Identification and Comparison of SARS-CoV-2 Peptides Binding to HLA-A*24:02 and HLA-A*24:07

Abstract

HLA-A*24:07 is unique to the Indonesian population, dominated by Sundanese and Javanese. As the Caucasian population handles the most worldwide research, a little study on the HLA-A*24:07 has been undertaken. Recently, the connection of SARS-CoV-2 peptides with HLA, notably HLAA* 24:02, has been investigated. The only distinction between HLA-A*24:02 and HLA-A*24:07 is the residue position 70. No SARS-COV-2 epitope related to HLA-A*24:07 in IEDB was reported until May 19, 2022. NetMHCPan EL 4.1 and IEDB Immunogenicity web servers were utilized in this study to find 42 immunogenic epitopes strongly interacting with HLA-A*24:07. Four top epitope candidates were used to examine the presence of glutamine70 of the HLA-A*24:02. The glutamine70 was compared to histidine70 of the HLA-A*24:02 for binding properties assessment. The assessment showed a lower affinity of the peptide-HLA-A*24:07 complex. A slightly different complex structure was influenced by glutamine and histidine's distinct side chains. Molecular docking using HPEPDOCK and CABS-Dock webserver was carried out along with the stability assessment using CABSFLEX. The 3D visualization and the non-covalent interaction were done using the Pymol and Protein-ligand interaction profiler (PLIP). Furthermore, the 2167NYMPYFFTL2176 and 1208QYIKWPWYI1217 peptides become the most promiscuous epitopes for both HLAs due to their large and aromatic side chain residues that contribute to higher CD8+ T cell response in the primary infection.