1
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Stocks BB, Thibeault MP, L'Abbé D, Umer M, Liu Y, Stuible M, Durocher Y, Melanson JE. Characterization of biotinylated human ACE2 and SARS-CoV-2 Omicron BA.4/5 spike protein reference materials. Anal Bioanal Chem 2024; 416:4861-4872. [PMID: 38942955 PMCID: PMC11330416 DOI: 10.1007/s00216-024-05413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Accurate diagnostic and serology assays are required for the continued management of the COVID-19 pandemic yet spike protein mutations and intellectual property concerns with antigens and antibodies used in various test kits render comparability assessments difficult. As the use of common, well-characterized reagents can help address this lack of standardization, the National Research Council Canada has produced two protein reference materials (RMs) for use in SARS-CoV-2 serology assays: biotinylated human angiotensin-converting enzyme 2 RM, ACE2-1, and SARS-CoV-2 Omicron BA.4/5 spike protein RM, OMIC-1. Reference values were assigned through a combination of amino acid analysis via isotope dilution liquid chromatography tandem mass spectrometry following acid hydrolysis, and ultraviolet-visible (UV-Vis) spectrophotometry at 280 nm. Vial-to-vial homogeneity was established using UV-Vis measurements, and protein oligomeric status, monitored by size exclusion liquid chromatography (LC-SEC), was used to evaluate transportation, storage, and freeze-thaw stabilities. The molar protein concentration in ACE2-1 was 25.3 ± 1.7 µmol L-1 (k = 2, 95% CI) and consisted almost exclusively (98%) of monomeric ACE2, while OMIC-1 contained 5.4 ± 0.5 µmol L-1 (k = 2) spike protein in a mostly (82%) trimeric form. Glycoprotein molar mass determination by LC-SEC with multi-angle light scattering detection facilitated calculation of corresponding mass concentrations. To confirm protein functionality, the binding of OMIC-1 to immobilized ACE2-1 was investigated with surface plasmon resonance and the resulting dissociation constant, KD ~ 4.4 nM, was consistent with literature values.
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Affiliation(s)
- Bradley B Stocks
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada.
| | - Marie-Pier Thibeault
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Denis L'Abbé
- Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Muhammad Umer
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Yali Liu
- Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Matthew Stuible
- Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Yves Durocher
- Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Jeremy E Melanson
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
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2
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Barrera A, Martínez-Valdebenito C, Angulo J, Palma C, Hormazábal J, Vial C, Aguilera X, Castillo-Torres P, Pardo-Roa C, Balcells ME, Nervi B, Corre NL, Ferrés M. SARS-CoV-2 infectivity and antigenic evasion: spotlight on isolated Omicron sub-lineages. Front Med (Lausanne) 2024; 11:1414331. [PMID: 39267969 PMCID: PMC11390582 DOI: 10.3389/fmed.2024.1414331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/16/2024] [Indexed: 09/15/2024] Open
Abstract
Since the SARS-CoV-2 outbreak in 2019, a diversity of viral genomic variants has emerged and spread globally due to increased transmissibility, pathogenicity, and immune evasion. By the first trimester of 2023 in Chile, as in most countries, BQ and XBB were the predominant circulating sub-lineages of Omicron. The molecular and antigenic characteristics of these variants have been mainly determined using non-authentic spike pseudoviruses, which is often described as a limitation. Additionally, few comparative studies using isolates from recent Omicron sub-lineages have been conducted. In this study, we isolated SARS-CoV-2 variants from clinical samples, including the ancestral B.1.1, Delta, Omicron BA.1, and sub-lineages of BA.2 and BA.5. We assessed their infectivity through cell culture infections and their antibody evasion using neutralization assays. We observed variations in viral plaque size, cell morphology, and cytotoxicity upon infection in Vero E6-TMPRSS2 cells for each variant compared to the ancestral B.1.1 virus. BA.2-derived sub-variants, such as XBB.1.5, showed attenuated viral replication, while BA.5-derived variants, such as BQ.1.1, exhibited replication rates similar to the ancestral SARS-CoV-2 virus. Similar trends were observed in intestinal Caco-2 cells, except for Delta. Antibody neutralization experiments using sera from individuals infected during the first COVID-19 wave (FWI) showed a consistent but moderate reduction in neutralization against Omicron sub-lineages. Interestingly, despite being less prevalent, BQ.1.1 showed a 6.1-fold greater escape from neutralization than XBB.1.5. Neutralization patterns were similar when tested against sera from individuals vaccinated with 3xBNT162b2 (PPP) or Coronavac-Coronavac-BNT162b2 (CCP) schedules. However, CCP sera showed 2.3-fold higher neutralization against XBB.1.5 than FWI and PPP sera. This study provides new insights into the differences between BA.2 and BA.5-derived variants, leading to their eventual outcompetition. Our analysis offers important evidence regarding the balance between infectivity and antigenic escape that drives the evolution of second-generation SARS-CoV-2 variants in the population.
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Affiliation(s)
- Aldo Barrera
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Martínez-Valdebenito
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jenniffer Angulo
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Palma
- Laboratorio de Infectología y Virología Molecular, Facultad de Medicina y Red de Salud UC CHRISTUS, Santiago, Chile
| | - Juan Hormazábal
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Ximena Aguilera
- Centro de Epidemiología y Políticas de Salud, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Pablo Castillo-Torres
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Salud del Niño y el Adolescente, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina Pardo-Roa
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Salud del Niño y el Adolescente, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Elvira Balcells
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bruno Nervi
- Departamento de Hematología y Oncología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Le Corre
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Laboratorio de Infectología y Virología Molecular, Facultad de Medicina y Red de Salud UC CHRISTUS, Santiago, Chile
| | - Marcela Ferrés
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Laboratorio de Infectología y Virología Molecular, Facultad de Medicina y Red de Salud UC CHRISTUS, Santiago, Chile
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3
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Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF. Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure 2024; 32:1055-1067.e6. [PMID: 39013463 DOI: 10.1016/j.str.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/16/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024]
Abstract
The recently emerged BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 variants have a growth advantage. In this study, we explore the structural bases of receptor binding and immune evasion for the Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Our findings reveal that BA.2.86 exhibits strong receptor binding, whereas its JN.1 sub-lineage displays a decreased binding affinity to human ACE2 (hACE2). Through complex structure analyses, we observed that the reversion of R493Q in BA.2.86 receptor binding domain (RBD) plays a facilitating role in receptor binding, while the L455S substitution in JN.1 RBD restores optimal affinity. Furthermore, the structure of monoclonal antibody (mAb) S309 complexed with BA.2.86 RBD highlights the importance of the K356T mutation, which brings a new N-glycosylation motif, altering the binding pattern of mAbs belonging to RBD-5 represented by S309. These findings emphasize the importance of closely monitoring BA.2.86 and its sub-lineages to prevent another wave of SARS-CoV-2 infections.
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MESH Headings
- Humans
- SARS-CoV-2/immunology
- SARS-CoV-2/metabolism
- SARS-CoV-2/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Immune Evasion
- Protein Binding
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- COVID-19/immunology
- COVID-19/virology
- COVID-19/metabolism
- Binding Sites
- Models, Molecular
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Mutation
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Affiliation(s)
- Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Beijing Life Science Academy, Beijing, China
| | - Kaiyuan Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Yuhang Gu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Junqing Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | | | - Xiaomei Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Guanghui Yu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hui Tan
- Shenzhen Children's Hospital, Shenzhen, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiaopeng Ma
- Shenzhen Children's Hospital, Shenzhen, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Beijing Life Science Academy, Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China; Beijing Life Science Academy, Beijing, China; College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China.
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4
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Fujimoto A, Kawai H, Kawamura R, Kitamura A. Interaction of Receptor-Binding Domain of the SARS-CoV-2 Omicron Variant with hACE2 and Actin. Cells 2024; 13:1318. [PMID: 39195208 DOI: 10.3390/cells13161318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/01/2024] [Accepted: 08/04/2024] [Indexed: 08/29/2024] Open
Abstract
The omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in 2021 as a variant with heavy amino acid mutations in the spike protein, which is targeted by most vaccines, compared to previous variants. Amino acid substitutions in the spike proteins may alter their affinity for host viral receptors and the host interactome. Here, we found that the receptor-binding domain (RBD) of the omicron variant of SARS-CoV-2 exhibited an increased affinity for human angiotensin-converting enzyme 2, a viral cell receptor, compared to the prototype RBD. Moreover, we identified β- and γ-actin as omicron-specific binding partners of RBD. Protein complex predictions revealed that many omicron-specific amino acid substitutions affected the affinity between RBD of the omicron variant and actin. Our findings indicate that proteins localized to different cellular compartments exhibit strong binding to the omicron RBD.
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Affiliation(s)
- Ai Fujimoto
- Laboratory of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan
| | - Haruki Kawai
- Laboratory of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan
| | - Rintaro Kawamura
- Laboratory of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan
| | - Akira Kitamura
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan
- PRIME, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo 100-0004, Japan
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5
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Du Q, Liang R, Wu M, Yang M, Xie Y, Liu Q, Tang K, Lin X, Yuan S, Shen J. Alisol B 23-acetate broadly inhibits coronavirus through blocking virus entry and suppresses proinflammatory T cells responses for the treatment of COVID-19. J Adv Res 2024; 62:273-290. [PMID: 37802148 PMCID: PMC11331179 DOI: 10.1016/j.jare.2023.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/11/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
INTRODUCTION Emerging severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 causes a global health disaster and pandemic. Seeking effective anti-pan-CoVs drugs benefit critical illness patients of coronavirus disease 2019 (COVID-19) but also may play a role in emerging CoVs of the future. OBJECTIVES This study tested the hypothesis that alisol B 23-acetate could be a viral entry inhibitor and would have proinflammatory inhibition for COVID-19 treatment. METHODS SARS-CoV-2 and its variants infected several cell lines were applied to evaluate the anti-CoVs activities of alisol B 23-aceate in vitro. The effects of alisol B 23-acetate on in vivo models were assessed by using SARS-CoV-2 and its variants challenged hamster and human angiotensin-converting enzyme 2 (ACE2) transgenic mice. The target of alisol B 23-acetate to ACE2 was analyzed using hydrogen/deuterium exchange (HDX) mass spectrometry (MS). RESULTS Alisol B 23-acetate had inhibitory effects on different species of coronavirus. By using HDX-MS, we found that alisol B 23-acetate had inhibition potency toward ACE2. In vivo experiments showed that alisol B 23-acetate treatment remarkably decreased viral copy, reduced CD4+ T lymphocytes and CD11b+ macrophages infiltration and ameliorated lung damages in the hamster model. In Omicron variant infected human ACE2 transgenic mice, alisol B 23-acetate effectively alleviated viral load in nasal turbinate and reduced proinflammatory cytokines interleukin 17 (IL17) and interferon γ (IFNγ) in peripheral blood. The prophylactic treatment of alisol B 23-acetate by intranasal administration significantly attenuated Omicron viral load in the hamster lung tissues. Moreover, alisol B 23-acetate treatment remarkably inhibited proinflammatory responses through mitigating the secretions of IFNγ and IL17 in the cultured human and mice lymphocytes in vitro. CONCLUSION Alisol B 23-acetate could be a promising therapeutic agent for COVID-19 treatment and its underlying mechanisms might be attributed to viral entry inhibition and anti-inflammatory activities.
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Affiliation(s)
- Qiaohui Du
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Ronghui Liang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Meiling Wu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Minxiao Yang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Yubin Xie
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Qing Liu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Kaiming Tang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Xiang Lin
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China.
| | - Jiangang Shen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong Special Administrative Region.
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6
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Cao C, Zhang G, Li X, Wang Y, Lü J. Nanomechanical collective vibration of SARS-CoV-2 spike proteins. J Mol Recognit 2024; 37:e3091. [PMID: 38773782 DOI: 10.1002/jmr.3091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/08/2024] [Accepted: 05/12/2024] [Indexed: 05/24/2024]
Abstract
The development of effective therapeutics against COVID-19 requires a thorough understanding of the receptor recognition mechanism of the SARS-CoV-2 spike (S) protein. Here the multidomain collective dynamics on the trimer of the spike protein has been analyzed using normal mode analysis (NMA). A common nanomechanical profile was identified in the spike proteins of SARS-CoV-2 and its variants. The profile involves collective vibrations of the receptor-binding domain (RBD) and the N-terminal domain (NTD), which may mediate the physical interaction process. Quantitative analysis of the collective modes suggests a nanomechanical property involving large-scale conformational changes, which explains the difference in receptor binding affinity among different variants. These results support the use of intrinsic global dynamics as a valuable perspective for studying the allosteric and functional mechanisms of the S protein. This approach also provides a low-cost theoretical toolkit for screening potential pathogenic mutations and drug targets.
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Affiliation(s)
- Changfeng Cao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guangxu Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- College of Pharmacy, Binzhou Medical University, Yantai, China
| | - Xueling Li
- College of Public Health, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Yadi Wang
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- College of Pharmacy, Binzhou Medical University, Yantai, China
| | - Junhong Lü
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- College of Pharmacy, Binzhou Medical University, Yantai, China
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7
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations. Phys Chem Chem Phys 2024; 26:17720-17744. [PMID: 38869513 DOI: 10.1039/d4cp01372g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In this study, we combined AlphaFold-based approaches for atomistic modeling of multiple protein states and microsecond molecular simulations to accurately characterize conformational ensembles evolution and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variants BA.1, BA.2, BA.2.75, BA.3, BA.4/BA.5 and BQ.1.1. We employed and validated several different adaptations of the AlphaFold methodology for modeling of conformational ensembles including the introduced randomized full sequence scanning for manipulation of sequence variations to systematically explore conformational dynamics of Omicron spike protein complexes with the ACE2 receptor. Microsecond atomistic molecular dynamics (MD) simulations provide a detailed characterization of the conformational landscapes and thermodynamic stability of the Omicron variant complexes. By integrating the predictions of conformational ensembles from different AlphaFold adaptations and applying statistical confidence metrics we can expand characterization of the conformational ensembles and identify functional protein conformations that determine the equilibrium dynamics for the Omicron spike complexes with the ACE2. Conformational ensembles of the Omicron RBD-ACE2 complexes obtained using AlphaFold-based approaches for modeling protein states and MD simulations are employed for accurate comparative prediction of the binding energetics revealing an excellent agreement with the experimental data. In particular, the results demonstrated that AlphaFold-generated extended conformational ensembles can produce accurate binding energies for the Omicron RBD-ACE2 complexes. The results of this study suggested complementarities and potential synergies between AlphaFold predictions of protein conformational ensembles and MD simulations showing that integrating information from both methods can potentially yield a more adequate characterization of the conformational landscapes for the Omicron RBD-ACE2 complexes. This study provides insights in the interplay between conformational dynamics and binding, showing that evolution of Omicron variants through acquisition of convergent mutational sites may leverage conformational adaptability and dynamic couplings between key binding energy hotspots to optimize ACE2 binding affinity and enable immune evasion.
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Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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8
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Xue S, Han Y, Wu F, Wang Q. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Protein Cell 2024; 15:403-418. [PMID: 38442025 PMCID: PMC11131022 DOI: 10.1093/procel/pwae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in various novel variants with distinct mutation profiles. Point mutations, particularly those within the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein, lead to the functional alteration in both receptor engagement and monoclonal antibody (mAb) recognition. Here, we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion. Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity. However, this weakened effect could be largely compensated by specific epistatic mutations, such as N501Y, thus maintaining the overall ACE2 affinity for the spike protein of all major variants. The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions. Together, this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is maintained, emphasizing the significance of comprehensive assessment of spike mutations.
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Affiliation(s)
- Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fan Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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9
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Leducq V, Zafilaza K, Fauchois A, Ghidaoui E, Sayon S, Dorival C, Meledje ML, Lusivika-Nzinga C, Yordanov Y, Martin-Blondel G, Carrat F, Marcelin AG, Soulie C. Spike Protein Genetic Evolution in Patients at High Risk of Severe Coronavirus Disease 2019 Treated by Monoclonal Antibodies. J Infect Dis 2024; 229:1341-1351. [PMID: 37996072 DOI: 10.1093/infdis/jiad523] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/16/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND High-risk patients, often immunocompromised and not responding to vaccine, continue to experience severe coronavirus disease 2019 (COVID-19) and death. Monoclonal antibodies (mAbs) were shown to be effective to prevent severe COVID-19 for these patients. Nevertheless, concerns about the emergence of resistance mutations were raised. METHODS We conducted a multicentric prospective cohort study, including 264 patients with mild to moderate COVID-19 at high risk for progression to severe COVID-19 and treated early with casirivimab/imdevimab, sotrovimab, or tixagevimab/cilgavimab. We sequenced the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during follow-up and searched for emerging spike mutations. RESULTS Immunocompromised patients have a 6-fold increased risk of developing mutations, which are associated with a prolonged duration of viral clearance but no clinical worsening. Emerging P337S/R/L/H, E340D/K/A/Q/V/G, and K356T/R substitutions in patients treated with sotrovimab are associated with higher viral RNA loads for up to 14 days post-treatment initiation. Tixagevimab/cilgavimab is associated with a 5-fold increased risk of developing mutations. R346K/I/T/S and K444R/N/M substitutions associated with tixagevimab/cilgavimab have been identified in multiple SARS-CoV-2 lineages, including BQ.1 and XBB. CONCLUSIONS The probability of emerging mutations arising in response to mAbs is significant, emphasizing the crucial need to investigate these mutations thoroughly and assess their impact on patients and the evolutionary trajectory of SARS-CoV-2.
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Affiliation(s)
- Valentin Leducq
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Karen Zafilaza
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Antoine Fauchois
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Emna Ghidaoui
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Sophie Sayon
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Céline Dorival
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Marie-Laure Meledje
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Clovis Lusivika-Nzinga
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Epidémiologie clinique des maladies virales chroniques (CLEPIVIR), Paris, France
| | - Youri Yordanov
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Service d'Accueil des Urgences, Paris, France
| | - Guillaume Martin-Blondel
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Toulouse, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Inserm, Université Toulouse III, Toulouse, France
| | - Fabrice Carrat
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Département de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
| | - Cathia Soulie
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de virologie, Paris, France
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10
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Fu Y, He X, Fang Q, Kong F, Zhang Y, Fu T, Chen L, Liu Y, Wang Z, Lyu J, Chen L. Rapid identification of SARS-CoV-2 variants using stable high-frequency mutation sites. APMIS 2024; 132:348-357. [PMID: 38488266 DOI: 10.1111/apm.13388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/25/2024] [Indexed: 04/16/2024]
Abstract
Respiratory infectious viruses, including SARS-CoV-2, undergo rapid genetic evolution, resulting in diverse subtypes with complex mutations. Detecting and differentiating these subtypes pose significant challenges in respiratory virus surveillance. To address these challenges, we integrated ARMS-PCR with molecular beacon probes, allowing selective amplification and discrimination of subtypes based on adjacent mutation sites. The method exhibited high specificity and sensitivity, detecting as low as 104 copies/mL via direct fluorescence analysis and ~106 copies/mL using real-time PCR. Our robust detection approach offers a reliable and efficient solution for monitoring evolving respiratory infections, aiding early diagnosis and control measures. Further research could extend its application to other respiratory viruses and optimize its implementation in clinical settings.
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Affiliation(s)
- Yu Fu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Xiaobai He
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Quan Fang
- Department of laboratory, Physical Examination Center, Air Force Hangzhou Special Service Convalescence Center Zone 1, Hangzhou, China
| | - Fei Kong
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Yan Zhang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Ting Fu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Liang Chen
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - YanXin Liu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Zhen Wang
- Center for Laboratory Medicine, Allergy center, Department of Transfusion medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jianxin Lyu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Linjie Chen
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
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11
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Shukla N, Roelle SM, Snell JC, DelSignore O, Bruchez AM, Matreyek KA. Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage. PLoS Pathog 2024; 20:e1012044. [PMID: 38768238 PMCID: PMC11142672 DOI: 10.1371/journal.ppat.1012044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/31/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike's interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.
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Affiliation(s)
- Nidhi Shukla
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Sarah M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - John C. Snell
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Olivia DelSignore
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anna M. Bruchez
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
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12
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Antia A, Alvarado DM, Zeng Q, Casorla-Perez LA, Davis DL, Sonnek NM, Ciorba MA, Ding S. SARS-CoV-2 Omicron BA.1 Variant Infection of Human Colon Epithelial Cells. Viruses 2024; 16:634. [PMID: 38675974 PMCID: PMC11055019 DOI: 10.3390/v16040634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The Omicron variant of SARS-CoV-2, characterized by multiple subvariants including BA.1, XBB.1.5, EG.5, and JN.1, became the predominant strain in early 2022. Studies indicate that Omicron replicates less efficiently in lung tissue compared to the ancestral strain. However, the infectivity of Omicron in the gastrointestinal tract is not fully defined, despite the fact that 70% of COVID-19 patients experience digestive disease symptoms. Here, using primary human colonoids, we found that, regardless of individual variability, Omicron infects colon cells similarly or less effectively than the ancestral strain or the Delta variant. The variant induced limited type III interferon expression and showed no significant impact on epithelial integrity. Further experiments revealed inefficient cell-to-cell spread and spike protein cleavage in the Omicron spike protein, possibly contributing to its lower infectious particle levels. The findings highlight the variant-specific replication differences in human colonoids, providing insights into the enteric tropism of Omicron and its relevance to long COVID symptoms.
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Affiliation(s)
- Avan Antia
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.A.); (Q.Z.)
| | - David M. Alvarado
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Qiru Zeng
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.A.); (Q.Z.)
| | - Luis A. Casorla-Perez
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Deanna L. Davis
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Naomi M. Sonnek
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Matthew A. Ciorba
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.A.); (Q.Z.)
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13
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Nguyen HL, Nguyen TQ, Li MS. SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study. J Phys Chem B 2024; 128:3340-3349. [PMID: 38564480 PMCID: PMC11017248 DOI: 10.1021/acs.jpcb.3c06270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high contagious ability. Studies have shown that the Omicron binds human ACE2 more strongly than the wild type. The prevalence of Omicron in new cases of COVID-19 promotes novel lineages with improved receptor binding affinity and immune evasion. To shed light on this open problem, in this work, we investigated the binding free energy of the receptor binding domain of the Omicron lineages BA.2, BA.2.3.20, BA.3, BA4/BA5, BA.2.75, BA.2.75.2, BA.4.6, XBB.1, XBB.1.5, BJ.1, BN.1, BQ.1.1, and CH.1.1 to human ACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. The results show that these lineages have increased binding affinity compared to the BA.1 lineage, and BA.2.75 and BA.2.75.2 subvariants bind ACE2 more strongly than others. However, in general, the binding affinities of the Omicron lineages do not differ significantly from each other. The electrostatic force dominates over the van der Waals force in the interaction between Omicron lineages and human cells. Based on our results, we argue that viral evolution does not further improve the affinity of SARS-CoV-2 for ACE2 but may increase immune evasion.
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Affiliation(s)
- Hoang Linh Nguyen
- Institute
of Fundamental and Applied Sciences, Duy
Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty
of Environmental and Natural Sciences, Duy
Tan University, Da Nang 550000, Vietnam
| | - Thai Quoc Nguyen
- Faculty
of Physics, VNU University of Science, Vietnam
National University, 334 Nguyen Trai, Hanoi 100000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap 81000, Vietnam
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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14
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587850. [PMID: 38617283 PMCID: PMC11014522 DOI: 10.1101/2024.04.02.587850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
In this study, we combined AlphaFold-based approaches for atomistic modeling of multiple protein states and microsecond molecular simulations to accurately characterize conformational ensembles and binding mechanisms of convergent evolution for the SARS-CoV-2 Spike Omicron variants BA.1, BA.2, BA.2.75, BA.3, BA.4/BA.5 and BQ.1.1. We employed and validated several different adaptations of the AlphaFold methodology for modeling of conformational ensembles including the introduced randomized full sequence scanning for manipulation of sequence variations to systematically explore conformational dynamics of Omicron Spike protein complexes with the ACE2 receptor. Microsecond atomistic molecular dynamic simulations provide a detailed characterization of the conformational landscapes and thermodynamic stability of the Omicron variant complexes. By integrating the predictions of conformational ensembles from different AlphaFold adaptations and applying statistical confidence metrics we can expand characterization of the conformational ensembles and identify functional protein conformations that determine the equilibrium dynamics for the Omicron Spike complexes with the ACE2. Conformational ensembles of the Omicron RBD-ACE2 complexes obtained using AlphaFold-based approaches for modeling protein states and molecular dynamics simulations are employed for accurate comparative prediction of the binding energetics revealing an excellent agreement with the experimental data. In particular, the results demonstrated that AlphaFold-generated extended conformational ensembles can produce accurate binding energies for the Omicron RBD-ACE2 complexes. The results of this study suggested complementarities and potential synergies between AlphaFold predictions of protein conformational ensembles and molecular dynamics simulations showing that integrating information from both methods can potentially yield a more adequate characterization of the conformational landscapes for the Omicron RBD-ACE2 complexes. This study provides insights in the interplay between conformational dynamics and binding, showing that evolution of Omicron variants through acquisition of convergent mutational sites may leverage conformational adaptability and dynamic couplings between key binding energy hotspots to optimize ACE2 binding affinity and enable immune evasion.
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15
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Li W, Xu Z, Niu T, Xie Y, Zhao Z, Li D, He Q, Sun W, Shi K, Guo W, Chang Z, Liu K, Fan Z, Qi J, Gao GF. Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins. EMBO J 2024; 43:1484-1498. [PMID: 38467833 PMCID: PMC11021471 DOI: 10.1038/s44318-024-00062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding and immune evasion are recognized as two major drivers for evolution of the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, the underlying mechanism of interplay between two factors remains incompletely understood. Herein, we determined the structures of human ACE2 complexed with BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5 RBDs. Based on the ACE2/RBD structures of these sub-variants and a comparison with the known complex structures, we found that R346T substitution in the RBD enhanced ACE2 binding upon an interaction with the residue R493, but not Q493, via a mechanism involving long-range conformation changes. Furthermore, we found that R493Q and F486V exert a balanced impact, through which immune evasion capability was somewhat compromised to achieve an optimal receptor binding. We propose a "two-steps-forward and one-step-backward" model to describe such a compromise between receptor binding affinity and immune evasion during RBD evolution of Omicron sub-variants.
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Affiliation(s)
- Weiwei Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Tianhui Niu
- Air Force Medical University, Air Force Medical center, PLA, Beijing, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Zhennan Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Qingwen He
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wenqiao Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Kaiyuan Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wenjing Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Chang
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zheng Fan
- Institutional Core Facility, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
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16
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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17
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Liu Y, Li D, Han J. COVID-19 vaccines and beyond. Cell Mol Immunol 2024; 21:207-209. [PMID: 38273150 PMCID: PMC10902311 DOI: 10.1038/s41423-024-01132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/01/2024] [Indexed: 01/27/2024] Open
Affiliation(s)
- Yiyuan Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Danying Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
- Laboratory Animal Center, Xiamen University, Xiamen, Fujian, China.
- Research Unit of Cellular Stress of CAMS, Cancer Research Center of Xiamen University, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China.
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18
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Shukla N, Roelle SM, Snell JC, DelSignore O, Bruchez AM, Matreyek KA. Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580056. [PMID: 38405739 PMCID: PMC10888787 DOI: 10.1101/2024.02.13.580056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike's interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.
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Affiliation(s)
- Nidhi Shukla
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Sarah M Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - John C Snell
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Olivia DelSignore
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Anna M Bruchez
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kenneth A Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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19
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Kesika P, Thangaleela S, Sisubalan N, Radha A, Sivamaruthi BS, Chaiyasut C. The Role of the Nuclear Factor-Kappa B (NF-κB) Pathway in SARS-CoV-2 Infection. Pathogens 2024; 13:164. [PMID: 38392902 PMCID: PMC10892479 DOI: 10.3390/pathogens13020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
COVID-19 is a global health threat caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is associated with a significant increase in morbidity and mortality. The present review discusses nuclear factor-kappa B (NF-κB) activation and its potential therapeutical role in treating COVID-19. COVID-19 pathogenesis, the major NF-κB pathways, and the involvement of NF-κB in SARS-CoV-2 have been detailed. Specifically, NF-κB activation and its impact on managing COVID-19 has been discussed. As a central player in the immune and inflammatory responses, modulating NF-κB activation could offer a strategic avenue for managing SARS-CoV-2 infection. Understanding the NF-κB pathway's role could aid in developing treatments against SARS-CoV-2. Further investigations into the intricacies of NF-κB activation are required to reveal effective therapeutic strategies for managing and combating the SARS-CoV-2 infection and COVID-19.
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Affiliation(s)
- Periyanaina Kesika
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand; (P.K.); (N.S.)
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Subramanian Thangaleela
- Institute of Biotechnology, Department of Medical Biotechnology and Integrative Physiology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
| | - Natarajan Sisubalan
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand; (P.K.); (N.S.)
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Arumugam Radha
- Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | | | - Chaiyavat Chaiyasut
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
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20
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Liu TW, Hsu SJ, Hsieh YSY, Liu HK, Lee CK. Polymethoxyflavone from Citrus depressa as an inhibitor against various variants of SARS-CoV-2 spike protein. JOURNAL OF ETHNOPHARMACOLOGY 2024; 320:117412. [PMID: 37995824 DOI: 10.1016/j.jep.2023.117412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In traditional Taiwanese medicine, Citrus depressa Hayata serves as the raw material of Chen-Pi which has been widely used to treat respiratory ailments. Scientific investigations have validated the attributes of C. depressa, elucidating its valuable properties, including antioxidative, anti-inflammatory, anticancer, neuroprotion, hepatoprotection, and hypolipidemic effects. AIM OF THE STUDY This study aims to isolate a universal inhibitor of the SARS-CoV-2 spike protein from C. depressa and confirm the mechanism by which these inhibitors disrupt the binding of the spike protein to hACE2. MATERIALS AND METHODS The whole fruit of C. depressa was subjected to ethanol extraction, following by partitioning to obtain water, butanol, and ethyl acetate fractions. To identify the inhibitory components in citrus fruits, we performed both the SPR assay and the SARS-CoV-2 pseudo-virus assays. Subsequently, we employed a bioassay-guided approach to efficiently isolate and characterize the bioactive constituents that hindered the interaction between the SARS-CoV-2 spike protein and hACE2, using a combination of MPLC and Semi-preparative HPLC for compound isolation. ELISA based spike protein binding assay evaluate the inhibitory activities of the extract and potential constituents against multiple spike protein variants. To further shed light on the inhibitory mechanism, candidate inhibitors were validated through the SPR assay and molecular docking. RESULTS The crude extract and ethyl acetate layer derived from C. depressa showed significant inhibitory activity on SARS-CoV-2 Omicron BA.4/5, with IC50 of 77.4 μg/mL and 100 μg/mL, respectively. Ten potential compounds from C. depressa have been identified with inhibitory activity against various SARS-CoV-2 spike proteins. 2'-hydroxy-4,4',5',6'-tetramethoxychalcone (Cd3) and 5-hydroxy-3',4',6,7,8-pentamethoxyflavone (Cd8) also showed good inhibitory activity to the spike protein, with KD of 0.79 μM and 37.3 nM, respectively. These findings are in line with prior study, indicating Cd3 and Cd8 can bind to key amino acid residue, disrupting the formation of the spike protein and h-ACE2 complex. CONCLUSION This study presents the initial evidence showcasing the inhibitory effect of polymethoxyflavones (PMFs) on the spike protein of SARS-CoV-2. Moreover, the inhibitory activity of C. depressa extracts indicates their potential to prevent infections of different SARS-CoV-2 variants.
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Affiliation(s)
- Ta-Wei Liu
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 11042, Taiwan.
| | - Su-Jung Hsu
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 11042, Taiwan.
| | - Yves S Y Hsieh
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 11042, Taiwan; Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei, 11042, Taiwan; Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, SE106 91, Sweden.
| | - Hui-Kang Liu
- National Research Institute of Chinese Medicine (NRICM), Ministry of Health and Welfare, Taipei City, Taiwan; Ph. D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Ching-Kuo Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 11042, Taiwan; Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei, 11042, Taiwan; Ph. D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei, Taiwan.
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21
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Lan PD, Nissley DA, O’Brien EP, Nguyen TT, Li MS. Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2. J Chem Phys 2024; 160:055101. [PMID: 38310477 PMCID: PMC11223169 DOI: 10.1063/5.0188053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
The binding of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein to the host cell receptor angiotensin-converting enzyme 2 (ACE2) is the first step in human viral infection. Therefore, understanding the mechanism of interaction between RBD and ACE2 at the molecular level is critical for the prevention of COVID-19, as more variants of concern, such as Omicron, appear. Recently, atomic force microscopy has been applied to characterize the free energy landscape of the RBD-ACE2 complex, including estimation of the distance between the transition state and the bound state, xu. Here, using a coarse-grained model and replica-exchange umbrella sampling, we studied the free energy landscape of both the wild type and Omicron subvariants BA.1 and XBB.1.5 interacting with ACE2. In agreement with experiment, we find that the wild type and Omicron subvariants have similar xu values, but Omicron binds ACE2 more strongly than the wild type, having a lower dissociation constant KD.
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Affiliation(s)
| | - Daniel A. Nissley
- Department of Statistics, University of Oxford, Oxford Protein Bioinformatics Group, Oxford OX1 2JD, United Kingdom
| | | | - Toan T. Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems and Department of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University - Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 11400, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
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22
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Liu W, Huang Z, Xiao J, Wu Y, Xia N, Yuan Q. Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness. Viruses 2024; 16:184. [PMID: 38399960 PMCID: PMC10893260 DOI: 10.3390/v16020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Over the last three years, the pandemic of COVID-19 has had a significant impact on people's lives and the global economy. The incessant emergence of variant strains has compounded the challenges associated with the management of COVID-19. As the predominant variant from late 2021 to the present, Omicron and its sublineages, through continuous evolution, have demonstrated iterative viral fitness. The comprehensive elucidation of the biological implications that catalyzed this evolution remains incomplete. In accordance with extant research evidence, we provide a comprehensive review of subvariants of Omicron, delineating alterations in immune evasion, cellular infectivity, and the cross-species transmission potential. This review seeks to clarify the underpinnings of biology within the evolution of SARS-CoV-2, thereby providing a foundation for strategic considerations in the post-pandemic era of COVID-19.
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Affiliation(s)
- Wenhao Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Jin Xiao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Yangtao Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Quan Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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23
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Li D, Sun C, Zhuang P, Mei X. Revolutionizing SARS-CoV-2 omicron variant detection: Towards faster and more reliable methods. Talanta 2024; 266:124937. [PMID: 37481886 DOI: 10.1016/j.talanta.2023.124937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The emergence of the highly contagious Omicron variant of SARS-CoV-2 has inflicted significant damage during the ongoing COVID-19 pandemic. This new variant's significant sequence changes and mutations in both proteins and RNA have rendered many existing rapid detection methods ineffective in identifying it accurately. As the world races to control the spread of the virus, researchers are urgently exploring new diagnostic strategies to specifically detect Omicron variants with high accuracy and sensitivity. In response to this challenge, we have compiled a comprehensive overview of the latest reported rapid detection techniques. These techniques include strategies for the simultaneous detection of multiple SARS-CoV-2 variants and methods for selectively distinguishing Omicron variants. By categorizing these diagnostic techniques based on their targets, which encompass protein antigens and nucleic acids, we aim to offer a comprehensive understanding of the utilization of various recognition elements in identifying these targets. We also highlight the advantages and limitations of each approach. Our work is crucial in providing a more nuanced understanding of the challenges and opportunities in detecting Omicron variants and emerging variants.
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Affiliation(s)
- Dan Li
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
| | - Cai Sun
- AECC Shenyang Liming Aero-Engine Co., Ltd., Shenyang, China
| | - Pengfei Zhuang
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Key Laboratory of Medical Tissue Engineering of Liaoning Province, Jinzhou Medical University, Jinzhou, Liaoning, China.
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24
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Rafaï CD, Heredeibona LS, Lango-Yaya E, Belizaire RD, Senzongo O, Mbala P, Fa-Ti-Gbia MO, Bengba JA, Pounguinza S, Kandou JEK, Gonessa DY, Koyaweda W, Vickos U, Kalla GC, Nambei WS, Somse P, Bélec L, Grésenguet G, Koffi B, Mbopi-Keou FX. Five successive waves of SARS-CoV-2 infection in the Central African Republic: a prospective observational study from 2020-2022. Pan Afr Med J 2023; 46:120. [PMID: 38465007 PMCID: PMC10924610 DOI: 10.11604/pamj.2023.46.120.39511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 11/30/2023] [Indexed: 03/12/2024] Open
Abstract
Introduction the National Laboratory of Clinical Biology and Public Health (NLBPH) in Bangui in the Central African Republic (CAR) carries out the vast majority of molecular screening tests for SARS-CoV-2 infection nationwide. This study aimed to show the contribution of molecular diagnosis and genomic surveillance in monitoring the evolution of longitudinal variations of the SARS-CoV-2 infection epidemic in CAR between 2020 and the end of 2022. Methods this is an observational study on the variations in the prevalence of detection of SARS-CoV-2 by RT-PCR at the NLCBPH from nasopharyngeal samples taken prospectively over a period of 3 years since the beginning of the COVID-19 epidemic. A subgroup of SARS-CoV-2 positive samples was selected for molecular sequencing performed by Illumina® and MinIon® at the National Institute for Biomedical Research in Kinshasa, Democratic Republic of the Congo. Results from March 2020 to December 31th, 2022, 88,442 RT-PCR tests were carried out (4/5 of the country) and detected 9,156 cases of SARS-CoV-2 infection in 5 successive waves. The average age of the patients was 39.8 years (extremes ranging from to 92 years). Age(P=0.001), sex(P=0.001) and symptom presentation(P=0.001) were significantly associated with RT-PCR test positivity. Among the different variants identified during successive waves, the Omicron variant predominated during the last two waves. Conclusion this prospective study over a period of 3 years, marked by 5 successive waves, made it possible to report that age, sex and the presence of clinical symptoms are associated with RT-PCR positivity. Among the different variants identified during successive waves, the Omicron variant predominated during the last two waves.
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Affiliation(s)
- Clotaire Donatien Rafaï
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
- Faculté des Sciences de la Santé, Université de Bangui, Centrafrique de la Santé et de la Population, Bangui, République Centrafricaine
| | | | - Ernest Lango-Yaya
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
- Faculté des Sciences de la Santé, Université de Bangui, Centrafrique de la Santé et de la Population, Bangui, République Centrafricaine
| | | | - Oscar Senzongo
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
| | - Placide Mbala
- National Institute of Biomedical Research of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Maurel Ouoko Fa-Ti-Gbia
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
| | - Javan Allon Bengba
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
| | - Simon Pounguinza
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
| | | | - Daniel Yvon Gonessa
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
| | - Wilfried Koyaweda
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
| | - Ulrich Vickos
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
| | - Ginette Claude Kalla
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Université Paris Cité, Paris, France
| | - Wilfried Sylvain Nambei
- Faculté des Sciences de la Santé, Université de Bangui, Centrafrique de la Santé et de la Population, Bangui, République Centrafricaine
| | - Pierre Somse
- Ministry of Health and population, Bangui, Central African Republic
| | - Laurent Bélec
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Université Paris Cité, Paris, France
| | - Gérard Grésenguet
- Faculté des Sciences de la Santé, Université de Bangui, Centrafrique de la Santé et de la Population, Bangui, République Centrafricaine
| | - Boniface Koffi
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine
- Faculté des Sciences de la Santé, Université de Bangui, Centrafrique de la Santé et de la Population, Bangui, République Centrafricaine
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25
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Parsons RJ, Acharya P. Evolution of the SARS-CoV-2 Omicron spike. Cell Rep 2023; 42:113444. [PMID: 37979169 PMCID: PMC10782855 DOI: 10.1016/j.celrep.2023.113444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/21/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern, first identified in November 2021, rapidly spread worldwide and diversified into several subvariants. The Omicron spike (S) protein accumulated an unprecedented number of sequence changes relative to previous variants. In this review, we discuss how Omicron S protein structural features modulate host cell receptor binding, virus entry, and immune evasion and highlight how these structural features differentiate Omicron from previous variants. We also examine how key structural properties track across the still-evolving Omicron subvariants and the importance of continuing surveillance of the S protein sequence evolution over time.
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Affiliation(s)
- Ruth J Parsons
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA.
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA.
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26
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Bains A, Fischer K, Guan W, LiWang PJ. The Antiviral Activity of the Lectin Griffithsin against SARS-CoV-2 Is Enhanced by the Presence of Structural Proteins. Viruses 2023; 15:2452. [PMID: 38140693 PMCID: PMC10747160 DOI: 10.3390/v15122452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Although COVID-19 transmission has been reduced by the advent of vaccinations and a variety of rapid monitoring techniques, the SARS-CoV-2 virus itself has shown a remarkable ability to mutate and persist. With this long track record of immune escape, researchers are still exploring prophylactic treatments to curtail future SARS-CoV-2 variants. Specifically, much focus has been placed on the antiviral lectin Griffithsin in preventing spike protein-mediated infection via the hACE2 receptor (direct infection). However, an oft-overlooked aspect of SARS-CoV-2 infection is viral capture by attachment receptors such as DC-SIGN, which is thought to facilitate the initial stages of COVID-19 infection in the lung tissue (called trans-infection). In addition, while immune escape is dictated by mutations in the spike protein, coronaviral virions also incorporate M, N, and E structural proteins within the particle. In this paper, we explored how several structural facets of both the SARS-CoV-2 virion and the antiviral lectin Griffithsin can affect and attenuate the infectivity of SARS-CoV-2 pseudovirus. We found that Griffithsin was a better inhibitor of hACE2-mediated direct infection when the coronaviral M protein is present compared to when it is absent (possibly providing an explanation regarding why Griffithsin shows better inhibition against authentic SARS-CoV-2 as opposed to pseudotyped viruses, which generally do not contain M) and that Griffithsin was not an effective inhibitor of DC-SIGN-mediated trans-infection. Furthermore, we found that DC-SIGN appeared to mediate trans-infection exclusively via binding to the SARS-CoV-2 spike protein, with no significant effect observed when other viral proteins (M, N, and/or E) were present. These results provide etiological data that may help to direct the development of novel antiviral treatments, either by leveraging Griffithsin binding to the M protein as a novel strategy to prevent SARS-CoV-2 infection or by narrowing efforts to inhibit trans-infection to focus on DC-SIGN binding to SARS-CoV-2 spike protein.
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Affiliation(s)
- Arjan Bains
- Chemistry and Biochemistry, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Kathryn Fischer
- Quantitative and Systems Biology, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Wenyan Guan
- Materials and Biomaterials Science and Engineering, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Patricia J. LiWang
- Molecular Cell Biology, Health Sciences Research Institute, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA
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27
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Yagüe Relimpio A, Fink A, Bui DT, Fabritz S, Schröter M, Ruggieri A, Platzman I, Spatz JP. Bottom-up Assembled Synthetic SARS-CoV-2 Miniviruses Reveal Lipid Membrane Affinity of Omicron Variant Spike Glycoprotein. ACS NANO 2023; 17:23913-23923. [PMID: 37976416 PMCID: PMC10722588 DOI: 10.1021/acsnano.3c08323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
The ongoing COVID-19 pandemic has been brought on by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike glycoprotein (S), which decorates the viral envelope forming a corona, is responsible for the binding to the angiotensin-converting enzyme 2 (ACE2) receptor and initiating the infection. In comparison to previous variants, Omicron S presents additional binding sites as well as a more positive surface charge. These changes hint at additional molecular targets for interactions between virus and cell, such as the cell membrane or proteoglycans on the cell surface. Herein, bottom-up assembled synthetic SARS-CoV-2 miniviruses (MiniVs), with a lipid composition similar to that of infectious particles, are implemented to study and compare the binding properties of Omicron and Alpha variants. Toward this end, a systematic functional screening is performed to study the binding ability of Omicron and Alpha S proteins to ACE2-functionalized and nonfunctionalized planar supported lipid bilayers. Moreover, giant unilamellar vesicles are used as a cell membrane model to perform competitive interaction assays of the two variants. Finally, two cell lines with and without presentation of the ACE2 receptor are used to confirm the binding properties of the Omicron and Alpha MiniVs to the cellular membrane. Altogether, the results reveal a significantly higher affinity of Omicron S toward both the lipid membrane and ACE2 receptor. The research presented here highlights the advantages of creating and using bottom-up assembled SARS-CoV-2 viruses to understand the impact of changes in the affinity of S for ACE2 in infection studies.
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Affiliation(s)
- Ana Yagüe Relimpio
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Andreas Fink
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Duc Thien Bui
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Department
for Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Martin Schröter
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Alessia Ruggieri
- Heidelberg
University, Medical Faculty, Centre for Integrative Infectious Disease Research (CIID), Department
of Infectious Diseases, Molecular Virology, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Ilia Platzman
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
- Max
Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, U.K.
| | - Joachim P. Spatz
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
- Max
Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, U.K.
- Max Planck
School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
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28
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Wang Q, Yeh AY, Guo Y, Mohri H, Yu J, Ho DD, Liu L. Impaired potency of neutralizing antibodies against cell-cell fusion mediated by SARS-CoV-2. Emerg Microbes Infect 2023; 12:2210237. [PMID: 37132357 PMCID: PMC10215017 DOI: 10.1080/22221751.2023.2210237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/30/2023] [Indexed: 05/04/2023]
Abstract
The SARS-CoV-2 Omicron subvariants have dominated the pandemic due to their high transmissibility and immune evasion conferred by the spike mutations. The Omicron subvariants can spread by cell-free virus infection and cell-cell fusion, the latter of which is more effective but has not been extensively investigated. In this study, we developed a simple and high-throughput assay that provides a rapid readout to quantify cell-cell fusion mediated by the SARS-CoV-2 spike proteins without using live or pseudotyped virus. This assay can be used to identify variants of concern and to screen for prophylactic and therapeutic agents. We further evaluated a panel of monoclonal antibodies (mAbs) and vaccinee sera against D614G and Omicron subvariants, finding that cell-cell fusion is substantially more resistant to mAb and serum inhibition than cell-free virus infection. Such results have important implications for the development of vaccines and antiviral antibody drugs against cell-cell fusion induced by SARS-CoV-2 spikes.
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Affiliation(s)
- Qian Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, USA
| | - Andre Yanchen Yeh
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, USA
- School of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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29
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567697. [PMID: 38045395 PMCID: PMC10690158 DOI: 10.1101/2023.11.18.567697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The latest wave SARS-CoV-2 Omicron variants displayed a growth advantage and the increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with all-atom MD simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that AlphaFold2-predicted conformational ensemble of the BA.2.86 spike protein complex can accurately capture the main dynamics signatures obtained from microscond molecular dynamics simulations. The ensemble-based dynamic mutational scanning of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 dissected the role of the BA.2 and BA.2.86 backgrounds in modulating binding free energy changes revealing a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 mutational sites R403K, F486P and R493Q. To examine immune evasion properties of BA.2.86 in atomistic detail, we performed large scale structure-based mutational profiling of the S protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against BA.2.86 variant. The results quantified specific function of the BA.2.86 mutations to ensure broad resistance against different classes of RBD antibodies. This study revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have primarily evolved to improve immune escape while modulating binding affinity with ACE2 through cooperative effect of R403K, F486P and R493Q mutations. The study supports a hypothesis that the impact of the increased ACE2 binding affinity on viral fitness is more universal and is mediated through cross-talk between convergent mutational hotspots, while the effect of immune evasion could be more variant-dependent.
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30
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Yang J, Lin S, Chen Z, Yang F, Guo L, Wang L, Duan Y, Zhang X, Dai Y, Yin K, Yu C, Yuan X, Sun H, He B, Cao Y, Ye H, Dong H, Liu X, Chen B, Li J, Zhao Q, Lu G. Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization. PLoS Pathog 2023; 19:e1011804. [PMID: 38033141 PMCID: PMC10688893 DOI: 10.1371/journal.ppat.1011804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023] Open
Abstract
The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility and profound immune-escape capacity makes it an urgent need to develop broad-spectrum therapeutics. Nanobodies have recently attracted extensive attentions due to their excellent biochemical and binding properties. Here, we report two high-affinity nanobodies (Nb-015 and Nb-021) that target non-overlapping epitopes in SARS-CoV-2 S-RBD. Both nanobodies could efficiently neutralize diverse viruses of SARS-CoV-2. The neutralizing mechanisms for the two nanobodies are further delineated by high-resolution nanobody/S-RBD complex structures. In addition, an Fc-based tetravalent nanobody format is constructed by combining Nb-015 and Nb-021. The resultant nanobody conjugate, designated as Nb-X2-Fc, exhibits significantly enhanced breadth and potency against all-tested SARS-CoV-2 variants, including Omicron sub-lineages. These data demonstrate that Nb-X2-Fc could serve as an effective drug candidate for the treatment of SARS-CoV-2 infection, deserving further in-vivo evaluations in the future.
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Affiliation(s)
- Jing Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fanli Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Wang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Duan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xindan Zhang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yushan Dai
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Keqing Yin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chongzhang Yu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xin Yuan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Honglu Sun
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haoyu Ye
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianbo Liu
- CHENGDU NB BIOLAB CO., LTD, Chengdu, Sichuan, China
| | - Bo Chen
- CHENGDU NB BIOLAB CO., LTD, Chengdu, Sichuan, China
| | - Jian Li
- School of Basic Medical Sciences, Chengdu University, Chengdu, Sichuan, China
| | - Qi Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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31
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Kimura I, Yamasoba D, Nasser H, Ito H, Zahradnik J, Wu J, Fujita S, Uriu K, Sasaki J, Tamura T, Suzuki R, Deguchi S, Plianchaisuk A, Yoshimatsu K, Kazuma Y, Mitoma S, Schreiber G, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Takaori-Kondo A, Ito J, Shirakawa K, Takayama K, Irie T, Hashiguchi T, Nakagawa S, Fukuhara T, Saito A, Ikeda T, Sato K. Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics. J Virol 2023; 97:e0101123. [PMID: 37796123 PMCID: PMC10781145 DOI: 10.1128/jvi.01011-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/16/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non-spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Medicine, Kobe University, Kobe, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuya Mitoma
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - The Genotype to Phenotype Japan (G2P-Japan) Consortium
MisawaNaoko1KosugiYusuke1PanLin1SuganamiMai1ChibaMika1YoshimuraRyo1YasudaKyoko1IidaKeiko1OhsumiNaomi1StrangeAdam P.1KakuYu1PlianchaisukArnon1GuoZiyi1HinayAlfredo Jr. Amolong1Mendoza TolentinoJarel Elgin1ChenLuo1ShimizuRyo2Monira BegumM. S. T.2TakahashiOtowa2IchiharaKimiko2JonathanMichael2MugitaYuka2SuzukiSaori3SuzukiTateki4KimuraKanako4NakajimaYukari4YajimaHisano4HashimotoRina4WatanabeYukio4SakamotoAyaka4YasuharaNaoko4NagataKayoko4NomuraRyosuke4HorisawaYoshihito4TashiroYusuke4KawaiYugo4ShibataniYuki5NishiuchiTomoko5YoshidaIsao6KawabataRyoko7MatsunoKeita8NaoNaganori9SawaHirofumi9TanakaShinya10TsudaMasumi10WangLei10OdaYoshikata10FerdousZannatul10ShishidoKenji10MotozonoChihiro11ToyodaMako11UenoTakamasa11TabataKaori12Institute of Medical Science, University of Tokyo, Tokyo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, JapanHokkaido University, Sapporo, JapanKyoto University, Kyoto, JapanUniversity of Miyazaki, Miyazaki, JapanTokyo Metropolitan Institute of Public Health, Tokyo, JapanHiroshima University, Hiroshima, JapanOne Health Research Center, Hokkaido University, Sapporo, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo, JapanHokkaido University, Sapporo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto, JapanKyushu University, Fukuoka, Japan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Medicine, Kobe University, Kobe, Japan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
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32
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Sun J, Liu X, Zhang S, Li M, Zhang Q, Chen J. Molecular insights and optimization strategies for the competitive binding of engineered ACE2 proteins: a multiple replica molecular dynamics study. Phys Chem Chem Phys 2023; 25:28479-28496. [PMID: 37846774 DOI: 10.1039/d3cp03392a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally, and rapid viral evolution and the emergence of new variants pose challenges to pandemic control. During infection, the spike protein of SARS-CoV-2 interacts with the human ACE2 protein via its receptor binding domain (RBD), and it is known that engineered forms of ACE2 can compete with wild-type (WT) ACE2 for binding to inhibit infection. Here, we conducted multiple replica molecular dynamics (MRMD) simulations to study the mechanisms of the engineered ACE2 variants 3N39 and 3N94 and provide directions for optimization. Our findings reveal that engineered ACE2 is notably more efficacious in systems that show weaker binding to WT ACE2 (i.e., WT and BA.1 RBD), but also faces immune escape as the virus evolves. Moreover, by modifying residue types near the binding interface, engineered ACE2 alters the electrostatic potential distribution and reconfigures the hydrogen bonding network, which results in modified binding to the RBD. However, this structural rearrangement does not occur in all RBD variants. In addition, we identified potentially engineerable beneficial residues and potentially engineerable detrimental residues in both ACE2 and RBD. Functional conservation can thus enable the optimization of these residues and improve the binding competitiveness of engineered ACE2, which therefore provides additional immune escape prevention. Finally, we conclude that these findings have implications for understanding the mechanisms responsible for engineered ACE2 and can help us to develop engineered ACE2 proteins that show superior performance.
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Affiliation(s)
- Jiahao Sun
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Meng Li
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
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33
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Carvalhal F, Magalhães AC, Rebelo R, Palmeira A, Resende DISP, Durães F, Maia M, Xavier CPR, Pereira L, Sousa E, Correia-da-Silva M, Vasconcelos MH. Evaluation of the Cytotoxic and Antiviral Effects of Small Molecules Selected by In Silico Studies as Inhibitors of SARS-CoV-2 Cell Entry. Molecules 2023; 28:7204. [PMID: 37894682 PMCID: PMC10609270 DOI: 10.3390/molecules28207204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
The spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) relies on host cell surface glycans to facilitate interaction with the angiotensin-converting enzyme 2 (ACE-2) receptor. This interaction between ACE2 and the spike protein is a gateway for the virus to enter host cells and may be targeted by antiviral drugs to inhibit viral infection. Therefore, targeting the interaction between these two proteins is an interesting strategy to prevent SARS-CoV-2 infection. A library of glycan mimetics and derivatives was selected for a virtual screening performed against both ACE2 and spike proteins. Subsequently, in vitro assays were performed on eleven of the most promising in silico compounds to evaluate: (i) their efficacy in inhibiting cell infection by SARS-CoV-2 (using the Vero CCL-81 cell line as a model), (ii) their impact on ACE2 expression (in the Vero CCL-81 and MDA-MB-231 cell lines), and (iii) their cytotoxicity in a human lung cell line (A549). We identified five synthetic compounds with the potential to block SARS-CoV-2 infection, three of them without relevant toxicity in human lung cells. Xanthene 1 stood out as the most promising anti-SARS-CoV-2 agent, inhibiting viral infection and viral replication in Vero CCL-81 cells, without causing cytotoxicity to human lung cells.
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Affiliation(s)
- Francisca Carvalhal
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, 4408-208 Matosinhos, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (A.C.M.); (C.P.R.X.); (L.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Ana Cristina Magalhães
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (A.C.M.); (C.P.R.X.); (L.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Rita Rebelo
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (A.C.M.); (C.P.R.X.); (L.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Andreia Palmeira
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, 4408-208 Matosinhos, Portugal
| | - Diana I. S. P. Resende
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, 4408-208 Matosinhos, Portugal
| | - Fernando Durães
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, 4408-208 Matosinhos, Portugal
| | - Miguel Maia
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, 4408-208 Matosinhos, Portugal
| | - Cristina P. R. Xavier
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (A.C.M.); (C.P.R.X.); (L.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Luísa Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (A.C.M.); (C.P.R.X.); (L.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Emília Sousa
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, 4408-208 Matosinhos, Portugal
| | - Marta Correia-da-Silva
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, 4408-208 Matosinhos, Portugal
| | - M. Helena Vasconcelos
- FFUP—Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal (R.R.); (A.P.); (D.I.S.P.R.); (F.D.); (M.M.); (E.S.)
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (A.C.M.); (C.P.R.X.); (L.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
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Hsiao YW, Bray DJ, Taddese T, Jiménez-Serratos G, Crain J. Structure adaptation in Omicron SARS-CoV-2/hACE2: Biophysical origins of evolutionary driving forces. Biophys J 2023; 122:4057-4067. [PMID: 37717145 PMCID: PMC10624932 DOI: 10.1016/j.bpj.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/20/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Since its emergence, the COVID-19 threat has been sustained by a series of transmission waves initiated by new variants of the SARS-CoV-2 virus. Some of these arise with higher transmissivity and/or increased disease severity. Here, we use molecular dynamics simulations to examine the modulation of the fundamental interactions between the receptor binding domain (RBD) of the spike glycoprotein and the host cell receptor (human angiotensin-converting enzyme 2 [hACE2]) arising from Omicron variant mutations (BA.1 and BA.2) relative to the original wild-type strain. Our key findings are that glycans play a vital role at the RBD···hACE2 interface for the Omicrons, and the interplay between glycans and sequence mutations leads to enhanced binding. We find significant structural differences in the complexes, which overall bring the spike protein and its receptor into closer proximity. These are consistent with and attributed to the higher positive charge on the RBD conferred by BA.1 and BA.2 mutations relative to the wild-type. However, further differences between subvariants BA.1 and BA.2 (which have equivalent RBD charges) are also evident: mutations reduce interdomain interactions between the up chain and its clockwise neighbor chain in particular for the latter, resulting in enhanced flexibility for BA.2. Consequently, we see occurrence of additional close contacts in one replica of BA.2, which include binding to hACE2 by a second RBD in addition to the up chain. Although this motif is not seen in BA.1, we find that the Omicrons can directly/indirectly bind a down-RBD to hACE2 through glycans: the role of the glycan on N90 of hACE2 switches from inhibiting to facilitating the binding to Omicron spike protein via glycan-protein lateral interactions. These structural and electrostatic differences offer further insight into the mechanisms by which viral mutations modulate host cell binding and provide a biophysical basis for evolutionary driving forces.
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Affiliation(s)
- Ya-Wen Hsiao
- The Hartree Centre, STFC Daresbury Laboratory, Warrington, United Kingdom; Scientific Computing Department, STFC Daresbury Laboratory, Warrington, United Kingdom.
| | - David J Bray
- The Hartree Centre, STFC Daresbury Laboratory, Warrington, United Kingdom
| | - Tseden Taddese
- The Hartree Centre, STFC Daresbury Laboratory, Warrington, United Kingdom
| | | | - Jason Crain
- IBM Research Europe, Hartree Centre, Warrington, United Kingdom; Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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35
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Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein. J Phys Chem B 2023; 127:8586-8602. [PMID: 37775095 PMCID: PMC10578311 DOI: 10.1021/acs.jpcb.3c01467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Indexed: 10/01/2023]
Abstract
SARS-CoV-2 strains have made an appearance across the globe, causing over 757 million cases and over 6.85 million deaths at the time of writing. The emergence of these variants shows the amplitude of genetic variation to which the wild-type strains have been subjected. The rise of the different SARS-CoV-2 variants resulting from such genetic modification has significantly affected COVD-19's major impact on proliferation, virulence, and clinics. With the emergence of the variants of concern, the spike protein has been identified as a possible therapeutic target due to its critical role in binding to human cells and pathogenesis. These mutations could be linked to functional heterogeneity and use a different infection strategy. For example, the Omicron variant's multiple mutations should be carefully examined, as they represent one of the most widely spread strains and hint to us that there may be more genetic changes in the virus. As a result, we applied a common protocol where we reconstructed SARS-CoV-2 variants of concern and performed molecular dynamics simulations to study the stability of the ACE2-RBD complex in each variant. We also carried out free energy calculations to compare the binding and biophysical properties of the different SARS-CoV-2 variants when they interact with ACE2. Therefore, we were able to obtain consistent results and uncover new crucial residues that were essential for preserving a balance between maintaining a high affinity for ACE2 and the capacity to evade RBD-targeted antibodies. Our detailed structural analysis showed that SARS-CoV-2 variants of concern show a higher affinity for ACE2 compared to the Wuhan strain. Additionally, residues K417N and E484K/A might play a crucial role in antibody evasion, whereas Q498R and N501Y are specifically mutated to strengthen RBD affinity to ACE2 and, thereby, increase the viral effect of the COVID-19 virus.
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Affiliation(s)
- Mariem Ghoula
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Audrey Deyawe Kongmeneck
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Rita Eid
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Anne-Claude Camproux
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Gautier Moroy
- Université de Paris, CNRS,
INSERM, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
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36
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Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites. Viruses 2023; 15:2073. [PMID: 37896850 PMCID: PMC10612107 DOI: 10.3390/v15102073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full-length trimer complexes with the ACE2 receptor complemented atomistic studies and enabled an in-depth analysis of mutational and binding effects on conformational dynamic and functional adaptability of the Omicron variants. Despite considerable structural similarities, Omicron variants BA.2, BA.2.75 and XBB.1 can induce unique conformational dynamic signatures and specific distributions of the conformational states. Using conformational ensembles of the SARS-CoV-2 Omicron spike trimer complexes with ACE2, we conducted a comprehensive cryptic pocket screening to examine the role of Omicron mutations and ACE2 binding on the distribution and functional mechanisms of the emerging allosteric binding sites. This analysis captured all experimentally known allosteric sites and discovered networks of inter-connected and functionally relevant allosteric sites that are governed by variant-sensitive conformational adaptability of the SARS-CoV-2 spike structures. The results detailed how ACE2 binding and Omicron mutations in the BA.2, BA.2.75 and XBB.1 spike complexes modulate the distribution of conserved and druggable allosteric pockets harboring functionally important regions. The results are significant for understanding the functional roles of druggable cryptic pockets that can be used for allostery-mediated therapeutic intervention targeting conformational states of the Omicron variants.
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Affiliation(s)
- Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75275, USA; (S.X.); (P.T.)
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75275, USA; (S.X.); (P.T.)
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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Ratswohl C, Vázquez García C, Ahmad AUW, Gonschior H, Lebedin M, Silvis CE, Spatt L, Gerhard C, Lehmann M, Sander LE, Kurth F, Olsson S, de la Rosa K. A design strategy to generate a SARS-CoV-2 RBD vaccine that abrogates ACE2 binding and improves neutralizing antibody responses. Eur J Immunol 2023; 53:e2350408. [PMID: 37435628 DOI: 10.1002/eji.202350408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023]
Abstract
The structure-based design of antigens holds promise for developing vaccines with higher efficacy and improved safety profiles. We postulate that abrogation of host receptor interaction bears potential for the improvement of vaccines by preventing antigen-induced modification of receptor function as well as the displacement or masking of the immunogen. Antigen modifications may yet destroy epitopes crucial for antibody neutralization. Here, we present a methodology that integrates deep mutational scans to identify and score SARS-CoV-2 receptor binding domain variants that maintain immunogenicity, but lack interaction with the widely expressed host receptor. Single point mutations were scored in silico, validated in vitro, and applied in vivo. Our top-scoring variant receptor binding domain-G502E prevented spike-induced cell-to-cell fusion, receptor internalization, and improved neutralizing antibody responses by 3.3-fold in rabbit immunizations. We name our strategy BIBAX for body-inert, B-cell-activating vaccines, which in the future may be applied beyond SARS-CoV-2 for the improvement of vaccines by design.
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Affiliation(s)
- Christoph Ratswohl
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Clara Vázquez García
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Ata Ul Wakeel Ahmad
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Hannes Gonschior
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Mikhail Lebedin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Casper Ewijn Silvis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Lisa Spatt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Cathrin Gerhard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Leif E Sander
- Charité - Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
| | | | - Simon Olsson
- Department of Computer Science and Engineering, Chalmers University of Technology, Göteborg, Västra Götalands län, Sweden
| | - Kathrin de la Rosa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
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38
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Case JB, Scheaffer SM, Darling TL, Bricker TL, Adams LJ, Harastani HH, Trende R, Sanapala S, Fremont DH, Boon ACM, Diamond MS. Characterization of the SARS-CoV-2 BA.5.5 and BQ.1.1 Omicron variants in mice and hamsters. J Virol 2023; 97:e0062823. [PMID: 37676002 PMCID: PMC10537574 DOI: 10.1128/jvi.00628-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/21/2023] [Indexed: 09/08/2023] Open
Abstract
The continued evolution and emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have resulted in challenges to vaccine and antibody efficacy. The emergence of each new variant necessitates the need to re-evaluate and refine animal models used for countermeasure testing. Here, we tested a recently circulating SARS-CoV-2 Omicron lineage variant, BQ.1.1, in multiple rodent models including K18-human ACE2 (hACE2) transgenic, C57BL/6J, and 129S2 mice, and Syrian golden hamsters. In contrast to a previously dominant BA.5.5 Omicron variant, inoculation of K18-hACE2 mice with BQ.1.1 resulted in substantial weight loss, a characteristic seen in pre-Omicron variants. BQ.1.1 also replicated to higher levels in the lungs of K18-hACE2 mice and caused greater lung pathology than the BA.5.5 variant. However, in C57BL/6J mice, 129S2 mice, and Syrian hamsters, BQ.1.1 did not cause increased respiratory tract infection or disease compared to animals administered BA.5.5. Moreover, the rates of direct contact or airborne transmission in hamsters were not significantly different after BQ.1.1 and BA.5.5 infections. Taken together, these data suggest that the BQ.1.1 Omicron variant has increased virulence in rodent species that express hACE2, possibly due to the acquisition of unique spike mutations relative to earlier Omicron variants. IMPORTANCE As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, there is a need to rapidly assess the efficacy of vaccines and antiviral therapeutics against newly emergent variants. To do so, the commonly used animal models must also be re-evaluated. Here, we determined the pathogenicity of the BQ.1.1 SARS-CoV-2 variant in multiple SARS-CoV-2 animal models including transgenic mice expressing human ACE2 (hACE2), two strains of conventional laboratory mice, and Syrian hamsters. While BQ.1.1 and BA.5.5 infection resulted in similar levels of viral burden and clinical disease in hamsters and the conventional strains of laboratory mice tested, increases in lung infection were detected in hACE2-expressing transgenic mice, which corresponded with greater levels of pro-inflammatory cytokines and lung pathology. Taken together, our data highlight important differences in two closely related Omicron SARS-CoV-2 variant strains and provide a foundation for evaluating countermeasures.
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Affiliation(s)
- James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Suzanne M. Scheaffer
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tamarand L. Darling
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Traci L. Bricker
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lucas J. Adams
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Houda H. Harastani
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Reed Trende
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shilpa Sanapala
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daved H. Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adrianus C. M. Boon
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, Missouri, USA
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39
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Andre M, Lau LS, Pokharel MD, Ramelow J, Owens F, Souchak J, Akkaoui J, Ales E, Brown H, Shil R, Nazaire V, Manevski M, Paul NP, Esteban-Lopez M, Ceyhan Y, El-Hage N. From Alpha to Omicron: How Different Variants of Concern of the SARS-Coronavirus-2 Impacted the World. BIOLOGY 2023; 12:1267. [PMID: 37759666 PMCID: PMC10525159 DOI: 10.3390/biology12091267] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
SARS-CoV-2, the virus that causes COVID-19, is prone to mutations and the generation of genetic variants. Since its first outbreak in 2019, SARS-CoV-2 has continually evolved, resulting in the emergence of several lineages and variants of concern (VOC) that have gained more efficient transmission, severity, and immune evasion properties. The World Health Organization has given these variants names according to the letters of the Greek Alphabet, starting with the Alpha (B.1.1.7) variant, which emerged in 2020, followed by the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. This review explores the genetic variation among different VOCs of SARS-CoV-2 and how the emergence of variants made a global impact on the pandemic.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nazira El-Hage
- Herbert Wertheim College of Medicine, Biomedical Sciences Program Florida International University, Miami, FL 33199, USA; (M.A.); (L.-S.L.); (M.D.P.); (J.R.); (F.O.); (J.S.); (J.A.); (E.A.); (H.B.); (R.S.); (V.N.); (M.M.); (N.P.P.); (M.E.-L.); (Y.C.)
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40
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Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557205. [PMID: 37745525 PMCID: PMC10515794 DOI: 10.1101/2023.09.11.557205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full length trimer complexes with the ACE2 receptor complemented atomistic studies and enabled an in-depth analysis of mutational and binding effects on conformational dynamic and functional adaptability of the Omicron variants. Despite considerable structural similarities, Omicron variants BA.2, BA.2.75 and XBB.1 can induce unique conformational dynamic signatures and specific distributions of the conformational states. Using conformational ensembles of the SARS-CoV-2 Omicron spike trimer complexes with ACE2, we conducted a comprehensive cryptic pocket screening to examine the role of Omicron mutations and ACE2 binding on the distribution and functional mechanisms of the emerging allosteric binding sites. This analysis captured all experimentally known allosteric sites and discovered networks of inter-connected and functionally relevant allosteric sites that are governed by variant-sensitive conformational adaptability of the SARS-CoV-2 spike structures. The results detailed how ACE2 binding and Omicron mutations in the BA.2, BA.2.75 and XBB.1 spike complexes modulate the distribution of conserved and druggable allosteric pockets harboring functionally important regions. The results of are significant for understanding functional roles of druggable cryptic pockets that can be used for allostery-mediated therapeutic intervention targeting conformational states of the Omicron variants.
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41
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Bains A, Guan W, LiWang PJ. The Effect of Select SARS-CoV-2 N-Linked Glycan and Variant of Concern Spike Protein Mutations on C-Type Lectin-Receptor-Mediated Infection. Viruses 2023; 15:1901. [PMID: 37766307 PMCID: PMC10535197 DOI: 10.3390/v15091901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The SARS-CoV-2 virion has shown remarkable resilience, capable of mutating to escape immune detection and re-establishing infectious capabilities despite new vaccine rollouts. Therefore, there is a critical need to identify relatively immutable epitopes on the SARS-CoV-2 virion that are resistant to future mutations the virus may accumulate. While hACE2 has been identified as the receptor that mediates SARS-CoV-2 susceptibility, it is only modestly expressed in lung tissue. C-type lectin receptors like DC-SIGN can act as attachment sites to enhance SARS-CoV-2 infection of cells with moderate or low hACE2 expression. We developed an easy-to-implement assay system that allows for the testing of SARS-CoV-2 trans-infection. Using our assay, we assessed how SARS-CoV-2 Spike S1-domain glycans and spike proteins from different strains affected the ability of pseudotyped lentivirions to undergo DC-SIGN-mediated trans-infection. Through our experiments with seven glycan point mutants, two glycan cluster mutants and four strains of SARS-CoV-2 spike, we found that glycans N17 and N122 appear to have significant roles in maintaining COVID-19's infectious capabilities. We further found that the virus cannot retain infectivity upon the loss of multiple glycosylation sites, and that Omicron BA.2 pseudovirions may have an increased ability to bind to other non-lectin receptor proteins on the surface of cells. Taken together, our work opens the door to the development of new therapeutics that can target overlooked epitopes of the SARS-CoV-2 virion to prevent C-type lectin-receptor-mediated trans-infection in lung tissue.
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Affiliation(s)
- Arjan Bains
- Chemistry and Biochemistry, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Wenyan Guan
- Materials and Biomaterials Science and Engineering, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Patricia J. LiWang
- Molecular Cell Biology, Health Sciences Research Institute, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA
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42
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Yang L, Wang Z. Bench-to-bedside: Innovation of small molecule anti-SARS-CoV-2 drugs in China. Eur J Med Chem 2023; 257:115503. [PMID: 37229831 PMCID: PMC10193775 DOI: 10.1016/j.ejmech.2023.115503] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/19/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
The ongoing COVID-19 pandemic has resulted in millions of deaths globally, highlighting the need to develop potent prophylactic and therapeutic strategies against SARS-CoV-2. Small molecule inhibitors (remdesivir, Paxlovid, and molnupiravir) are essential complements to vaccines and play important roles in clinical treatment of SARS-CoV-2. Many advances have been made in development of anti-SARS-CoV-2 inhibitors in China, but progress in discovery and characterization of pharmacological activity, antiviral mechanisms, and clinical efficacy are limited. We review development of small molecule anti-SARS-CoV-2 drugs (azvudine [approved by the NMPA of China on July 25, 2022], VV116 [approved by the NMPA of China on January 29, 2023], FB2001, WPV01, pentarlandir, and cepharanthine) in China and summarize their pharmacological activity, potential mechanisms of action, clinical trials and use, and important milestones in their discovery. The role of structural biology in drug development is also reviewed. Future studies should focus on development of diverse second-generation inhibitors with excellent oral bioavailability, superior plasma half-life, increased antiviral activity against SARS-CoV-2 and its variants, high target specificity, minimal side effects, reduced drug-drug interactions, and improved lung histopathology.
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Affiliation(s)
- Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu, 273165, PR China; Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, PR China; School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus, Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, PR China.
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43
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Chen J, Woldring DR, Huang F, Huang X, Wei GW. Topological deep learning based deep mutational scanning. Comput Biol Med 2023; 164:107258. [PMID: 37506452 PMCID: PMC10528359 DOI: 10.1016/j.compbiomed.2023.107258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
Abstract
High-throughput deep mutational scanning (DMS) experiments have significantly impacted protein engineering, drug discovery, immunology, cancer biology, and evolutionary biology by enabling the systematic understanding of protein functions. However, the mutational space associated with proteins is astronomically large, making it overwhelming for current experimental capabilities. Therefore, alternative methods for DMS are imperative. We propose a topological deep learning (TDL) paradigm to facilitate in silico DMS. We utilize a new topological data analysis (TDA) technique based on the persistent spectral theory, also known as persistent Laplacian, to capture both topological invariants and the homotopic shape evolution of data. To validate our TDL-DMS model, we use SARS-CoV-2 datasets and show excellent accuracy and reliability for binding interface mutations. This finding is significant for SARS-CoV-2 variant forecasting and designing effective antibodies and vaccines. Our proposed model is expected to have a significant impact on drug discovery, vaccine design, precision medicine, and protein engineering.
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Affiliation(s)
- Jiahui Chen
- Department of Mathematical Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Daniel R Woldring
- Department of Chemical Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, MI 48824, USA; Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA; The Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA; Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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44
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Qing E, Gallagher T. Adaptive variations in SARS-CoV-2 spike proteins: effects on distinct virus-cell entry stages. mBio 2023; 14:e0017123. [PMID: 37382441 PMCID: PMC10470846 DOI: 10.1128/mbio.00171-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/14/2023] [Indexed: 06/30/2023] Open
Abstract
Evolved SARS-CoV-2 variants of concern (VOCs) spread through human populations in succession. Major virus variations are in the entry-facilitating viral spike (S) proteins; Omicron VOCs have 29-40 S mutations relative to ancestral D614G viruses. The impacts of this Omicron divergence on S protein structure, antigenicity, cell entry pathways, and pathogenicity have been extensively evaluated, yet gaps remain in correlating specific alterations with S protein functions. In this study, we compared the functions of ancestral D614G and Omicron VOCs using cell-free assays that can reveal differences in several distinct steps of the S-directed virus entry process. Relative to ancestral D614G, Omicron BA.1 S proteins were hypersensitized to receptor activation, to conversion into intermediate conformational states, and to membrane fusion-activating proteases. We identified mutations conferring these changes in S protein character by evaluating domain-exchanged D614G/Omicron recombinants in the cell-free assays. Each of the three functional alterations was mapped to specific S protein domains, with the recombinants providing insights on inter-domain interactions that fine-tune S-directed virus entry. Our results provide a structure-function atlas of the S protein variations that may promote the transmissibility and infectivity of current and future SARS-CoV-2 VOCs. IMPORTANCE Continuous SARS-CoV-2 adaptations generate increasingly transmissible variants. These succeeding variants show ever-increasing evasion of suppressive antibodies and host factors, as well as increasing invasion of susceptible host cells. Here, we evaluated the adaptations enhancing invasion. We used reductionist cell-free assays to compare the entry steps of ancestral (D614G) and Omicron (BA.1) variants. Relative to D614G, Omicron entry was distinguished by heightened responsiveness to entry-facilitating receptors and proteases and by enhanced formation of intermediate states that execute virus-cell membrane fusion. We found that these Omicron-specific characteristics arose from mutations in specific S protein domains and subdomains. The results reveal the inter-domain networks controlling S protein dynamics and efficiencies of entry steps, and they offer insights on the evolution of SARS-CoV-2 variants that arise and ultimately dominate infections worldwide.
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Affiliation(s)
- Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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45
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Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. J Chem Inf Model 2023; 63:5272-5296. [PMID: 37549201 PMCID: PMC11162552 DOI: 10.1021/acs.jcim.3c00778] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
The new generation of SARS-CoV-2 Omicron variants displayed a significant growth advantage and increased viral fitness by acquiring convergent mutations, suggesting that the immune pressure can promote convergent evolution leading to the sudden acceleration of SARS-CoV-2 evolution. In the current study, we combined structural modeling, microsecond molecular dynamics simulations, and Markov state models to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the recently emerged highly transmissible XBB.1, XBB.1.5, BQ.1, and BQ.1.1 Omicron variants. Microsecond simulations and Markovian modeling provided a detailed characterization of the functional conformational states and revealed the increased thermodynamic stabilization of the XBB.1.5 subvariant, which can be contrasted to more dynamic BQ.1 and BQ.1.1 subvariants. Despite considerable structural similarities, Omicron mutations can induce unique dynamic signatures and specific distributions of the conformational states. The results suggested that variant-specific changes of the conformational mobility in the functional interfacial loops of the receptor-binding domain in the SARS-CoV-2 spike protein can be fine-tuned through crosstalk between convergent mutations which could provide an evolutionary path for modulation of immune escape. By combining atomistic simulations and Markovian modeling analysis with perturbation-based approaches, we determined important complementary roles of convergent mutation sites as effectors and receivers of allosteric signaling involved in modulation of conformational plasticity and regulation of allosteric communications. This study also revealed hidden allosteric pockets and suggested that convergent mutation sites could control evolution and distribution of allosteric pockets through modulation of conformational plasticity in the flexible adaptable regions.
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Affiliation(s)
- Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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46
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Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships. Phys Chem Chem Phys 2023; 25:21245-21266. [PMID: 37548589 PMCID: PMC10536792 DOI: 10.1039/d3cp02042h] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 spike protein complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which can be contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using the dynamics-based mutational scanning of spike residues, we identified structural stability and binding affinity hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational profiling approaches probed the effect of the Omicron mutations on allosteric interactions and communications in the complexes. The results of this analysis revealed specific roles of Omicron mutations as conformationally plastic and evolutionary adaptable modulators of binding and allostery which are coupled to the major regulatory positions through interaction networks. Through perturbation network scanning of allosteric residue potentials in the Omicron variant complexes performed in the background of the original strain, we characterized regions of epistatic couplings that are centered around the binding affinity hotspots N501Y and Q498R. Our results dissected the vital role of these epistatic centers in regulating protein stability, efficient ACE2 binding and allostery which allows for accumulation of multiple Omicron immune escape mutations at other sites. Through integrative computational approaches, this study provides a systematic analysis of the effects of Omicron mutations on thermodynamics, binding and allosteric signaling in the complexes with ACE2 receptor.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA.
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA.
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA.
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47
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Wrobel AG. Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike. Curr Opin Struct Biol 2023; 81:102619. [PMID: 37285618 PMCID: PMC10183628 DOI: 10.1016/j.sbi.2023.102619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023]
Abstract
Spike glycoprotein of SARS-CoV-2 mediates viral entry into host cells by facilitating virus attachment and membrane fusion. ACE2 is the main receptor of SARS-CoV-2 and its interaction with spike has shaped the virus' emergence from an animal reservoir and subsequent evolution in the human host. Many structural studies on the spike:ACE2 interaction have provided insights into mechanisms driving viral evolution during the on-going pandemic. This review describes the molecular basis of spike binding to ACE2, outlines mechanisms that have optimised this interaction during viral evolution, and suggests directions for future research.
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Affiliation(s)
- Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, United Kingdom.
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48
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Wei X, Chen J, Wei GW. Persistent topological Laplacian analysis of SARS-CoV-2 variants. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2023; 22:569-587. [PMID: 37829318 PMCID: PMC10569362 DOI: 10.1142/s2737416523500278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Topological data analysis (TDA) is an emerging field in mathematics and data science. Its central technique, persistent homology, has had tremendous success in many science and engineering disciplines. However, persistent homology has limitations, including its inability to handle heterogeneous information, such as multiple types of geometric objects; being qualitative rather than quantitative, e.g., counting a 5-member ring the same as a 6-member ring, and a failure to describe non-topological changes, such as homotopic changes in protein-protein binding. Persistent topological Laplacians (PTLs), such as persistent Laplacian and persistent sheaf Laplacian, were proposed to overcome the limitations of persistent homology. In this work, we examine the modeling and analysis power of PTLs in the study of the protein structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike receptor binding domain (RBD). First, we employ PTLs to study how the RBD mutation-induced structural changes of RBD-angiotensin-converting enzyme 2 (ACE2) binding complexes are captured in the changes of spectra of the PTLs among SARS-CoV-2 variants. Additionally, we use PTLs to analyze the binding of RBD and ACE2-induced structural changes of various SARS-CoV-2 variants. Finally, we explore the impacts of computationally generated RBD structures on a topological deep learning paradigm and predictions of deep mutational scanning datasets for the SARS-CoV-2 Omicron BA.2 variant. Our results indicate that PTLs have advantages over persistent homology in analyzing protein structural changes and provide a powerful new TDA tool for data science.
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Affiliation(s)
- Xiaoqi Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Jiahui Chen
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA
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49
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Guo S, Zheng Y, Gao Z, Duan M, Liu S, Du P, Xu X, Xu K, Zhao X, Chai Y, Wang P, Zhao Q, Gao GF, Dai L. Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine. Cell Discov 2023; 9:79. [PMID: 37507370 PMCID: PMC10382582 DOI: 10.1038/s41421-023-00585-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Vaccination with different vaccines has been implemented globally to counter the continuous COVID-19 pandemic. However, the vaccine-elicited antibodies have reduced efficiency against the highly mutated Omicron sub-variants. Previously, we developed a protein subunit COVID-19 vaccine called ZF2001, based on the dimeric receptor-binding domain (RBD). This vaccine has been administered using different dosing intervals in real-world setting. Some individuals received three doses of ZF2001, with a one-month interval between each dose, due to urgent clinical requirements. Others had an extended dosing interval of up to five months between the second and third dose, a standard vaccination regimen for the protein subunit vaccine against hepatitis B. In this study, we profile B cell responses in individuals who received three doses of ZF2001, and compared those with long or short dosing intervals. We observed that the long-interval group exhibited higher and broader serologic antibody responses. These responses were associated with the increased size and evolution of vaccine-elicited B-cell receptor repertoires, characterized by the elevation of expanded clonotypes and somatic hypermutations. Both groups of individuals generated substantial amounts of broadly neutralizing antibodies (bnAbs) against various SARS-CoV-2 variants, including Omicron sub-variants such as XBB. These bnAbs target four antigenic sites within the RBD. To determine the vulnerable site of SARS-CoV-2, we employed cryo-electron microscopy to identify the epitopes of highly potent bnAbs that targeted two major sites. Our findings provide immunological insights into the B cell responses elicited by RBD-based vaccine, and suggest that a vaccination regimen of prolonging time interval should be used in practice.
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Affiliation(s)
- Shuxin Guo
- Faculty of Health Sciences, University of Macau, Macau SAR, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxuan Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhengrong Gao
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
- Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Minrun Duan
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Sheng Liu
- Department of Biology, Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Pan Du
- Vazyme Biotech, Nanjing, Jiangsu, China
| | - XiaoYu Xu
- Vazyme Biotech, Nanjing, Jiangsu, China
| | - Kun Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Peiyi Wang
- Department of Biology, Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Qi Zhao
- MoE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - George F Gao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Lianpan Dai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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50
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Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J. Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants. Nat Commun 2023; 14:4405. [PMID: 37479708 PMCID: PMC10362042 DOI: 10.1038/s41467-023-39942-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/29/2023] [Indexed: 07/23/2023] Open
Abstract
Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly increasing in some countries. Exploring their receptor binding and interspecies transmission risk is urgently needed. Herein, we examine the binding capacities of human and other 28 animal ACE2 orthologs covering nine orders towards S proteins of these sub-variants. The binding affinities between hACE2 and these sub-variants remain in the range as that of previous variants of concerns (VOCs) or interests (VOIs). Notably, R493Q reverse mutation enhances the bindings towards ACE2s from humans and many animals closely related to human life, suggesting an increased risk of cross-species transmission. Structures of S/hACE2 or RBD/hACE2 complexes for these sub-variants and BA.2 S binding to ACE2 of mouse, rat or golden hamster are determined to reveal the molecular basis for receptor binding and broader interspecies recognition.
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Affiliation(s)
- Zhennan Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunliang Luo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Jingya Zhou
- University of Chinese Academy of Sciences, Beijing, China
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Weiwei Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yumin Meng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaomei Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Xiaoxiong Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Xiaoyun Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junqing Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Yeping Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zheng Fan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linhuan Wu
- Chinese National Microbiology Data Center (NMDC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Juncai Ma
- Chinese National Microbiology Data Center (NMDC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Odel Y Li
- NHC Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Guijun Shang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Peiyi Wang
- Cryo-EM Center, Department of Biology, Southern University of Science and Technology, Shenzhen, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
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