Defining neutralization and allostery by antibodies against COVID … – Nature.com

Varying binding affinities and neutralization efficacies of Spike by antibodies

We performed biophysical characterization of nine human monoclonal IgG antibodies (HuMAbs), namely LSI-CoVA-014, LSI-CoVA-015, LSI-CoVA-016, LSI-CoVA-017 which were discovered in this study, along with 4A833, 5A634, CR302235, CoVA-0236, and CoVA-3936. These monoclonal antibodies were principally discovered from convalescent patients of COVID-19 with the exception of CR3022 that was derived from a SARS-CoV-1 patient35, and 5A6 which was derived from a nave human phage-FAB library. The binding activity of each antibody to SARS-CoV-2 Spike trimer (Spike) and isolated RBD (RBD) from the Wuhan-Hu-1 strain was determined using Quartz Crystal Microbalance (QCM) and enzyme-linked immunosorbent assay (ELISA). As indicated by the half-maximal effective concentration (EC50) values, seven of the nine antibodies bound strongly to both Spike trimer and RBD (Fig.1b). Antibody LSI-CoVA-017 binds strongly to Spike but not RBD, suggestive of an epitope outside RBD. Antibody 4A8 binds weakly to Spike and showed negligible binding to RBD, consistent with previous studies that show 4A8 binds NTD33. Next, we determined the binding kinetics of these HuMAbs against Spike and observed high affinity binding with slow off-rates (Supplementary Fig.1 and Supplementary Table1). The affinity constants (KD) were in the sub-nM range, with LSI-CoVA-017 being the lowest (0.088nM). The association-dissociation kinetics clearly indicate stable binding of the HuMAbs to the Spike trimer.

We next investigated their neutralization efficacies using a pseudotyped virus neutralization test (PVNT). A neutralization capacity of >50% was considered significant in accordance with WHO standards. Correspondingly, we observed differential levels of neutralization, wherein LSI-CoVA-014, LSI-CoVA-015, LSI-CoVA-016, and CR3022 showed less than 50% efficacy. On the other hand, 4A8, LSI-CoVA-017, and CoVA2-04 showed significant neutralization capacities, while the highest neutralization was observed for CoVA2-39 and 5A6. On this basis, the antibodies were classified as (i) weak, (ii) moderate, and (iii) strong neutralizing HuMAbs (Fig.1ce).

The epitopes of the HuMAbs were mapped by comparative HDXMS analysis of complexes with Spike and RBD. We observed extensive protection against deuterium exchange across peptides spanning RBD of Spike and isolated RBD, in the presence of LSI-CoVA-014, LSI-CoVA-015, LSI-CoVA-016. This indicates binding to eitherthereceptor-binding motif (RBM) or at a site distal to RBM (Fig.2af). Overlapping peptides covering residues 361395 showed large-scale protection against deuterium exchange in both Spike (Fig.2h, i) and RBD complexes with LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016, indicating that these three antibodies bind RBD at a site distal to the RBM site. In the trimeric Spike, the region spanning residues 361395 becomes accessible only when the RBD adopts an up-position. These changes indicate that the epitope sites identified for LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016 are similar to the site observed for the CR3022 antibody (Supplementary Fig.2a), previously characterized as a cryptic site binder37. Alongside antibodies discovered in the current study, we mapped the binding interfaces of known RBD-binding IgGsCoVA2-04, CoVA2-39, and CR3022 (Supplementary Fig.2). The binding hotspots mapped using HDXMS agree with reported cryo-EM structures38. Consistent with our expectations, increased deuterium exchange was observed across the peptides spanning the RBM/ACE2 binding site upon binding of either of these three antibodies (Fig.2af and Supplementary Fig.2a). This correlates to increased conformational dynamics at the ACE2 binding site, suggesting that binding of LSI-CoVA-014, LSI-CoVA-015, or LSI-CoVA-016 locks the RBD in the up- position resulting in higher solvent exposure (Fig.2g). Also, binding of LSI-CoVA 014, 015, 016 may induce allosteric destabilization at RBM, which further needs to be probed (Fig.2g).

Difference plots showing changes in deuterium exchange (D) for a LSI-CoVA-014, b LSI-CoVA-015, and c LSI-CoVA-016 antibody complexes with isolated RBD compared to free RBD, at different labelling times as indicated. Pepsin-proteolyzed fragment peptides are represented by a dot and their residue numbers are indicated. Average values (n=3 independent experiments) and the standard deviations are plotted using Microsoft Excel. A significant value of 0.5D was considered as threshold and is indicated by red-dashed line. Epitope sites are highlighted in yellow. Differences in deuterium exchange values at 1min labeling time for d LSI-CoVA-014, e LSI-CoVA-015, and f LSI-CoVA-016 antibody complexes are mapped on to the structure of RBD shown in surface representation, as per key. g The effects of ACE2 binding to RBDWuhan are mapped and shown for reference, with the RBM-site highlighted in pink box. Comparative HDXMS analysis of Spike trimer (purified from insect cell culture) in the presence and absence of h LSI-CoVA-014 and i LSI-CoVA-015 and LSI-CoVA-016 highlighting S1 subunit (left), S2 subunit (centre), and Spike monomer (right, 11208 residues), with the other two monomers shown in grey. Peptides spanning key regions are highlighted by arrows. Epitopes on RBD (345361, 375390, 471495) are indicated in yellow. Inset highlights a close-up view of Spike trimer (cartoon representation) along the transverse axis. Differences are mapped onto all the three monomers of Spike. RBD-binding antibodies (LSI-CoVA-014, LSI-CoVA-015, and LSI-COVA-016) induce destabilizing effects at the inter-protomer contacts. Peptides spanning residues 304317, fusion peptide (FP), and heptad repeat 1 (HR1) constituting a part of intermonomer interaction interface are indicated. Source data is provided as Source data file.

Similar effects were observed across the other regions of Spike upon binding of LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016 (Supplementary Fig.2bd). Notably, peptides spanning residues 516533 showed increased deuterium exchange (Fig.2h, i, left panels), confirming that antibody-binding stabilized RBD in an up-conformation. This is accompanied by the loss of inter- and intra-monomer contacts between RBD and NTD, with residues 166182 which interact with RBD, and 289305 that connect NTD to the central Spike core showing the most significant changes (Fig.2h, i, left panels). In the presence of LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016, an overall increased deuterium exchange was observed for peptides spanning the NTD regions of the Spike trimer. Further, multiple regions of the S2 subunit including the fusion peptide (FP), heptad repeats (HR1 and HR2) and residues 902916 also showed increased deuterium exchange in the presence of these three HuMAbs (Fig.2h, i, centre panels and Supplementary Fig.3ac), except the S1/S2 cleavage site which was associated with a decreased deuterium exchange. These sites are essential for intermonomer interactions (Fig.2h, i, right panels). Taken together, the conformational changes observed at the NTD and the S2 subunit suggest antibody-binding at RBD induces allosteric changes across the Spike trimer, resulting in its global destabilization that may lead to dissociation of adjacent monomers.

These observations were further supported by the HDX changes at the paratope sites of LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016 (Supplementary Figs.3d, e and4). Peptides spanning CDRL1-3 and CDRH1-3 showed greater differences in deuterium exchange in the RBD-bound complex, as compared to Spike-bound antibody complexes (Supplementary Table2). The epitope sites are not hidden in the isolated RBD construct but are readily accessible to stably bind the paratope sites. On the other hand, in the Spike trimer, the RBDs must move from a down- to an up- position, and antibody binding is further hindered spatially by the NTD and the S2 subunit, leading to less stable antibody binding.

We next investigated the effects of LSI-CoVA-017, which shows moderate neutralization. In the LSI-CoVA-017-bound state, protection against deuterium exchange was observed across the Spike trimer, with only a few peptides showing deprotection (Fig.3a and Supplementary Fig.5a). Upon closer examination, peptides spanning residues 92110, 136143 (N3 loop), and 243265 (N5 loop) showed large-scale decreases in deuterium exchange in the LSI-CoVA-017-bound state (Fig.3a). These peptides are positioned towards the outer edge of NTD, and are likely the epitope sites bound by LSI-CoVA-017. This region also corresponds to the NTD antigenic supersite20,39. Reduction in deuterium exchange at short labeling times was observed across residues 3648, 166182, and 303318, while increased deuterium exchange was observed for residues 6083, 107117, 213228, and 266276. These differences, mapped onto the structure of NTD (Fig.3a, right panels), revealed that peptides encompassing the epitope site are clustered closely to form a structural epitope and facilitate complexation of Spike with LSI-CoVA-017. These peptides also showed a reduction in deuterium exchange in our comparative HDX analysis of free Spike and its complex with 4A8, which has been previously characterized as an NTD-binding antibody40 (Fig.3b and Supplementary Fig.5b). Thus, our binding assays and HDX data identify LSI-CoVA-017 as an NTD-binding antibody, with both LSI-CoVA-017 and 4A8 being moderate neutralizers.

Difference plots for NTD showing changes in deuterium exchange for a LSI-CoVA-017 and b 4A8 antibody complexes with Spike (purified from insect cell culture) compared to apo Spike, at different labelling times as indicated. Pepsin-proteolyzed fragment peptides spanning NTD of the Spike are represented by a dot and their residue numbers are indicated on the x axis. Average values (n=3 independent experiments each for two biological replicates) and the standard deviations (error bars) are plotted using Microsoft Excel. A significant value of 0.5D was considered as threshold and is indicated by red-dashed line. Epitope sites are highlighted in yellow. Right panels: Differences at 1min labeling time mapped on to NTD of Spike is shown in cartoon representation. Comparative HDXMS analysis of Spike trimer in the presence and absence of c LSI-CoVA-017 and d 4A8 mapped onto the S1 subunit (left) and trimeric Spike protein (right), as indicated. Peptides spanning key regions are highlighted by arrows with epitopes on NTD (92110, 136143, 243265) indicated by yellow ellipse. Inset highlights a close-up view of Spike trimer along the transverse axis. Differences are mapped onto all the three monomers of Spike. NTD-binding LSI-CoVA-017 reduce overall conformational dynamics (shades of blue). Peptides spanning residues 304317, fusion peptide (FP), and heptad repeat 1 (HR1) constituting a part of intermonomer interaction interface are indicated. Source data is provided as Source data file.

Large-magnitude decreases in deuterium exchange were observed across all peptides (including residues 320-350, 516533) spanning the RBD of Spike bound to LSI-CoVA-017 (Supplementary Fig.5a and Supplementary Table2). This indicates significantly reduced conformational dynamics across RBD, suggesting restricted domain motions in the LSI-CoVA-017-bound state. HDXMS analysis of LSI-CoVA-017 and 4A8 with isolated RBD, revealed no significant changes in deuteration levels of RBD (Supplementary Fig.5a). Hence, it is clear that the antibodies binding at NTD induce distinct conformational changes across RBD and the S2 subunit compared to RBD-binding antibodies. Decreased deuterium exchange was observed for peptides spanning the S2 subunit of the Spike-LSI-CoVA-017 complex (Fig.3c, d and Supplementary Fig.5b). Upon LSI-CoVA-017 binding, notable changes in conformational dynamics were observed at the S1/S2 cleavage site, FP, central helix, and HR (Fig.3c, inset). While both LSI-CoVA-017 and 4A8 binding resulted in similar effects on the Spike trimer, the changes induced by 4A8 HuMAb were less prominent. Overall, these HDXMS results reveal that LSI-CoVA-017 binding at NTD induces global stabilization of the Spike trimer.

HDXMS analysis of the LSI-CoVA-017 antibody showed significant changes across both heavy and light chains in the presence of Spike (Supplementary Fig.5c and Supplementary Table2). Peptides overlapping CDRH2 (residues 4870), CDRH3 (96103), and CDRL2 (4871) showed protection against deuterium exchange, while CDRL3 (101129) showed increased deuterium exchange. Interestingly, similar changes were observed for 4A8 complexed to Spike. No significant changes were observed for the light chain of 4A8 with or without Spike, consistent with available high-resolution structures33.

The commonalities in effects of 4A8 and LSI-CoVA-017 upon Spike suggest similar modes of neutralization, as reflected in their neutralization capacities. However, our biophysical data showed LSI-CoVA-017 binds Spike trimer with an affinity much greater than 4A8 (Fig.1b). To rationalize this, we determined the stoichiometry of the Spike-LSI-CoVA-017 complex by size-exclusion chromatography (Supplementary Fig.6 and Supplementary Table3). Three chromatographic peaks were detected and analyzed by denaturing polyacrylamide electrophoresis. Densitometry analysis of different amounts of peak B suggested a binding stoichiometry of three LSI-CoVA-017 antibodies per Spike trimer. With a 1:3 Spike:IgG stoichiometry, two models are plausible where: (i) Fab arms from three LSI-CoVA-017 antibodies bind to three monomers of a single Spike trimer; or (ii) two Fab arms of the same LSI-CoVA-017 bind monomers of two different Spike trimers. This is similar to the model predicted for the Spike:4A8 complex33. We further probed this computationally, as discussed below.

Multiple studies have reported high-resolution structures of HuMAbs bound to RBM, including CoVA2-04, 5A6, and CoVA2-39, showing direct competition with ACE2 binding38. However, given that these HuMAbs display varying neutralization potencies in inhibiting viral entry while binding to overlapping epitopes, a mechanistic explanation for their contrasting behavior remains elusive, particularly for CoVA2-04, a moderate neutralizer, as opposed to 5A6 and CoVA2-39 that are strong neutralizers. We therefore monitored the binding of CoVA2-04, 5A6, and CoVA2-39 to the Spike trimer and observed a distinct impact on its conformational dynamics (Fig.4 and Supplementary Fig.7). A large-magnitude decrease in deuterium exchange was observed across RBD, particularly the peptide clusters spanning RBM (485-502) of Spike complexes with 5A6, CoVA2-04 and CoVA2-39 (Fig.4d, e and Supplementary Fig.7a). Interestingly, HDXMS analysis of CoVA2-04 and CoVA2-39 complexes with the isolated RBD construct showed lower deuterium exchange across RBM, and only minor changes at other regions (Fig.4a). These results indicate that binding of HuMAbs at RBM induces localized changes that lead to a significant reduction in the structural dynamics of RBD, including the peptides spanning the base and linker regions that connect RBD to the Spike trimer. Notably, the Spike variants contain mutations at different sites including E484K, N501Y- or K417N/E484K/N501 that are localized at RBM, and are reported to reduce the neutralization efficacy of antibodies1,26,41.

Difference plots showing changes in deuterium exchange for a CoVA2-39 and b CoVA2-04 antibody complexes with isolated RBD, and c 5A6 antibody with RBD of Spike compared to apo RBD, at 1- and 10-min labelling times. Pepsin-proteolyzed fragment peptides spanning NTD of the Spike are represented by a dot and their residue numbers are indicated. Average values (n=3 independent experiments each for two biological replicates) and their standard deviations (error bars) are plotted using Microsoft Excel. A significant value of 0.5D was considered as threshold and is indicated by red-dashed line. Epitope sites are highlighted in yellow. (right panels) Differences at 1min labeling time mapped on to NTD of Spike is shown. Comparative HDXMS analysis of Spike trimer (purified from insect cell culture) in the presence and absence of d CoVA2-39 and e 5A6 mapped onto the S1 subunit (left), and Spike monomer (right), as indicated. Peptides spanning RBM epitope site are highlighted in yellow. Inset highlights a close-up view of Spike trimer along the transverse axis. Differences are mapped onto all the three monomers of Spike. Peptides spanning residues 304317, fusion peptide (FP), and heptad repeat 1 (HR1) constituting a part of intermonomer interaction interface are indicated. Source data is provided as Source data file.

Binding of CoVA2-04, 5A6, and CoVA2-39 to Spike resulted in increased deuterium exchange across peptide clusters covering residues 3142, 92110, 177191, 265276 of NTD (Fig.4d, e and Supplementary Fig.7a). Some of these peptides span the interface interacting with the RBD and the C-terminal region of NTD. As binding of these HuMAbs leads to RBD domain movement, it induces NTD movement as well, disrupting their interaction. Significant protection against deuterium exchange was observed at the S1/S2 cleavage site (residues 672695), regions flanking the FP (residues 770782, 878898), HR1 (residues 927962), central helix (10031031), and 11031117 of the S2 subunit (Fig.4d, e, right panels, Supplementary Fig.7b). These sites are essential for the Spike trimer to transition from its pre-fusion state to post-fusion state. Decreased deuterium exchange across the S2 subunit suggests that binding of these strong neutralizing HuMAbs leads to global reduction in the conformational dynamics of the Spike trimer, which may prevent the transition to the fusogenic intermediate. Collectively, the HDXMS results provide detailed insights into the mechanism of action of CoVA2-04, 5A6, and CoVA2-39, wherein they compete with ACE2 binding and induce stabilization throughout the Spike trimer to restrict its mobility.

Next, we performed molecular docking to model the Fab domains of LSI-CoVA-014, LSI-CoVA-015, LSI-CoVA-016, and LSI-CoVA-017 at their respective epitope sites of the Spike protein (RBD or NTD) using HDXMS footprints as restraints (Fig.5 and Supplementary Table4), followed by atomic-resolution MD simulations. Out of 100 Fab:RBD/NTD complexes generated, five top-scoring binding poses were selected for 200ns simulations (Fig.5ad). Among the simulated models of Fab:RBD/NTD complexes, multiple models were observed to either displace from the epitope site (Model 3, RBD-LSI-CoVA-014) or completely detach from RBD (Model 4, RBD-LSI-CoVA-014 and Model 3 of RBD-LSI-CoVA-016), and were not considered for further analysis(Supplemenary Fig. 8a). To select the best models from the stable complexes with each antibody, we next calculated the root mean square deviation (RMSD) of backbone atoms of the Fab domain (Supplementary Fig.8b) and the model with the lowest RMSD was selected for additional replicate simulations to improve the conformational sampling (Supplementary Table4 and Supplementary Fig.9). A stable Fab binding orientation from the most populated cluster was identified via cluster analysis, of each Fab:RBD/NTD complex (Supplementary Fig.9a) and the cluster analysis identified 34, 79, 52 and 65 clusters sampled for LSI-CoVA-014, LSI-CoVA-015, LSI-CoVA-016 and LSI-CoVA-017, respectively (Fig.5eh and Supplementary Fig.9). Further, contact frequencies were calculated between the glycan moieties and Fab from RBD/NTD simulations of the top 5 docking poses and triplicate MD trajectories of selected poses, revealing that N-glycans interact with residues across Fab arms of LSI-CoVA-014, LSI-CoVA-015, LSI-CoVA-016 and LSI-CoVA-017 (Fig.5il, Supplementary Fig.8b, and Supplementary Fig.9c). Interestingly, the glycan moieties at N343 of RBD and N74, N122 and N149 on NTD were observed to interact with the Fab (Fig.5c). For the residues interacting with the N-glycans at N331 and N343, contact frequency maps showed the highest number and magnitude of contact frequencies made by LSI-CoVA-014 Fab, as compared to those by LSI-CoVA-015 and LSI-CoVA-016 (Supplementary Fig.8b and Supplementary Fig.9c). Similarly, simulation trajectories of the NTD-LSI-CoVA-017 complex showed prominent interactions between the N74, N122 and N149 N-glycans and the Fab (Supplementary Fig.8b and Supplementary Fig.9c). The contact frequencies measured for the NTD-LSI-CoVA-017 Fab complex indicated stable interactions with a larger surface compared to any of the RBD-Fab complexes, suggesting a potential role for glycans in forming the antibody epitope.

Surface representation of central structures of the five most populated clusters from a RBD-LSI-CoVA-014, b RBD-LSI-CoVA-015, c RBD-LSI-CoVA-016, and d NTD-LSI-CoVA-017 complexes. RBD and NTD are in gray, with LSI-CoVA-014 (brown), LSI-CoVA-015 (green), LSI-CoVA-016 (orange), and LSI-CoVA-017 (yellow). Representative structures from the most populated cluster from MD simulation trajectories are depicted in two orientations for RBD (grey) complexes with Fab of e LSI-CoVA-014 (brown), f LSI-CoVA-015 (green), g LSI-CoVA-016 (orange); and NTD (grey) in complex with h LSI-CoVA-017 (yellow). Glycans are shown in ball-and-stick representation. il Maximum contact frequencies between glycan moieties and Fab from simulations of top five RBD/NTD:Fab docking poses are mapped onto the structure of each Fab. Plots showing the binding of varying concentrations of m LSI-CoVA-014, n LSI-CoVA-015, o LSI-CoVA-016, and p LSI-CoVA-017 antibodies with Spike (red circles) and deglycosylated Spike (blue squares) as determined by ELISA. Data is represented as mean SEM (n=3 independent experiments). Source data is provided as Source data file.

To verify this, we tested the binding of four novel HuMAbs (LSI-CoVA) with a deglycosylated Spike trimer. Binding of LSI-CoVA-017 was completely abolished with deglycosylated Spike, in contrast to the minor changes observed for LSI-CoVA-014, LSI-CoVA-015 and LSI-CoVA-016 (Fig.5mp and Supplementary Fig.10). Furthermore, significant reduction in binding kinetics of these four HuMAbs with deglycosylated Spike was observed, as compared to the glycosylated Spike trimer (Supplementary Fig.10b). To further validate the significance of glycosylation to RBD-binding HuMAbs, we tested 5A6 as a control, which showed a partial reduction. Collectively, these results demonstrate that the LSI-CoVA-017 epitope encompasses glycan moieties on the Spike protein surface. For other antibodies (LSI-CoVA-014/LSI-CoVA-015/LSI-CoVA-016/5A6) the primary binding sites were non-glycosylated epitopes, as identified by HDXMS, with only secondary interactions contributed by glycans. These results provide a view contrary to the prevailing notion that glycans only act as a shield for Spike protein to hide epitope sites from host immune recognition42,43 and suggest that non-specific interactions of glycans with the antibodies can play a substantial role in stabilizing Fab arm binding at the epitope site.

A competitive ELISA was performed to evaluate the extent of epitope site overlap among antibodies (Fig.6ad) and also to characterize the cooperative binding to Spike monomers in the trimeric Spike. This allowed us to distinguish the mechanisms of binding and neutralization of RBD-specific antibodies that share the same or highly overlapping epitopes, yet have different affinities and neutralization activities. Competitive binding ELISA results indicated similar OD450 values between LSI-CoVA-015 and LSI-CoVA-016 as detection or capture antibodies, suggesting a significant overlap in their binding orientation, which is in-line with our HDXMS-guided docking and MD simulations (Fig.6ej). On the other hand, LSI-CoVA-014 did not prevent binding of LSI-CoVA-015 or LSI-CoVA-016. Our simulation cluster analysisof trajectories showed that LSI-CoVA-014 bound to Spike in a different orientation than LSI-CoVA-015 or LSI-CoVA-016, and thus could, in principle, pair with either LSI-CoVA-015 or LSI-CoVA-016 (Fig.6eh). Competitive assays between RBD- and NTD- recognizing antibodies showed that the binding sites for these two antibody classes do not overlap with each other, as observed for LSI-CoVA-014 and LSI-CoVA-017 with LSI-CoVA-015/LSI-CoVA-016 antibodies (Fig.6ac).

Plots showing capture ELISA for pairs of selected antibodies. 0.1g SpikeWuhan (hexapro (purified from mammalian cell culture) was captured by a LSI-CoVA-014, LSI-CoVA-015, LSI-CoVA-016 and CR3022, b LSI-CoVA-017 and 4A8, and c 5A6, CoVA2-04 and CoVA2-39, detected using peroxidase-labelled monoclonal antibodies. A low OD450 value is indicative of impaired binding of the peroxidase-labelled detection antibody, as listed. Data (n=3 independent experiments) and represented as meanSEM. d Neutralization of pseudo SARS-CoV-2 virus using antibody cocktail (described in methods). Pair-mAb cocktail in the ratio of 1:9 to a final total concentration of 10g/ml or the single huMAb at a concentration of 10g/ml were incubated with pseudovirus lentiviral construct expressing the SARS-CoV-2 Spike protein. The chemiluminescence readout from the luciferase-tagged reporter in the lentiviral construct, is plotted and represented as percentage neutralization. The plots and one-way ANOVA statistical analysis were done using GraphPad prism 9.0. P values determined were 0.0026 (LSI-CoVA-017 vs LSI-CoVA-017+CoVA2-04) and 0.0339 (CoVA2-04 vs LSI-CoVA-017+CoVA2-04) using 6 degrees of freedom, as indicated in the figure. Different antibodies are indicated by alternative colors. Data is reported as meanSEM (n=3 independent experiments). Lateral (upper panel) and top (lower panel) views of surface representations showing Fab arms of e LSI-CoVA-014 (brown), f LSI-CoVA-015 (green), g LSI-CoVA-016 (orange), and h LSI-CoVA-017 (yellow) aligned onto a Spike trimer (grey, PDB 7A98). Representative structures from most populated cluster of Fab:RBD and Fab:NTD cluster analysis were used respectively. Predicted models showing two Spike trimers (grey and blue) bound to both Fab arms of i LSI-CoVA-014 (brown) and j LSI-CoVA-017 (yellow). Source data is provided as Source data file.

To infer stoichiometry and plausible mechanisms of neutralization, we then modelled the binding of full-length IgGs to Spike using a representative structure of Fab:RBD/NTD from the cluster analysis described above (Fig.6eh). Modelled full-length antibodies showed that RBD-binding antibodies specifically bind to RBD in the up-position. Models of LSI-CoVA-015 and LSI-CoVA-016 complexes with the Spike trimer indicate that IgG binding to a single RBD of a Spike monomer sterically hinders the binding of a second IgG to the same Spike trimer. In the case of LSI-CoVA-014 and LSI-CoVA-017, the predicted orientation allows the respective full-length antibody to bind all three RBDs or NTDs of the same Spike protein trimer. These results are consistent with our competitive ELISA and neutralization assays. Additionally, the second Fab arm of LSI-CoVA-017 and LSI-CoVA-014 can bind to a second Spike protein trimer, cross-linking two Spike trimers (Fig.6i, j and Supplementary Fig.6). Taken together, the Spike-IgG complex models suggest that the novel antibodies characterized in this study indirectly interfere with ACE2 binding by either cross-linking Spike trimers on the viral surface (LSI-CoVA-014 and LSI-CoVA-017), or by blocking RBD-ACE2 interaction on a single Spike trimer (LSI-CoVA-015 and LSI-CoVA-016).

The four novel antibodies isolated here from convalescent patients showed suboptimal levels of neutralisation efficacy compared to RBM binding antibodies. However, considering the mutually exclusive epitope sites complemented by high affinity binding to Spike protein, it would be of interest to investigate their use in antibody cocktails. We explored the possibility to induce destabilisation in individual monomers or stabilization to reduce the hinge dynamics between the region connecting S1 and S2 subunits in order to effectively neutralise the SARS-CoV-2. Synergistic effects of selected HuMAbs used in this study were thus evaluated. The selected HuMAbs were used in a pairwise cocktail to study the potential synergistic enhancement of neutralization efficacy, amongst which the paired Mab cocktail of LSI-CoVA-017 and CoVA2-04 displayed a significantly higher percentage neutralization in comparison to the treatment of either of the single HuMAbs (Fig.6d). We did not observe any enhancement in the neutralization efficacies of the two potent HuMAbs (CoVA2-39, 5A6) with NTD-binding LSI-CoVA-017. This could possiblybe due to the limitation of the method and warrants alternative method for quantification purposes. Surprisingly, a combination of NTD- (LSI-CoVA-017) with RBD- (LSI-CoVA-014) antibodies resulted in lower neutralization, than when added alone.

Emergence of new variants as a result of mutations of the Spike protein, have led to many antibody-mediated therapies faltering. Therefore, we assessed the impact of defined variant-linked mutations on binding and neutralization of the novel antibodies characterized in this study with isolated RBD and Spike proteins of the two former variants Delta () and Omicron (o1 for BA.1 and o2 for BA.2 lineages). LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016 bind to Spike and isolated RBD of all strains tested, although the binding activities to Omicron variants were slightly lower (Fig.7), akin to CR3022 (Fig.7). Binding of these antibodies was preserved as the mutations among the variants are distant from the cryptic epitopes site. Interestingly, 4A8 bound to Spike of all strains tested, although the binding activity was drastically reduced among all variants compared to Wuhan-Hu-1 Spike. On the other hand, the other NTD-binding antibody LSI-CoVA-017 bound only to SpikeWuhan. This lack of binding of LSI-CoVA-017 and 4A8 to Spike or Spikeo is due to the deletions and mutations spanning the NTD antigenic supersite. Most importantly, 5A6, CoVA2-04, and CoVA2-39 which strongly bind and neutralize SpikeWuhan, bound only to Spike and RBD, but not the Omicron variants (Fig.7a, open symbol plots). We also observed that upon deglycosylation, the binding activity of LSI-CoVA-017 and 4A8 was lost for all Spike variants, while minimal reduction was detected for anti-RBD antibodies against the Spike variants (Supplementary Fig.10).

a Antibody binding activity to Delta and Omicron variants of Spike compared with Wuhan-Hu-1 strain (HexaPro, purified from mammalian cell culture). Antibodies at concentrations from 10pg/mL10g/mL were tested for binding to SARS-CoV-2 Spike and MBP-RBD by ELISA, shown with their EC50 values indicated. Data was collected (n=3 independent experiments) and represented as meanerror bars (SEM). Heat map of differences in deuterium exchange for bd LSI-CoVA-014 and eg LSI-CoVA-016 antibody complexes with isolated RBD variants (b, e) RBD (PDB: 7W98), c, f RBDo1 (PDB: 7WPA), and d, g RBDo2 (PDB: 7WPA) as compared to apo states. Cryptic epitope sites are highlighted in yellow. Source data is provided as Source data file.

Many studies have reported higher binding affinities of Spike variants with the ACE2 receptor44,45. We therefore set out to probe if any of the nine HuMAbs competed with ACE2 binding to Spike variants. We performed ACE2-binding inhibition assays and observed a lack of any inhibitory activity by the cryptic site binders or the NTD-binding antibodies (Fig.8a). Interestingly, LSI-CoVA-015 and LSI-CoVA-016 seemed to enhance ACE2 interaction with RBDo1, as indicated by the negative inhibition (Fig.8a, green arrows). These antibodies bind at the cryptic site, and maintain RBD in an up-position, making the RBM site accessible, which may lead to increased ACE2 binding. This is similar to the effects of antibodies (e.g., S309) recognizing epitopes outside the RBM locus, and show some efficacy against the Omicron variant46,47. Also, 5A6, CoVA2-04, and CoVA2-39 inhibited interactions between ACE2 and Spike Wuhan/Delta strains, but this was not the case for in Spikeo1 or RBDo1 (Fig.8a, bottom panels). For ACE2 inhibition assays, neutralizers that bind RBD often exhibit >40% inhibition. Therefore, the binding and ACE2-inhibition results suggest that only the cryptic-site binding antibodies retain binding to Spike and Spikeo2, and hence only their interactions were further explored.

a ACE2-binding inhibition assays for the nine antibodies at varying concentrations for Spike (purified from mammalian cell culture) and RBD constructs of Wuhan-Hu-1(HexaPro), Delta () and Omicron (o1, o2) variants. Negative values indicate enhanced ACE2 binding (green arrows), while positive values indicate inhibition of ACE2 binding by the antibody (Source data 8). Data was collected (n=3 independent experiments) and represented as meanerror bars (SEM). b Differences in HDX in the presence and absence of ACE2 for isolated RBD constructs of (left) Delta (PDB: 7W98), (centre) Omicron BA.1 (PDB: 7WPA), and (right) Omicron BA.2 (PDB: 7WPA) variants are mapped on to high-resolution structure of RBD, shown in cartoon. Shades of blue correspond to decreased deuterium exchange upon binding to ACE2. c Heat map of differences in deuterium exchange of (left) Spike Delta (PDB: 7W98) and (right) Spike Omicron BA.2 (PDB: 7WPA) in the presence and absence of ACE2 (yellow, cartoon) at 1min labeling time is shown. d, e Plots comparing differences in deuterium exchange (D) in the presence and absence of ACE2 for various peptides across the S1 subunit of Spike variants d Delta and e Omicron BA.2. Various labelling timepoints are indicated with peptide numbers are indicated in accompanying Source data. Data was collected (n=3 independent experiments) and represented as meanerror bars (standard deviation). Peptides covering NTD and RBD are grouped as per domain organization shown. ACE2-binding sites on RBM are highlighted in yellow. Source data is provided as Source data file.

We examined the effects of ACE2 binding on the conformational dynamics of the isolated RBD and trimeric Spike variants by HDXMS, and compared this with ACE2-binding footprints previously reported5,44,48. Binding of ACE2 elicited large-scale protection against deuterium uptake across all regions of isolated RBD, RBDo1 and RBDo2 (Fig.8b). This altered conformational dynamics of RBD variants upon ACE2 binding is reflective of their higher binding affinities44,48. Despite this, mutations of key residues of RBM disrupted specific contacts between the RBD and ACE2, as reflected by available cryo-electron microscopy structures45, and structural dynamics studies49. Upon closer examination of the HDX results, the ACE2 binding footprints were smaller for variants of RBD, as compared to RBDWuhan. Peptides spanning the mutation sites of the loop region (475-495) showed a lower degree of deuterium exchange, while residues 445-455 and 493-510 showed greater protection (Fig.8b and Supplementary Fig.11 ac). We further determined the effects of ACE2 bindingusing trimeric Spike and Spikeo2 (Fig.8c, d and Supplementary Fig.11d, e). Binding of ACE2 elicited conformational changes across RBD of Spike (Fig.8c, left, 8d) akin to those of isolated RBD (Fig.8b, left, 8d), as well as RBD of SpikeWuhan. Surprisingly, we observed marked differences between the ACE2-bound states of RBDo2 and Spikeo2 (Fig.8c, right, 8e). While domain-wide decreased deuterium exchange was observed for the RBDo2-ACE2 complex (Fig.8b, right and Supplementary Fig.11c), for RBD of the Spikeo2-ACE2 complex decreased deuterium exchange was observed only at residues 390417 and 450467 (Fig.8e), and at 1min labeling time for residues 488507, as observed in high-resolution structures. Peptides spanning residues 373384, 429446, and 468483 showed significantly increased deuterium exchange at all labeling time points, and residues 488507 showed increased deuterium exchange at longer labeling times. Peptides showing deprotection overlapped the RBD-specific mutation sites observed for the Omicron variant, while increased protection against HDX was observed for Wuhan-Hu-1and Delta variants (Fig.8c and Supplementary Fig.11d, e). These results describe the molecular mechanism of ACE2-binding by the Omicron variant, whereby the specific amino acid residues promote receptor-binding by maintaining the essential conformational dynamics, yet evade immune responses. Furthermore, these HDX findings also explain how ACE2 binding enhances the conformational sampling of variants, as observed by their high flexibility and fuzzy densities in cryo-EM maps44,45 as well as the comparative structural dynamics of Spike variants containing the D614G mutation.

Using HDXMS, we also mapped and characterized the interactions of LSI-CoVA-014, LSI-CoVA-015, LSI-CoVA-016 antibodies with Delta and Omicron variants. Firstly, we characterized the interactions of the cryptic site binding antibodies LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016 with isolated RBD constructs of Delta (Supplementary Fig.12), Omicron BA.1 (Supplementary Fig.13), and Omicron BA.2 (Supplementary Fig.14) variants. Consistent with our expectations, the most notable differences in deuterium exchange were observed for peptides covering the cryptic site, with LSI-CoVA-014, showing lower deuterium exchange values, compared to the LSI-CoVA-015 and LSI-CoVA-016 antibodies. These varying deuterium exchange values are reflective of the differences in conformations of RBD induced by variant-specific mutations. Further, we observed enhanced conformational dynamics for peptides spanning the ACE2-binding sites of the Delta and Omicron variants.

Next, we monitored the effects of these three antibodies binding to Spike and Spikeo2 variants, which showed similar deuterium exchange profiles across the S1 (Fig.9) and the S2 (Supplementary Fig.15) subunits. Peptides flanking the mutated sites of NTD showed no significant change in deuteration as compared to SpikeWuhan, which exhibited lower deuterium exchange upon binding to these three antibodies (Fig.2). Importantly, the linker regions of NTD and RBD showed large-scale protection against deuterium exchange, due to reduced conformational flexibility, indicating that their domain motions were severely restricted. Specifically, peptides spanning residues 365390 of RBD showed protection from deuterium exchange in the antibody-bound states of Spike (Fig.9a, b) and Spikeo2 (Fig.9c, d), indicating that these three HuMabs bind at the same epitopes, akin to SpikeWuhan. Upon closer examination, the magnitude of HDX changes across SpikeWuhan, Spike and Spikeo2 were different, owing to the differences in their binding affinities (Fig.9ad and Supplementary Fig.15). Overall LSI-CoVA-015 and LSI-CoVA-016 (Fig.9e, f, right panels) showed similar deuterium exchange values for peptides spanning the S1 subunit of Omicron Spike and were different compared to changes observed upon binding of LSI-CoVA-014 to Omicron Spike (Fig.9e, f, left panels). Furthermore, HDX kinetics observed across the epitope sites of individual RBD variants (RBD, RBDo1, and RBDo2) in the presence of LSI-CoVA-015, LSI-CoVA-016, and LSI-CoVA-014, were stronger than their corresponding Spike trimers. This indicates that variant-specific mutations on Spike induce subtle changes in the conformational dynamics, which alter the binding strengths of antibodies even though the epitope sites are conserved. This is further supported by the varying HDX effects observed across peptides spanning RBM in antibody-bound Spike and Spikeo2 (Fig.9). This effect was more prominent for RBD, RBDo1 and RBDo2, where binding of LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016 antibodies led to significant protection against deuterium exchange at the ACE2-binding sites (Fig.9d). Our results show destabilization of the RBD of Spike and Spikeo2upon antibody binding and explain why the up-position of RBD is favored in the variants50.

Plots comparing differences in deuterium exchange across the S1 subunit of a, b Spikeo2 and c, d Spike complexed to a, c LSI-CoVA-014 and b, d LSI-CoVA-016 versus the apo states are shown at various labelling times. Residue numbers for the peptides are labeled on x axis of the bottom plots of a, b Spikeo2 and c, d Spike, with domain organization shown. Average (n=3 independent experiments) values with standard deviations (error bars) were used to generate the plots (Microsoft Excel). Yellow zones highlight the peptides spanning the cryptic epitope site, as observed for SpikeWuhan. LSI-CoVA-016 showed larger decreases in deuterium exchange to the two variants. Differences in HDX of Spike variantse Delta and f Omicron BA.2 in the presence and absence of (left) LSI-CoVA-014 and (right) LSI-CoVA-016 antibody are mapped onto a monomer of delta Spike (PDB: 7W98) and Omicron Spike (PDB: 7WPA), shown in surface representation. The insets show a transverse view of the conformational changes across the trimer. Source data is provided as Source data file.

Within the S2 subunit of Spike, the LSI-CoVA-014/015/016 deuterium exchange profiles (Fig.9e, Supplementary Fig.15b) were similar to that of SpikeWuhan, but were significantly different from Spikeo2 (Fig.9f and Supplementary Fig.15a). Peptides spanning the S1/S2 cleavage site showed minor differences in deuterium exchange and were lower than those observed for SpikeWuhan. The reduced deuterium exchange indicates that the S1/S2 cleavage site is more concealed in Spike and Spikeo2, and is further occluded by antibody binding. These results also help to explain the reduced propensity for cleavage of variants and the inaccessibility to host proteases observed for the Omicron variant29,51. The most notable changes in conformation upon antibody binding were observed across peptide clusters spanning FP1, FP2 and HR1 (Supplementary Fig.15). Large-magnitude increases in deuterium exchange were observed across these sites for Spike and Spikeo2, as compared to the effects observed for SpikeWuhan. Higher deuterium uptake correlates with increased dynamics and/or solvent accessibility across regions which span peptide clusters including residues 539565 (subdomain 1), 757779, and 936974 (Fig.9e, f right panels,). Increased deuterium exchange at these sites reflects greater solvent accessibility accompanied by the loss of intermonomer contacts. This translates to a long-range effect induced effect by LSI-CoVA-014, LSI-CoVA-015, and LSI-CoVA-016 across the Spike and Spikeo2 trimers. Overall, these antibodies likely cause destabilization of the Spike trimers into antibody-bound monomers. This destabilization ofthe trimer, likely into individual monomers also reflects the altered interaction of ACE2 with Spikeo2 by LSI-CoVA-015/016, accompanied by weak neutralization efficacy.

Our binding assays indicated that 5A6, CoVA2-39, and CoVA2-04 bound to the Delta variant, but not the Omicron variant (Fig.7a). We then compared the effects of binding of 5A6 and CoVA2-04 to Spike and RBD, using HDXMS. Upon binding of these HuMAbs, significant protection against deuterium exchange was observed across the RBDs, both in isolated constructs (Supplementary Fig.16a) and in Spike (Supplementary Fig.16b, c). While the HDX changes observed across the RBM-sites of SpikeWuhan were about ~4Da, the average changes observed for the Delta variant were lower in magnitude (~2.5Da) with a relatively smaller antibody-binding footprint. As the Delta variant has two key mutations at the RBM-site26, the antibody footprint at the epitope site is reduced, affecting the overall conformational dynamics of the RBDs of Spike. Although 5A6, CoVA2-39 and CoVA2-04 directly compete with ACE2 binding, various studies have reported that both CoVA2-39 and CoVA2-04 are unable to neutralize Delta or Omicron variants52,53.

We further determined the effects of 5A6 (Supplementary Fig.16b) and CoVA2-04 on the S2 subunit of Spike. No significant change was observed for peptides covering the S1/S2 cleavage site. Decreased deuterium exchange was observed for peptides spanning FP2, HR1, connector domain (CD) and HR2. Importantly, peptides spanning the central helix (residues 9901010), showed increased deuterium exchange in the presence of these two antibodies, suggesting higher localized conformational dynamics. This is in contrast to the effects observed for SpikeWuhan (Fig.4). While the sites essential for trimerization of Spike showed increased conformational rigidity induced by 5A6 and CoVA2-04 HuMAbs, increased conformational mobility was observed across the central helix. Collectively, the binding assays and HDX results indicate that the HuMAbs recognizing the RBM antigenic supersite cannot bind Omicron at all, and bind Spike variant with reduced affinity, by allosterically reducing the conformational dynamics of the S1 and the S2 subunit, thereby mediating overall stabilization.

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