Discovery of a potent human monoclonal antibody specific for SARS-CoV-2 RBD

A recent article published on the website of the bioRxiv* preprint server demonstrated the structural basis for the neutralization of Omicron variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by 002-S21F2, an extended neutralizing antibody of SARS-CoV-2.

Study: Structural perspectives for the neutralization of BA.1 and BA.2 Omicron variants by a broadly neutralizing SARS-CoV-2 antibody. Image Credit: Huen Structure Bio/Shutterstock

context

The current pandemic of the 2019 coronavirus disease (COVID-19), caused by SARS-CoV-2, has resulted in more than 524 million cases and six million deaths worldwide. Intensive efforts are underway worldwide to develop, analyze and deploy vaccines or other medical alternatives against COVID-19, such as monoclonal antibody (mAb) treatment. However, as a result of widespread viral transmission and critical mutations, SARS-CoV-2 variants have emerged that evade neutralization conferred by therapeutic COVID-19 antibodies and immunity obtained through vaccination or infection.

In particular, most of the currently approved therapeutic antibodies against COVID-19 have shown reduced neutralizing efficacy against the Omicron variant of SARS-CoV-2 and its sublines, such as BA.2 and BA.1, due to approximately 30 mutations in its peak (S) protein. This underscores the ongoing need to discover mAbs that are effective against novel SARS-CoV-2 mutants.

About the study

The authors of the current study previously assessed humoral immunity in 42 COVID-19 rehab patients who experienced mild symptoms after transmission of the ancestral Wuhan (WA.1) strain of SARS-CoV-2 in 2020.

Identification of a broad and potent SARS-CoV-2 RBD-specific human monoclonal antibody 002-S21F2.  (A) General strategy for the isolation of RBD-specific mAbs described in this study.  (B) 002-S21F2 was tested for binding to SARS-CoV-2 variants of concern (VOC) WA.1, Alpha, Beta, Gamma, Delta and Omicron spike proteins.  (C) Authentic live virus neutralization curves of 002-S21F2 for SARS-CoV-2 VOCs WA.1, Alpha, Beta, Gamma, Delta and Omicron (BA.1 and BA.2).  Neutralization was determined on Vero-TMPRSS2 cells using a focus reduction assay.  (D) IC50 values ​​of the 50% inhibitory concentration of 002-S21F2-mediated neutralization were obtained from live SARS-CoV-2 COV neutralization assays.  Affinity constant (KD) values ​​calculated from binding curves for two mAbs, as measured by MSD binding assays, are plotted.

Identification of a broad and potent SARS-CoV-2 RBD-specific human monoclonal antibody 002-S21F2. (A) The general strategy for the isolation of RBD-specific mAbs described in this study. (B) 002-S21F2 was tested for binding to SARS-CoV-2 variants of concern (VOC) WA.1, Alpha, Beta, Gamma, Delta and Omicron spike proteins. (C) Authentic live virus neutralization curves of 002-S21F2 for SARS-CoV-2 WA.1, Alpha, Beta, Gamma, Delta and Omicron (BA.1 and BA.2) VOCs. Neutralization was determined on Vero-TMPRSS2 cells using a focus reduction assay. (D) IC50 values ​​of the 50% inhibitory concentration of 002-S21F2-mediated neutralization were obtained from live SARS-CoV-2 COV neutralization assays. Affinity constant (KD) values ​​calculated from binding curves for two mAbs, as measured by MSD binding assays, are plotted.

In the present study, researchers selected five subjects from previous research with measurable frequencies of SARS-CoV-2 receptor binding domain (RBD)-specific memory B cells, high concentrations of RBD binding, and significant neutralization levels of live SARS-CoV-2 strain. WA.1 for the production of mAbs targeting the RBD of SARS-CoV-2.

The team screened 804 class-switched B cells involved in the SARS-CoV-2 fluorescent RBD probe and amplified 398 linked gene sequences for light and heavy chains. In addition, they performed enzyme-linked immunosorbent assay (ELISA) profiling of the selected mAbs.

Scientists assessed the protein S-binding ability of antibody 002-S21F2 from several SARS-CoV-2 variants of concern (VOCs) through a multiplex electrochemiluminescence experiment. They used cryogenic electron microscopy (cryo-EM) structures of full-length immunoglobulin G (IgG) 002-S21F2 complexed with the S proteins Omicron and WA.1 to delineate the molecular features and mechanisms of broad-spectrum neutralization of SARS-CoV. 2 of 002-S21F2.

Results

The results of the study indicate that the authors successfully cloned and produced 208 mAbs targeting the SARS-CoV-2 RBD from the 398 matched amplified light and heavy chain antibody sequences. In addition, ELISA screening yielded 92 mAbs binding to SARS-CoV-2 RBD. Most of these mAbs showed low levels of somatic hypermutations (SHMs) in their light and heavy chains, indicating that they were recently generated from a naive B cell population. Of these antibodies, 48 ​​mAbs successfully prevented contact between host angiotensin-converting enzyme 2 (ACE2) and viral RBD, and 18 effectively neutralized live virus at half-maximal inhibitory concentrations (IC).50) ranging from 0.05 to 17 µg/ml.

The 002-S21F2 antibody has different genetic and epitope contact characteristics compared to therapeutic antibodies against SARS-CoV-2.  (A) Comparison of the genetic characteristic of the 002-S21F2 antibody with therapeutic antibodies in the clinic.  The mAbs that neutralize the Omicron are shown in bold and highlighted in red.  (B) Comparison of the epitope site of 002-S21F2 (green) with the S309 (Sotrovimab) (red outline), Ly-CoV1404 (Bebtelovimab) (yellow outline) epitopes on the RBD of SARS-CoV-2.

The 002-S21F2 antibody has different genetic and epitope contact characteristics compared to therapeutic SARS-CoV-2 antibodies.(HAS) Comparison of the genetic characteristic of mAb 002-S21F2 with therapeutic mAbs in the clinic. The mAbs that neutralize the Omicron are shown in bold and highlighted in red. (B) Comparison of epitope site 002-S21F2 (green) with S309 (Sotrovimab) (red outline), Ly-CoV1404 (Bebtelovimab) (yellow outline) epitopes on the RBD of SARS-CoV-2.

The authors noted that of all the mAbs that neutralized the live WA.1 sequence of SARS-CoV-2, the 002-S21F2 antibody was the most effective. They found that the 002-S21F2 antibody adhered to all SARS-CoV-2 variant S proteins analyzed with the same affinity. In addition, the 002-S21F2 antibody bound to the prefusion-stabilized S protein WA.1 and showed picomolar affinity by bilayer interferometry. In addition, the human antibody 002-S21F2, which targets the RBD of SARS-CoV-2, effectively neutralized live viral isolates of SARS-CoV-2 VOCs, including VOCs Beta, Alpha, Delta, Gamma and Omicron BA.2 and BA .1 with CI50 ranging from 0.02 to 0.05 µg/ml.

This quasi-germline antibody has genetic features that distinguish it from other SARS-CoV-2 mAbs. 002-S21F2 identified an epitope on the outer surface of RBD, ie, the class 3 surface, according to structural cryo-EM studies. In addition, this epitope fell outside the ACE2 joining motif, and its different molecular properties allowed it to overcome the mutations seen in Omicron variants.

The antigenic residues addressed by the broad neutralizing antibody (bnAb), 002-S21F2, were significantly conserved between previous and current SARS-CoV-2 COVs. Structural data revealed that antibody 002-S21F2 maintained effective neutralization against Omicron BA.2 and BA.1 variants containing epitope mutations at N440K and G339D. Since the recently reported Omicron variants BA.2.12.1, BA.2.13, BA.5, BA.4 and BA.3 showed no additional changes in the epitope region 002-S21F2, scientists assumed that the neutralizing ability of this monoclonal antibody against them would persist. Furthermore, the sequence alignment of Sarbecovirus RBDs showed that 10 of the 19 conserved SARS-CoV residues were addressed by 002-S21F2, indicating the possibility of cross-reactivity with other Sarbecoviruses.

The structural comparison of other class 3 mAbs, such as the two current therapeutic mAbs targeting Omicron, Bebtelovimab (Ly-CoV1404) and Sotrovimab (S309), and the 002-S21F2 epitope revealed certain similarities between the C135 and 002 -S21F binding sites. However, C135 did not neutralize Omicron’s VOC.

In addition, structural analysis revealed that the small number of SHMs found in this nearly germline bnAb 002-S21F2 were not involved in antigen recognition, suggesting that the fingerprints of these bnAbs could provide a model for the rational development of the COVID-19 vaccine.

Overall, the authors reported that the identification and detailed structural characterization of 002-S21F2 in this study provided important information about their broad and efficient neutralization of SARS-CoV-2 VOCs.

*Important announcement

bioRxiv publishes preliminary scientific reports that have not been peer-reviewed and therefore should not be considered conclusive, should guide clinical practice/health behavior or be treated as established information.

Reference magazine:

  • Structural perspectives for the neutralization of Omicron BA.1 and BA.2 variants by a broad neutralizing SARS-CoV-2 antibody. Sanjeev Kumar, Anamika Patel, Lilin Lai, Chennareddy Chakravarthy, Rajesh Valanparambil, Meredith E. Davis-Gardner, Venkata Viswanadh Edara, Susanne Linderman, Elluri Seetharami Reddy, Kamalvishnu Gottimukkala, Kaustuv Nayak Vankaray, Prashant Vankarayana Andrew S. Neish, John D. Roback, Grace Mantus, Pawan Kumar Goel, Manju Rahi, Carl W. Davis, Jens Wrammert, Mehul S. Suthar, Rafi Ahmed, Eric Ortlund, Amit Sharma, Kaja Murali Krishna, Anmol Chandele. bioRxiv preprint 2022, DOI: https://doi.org/10.1101/2022.05.13.491770, https://www.biorxiv.org/content/10.1101/022.05.13.491770v1

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