Developing therapeutics against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be guided by the distribution of epitopes, not only on the receptor binding domain (RBD) of the Spike (S) protein but also across the full Spike (S) protein. We isolated and characterized monoclonal antibodies (mAbs) from 10 convalescent COVID-19 patients. Three mAbs showed neutralizing activities against authentic SARS-CoV-2. One mAb, named 4A8, exhibits high neutralization potency against both authentic and pseudotyped SARS-CoV-2 but does not bind the RBD. We defined the epitope of 4A8 as the N-terminal domain (NTD) of the S protein by determining with cryo–eletron microscopy its structure in complex with the S protein to an overall resolution of 3.1 angstroms and local resolution of 3.3 angstroms for the 4A8-NTD interface. This points to the NTD as a promising target for therapeutic mAbs against COVID-19.
There is an urgent need for prophylactic and therapeutic interventions for SARS-CoV-2 infections given the ongoing COVID-19 pandemic. Our work reveals that naturally occurring human SARS-CoV-2 mAbs isolated from the B cells of 10 recovered donors are diverse in gene usage and epitope recognition of S protein. The majority of the isolated mAbs did not recognize the RBD, and all the mAbs that neutralize authentic SARS-CoV-2 failed to inhibit the binding of S protein to ACE2. These unexpected results suggest the presence of other important mechanisms for SARS-CoV-2 neutralization in addition to suppressing the viral interaction with the receptor.
The S1-targeting mAb 4A8 does not block the interaction between ACE2 and S protein but exhibits high levels of neutralization against both authentic and pseudotyped SARS-CoV-2 in vitro. Many neutralizing antibodies against SARS-CoV-2 were reported to target the RBD of the S protein and block the binding between RBD and ACE2. Our results show that 4A8 binds to the NTD of S protein with potent neutralizing activity. Previous study has shown that mAb 7D10 could bind to the NTD of S protein of MERS-CoV probably by inhibiting the RBD-DPP4 binding and the prefusion-to-postfusion conformational change of S protein. We aligned the crystal structure of 7D10 in complex with the NTD of S protein of MERS-CoV with our complex structure and found that the interfaces between the mAb and the NTDs are partially overlapped (fig. S7). 7D10 may inhibit the interaction between MERS-CoV and DPP4 through its light chain, which is close to the RBD. In our complex, the light chain of 4A8 is away from the RBD (fig. S7). Therefore, we speculate that 4A8 may neutralize SARS-CoV-2 by restraining the conformational changes of the S protein. Furthermore, sequence alignment of the S proteins from SARS-CoV-2, SARS-CoV, and MERS-CoV revealed varied NTD surface sequences that are respectively recognized by different mAbs (fig. S8).
This work reports a fully human neutralizing mAb recognizing a vulnerable epitope of NTD on S protein of SARS-CoV-2, functioning with a mechanism that is independent of receptor binding inhibition. Combination of 4A8 with RBD-targeting antibodies may avoid the escaping mutations of the virus and serve as promising “cocktail” therapeutics. The information obtained from these studies can be used for development of the structure-based vaccine design against SARS-CoV-2.
Reference & Source information: https://science.sciencemag.org/
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