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

Allah Rakha Yaseen; Muhammad Suleman; Abdul Salam Qadri; Ali Asghar; Iram Arshad; Daulat Munaza Khan

doi:10.1007/s40203-023-00156-2

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

In Silico Pharmacol. 2023 Jul 27;11(1):18. doi: 10.1007/s40203-023-00156-2. eCollection 2023.

Authors

Allah Rakha Yaseen¹, Muhammad Suleman¹, Abdul Salam Qadri², Ali Asghar², Iram Arshad³, Daulat Munaza Khan⁴

Affiliations

¹ School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590 Pakistan.
² Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000 Pakistan.
³ Institute of Biochemistry and Biotechnology, University of Veterinary & Animal Sciences, Lahore, 54000 Pakistan.
⁴ Institute of Molecular Biology and Biotechnology, Faculty of Life Sciences, University of Lahore, Lahore, 54000 Pakistan.

PMID: 37519944
PMCID: PMC10374517 (available on 2024-07-27)
DOI: 10.1007/s40203-023-00156-2

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s40203-023-00156-2.

Keywords: Envelope protein; Immune simulation; Membrane protein; Molecular docking; Multi-epitope; Nucleocapsid; SARS-COV-2; Spike protein.

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