4.1  Anti-S1 & RBD antibodies
Neutralizing Abs can fight against viral infections by blocking binding to cellular receptors or by interfering with viral fusion. Besides, in the case of enveloped viruses, the Abs can recruit effector cells or the complement, thus allowing the destruction of the infected cells or the lysis of the viral particles [6]. The S1 domain contains most of the epitopes recognized by nAbs during infection. The RBD located in this S1 domain would be the most important target for nAbs against SARS-CoV, MERS-CoV and the novel coronavirus SARS-CoV-2 [[26], [27], [28], [29]]. More specifically, certain secondary structures such as extended loops seem to be particularly immunogenic.
RBD of SARS-CoV is composed of 193 amino acids (N318-V510) within S protein. Five regions on the S glycoprotein of SARS-CoV (residues 274–306, 510–586, 587–628, 784–803 and 870–893), in which three first regions belong to S1 subunit in the CTD2 and CTD3 (C-terminal domain) and two later belong to HR1 domain of the S2 subunit, were predicted to be associated with a robust immune response to SARS-CoV [30]. Several specific-nAbs for SARS-CoV were discovered; unfortunately none of them are under clinical trial [31] (Fig. 2 ).
Fig. 2 S protein of SARS-CoV, MERS-CoV, SARS-CoV-2 with its subdomains are the target of antibodies. The antibodies cited in this review have different origins or techniques, and some of them have specific targets such as the receptor binding domain (RBD) containing the receptor binding motif (RBM), the heptad repeat regions (HR1 and HR2). Some antibodies could bind SARS-CoV and SARS-CoV-2. Background color: Black for SARS-CoV, dark grey for MERS-CoV, grey for SARS-CoV-2. SP: Signal peptide, FP: Fusion peptide, TM: Transmembrane domain, CP: Cytoplasm domain.
The human single-chain variable region fragment (scFv) antibody 80R blocked ACE-RBD interaction (epitope aa 324–503) [32] but some 80R-escape variants were found with the mutations mostly locating at lysine D480 [33]. The target epitope of 80R is not conserved in SARS-CoV-2 then it does not affect this novel virus [34]. Another nAb generated from a non-immune scFv library, named 256, could bind to an epitope of RBD but did not inhibit RBD binding. 256 is weak but specific to D480A-muted strains of 80R-escape variants. Some engineered broad nAbs, fm6 and fm39, also showed a high affinity to D480A-muted strains [33]. m396 (epitope aa 482–491) from human antibody fab library was cross-reactive [35] and used the D95 of m396 to form a salt bridge with R395 or an electrostatic interaction with D408 of SARS-CoV RBD [34]. m396 potently neutralized GD03 strain isolated from the second outbreak which resisted neutralization by 80R and S3.1. m396 also neutralized isolates from the first SARS-CoV outbreak (Urbani, Tor2) and from palm civets (SZ3, SZ16) [36]. Another human monoclonal antibody from scFv libraries CR3014 (epitope aa 318–510) showed potent effects on SARS-CoV neutralization; however, this virus can escape CR3014 upon P426L mutation in the S glycoprotein [37]. Same as 80R, m396 and CR3014 RBD-specific SARS-CoV antibodies failed to bind the S protein of SARS-CoV-2 [34]. CR3022, always from scFv libraries, could bind noncompetitively the SARS-CoV RBD (epitope aa 318–510) and had a synergistic neutralizing effect with CR3014 on SARS-CoV, even with the escaped P426L-muted variants [37].
By using Xenomouse in which mouse immunoglobulin genes were replaced by human immunoglobulin genes, 19 neutralizing mAbs bound S1 were found. 18 of them, 1B5 [38], 3A7, 3C7, 3F3, 3H12, 4A10, 4E2, 4G2, 5A5, 5A7, 5D3, 5D6, 5E4, 6B1, 6B5, 6B8, 6C1 and 6C2 bound RBD (aa 318–510) to avoid virus binding to the ACE2 receptor. The last one, 4D4, bound an epitope (aa 12–261) located on the N-terminal of RBD and inhibited post-binding event but not the RBD binding. Truncation of the first 300 amino acids of S1 blocked the trimerization and the fusion of S protein [39]. Synergistic effects in some SARS-CoV strains of 4D4 with other mAbs targeting S1 or S2 proteins such as 3C7 (S1), 1F8 (HR1) or 5E9 (HR2) were also reported [38,40]. The tri-combination of 3C7, 3H12 and 4D4 could effectively neutralize escape variants.
Other neutralizing human monoclonal Abs from transgenic mice were also reported. Ab 201 interfered with ACE2 binding by targeting S1 protein at the epitope aa 490–510. In contrast to 201, Ab 68 bound epitope aa 130–150 at the N-terminal of RBD but did not affect ACE2 binding [41].
F26 family of monoclonal Abs generated from mice (F26G9, F26G10, F26G18 and F26G19) showed neutralizing effect against SARS-CoV [42]. F26G18 binding RBD at the epitope aa 460–476 showed the most potent effect [43]. F26G19 (epitope aa 486–492 on RBD [44]) or 80R could also bind SARS-CoV by forming salt bridge R426 (RBD)-D56 or D480 (RBD)-R162, respectively [34].
SARS-CoV mouse antibody 240CD had a nanomolar affinity for the SARS-CoV-2 RBD but did not significantly block ACE-2 receptor binding [45]. As 240CD, CR3022 also has high affinity to SARS-CoV-2 and moreover, CR3022 had cross-neutralizing activity with this novel coronavirus [34].
The effects of neutralizing human monoclonal antibodies, S3.1, S215.13 [46] and S230.15, from Epstein-Bar virus transformation of human B cells were observed. As m396, S230.15 had potent inhibitory activity against isolates from the first, second SARS-CoV outbreaks and from palm civets (SZ3, SZ16) [36].