Designing of Nucleocapsid Protein Based Novel Multi-epitope Vaccine Against SARS-COV-2 Using Immunoinformatics Approach
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Designing of Nucleocapsid Protein Based Novel Multi‑epitope Vaccine Against SARS‑COV‑2 Using Immunoinformatics Approach Janish Kumar1 · Rahila Qureshi2 · Someswar R. Sagurthi2 · Insaf Ahmed Qureshi1 Accepted: 3 November 2020 © Springer Nature B.V. 2020
Abstract The COVID-19 disease is caused by SARS-CoV-2 and spreading rapidly worldwide with extremely high infection rate. Since effective and specific vaccine is not available to combat the deadly COVID-19, the objective of our study was to design a multi-epitope vaccine using immunoinformatics approach with translational implications. Nucleocapsid (N) protein of SARS-CoV-2 is stable, conserved and highly immunogenic along with being less prone to mutations during infection, which makes it a suitable candidate for designing vaccine. In our study, B- and T-cells epitopes were identified from N protein and screened based on crucial parameters to design the multi-epitope vaccine construct. Additionally, human beta-defensin-2 was incorporated into the vaccine construct as an adjuvant along with suitable linkers followed by its further evaluation based on crucial parameters including allergenicity, antigenicity, stability etc. Combined major histocompatibility complexes (MHC-I and MHC-II) binding epitopes presented broader population coverage of the vaccine throughout the world. The three-dimensional structure of vaccine candidate implied strong interaction with toll-like receptor 3 (TLR3) using molecular docking. The vaccine-TLR3 complex was observed to be highly stable during simulation and electrostatic free energy was foremost contributor for stabilization of the structure. Subsequently, in silico cloning of vaccine candidate was carried out to generate the construct into pET-28a(+) expression vector succeeded by its virtual confirmation. Altogether, our results advocate that the designed vaccine candidate could be an effective and promising weapon to fight with COVID-19 infection worldwide. Keywords SARS-CoV-2 · Nucleocapsid protein · Multi-epitope vaccine · Immunoinformatics approach · TLR3 receptor · Molecular dynamics simulation
Introduction A new betacoronavirus, SARS-CoV-2 (Severe Acute Respiratory Syndrome Corona Virus 2), which belongs to Coronaviridae family is the causative agent of the recent world health hazard COVID-19 (coronavirus disease 2019). SARS-CoV-2 represents 79.6% sequence identity to SARSCoV (Zhou et al. 2020), which was the causative agent of an epidemic in the year 2003. The recent outbreak of COVID19 has been declared as a public health crisis of global concern by World Health Organization (WHO), which has * Insaf Ahmed Qureshi [email protected] 1
Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Hyderabad 500046, India
Department of Genetics, Osmania University, Hyderabad 500007, India
2
reached to over 216 countries in a short span with affecting approximately thirty million people worldwide (https: //covid 19.who.int/). The case fatality rate (CFR) is appro
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