SARS-CoV-2 spike S2-specific neutralizing antibodies

Abstract

Since the onset of the coronavirus disease 2019 (COVID-19), numerous neutralizing antibodies (NAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed and authorized for emergency use to control the pandemic. Most COVID-19 therapeutic NAbs prevent the S1 subunit of the SARS-CoV-2 spike (S) protein from binding to the human host receptor. However, the emergence of SARS-CoV-2 immune escape variants, which possess frequent mutations on the S1 subunit, may render current NAbs ineffective. In contrast, the relatively conserved S2 subunit of the S protein can elicit NAbs with broader neutralizing potency against various SARS-CoV-2 variants. In this review, the binding specificity and functional features of SARS-CoV-2 NAbs targeting different domains of the S2 subunit are collectively discussed. The knowledge learned from the investigation of the S2-specific NAbs provides insights and potential strategies for developing antibody cocktail therapy and next-generation coronavirus vaccine.

Keywords: S2 subunit; SARS-CoV-2; antibody cocktail therapy; neutralizing antibody; spike protein.

Figure 1.

The molecular structure of SARS-CoV-2 S protein. (A) The schematic diagram of the domain structure of SARS-CoV-2 S protein. NTD, N-terminal domain (yellow). RBD, receptor-binding domain (cyan). S1/S2, S1/S2 furin cleavage site. S2’, S2’ cleavage site R815 (blue spheres). FP, fusion peptide (bright purple). HR1, heptad repeat 1 (green). HR2, heptad repeat 2 (brown). (B) The trimeric S protein ectodomain. (C) The prefusion (left) and postfusion (right) structures of the trimeric S2 subunits. HR2 was not seen in the crystal structure of the trimeric S protein ectodomain (PDB ID: 6XR8).

Figure 2.

An immunodominant S2 peptide recognized by various S2 stem helix-specific antibodies. (A) Sequence alignment of the S2 stem helix regions (S_1141-1160) of SARS-CoV-2 VOCs, including Wuhan-Hu-1, Alpha, Beta, Gamma, Epsilon, Delta, and Omicron strains. (B) Sequence alignment of the S2 stem helix regions of SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E. S_1141-1160 is shown as SARS-CoV-2 numbering. Residues identical to the sequence of SARS-CoV-2 S2 stem helix are marked with black backgrounds. (C) The key binding epitopes of the S2 stem helix-specific antibodies. Hydrophobic, negatively charged, and positively charged residues of S_1141-1160 are coloured in grey, magenta, and brown, respectively. Residues recognized by S2P6 and 1249A8 that broadly neutralize SARS-CoV-2, SARS-CoV, and MERS-CoV are coloured in cyan and marine blue, respectively. Residues recognized by CC40.8, CC68.109, and CC99.103 that neutralize SARS-CoV-2 and SARS-CoV but not MERS-CoV are coloured yellow. Residues recognized by WS6 that neutralizes SARS-CoV-2 and SARS-CoV but not MERS-CoV are coloured in orange. Residues E1144, F1148, L1152, and F1156 recognized by S2-4D, S2-5D, S2-8D, and S2-4A that neutralize SARS-CoV-2 are coloured in pink. Residues recognized by B6, IgG22, 1.6C7, and 28D9 that only neutralize MERS-CoV but not SARS-CoV-2 are coloured in green, purple, and light purple, respectively.

Figure 3.

Superimposition of S2 stem helix-specific antibodies upon binding with their epitopes. (A) The Fabs of S2P6 (cyan, PDB: 7RNJ), CC40.8 (yellow, PDB: 7SJS), WS6 (orange, PDB: 7TCQ), B6 (green, PDB: 7M53), IgG22 (purple, PDB: 7S3N), and CV3-25 (magenta, PDB: 7RAQ) are superimposed with the prefusion S trimer (grey, PDB: 6XR8). (B) Alignment of the Fabs of S2P6, CC40.8, WS6, B6, IgG22, and CV3-25 upon binding with residues 1141-1162 of the S2 stem helix. Superimposition of the Fabs of S2P6 and B6 (C), CC40.8 and WS6 (D), or B6 and IgG22 (E) for comparison.

Figure 4.

Sequence alignment of the partial FP residues recognized by S2’/FP-specific antibodies. (A) Sequence alignment of the partial S2’/FP regions (S_815-830) of SARS-CoV-2 VOCs, including Wuhan-Hu-1, Alpha, Beta, Gamma, Epsilon, Delta, and Omicron strains. (B) Sequence alignment of the partial S2’/FP regions of SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E. S_815-830 is shown as SARS-CoV-2 numbering. Residues identical to the S2’/FP sequence of SARS-CoV-2 are marked with black backgrounds. (C) The key residues recognized by 76E1, COV44-62, COV44-79, and VN01H1 that can neutralize both of α- and β-CoVs are coloured in cyan, yellow, magenta, and green, respectively. The key residues recognized by C77G12 that can only neutralize β-CoVs are coloured in orange.

Figure 5.

Superimposition of S2’/FP-specific antibodies upon binding with their epitopes. The Fabs of 76E1 (cyan, PDB: 7X9E), COV44-62 (yellow, PDB: 8D36), COV44-79 (magenta, PDB: 8DAO), VN01H1 (green, PDB: 7SKZ), and C77G12 (orange, PDB: 7U0A) are superimposed with the FP (bright purple) of SARS-CoV-2 S protein. N’ and C’ stand for the N- and C-termini of FP.

Figure 6.

Sequence alignment of the partial HR2 residues recognized by hMab5.17. (A) Sequence alignment of the partial HR2 residues of SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E. S_1163-1176 is shown as SARS-CoV-2 numbering. Residues identical to the sequence of SARS-CoV-2 HR2 are marked with black backgrounds. (B) Sequence alignment of the partial HR2 residues (S_1163-1176) of SARS-CoV-2 VOCs, including Wuhan-Hu-1, Alpha, Beta, Gamma, Epsilon, Delta, and Omicron strains. F1176 in Gamma strain is marked with black background. (C) The binding epitope of hMab5.17 on the SARS-CoV-2 S protein is coloured in grey.