Structure of monoclonal antibody that can potently neutralize SARS-CoV-2 and variants of concern

The coronavirus disease 2019 (COVID-19) pandemic has caused more than 223 million cases, of whom over 4.78 million have been fatal. Vaccination has been very patchy, leading to the emergence of new variants that reduce vaccine efficacy.

Study: Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody. Image Credit: Kateryna Kon/ Shutterstock

New therapeutic modalities are urgently needed to counter the threat posed by the virus to the susceptible population. A new preprint deals with the analysis of the monoclonal antibody J08, which was capable of powerful neutralization of the wildtype severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as well as its variants of concern (VOCs).

A preprint version of the study is available on the bioRxiv* server, while the article undergoes peer review.

Background

Vaccine roll-outs have led to the administration of millions of doses worldwide, but mostly in the high-income bloc. As a result, viral variants have emerged, mostly in the low- and middle-income countries (LMIC), with greater transmissibility and mortality.

Especially disturbing is that these seem to reduce vaccine efficacy, prompting the development of booster shots, which pose many ethical and logistical challenges.

Most vaccines target the viral spike antigen, a glycoprotein that exists as a homotrimer, mediating viral attachment to the host cell and entry into the cell. The spike interacts with the target host cell at the angiotensin-converting enzyme 2 (ACE2) via its receptor-binding domain (RBD).

The spike protein comprises an S1 and S2 subunit, the first containing the RBD and the N-terminal domain (NTD). The second contains the fusion peptide that mediates the entry of the virus into the host cell by fusing the cell membrane with the viral membrane.

Most neutralizing antibodies target both the RBD and NTD. Earlier monoclonal antibodies (mAbs) have had mixed results. However, some have received emergency use authorization from the Food and Drugs Administration (FDA).

The current study aimed at identifying the structural interactions responsible for the potent neutralization of the virus by J08. The researchers tested the binding of the antibody, its ACE2 inhibition, and neutralization against the SARS-CoV-2 virus with the following variants: the D614G strain, the VOCs alpha, beta, gamma, and delta (B.1.1.7, B.1.351, P.1, and B.1.617.2, respectively.)

What did the study show?

The results show that J08 bound all the tested variants of the viral RBD and inhibited the binding of the RBD variants and the ACE2 receptor. The mAb was also able to neutralize both authentic wildtype and VOC strains.

J08 blocked RBD-ACE2 binding by the D614G strain, with 100% inhibition at a concentration of ~4 ng/mL (IC100). It also showed potent neutralizing activity against all tested VOCs. The IC100 values were ~4, 10, 5, and 6 ng/mL for the alpha, beta, gamma, and delta strains, respectively.

J08 showed complete neutralization of all tested variants of the virus. With such high potency, the IC50 against the D614G, Alpha, and Delta variants was assigned as <1 ng/mL because of the inability to define the half-maximal inhibitory concentration (IC50) against them.

The lentiviral pseudovirus neutralization assay was performed with a spike variant containing a 19-residue deletion in the cytoplasmic tail. This modification led to an observed increase in the incorporation of the spike into the pseudovirions and a higher rate of viral entry into the cells relative to the full-length spike protein.

However, the pseudovirus neutralization assay showed a decrease in the neutralization IC50 value. This could be an unforeseen effect of the platform used since it allows enhanced spike incorporation into the pseudovirions. Alternatively, it might result from using cell lines that have varying levels of human ACE2 expression on the cell surface.

Despite the drop observed, the antibody could neutralize all these variants, though the IC50 rose in all cases, from 22 to 226 ng/mL for the D614G to the delta variants, respectively.

Structural Analysis

The structural analysis shows the antibody’s antigen-binding fragment (Fab) in complex with two types of RBD, one with unrestricted RBD movement and one where the RBD has to be in the down conformation.

Two conformations of Fab J08 were captured, in both of which three Fab molecules are bound to one spike trimer. In the first conformation, the Fabs of J08 are further apart, and the apex is more closed, indicating the RBD to be more down. In the second, the Fabs are closer to one another, and the RBD is more open.

The bound epitopes in each case were constant, but the epitope-paratope interactions were slightly different in each case. The heavy chain complementarity-determining region 2 (CDRH2) loops of the antibody were responsible for anchoring the antibody to the RBD. The CDHR3 was capable of fitting either RBD-up or RBD-down conformation. The buried surface area (BSA) for the Fab J08 differed in each of the three conformations.

J08 can tolerate the RBD’s dynamic movement, with CDHR2 playing the anchoring role in conformation one and two, while in conformation three, the CDHR3 contacts are increased. More contacts are found in CDHR2 and CDHR3 in conformations one and three, but in conformation two, CDHR1 provides some contacts between the protomers.

There are fewer contacts between the antibody light chain. In all three conformations, CDRL1 and CDRL3 form part of the RBD interface. The researchers think that J08 is a highly potent neutralizing antibody partly because of its ability to bind the RBD in up and down conformations.

J08 resists immune escape

The antibody binds high on the RBD ridge and thus escapes common mutations of the receptor-binding site (RBS). The RBS has four epitopes, titled A-D, and J08 binds RBS-B, which is rarely mutated, unlike the other epitopes. The latter escape neutralization because of these mutations.

Key residues such as the E484K, common to the alpha, beta, and gamma variants of concern, and K417N/T in beta and gamma, respectively, seem to avoid immune escape. This may be because alternate contacts are found.

Antibodies binding high on the RBD-ridge approach the RBD similarly to J08 to cause steric hindrance to ACE2 binding. Almost half the RBD residues that participate in the RBD-ACE2 interface belong to the J08 interface, making up more than three-quarters of the interface between this antibody and the RBD. This indicates that the escape mutations that may allow the virus to avoid neutralization are also likely to reduce viral fitness.

*Important notice

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

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.