Determination and Validation of Iron-Regulated Protein from Escherichia coli

2018 ◽  
Vol 25 (4) ◽  
pp. 1523-1537 ◽  
Author(s):  
Fateme Sefid ◽  
Armina Alagheband Bahrami ◽  
Maryam Darvish ◽  
Robab Nazarpour ◽  
Zahra Payandeh
Keyword(s):  
Escherichia Coli ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis

A novel multi-epitope peptide vaccine against cancer: An in silico approach

2014 ◽  
Vol 349 ◽  
pp. 121-134 ◽  
Author(s):  
Navid Nezafat ◽  
Younes Ghasemi ◽  
Gholamreza Javadi ◽  
Mohammad Javad Khoshnoud ◽  
Eskandar Omidinia
Keyword(s):  
In Silico ◽  
Peptide Vaccine ◽  
Epitope Peptide

scholarly journals EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations

2008 ◽  
Vol 25 (2) ◽  
pp. 163-166 ◽  
Author(s):  
Richard S. P. Horler ◽  
Andrew Butcher ◽  
Nikitas Papangelopoulos ◽  
Peter D. Ashton ◽  
Gavin H. Thomas
Keyword(s):  
Escherichia Coli ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis

scholarly journals Immuno-informatics Design of a Multimeric Epitope Peptide Based Vaccine Targeting SARS-CoV-2 Spike Glycoprotein

2020 ◽  
Author(s):  
Onyeka S. Chukwudozie ◽  
Clive M. Gray ◽  
Tawakalt A. Fagbayi ◽  
Rebecca C. Chukwuanukwu ◽  
Victor O. Oyebanji ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Peptide Vaccine ◽  
Spike Protein ◽  
Cell Mediated Immunity ◽  
Epitope Peptide ◽  
Mhc I ◽  
B Cell Epitopes ◽  
Antibody Recognition

ABSTRACTDeveloping an efficacious vaccine to SARS-CoV-2 infection is critical to stem COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in the design of an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers along with 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC-I and II alleles respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. The vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, with triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We therefore propose that potential vaccine designs consider this approach.

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