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Shafiq A, Khalid U, Abdur Rehman U, Abdullah Almuqri E, Muddassir M, Ahmad S, Khan MI, Khan A, Wei DQ. Structural basis for the mechanism of interaction of SARS-CoV-2 B.1.640.2 variant RBD with the host receptors hACE2 and GRP78. J Biomol Struct Dyn 2024; 42:2034-2042. [PMID: 37286365 DOI: 10.1080/07391102.2023.2220053] [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: 01/23/2023] [Accepted: 04/09/2023] [Indexed: 06/09/2023]
Abstract
The inflicted chaos instigated by the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) globally continues with the emergence of novel variants. The current global outbreak is aggravated by the manifestation of novel variants, which affect the effectiveness of the vaccine, attachment with hACE2 (human Angiotensin-converting enzyme 2) and immune evasion. Recently, a new variant named University Hospital Institute (IHU) (B.1.640.2) was reported in France in November 2021 and is spreading globally affecting public healthcare. The B.1.640.2 SARS-CoV-2 strain revealed 14 mutations and 9 deletions in spike protein. Thus, it is important to understand how these variations in the spike protein impact the communication with the host. A protein coupling approach along with molecular simulation protocols was used to interpret the variation in the binding of the wild type (WT) and B.1.640.2 variant with hACE2 and Glucose-regulating protein 78 (GRP78) receptors. The initial docking scores revealed a stronger binding of the B.1.640.2-RBD with both the hACE2 and GRP78. To further understand the crucial dynamic changes, we looked at the structural and dynamic characteristics and also explored the variations in the bonding networks between the WT and B.1.640.2-RBD (receptor-binding domain) in association with hACE2 and GRP78, respectively. Our findings revealed that the variant complex demonstrated distinct dynamic properties in contrast to the wild type due to the acquired mutations. Finally, to provide conclusive evidence on the higher binding by the B.1.640.2 variant the TBE was computed for each complex. For the WT with hACE2 the TBE was quantified to be-61.38 ± 0.96 kcal/mol and for B.1.640.2 variant the TBE was estimated to be -70.47 ± 1.00 kcal/mol. For the WT-RBD-GRP78 the TBE -was computed to be 32.32 ± 0.56 kcal/mol and for the B.1.640.2-RBD a TBE of -50.39 ± 0.88 kcal/mol was reported. This show that these mutations are the basis for higher binding and infectivity produced by B.1.640.2 variant and can be targeted for drug designing against it.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Athar Shafiq
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ujala Khalid
- Fatima Jinnah Medical University, Lahore, Punjab, Pakistan
| | - Umar Abdur Rehman
- Aziz Fatimah Medical and Dental College, Faisalabad, Punjab, Pakistan
| | - Eman Abdullah Almuqri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Maria Muddassir
- Institute of Molecular Biology & Biotechnology, The University of Lahore (UOL), Lahore, Punjab, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Idrees Khan
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Nayang, Henan, P.R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Nayang, Henan, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Peng Cheng Laboratory, Shenzhen, Guangdong, P.R. China
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Lusiany T, Terada T, Kishikawa JI, Hirose M, Chen DV, Sugihara F, Ismanto HS, van Eerden FJ, Li S, Kato T, Arase H, Yoshiharu M, Okada M, Standley DM. Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies. Viruses 2023; 15:2421. [PMID: 38140662 PMCID: PMC10747171 DOI: 10.3390/v15122421] [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: 11/14/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The entry of SARS-CoV-2 into host cells is mediated by the interaction between the spike receptor-binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2). Certain human antibodies, which target the spike N-terminal domain (NTD) at a distant epitope from the host cell binding surface, have been found to augment ACE2 binding and enhance SARS-CoV-2 infection. Notably, these antibodies exert their effect independently of the antibody fragment crystallizable (Fc) region, distinguishing their mode of action from previously described antibody-dependent infection-enhancing (ADE) mechanisms. Building upon previous hypotheses and experimental evidence, we propose that these NTD-targeting infection-enhancing antibodies (NIEAs) achieve their effect through the crosslinking of neighboring spike proteins. In this study, we present refined structural models of NIEA fragment antigen-binding region (Fab)-NTD complexes, supported by molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry (HDX-MS). Furthermore, we provide direct evidence confirming the crosslinking of spike NTDs by NIEAs. Collectively, our findings advance our understanding of the molecular mechanisms underlying NIEAs and their impact on SARS-CoV-2 infection.
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Affiliation(s)
- Tina Lusiany
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan;
| | - Jun-ichi Kishikawa
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - Mika Hirose
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - David Virya Chen
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan;
| | - Fuminori Sugihara
- Core Facility, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka 565-0871, Japan;
| | - Hendra Saputra Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
| | - Floris J. van Eerden
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
| | - Takayuki Kato
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan;
- Department of Immunochemistry, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Matsuura Yoshiharu
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan;
| | - Masato Okada
- Center for Advanced Modalities and DDS, Osaka University, 2-8 Yamadaoka, Suita 565-0871, Japan;
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
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Le K, Kannappan S, Kim T, Lee JH, Lee HR, Kim KK. Structural understanding of SARS-CoV-2 virus entry to host cells. Front Mol Biosci 2023; 10:1288686. [PMID: 38033388 PMCID: PMC10683510 DOI: 10.3389/fmolb.2023.1288686] [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: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health concern associated with millions of fatalities worldwide. Mutant variants of the virus have further exacerbated COVID-19 mortality and infection rates, emphasizing the urgent need for effective preventive strategies. Understanding the viral infection mechanism is crucial for developing therapeutics and vaccines. The entry of SARS-CoV-2 into host cells is a key step in the infection pathway and has been targeted for drug development. Despite numerous reviews of COVID-19 and the virus, there is a lack of comprehensive reviews focusing on the structural aspects of viral entry. In this review, we analyze structural changes in Spike proteins during the entry process, dividing the entry process into prebinding, receptor binding, proteolytic cleavage, and membrane fusion steps. By understanding the atomic-scale details of viral entry, we can better target the entry step for intervention strategies. We also examine the impacts of mutations in Spike proteins, including the Omicron variant, on viral entry. Structural information provides insights into the effects of mutations and can guide the development of therapeutics and vaccines. Finally, we discuss available structure-based approaches for the development of therapeutics and vaccines. Overall, this review provides a detailed analysis of the structural aspects of SARS-CoV-2 viral entry, highlighting its significance in the development of therapeutics and vaccines against COVID-19. Therefore, our review emphasizes the importance of structural information in combating SARS-CoV-2 infection.
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Affiliation(s)
- Kim Le
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Shrute Kannappan
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
| | - Truc Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
- School of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
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Fan T, Li C, Liu X, Xu H, Li W, Wang M, Mei X, Li D. Development of practical techniques for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. ANAL SCI 2023; 39:1839-1856. [PMID: 37517003 DOI: 10.1007/s44211-023-00396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Countless individuals have fallen victim to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have generated antibodies, reducing the risk of secondary infection in the short term. However, with the emergence of mutated strains, the probability of subsequent infections remains high. Consequently, the demand for simple and accessible methods for distinguishing between different variants is soaring. Although monitoring viral gene sequencing is an effective approach for differentiating between various types of SARS-CoV-2 variants, it may not be easily accessible to the general public. In this article, we provide an overview of the reported techniques that use combined approaches and adaptable testing methods that use editable recognition receptors for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. These techniques employ straightforward detection strategies, including tests capable of simultaneously identifying and differentiating between different variants. Furthermore, we recommend advancing the development of uncomplicated protocols for distinguishing between current and emerging variants. Additionally, we propose further development of facile protocols for the differentiation of existing and emerging variants.
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Affiliation(s)
- Tuocen Fan
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Chengjie Li
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Xinlei Liu
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Hongda Xu
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Wenhao Li
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Minghao Wang
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Jinzhou Medical University, Jinzhou, 121000, China.
| | - Dan Li
- Jinzhou Medical University, Jinzhou, 121000, China.
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
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Cox M, Peacock TP, Harvey WT, Hughes J, Wright DW, Willett BJ, Thomson E, Gupta RK, Peacock SJ, Robertson DL, Carabelli AM. SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nat Rev Microbiol 2023; 21:112-124. [PMID: 36307535 PMCID: PMC9616429 DOI: 10.1038/s41579-022-00809-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 01/20/2023]
Abstract
Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in vitro neutralization data for mAbs against live variants and viral constructs containing spike mutations of interest. Unfortunately, evasion of mAb-induced protection is being reported with new SARS-CoV-2 variants. The magnitude of neutralization reduction varied greatly among mAb-variant pairs. For example, sotrovimab retained its neutralization capacity against Omicron BA.1 but showed reduced efficacy against BA.2, BA.4 and BA.5, and BA.2.12.1. At present, only bebtelovimab has been reported to retain its efficacy against all SARS-CoV-2 variants considered here. Resistance to mAb neutralization was dominated by the action of epitope single amino acid substitutions in the spike protein. Although not all observed epitope mutations result in increased mAb evasion, amino acid substitutions at non-epitope positions and combinations of mutations also contribute to evasion of neutralization. This Review highlights the implications for the rational design of viral genomic surveillance and factors to consider for the development of novel mAb therapies.
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Affiliation(s)
- MacGregor Cox
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Derek W Wright
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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