In a survey of novel interactions between an IgG1 antibody and different Fcγ receptors (FcγR), molecular dynamics simulations were performed of interactions of monoclonal antibody involved complexes with FcγRs. Free energy simulations were also performed of isolated wild-type and substituted Fc regions bound to FcγRs with the aim of assessing their relative binding affinities. Two different free energy calculation methods, Molecular Mechanical/Generalized Born Molecular Volume (MM/GBMV) and Bennett Acceptance Ratio (BAR), were used to evaluate the known effector substitution G236A that is known to selectively increase antibody dependent cellular phagocytosis. The obtained results for the MM/GBMV binding affinity between different FcγRs are in good agreement with previous experiments, and those obtained using the BAR method for the complete antibody and the Fc-FcγR simulations show increased affinity across all FcγRs when binding to the substituted antibody. The FcγRIIa, a key determinant of antibody agonistic efficacy, shows a 10-fold increase in binding affinity, which is also consistent with the published experimental results. Novel interactions between the Fab region of the antibody and the FcγRs were discovered with this in silico approach, and provide insights into the antibody-FcγR binding mechanism and show promise for future improvements of therapeutic antibodies for preclinical studies of biological drugs.
On the Improvement of Free-Energy Calculation from Steered Molecular Dynamics Simulations Using Adaptive Stochastic Perturbation Protocols
