In Silico Analysis of SARS-CoV-2 Envelope Protein-IgM Antibody Complex

Abstract

The SARS-CoV-2 envelope protein (protein E) is a small but multifunctional structural protein that plays a critical role in viral assembly, budding, and pathogenesis, making it an attractive target for therapeutic intervention. This study investigated the interaction between the SARS-CoV-2 envelope protein (wild type and T9I mutant) and Immunoglobulin M (IgM) antibody through a molecular docking approach. The IgM antibody structure was retrieved from the Protein Data Bank (PDB) with the code 1IGM, while the envelope protein structures were modeled using I-TASSER based on available sequence data. Molecular docking of the antigen-antibody complexes was performed using ClusPro 2.0 with Antibody Mode activated. The docking results demonstrated favorable antigen-antibody interactions, visualized by LigPlot+ software. Binding energy analysis using the PRODIGY program revealed ΔG values of -9.0 kcal/mol (wild type) and -7.4 kcal/mol (T9I mutant), with corresponding Kd values of 2.6×10⁻⁷ M and 3.5×10⁻⁶ M, respectively. The wild type complex exhibited a stronger binding affinity compared to the T9I mutant. Persistent hydrogen bonding interactions observed at the binding interface further support the stability of the envelope protein-IgM complex. These results indicate that the wild type envelope protein exhibits strong and favorable binding to IgM antibody, underscoring its potential as a basis for COVID-19 therapeutic antibody development.