Compatibility of the Ligand Binding Sites in the Spike Glycoprotein of COVID-19 with those in the Aminopeptidase and the Caveolins 1, 2 Proteins

Abstract

A novel severe viral pneumonia emerged in Wuhan city, China, in December 2019. The spike glycoprotein of the SARS-CoV-2 plays a crucial role in the viral entry to the host cell and eliciting a strong response for antibody-mediated neutralization in mice. Caveolins 1,2 are scaffolding proteins dovetailed as a co-stimulatory signal essential for T-cell receptor and activation. Aminopeptidase is a membrane protein acting as a receptor for human coronavirus within the S1 subunit of the spike glycoprotein. Vaccines for COVID-19 have become a priority for predisposition against the outbreak, so that our study aimed to find interaction sites between SP of SARS-CoV-2 and CAV1, CAV2, and AMPN. Methods: Amino acids motif search was employed to predict the possible CAV1, CAV2, and AMPN related interaction domains in the SARS-CoV-2 SP In silico analysis. Results: Interactions between proteins revealed 5 and16 residues. ZN ligand binding site is matched between AMPN and SARS- CoV-2 SP. HLA-A*74:01 allele is the best CTL epitope for SP. We identified seven B-cell epitopes specifically for SARS-CoV-2 SP. Conclusions: SARS-CoV-2 SP binding sites might be compatible with AMPN ligand binding sites. The limit score was detected for ligand binding sites of CAV1 and CAV2. Our findings might be critical for the further substantial study of vaccine production strategy.