Study: Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies. Image Credit: Lightspring / Shutterstock

Discovery of antibodies that may eliminate the need for COVID vaccines

In a recent study published in the journal Communication biologyresearchers evaluated the efficacy of monoclonal antibodies (mAb) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent donors infected with the Wuhan-1 strain against SARS-CoV-2 VOCs (variants of interest) such as Alpha, Beta, Gamma, Delta and Omicron.

Study: Conformational flexibility in neutralization of SARS-CoV-2 by naturally induced anti-SARS-CoV-2 antibodies. Image credit: Lightspring / Shutterstock

The continued emergence of SARS-CoV-2 VOCS threatens the efficacy of vaccines and the immune protection conferred by natural SARS-CoV-2 infections with the original Wuahn-Hu-1 strain. Therefore, it is essential to assess the cross-neutralizing ability of serological antibodies. Furthermore, the structural basis for SARS-CoV-2 neutralization needs to be explored to predict the effects that VOC modifications would have on Ab cross-reactivity.

The authors of this study previously identified nine SARS-CoV-2 neutralizing mAbs from the sera of two convalescents with coronavirus disease 2019 (COVID-19) infected with a likely ancestral strain. Of these, seven mAbs (TAU-2310, TAU-2303, TAU-2230, TAU-2212, TAU-2189, TAU-1145, and TAU-1109) demonstrated potent neutralization of SARS-CoV-2, while the remaining two mAbs ( TAU-2220 and TAU-1115) showed lower efficacy.

All mAbs (except TAU-2212) were highly bound to the spike (S) protein of SARS-CoV-2 and its receptor binding domain (RBD), while TAU-2212 bound to an unidentified conformational site on SARS-CoV-2 S. While The mAbs neutralized the parent strain, their ability to cross-neutralize against SARS-CoV-2 VOCs was unknown.

About studying

In this study, the researchers extended their previous analysis by examining the breadth of neutralization and the mechanistic basis for SARS-CoV-2 VOC neutralization using mAbs previously isolated from convalescent Wuhan-Hu-1-infected donors.

Flow cytometry (FC) analysis was performed to assess the ability of mAbs to inhibit the binding interactions between human angiotensin-converting enzyme 2 (hACE2) and S proteins of the ancestral strain and VOCs Alpha, Beta and Delta. In addition, the prevention of SARS-CoV-2 infection by the mAb was evaluated by pseudovirus and authentic virus neutralization assays using Vero-TMPRSS2 (transmembrane serine protease 2) cells.

Structural analyzes were performed using X-ray crystallography and cryo-EM (cryo-electron microscopy) to investigate the mechanistic basis of SARS-CoV-2 neutralization of VOCs by TAU-2212 and TAU-2303 and to investigate the contribution of VOC mutations to Ab escape. Abs conformational structures were determined at 3.3 Å, 4.7 Å, 6.4 Å, 7.3 Å, and 9.4 Å resolution, respectively.

Dr Natalia Freund / Tel Aviv University

Dr Natalia Freund / Tel Aviv University

Result

The most potent mAbs detected were predominantly directed against the ACE2 binding site (ACE2bs) and showed higher sensitivity to SARS-CoV-2 devolution than non-ACE2bs mAbs (TAU-2310, TAU-2220, TAU-1109 and TAU-1115). two of them retained their neutralizing ability against all analyzed VOCs. The binding efficiency of all ACE2bs mAbs (mAb TAU-1145, TAU-2189, TAU-2230, and TAU-2303) to all VOCs was reduced except for Alpha, with the most significant reductions for Beta VOCs, Delta VOCs, and Omicron VOCs, and less for Gamma VOCs.

Among the ACE2bs mAbs, none retained their original neutralizing potency against Beta VOCs, and only TAU-2303 retained (and showed higher than original) neutralizing potency against Delta VOCs. No effects were observed with TAU-1109, -2310, -1115, and -2220 mAbs because neutralization of SARS-CoV-2 did not occur by blocking the receptor.

The L452R mutation (in Delta VOC) and the E484K mutation (in Beta VOC and Gamma VOC) significantly affected Ab binding. Furthermore, RBDs containing the individual mutations N439K, Y453F, and A475V showed binding to all mAbs as efficiently as to the parental strain RBD. Binding of TAU-2303 to the K417N/N501Y double-mutated RBD was reduced, although individual mutations had no significant effect.

TAU-2212 demonstrated 25 to 40% inhibition of ACE2:S when tested against the ancestral strain, Alpha and Delta VOC, but showed no activity against Beta VOC. Alpha VOC and the parent strain showed similar behavior, while Beta and Omicron VOC showed the highest resistance to neutralization, followed by Gamma VOC and Delta VOC.

Structural analysis of Delta VOC-neutralizing ACE2bs mAb, antigen-binding fragment (Fab) TAU-2303 (Fab2303) in complex with SARS-CoV-2 S at 4.5 Å and S RBD at 2.4 Å showed similar binding modes as between With RBD and hACE2 with RBD in RBD “up” conformation. Most of the Fab2303-RBD contact surface (64%) was derived from the Fab2303 heavy chain (HC, 19 residues), while only 36% (10 residues) was derived from the light chain.

A combination of RBD mutations can alter resistance to SARS-CoV-2; Omicron has mutations in seven residues in the Fab2303 binding epitope, including Q493, Q498, Y505, and K417, providing a structural explanation for the lack of neutralization of omicron by TAU-2303 mAb. The E484K mutation disrupted the hydrogen bonds between TAU-2212 and the RBD, providing a structural explanation for the lack of neutralization of beta and gamma VOCs by TAU-2212.

Five conformational structures of the TAU-2212-SARS-CoV-2 S complex were evaluated at several resolutions. TAU-2212 showed binding with an exclusive quaternary epitope and flexible [fragment crystallizable (Fc) region] and a unique neutralization mode involving transitions between conformations.

TAU-2212 showed that one to three Fabs either bind to a single SARS-CoV-2 S trimer or cross-link neighboring S trimers by making both intra-S and inter-S contacts and favoring the RBD in the “down” position. Epitope recognition by TAU-2212 primarily involved HCDR (heavy complementarity determining region) loops and S regions of RBD1 and RBD2 and 57 residues.

Overall, the study results provided valuable mechanistic and structural insights into the neutralization of SARS-CoV-2 VOCs by mAbs with molecular modeling predictions of mAb interactions with Omicron.

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