Assessing Computational Strategies for the Evaluation of Antibody Binding Affinities

Accurate evaluation of binding affinity is critical in drug discovery to identify molecules that bind strongly to their targets while minimizing off-target effects. Although binding affinity calculations are theoretically well defined, they require exhaustive sampling of configurational space, a step that often requires significant computational resources. In this study, we compare different methods for calculating the binding energy of antibodies targeting a peptide derived from the N-terminus of CXCR2, a GPCR-family protein. Contrary to some previous reports, we find that equilibrium molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations yield better agreement with experimental binding affinities than nonequilibrium potential of mean force evaluations, underscoring the system-dependent performance of these methods. We also observed a modest improvement in accuracy when MMPBSA is combined with replica exchange molecular dynamics, albeit at a significantly higher computational cost. Calculation based on the Rosetta force field, instead, produced results that did not correlate with the experimental data. We attribute these findings to two factors, which could limit the applicability of some methodologies that are widely used in computing the binding energy: the high potency of the antibodies studied and the dominance of hydrophobic interactions between the antibodies and the peptide. Overall, this work provides important insights for optimizing in silico antibody screening strategies.