Structural Basis of Pan-Ebolavirus Neutralization by a Human Antibody against a Conserved, yet Cryptic Epitope

Abstract

Only one naturally occurring human antibody has been described thus far that is capable of potently neutralizing all five ebolaviruses. Here we present two crystal structures of this rare, pan-ebolavirus neutralizing human antibody in complex with Ebola virus and Bundibugyo virus glycoproteins (GPs), respectively. The structures delineate the key protein and glycan contacts for binding that are conserved across the ebolaviruses, explain the antibody's unique broad specificity and neutralization activity, and reveal the likely mechanism behind a known escape mutation in the fusion loop region of GP2. We found that the epitope of this antibody, ADI-15878, extends along the hydrophobic paddle of the fusion loop and then dips down into a highly conserved pocket beneath the N-terminal tail of GP2, a mode of recognition unlike any other antibody elicited against Ebola virus, and likely critical for its broad activity. The fold of Bundibugyo virus glycoprotein, not previously visualized, is similar to the fold of Ebola virus GP, and ADI-15878 binds to each virus's GP with a similar strategy and angle of attack. These findings will be useful in deployment of this antibody as a broad-spectrum therapeutic and in the design of immunogens that elicit the desired broadly neutralizing immune response against all members of the ebolavirus genus and filovirus family.IMPORTANCE There are five different members of the Ebolavirus genus. Provision of vaccines and treatments able to protect against any of the five ebolaviruses is an important goal of public health. Antibodies are a desired result of vaccines and can be delivered directly as therapeutics. Most antibodies, however, are effective against only one or two, not all, of these pathogens. Only one human antibody has been thus far described to neutralize all five ebolaviruses, antibody ADI-15878. Here we describe the molecular structure of ADI-15878 bound to the relevant target proteins of Ebola virus and Bundibugyo virus. We explain how it achieves its rare breadth of activity and propose strategies to design improved vaccines capable of eliciting more antibodies like ADI-15878.

Keywords: Bundibugyo virus; Ebola virus; antibody; broadly neutralizing; glycoprotein; pan-ebolavirus; structure.

FIG 1

GP organization and ADI-15878 complexes. (A) Schematic comparing full-length GP and cleaved EBOV GP (GP_CL), and crystal structure of the ADI-15878–EBOV GP_CL complex. Components are indicated by different colors. GP_CL is gray. The ADI-15878 light chain is light blue, and the heavy chain is dark blue. Top and side views are shown. One monomer is shown in a ribbon format, and the other two are shown as molecular surfaces. The buried surface contributed by each CDR is indicated in the table to the right. IFL, internal fusion loop; HR1, heptad repeat 1. (B) Schematic of BDBV GP and GP_CL and the ADI-15878–BDBV GP_CL crystal structure. BDBV GP_CL is shown in orange, with GP1 dark orange and GP2 light orange. The ADI-15878 light chain is light blue, and the heavy chain is dark blue. The values for CDR buried surface area in the table differ significantly between EBOV and BDBV especially within CDRs H3 and L2 and framework region L3. This difference is due to the lack of density for the GP2 glycan at position N563 in the lower-resolution ADI-15878–BDBV GP complex structure compared to the ADI-15878–EBOV GP structure. CDR H3 makes extensive contacts with this glycan, and glycan contacts account for all of the interactions between GP and CDR L2 as well as framework region L3.

FIG 2

Comparison of the footprint of broadly neutralizing ADI-15878 with monospecific antibodies. In sequence alignments, footprint residues are highlighted, residues that are not identical, but similar across the ebolaviruses are indicated by light gray arrowheads, and residues that differ significantly across the ebolaviruses are indicated by blue arrowheads. (A) Footprint of ADI-15878 (light blue) on GP (white). ADI-15878 recognizes only 100% conserved or highly similar residues among the ebolaviruses. (B) The footprint of MAb100 (orange), like that of ADI-15878, is also a quaternary epitope; however, MAb100 binds to the top of the nonconserved GP2 N-terminal tail. (C) Footprint of the SUDV-specific MAb 16F6 (green) in complex with SUDV GP (white). (D) Footprint of EBOV-specific MAb KZ52 (pink), which binds the GP2 N-terminal peptide and the base of the GP complex.

FIG 3

Position of the GP2 N-terminal peptide and Marburg virus-specific wing relative to the ADI-15878 footprint. (A) ADI-15878-bound EBOV GP, in which the N-terminal GP2 tail (pink) is lifted from the GP core and disordered (broken line). The footprint of antibody ADI-15878 is indicated by the light blue line. GP1 is shown in gray, and GP2 is white. (B) In EBOV GP without bound receptor or antibody (26) (pictured; PDB 5JQ3) and all other EBOV GP-antibody complexes, the N-term GP2 tail is visible (pink) and tethered along the GP core, occupying the lower portion of the ADI-15878 footprint (blue). The GP glycan cap and HR2 are not shown for simplicity. (C) In Marburg virus (MARV) GP (PDB 6BP2), a MARV-specific wing domain (also pink) hugs the GP core, also in the space that would be occupied by the ADI-15878 footprint, with GP2 N-terminal tail (pink broken line) extending outward and disordered. MARV GP1 is dark green, and GP2 is light green. (D) ADI-15878 residues L53 of CDR H2 and W99 of CDR H3 bind the GP core in a site previously occupied by the lifted GP2 N-terminal peptide (pink). The bound ADI-15878 heavy chain is dark blue and the light chain is light blue. The glycan attached to N563 is shown as sticks. (E) The standard position of the GP2 N-terminal peptide lining the outside of the GP core. GP2 I504 occupies the position of ADI-15878’s L53. (F) The extensive MARV wing domain wraps about the outside of the MARV GP core in the site that would be occupied by ADI-15878. The glycan equivalent to that of EBOV N563 (MARV N564) is illustrated in green stick representation.

FIG 4

The internal fusion loop of GP2 shifts inward when bound by ADI-15878. (A) EBOV GP1 and GP2 are dark and light gray, respectively, with visible glycans illustrated in ball and stick. The fusion loop is illustrated in the standard conformation (yellow) and ADI-15878-bound conformation (white). (B) The shift in position, particularly at G528, is noted when looked at from the top of the spike down (a 90° rotation about the x axis) in the zoomed-in view of the internal fusion loop. (C) Interaction of ADI-15878 with the fusion loop I527 (yellow dotted line) in the standard conformation of the fusion loop sterically interferes with the bound conformation of the ADI-15878 light chain. In the ADI-15878-bound conformation (white), the fusion loop is adjusted so that I527 is accommodated between light chains (LC) (light blue) and heavy chains (HC) (dark blue). (D) Electrostatic surface of ADI-15878 with a limit of 10 k_bTe_c⁻¹ (k_b is Boltzmann’s constant, T is temperature, and e_c is the charge of an electron) indicated in blue and red, respectively. The position of G528 is noted. Escape mutation G528E may introduce an unfavorable charge clash with the somewhat acidic outer surface of the antibody. The basic charge in the nearby pit is buried.

FIG 5

Continuum of antibody epitopes at the GP “waist.” Sites A to D are shown. (A) The approximate locations of the various epitopes are shown mapped along the surface of GP in a side view. (B) A top-down view of the GP trimer highlights the repeating nature of these epitopes around the circumference of GP.