IgG1 effector functions: elucidation of glycans role by in silico structural analysis

Monoclonal antibodies (mAbs) represent one of the most innovative class of biopharmaceuticals, due the ability of their Fab portion to specifically recognize unique epitopes on the target molecule. mAbs can also act as stimulators of immune and anti-inflammatory reactions, like Antibody-Dependent Cell Cytotoxicity (ADCC), Complement-Dependent Cytotoxicity (CDC) and Antibody-Dependent Cell Phagocytosis (ADCP), which are determined by the interaction between Fc portion and its receptors and may depend upon glycosylation. Assessment of Fc effector functions is therefore a critical step for pharmaceutical companies. In silico structural investigation could be a powerful tool to clarify the role of different glycan patterns in the recognition mechanism of Fc::FcRs complexes. The whole atomistic structure of mAb1 was built by chimeric homology modeling, performed by MOE 2018.01.01 (Molecular Operating Environment) suite. Then, the impact of a fucose core on a representative IgG1 structure is under investigation in three different models: glycosylated-fucosylated (G0F), glycosylated-afucosylated (G0) and aglycosylated mAb. A molecular dynamics simulation (MD) was performed on the aglycosylated mAb in an explicit solvent model with AMBER10:EHT forcefield for 100ns. Preliminary analysis of the trajectory revealed that the mAb reaches an equilibrium state after 50 ns of simulation, suggesting a good stability of the protein in our system. A second MD simulation was run in parallel on G0F chain at same conditions to validate the forcefield also for glycan calculations. All the calculations were carried on by NAMD 2.13 package handled by MOE graphical interface. Ongoing simulations of fucosylated and afucosylated models will clarify the impact of different glycosylation patterns on mAbs tertiary and quaternary structure. These data may pave the way for the understanding of molecular basis of Fc::FcgammaRs recognition and of the impact of different glycosylation patterns on this interaction.