Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins

All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.

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Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2

Infectious Diseases of Poverty ◽

10.1186/s40249-020-00752-w ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

Muhammad Tahir ul Qamar ◽

Farah Shahid ◽

Sadia Aslam ◽

Usman Ali Ashfaq ◽

Sidra Aslam ◽

...

Keyword(s):

In Silico ◽

Subunit Vaccine ◽

Human Leukocyte ◽

Surface Glycoprotein ◽

Structural Proteins ◽

Effective Vaccine ◽

Severe Illness ◽

T Cell Epitopes ◽

Hla Binding ◽

K 12

Abstract Background Coronavirus disease 2019 (COVID-19) linked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause severe illness and life-threatening pneumonia in humans. The current COVID-19 pandemic demands an effective vaccine to acquire protection against the infection. Therefore, the present study was aimed to design a multiepitope-based subunit vaccine (MESV) against COVID-19. Methods Structural proteins (Surface glycoprotein, Envelope protein, and Membrane glycoprotein) of SARS-CoV-2 are responsible for its prime functions. Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B- and T- cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. Results Predicted epitopes suggested high antigenicity, conserveness, substantial interactions with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 88.40%. Taken together, 276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes (CTL), 6 helper T lymphocyte (HTL) and 4 B-cell epitopes with suitable adjuvant and linkers. The MESV construct was non-allergenic, stable, and highly antigenic. Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3 (TLR3). Furthermore, in silico immune simulation revealed significant immunogenic response of MESV. Finally, MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system, to ensure its increased expression. Conclusion The MESV developed in this study is capable of generating immune response against COVID-19. Therefore, if designed MESV further investigated experimentally, it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19.

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Structural modeling and conserved epitopes prediction against SARS-COV-2 structural proteins for vaccine development

10.21203/rs.2.23973/v1 ◽

2020 ◽

Cited By ~ 3

Author(s):

Muhammad Tahir ul Qamar ◽

Farah Shahid ◽

Usman Ali Ashfaq ◽

Sidra Aslam ◽

Israr Fatima ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

Mhc Class I ◽

Mhc Class Ii ◽

Class Ii ◽

Class I ◽

Structural Proteins ◽

Severe Illness ◽

T Cell Epitopes ◽

B Cell Epitopes

Abstract Background: Coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Corona virus 2 (SARS-COV-2) was first diagnosed in December 2019, Wuhan, China. Little is known about this new virus and it has the potential to cause severe illness and pneumonia in some people, therefore the development of an effective vaccine is highly desired.Methods: Immunoinformatics and statistical approaches were used in this study to forecast B- and T- cell epitopes for the SARS-COV-2 structural proteins (Surface glycoprotein, Envelope protein, and Membrane glycoprotein) that may play a key role in eliciting immune response against COVID-19. Different types of B cell epitopes (linear as well as discontinuous) and T cell (MHC class I and MHC class II) were determined. Moreover, their antigenicity and allergenicity were also estimated.Results: The antigenic B-cell epitopes exposed to the outer surface were screened out and 23 linear B cell epitopes were selected. “SPTKLNDLCFTNVY” had the highest antigenicity score among B cell epitopes. The T-cell epitopes bound to multiple alleles, antigenic, non-allergen, non-toxic, and conserved in the protein sequence were shortlisted. In total, 16 epitopes (9 from MHC class I and 7 from MHC class II) were selected. Among the T-cell epitopes, MHC class I (IPFAMQMAYRFN) and MHC class II (VTLACFVLAAVYRIN) were classified as strongly antigenic. Digestion analysis verified the safety and stability of the peptides predicted during this study. Furthermore, docking analyses of predicted peptides showed significant interactions with the HLA-B7 allele.Conclusion: The putative antigen epitopes identified in this study may serve as vaccine candidates and can help to eliminate/control growing health threat of COVID-19.

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A Candidate Multi-epitope Vaccine Against Porcine Reproductive and Respiratory Syndrome Virus and Mycoplasma Hyopneumoniae

10.21203/rs.3.rs-536687/v1 ◽

2021 ◽

Author(s):

Zhisong Gao ◽

Lingxiao Chen ◽

Xuan Pan ◽

Xiaojing Li ◽

Guangzong Lu ◽

...

Keyword(s):

High Surface ◽

Mycoplasma Hyopneumoniae ◽

Economic Losses ◽

Effective Vaccine ◽

Respiratory Syndrome Virus ◽

Potential Candidate ◽

T Cell Epitopes ◽

Swine Industry ◽

Combined Vaccine ◽

Epitope Vaccines

Abstract Background: Porcine reproductive and respiratory syndrome virus (PRRSV) and Mycoplasma hyopneumoniae (M. hyopneumoniae, Mhp) are two of the most common pathogens involved in the porcine respiratory disease complex (PRDC) which results in significant worldwide economic losses. Vaccination is reported to be the most effective approach to prevent the disease. Since PRRSV and Mhp co-infections are very common, an efficient dual vaccine against PRRSV and Mhp co-infections is required for the global swine industry. Compare with the traditional vaccine, the multi-epitope vaccines have several advantages, such as comparatively easy production and construction, chemical stability, and lack of infectious potential.Results: In this study, to develop a safe and effective vaccine, B cell epitopes and T cell epitopes of PRRSV-GP5, PRRSV-M, Mhp-P46 and Mhp-P65 protein had been screened to construct a recombinant epitope protein rEP-PM which has good hydrophilicity, strong antigenicity and high surface accessibility, and each epitope is independent and complete. After immunization in mice, rEP-PM could induce the production of high levels of antibodies and effective cellular immune response.Conclusions: Our results showed that the rEP-PM protein could be potential candidate to develop into a safe and effective multi-epitope peptide combined vaccine used in the control of PRRSV and Mhp infection.

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Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2

10.21203/rs.3.rs-31779/v1 ◽

2020 ◽

Author(s):

Vipul Kumar ◽

Manoj Jena

Keyword(s):

T Cell ◽

Vaccine Development ◽

Gc Content ◽

Cytotoxic T Cell ◽

Effective Vaccine ◽

T Cell Epitopes ◽

Online Tools ◽

Efficient Expression ◽

Experimental Validations ◽

Dynamics Simulations

Abstract The novel severe acute respiratory syndrome related corona virus-2 (SARS-CoV-2) belongs to the “Coronaviridae” family and order “Nidovirales” cause coronavirus disease (COVID19). The SARS-CoV-2 has been spread in more than a hundred countries, and more than a million have lost their lives. Recently COVID-19 has been declared as pandemic worldwide. Vaccination and immunization could only be an effective strategy to combat this fatal COVID-19. For identification of the effective vaccine candidate against COVID-19, various immunoinformatics online tools and software were used to predict the epitopes. The cytotoxic T cell epitopes, Helper T cell epitopes, and B cell epitopes from three structural polyproteins ( Spike, Membrane, and Nucleocapsid (SMN) ) based on the binding affinity towards MHC , antigenicity, non-allergenicity, and non-toxicity were identified for vaccine development. The multiepitope based vaccine was constructed linking two additional adjuvants human betadefensin-3 and human beta-defensin-2 at N and C terminal, respectively. Constructed vaccine sequence was found to be a good antigen and non-allergen for the human body. The constructed vaccine was docked with the TLR-3 receptor. And the docked complex then further taken for Molecular dynamics simulations and RMSD was calculated, which showed stable binding of the complex. The codon adaptation index (CAI) of 0.92 and GC content of 55.5% for E.coli (k12) strain suggested the efficient expression of the predicted vaccine. The current study can be helpful in the reduction of time and cost for further experimental validations and could give a valuable contribution against this pandemic.

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Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2

F1000Research ◽

10.12688/f1000research.36371.1 ◽

2021 ◽

Vol 10 ◽

pp. 44

Author(s):

Vipul Kumar ◽

Sudhakar Kancharla ◽

Prachetha Kolli ◽

Manoj Jena

Keyword(s):

T Cell ◽

Vaccine Development ◽

Gc Content ◽

Cytotoxic T Cell ◽

Effective Vaccine ◽

T Cell Epitopes ◽

Online Tools ◽

Efficient Expression ◽

Experimental Validations ◽

Dynamics Simulations

Background: The novel severe acute respiratory syndrome related corona virus-2 (SARS-CoV-2) belongs to the “Coronaviridae” family and order “Nidovirales”, which has caused the pandemic coronavirus disease 2019 (COVID-19). SARS-CoV-2 has been spread in more than a 100 countries, and more than a million have lost their lives. Vaccination and immunization could be an effective strategy to combat fatal COVID-19. Methods: For identification of effective vaccine candidate against COVID-19, various immunoinformatics online tools and softwares were used to predict epitopes. Cytotoxic T cell epitopes, helper T cell epitopes, and B cell epitopes from three structural polyproteins (Spike, Membrane, and Nucleocapsid (SMN) based on the binding affinity towards MHC, antigenicity, non-allergenicity, and non-toxicity) were identified for vaccine development. The multiepitope based vaccine was constructed linking two additional adjuvants human beta-defensin-3 and human beta-defensin-2 at N and C terminal, respectively. Results: The constructed vaccine sequence was found to be a good antigen and non-allergen for the human body. The constructed vaccine was docked with the TLR-3 receptor. The docked complex was further taken for molecular dynamics simulations and RMSD was calculated, which showed stable binding of the complex. The codon adaptation index (CAI) of 0.92 and GC content of 55.5% for E. coli (K12 strain) suggested efficient expression of the predicted vaccine. Conclusion: The current study can be helpful in the reduction of time and cost for further experimental validations and could give a valuable contribution against this pandemic.

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In Silico Prediction of T and B Cell Epitopes of SAG1-Related Sequence 3 (SRS3) Gene for Developing Toxoplasma gondii Vaccine

Archives of Clinical Infectious Diseases ◽

10.5812/archcid.69241 ◽

2020 ◽

Vol In Press (In Press) ◽

Author(s):

Abolfazl Mirzadeh ◽

Geita Saadatnia ◽

Majid Golkar ◽

Jalal Babaie ◽

Samira Amiri ◽

...

Keyword(s):

Toxoplasma Gondii ◽

Dna Vaccine ◽

In Silico ◽

Effective Vaccine ◽

T Cell Epitopes ◽

In Silico Prediction ◽

Vaccine Strategy ◽

Related Sequence ◽

Ideal Tool ◽

Major Surface

: Toxoplasmosis is a worldwide infection that can lead to serious problems in immune-compromised individuals and fetuses. A DNA vaccine strategy would be an ideal tool against Toxoplasma gondii. One of the necessary measures to provide an effective vaccine is the selection of proteins with high antigenicity. The SAG1-related sequence 3 (SRS3) protein is a major surface antigen in T. gondii that can be used as a vaccine candidate. In the present study, bioinformatics and computational methods were utilized to predict protein characteristics, as well as secondary and tertiary structures. The in silico approach is highly suited to analyze, design, and evaluate DNA vaccine strategies. Hence, in silico prediction was used to identify B and T cell epitopes and compare the antigenicity of SRS3 and other candidate genes of Toxoplasma previously applied in the production of vaccines. The results of the analysis theoretically showed that SRS3 has multiple epitopes with high antigenicity, proposing that SRS3 is a promising immunogenic candidate for the development of DNA vaccines against toxoplasmosis.

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Designing of a novel multisubunit vaccine against Nipah virus structural proteins: A reverse vaccinology approach

10.21203/rs.3.rs-935912/v1 ◽

2021 ◽

Author(s):

khalid Mohamed Adam

Keyword(s):

Nipah Virus ◽

Reverse Vaccinology ◽

Structural Proteins ◽

Effective Vaccine ◽

Compact Structure ◽

Grand Average ◽

Physiochemical Parameters ◽

Significant Public Health ◽

Aliphatic Index ◽

Stable Molecule

Abstract Background The significant public health risk posed by NiV zoonosis and the lack of effective countermeasures against the intermittent outbreaks of the disease in the South and Southeast Asia region have entailed an imperative search for a protective vaccine to prevent or mitigate its epidemic potentiality. This is an endeavor to design an effective, safe multisubunit vaccine using an in silico reverse vaccinology approach. Methods The epitopes used for the construction of the candidate vaccine were meticulously predicted from five viral structural proteins (G, F, M, N, P) using several immunoinformatics tools to assess different epitope characteristics, namely, VaxiJen server for antigenicity, IEDB immunogenicity tool for immunogenicity, AlgPred server for allergenicity, ToxinPred for toxigenicity, IFNepitope server for interferon-gamma induction, Protparam server for physicochemical properties, GROMACS for simulation and simulation dynamics analysis, and finally, SnapGene tool for molecular cloning. Results The proposed vaccine molecule consisted of 501 amino acids, encompassing 7 B cell epitopes, 14 CTL epitopes, and 4 HTL epitopes. The physiochemical parameters of the vaccine construct showed a molecular weight of 54.6 kDa, an acidic stable molecule with an instability index of 38.3, aliphatic index of 62.89, and grand average of hydropathicity of -0.476. Moreover, the docking results and simulation dynamics of the vaccine molecule and TLR-3 showed global energy of 1.58 Kcal/mol, atomic contact energy of 2.98 Kcal/mol, and RMSD of 0.65 nm. The radius gyration showed a relatively steady value throughout the simulation period. a suggestive result of a stable compact structure and a promisingly effective vaccine construct. Conclusion In summary, the overall results of the multi-subunit vaccine molecule are suggestive of a promisingly effective vaccine against NiV infection in humans with a relatively stable compact structure, however, further experimental validation and assessment of pathogenic priming and autoimmunity induction are recommended.

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Immunoinformatics and Structural Analysis for Identification of Immunodominant Epitopes in SARS-CoV-2 as Potential Vaccine Targets

Vaccines ◽

10.3390/vaccines8020290 ◽

2020 ◽

Vol 8 (2) ◽

pp. 290 ◽

Cited By ~ 13

Author(s):

Sumit Mukherjee ◽

Dmitry Tworowski ◽

Rajesh Detroja ◽

Sunanda Biswas Mukherjee ◽

Milana Frenkel-Morgenstern

Keyword(s):

Peptide Vaccine ◽

Vaccine Design ◽

Computational Prediction ◽

Effective Vaccine ◽

Cell Mediated Immunity ◽

T Cell Epitopes ◽

Protective Antigens ◽

Global Pandemic ◽

Time Required ◽

Immunodominant Epitopes

A new coronavirus infection, COVID-19, has recently emerged, and has caused a global pandemic along with an international public health emergency. Currently, no licensed vaccines are available for COVID-19. The identification of immunodominant epitopes for both B- and T-cells that induce protective responses in the host is crucial for effective vaccine design. Computational prediction of potential epitopes might significantly reduce the time required to screen peptide libraries as part of emergent vaccine design. In our present study, we used an extensive immunoinformatics-based approach to predict conserved immunodominant epitopes from the proteome of SARS-CoV-2. Regions from SARS-CoV-2 protein sequences were defined as immunodominant, based on the following three criteria regarding B- and T-cell epitopes: (i) they were both mapped, (ii) they predicted protective antigens, and (iii) they were completely identical to experimentally validated epitopes of SARS-CoV. Further, structural and molecular docking analyses were performed in order to understand the binding interactions of the identified immunodominant epitopes with human major histocompatibility complexes (MHC). Our study provides a set of potential immunodominant epitopes that could enable the generation of both antibody- and cell-mediated immunity. This could contribute to developing peptide vaccine-based adaptive immunotherapy against SARS-CoV-2 infections and prevent future pandemic outbreaks.

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Potent HIV-1-Specific CD8 T Cell Responses Induced in Mice after Priming with a Multiepitopic DNA-TMEP and Boosting with the HIV Vaccine MVA-B

Viruses ◽

10.3390/v10080424 ◽

2018 ◽

Vol 10 (8) ◽

pp. 424 ◽

Cited By ~ 5

Author(s):

Beatriz Perdiguero ◽

Suresh C. Raman ◽

Cristina Sánchez-Corzo ◽

Carlos Oscar S. Sorzano ◽

José Ramón Valverde ◽

...

Keyword(s):

T Cell ◽

Immune Responses ◽

T Cell Responses ◽

Cd8 T Cell ◽

T Cell Response ◽

Effective Vaccine ◽

T Cell Epitopes ◽

Cell Responses ◽

Modified Vaccinia Virus Ankara ◽

Hiv 1

An effective vaccine against Human Immunodeficiency Virus (HIV) still remains the best solution to provide a sustainable control and/or eradication of the virus. We have previously generated the HIV-1 vaccine modified vaccinia virus Ankara (MVA)-B, which exhibited good immunogenicity profile in phase I prophylactic and therapeutic clinical trials, but was unable to prevent viral rebound after antiretroviral (ART) removal. To potentiate the immunogenicity of MVA-B, here we described the design and immune responses elicited in mice by a new T cell multi-epitopic B (TMEP-B) immunogen, vectored by DNA, when administered in homologous or heterologous prime/boost regimens in combination with MVA-B. The TMEP-B protein contained conserved regions from Gag, Pol, and Nef proteins including multiple CD4 and CD8 T cell epitopes functionally associated with HIV control. Heterologous DNA-TMEP/MVA-B regimen induced higher HIV-1-specific CD8 T cell responses with broader epitope recognition and higher polyfunctional profile than the homologous DNA-TMEP/DNA-TMEP or the heterologous DNA-GPN/MVA-B combinations. Moreover, higher HIV-1-specific CD4 and Tfh immune responses were also detected using this regimen. After MVA-B boost, the magnitude of the anti-VACV CD8 T cell response was significantly compromised in DNA-TMEP-primed animals. Our results revealed the immunological potential of DNA-TMEP prime/MVA-B boost regimen and supported the application of these combined vectors in HIV-1 prevention and/or therapy.

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Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae

Vaccines ◽

10.3390/vaccines7030088 ◽

2019 ◽

Vol 7 (3) ◽

pp. 88 ◽

Cited By ~ 11

Author(s):

Dar ◽

Zaheer ◽

Shehroz ◽

Ullah ◽

Naz ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Bacterial Infections ◽

Dynamics Simulation ◽

Effective Vaccine ◽

High Morbidity ◽

T Cell Epitopes ◽

Toll Like Receptor ◽

Epitope Vaccine ◽

The Core ◽

Core Proteins

Klebsiella pneumoniae is an opportunistic gram-negative bacterium that causes nosocomial infection in healthcare settings. Despite the high morbidity and mortality rate associated with these bacterial infections, no effective vaccine is available to counter the pathogen. In this study, the pangenome of a total of 222 available complete genomes of K. pneumoniae was explored to obtain the core proteome. A reverse vaccinology strategy was applied to the core proteins to identify four antigenic proteins. These proteins were then subjected to epitope mapping and prioritization steps to shortlist nine B-cell derived T-cell epitopes which were linked together using GPGPG linkers. An adjuvant (Cholera Toxin B) was also added at the N-terminal of the vaccine construct to improve its immunogenicity and a stabilized multi-epitope protein structure was obtained using molecular dynamics simulation. The designed vaccine exhibited sustainable and strong bonding interactions with Toll-like receptor 2 and Toll-like receptor 4. In silico reverse translation and codon optimization also confirmed its high expression in E. coli K12 strain. The computer-aided analyses performed in this study imply that the designed multi-epitope vaccine can elicit specific immune responses against K. pneumoniae. However, wet lab validation is necessary to further verify the effectiveness of this proposed vaccine candidate.

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