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Minerva Biotechnology and Biomolecular Research 2022 September;34(3):97-113

DOI: 10.23736/S2724-542X.22.02868-1


lingua: Inglese

In-silico analysis of multiepitope based vaccine targeting respiratory viruses SARS, MERS and SARS-CoV-2

Anamitra SEN 1, Ritu BANSAL 1, Sanika MOHAGAONKAR 1, Tulika BHARDWAJ 2, Bhawna RATHI 1 , Atiah H. ALMALKI 3, 4, Essam M. JANAHI 5, Ahmad ALSULIMANI 6, Brij N. TEWARI 7, Pallavi SOMVANSHI 2, 8, Shafiul HAQUE 9, 10

1 Department of Biotechnology, Amity University Campus, Noida, India; 2 School of Computational and Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi, India; 3 Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia; 4 Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Al-Hawiah, Taif, Saudi Arabia; 5 Independent Researcher, Al Janabiyah, Bahrain; 6 Medical Laboratory, Department of Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia; 7 Department of Microbiology, King George’s Medical University, Lucknow, India; 8 Special Center of Systems Medicine (SCSM), Jawaharlal Nehru University, New Delhi, India; 9 Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia; 10 Bursa Uludağ University Faculty of Medicine, Nilüfer, Turkey

BACKGROUND: Recurrent outbreaks of respiratory viruses like SARS-CoV (severe acute respiratory syndrome-coronavirus, 2002), MERS (Middle East respiratory syndrome, 2012) including the ongoing SARS-CoV-2 (2019) pandemic warrants for a single-broad-spectrum vaccine against these respiratory viruses.
METHODS: In the present study, phylogenetic analysis followed by in-silico identification of vaccine candidates for SARS, MERS and SARS-CoV-2 was performed by exploiting T-cell and B-cell mapping to ascertain the best possible epitopes for effector humoral- and cell-mediated immune response. Further, population-coverage analysis of the identified epitopes followed by the designing of chimera of epitope-based vaccine was done using linkers and adjuvants. Docking study was done to appraise the interaction of the proposed vaccine with ACE2 (angiotensin converting enzyme-2) receptor (SARS and SARS-CoV-2) and HLA-B7 (human leukocyte antigen) receptor (MERS). The stability of the vaccine chimera was confirmed by molecular dynamics performed for 20 ns; this was followed by codon optimization and in-silico cloning.
RESULTS: Phylogenetic analysis revealed similarity among SARS-CoV-2, SARS-CoV and bat SARS-like coronavirus. Both, SARS-CoV and SARS-CoV-2 were from different class than MERS, whereas SARS-CoV-2 showed more relatedness with Bat SARS-like coronaviruses. The most suitable epitopes found were LSFELLNAPATVCGP (SARS), LVTLAILTALRLCAY (SARS-CoV-2) and YTSAFNWLL (MERS) with nearly 98% population coverage. Molecular docking followed by simulation studies revealed high number of hydrogen bonds, stable RMSD values and acceptable RMSF flexibility scores, indicating stable interactions of the vaccine with ACE2 and MHC receptors (Major histocompatibility complex). Expression of the designed multiepitope vaccine in E. coli (Escherichia coli) expression system was confirmed by in-silico cloning/codon optimization.
CONCLUSIONS: Further, in-vitro and in-vivo experimental validation studies are required to endorse our current findings.

KEY WORDS: COVID-19; Mass vaccination; T-lymphocytes; B-lymphocytes; Molecular docking simulation; SARS-CoV-2

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