Structural insights into hybridoma-derived neutralizing monoclonal antibodies against Omicron BA.5 and XBB.1.16 variants of SARS-CoV-2

Journal of Virology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 7, 2025

ABSTRACT The emergence of novel variants severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to pose an ongoing challenge for global public health services, highlighting the urgent need effective therapeutic interventions. Neutralizing monoclonal antibodies (mAbs) are a major strategy treatment COVID-19 and other viral diseases. In this study, we employed hybridoma technology generate mAbs that target BA.5 receptor-binding domain (RBD) SARS-CoV-2 spike protein. Through comprehensive screening process, identified four capable effectively neutralizing BA.5, XBB.1.16, related variant infections in vitro , among which ORB10 was found neutralize with plaque reduction neutralization test (PRNT 50 ) 8.7 ng/mL. Additionally, competitive binding assays, sequencing heavy light chain variable regions, kinetics characterization provided insights into epitopes affinities mAbs. Moreover, vivo experiments K18-hACE2 mouse model demonstrated protective efficacy against both XBB.1.16 variants. Finally, cryo-electron microscopy structural analysis ORB10–RBD complex key residues involved antibody–antigen interactions, providing molecular mechanisms immune escape Omicron from IMPORTANCE evolution has led evading responses elicited by natural infection vaccination, especially highly transmissible immune-evasive This study generated characterized panel specifically targeting RBD variant, showed . Cryo-EM further elucidated epitope interactions mechanism between enhances our understanding antibody-mediated provides valuable development strategies combat infections.

Язык: Английский

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SARS-CoV-2 Variants: Genetic Insights, Epidemiological Tracking, and Implications for Vaccine Strategies

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(3), С. 1263 - 1263

Опубликована: Янв. 31, 2025

The emergence of SARS-CoV-2 variants has significantly impacted the global response to COVID-19 pandemic. This review examines genetic diversity variants, their roles in epidemiological tracking, and influence on viral fitness. Variants concern (VOCs) such as Alpha, Beta, Gamma, Delta, Omicron have demonstrated increased transmissibility, altered pathogenicity, potential resistance neutralizing antibodies. Epidemiological tracking these is crucial for understanding spread, informing public health interventions, guiding vaccine development. also explores how specific mutations spike protein other genomic regions contribute fitness, affecting replication efficiency, immune escape, transmission dynamics. By integrating surveillance data with clinical findings, this provides a comprehensive overview ongoing evolution its implications strategies new

Язык: Английский

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Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies

Biomolecules, Год журнала: 2025, Номер 15(2), С. 249 - 249

Опубликована: Фев. 8, 2025

A growing body of experimental and computational studies suggests that the cross-neutralization antibody activity against Omicron variants may be driven by balance tradeoff between multiple energetic factors interaction contributions evolving escape hotspots involved in antigenic drift convergent evolution. However, dynamic details quantifying contribution these factors, particularly balancing nature specific interactions formed antibodies with epitope residues, remain largely uncharacterized. In this study, we performed molecular dynamics simulations, an ensemble-based deep mutational scanning SARS-CoV-2 spike binding free energy computations for two distinct groups broadly neutralizing antibodies: E1 group (BD55-3152, BD55-3546, BD5-5840) F3 (BD55-3372, BD55-4637, BD55-5514). Using approaches, examined determinants which potent can evade immune resistance. Our analysis revealed emergence a small number positions correspond to R346 K444 strong van der Waals act synchronously, leading large contribution. According our results, Abs effectively exploit hotspot clusters hydrophobic sites are critical functions along selective complementary targeting positively charged important ACE2 binding. Together conserved epitopes, lead expand breadth resilience neutralization shifts associated viral The results study demonstrate excellent qualitative agreement predicted mutations respect latest experiments on average scores. We argue epitopes leverage stability binding, while tend emerge synergistically electrostatic interactions.

Язык: Английский

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Mutational Scanning and Binding Free Energy Computations of the SARS-CoV-2 Spike Complexes with Distinct Groups of Neutralizing Antibodies: Energetic Drivers of Convergent Evolution of Binding Affinity and Immune Escape Hotspots

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(4), С. 1507 - 1507

Опубликована: Фев. 11, 2025

The rapid evolution of SARS-CoV-2 has led to the emergence variants with increased immune evasion capabilities, posing significant challenges antibody-based therapeutics and vaccines. In this study, we conducted a comprehensive structural energetic analysis spike receptor-binding domain (RBD) complexes neutralizing antibodies from four distinct groups (A–D), including group A LY-CoV016, B AZD8895 REGN10933, C LY-CoV555, D AZD1061, REGN10987, LY-CoV1404. Using coarse-grained simplified simulation models, energy-based mutational scanning, rigorous MM-GBSA binding free energy calculations, elucidated molecular mechanisms antibody escape mechanisms, identified key hotspots, explored evolutionary strategies employed by virus evade neutralization. residue-based decomposition revealed thermodynamic factors underlying effect mutations on binding. results demonstrate excellent qualitative agreement between predicted hotspots latest experiments escape. These findings provide valuable insights into determinants viral escape, highlighting importance targeting conserved epitopes leveraging combination therapies mitigate risk evasion.

Язык: Английский

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Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor

Physchem, Год журнала: 2025, Номер 5(1), С. 8 - 8

Опубликована: Фев. 20, 2025

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continually undergoes mutation, leading to variants with altered pathogenicity and transmissibility. The Omicron variant (B.1.1.529), first identified in South Africa 2021, has become dominant strain worldwide. It harbors approximately 50 mutations compared original strain, 15 located receptor-binding domain (RBD) spike protein that facilitates viral entry via binding human angiotensin-converting enzyme (ACE2) receptor. How do these mutated residues modulate intermolecular interactions affinity between RBD ACE2? This is a question great theoretical importance practical implication. In this study, we employed quantum chemical calculations at B2PLYP-D3/def2-TZVP level theory investigate molecular determinants governing Omicron’s ACE2 interaction. Comparative analysis wild-type RBD–ACE2 interfaces revealed including S477N, Q493R, Q498R, N501Y enhance through formation bifurcated hydrogen bonds, π–π stacking, cation–π interactions. These favorable counterbalance such destabilizing as K417N, G446S, G496S, Y505H, which disrupt salt bridges bonds. Additionally, allosteric effects improve contributions non-mutated (notably A475, Y453, F486) structural realignment novel bonding S19, an overall increase electrostatic π-system interaction energy. conclusion, our findings provide mechanistic basis for increased infectivity offer valuable insights development targeted antiviral therapies. Moreover, from methodological perspective, directly calculated mutation-induced energy changes residue using advanced methods rather than relying on indirect decomposition schemes typical dynamics-based free analyses. strong correlation differences experimental deep mutational scanning (DMS) data underscores robustness framework predicting affinity. demonstrates potential predictive tools studying protein–protein guiding rational therapeutic design.

Язык: Английский

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Biophysics of SARS-CoV-2 spike protein’s receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights

Biophysical Reviews, Год журнала: 2025, Номер unknown

Опубликована: Март 8, 2025

Язык: Английский

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Anti-S2 antibodies responsible for the SARS-CoV-2 infection-induced serological cross-reactivity against MERS-CoV and MERS-related coronaviruses

Frontiers in Immunology, Год журнала: 2025, Номер 16

Опубликована: Март 28, 2025

Sarbecoviruses, such as SARS-CoV-2, utilize angiotensin-converting enzyme 2 (ACE2) the entry receptor; while merbecoviruses, MERS-CoV, use dipeptidyl peptidase 4 (DPP4) for viral entry. Recently, several MERS-related coronaviruses, NeoCoV and PDF-2180, were reported to ACE2, same receptor enter cells, raising possibility of potential recombination between SARS-CoV-2 coronaviruses within co-infected ACE2-expressing cells. However, facing this risk, serum antibody cross-reactivity against MERS/MERS-related after vaccination and/or infection is still elusive. Here, in study, we showed that serological S proteins could be induced by but not inactivated vaccination. Further investigation revealed due monoclonals recognizing relatively conserved S2 epitopes, fusion peptide stem helix, antibodies receptor-binding domain (RBD), N-terminal (NTD) or subdomain-1 (SD1). Some these anti-S2 cross-reactive mAbs cross-neutralizing activity, none them exhibited antibody-dependent enhancement (ADE) effect vitro. Together, results dissected infection-induced highlighted significance region design development pan-β-coronaviruses vaccines.

Язык: Английский

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Severe Acute Respiratory Syndrome Coronavirus 2 Variant Infection Dynamics and Pathogenesis in Transgenic K18-hACE2 and Inbred Immunocompetent C57BL/6J Mice

Viruses, Год журнала: 2025, Номер 17(4), С. 500 - 500

Опубликована: Март 30, 2025

The global impact of the COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), persists in part due to emergence new variants. Understanding variant-specific infection dynamics and pathogenesis murine models is crucial for identifying phenotypic changes guiding development countermeasures. To address limitations earlier studies that investigated only a few variants or used small sample sizes, we evaluated clinical disease, kinetics, viral titers, cellular localization, histopathologic lungs brains transgenic B6.Cg-Tg(K18-ACE2)2Prlmn/J (“K18”) corresponding genetic control (C57BL/6J) mice expressing human angiotensin-converting enzyme (hACE2). Six SARS-CoV-2 were assessed: B.1 (WA1-like), alpha, beta, delta, omicron, omicron XBB.1.5, using cohorts ≥18 mice. Following intranasal inoculation with B.1, delta variants, K18 experienced rapid weight loss reached euthanasia criteria 5–6 days post-inoculation (dpi). In contrast, inoculated both recovered their starting within 4–6 dpi. Infectious was detected oropharynx at 1 and2 dpi, 2, 4, 6 brain 4 dpi all except omicron. nucleoprotein detected, interstitial pneumonia varying severity observed infected Brain lesions identified As express hACE2 brain—a feature not present humans—we also compared three those mouse-adapted WA1 strain C57BL/6J lacking ACE2 gene. did experience lethal exhibited milder pneumonia, had no evidence neuroinvasion despite similar kinetics These findings demonstrate contrasting phenotypes across two reduced tropism pathology models. This comprehensive analysis mouse provides valuable insights model variant selection future studies.

Язык: Английский

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Structural and Energetic Insights into SARS-CoV-2 Evolution: Analysis of hACE2–RBD Binding in Wild-Type, Delta, and Omicron Subvariants

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(8), С. 3776 - 3776

Опубликована: Апрель 17, 2025

The evolution of SARS-CoV-2, particularly the emergence Omicron variants, has raised questions regarding changes in its binding affinity to human angiotensin-converting enzyme 2 receptor (hACE2). Understanding impact mutations on interaction between receptor-binding domain (RBD) spike protein and hACE2 is critical for evaluating viral transmissibility, immune evasion, efficacy therapeutic strategies. Here, we used molecular dynamics (MD) simulations energy calculations investigate structural energetic differences hACE2- RBD complexes wild-type (WT), Delta, subvariants. Our results indicate that Delta first variants showed highest second-highest among studied. Furthermore, while exhibit increased stability altered electrostatic potential at hACE2–RBD interface when compared ancestral WT, their strength does not consistently increase with evolution. Moreover, newer subvariants like JN.1 a bimodal conformational strategy, alternating high-affinity state low-affinity state, which could potentially facilitate evasion. These findings suggest that, addition enhanced affinity, other factors, such as evasion adaptability, shape SARS-CoV-2

Язык: Английский

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An engineered miniACE2 protein secreted by mesenchymal stromal cells effectively neutralizes multiple SARS-CoV- 2 variants in vitro

Molecular Medicine, Год журнала: 2025, Номер 31(1)

Опубликована: Апрель 23, 2025

Язык: Английский

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