Structural diversity in malaria vaccine candidates CSP and MSP2

Polymorphism in the Plasmodium?falciparum antigens circumsporozoite protein (CSP) and merozoite-surface protein 2 (MSP2) limit the valence and strain-transcendency of current malaria vaccines. We sought to define the structural and antigenic landscape of field variants and to identify attributes relevant for multivalent vaccine design and for potential host-pathogen interplay with neuro-amyloid disorders. Seventy-two CSP and 71 MSP2 open-reading frames, sequenced from clinical P. falciparum isolates collected between 1994 and?2016, were trimmed of signal peptide and GPI anchor and modelled with AlphaFold?2. Variant backbones were structurally clustered with FoldMason; linear-epitope repertoires were derived from exhaustive in silico 13-mer digestions. Antibody complexes and MSP2 oligomers were predicted with AlphaFold?3. Thioflavin-T kinetics and electron microscopy assessed intrinsic fibrillation and the influence of malaria-exposed plasma on Aß42 aggregation. Both antigens were intrinsically disordered except for a conserved CSP thrombospondin type I repeat and an amyloid-like domain present in 10?(14·0?%) MSP2 variants. Structural clustering separated CSP into six and MSP2 into nine backbone families; epitope-count matrices defined comparable numbers of antigenic “families”. The prophylactic antibody CIS43 was predicted to bind 55?(76·4?%) of CSP variants and two non-human Laverania orthologues, but not alleles carrying a 19-residue N-terminal insertion. MSP2 amyloid-like domains did not accelerate self-aggregation, yet malaria-exposed plasma increased Aß42 fibrillation in vitro. Deep-learning structure prediction plus high-throughput epitope mapping resolves the diversity of disordered malaria antigens, pinpoints variants for inclusion, or exclusion, in multivalent vaccines, and reveals a plausible molecular intersection between malaria immunity and amyloid biology that requires further epidemiological investigation