scholarly journals Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display

2021 ◽  
Author(s):  
Shiho Tanaka ◽  
C. Anders Olson ◽  
Christopher O. Barnes ◽  
Wendy Higashide ◽  
Marcos Gonzalez ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Rapid Identification ◽  
Mrna Display ◽  
Receptor Binding Domain ◽  
Structural Studies ◽  
Binding Modes ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Previous Infection ◽  
Cryptic Epitopes

AbstractThe increasing prevalence of SARS-CoV-2 variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly-reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identified a set of antibodies against SARS-CoV-2 spike (S) proteins and characterized the structures of nAbs that recognized epitopes in the S1 subunit of the S glycoprotein. These structural studies revealed distinct binding modes for several antibodies, including targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interacts with angiotensin- converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. A potent ACE2-blocking nAb was further engineered to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is a promising approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.

scholarly journals Amino acids 484 and 494 of SARS-CoV-2 spike are hotspots of immune evasion affecting antibody but not ACE2 binding

2021 ◽  
Author(s):  
Marta Alenquer ◽  
Filipe Ferreira ◽  
Diana Lousa ◽  
Mariana Valério ◽  
Mónica Medina-Lopes ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Angiotensin Converting Enzyme ◽  
Immune Evasion ◽  
Neutralizing Antibodies ◽  
Receptor Binding Domain ◽  
Converting Enzyme ◽  
Antibody Neutralization ◽  
Angiotensin Converting Enzyme 2 ◽  
The Core

AbstractUnderstanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike and, predominantly, of its receptor-binding-domain (RBD). Mutations in spike impacting antibody or ACE2 binding are known, but the effect of mutation synergy is less explored. We engineered 22 spike-pseudotyped lentiviruses containing individual and combined mutations, and confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent sera. This amino acid emerges as an additional hotspot for immune evasion and a target for therapies, vaccines and diagnostics.One-Sentence SummaryAmino acids in SARS-CoV-2 spike protein implicated in immune evasion are biased for binding to neutralizing antibodies but dispensable for binding the host receptor angiotensin-converting enzyme 2.

scholarly journals An Ultrapotent Neutralizing Bispecific Antibody with Broad Spectrum Against SARS-CoV-2 Variants

2021 ◽  
Author(s):  
Hui Zhang ◽  
Haohui Huang ◽  
Rong Li ◽  
Lu Zhang ◽  
Zhiwei Wang ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Bispecific Antibody ◽  
Herd Immunity ◽  
Therapeutic Effects ◽  
Bodyweight Loss ◽  
Receptor Binding Domain ◽  
Single Administration ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
High Affinity

Abstract Some variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are threatening our global efforts of herd immunity, novel and more efficacious agents are urgently needed. We have developed a bispecific antibody, 2022, which bonds with high affinity to two non-overlapping epitopes on the receptor-binding domain (RBD) simultaneously, blocks the binding of RBD to human angiotensin-converting enzyme 2 (ACE2), and potently neutralizes SARS-CoV-2 and all of the variants tested, including variants carrying mutations known to resist neutralizing antibodies approved under Emergency Use Authorization (EUA) and reduce the efficacy of existing vaccines. In a mouse model of SARS-CoV-2, 2022 showed strong prophylactic and therapeutic effects. A single administration of 2022 completely protected all mice from bodyweight loss, as compared with up to 20% loss of bodyweight in placebo treated mice, reduced the lung viral titers to undetectable in all mice treated with 2022 either prophylactically or therapeutically, as compared with around 1X105 pfu/g lung tissue in placebo treated mice. In summary, bispecific antibody 2022 showed potent binding and neutralizing activity across a variety of SARS-CoV-2 variants and could be an attractive weapon to combat the ongoing waves of the COVID-19 pandemic.

scholarly journals mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection

Science ◽  
2021 ◽  
pp. eabg9175 ◽  
Author(s):  
Leonidas Stamatatos ◽  
Julie Czartoski ◽  
Yu-Hsin Wan ◽  
Leah J. Homad ◽  
Vanessa Rubin ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Binding Domain ◽  
Receptor Binding Domain ◽  
Previous Infection

Emerging SARS-CoV-2 variants have raised concerns about resistance to neutralizing antibodies elicited by previous infection or vaccination. We examined whether sera from recovered and naïve donors collected prior to, and following immunizations with existing mRNA vaccines, could neutralize the Wuhan-Hu-1 and B.1.351 variants. Pre-vaccination sera from recovered donors neutralized Wuhan-Hu-1 and sporadically neutralized B.1.351, but a single immunization boosted neutralizing titers against all variants and SARS-CoV-1 by up to 1000-fold. Neutralization was due to antibodies targeting the receptor binding domain and was not boosted by a second immunization. Immunization of naïve donors also elicited cross-neutralizing responses, but at lower titers. Our study highlights the importance of vaccinating both uninfected and previously infected persons to elicit cross-variant neutralizing antibodies.

scholarly journals Comprehensive Deep Mutational Scanning Reveals the Immune-Escaping Hotspots of SARS-CoV-2 Receptor-Binding Domain Targeting Neutralizing Antibodies

2021 ◽  
Vol 12 ◽  
Author(s):  
Keng-Chang Tsai ◽  
Yu-Ching Lee ◽  
Tien-Sheng Tseng
Keyword(s):  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Binding Domain ◽  
Receptor Binding Domain ◽  
Human Immune System ◽  
Angiotensin Converting Enzyme 2 ◽  
Study Results ◽  
Rapid Spread ◽  
Care Systems ◽  
Computational Analyses

The rapid spread of SARS-CoV-2 has caused the COVID-19 pandemic, resulting in the collapse of medical care systems and economic depression worldwide. To combat COVID-19, neutralizing antibodies have been investigated and developed. However, the evolutions (mutations) of the receptor-binding domain (RBD) of SARS-CoV-2 enable escape from neutralization by these antibodies, further impairing recognition by the human immune system. Thus, it is critical to investigate and predict the putative mutations of RBD that escape neutralizing immune responses. Here, we employed computational analyses to comprehensively investigate the mutational effects of RBD on binding to neutralizing antibodies and angiotensin-converting enzyme 2 (ACE2) and demonstrated that the RBD residues K417, L452, L455, F456, E484, G485, F486, F490, Q493, and S494 were consistent with clinically emerging variants or experimental observations of attenuated neutralizations. We also revealed common hotspots, Y449, L455, and Y489, that exerted comparable destabilizing effects on binding to both ACE2 and neutralizing antibodies. Our results provide valuable information on the putative effects of RBD variants on interactions with neutralizing antibodies. These findings provide insights into possible evolutionary hotspots that can escape recognition by these antibodies. In addition, our study results will benefit the development and design of vaccines and antibodies to combat the newly emerging variants of SARS-CoV-2.

Identification of the interaction between Angiotensin-converting Enzyme Residues and Severe Acute Respiratory Syndrome Coronavirus 2.

2021 ◽  
Vol 27 ◽  
Author(s):  
Youness Kadil ◽  
Mohammed Mouhcine ◽  
Imane Rahmoune ◽  
Houda Filali
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Angiotensin Converting Enzyme ◽  
Receptor Binding Domain ◽  
Converting Enzyme ◽  
Methodological Study ◽  
Angiotensin Converting Enzyme 2 ◽  
Enveloped Virus ◽  
Positive Sense ◽  
Contact Residues ◽  
Cell Membrane Protein

Introduction: Coronaviruses are an enveloped virus with a positive-sense single-stranded RNA genome. It has been shown that the viral spike S glycoprotein binds to the cell membrane protein angiotensin-converting enzyme 2 as an invasive process of the virus. The aim of this research is the application of a computational approach in the identification of the interaction residues ACE2 with severe acute respiratory syndrome Coronavirus 2. A methodological study to understand the interactions between SARS CoV2 and ACE2, which is essential for the development of a vaccine and an antiviral. Methods: The S protein is cleaved into two subunits, S1 and S2. S1 contains the receptor-binding domain (RBD) which allows the virus to bind directly to the peptidase domain of ACE2. Results: Our results present the overall differences in contact residues between the different chains, and an alignment between the two SARS Viruses, along with a presentation of similarity between them.Then S2 likely plays a role in membrane fusion. Conclusions : The synthesis of our results appears to provide potentially a rational set of objectives that can help in the development of a SARS-CoV-2 vaccine.

scholarly journals Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus

2020 ◽  
Vol 94 (7) ◽  
Author(s):  
Yushun Wan ◽  
Jian Shang ◽  
Rachel Graham ◽  
Ralph S. Baric ◽  
Fang Li
Keyword(s):  
Animal Species ◽  
Atomic Level ◽  
Spike Protein ◽  
Structural Studies ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Receptor Usage ◽  
Receptor Recognition ◽  
Critical Residues ◽  
Novel Coronavirus

ABSTRACT Recently, a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by severe acute respiratory syndrome coronavirus (SARS-CoV). Since the SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between the SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here, we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV’s capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV and may help epidemic surveillance and preventive measures against 2019-nCoV. IMPORTANCE The recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002 to 2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational, and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV.

Cross-neutralization antibodies against SARS-CoV-2 and RBD mutations from convalescent patient antibody libraries

2020 ◽  
Author(s):  
Yan Lou ◽  
Wenxiang Zhao ◽  
Haitao Wei ◽  
Min Chu ◽  
Ruihua Chao ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Viral Infections ◽  
Therapeutic Agents ◽  
Therapeutic Interventions ◽  
Receptor Binding Domain ◽  
Angiotensin Converting Enzyme 2 ◽  
Human Antibodies ◽  
Global Pandemic ◽  
Antibody Libraries ◽  
Cross Neutralization

AbstractThe emergence of coronavirus disease 2019 (COVID-19) pandemic led to an urgent need to develop therapeutic interventions. Among them, neutralizing antibodies play crucial roles for preventing viral infections and contribute to resolution of infection. Here, we describe the generation of antibody libraries from 17 different COVID-19 recovered patients and screening of neutralizing antibodies to SARS-CoV-2. After 3 rounds of panning, 456 positive phage clones were obtained with high affinity to RBD (receptor binding domain). Then the positive clones were sequenced and reconstituted into whole human IgG for epitope binning assays. After that, all 19 IgG were classified into 6 different epitope groups or Bins. Although all these antibodies were shown to have ability to bind RBD, the antibodies in Bin2 have more superiority to inhibit the interaction between spike protein and angiotensin converting enzyme 2 receptor (ACE2). Most importantly, the antibodies from Bin2 can also strongly bind with mutant RBDs (W463R, R408I, N354D, V367F and N354D/D364Y) derived from SARS-CoV-2 strain with increased infectivity, suggesting the great potential of these antibodies in preventing infection of SARS-CoV-2 and its mutations. Furthermore, these neutralizing antibodies strongly restrict the binding of RBD to hACE2 overexpressed 293T cells. Consistently, these antibodies effectively neutralized pseudovirus entry into hACE2 overexpressed 293T cells. In Vero-E6 cells, these antibodies can even block the entry of live SARS-CoV-2 into cells at only 12.5 nM. These results suggest that these neutralizing human antibodies from the patient-derived antibody libraries have the potential to become therapeutic agents against SARS-CoV-2 and its mutants in this global pandemic.

scholarly journals Pathology and pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

2020 ◽  
Vol 245 (15) ◽  
pp. 1299-1307
Author(s):  
Henok Kessete Afewerky
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Indirect Effects ◽  
Clinical Characteristics ◽  
Receptor Binding Domain ◽  
Structural Studies ◽  
Direct And Indirect Effects ◽  
Basic Information ◽  
Angiotensin Converting Enzyme 2 ◽  
High Affinity ◽  
Current Survey

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta coronavirus that causes infectious respiratory disease, named as coronavirus disease of 2019 (COVID-19). While extensive studies have provided basic information on clinical characteristics of COVID-19, the disease pathology is not fully known. The SARS-CoV-2 virus structural studies and biochemical experiments have also indicated that the virus receptor-binding domain (RBD) binds with a high affinity to angiotensin-converting enzyme-2 (ACE-2) receptor from humans; however, the mechanism remains unclear. Hereunder, a summary of relevant findings in the SARS-CoV-2 virus pathology and major pathogenicity mechanisms are discussed. This review of studies provides additional enlightenments on the way forward to prevent further spread or even cure for the SARS-CoV-2 virus-caused COVID-19 disease, either-or should a similar viral plague occur in the future. Impact statement The current survey of studies outlines the direct and indirect effects of SARS-CoV-2 on the specific body systems and summarizes the SARS-CoV-2 main pathogenicity mechanisms that require attention during patient hospitalization and for further research.

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