scholarly journals A Bioinformatics Approach for the Prediction of Immunogenic Properties and Structure of the SARS-COV-2 B.1.617.1 Variant Spike Protein

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Vijay Kumar Srivastava ◽  
Sanket Kaushik ◽  
Gazal Bhargava ◽  
Ajay Jain ◽  
Juhi Saxena ◽  
...  
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Tertiary Structure ◽  
In Silico Analysis ◽  
Respiratory Illness ◽  
T Cell Epitopes ◽  
S Protein ◽  
Immunogenic Properties

Background. B.1.617.1, a variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causing respiratory illness is responsible for the second wave of COVID-19 and associated with a high incidence of infectivity and mortality. To mitigate the B.1.617.1 variant of SARS-CoV-2, deciphering the protein structure and immunological responses by employing bioinformatics tools for data mining and analysis is pivotal. Objectives. Here, an in silico approach was employed for deciphering the structure and immune function of the subunit of spike (S) protein of SARS-CoV-2 B.1.617.1 variant. Methods. The partial amino acid sequence of SARS-CoV-2 B.1.617.1 variant S protein was analyzed, and its putative secondary and tertiary structure was predicted. Immunogenic analyses including B- and T-cell epitopes, interferon-gamma (IFN-γ) response, chemokine, and protective antigens for SARS-CoV 2 S proteins were predicted using appropriate tools. Results. B.1.617.1 variant S protein sequence was found to be highly stable and amphipathic. ABCpred and CTLpred analyses led to the identification of two potential antigenic B cell and T cell epitopes with starting amino acid positions at 60 and 82 (for B cell epitopes) and 54 and 98 (for T cell epitopes) having prediction scores > 0.8 . Further, RAMPAGE tool was used for determining the allowed and disallowed regions of the three-dimensional predicted structure of SARS-CoV-2 B.1.617.1 variant S protein. Conclusion. Together, the in silico analysis revealed the predicted structure of partial S protein, immunogenic properties, and possible regions for S protein of SARS-CoV-2 and provides a valuable prelude for engineering the targeted vaccine or drug against B.1.617.1 variant of SARS-CoV-2.

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

2020 ◽  
Vol 2020 ◽  
pp. 1-17
Author(s):  
Onyeka S. Chukwudozie ◽  
Rebecca C. Chukwuanukwu ◽  
Onyekachi O. Iroanya ◽  
Daniel M. Eze ◽  
Vincent C. Duru ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Rna Binding ◽  
Peptide Vaccine ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
Translation Efficiency ◽  
T Cell Epitopes

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.

An Integrated In-Silico Approach to Develop Epitope-Based Peptide Vaccine against SARS-CoV-2

Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Prekshi Garg ◽  
Neha Srivastava ◽  
Prachi Srivastava
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Peptide Vaccine ◽  
Cell Epitope ◽  
Peptide Sequence ◽  
T Cell Epitopes ◽  
Mhc I ◽  
In Silico Study

Background: SARS-CoV-2 has been the talk of the town ever since the beginning of 2020. Every country is trying all possible steps to combat the disease ranging from shutting the complete economy of the country to the repurposing of drugs and vaccine development. The rapid data analysis and widespread tools have made bioinformatics capable of giving new insights to deal with the current scenario more efficiently through an emerging field, Vaccinomics. Objective: The present in-silico study was attempted to identify peptide fragments from spike surface glycoprotein of SARS-CoV-2 that can be efficiently used for the development of an epitope-based vaccine designing approach. Methodology: The epitopes of B and T-cell are predicted using integrated computational tools. VaxiJen server, NetCTL, and IEDB tools were used to study, analyze, and predict potent T-cell epitopes, its subsequent MHC-I interactions, and B-cell epitopes. The 3D structure prediction of peptides and MHC-I alleles (HLA-C*03:03) was further done using AutoDock4.0. Result: Based on result interpretation, the peptide sequence from 1138-1145 amino acid and sequence WTAGAAAYY and YDPLQPEL were obtained as potential B-cell and T-cell epitopes respectively. Conclusion: The peptide sequence WTAGAAAYY and the amino acid sequence from 1138-1145 of the spike protein of SARS-CoV-2 can be used as a probable B-cell epitope candidate. Also, the amino acid sequence YDPLQPEL can be used as a potent T-cell epitope. This in-silico study will help us to identify novel epitope-based peptide vaccine targets in the spike protein of SARS-CoV-2. Further, the in-vitro and in-vivo study needed to validate the findings.

scholarly journals Epitope‐based peptide vaccine design and target site depiction against Middle East Respiratory Syndrome Coronavirus: an immune-informatics study

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Muhammad Tahir ul Qamar ◽  
Saman Saleem ◽  
Usman Ali Ashfaq ◽  
Amna Bari ◽  
Farooq Anwar ◽  
...  
Keyword(s):  
T Cell ◽  
Middle East ◽  
B Cell ◽  
Mhc Class Ii ◽  
Peptide Vaccine ◽  
Middle East Respiratory Syndrome ◽  
T Cell Epitopes ◽  
Resistance Response ◽  
B Cell Epitopes ◽  
S Protein

Abstract Background Middle East Respiratory Syndrome Coronavirus (MERS-COV) is the main cause of lung and kidney infections in developing countries such as Saudi Arabia and South Korea. This infectious single-stranded, positive (+) sense RNA virus enters the host by binding to dipeptidyl-peptide receptors. Since no vaccine is yet available for MERS-COV, rapid case identification, isolation, and infection prevention strategies must be used to combat the spreading of MERS-COV infection. Additionally, there is a desperate need for vaccines and antiviral strategies. Methods The present study used immuno-informatics and computational approaches to identify conserved B- and T cell epitopes for the MERS-COV spike (S) protein that may perform a significant role in eliciting the resistance response to MERS-COV infection. Results Many conserved cytotoxic T-lymphocyte epitopes and discontinuous and linear B-cell epitopes were predicted for the MERS-COV S protein, and their antigenicity and interactions with the human leukocyte antigen (HLA) B7 allele were estimated. Among B-cell epitopes, QLQMGFGITVQYGT displayed the highest antigenicity-score, and was immensely immunogenic. Among T-cell epitopes, MHC class-I peptide YKLQPLTFL and MHC class-II peptide YCILEPRSG were identified as highly antigenic. Furthermore, docking analyses revealed that the predicted peptides engaged in strong bonding with the HLA-B7 allele. Conclusion The present study identified several MERS-COV S protein epitopes that are conserved among various isolates from different countries. The putative antigenic epitopes may prove effective as novel vaccines for eradication and combating of MERS-COV infection.

scholarly journals In silico analysis and modeling of putative T cell epitopes for vaccine design of Toscana virus

3 Biotech ◽  
2014 ◽  
Vol 5 (4) ◽  
pp. 497-503 ◽  
Author(s):  
Amisha Jain ◽  
Pranav Tripathi ◽  
Aniket Shrotriya ◽  
Ritu Chaudhary ◽  
Ajeet Singh
Keyword(s):  
T Cell ◽  
In Silico ◽  
In Silico Analysis ◽  
Vaccine Design ◽  
T Cell Epitopes ◽  
Toscana Virus ◽  
Silico Analysis

scholarly journals Molecular cloning, expression, purification and in silico epitope prediction of cobalamin-independent methionine synthase (Mor a 2), as a novel allergen from Morus alba pollen

2021 ◽  
Author(s):  
Yunus AKSÜT
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Allergic Diseases ◽  
Structural Features ◽  
Morus Alba ◽  
Methionine Synthase ◽  
Antigenic Peptides ◽  
T Cell Epitopes ◽  
B Cell Epitopes

IntroductionMorus alba (white mulberry) pollen is an aero-allergen source that can trigger allergic diseases. Cobalamin-independent methionine synthase (MetE) in M. alba pollen has been proved to be one of the major allergens for some patients living in Istanbul (Turkey). The aim of the present study was the recombinant production and identification of MetE (Mor a 2), a novel allergen from M. alba pollen. The IgE binding reactivity of rMor a 2 produced for the first time was evaluated and some structural features were investigated by in silico methods to better understand its immunogenicity.Material and methodsThe gene encoding Mor a 2 was cloned in fission yeast, Schizosaccharomyces pombe ura4-D18h- strain, using pSLF1073 vector. This is the first report of the production of recombinant pollen allergen in S. pombe. After the purification, immunoreactivity of rMor a 2 was confirmed by immunoblotting using sera of patient allergic to M. alba pollen. Besides, B-cell epitopes of rMor a 2 were predicted using various bioinformatic tools, namely Bioinformatics Predicted Antigenic Peptides, BepiPred 2.0 and Immune Epitope Database whereas T-cell epitopes were estimated using NetMHCIIpan-3.2 and NetMHCII 2.3 servers.ResultsThe immunoblotting analysis yielded 11 of 11 positive reactions to rMor a 2. In silico predictions exerted seven B-cell epitopes (22-33, 384-394, 407-423, 547-553, 571-577, 671-678, 736-741) and seven T-cell epitopes (54-62, 161-170, 197-205, 347-358, 622-630, 657-665, 756-764).ConclusionsThese findings may help the use of rMor a 2 in the diagnosis and treatment of allergic diseases associated with M. alba and/or MetE.

scholarly journals Vaccine Design against Coronavirus Spike (S) Glycoprotein in Chicken: Immunoinformatic and Computational Approaches

2020 ◽  
Author(s):  
Sumaia Awad Elkariem Ali ◽  
Eman Ali Awadelkareem
Keyword(s):  
T Cell ◽  
B Cell ◽  
Rna Virus ◽  
Economic Loss ◽  
T Cell Epitopes ◽  
Resistance Response ◽  
Docking Analysis ◽  
S Protein ◽  
Infectious Bronchitis ◽  
Mhc Alleles

Abstract Background: Infectious bronchitis (IB) is a highly contagious respiratory disease in chickens and produces economic loss within the poultry industry. It is caused by a single stranded RNA virus belonging to Cronaviridae family. Methods: The present study used various tools in Immune Epitope Database (IEDB) to predict conserved B and T cell epitopes against IBV spike (S) protein that may perform a significant role in provoking the resistance response to IBV infection. Results: In B cell prediction methods, three epitopes (1139KKSSYY1144, 1140KSSYYT1145, 1141SSYYT1145) were selected as surface, linear and antigenic epitopes. Many MHCI and MHCII epitopes were predicted for IBV S protein. Among them 982YYITARDMY990 and 983YITARDMYM991 epitopes displayed high antigenicity, no allergenicity and no toxicity as well as great linkage with MHCI and MHCII alleles. Moreover, docking analysis of MHCI epitope produced strong binding affinity with BF2 alleles. Conclusion: Five conserved epitopes were expected from spike glycoprotein of IBV as the best B cell and T cell epitopes due to high antigenicity, no allergenicity and no toxicity. In addition, MHC epitopes showed great linkage with MHC alleles as well as strong interaction with BF2 alleles. These epitopes should be designed and incorporated and then tested as multi-epitope vaccine against IBV.

scholarly journals SARS-CoV-2 Spike Protein Evolution may Cause Difficulties for Vaccine

2020 ◽  
Author(s):  
Jian Zhou ◽  
Sun Jingjing ◽  
Gang Lu ◽  
Wanchun Wang ◽  
Lin Wang
Keyword(s):  
T Cell ◽  
B Cell ◽  
3D Model ◽  
Bioinformatics Analysis ◽  
Cell Epitope ◽  
Amino Acid Sequences ◽  
T Cell Epitopes ◽  
Sequence Structure ◽  
B Cell Epitopes ◽  
S Protein

Abstract Background: Coronavirus disease 2019 (COVID-19) poses a great threat to human health and life. We performed a bioinformatics analysis to compare the sequence, structure, and epitopes of SARS-CoV-2 spike (S) protein in 10 different countries. Methods: The amino acid sequences of SARS-CoV-2 S protein were obtained from the NCBI database. We used DNASTAR Lasergene software to analyze the protein’s secondary structures. SWISS-MODEL combined with VMD software was used to construct a 3D model of SARS-CoV-2 S protein. DNASTAR Protean and the IEDB database were used to analyze the B cell epitopes and T cell epitopes, respectively. Results: The results of B cell epitopes analysis indicated that the epitopes of SARS-CoV-2 S protein in Korea and American increased, which suggested that the antigenicity of SARS-CoV-2 in Czech, Korea and American might be enhanced. A small number of B cell epitopes disappeared in the SARS-CoV-2 S protein sequence from Greece, Australia, Sweden and India, which suggested that the antigenicity of SARS-CoV-2 in Greece, Australia, Sweden and India may be weakened. T cell epitope analysis indicated that the antigenicity of SARS-CoV-2 in Czech, Korea and American was enhanced, while antigenicity of SARS-CoV-2 in Greece, Australia, Inida, Sweden and Thailand may be weakened. The sequence of SARS-CoV-2 S protein has changed as the virus has spread, and the structures and epitopes have changed accordingly. Conclusion: The mutation leads to a decrease in the antigenicity of SARS-CoV-2, which may be a mechanism for the virus to evade surveillance by the immune system.

scholarly journals Designing of multiepitope-based vaccine against Leptospirosis using Immuno-Informatics approaches

2021 ◽  
Author(s):  
Mohd Abdullah ◽  
Mohammad Kadivella ◽  
Rolee Sharma ◽  
Syed M. Faisal ◽  
Sarwar Azam
Keyword(s):  
T Cell ◽  
B Cell ◽  
Cellular Localization ◽  
Tertiary Structure ◽  
Vaccine Candidate ◽  
Surface Proteins ◽  
World Population ◽  
T Cell Epitopes ◽  
Universal Vaccine ◽  
Vaccine Candidates

AbstractLeptospira is a zoonotic pathogen causing significant morbidity and mortality both in animals and humans. Although several surface proteins have been identified as vaccine candidate, they failed to induce sterilizing immunity and cross protection against different serovars. Thus, identification of highly immunogenic antigens that are conserved among pathogenic serovars would be first step towards development of universal vaccine for Leptospirosis. Here we used reverse vaccinology pipeline to screen core genome of pathogenic Leptospira spp.in order to identify suitable vaccine candidates. Based on properties like sub cellular localization, adhesin, homology to human proteins, antigenicity and allergenicity, 18 antigenic proteins were identified and were further investigated for immunological properties. Based on immunogenicity, Protegenicity, Antigenicity, B-cell and promiscuous T-cell epitopes, 6 Potential Vaccine Candidates (PVCs) were finally selected which covered most of the affected world population. For designing a Multi-Epitope Vaccine (MEV), 6 B-cell and 6 promiscuous MHC-I and MHC-II epitopes from each candidate were clustered with linkers in between and stitched along with a TLR4 adjuvant (APPHALS) at the N-terminal to form a construct of 361 amino acids. The physiochemical properties, secondary and tertiary structure analysis revealed that MEV was highly stable. Molecular docking analysis revealed the deep binding interactions of the MEV construct within the grooves of human TLR4 (4G8A). In-silico codon optimization and cloning of the vaccine construct assured good expression. Further, immune simulations have shown that MEV could induce strong and diverse B and T cell responses. Taken together our results indicate that the designed MEV could be a promising subunit vaccine candidate against Leptospirosis, however it requires experimental validation.

scholarly journals Frequency of Interferon-Resistance Conferring Substitutions in Amino Acid Positions 70 and 91 of Core Protein of the Russian HCV 1b Isolates Analyzed in the T-Cell Epitopic Context

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
V. S. Kichatova ◽  
K. K. Kyuregyan ◽  
N. V. Soboleva ◽  
A. A. Karlsen ◽  
O. V. Isaeva ◽  
...  
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
Immune Escape ◽  
Core Protein ◽  
Significant Proportion ◽  
In Silico Analysis ◽  
Hla Class I ◽  
T Cell Epitopes ◽  
Hla Class I Molecules ◽  
Negative Effect

Amino acid substitutions R70Q/H and L91M in HCV subtype 1b core protein can affect the response to interferon and are associated with the development of hepatocellular carcinoma. We found that the rate of R70Q/H in HCV 1b from Russia was 31.2%, similar to that in HCV strains from Asia (34.0%), higher than that in the European (18.0%, p=0.0010), but lower than that in the US HCV 1b strains (62.8%, p<0.0001). Substitution L91M was found in 80.4% of the Russian HCV 1b isolates, higher than in Asian isolates (43.8%, p<0.0001). Thus, a significant proportion of Russian HCV 1b isolates carry the unfavorable R70Q/H and/or L91M substitution. In silico analysis of the epitopic structure of the regions of substitutions revealed that both harbor clusters of T-cell epitopes. Peptides encompassing these regions were predicted to bind to a panel of HLA class I molecules, with substitutions impairing peptide recognition by HLA I molecules of the alleles prevalent in Russia. This indicates that HCV 1b with R70Q/H and L91M substitutions may have evolved as the immune escape variants. Impairment of T-cell recognition may play a part in the negative effect of these substitutions on the response to IFN treatment.

In silico identification of immunodominant B-cell and T-cell epitopes of non-structural proteins of Usutu Virus

2018 ◽  
Vol 125 ◽  
pp. 129-143 ◽  
Author(s):  
Rohit Satyam ◽  
Essam Mohammed Janahi ◽  
Tulika Bhardwaj ◽  
Pallavi Somvanshi ◽  
Shafiul Haque ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Structural Proteins ◽  
T Cell Epitopes ◽  
Usutu Virus ◽  
In Silico Identification
Sign in / Sign up

Export Citation Format

Share Document