Free energy perturbation approach for the rational engineering of the antibody for human hepatitis B virus

HzKR127 is the humanized monoclonal antibody effective for the neutralization of human hepatitis B virus. By means of the free energy perturbation (FEP) calculations based on molecular dynamic (MD) simulations, we examine the mutation-induced variations in the energetic and structural features associated with the interactions between HzKR127 and its antigen. N58A, Y96A, D97A, and D97A/Y102A mutants of HzKR127 are taken in account in this study for which the experimental data for relative efficacies with respect to the wild-type antibody are available. The results of the present MD–FEP simulation studies show that in order to enhance the affinity for the antigen, the engineering of HzKR127 should be made in such a way as to promote the dynamic stability of the overall protein conformation and that of the translational motion of the antigen in the antibody–antigen complex. The relative binding free energies of the four mutant antibodies obtained from MD–FEP calculations compare pretty well with the experimental mutagenesis data with the associated squared correlation coefficient of 0.96. This indicates that MD–FEP calculations may serve as a useful computational tool for rational antibody engineering. Discussed in detail are the differences in the structural features of antibody–antigen interactions between the wild-type and the mutant antibodies that are responsible for the change in binding affinities for the antigen.

Free energy perturbation calculations may elucidate the mutational effect on the changes in the binding mode and the binding free energy associated with the antibody–antigen interaction.Figure optionsDownload high-quality image (114 K)Download as PowerPoint slideResearch highlights▶ Free energy perturbation (FEP) calculations are performed on antibody-antigen complexes. ▶ Mutational effects on the binding affinity for antigen can be explained. ▶ Various affinity-enhancing factors are found in these calculations. ▶ FEP calculations can be very useful for antibody engineering.