Comparative nanomechanical analysis of antibodies and nanobodies against SARS-CoV-2 variants

Abstract

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is the main target of neutralizing antibodies (Abs) and nanobodies (Nbs). Although their binding affinities are well characterized, their mechanical stability under force remains poorly understood, despite its relevance in viral attachment, immune recognition, and receptor engagement. Here, we present a comparative nanomechanical analysis of three Abs (PDI-231, S2X259, and R1-32) and three Nbs (R14, C1, and n3113.1) bound to the RBD from the WT and Omicron variants BA.4 and JN.1. Using steered molecular dynamics within the Martini 3 coarse-grained framework, we identified distinct mechanical signatures determined by epitope topology, binding architecture, and variant-specific mutations. Ab/RBD complexes display asymmetric rupture events in which the heavy chain serves as the main pathway for force transmission, while the light chain provides secondary reinforcement. The cooperative action of both chains enhances mechanical resilience, supporting rupture forces near 500 pN. In contrast, Nb/RBD complexes exhibit rigid-body dissociation with direct force transmission through compact single-domain scaffolds and minimal structural deformation. Variant-dependent unfolding of RBD regions, particularly residues 438–507 and 516–529, appears as a recurrent fracture motif contributing to adaptive mechanical response. These results establish mechanical stability as a key descriptor of immune complex robustness, complementing thermodynamic affinity. By linking architecture, epitope geometry, and force propagation, this study provides a quantitative framework for designing antibodies and nanobodies with improved mechanical resilience against viral evolution