Application of 3D Zernike Descriptors in Antibody Structural Clustering and Repurposing

Antibodies generally exhibit high specificity for their cognate epitopes, but structural and physicochemical similarities between distinct epitopes can enable an antibody to recognize different antigens, resulting in cross-reactivity. This property can be exploited for antibody repurposing. To identify epitopes that share such similarities, both sequence- and structure-based approaches can be employed. In this context, 3D Zernike descriptors provide a compact representation of protein surface geometry as numerical feature vectors, enabling quantitative comparisons independently of structural alignment and orientation. Thus, this study aimed to evaluate the application of 3D Zernike descriptors for the structural clustering of antibodies and epitopes and to explore their use in antibody repurposing for the recognition of new targets. To this end, antibody binding sites previously associated with recognition of similar epitopes were analyzed at different structural levels, considering the CDRs, CDRH3, and complete paratopes. Surface similarity was subsequently quantified by calculating the Euclidean distance between their corresponding 3D Zernike feature vectors. Performance was benchmarked against SPACE2. Additionally, different distance thresholds were evaluated based on their ability to recover antibody pairs recognizing the same epitope. The paratope-based approach provided the best balance between the number of identified pairs and precision at a distance threshold of 2.7, whereas epitope clustering showed robust performance up to a distance of 3.0. At these thresholds, the 3D Zernike descriptors identified a greater number of functional pairs than SPACE2 while maintaining comparable precision and identifying complementary sets of antibody pairs.. BTaken together, these findings support the use of 3D Zernike descriptors for structural clustering of antibodies and epitopes and for guiding antibody repurposing G, a highly lethal zoonotic pathogen. Structural screening identified three antibodies with epitopes similar to the NiV target that also showed a consistent binding preference for the target epitope in molecular docking assays. Notably, one candidate, originally directed against a SARS-CoV-2 epitope, formed a stable complex with the NiV epitope, remaining within the 5 [A] RMSD threshold during heated molecular dynamics simulations and emerging as a potential cross-reactive candidate.These results support the use of this computational framework for biopharmaceutical discovery against emerging targets. Taken together, these findings support the use of 3D Zernike descriptors for structural clustering of antibodies and epitopes and for guiding antibody repurposing.