DESIGNING OF CELL-MEDIATED EPITOPE VACCINE FOR COVID-19 VIRUS SPIKE PROTEIN

Zahra M. Al-Khafaji*, Aaisha B. Mahmood and Marium B. Mahmood

ABSTRACT

Another attack of coronaviruses comes again, it causes a sever and fatal disease by COVID-19.Immunity is considered as the main way to face viral disease, it becomes more effective if it develops long-lasting activity through cellular immunity. Different short epitopes were derived from COVID-19 spike protein. For cytotoxic cell (CD8+), 7 epitopes were derived 240- TLLALHRSY-248, 628- QLTPTWRVY-636, 714-IPTNFTISV-722, 894- LQIPFAMQM-902, 896- IPFAMQMAY-904, 898- FAMQMAYRF-906, 1065-VTYVPAQEK-1073. For helper cells (CD4+) the following epitopes were derived 199-GYFKIYSKHTPINLV-213,405 GYQPYRVVVLSFELL-518, 505-YQPYRVVVLSFELLH-519, 506-QPYRVVVLSFELLHA-520, 715-PTNFTISVTTEILPV-729, 892-AALQIPFAMQMAYRF-906, 893-ALQIPFAMQMAYRFN-907, 898-FAMQMAYRFNGIGVT-912,895-QIPFAMQMAYRFNGI-909. These epitopes were checked for antigenicity, toxicity, allergenicity, similarity to human proteome, they were highly conserved with the reference protein, and with resemble population coverage. Docking studies revealed desired engagement with selected HLA alleles as indicated by binding affinity energy and RMSD values. Theses epitopes are worth to go for real applications.

Keywords: COVID-19, spike protein, coronaviruses, cellular immunity, epitope vaccine Docking MHCs, Iraq.