SARS-CoV-2 spike mutations alter structure and energetics to modulate ACE2 binding immune evasion and viral adaptation

The persistent evolution of SARS-CoV-2 is driven by mutations in the spike protein that modulate receptor binding, immune evasion, and structural stability. In this study, we deciphered the complex host-virus protein-protein interactions using an integrated molecular dynamics (MD) approach to assess the biophysical impacts of key spike mutations, including T478K, T478A, T478E, E484K, G496S, F490S, Q493E, and Y369C. Our findings reveal that viral adaptation hinges on trade-offs between transmissibility and immune escape. For instance, T478K enhances ACE2 binding through structural rigidification and salt bridge formation (e.g., K478-D30), favoring Omicron's increased transmissibility. In contrast, T478A introduces polarity loss and interface relaxation, while T478E leads to electrostatic repulsion and weakened binding, both of which compromise interface stability. E484K balances antibody evasion (e.g., against LY-CoV555) with receptor stabilization via compensatory interactions (e.g., K484-D38). In vivo studies support these findings, showing that T478K and E484K enhance viral fitness and immune evasion in animal models. Mutations like G496S and F490S act as stealth adaptations, subtly destabilizing ACE2 or introducing metastability without fully disrupting binding. The high-risk Y369C mutation collapses the N-terminal domain supersite, enhancing immune evasion but requiring compensatory mutations (e.g., G142D) to maintain viability. Evolutionary strategies favor co-mutations (e.g., T478K + Q498R) that distribute fitness costs across residues. Notably, functionally conserved energetic hotspots such as T430, L390, V382, K386, F486, Q493 (RBD), and Q102, R192 (ACE2) consistently contributed to ACE2 engagement across all variants, representing potential targets for broad-spectrum therapeutics. Our work provides the importance of real-time surveillance for mutations that exploit conformational flexibility or compensatory networks, informing the design of durable vaccines and multi-specific antibodies. These insights bridge molecular mechanisms with evolutionary dynamics, offering a framework to anticipate and counter emerging variants.