Antibody Treatment of Ebola and Sudan Virus Infection via a Uniquely Exposed Epitope within the Glycoprotein Receptor-Binding Site

Abstract

Previous efforts to identify cross-neutralizing antibodies to the receptor-binding site (RBS) of ebolavirus glycoproteins have been unsuccessful, largely because the RBS is occluded on the viral surface. We report a monoclonal antibody (FVM04) that targets a uniquely exposed epitope within the RBS; cross-neutralizes Ebola (EBOV), Sudan (SUDV), and, to a lesser extent, Bundibugyo viruses; and shows protection against EBOV and SUDV in mice and guinea pigs. The antibody cocktail ZMapp™ is remarkably effective against EBOV (Zaire) but does not cross-neutralize other ebolaviruses. By replacing one of the ZMapp™ components with FVM04, we retained the anti-EBOV efficacy while extending the breadth of protection to SUDV, thereby generating a cross-protective antibody cocktail. In addition, we report several mutations at the base of the ebolavirus glycoprotein that enhance the binding of FVM04 and other cross-reactive antibodies. These findings have important implications for pan-ebolavirus vaccine development and defining broadly protective antibody cocktails.

Graphical abstract

Figure 1

Identification of Critical Residues for FVM04 Binding (A) A shotgun mutagenesis mutation library was constructed for EBOV GP protein, where each of the 641 amino acids were individually mutated to alanine. Human HEK293T cells expressing the mutation library were tested for reactivity to mAbs using an Intellicyt flow cytometer. A typical reactivity pattern (red wells) is shown for a representative assay plate. Eight positive (wild-type EBOV GP) and eight negative (mock-transfected) control wells were included on each plate. (B) The library was tested for reactivity with FVM04. Clones with <30% binding relative to that of wild-type (WT) EBOV GP yet >65% reactivity for a control mAb were initially identified to be critical for FVM04 binding. (C) Mutation of three individual residues reduced FVM04 binding (red bars) but had little effect on the binding of FVM02 and FVM09 (gray bars; Keck et al., 2015). Bars represent the mean and range ([max−min]/2) of at least two replicate data points. (D) The FVM04 binding residues are shown in red in the crystal structure of EBOV GP. The glycan cap is shown in cyan, and the attachment points for N-linked glycans in orange. The GP1 core is shown in purple, and parts of GP2 are seen in yellow. The RBS crest is shown in red outline and the occluded trough region is shown in black outline. (E) Sequence homology between filoviruses within the RBS crest region containing putative FVM04 epitope. Identical sequences among ebolavirus species and between ebolavirus and marburgvirus are shown in red. The FVM04 binding site is boxed. (F–H) The EBOV GP monomer is depicted as a cartoon overlay with GP_CL (F), SUDV GP (G), and MARV RAVN GP (H). Putative critical EBOV contacts made by FVM04 are shown as sticks (red) overlaid with corresponding contact residues from the overlay structure (green).

Figure 2

Mutations in the GP Base Affect the Exposure of the FVM04 Epitope (A) Crystal structure of the trimeric EBOV GP complexed with KZ52 (PDB: 3CSY). The specific domains are color coded as indicated in the figure. (B and C) Relative binding of individual point mutants of mature EBOV GP to the base binder KZ52 (B) or FVM04 (C) compared to binding to wild-type (WT) GP set at 100%. Individual mutants are color coded in (B) and (C) based on the positioning of each residue in various structural domains according to the key shown in (B). See also Table S1 and Figures S1 and S2.

Figure 3

Single-Particle Negative-Stain EM Analysis of FVM04 Fab Bound to EBOV GPΔMuc (A) Reference-free 2D class averages of the complex illustrate that only a single FVM04 Fab binds to the GP trimer near the glycan cap at the trimer apex. Scale bar represents 100 Å. (B) Two exemplar class averages have been colored to highlight FVM04 (blue) and the GP trimer (green). (C) Example class average of the glycan-cap-binding antibody c13C6 (orange) (Murin et al., 2014) that also binds at the GP trimer (green) apex. Relative to c13C6, FVM04 binds closer to the trimer 3-fold axis and is bent inward. See also Figures S3 and S4.

Figure 4

Neutralization of Filoviruses and Inhibition of EBOV GP/NPC-1 Interaction by FVM04 (A) FVM04 was preincubated at different concentrations with VSV-EBOV GP-Luc or VSV-SUDV GP-Luc and added to Vero cells in 96-well plates. Luciferase activity was measured after 48 hr and percent neutralization was calculated in comparison with untreated virus. (B) Neutralization assay was performed as in (A) using purified FVM04 Fab fragment. (C) Neutralization of rVSV-GFP expressing full-length GP of EBOV, SUDV, or TAFV, or GPΔMuc of BDBV. (D) Plaque reduction neutralization of wild-type EBOV, SUDV, BDBV, or MARV by FVM04. (E) Neutralization of VSV-EBOVGP_CL and VSV-SUDVGP_CL by FVM04. (F) VSV-EBOVGP_CL was immobilized on streptavidin-coated plates and incubated with Flag-NPC1 in the presence or absence of various concentrations of FVM04. Bound NPC1 was detected using anti-Flag antibody-HRP conjugate. The relative binding of NPC1 was calculated in the presence of inhibiting antibody in comparison to the no-antibody control and plotted as percent binding. Error bars represent SEM.

Figure 5

Kinetic Analysis of FVM04 Binding to GP (A–C) The sensograms show the association and dissociation of EBOV (A), SUDV (B), or BDBV (C) GPΔTM binding to FVM04 immobilized on protein G sensors. Binding to EBOV GPΔTM and SUDV GPΔTM fit to a 1:1 binding model, whereas BDBV GPΔTM fit to a 2:1 binding model. Analyzed concentration ranges are indicated (colored), and the fits are shown as red dashes. On-rate, off-rate, and K_D values for each of the three proteins are shown below the sensograms.

Figure 6

Post-exposure Efficacy of FVM04 in a Mouse Model of EBOV and SUDV Infection (A and B) Groups of ten BALB/c mice were infected intraperitoneally with 100 PFU of MA-EBOV and treated intraperitoneally with the doses and at time points indicated in the figure or left untreated. (C) Three groups of IFNαβR^−/− mice were infected with 1,000 PFU of SUDV; one group (n = 7) received two i.p. injections of 16F6 at 1 and 3 dpi, a second group received FVM04 once at 1 dpi, and a third group was left untreated. Mice were monitored for 21 days for survival, weight change, and signs of disease.

Figure 7

Efficacy of FVM04 Treatment and an FVM04-Containing Cocktail in Guinea Pig Models of SUDV and EBOV Infection (A and B) Efficacy of a single i.p. dose of 5 mg per animal FVM04 (∼15 mg/kg) injected at 1 dpi compared to control group receiving DPBS in animals challenged with GPA-SUDV (A) or GPA-EBOV (B), with six animals per group. (C) Groups of six guinea pigs were challenged with GPA-SUDV and treated with either DPBS; 5 mg per animal of FVM04; or 1.6 mg per animal each of FVM04, c2G4, and c13C6 at 3 dpi. (D) Guinea pigs (six animals per group) were infected with GPA-EBOV and treated with 1.6 mg per animal each of FVM04, c2G4, and c13C6 at 3 dpi. (E) Compiled data of three experiments with ZMapp™. Guinea pigs were infected with GPA-EBOV and treated with DPBS (n = 19) or 5 mg per animal of ZMapp™ (n = 20) at 3 dpi. Challenge was performed with 1,000 × LD₅₀ of GPA-SUDV or GPA-EBOV as indicated. Survival was monitored for 21 dpi, and weights were monitored for 16 days dpi.