Unraveling the Tomaralimab Epitope on the Toll-like Receptor 2 via Molecular Dynamics and Deep Learning

[Image: see text] Tomaralimab (OPN-305) is the first humanized immunoglobulin G4 monoclonal antibody against TLR2 and is designed to prevent inflammation that is driven by inappropriate or excessive activation of innate immune pathways. Here, we constructed a homology model of Tomaralimab and its complex with TLR2 at different mapped epitopes and unraveled their behavior at the atomistic level. Furthermore, we predicted a novel epitope (leucine-rich region 9–12) near the lipopeptide-binding site that can be targeted and studied for the utility of therapeutic antibodies. A geometric deep learning algorithm was used to envisage Tomaralimab binding affinity changes upon mutation. There was a significant difference in binding affinity for Tomaralimab following epitope-mutated alanine substitutions of Val266, Pro294, Arg295, Asn319, Pro326, and His372. Using deep learning-based ΔΔG prediction, we computationally contrasted human TLR2–TLR2, TLR2–TLR1, and TLR2–TLR6 dimerization. These results reveal the mechanism that underlies Tomaralimab binding to TLR2 and should help to design structure-based mimics or bispecific antibodies that can be used to inhibit both lipopeptide-binding and TLR2 dimerization.