Structural insights into the mechanism of malaria-protective antibodies from the IGHV3-49/IGKV2D-29 lineage

Malaria remains a global health concern and continues to be endemic in many tropical regions, particularly in Southeast Asia and sub-Saharan Africa. Effective vaccines and monoclonal antibody (mAb) therapies are urgently needed, especially for people living in endemic areas. Structural studies using X-ray crystallography and cryo-electron microscopy have revealed the molecular interactions of antigen-binding fragments (Fabs) from protective mAbs targeting Plasmodium falciparum circumsporozoite protein (PfCSP) of the liver stage sporozoites. Notably, several mAbs including 850, 1210, 399, and 311 form inter-Fab homotypic contacts upon binding the central NANP repeat region of PfCSP and demonstrate potent neutralizing activity. Among these, mAb 399, derived from the IGHV3-49/IGKV2D-29 germline, engages in head-to-head inter-Fab contacts upon CSP binding. In this study, we determined high-resolution X-ray crystal structures of additional Fabs, 7160 and 7118, both originating from the same IGHV3-49/IGKV2D-29 germline lineage, in complex with PfCSP-derived peptides. Both antibodies showed strong inhibitory activity, reducing liver-stage sporozoite burden by 90–95% in a murine challenge model, and exhibited high-affinity binding to the CSP repeat region. Strikingly, Fab 7160 formed inter-Fab homotypic interactions upon binding to an extended repeat peptide (NANP6), similar to the binding mode observed with Fab 399. In contrast, Fab 7118 did not engage in such contacts. Structural analysis suggests that variations in the complementarity-determining region (CDRH3), particularly in Fab 7118 which features a longer loop may introduce steric hindrance and electrostatic repulsion, thereby preventing homotypic Fab-Fab interactions that have been found to be beneficial in mouse models of protection for other antibodies.