Differential conformational selections of three therapeutic antibodies binding to polymorphic Aβ oligomers

Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of amyloid-β (Aβ) aggregates, which play a central role in disease pathogenesis according to the amyloid cascade hypothesis. While soluble Aβ oligomers and protofibrils have been identified as the most neurotoxic species, their structural heterogeneity has posed significant challenges for therapeutic development. Current antibody therapies targeting Aβ show differential clinical efficacy, but the molecular basis for their selective recognition of various Aβ polymorphs remains unclear. This critical knowledge gap stems from the lack of experimental structures of antibody-oligomer complexes, which hinders rational drug design. In this study, we thoroughly simulated possible interactions between Aβ oligomer and three antibodies recently approved for targeting Aβ as AD therapy. Our results reveal fundamental differences in their recognition mechanisms. Aducanumab shows polymorph-dependent binding, targeting N-terminal epitopes in full-length Aβ but maintaining non-specific contacts to cross-β structures. Lecanemab uniquely engages multiple N-termini simultaneously through an extended flat-binding interface. Donanemab employs a conserved CDRL1-dominated mode to recognize F4-H13 aggregates, with the pE3 modification acting as a structural anchor that reinforces binding stability. These structural insights provide a molecular basis for observed clinical outcomes and establish design principles for improved therapeutics targeting specific pathological aggregates.