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Aloufi AS, El-Arabey AA, Eltayb WA, Elsayim R, Marenga HS, Modafer Y, Awadalla ME, Mohapatra PK, Mohapatra RK, Abdalla M. Molecular dynamic analyses of the interaction of SARS-CoV-1 or 2 variants with various angiotensin-converting enzyme-2 species. J Biomol Struct Dyn 2024:1-10. [PMID: 38344933 DOI: 10.1080/07391102.2024.2314745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/18/2024] [Indexed: 10/04/2024]
Abstract
The transmembrane glycoprotein angiotensin-converting enzyme 2 (ACE2) is a key component of the renin-angiotensin system (RAS). It was shown to be the receptor of severe acute respiratory syndrome coronavirus 2 in the COVID-19 outbreak (SARS-COV-2). Furthermore, ACE2 aids in the transport of amino acids across the membrane. ACE2 is lost from the membrane, resulting in soluble ACE2 (sACE2). We aim to examine the structural conformation alterations between SARS-CoV-1 or 2 variants at various periods with ACE2 from various sources, particularly in the area where it interacts with the viral protein and the receptor. It is important to study the molecular dynamics of ACE2/SARS-COV RBD when the structure is available on the database. Here we analyzed the crystal structure of ACE2 from Human, Dog, Mus, Cat, and Bat ACE2 in complex with RBD from SARS-COV-1 and SARS-COV-2. The result shows, there is a variation in the type of residues, number of contact atoms and hydrogen bonds in ACE2 and RBD during the interaction interfaces. By using molecular dynamics simulation, we can measure RMSD, RMSF, SASA, Rg and the difference in the percentage of α helix and β strand. As bat ACE2 & SARS-CoV-2 RBD found to have a high amount of β strand compared to another structure complex, while hACE2 & SARS-CoV-1 RBD has fewer amounts of β strand. Our study provides a deep view of the structure which is available and a summary of many works around ACE2/SARS-CoV RBD interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abeer S Aloufi
- Department of Biology, College of Science, princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amr Ahmed El-Arabey
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Wafa Ali Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi, Nher Anile, Sudan
| | - Rasha Elsayim
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hanin S Marenga
- Department of Pharmaceutical chemistry, College of pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Yosra Modafer
- Department of Biology, Faculty of Science, Jazan university, Jazan, Saudi Arabia
| | | | - Pranab K Mohapatra
- Department of Chemistry, C. V. Raman Global University, Bhubaneswar, Odisha, India
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Odisha, India
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
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Gan M, Cao J, Zhang Y, Fu H, Lin X, Ouyang Q, Xu X, Yuan Y, Fan X. Landscape of T cell epitopes displays hot mutations of SARS-CoV-2 variant spikes evading cellular immunity. J Med Virol 2024; 96:e29452. [PMID: 38314852 DOI: 10.1002/jmv.29452] [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: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024]
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been accompanied by the emergence of viral mutations that pose a great challenge to existing vaccine strategies. It is not fully understood with regard to the role of mutations on the SARS-CoV-2 spike protein from emerging viral variants in T cell immunity. In the current study, recombinant eukaryotic plasmids were constructed as DNA vaccines to express the spike protein from multiple SARS-CoV-2 strains. These DNA vaccines were used to immunize BALB/c mice, and cross-T cell responses to the spike protein from these viral strains were quantitated using interferon-γ (IFN-γ) Elispot. Peptides covering the full-length spike protein from different viral strains were used to detect epitope-specific IFN-γ+ CD4+ and CD8+ T cell responses by fluorescence-activated cell sorting. SARS-CoV-2 Delta and Omicron BA.1 strains were found to have broad T cell cross-reactivity, followed by the Beta strain. The landscapes of T cell epitopes on the spike protein demonstrated that at least 30 mutations emerging from Alpha to Omicron BA.5 can mediate the escape of T cell immunity. Omicron and its sublineages have 19 out of these 30 mutations, most of which are new, and a few are inherited from ancient circulating variants of concerns. The cross-T cell immunity between SARS-CoV-2 prototype strain and Omicron strains can be attributed to the T cell epitopes located in the N-terminal domain (181-246 aa [amino acids], 271-318 aa) and C-terminal domain (1171-1273 aa) of the spike protein. These findings provide in vivo evidence for optimizing vaccine manufacturing and immunization strategies for current or future viral variants.
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Affiliation(s)
- Mengze Gan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Jinge Cao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Yandi Zhang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Fu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaosong Lin
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Ouyang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Xinyue Xu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Yin Yuan
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xionglin Fan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
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Li E, Han Q, Bi J, Wei S, Wang S, Zhang Y, Liu J, Feng N, Wang T, Wu J, Yang S, Zhao Y, Liu B, Yan F, Xia X. Therapeutic equine hyperimmune antibodies with high and broad-spectrum neutralizing activity protect rodents against SARS-CoV-2 infection. Front Immunol 2023; 14:1066730. [PMID: 36875106 PMCID: PMC9981790 DOI: 10.3389/fimmu.2023.1066730] [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: 10/11/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
The emergence of SARS-CoV-2 variants stresses the continued need for broad-spectrum therapeutic antibodies. Several therapeutic monoclonal antibodies or cocktails have been introduced for clinical use. However, unremitting emerging SARS-CoV-2 variants showed reduced neutralizing efficacy by vaccine induced polyclonal antibodies or therapeutic monoclonal antibodies. In our study, polyclonal antibodies and F(ab')2 fragments with strong affinity produced after equine immunization with RBD proteins produced strong affinity. Notably, specific equine IgG and F(ab')2 have broad and high neutralizing activity against parental virus, all SARS-CoV-2 variants of concern (VOCs), including B.1.1,7, B.1.351, B.1.617.2, P.1, B.1.1.529 and BA.2, and all variants of interest (VOIs) including B.1.429, P.2, B.1.525, P.3, B.1.526, B.1.617.1, C.37 and B.1.621. Although some variants weaken the neutralizing ability of equine IgG and F(ab')2 fragments, they still exhibited superior neutralization ability against mutants compared to some reported monoclonal antibodies. Furthermore, we tested the pre-exposure and post-exposure protective efficacy of the equine immunoglobulin IgG and F(ab')2 fragments in lethal mouse and susceptible golden hamster models. Equine immunoglobulin IgG and F(ab')2 fragments effectively neutralized SARS-CoV-2 in vitro, fully protected BALB/c mice from the lethal challenge, and reduced golden hamster's lung pathological change. Therefore, equine pAbs are an adequate, broad coverage, affordable and scalable potential clinical immunotherapy for COVID-19, particularly for SARS-CoV-2 VOCs or VOIs.
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Affiliation(s)
- Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qiuxue Han
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, Jilin Agriculture University, Changchun, China
| | - Jinhao Bi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,Institute of Laboratory Animal Science, Chinese Academy of Medical Science and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Shimeng Wei
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,Institute of Laboratory Animal Science, Chinese Academy of Medical Science and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Shen Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ying Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jun Wu
- Department of Microorganism Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Songtao Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yongkun Zhao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bo Liu
- Department of Microorganism Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
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Yang S, Tong Y, Chen L, Yu W. Human Identical Sequences, hyaluronan, and hymecromone ─ the new mechanism and management of COVID-19. MOLECULAR BIOMEDICINE 2022; 3:15. [PMID: 35593963 PMCID: PMC9120813 DOI: 10.1186/s43556-022-00077-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/04/2022] [Indexed: 02/08/2023] Open
Abstract
COVID-19 caused by SARS-CoV-2 has created formidable damage to public health and market economy. Currently, SARS-CoV-2 variants has exacerbated the transmission from person-to-person. Even after a great deal of investigation on COVID-19, SARS-CoV-2 is still rampaging globally, emphasizing the urgent need to reformulate effective prevention and treatment strategies. Here, we review the latest research progress of COVID-19 and provide distinct perspectives on the mechanism and management of COVID-19. Specially, we highlight the significance of Human Identical Sequences (HIS), hyaluronan, and hymecromone ("Three-H") for the understanding and intervention of COVID-19. Firstly, HIS activate inflammation-related genes to influence COVID-19 progress through NamiRNA-Enhancer network. Accumulation of hyaluronan induced by HIS-mediated HAS2 upregulation is a substantial basis for clinical manifestations of COVID-19, especially in lymphocytopenia and pulmonary ground-glass opacity. Secondly, detection of plasma hyaluronan can be effective for evaluating the progression and severity of COVID-19. Thirdly, spike glycoprotein of SARS-CoV-2 may bind to hyaluronan and further serve as an allergen to stimulate allergic reaction, causing sudden adverse effects after vaccination or the aggravation of COVID-19. Finally, antisense oligonucleotides of HIS or inhibitors of hyaluronan synthesis (hymecromone) or antiallergic agents could be promising therapeutic agents for COVID-19. Collectively, Three-H could hold the key to understand the pathogenic mechanism and create effective therapeutic strategies for COVID-19.
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Affiliation(s)
- Shuai Yang
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Shanghai Public Health Clinical Center & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Key Laboratory of Medical Epigenetics, Shanghai, 200032, People's Republic of China
| | - Ying Tong
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Shanghai Public Health Clinical Center & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Key Laboratory of Medical Epigenetics, Shanghai, 200032, People's Republic of China
| | - Lu Chen
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Shanghai Public Health Clinical Center & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Key Laboratory of Medical Epigenetics, Shanghai, 200032, People's Republic of China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Shanghai Public Health Clinical Center & Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
- Shanghai Key Laboratory of Medical Epigenetics, Shanghai, 200032, People's Republic of China.
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Affiliation(s)
- Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, PR China
| | - Amr Ahmed El-Arabey
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Xinyi Jiang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, PR China
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Abdalla M, Eltayb WA, El-Arabey AA, Singh K, Jiang X. Molecular dynamic study of SARS-CoV-2 with various S protein mutations and their effect on thermodynamic properties. Comput Biol Med 2021; 141:105025. [PMID: 34772510 PMCID: PMC8576119 DOI: 10.1016/j.compbiomed.2021.105025] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 11/30/2022]
Abstract
Studying the structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein is important to understand the infection process. The S protein is necessary in completing the virus life cycle and is responsible for the appearance of new variants and drug and vaccine resistance. Understanding the structure and dynamics of biological macromolecules is essential for understanding how they function. In this work, we investigated the effects of mutations on S protein stability and solubility through molecular dynamic (MD) simulation in a 100 ns (ns) period. We screened four variants in addition to the wild type (WT). Results show that changes on MD simulation parameters of S protein indicate fluctuations and changes in the conformation, especially in the area between 300 and 600 amino acids (aa). This provides us an image of how the virus protein can reshape itself to adapt to any changes that occur in human angiotensin-converting enzyme 2 or drugs that can target the protein region. Our results also show that the Brazil variant has high fluctuations and unstable folding at some stages compared with other variants.
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Affiliation(s)
- Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China.
| | - Wafa Ali Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi, Nher Anile, Sudan
| | - Amr Ahmed El-Arabey
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Xinyi Jiang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China.
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