Bapineuzumab captures the N-terminus of the Alzheimer's disease amyloid-beta peptide in a helical conformation

Bapineuzumab is a humanized antibody developed by Pfizer and Johnson & Johnson targeting the amyloid (Aβ) plaques that underlie Alzheimer's disease neuropathology. Here we report the crystal structure of a Fab-Aβ peptide complex that reveals Bapineuzumab surprisingly captures Aβ in a monomeric helical conformation at the N-terminus. Microscale thermophoresis suggests that the Fab binds soluble Aβ(1–40) with a K_D of 89 (±9) nM. The structure explains the antibody's exquisite selectivity for particular Aβ species and why it cannot recognize N-terminally modified or truncated Aβ peptides.

Structure of the humanized 3D6 Fab-Aβ peptide complex.

Both panels show Aβ nestled in the surface of the Fab CDRs. The peptide is shown in green sticks with the light chain in light blue surface and heavy chain in a darker blue surface. (a) A 2F_o - F_c electron density map in the vicinity of the peptide contoured at 1.5σ. (b) Intra-Aβ hydrogen bonding, shown as dashed lines, stabilizes the helical conformation of the peptide.

Different conformations of the Aβ peptide.
(a) The helical conformational epitope of Aβ recognized by Bapineuzumab highlighted in green ribbon. (b) Superposition of the main-chain heavy atoms of TFE-stabilized Aβ (residues 1 to 6) NMR structures (9) (in purple) with those of Aβ as recognized by Bapineuzumab (in green). (c), (d) Superposition over light chain of Fab-Aβ complexes with murine antibody Fabs in (c) WO2-Aβ is in orange ribbon, PFA1-Aβ in yellow and (d) Bapineuzumab related Fab in grey with Aβ in green sticks.




Aβ-Fab interactions.

The Aβ residues are shown as green sticks. Amino acid sequences corresponding to the CDRs of Bapineuzumab are shown in light blue and darker blue for light and heavy chains respectively. Amino acids involved in Fab binding to Aβ are underlined and italicized in the CDR sequences common to 3D6 antibodies including Bapineuzumab. Direct polar contacts between the Fab and Aβ are shown graphically as red dashed lines. Waters involved in the hydrogen bonding network are shown as aquamarine spheres, and their putative hydrogen bonds are shown as aquamarine dashed lines. Fab residue labels and carbon atoms are colored by chain (shades of blue), whereas nitrogen, oxygen and sulfur atoms are shown in dark blue, red and yellow respectively. Surfaces represent non-polar contacts to Fab residues. Intra-chain contacts have been omitted for clarity. Figure produced using LigPlus