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Development of conserved multi-epitopes based hybrid vaccine against SARS-CoV-2 variants: an immunoinformatic approach

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Abstract

The world has faced unprecedented disruptions like global quarantine and the COVID-19 pandemic due to SARS-CoV-2. To combat these unsettling situations, several effective vaccines have been developed and are currently being used. However, the emergence of new variants due to the high mutation rate of SARS-CoV-2 challenges the efficacy of existing vaccines and has highlighted the need for novel vaccines that will be effective against various SARS-CoV-2 variants. In this study, we exploited the four structural proteins of SARS-CoV-2 to execute a potential multi-epitope vaccine against SARS-CoV-2 and its variants. The vaccine was designed by utilizing the antigenic, non-toxic, and non-allergenic B-cell and T-cell epitopes, which were selected from conserved regions of viral proteins. To build a vaccine construct, epitopes were connected through different linkers and an adjuvant was also attached at the start of the construct to enhance the immunogenicity and specificity of the epitopes. The vaccine construct was then screened through the aforementioned filters and it scored 0.6019 against the threshold of 0.4 on VexiJen 2.0 which validates its antigenicity. Toll-like receptors (i.e., TLR2, TLR3, TLR4, TLR5, and TLR8) and vaccine construct were docked by Cluspro 2.0, and TLR8 showed strong interaction with construct having a maximum negative binding energy of − 1577.1 kCal/mole. C-IMMSIM's immune simulations over three doses of the vaccine and iMODS' molecular dynamic simulations were executed to assess the reliability of the docked complexes. The stability of the vaccine construct was evaluated through the physicochemical analyses and the findings suggested that the manufactured vaccine is stable under a wide range of circumstances and can trigger immune responses against various SARS-CoV-2 variants (due to conserved epitopes). However, to strengthen the formulation of the vaccine and assess its safety and effectiveness, additional investigations and studies are required to support the computational data of this research at in-vitro and in-vivo levels.

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Data availability

More data related to this study can be accessed by sending a rea-sonable email to 123allah.rakha@gmail.com.

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Authors and Affiliations

  1. School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan

    Allah Rakha Yaseen & Muhammad Suleman

  2. Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan

    Abdul Salam Qadri & Ali Asghar

  3. Institute of Biochemistry and Biotechnology, University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan

    Iram Arshad

  4. Institute of Molecular Biology and Biotechnology, Faculty of Life Sciences, University of Lahore, Lahore, 54000, Pakistan

    Daulat Munaza Khan

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  1. Allah Rakha Yaseen
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Contributions

Conceptualization, A.R.Y.; methodology, A.R.Y., and M.S.; software, A.R.Y., D.M.K., and M.S.; validation, A.R.Y., and M.S.; formal analysis, A.R.Y., A.S.Q., and I.A.; investigation, A.R.Y., and M.S.; resources, A.R.Y., and M.S.; data curation, A.R.Y., A.A., and M.S.; writing—original draft preparation, A.R.Y., and M.S.; writing—review and editing A.R.Y., M.S., A.S.Q., A.A., I.A., and D.M.K. supervision, A.R.Y., and M.S., project administration, A.R.Y.; prepared figures 1-12, A.S.Q., A.A., I.A., and D.M.K. All authors have read and agreed to the published version of the manuscript.

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40203_2023_156_MOESM1_ESM.rar

Supplementary file1 Figure S1a: Conservancy analysis of Spike protein for the filtration of epitopes; Figure S2b: Conservancy analysis of Envelope protein for the filtration of epitopes; Figure S1c: Conservancy analysis of Membrane protein for the filtration of epitopes; Figure S1d: Conservancy analysis of Nucleocapsid protein for the filtration of epitopes; Figure S2: The wireframe model of original and mutant model after the disulfide engineering: The yellow colored rods represents the disulfide bond formation after disulfide engineering; Figure S3a: Graphical representation of various Normal mode Analyses (NMA) generated by iMODS for the docked complex (Vaccine + TLR2); Figure S3b: Graphical representation of various Normal mode Analyses (NMA) generated by iMODS for the docked complex (Vaccine + TLR3); Figure S3c: Graphical representation of various Normal mode Analyses (NMA) generated by iMODS for the docked complex (Vaccine + TLR4); Figure S3d: Graphical representation of various Normal mode Analyses (NMA) generated by iMODS for the docked complex (Vaccine + TLR5); Figure S4: Immune simulation analysis: a) Represents the production of Dendritic cells per state (mm-3) while b) showed the generation of MA population per state (mm-3); Figure S5: Immune simulation analysis: a) Represents the production of EP population per state (mm-3) while b) showed the generation of NK cell population per state (mm-3); Table S1a: List of B-cell restricted epitopes predicted for Spike (S) protein; Table S1b: The list of B-cell-specific epitopes predicted from Envelope (E) protein; Table S1c: List of all the B-cell restricted protein predicted from Membrane (M) protein; Table S1d: The list of linear B-cell restricted epitope predicted from Nucleocapsid (N); Table S2a: List of reference HLA alleles used for the prediction of MHC-I restricted epitopes; Table S2b: The selected HLA alleles as reference for the prediction of MHC-II restricted epitopes; Table S3a: The set alleles for individual MHC-I epitopes used in Population Coverage Analysis; Table S3b: The set alleles for individual MHC-II epitopes used in Population Coverage Analysis; Table S4a: Cumulative population coverage against individual MHC-I restricted epitopes and HLA hits; Table S4b: Percentage genotype frequencies of each HLA allele against individual MHC-I restricted epitopes; Table S4c: Cumulative population coverage against individual MHC-II restricted epitopes and HLA hits; Table S4d: Percentage genotype frequencies of each HLA allele against individual MHC-II restricted epitopes; Table S5: C-score for the designed 3D model by I-TASSAR; Table S6: List of predicted (black) and selected (Green) pairs for Disulfide engineering; Table S7: List of cluster members and lowest energies obtained from Cluspro docking analysis against various TLRs and vaccine construct; Table S8: The eigenvalue of various docked complexes that were obtained from ClusPro analysis. File named Tools and access dates contained the links and access dates of all the software, servers, and tools used in this study (RAR 19896 KB)

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Yaseen, A.R., Suleman, M., Qadri, A.S. et al. Development of conserved multi-epitopes based hybrid vaccine against SARS-CoV-2 variants: an immunoinformatic approach. In Silico Pharmacol. 11, 18 (2023). https://doi.org/10.1007/s40203-023-00156-2

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