Exploring the Interaction of RBD with Human β Defensin Type 2 Point Mutants: Insights from Molecular Dynamics Simulations

Abstract

The global health crisis triggered by the SARS-CoV-2 virus has highlighted the urgent need for effective treatments. As existing drugs are not specifically targeted at this virus, there is a growing interest in exploring natural antimicrobial peptides such as defensin as potential therapeutic options. Human β defensin type 2 (hBD-2), which is a cationic cysteine-rich peptide, serves as the initial barrier against bacterial and fungal invaders in mammals. It can bind with Spike-RBD and occupy the same site as the ACE2 receptor, thereby hindering viral entry into cells expressing ACE2. To explore the effect of different point mutations on the binding of hBD-2 with RBD, the binding dynamics and interactions between hBD-2 point mutants with RBD were studied and compared with that of RBD&hBD-2 wild-type complex. In total, 247 hBD-2 point mutants were built with the mutation sites at the binding region of hBD-2 (RES18-30) with the RBD of CoV-2. All-atom molecular dynamics simulations were carried out on RBD binding with hBD-2 point mutants. Analysis based on root-mean-square deviation (RMSD), hydrogen bonds analysis, and binding free energy using the MM/PBSA method revealed that many point mutants of hBD-2 exhibit weaker binding with RBD compared to the wild type; however, a subset of mutants, including C20I, C20K, R22W, R23H, R23L, Y24L, K25F, K25H, G28Y, T29R, and C30K, displayed enhanced binding with RBD. The findings can offer insights designing hBD-2-based novel drugs to combat SARS-CoV-2 in the long term.

1

Binding structure of hBD-2 (cyan) with RBD (green) used as a starting structure for the MD simulations in wild type (WT) and for spot mutants with the binding region of V18–C30 highlighted in red lines and mostly labeled.

2

Change of binding interaction energy heat map plot of 247 hBD-2 point mutants binding with RBD.

3

ΔΔG of 11 hBD-2 point mutants binding with RBD which have a binding interaction energy lower than the complex in wild type.

4

ΔG of the residues of wild-type hBD-2&RBD complex involved in interaction during the last 100 ns of the MD simulations.

5

RMSD of the backbone atoms of C20I, C20K, R22W, R23H, R23L, Y24L, K25H, K25F, G28Y, T29R, and C30K mutants of hBD-2&RBD complex. Here, WT is the abbreviation of wild type.

6

Heat map plot illustrating the average number of hydrogen bonds formed between hBD-2&RBD in wild type and the 247 point mutants over the course of the MD simulations.