Immunoglobulins G (IgG) are the most abundant class of antibodies in the human body and play a central role in the humoral immune response. In medicine, they are used as therapeutic agents for the treatment of cancer, autoimmune, infectious, and other diseases. Their Fc region, composed of the CH2 and CH3 domains, mediates effector functions and is responsible for binding effector receptors and complement molecules. At the same time, this region serves as a binding site for bacterial Ig-binding proteins, staphylococcal Protein A (SpA) and streptococcal Protein G, which are traditionally used in affinity chromatography for the purification and isolation of antibodies. Due to the risk of ligand leaching, its immunogenicity, and the high production costs of protein-based affinity ligands, shorter and more stable peptide ligands have been developed as an alternative. These include the peptide min19Fc (GSYWYQVWF) and its derivatives, which were obtained using phage display technology. Since an in-depth understanding of the basis of their binding to the Fc region of IgG requires insight at the atomic level, molecular modelling methods are increasingly used. These include protein structure prediction with artificial intelligence (AI) models (e.g., AlphaFold), molecular docking, and molecular dynamics (MD) simulations. These methods provide insight into binding interactions at a level that is difficult to achieve with experimental methods alone. In this master's thesis, we used molecular modelling approaches to investigate the binding of the peptide min19Fc and its derivatives to human IgG subclasses (IgG1–IgG4). The binding site and binding conformations of the peptides were predicted using co-folding in AlphaFold3 and AlphaFold2-Multimer v3, molecular docking using the Peptide Docking workflow in Maestro, and further evaluated through MD simulations in Desmond. The results were compared with prior experimental data and with experimentally determined structures of related Fc-region ligands. Based on the results obtained using the AI models, we showed that the peptides bind at the hinge between the CH2 and CH3 domains of the Fc fragment, where their binding site partially overlaps with that of SpA. Through molecular docking and MD, we determined the key interactions and the minimal binding motif. Substitution analysis showed that the V7F substitution increases binding affinity but reduces binding specificity, while the negative control with the W4F substitution confirms the importance of the aromatic YWY motif. The peptide min19Fc exhibits the highest affinity for IgG1, followed by IgG3, IgG2, and IgG4, which is consistent with experimental data. These findings provide a starting point for the further rational development of affinity peptide ligands with improved affinity and selectivity.
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