Structural analysis of the SARS-CoV-2 Spike N-terminal domain across wild-type and recent variants: a comparative study

Since its first appearance in China, the molecular evolution of SARS-CoV-2 has progressed through altering the properties of the Spike protein, changing the virus ability to transmit and to evade host immune surveillance. Despite receiving less attention than the Receptor Binding Domain (RBD), the Spike N-Terminal Domain (NTD) is crucial to SARS-CoV-2 biology and pathogenesis. This study provides a comparative structural analysis of the NTD from the wild-type strain and different variants (BA.2, XBB.1, XBB.1.5, BA.2.86, JN.1, HV.1, KP.2, KP.3, and KP.3.1.1), aiming to clarify the structural impact of mutations in each variant. To assess the impact of mutations on the interaction of NTD with antibodies, we selected as a test case the neutralizing antibody 4A8, which has proven highly effective against the WT. The results obtained from molecular dynamics simulations, surface electrostatic potential analysis, and binding energy predictions show a clear trend in the evolution of the virus. The net charge of the NTD decreases as the variants progress, reaching a minimum charge of −1.84 observed for KP.3.1.1. This is in clear contrast to the RBD net charge, which follows an opposite trend toward higher positive values. Binding energy predictions show that the antibody's efficacy decreases as the virus evolves. While the WT exhibited an interaction energy of −96.28 kcal/mol with 4A8, more recent variants like KP.3 show no interaction stronger than −64.00 kcal/mol. These results reveal a clear trend of modifications aimed at favoring immune escape in the virus' evolutionary trajectory.