Binding Affinity of Trastuzumab and Pertuzumab Monoclonal Antibodies to Extracellular HER2 Domain

The binding affinity of trastuzumab and pertuzumab to HER2 has been studied using both experimental and in silico methods. The experiments were conducted using the antibodies in their complete IgG form, as used in clinical therapy, and the extracellular domain of the HER2 protein in solution. This approach provides a precise, reproducible, and reliable view of the interaction between them in physicochemical conditions similar to those found in the tumoral environment. Dynamic light scattering and size exclusion chromatography coupled with tetra detection were utilized to characterize the protein complexes, measure their concentrations, and calculate the equilibrium-free binding energy, & UDelta;G(bind). In addition, PRODIGY, a QSAR-like model with excellent predictive ability, was employed to obtain in silico & UDelta;G(bind) estimations. The results obtained indicate that pertuzumab exhibits a slightly higher binding affinity to HER2 than trastuzumab. The difference in binding affinity was explained based on the contribution of the different interfacial contact (IC) descriptors to the & UDelta;G(bind) value estimated by the PRODIGY model. Furthermore, experiments revealed that the pertuzumab IgG antibody binds preferentially to two HER2 proteins, one per Fab fragment, while trastuzumab mainly forms a monovalent complex. This finding was interpreted based on a geometrical model that identified steric crowding in the trastuzumab-HER2 complex as compared with the pertuzumab-HER2 complex.

Automated summary

The binding affinity of trastuzumab and pertuzumab to HER2 was studied using experimental and computational methods. The experiments were conducted using complete IgG antibodies and the extracellular domain of HER2 in solution. The results showed that pertuzumab had slightly higher binding affinity than trastuzumab, possibly due to different interfacial contact descriptors. Furthermore, the experiments revealed that pertuzumab preferred to bind to two HER2 proteins, while trastuzumab mainly formed a monovalent complex, possibly due to steric crowding.