Exploration of antigenic determinants in spike glycoprotein of SARS-CoV2 and identification of five salient potential epitopes

Agrawal, Aditya; Varshney, Rajat; Pathak, Mamta; Patel, Shailesh Kumar; Rai, Vishal; Sulabh, Sourabh; Gupta, Rohini; Solanki, Khushal Singh; Varshney, Ritu; Nimmanapalli, Ramadevi

Emerging pathogens have been an eternal threat to mankind. In a series of pandemics caused by notorious coronaviruses, a newly emerged SARS-CoV2 virus is creating panic among the world population. The unavailability of reliable theranostics insists the exploration of antigenic determinants in spike glycoprotein of SARS-CoV2. The four novel inserts (‘(70)VSGTNGT(76)’, ‘(150)KSWM(153)’, (247)SYLTPG(252) and (674)QTQTNSPRR(682)) in SARS-CoV2 spike protein were unraveled via multiple sequence alignment of spike proteins of SARS-CoV2, SARS-CoV, and MERS-CoV. The three-dimension (3D) modeling of the spike protein of the SARS-CoV2 and their interaction with the ACE2 receptor was delineated with the help of SWISS-MODEL and 3DLigandSite web servers. The predicted 3D model of SARS-CoV2 was further verified by SAVES, RAMPAGE, and ProSA-web tools. The potential B-cell immunogenic epitopes of SARS-CoV2 were predicted out by using various software viz. IEDB B-cell epitopes prediction tool, BepiPred linear epitope prediction tool, Emini Surface Accessibility Prediction tool, and Kolaskar-Tongaonkar antigenicity web tool. The five epitopes (i.e. ‘(71)SGTNGTKRFDN(81), (247)SYLTPG(252), (634)RVYST(638), (675)QTQTNSPRRARSV(687), and (1054)QSAPH(1058)) were selected as potent antigenic determinants. The quantum of information generated by this study will prove beneficial for the development of effective therapeutics, diagnostics, and multi-epitopic vaccines to combat this ongoing menace.