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Abstract S03-03: A computational approach to identify a possible SARS-CoV-2 vaccine from receptor binding domain peptide sequence on spike glycoproteins

The novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a pathogenic virus responsible for thecoronavirus disease 2019 (COVID-19) outbreak The virus has rapidly spread worldwide and caused serious globalhealth and economic issues The World Health Organization has declared COVID-19 a pandemic and suggestedthat all countries should take extreme countermeasures to stop it from spreading SARS-CoV-2 targets theangiotensin-converting enzyme 2 (ACE2) receptor on human lung cells through receptor binding domain on thespike proteins (S-RBD) via N487, Y489, and G496 residues as previously reported The virus uses ACE2 toinoculate mRNA and to replicate inside the cells, which results in a severe respiratory syndrome Patients mightexperience serious symptoms including fever, cough, inability to taste, shortness of breath, and sometimesrespiratory failure Therefore, developing a vaccine is highly necessary to control the outbreak, which led to our goalin this study to identify antigenic peptide sequences on the S-RBD domain that may induce the immune response toprovide protection from the virus We virtually analyzed S-RBD protein structure by multiple sequence alignment(MSA) via CLUSTAL OMEGA to study the homology of the S-RBD domain in both strains (SARS-CoV and SARS-CoV-2), and the results showed 76% identical shared amino acids Moreover, the S-RBD sequence for SARS-CoV-2was blasted against the sequence “486-FNCYFPLQSYGFQ-498” on Drugbank database with a penalty of -1 foreach indel, -3 for the mismatch, and with an expected value of 8 to screen for potential molecules that might interact with the target sequence The blast results showed a possible alignment with complement component 4A (C4-A) protein, a protein involved in autoimmunity and antibody signaling, on the residues F490, C488, P491, Y495, G496, F497, and Q498 Lastly, a molecular docking analysis was performed by ClusPro 2 0 docking system to analyze thebinding affinity of C4-A protein to the S-RBD-protein, and the results of the docking analysis showed 30 differentbindings with different weighted energy coefficient scores The top 10 binding conformations were chosen based onthe coefficient score values between -856 2 to -985 4 The highest binding affinity of C4-A protein was observed onthe target sequence, which might be a therapeutic approach for a possible COVID-19 vaccine Further experimentsare required to synthesize recombinant peptides for S-RBD protein and test it on animal models to check if it willinduce C4-A production in response to recombinant S-RBD peptide and antibodies signaling to counter SARS-CoV-2 virus and, hopefully, competing with ACE2 binding to S-protein