Affinity enhancement of an anti-VEGF humanized nanobody as a superior candidate to bevacizumab: integrative in silico and in vitro studies

BACKGROUND: Although nanobodies have superior characteristics to conventional antibodies, their affinities are often lower because of a single interaction site for antigen binding. Therefore, in the current study, a bioinformatics approach was employed to enhance the affinity of a humanized anti-VEGF nanobody even that of the commercially available antibody, bevacizumab. METHODS: The in vitro safe dose and the affinity of the wild and mutated nanobodies were determined and compared to bevacizumab. The best mutated nanobodies (MHNb136 and MHNb256) were selected by implementing umbrella sampling simulation to improve the binding affinity of the wild-type nanobody (WHNb) to VEGF. In vitro safety investigations were performed on nanobodies with doses of 12.5, 25, 50, and 100 µg, equivalent to the dose of bevacizumab as the conventional treatment. RESULTS: Ultimately, umbrella sampling results showed that MHNb136 and MHNb256 bind to VEGF more strongly, with ΔG values of -39.3 and -32.64 kcal/mol, respectively, than WHNb, which has a ΔG value of -19.05 kcal/mol. BIACORE assay results indicated that MHNb136 and MHNb256 bind to VEGF with higher affinity than bevacizumab as a reference. CONCLUSION: Eventually, MHNb136 and MHNb256 can be subjected for further clinical investigation due to the superiority to bevacizumab.