This is a project for the class 22117 at DTU. Here you can find the material used for the study: Structural and Binding Analysis of SARS-CoV-2 Spike Protein Variants with Human ACE2 Receptor.
The SARS-CoV-2 virus continues to mutate and produce new variants, with the Omi- cron variant being of particular concern due to its high virulence and potential to evade immune responses. This study, focuses on the analysis of the structural and functional changes in the receptor binding domain (RBD) of XBB.1.16 compared to the wild-type and B.1.1.529. Molecular dynamics simulations and docking analysis were performed to investigate the differences in protein-protein interactions between the wild-type and B.1.1.529. The results showed that B.1.1.529 has a higher number of interactions and stronger binding to ACE2, which may contribute to its higher virulence. Furthermore, the flexibility of certain residues of the RBD was analyzed and found that the wild-type structure had significantly higher flexibility than the Omicron and XBB.1.16 variants, especially for residues 445 and 449. Finally, a mutational scan of XBB.1.16 for variants of concern such as 417, 484 and 501 was conducted. The results indicate that Y501 might remain in future variants while 417 and 484 could mutate back to the origial wildtypes variants.The findings highlight the structural differences between the analyzed variants of SARS-COV2 and their potential impact on the virus’s virulence and infectivity and give an outlook to potential mutations in the future.