key: cord-0996492-m4u96x2v authors: Bhattacharya, Manojit; Sharma, Ashish R.; Patra, Prasanta; Ghosh, Pratik; Sharma, Garima; Patra, Bidhan C.; Lee, Sang‐Soo; Chakraborty, Chiranjib title: Development of epitope‐based peptide vaccine against novel coronavirus 2019 (SARS‐COV‐2): Immunoinformatics approach date: 2020-03-05 journal: J Med Virol DOI: 10.1002/jmv.25736 sha: a7278f3a272ea92ab740d6863e94afd9cd266621 doc_id: 996492 cord_uid: m4u96x2v Recently, a novel coronavirus (SARS‐COV‐2) emerged which is responsible for the recent outbreak in Wuhan, China. Genetically, it is closely related to SARS‐CoV and MERS‐CoV. The situation is getting worse and worse, therefore, there is an urgent need for designing a suitable peptide vaccine component against the SARS‐COV‐2. Here, we characterized spike glycoprotein to obtain immunogenic epitopes. Next, we chose 13 Major Histocompatibility Complex‐(MHC) I and 3 MHC‐II epitopes, having antigenic properties. These epitopes are usually linked to specific linkers to build vaccine components and molecularly dock on toll‐like receptor‐5 to get binding affinity. Therefore, to provide a fast immunogenic profile of these epitopes, we performed immunoinformatics analysis so that the rapid development of the vaccine might bring this disastrous situation to the end earlier. Therefore, as the situation was getting worse and worse, the need for designing a suitable peptide vaccine component against the SARS-COV-2 was growing. Our work was to find suitable epitopes, which can generate enough immune response against the SARS-COV-2 infection. Using immunoinformatics, we could recognize and characterize potential B and T-cell epitopes for the generation of the The amino acid sequence of the targeted protein on SARS-COV-2 was collected from the National Centre for Biotechnological Information (NCBI) database. 11 The protein sequence is very crucial for identifying the potential epitopes of the targeted protein. In this subsection, we used the Immune Epitope Database (IEDB) to identify linear B-cell epitopes using the incorporated BepiPred 2.0 prediction module. 12, 13 We provided the FASTA sequence of the targeted protein as an input considering all default parameters. Molecular docking is the most promising part of the modern drugdiscovery method. Here, in this study, we adopted PatchDock (Beta We obtained a total of 34 sequential linear B-cell epitopes of varying lengths from the IEDB server within spike glycoprotein of SARS-COV-2. Those B-cell epitopes were placed into Table 1 based on their positional value, sequence, and length. In Figure 1 the yellow-colored peaks represent the epitopic region, while the green-colored slopes, represent the nonepitopic region. We identified 29 MHC-I epitopes and 8 MHC-II epitopes, which fall within the preidentified B-cell epitopic region. Among them, Tables 2 and 3 with encountering MHC alleles and antigenic scores. In this study, we linked the 13 MHC-I and 3 MHC-II antigenic epitopes with (EAAAK) 3 linker peptide to construct a vaccine component. This linker peptide was easily fused with the virus coat protein and increased stability as well as folding of the vaccine component. 22 The predicted structure of the vaccine component is shown in Figure 2 . It has 90.0%, 7.1%, 1.6%, and 1.3% residues in most favored, additionally allowed, generously allowed and disallowed regions respectively within PROCHECK as the validation server to generate Ramachandran plot. Using the ProSA server, the "Z" score was −3.82 and most of the residues had negative energy value as shown in All the observations of our present work depict the effectiveness of selected epitopes within the spike glycoprotein of SARS-COV-2. These epitopes can be used to make an immunogenic multi-epitopic peptide vaccine against SARS-COV-2. Present immunoinformatic analysis pointed out 13 MHC-I and 3 MHC-II epitopes within the spike glycoprotein of SARS-COV-2. These epitopes are the ideal candidate to formulate a multi-epitopic peptide vaccine, not only because of being selected from the linear B-cell epitopic region but also because of their antigenic property was confirmed. Moreover, the molecular docking of vaccine components with the TLR-5 proves the significance and effectiveness of these epitopes as an ideal vaccine candidate against SARS-COV-2. However, these immunoinformatic analyses require several in vitro and in vivo validations before formulating the vaccine to resist COVID-19. 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