Antibodies are increasingly attractive biological drugs, and at present are at the forefront of vaccine and therapeutic developments against COVID-19, a pandemic that has caused over 2.9 million deaths as of April 2021. The majority of an antibody’s high affinity and specificity is dictated via six hypervariable loops at the antigen binding site, known as Complementarity Determining Regions (CDRs). These make antibody binding difficult to predict and understand at the atomic level. So far, computational antibody design attempts have developed binders of therapeutic affinity, but often require human intervention to filter out false positives. A possible reason for human involvement is a limited understanding on the nature of antibody-antigen interactions, and consequently the use of methods that may not account for all features affecting affinity. These computational methods include scoring designs with implicit solvent, and using static crystal structures or models despite the potential for CDRs to be flexible.<br/><br/>To further our understanding on the potential role of water and CDR flexibility at these interfaces, we have carried out a long-timescale simulation study on sixteen antibody crystal structures. Using Replica Exchange with Solute Scaling and an explicit water model to explore interface conformation and hydration, we find significant numbers of bridging water molecules at the antibody-antigen interface. Additionally, a higher proportion of antibody-antigen interactions, including those mediated by water, are correlated with higher antibody affinity. While the difference in CDR flexibility between bound and unbound structures is not correlated with affinity, we find that fewer CDR conformers in the bound form is associated with enhanced binding. This observation is consistent with the fact that antibody-antigen binding is often enthalpically driven. We thus propose that interactions with waters and CDR flexibility are important in moderating antibody-antigen binding, and that explicit hydration and CDR sampling must be considered to improve antibody affinity prediction and computational design workflows.

Understanding the role of hydration and flexibility in antibody binding

ACS Fall 2021

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