Investigating and evaluating potential antigen binding sites for monoclonal anti-HER2 antibodies: The LightDock approach.

Monoclonal antibodies targeting HER2, a receptor overexpressed in certain cancer cells, have greatly improved the treatment of HER2-positive cancers. In addition, anti-HER2 antibodies play a critical role in diagnostic applications, enabling accurate detection of HER2 expression levels. Advancing antibody-based therapies and diagnostic tools require a thorough understanding of binding interactions, but it remains challenging due to complex antibody protein structure and its flexibility, particularly within their complementarity-determining regions. In this study we utilized LightDock, a molecular docking tool simulating protein-protein interactions which can incorporate flexibility that allows the in silico analysis of flexible proteins like antibody. Using LightDock we investigated interaction sites between the recently developed by our group anti-HER2 antibodies and their specific antigen HER2 protein. Despite the high variability in the obtained results, a statistics-based approach identified two recurring HER2 regions as potential binding sites and functionally relevant areas in receptor biology. This variability in predicted docking interfaces reflects the inherent complexity of antibody-antigen interactions. This structure based docking approach provides a cost-effective method to analyze antibody-protein interactions and offers preliminary insight into possible epitopes targeted by the novel anti-HER2 antibodies. However, our data indicates that at this time point further validation using experimental techniques will be beneficial to refine and increase the accuracy of the results obtained in silico. This report highlights the value of the computational docking in antibody-protein interaction studies, demonstrating significant potential with present and upcoming advancements in computer-based approaches.