Molecular Dynamics Simulations on Spike Protein Mutants Binding with Human β Defensin Type 2.

Area of Science:

• Immunology
• Virology
• Computational Biology

Background:

• Human beta defensin 2 (hBD-2) is an innate immune peptide that inhibits SARS-CoV-2 by binding the Spike-RBD.
• Understanding how SARS-CoV-2 mutations affect hBD-2 binding is crucial for developing effective antiviral strategies.

Purpose of the Study:

• To investigate the impact of key SARS-CoV-2 Spike-RBD mutations on the binding and interaction with hBD-2.
• To assess the stability and binding affinity of hBD-2 with various RBD mutants.

Main Methods:

• All-atom molecular dynamics simulations were performed on hBD-2 complexed with wild-type and mutant RBDs (N501Y, E484K, P479S, T478I, S477N, N439K, K417N, and a triple mutant).
• Structure and dynamics analysis, including hydrogen bonding and buried surface area (BSA) calculations, were conducted.
• Free energy perturbation (FEP) and MM-GBSA methods were used to calculate binding free energy and interaction energies.

Main Results:

• Most RBD mutants exhibited similar hydrogen bonding, BSA, and binding interfaces with hBD-2 compared to the wild-type.
• The RBD triple mutant (N501Y-E484K-K417N) showed reduced binding stability with hBD-2.
• FEP analysis indicated that N439K, K417N, and the triple mutation increased binding free energy, suggesting less stable binding, while E484K decreased it, indicating more stable binding.

Conclusions:

• hBD-2 maintains binding with most individual SARS-CoV-2 RBD mutations, but the triple mutant exhibits significantly reduced binding stability.
• Specific mutations like E484K enhance hBD-2 binding stability, while others like N439K and K417N decrease it.
• These findings provide insights into hBD-2's mechanism against SARS-CoV-2 variants and potential implications for viral escape.