Modeling the Disruption of Binding of Three IgE Antibodies with Six Mutated Interaction Sites on the Arah2 Allergen

Modeling the Disruption of Binding of Three IgE Antibodies with Six Mutated Interaction Sites on the Arah2 Allergen

Alvin Sherman Library

Peanut allergy is a life-threatening food allergy that affects millions of children and adults across the world. This issue presents serious public health concerns and heavy interest from the scientific community to find viable treatments that minimize immunological side effects. To better understand and explain the peanut allergy response, the literature was examined, and a 3D model was printed based on two protein database files. Arachis hypogaea 2 (Arah2) is the dominant peanut allergen protein. When Arah2 binds IgE antibodies, a strong allergic response is triggered. This reaction makes treating allergy patients with Oral Immunotherapy (OIT) difficult due to adverse effects from allergic reactions. Existing PDBs 8G4P and 8DB4 from the literature reveal three monoclonal antibodies (mAbs) which bind the dominant IgE binding sites to elicit this inflammatory allergic reaction cascade. The structural epitopes of each of these antibodies interact with specific amino acid residues on the Arah2 allergen. In these PDBs, six mutations on the allergen, E46R, E89R, E97R, E114R, Q146A, and R147E, were targeted to generate a hexamutant Arah2 hypoallergen. These modifications demonstrated reduced IgE reactivity while maintaining the native Arah2 structure. The study concludes that allergic reactions can be reduced through rational amino acid substitutions that disrupt antibody binding. The study provides a basis for immunotherapies by using structurally similar but less reactive allergens. Here, we prepared a 3D model of the hexamutant hypoallergen using AlphaFold 3 to predict the hexamutant structure, while ensuring that the overall conformation was conserved. Using Pymol and Jmol, a 3D printed molecular model was prepared with the 8G4P and 8DB4 PDB files in order to dock three antibodies to the hexamutant structure. This 3D printed model highlights the binding of mAbs 13T1, 13T5, and 22S1 to three different sites and demonstrates why the hypoallergen mutations disrupt binding while conserving Arah2's tertiary structure. Molecular interactions are compared, including hydrogen bonds and possible ionic interactions, with specific attention to key amino acid mutations in the binding sites. Through this work, we can show that details of the molecular stories in the protein data bank can be better visualized and understood with the development and use of 3D models.