Epitope Mapping with Sidewinder: An XL-MS and Structural Modeling Approach

Area of Science:

• Immunology
• Structural Biology
• Computational Biology

Background:

• Antibodies are crucial for immune defense against bacterial pathogens.
• Understanding antibody-antigen interactions is vital for developing targeted immunotherapies.
• High-throughput computational methods are needed to map these interactions.

Purpose of the Study:

• To introduce Sidewinder, a novel computational pipeline for analyzing antibody-antigen interactions.
• To enable high-throughput mapping of antibody-antigen interfaces.
• To advance the development of targeted immunotherapies.

Main Methods:

• Integrated cross-linking mass spectrometry (XL-MS) with computational structural prediction and molecular docking.
• Developed a modular, high-throughput pipeline named Sidewinder.
• Validated the pipeline on antibodies targeting *Streptococcus pyogenes* virulence factors.

Main Results:

• Successfully identified a monoclonal antibody epitope on Streptolysin O using Sidewinder.
• Demonstrated the pipeline's utility in analyzing complex antibody-antigen systems, including antibodies against the M1 protein.
• Validated the accuracy and efficiency of the Sidewinder pipeline.

Conclusions:

• Sidewinder provides a robust and flexible framework for interrogating antibody-antigen systems.
• This pipeline can accelerate the study of complex immune interactions.
• The findings have potential implications for developing novel therapeutic strategies.