Molecular dynamics simulation of engineered Fc-FcγRIIIa complexes as a framework for anticancer monoclonal antibody development
Therapeutic monoclonal antibodies exert immune-activating functions partly through the interaction between the antibody Fc region and the FcγRIIIa receptor on the effector cells. Increasing or decreasing binding affinity by engineering this interaction is a key approach taken in antibody drug development for cancer, but whether the changes in affinity are due to global transformation of protein conformation or due to localized changes only is unclear. Here, we address this using comparative 200-ns all-atom molecular dynamics simulations of three Fc-FcγRIIIa complexes: the wild type, the affinity-enhanced S239D/I332E double mutant, and the affinity-abolished V263D mutant, analyzed across seven analytical metrics. The affinity-enhanced complex remained structurally convergent, with backbone root mean square deviation stabilizing at 3.8 ± 0.3 Å, the first principal component capturing 51% of total positional variance, and a free-energy landscape confined to a single basin (~5 kJ/mol ceiling). The affinity-abolished complex showed progressive structural instability, with RMSD rising to 7.1 ± 1.2 Å in the second half of the simulation and conformational sampling dispersed across multiple free-energy basins (~7 kJ/mol ceiling). The wild type occupied a dynamically intermediate regime, with RMSD rising from 4.5 Å to 6–11 Å at approximately 95 ns. These results indicate that binding affinity is consistently associated with global conformational dynamics of the Fc-FcγRIIIa complex. Electrostatic stabilization through three salt bridges drives the enhanced mutant, while hydrophobic core disruption at Val263 drives the abolished mutant. These findings support multi-scale molecular dynamics simulation as a candidate screening approach for engineered therapeutic antibodies in cancer immunotherapy, pending validation with independent replicate simulations and variants of unknown affinity.
Petrina J, Lingayat N, Mukilan M, Krishna RA, Prabhu D. Molecular dynamics simulation of engineered Fc-FcγRIIIa complexes as a framework for anticancer monoclonal antibody development. J Appl Biol Biotech 2026. Article in Press. http://doi.org/10.7324/JABB.2026.326155
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