Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2

Abstract

The SARS-CoV-2 viral spike (S) protein mediates attachment and entry into host cells and is a major target of vaccine and drug design. Potent SARS-CoV-2 neutralizing antibodies derived from closely related antibody heavy chain genes (IGHV3-53 or 3-66) have been isolated from multiple COVID-19 convalescent individuals. These usually contain minimal somatic mutations and bind the S receptor-binding domain (RBD) to interfere with attachment to the cellular receptor angiotensin-converting enzyme 2 (ACE2). We used antigen-specific single B cell sorting to isolate S-reactive monoclonal antibodies from the blood of a COVID-19 convalescent individual. The seven most potent neutralizing antibodies were somatic variants of the same IGHV3-53-derived antibody and bind the RBD with varying affinity. We report X-ray crystal structures of four Fab variants bound to the RBD and use the structures to explain the basis for changes in RBD affinity. We show that a germline revertant antibody binds tightly to the SARS-CoV-2 RBD and neutralizes virus, and that gains in affinity for the RBD do not necessarily correlate with increased neutralization potency, suggesting that somatic mutation is not required to exert robust antiviral effect. Our studies clarify the molecular basis for a heavily germline-biased human antibody response to SARS-CoV-2.

Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain

“…Additional common SHMs among IGHV3-53/3-66 RBD antibodies with a short CDR H3 include S31R in CDR H1 and V50L in CDR H2 (Figure 5a). As a result, while IGHV3-53/3-66 RBD antibodies do not require any SHM to neutralize SARS-CoV-2 57 , this study along with others have shown that SHM can substantially improve the binding affinity of IGHV3-53/3-66 antibodies to RBD 38,57 . Consistently, RBD antibodies from convalescent SARS-CoV-2 patients have significantly more SHMs and higher neutralization potency at 6 months postinfection than at 1-month post-infection 62 .…”

“…Interestingly, a Y58F mutation results in a loss of hydrogen bonding interactions between residue 58 of the heavy chain and T415 of the RBD ( Supplementary Figure 10), yet the mutation significantly increases the binding affinity of the antibody to the RBD. We then performed a structural analysis on seven IGHV3-53/66 RBD antibodies with Y58F mutation and nine without 26,29,38,40,47,[54][55][56][57] . Our results indicate that, by removal of the hydroxyl group, the side chain of Y58F moves closer to the backbone carbon of RBD T415 (Supplementary Figure 10).…”

Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies

“…43 The mutations on the RBD are considered for the predictions of BFE changes. Our predictions are built from the X-ray crystal structure of SARS-CoV-2 S protein and ACE2 (PDB 6M0J), 57 76 and 7KFY 76 ). The BFE change following mutation (DDG) is dened as the subtraction of the BFE of the mutant type from the BFE of the wild type: DDG ¼ DG W À DG M , where DG W is the BFE of the wild type and DG M is the BFE of the mutant.…”

Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants

“…E484 (left) and K417 (right) are represented by red and blue spheres, respectively, and are also labeled in the first panel. All available RBD-targeting IGHV3- 53/3-66 antibody structures in the PDB at time of analysis (January 2021) are shown: CC12.1 (PDB ID: 6XC3), CC12.3 (PDB ID: 6XC4) ( 20 ), COVA2-04 (PDB ID: 7JMO) ( 21 ), B38 (PDB ID: 7BZ5) ( 22 ), CB6 (PDB ID: 7C01) ( 23 ), CV30 (PDB ID: 6XE1) ( 24 ), C105 (PDB ID: 6XCN) ( 25 ), BD-236 (PDB ID: 7CHB), BD-604 (PDB ID: 7CH4), BD-629 (PDB ID: 7CH5) ( 26 ), C102 (PDB ID: 7K8M) ( 27 ), C1A-B3 (PDB ID: 7KFW), C1A-C2 (PDB ID: 7KFX), C1A-B12 (PDB ID: 7KFV), C1A-F10 (PDB ID: 7KFY) ( 28 ), P4A1 (PDB ID: 7JCF) ( 29 ), COVA2-39 (PDB ID: 7JMP) ( 21 ), and C144 (PDB ID: 7K90) ( 25 ).…”

“…Previously, we and others demonstrated that IGHV3-53/3-66 RBD antibodies can adopt two different binding modes ( 44, 46 ), which we now refer to as binding modes 1 and 2, with distinct epitopes and angles of approach to the receptor binding site (RBS) (Figure 2B, Figure S3). All known IGHV3-53/3-66 RBD antibodies with binding mode 1 have a short CDR H3 of < 15 amino acids and bind to the RBS-A epitope ( 11, 15, 31 ), while those with binding mode 2 contain a longer CDR H3 (≥ 15 amino acids) and target RBS-B ( 44, 46, 47 ). These dual binding modes enhance the recognition potential of this antibody family for the SARS-CoV-2 RBD, although 16 of 18 IGHV3-53/3-66 RBD antibodies with structural information adopt binding mode 1 (Figure S3).…”