In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2

Abstract

The COVID-19 epidemic, caused by virus SARS-CoV-2, has turned into a pandemic and threatened everyone's health for the past two years. In SARS-CoV-2, ORF8 is one of the most important accessory proteins with a role in immune modulation. There are multiple disulfide bonds in the wild type (WT) ORF8. Here, we present an in silico study on the effects of the disulfide bonds in ORF8 on the aspects of the structural properties and binding properties with the human leukocyte antigen (HLA-A). We first define five possible states for ORF8 with different disulfide bond reduction schemes. For each state, we collect the conformational ensemble using molecular dynamics (MD) simulations in an explicit solvent. From the analysis of the structural properties, we find that the reduction of the disulfide bonds has small effects on the global properties but much larger effects on the ORF8-specific region that is located on the surface of the ORF8 dimer. Interestingly, we find that the dimer does not break into two monomers at room temperature even if all the disulfide bonds get reduced. Further, we investigate the role of the disulfide bonds in the interactions with the human leukocyte antigen (HLA) by performing docking between HLA-A and the conformational ensembles of ORF8 in different states. We give predictions on the preferred binding sites for each state and validate the predictions for the WT dimer with the experimental data on epitopes. In the end, we evaluate the stability of the complexes formed between HLA-A and ORF8 in each state using MD simulations. Our observations can provide inspiration for inhibitor/drug design against ORF8 based on the binding pathway with HLA-A.