Molecular Dynamics of the Neutralizing Potential of Dimeric IgA Antibodies against SARS-CoV-2 Antigen

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stands for being the most serious epidemic (so far) of the 21st century. However, only a few computational studies have investigated the molecular mechanisms underlying the neutralization of the spike protein by antibodies of different classes. Hence, bioinformatic methods were employed to unravel the factors contributing to the remarkable neutralization capacity exhibited by specific antibodies. Initially, crystallographic structures of IgA monomeric / dimeric, IgG, and IgM antibodies binding with the receptor-binding domain region of the SARS-CoV-2 spike protein were retrieved. Subsequently, rigid molecular docking and molecular dynamic simulations were performed over 100 ns with explicit water solvation. Lastly, an energy decomposition was conducted to estimate the binding affinity using the last frames from molecular dynamics. The results revealed a higher binding affinity for both monomeric and dimeric forms of IgA antibodies against the spike protein. Additionally, a greater number of hydrogen bonds were observed during their interaction with the spike protein, as well as greater structural instability along the time and especially a more thermodynamically favorable interaction affinity. In this way, the research contributes a small piece to the complex puzzle of understanding the humoral immune response induced by the SARS-CoV-2 virus.