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An K, Yang X, Luo M, Yan J, Xu P, Zhang H, Li Y, Wu S, Warshel A, Bai C. Mechanistic study of the transmission pattern of the SARS-CoV-2 omicron variant. Proteins 2024; 92:705-719. [PMID: 38183172 PMCID: PMC11059747 DOI: 10.1002/prot.26663] [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: 10/18/2023] [Revised: 11/25/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]
Abstract
The omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) characterized by 30 mutations in its spike protein, has rapidly spread worldwide since November 2021, significantly exacerbating the ongoing COVID-19 pandemic. In order to investigate the relationship between these mutations and the variant's high transmissibility, we conducted a systematic analysis of the mutational effect on spike-angiotensin-converting enzyme-2 (ACE2) interactions and explored the structural/energy correlation of key mutations, utilizing a reliable coarse-grained model. Our study extended beyond the receptor-binding domain (RBD) of spike trimer through comprehensive modeling of the full-length spike trimer rather than just the RBD. Our free-energy calculation revealed that the enhanced binding affinity between the spike protein and the ACE2 receptor is correlated with the increased structural stability of the isolated spike protein, thus explaining the omicron variant's heightened transmissibility. The conclusion was supported by our experimental analyses involving the expression and purification of the full-length spike trimer. Furthermore, the energy decomposition analysis established those electrostatic interactions make major contributions to this effect. We categorized the mutations into four groups and established an analytical framework that can be employed in studying future mutations. Additionally, our calculations rationalized the reduced affinity of the omicron variant towards most available therapeutic neutralizing antibodies, when compared with the wild type. By providing concrete experimental data and offering a solid explanation, this study contributes to a better understanding of the relationship between theories and observations and lays the foundation for future investigations.
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Affiliation(s)
- Ke An
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang, 310005, P.R. China
| | - Xianzhi Yang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen 518000, China
| | - Mengqi Luo
- College of Management, Shenzhen University, Shenzhen, 518060, China
| | - Junfang Yan
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Peiyi Xu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Honghui Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Yuqing Li
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518116, China
| | - Song Wu
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518116, China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang, 310005, P.R. China
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Žáčková S, Pávová M, Trylčová J, Chalupová J, Priss A, Lukšan O, Weber J. Upregulation of mRNA Expression of ADGRD1/GPR133 and ADGRG7/GPR128 in SARS-CoV-2-Infected Lung Adenocarcinoma Calu-3 Cells. Cells 2024; 13:791. [PMID: 38786015 PMCID: PMC11119037 DOI: 10.3390/cells13100791] [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: 03/26/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Adhesion G protein-coupled receptors (aGPCRs) play an important role in neurodevelopment, immune defence and cancer; however, their role throughout viral infections is mostly unexplored. We have been searching for specific aGPCRs involved in SARS-CoV-2 infection of mammalian cells. In the present study, we infected human epithelial cell lines derived from lung adenocarcinoma (Calu-3) and colorectal carcinoma (Caco-2) with SARS-CoV-2 in order to analyse changes in the level of mRNA encoding individual aGPCRs at 6 and 12 h post infection. Based on significantly altered mRNA levels, we identified four aGPCR candidates-ADGRB3/BAI3, ADGRD1/GPR133, ADGRG7/GPR128 and ADGRV1/GPR98. Of these receptors, ADGRD1/GPR133 and ADGRG7/GPR128 showed the largest increase in mRNA levels in SARS-CoV-2-infected Calu-3 cells, whereas no increase was observed with heat-inactivated SARS-CoV-2 and virus-cleared conditioned media. Next, using specific siRNA, we downregulated the aGPCR candidates and analysed SARS-CoV-2 entry, replication and infectivity in both cell lines. We observed a significant decrease in the amount of SARS-CoV-2 newly released into the culture media by cells with downregulated ADGRD1/GPR133 and ADGRG7/GPR128. In addition, using a plaque assay, we observed a reduction in SARS-CoV-2 infectivity in Calu-3 cells. In summary, our data suggest that selected aGPCRs might play a role during SARS-CoV-2 infection of mammalian cells.
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Affiliation(s)
- Sandra Žáčková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic; (S.Ž.); (M.P.); (J.T.); (J.C.); (A.P.); (O.L.)
- Department of Genetics and Microbiology, Charles University, Faculty of Sciences, 128 44 Prague, Czech Republic
| | - Marcela Pávová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic; (S.Ž.); (M.P.); (J.T.); (J.C.); (A.P.); (O.L.)
| | - Jana Trylčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic; (S.Ž.); (M.P.); (J.T.); (J.C.); (A.P.); (O.L.)
| | - Jitka Chalupová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic; (S.Ž.); (M.P.); (J.T.); (J.C.); (A.P.); (O.L.)
| | - Anastasiia Priss
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic; (S.Ž.); (M.P.); (J.T.); (J.C.); (A.P.); (O.L.)
| | - Ondřej Lukšan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic; (S.Ž.); (M.P.); (J.T.); (J.C.); (A.P.); (O.L.)
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic; (S.Ž.); (M.P.); (J.T.); (J.C.); (A.P.); (O.L.)
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3
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [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: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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Olumuyide E, Agwuegbo CC, Ahmed EN. Exploring the Heart Failure Connection in Long COVID Patients: A Narrative Review. Cureus 2024; 16:e58694. [PMID: 38774167 PMCID: PMC11108637 DOI: 10.7759/cureus.58694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/24/2024] Open
Abstract
In this narrative review, we explore the relationship between long COVID patients and their risk of developing heart failure (HF). Patients with long COVID face a heightened risk of HF, a critical cardiovascular complication linked to the prolonged effects of COVID-19. Clinical manifestations of long COVID-associated HF present diagnostic challenges, complicating patient management. Multidisciplinary care is essential to address these complexities effectively. We found that long COVID can result in various cardiovascular issues including HF. The current view is long COVID leads to HF by activating systemic inflammation by causing endothelial dysfunction, which leads to activation of the complement pathways, tissue factor pathways, and Von Willebrand factor; activation of all these factors leads to venous and arterial thrombosis, which could lead to clogging of blood vessel of the heart leading to cardiovascular complications. The association between long COVID and HF can be challenging despite being recognized as comorbidity because biomarkers are not dependable in determining whether a patient had HF before or after contracting COVID-19. Emerging therapeutic modalities offer hope for improving outcomes, but further research is needed to refine management strategies and mitigate long-term cardiovascular consequences of COVID-19.
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Affiliation(s)
- Emmanuel Olumuyide
- Internal Medicine, Advocate Illinois Masonic Medical Center, Chicago, USA
| | | | - Eman N Ahmed
- Internal Medicine, Alfaisal University College of Medicine, Riyadh, SAU
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Biswas S, Mita MA, Afrose S, Hasan MR, Shimu MSS, Zaman S, Saleh MA. An in silico approach to develop potential therapies against Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Heliyon 2024; 10:e25837. [PMID: 38379969 PMCID: PMC10877303 DOI: 10.1016/j.heliyon.2024.e25837] [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: 05/25/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
A deadly respiratory disease Middle East Respiratory Syndrome (MERS) is caused by a perilous virus known as MERS-CoV, which has a severe impact on human health. Currently, there is no approved vaccine, prophylaxis, or antiviral therapeutics for preventing MERS-CoV infection. Due to its inexorable and integral role in the maturation and replication of the MERS-CoV virus, the 3C-like protease is unavoidly a viable therapeutic target. In this study, 2369 phytoconstituents were enlisted from Japanese medicinal plants, and these compounds were screened against 3C-like protease to identify feasible inhibitors. The best three compounds were identified as Kihadanin B, Robustaflavone, and 3-beta-O- (trans-p-Coumaroyl) maslinic acid, with binding energies of -9.8, -9.4, and -9.2 kcal/mol, respectively. The top three potential candidates interacted with several active site residues in the targeted protein, including Cys145, Met168, Glu169, Ala171, and Gln192. The best three compounds were assessed by in silico technique to determine their drug-likeness properties, and they exhibited the least harmful features and the greatest drug-like qualities. Various descriptors, such as solvent-accessible surface area, root-mean-square fluctuation, root-mean-square deviation, hydrogen bond, and radius of gyration, validated the stability and firmness of the protein-ligand complexes throughout the 100ns molecular dynamics simulation. Moreover, the top three compounds exhibited better binding energy along with better stability and firmness than the inhibitor (Nafamostat), which was further confirmed by the binding free energy calculation. Therefore, this computational investigation could aid in the development of efficient therapeutics for life-threatening MERS-CoV infections.
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Affiliation(s)
- Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | | | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
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Ding C, Chen Y, Miao G, Qi Z. Research Advances on the Role of Lipids in the Life Cycle of Human Coronaviruses. Microorganisms 2023; 12:63. [PMID: 38257890 PMCID: PMC10820681 DOI: 10.3390/microorganisms12010063] [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: 11/13/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Coronaviruses (CoVs) are emerging pathogens with a significant potential to cause life-threatening harm to human health. Since the beginning of the 21st century, three highly pathogenic and transmissible human CoVs have emerged, triggering epidemics and posing major threats to global public health. CoVs are enveloped viruses encased in a lipid bilayer. As fundamental components of cells, lipids can play an integral role in many physiological processes, which have been reported to play important roles in the life cycle of CoVs, including viral entry, uncoating, replication, assembly, and release. Therefore, research on the role of lipids in the CoV life cycle can provide a basis for a better understanding of the infection mechanism of CoVs and provide lipid targets for the development of new antiviral strategies. In this review, research advances on the role of lipids in different stages of viral infection and the possible targets of lipids that interfere with the viral life cycle are discussed.
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Affiliation(s)
- Cuiling Ding
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (C.D.); (Y.C.)
| | - Yibo Chen
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (C.D.); (Y.C.)
| | - Gen Miao
- Department of Nutrition and Food Hygiene, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China;
| | - Zhongtian Qi
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (C.D.); (Y.C.)
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Ghafouri E, Bigdeli M, Khalafiyan A, Amirkhani Z, Ghanbari R, Hasan A, Khanahmad H, Boshtam M, Makvandi P. Unmasking the complex roles of hypocalcemia in cancer, COVID-19, and sepsis: Engineered nanodelivery and diagnosis. ENVIRONMENTAL RESEARCH 2023; 238:116979. [PMID: 37660871 DOI: 10.1016/j.envres.2023.116979] [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: 07/10/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
Calcium (Ca2+) homeostasis is essential for maintaining physiological processes in the body. Disruptions in Ca2+ signaling can lead to various pathological conditions including inflammation, fibrosis, impaired immune function, and accelerated senescence. Hypocalcemia, a common symptom in diseases such as acute respiratory distress syndrome (ARDS), cancer, septic shock, and COVID-19, can have both potential protective and detrimental effects. This article explores the multifaceted role of Ca2+ dysregulation in inflammation, fibrosis, impaired immune function, and accelerated senescence, contributing to disease severity. Targeting Ca2+ signaling pathways may provide opportunities to develop novel therapeutics for age-related diseases and combat viral infections. However, the role of Ca2+ in viral infections is complex, and evidence suggests that hypocalcemia may have a protective effect against certain viruses, while changes in Ca2+ homeostasis can influence susceptibility to viral infections. The effectiveness and safety of Ca2+ supplements in COVID-19 patients remain a subject of ongoing research and debate. Further investigations are needed to understand the intricate interplay between Ca2+ signaling and disease pathogenesis.
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Affiliation(s)
- Elham Ghafouri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Anis Khalafiyan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zohre Amirkhani
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Roham Ghanbari
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China; School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh, EH9 3JL, UK.
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Boumaiza M, Chaabene A, Akrouti I, Ben Zakour M, Askri H, Salhi S, Ben Hamouda W, Marzouki S, Benabdessalem C, Ben Ahmed M, Trabelsi K, Rourou S. Development of an Optimized Process for Functional Recombinant SARS-CoV-2 Spike S1 Receptor-Binding Domain Protein Produced in the Baculovirus Expression Vector System. Trop Med Infect Dis 2023; 8:501. [PMID: 37999620 PMCID: PMC10674791 DOI: 10.3390/tropicalmed8110501] [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: 08/21/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 11/25/2023] Open
Abstract
To map the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and evaluate immune response variations against this virus, it is essential to set up efficient serological tests locally. The SARS-CoV-2 immunogenic proteins were very expensive and not affordable for lower- middle-income countries (LMICs). For this purpose, the commonly used antigen, receptor-binding domain (RBD) of spike S1 protein (S1RBD), was produced using the baculovirus expression vector system (BEVS). In the current study, the expression of S1RBD was monitored using Western blot under different culture conditions. Different parameters were studied: the multiplicity of infection (MOI), cell density at infection, and harvest time. Hence, optimal conditions for efficient S1RBD production were identified: MOI 3; cell density at infection 2-3 × 106 cells/mL; and time post-infection (tPI or harvest time) of 72 h and 72-96 h, successively, for expression in shake flasks and a 7L bioreactor. A high production yield of S1RBD varying between 4 mg and 70 mg per liter of crude cell culture supernatant was achieved, respectively, in the shake flasks and 7L bioreactor. Moreover, the produced S1RBD showed an excellent antigenicity potential against COVID-19 (Wuhan strain) patient sera evaluated by Western blot. Thus, additional serological assays, such as in-house ELISA and seroprevalence studies based on the purified S1RDB, were developed.
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Affiliation(s)
- Mohamed Boumaiza
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Ameni Chaabene
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Ines Akrouti
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Meriem Ben Zakour
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Hana Askri
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Said Salhi
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Wafa Ben Hamouda
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR11IPT-02, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur. BP. 74, Tunis 1002, Tunisia
| | - Soumaya Marzouki
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR11IPT-02, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur. BP. 74, Tunis 1002, Tunisia
| | - Chaouki Benabdessalem
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR11IPT-02, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur. BP. 74, Tunis 1002, Tunisia
| | - Melika Ben Ahmed
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR11IPT-02, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur. BP. 74, Tunis 1002, Tunisia
| | - Khaled Trabelsi
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Samia Rourou
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
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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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Bodakuntla S, Kuhn CC, Biertümpfel C, Mizuno N. Cryo-electron microscopy in the fight against COVID-19-mechanism of virus entry. Front Mol Biosci 2023; 10:1252529. [PMID: 37867557 PMCID: PMC10587472 DOI: 10.3389/fmolb.2023.1252529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) and electron tomography (cryo-ET) have become a critical tool for studying viral particles. Cryo-EM has enhanced our understanding of viral assembly and replication processes at a molecular resolution. Meanwhile, in situ cryo-ET has been used to investigate how viruses attach to and invade host cells. These advances have significantly contributed to our knowledge of viral biology. Particularly, prompt elucidations of structures of the SARS-CoV-2 spike protein and its variants have directly impacted the development of vaccines and therapeutic measures. This review discusses the progress made by cryo-EM based technologies in comprehending the severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2), the virus responsible for the devastating global COVID-19 pandemic in 2020 with focus on the SARS-CoV-2 spike protein and the mechanisms of the virus entry and replication.
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Affiliation(s)
- Satish Bodakuntla
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christopher Cyrus Kuhn
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christian Biertümpfel
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
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11
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Liu Y, Chen D, Wang Y, Li X, Qiu Y, Zheng M, Song Y, Li G, Song C, Liu T, Zhang Y, Guo JT, Lin H, Zhao X. Characterization of CCoV-HuPn-2018 spike protein-mediated viral entry. J Virol 2023; 97:e0060123. [PMID: 37676001 PMCID: PMC10537617 DOI: 10.1128/jvi.00601-23] [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: 04/23/2023] [Accepted: 07/25/2023] [Indexed: 09/08/2023] Open
Abstract
Canine coronavirus-human pneumonia-2018 (CCoV-HuPn-2018) was recently isolated from a child with pneumonia. This novel human pathogen resulted from cross-species transmission of a canine coronavirus. It has been known that CCoV-HuPn-2018 uses aminopeptidase N (APN) from canines, felines, and porcines, but not humans, as functional receptors for cell entry. The molecular mechanism of cell entry in CCoV-HuPn-2018 remains poorly understood. In this study, we demonstrated that among the nine APN orthologs tested, the APN of the Mexican free-tailed bat could also efficiently support CCoV-HuPn-2018 spike (S) protein-mediated entry, raising the possibility that bats may also be an alternative host epidemiologically important for the transmission of this virus. The glycosylation at residue N747 of canine APN is critical for its receptor activity. The gain of glycosylation at the corresponding residues in human and rabbit APNs converted them to functional receptors for CCoV-HuPn-2018. Interestingly, the CCoV-HuPn-2018 spike protein pseudotyped virus infected multiple human cancer cell lines in a human APN-independent manner, whereas sialic acid appeared to facilitate the entry of the pseudotyped virus into human cancer cells. Moreover, while host cell surface proteases trypsin and TMPRSS2 did not promote the entry of CCoV-HuPn-2018, endosomal proteases cathepsin L and B are required for the entry of CCoV-HuPn-2018 in a pH-dependent manner. IFITMs and LY6E are host restriction factors for the CCoV-HuPn-2018 entry. Our results thus suggest that CCoV-HuPn-2018 has not yet evolved to be an efficient human pathogen. Collectively, this study helps us understand the cell tropism, receptor usage, cross-species transmission, natural reservoir, and pathogenesis of this potential human coronavirus. IMPORTANCE Viral entry is driven by the interaction between the viral spike protein and its specific cellular receptor, which determines cell tropism and host range and is the major constraint to interspecies transmission of coronaviruses. Aminopeptidase N (APN; also called CD13) is a cellular receptor for HCoV-229E, the newly discovered canine coronavirus-human pneumonia-2018 (CCoV-HuPn-2018), and many other animal alphacoronaviruses. We examined the receptor activity of nine APN orthologs and found that CCoV-HuPn-2018 utilizes APN from a broad range of animal species, including bats but not humans, to enter host cells. To our surprise, we found that CCoV-HuPn-2018 spike protein pseudotyped viral particles successfully infected multiple human hepatoma-derived cell lines and a lung cancer cell line, which is independent of the expression of human APN. Our findings thus provide mechanistic insight into the natural hosts and interspecies transmission of CCoV-HuPn-2018-like coronaviruses.
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Affiliation(s)
- Yongmei Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Danying Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yuanyuan Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Peking University Ditan Teaching Hospital, Beijing, China
| | - Xinglin Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yaruo Qiu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Peking University Ditan Teaching Hospital, Beijing, China
| | - Mei Zheng
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yanjun Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Guoli Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Chuan Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Tingting Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Hepatitis B Foundation, Doylestown, Pennsylvania, USA
| | - Hanxin Lin
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
- Molecular Genetics Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Xuesen Zhao
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
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12
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Niort K, Dancourt J, Boedec E, Al Amir Dache Z, Lavieu G, Tareste D. Cholesterol and Ceramide Facilitate Membrane Fusion Mediated by the Fusion Peptide of the SARS-CoV-2 Spike Protein. ACS OMEGA 2023; 8:32729-32739. [PMID: 37720777 PMCID: PMC10500581 DOI: 10.1021/acsomega.3c03610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/17/2023] [Indexed: 09/19/2023]
Abstract
SARS-CoV-2 entry into host cells is mediated by the Spike (S) protein of the viral envelope. The S protein is composed of two subunits: S1 that induces binding to the host cell via its interaction with the ACE2 receptor of the cell surface and S2 that triggers fusion between viral and cellular membranes. Fusion by S2 depends on its heptad repeat domains that bring membranes close together and its fusion peptide (FP) that interacts with and perturbs the membrane structure to trigger fusion. Recent studies have suggested that cholesterol and ceramide lipids from the cell surface may facilitate SARS-CoV-2 entry into host cells, but their exact mode of action remains unknown. We have used a combination of in vitro liposome-liposome and in situ cell-cell fusion assays to study the lipid determinants of S-mediated membrane fusion. Our findings reveal that both cholesterol and ceramide lipids facilitate fusion, suggesting that targeting these lipids could be effective against SARS-CoV-2. As a proof of concept, we examined the effect of chlorpromazine (CPZ), an antipsychotic drug known to perturb membrane structure. Our results show that CPZ effectively inhibits S-mediated membrane fusion, thereby potentially impeding SARS-CoV-2 entry into the host cell.
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Affiliation(s)
- Kristina Niort
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| | - Julia Dancourt
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - Erwan Boedec
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| | - Zahra Al Amir Dache
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - Grégory Lavieu
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - David Tareste
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
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13
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Xie E, Ahmad S, Smyth RP, Sieben C. Advanced fluorescence microscopy in respiratory virus cell biology. Adv Virus Res 2023; 116:123-172. [PMID: 37524480 DOI: 10.1016/bs.aivir.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory viruses are a major public health burden across all age groups around the globe, and are associated with high morbidity and mortality rates. They can be transmitted by multiple routes, including physical contact or droplets and aerosols, resulting in efficient spreading within the human population. Investigations of the cell biology of virus replication are thus of utmost importance to gain a better understanding of virus-induced pathogenicity and the development of antiviral countermeasures. Light and fluorescence microscopy techniques have revolutionized investigations of the cell biology of virus infection by allowing the study of the localization and dynamics of viral or cellular components directly in infected cells. Advanced microscopy including high- and super-resolution microscopy techniques available today can visualize biological processes at the single-virus and even single-molecule level, thus opening a unique view on virus infection. We will highlight how fluorescence microscopy has supported investigations on virus cell biology by focusing on three major respiratory viruses: respiratory syncytial virus (RSV), Influenza A virus (IAV) and SARS-CoV-2. We will review our current knowledge of virus replication and highlight how fluorescence microscopy has helped to improve our state of understanding. We will start by introducing major imaging and labeling modalities and conclude the chapter with a perspective discussion on remaining challenges and potential opportunities.
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Affiliation(s)
- Enyu Xie
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shazeb Ahmad
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany; Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Christian Sieben
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany.
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14
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Sharifi E, Yousefiasl S, Trovato M, Sartorius R, Esmaeili Y, Goodarzi H, Ghomi M, Bigham A, Moghaddam FD, Heidarifard M, Pourmotabed S, Nazarzadeh Zare E, Paiva-Santos AC, Rabiee N, Wang X, Tay FR. Nanostructures for prevention, diagnosis, and treatment of viral respiratory infections: from influenza virus to SARS-CoV-2 variants. J Nanobiotechnology 2023; 21:199. [PMID: 37344894 PMCID: PMC10283343 DOI: 10.1186/s12951-023-01938-8] [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: 12/21/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023] Open
Abstract
Viruses are a major cause of mortality and socio-economic downfall despite the plethora of biopharmaceuticals designed for their eradication. Conventional antiviral therapies are often ineffective. Live-attenuated vaccines can pose a safety risk due to the possibility of pathogen reversion, whereas inactivated viral vaccines and subunit vaccines do not generate robust and sustained immune responses. Recent studies have demonstrated the potential of strategies that combine nanotechnology concepts with the diagnosis, prevention, and treatment of viral infectious diseases. The present review provides a comprehensive introduction to the different strains of viruses involved in respiratory diseases and presents an overview of recent advances in the diagnosis and treatment of viral infections based on nanotechnology concepts and applications. Discussions in diagnostic/therapeutic nanotechnology-based approaches will be focused on H1N1 influenza, respiratory syncytial virus, human parainfluenza virus type 3 infections, as well as COVID-19 infections caused by the SARS-CoV-2 virus Delta variant and new emerging Omicron variant.
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Affiliation(s)
- Esmaeel Sharifi
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran.
| | - Satar Yousefiasl
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maria Trovato
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131, Naples, Italy
| | - Rossella Sartorius
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131, Naples, Italy
| | - Yasaman Esmaeili
- School of Advanced Technologies in Medicine, Biosensor Research Center, Isfahan University of Medical Sciences, Isfahan, 8174673461, Iran
| | - Hamid Goodarzi
- Centre de recherche, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
- Départment d'Ophtalmologie, Université de Montréal, Montreal, QC, Canada
| | - Matineh Ghomi
- School of Chemistry, Damghan University, Damghan, 36716-45667, Iran
| | - Ashkan Bigham
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran
| | - Farnaz Dabbagh Moghaddam
- Institute for Photonics and Nanotechnologies, National Research Council, Via Fosso del Cavaliere, 100, 00133, Rome, Italy
| | - Maryam Heidarifard
- Centre de recherche, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
- Départment d'Ophtalmologie, Université de Montréal, Montreal, QC, Canada
| | - Samiramis Pourmotabed
- Department of Emergency Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran
| | | | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal
- Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA, 30912, USA.
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15
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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16
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Su M, Zheng G, Xu X, Song H. Antigen epitopes of animal coronaviruses: a mini-review. ANIMAL DISEASES 2023; 3:14. [PMID: 37220551 PMCID: PMC10189233 DOI: 10.1186/s44149-023-00080-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023] Open
Abstract
Coronaviruses are widespread in nature and can infect mammals and poultry, making them a public health concern. Globally, prevention and control of emerging and re-emerging animal coronaviruses is a great challenge. The mechanisms of virus-mediated immune responses have important implications for research on virus prevention and control. The antigenic epitope is a chemical group capable of stimulating the production of antibodies or sensitized lymphocytes, playing an important role in antiviral immune responses. Thus, it can shed light on the development of diagnostic methods and novel vaccines. Here, we have reviewed advances in animal coronavirus antigenic epitope research, aiming to provide a reference for the prevention and control of animal and human coronaviruses. Supplementary Information The online version contains supplementary material available at 10.1186/s44149-023-00080-0.
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Affiliation(s)
- Mingjun Su
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Guanghui Zheng
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Xiangwen Xu
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Houhui Song
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
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17
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Zhang J, Yang W, Roy S, Liu H, Roberts R, Wang L, Shi L, Ma W. Tight junction protein occludin is an internalization factor for SARS-CoV-2 infection and mediates virus cell-to-cell transmission. Proc Natl Acad Sci U S A 2023; 120:e2218623120. [PMID: 37068248 PMCID: PMC10151465 DOI: 10.1073/pnas.2218623120] [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: 10/31/2022] [Accepted: 03/13/2023] [Indexed: 04/19/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads efficiently by spike-mediated, direct cell-to-cell transmission. However, the underlying mechanism is poorly understood. Herein, we demonstrate that the tight junction protein occludin (OCLN) is critical to this process. SARS-CoV-2 infection alters OCLN distribution and expression and causes syncytium formation that leads to viral spread. OCLN knockdown fails to alter SARS-CoV-2 binding but significantly lowers internalization, syncytium formation, and transmission. OCLN overexpression also has no effect on virus binding but enhances virus internalization, cell-to-cell transmission, and replication. OCLN directly interacts with the SARS-CoV-2 spike, and the endosomal entry pathway is involved in OCLN-mediated cell-to-cell fusion rather than in the cell surface entry pathway. All SARS-CoV-2 strains tested (prototypic, alpha, beta, gamma, delta, kappa, and omicron) are dependent on OCLN for cell-to-cell transmission, although the extent of syncytium formation differs between strains. We conclude that SARS-CoV-2 utilizes OCLN as an internalization factor for cell-to-cell transmission.
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Affiliation(s)
- Jialin Zhang
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO65211
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO65211
| | - Wenyu Yang
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO65211
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO65211
| | - Sawrab Roy
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO65211
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO65211
| | - Heidi Liu
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO65211
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO65211
| | - R. Michael Roberts
- Division of Animal Sciences, College of Agriculture, Food, & Natural Resources, University of Missouri, Columbia, MO65211
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO65211
| | - Liping Wang
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO65211
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO65211
| | - Lei Shi
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO65211
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO65211
| | - Wenjun Ma
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO65211
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO65211
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18
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Milogrodzka I, Nguyen Pham DT, Sama GR, Samadian H, Zhai J, de Campo L, Kirby NM, Scott TF, Banaszak Holl MM, van 't Hag L. Effect of Cholesterol on Biomimetic Membrane Curvature and Coronavirus Fusion Peptide Encapsulation. ACS NANO 2023; 17:8598-8612. [PMID: 37078604 DOI: 10.1021/acsnano.3c01095] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Biomimetic cubic phases can be used for protein encapsulation in a variety of applications such as biosensors and drug delivery. Cubic phases with a high concentration of cholesterol and phospholipids were obtained herein. It is shown that the cubic phase structure can be maintained with a higher concentration of biomimetic membrane additives than has been reported previously. Opposing effects on the curvature of the membrane were observed upon the addition of phospholipids and cholesterol. Furthermore, the coronavirus fusion peptide significantly increased the negative curvature of the biomimetic membrane with cholesterol. We show that the viral fusion peptide can undergo structural changes leading to the formation of hydrophobic α-helices that insert into the lipid bilayer. This is of high importance, as a fusion peptide that induces increased negative curvature as shown by the formation of inverse hexagonal phases allows for greater contact area between two membranes, which is required for viral fusion to occur. The cytotoxicity assay showed that the toxicity toward HeLa cells was dramatically decreased when the cholesterol or peptide level in the nanoparticles increased. This suggests that the addition of cholesterol can improve the biocompatibility of the cubic phase nanoparticles, making them safer for use in biomedical applications. As the results, this work improves the potential for the biomedical end-use applications of the nonlamellar lipid nanoparticles and shows the need of systematic formulation studies due to the complex interplay of all components.
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Affiliation(s)
- Izabela Milogrodzka
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Duy Tue Nguyen Pham
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Gopal R Sama
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Hajar Samadian
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Jiali Zhai
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Liliana de Campo
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Kirrawee, NSW 2234, Australia
| | - Nigel M Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Timothy F Scott
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Mark M Banaszak Holl
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- Department of Mechanical and Materials Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Leonie van 't Hag
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
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19
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Minasi A, Andreadi A, Maiorino A, Giudice L, De Taddeo S, D'Ippolito I, de Guido I, Laitano R, Romano M, Ruotolo V, Magrini A, Di Daniele N, Rogliani P, Bellia A, Lauro D. Hypocalcemia is associated with adverse outcomes in patients hospitalized with COVID-19. Endocrine 2023; 79:577-586. [PMID: 36350462 PMCID: PMC9643940 DOI: 10.1007/s12020-022-03239-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
PURPOSE Calcium ions are involved in the regulation of several cellular processes and may also influence viral replication. Hypocalcemia has been frequently reported during infectious diseases and in critically ill patients, including also COVID-19 patients, significantly related with the pro-inflammatory state and mortality. The aim of this study is to investigate the prevalence of hypocalcemia at admission in patients hospitalized for COVID-19 (Coronavirus disease 2019) and to evaluate association of hypocalcemia with in-hospital COVID-19 outcomes. METHODS Retrospective analysis on 118 consecutive patients, hospitalized for COVID-19 between March and May 2020. Clinical characteristics, inflammation markers, biochemical routine and mineral metabolism parameters at admission were collected. Hypocalcemia was defined as total serum calcium <2.2 mmol/L. Population was stratified by tertiles of total serum calcium. Primary outcome was the composite of in-hospital death or admission to intensive care unit (ICU). Secondary outcomes included in-hospital death, admission to ICU and need for non-invasive ventilation as separate events. Associations were tested by logistic regression and Cox-regression analysis with survival curves. RESULTS Overall prevalence of hypocalcemia was 76.6%, with just 6.7% of patients reporting levels of 25-(OH)-vitamin D > 30 ng/ml. Total serum calcium was inversely related with selected inflammatory biomarkers (p < 0.05) and poorer outcome of COVID-19 during hospitalization. Lower tertile of total calcium (≤2.02 mmol/L) had increased risk of in-hospital mortality (HR 2.77; 1.28-6.03, p = 0.01) compared with other groups. CONCLUSION Total serum calcium detected on admission is inversely related with proinflammatory biomarkers of severe COVID-19 and is useful to better define risk stratification for adverse in-hospital outcome.
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Affiliation(s)
- Alessandro Minasi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Aikaterini Andreadi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Alessio Maiorino
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Luca Giudice
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Sofia De Taddeo
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Ilenia D'Ippolito
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Ilaria de Guido
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Respiratory Medicine, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Rossella Laitano
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Respiratory Medicine, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Maria Romano
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Valeria Ruotolo
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Andrea Magrini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Nicola Di Daniele
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Paola Rogliani
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Respiratory Medicine, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Alfonso Bellia
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy
| | - Davide Lauro
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy.
- Division of Endocrinology and Diabetes, University Hospital Fondazione Policlinico Tor Vergata, Rome, Italy.
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20
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Qiu C, Whittaker GR, Gellman SH, Daniel S, Abbott NL. Interactions of SARS-CoV-2 and MERS-CoV fusion peptides measured using single-molecule force methods. Biophys J 2023; 122:646-660. [PMID: 36650897 PMCID: PMC9841730 DOI: 10.1016/j.bpj.2023.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/07/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
We address the challenge of understanding how hydrophobic interactions are encoded by fusion peptide (FP) sequences within coronavirus (CoV) spike proteins. Within the FPs of severe acute respiratory syndrome CoV 2 and Middle East respiratory syndrome CoV (MERS-CoV), a largely conserved peptide sequence called FP1 (SFIEDLLFNK and SAIEDLLFDK in SARS-2 and MERS, respectively) has been proposed to play a key role in encoding hydrophobic interactions that drive viral-host cell membrane fusion. Although a non-polar triad (Leu-Leu-Phe (LLF)) is common to both FP1 sequences, and thought to dominate the encoding of hydrophobic interactions, FP1 from SARS-2 and MERS differ in two residues (Phe 2 versus Ala 2 and Asn 9 versus Asp 9, respectively). Here we explore whether single-molecule force measurements can quantify hydrophobic interactions encoded by FP1 sequences, and then ask whether sequence variations between FP1 from SARS-2 and MERS lead to significant differences in hydrophobic interactions. We find that both SARS-2 and MERS wild-type FP1 generate measurable hydrophobic interactions at the single-molecule level, but that SARS-2 FP1 encodes a substantially stronger hydrophobic interaction than its MERS counterpart (1.91 ± 0.03 nN versus 0.68 ± 0.03 nN, respectively). By performing force measurements with FP1 sequences with single amino acid substitutions, we determine that a single-residue mutation (Phe 2 versus Ala 2) causes the almost threefold difference in the hydrophobic interaction strength generated by the FP1 of SARS-2 versus MERS, despite the presence of LLF in both sequences. Infrared spectroscopy and circular dichroism measurements support the proposal that the outsized influence of Phe 2 versus Ala 2 on the hydrophobic interaction arises from variation in the secondary structure adopted by FP1. Overall, these insights reveal how single-residue diversity in viral FPs, including FP1 of SARS-CoV-2 and MERS-CoV, can lead to substantial changes in intermolecular interactions proposed to play a key role in viral fusion, and hint at strategies for regulating hydrophobic interactions of peptides in a range of contexts.
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Affiliation(s)
- Cindy Qiu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Susan Daniel
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Nicholas L Abbott
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York.
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21
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Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes. Nat Commun 2023; 14:945. [PMID: 36806058 PMCID: PMC9940680 DOI: 10.1038/s41467-023-36234-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 01/20/2023] [Indexed: 02/22/2023] Open
Abstract
The phenomenon of protein aggregation is associated with a wide range of human diseases. Our knowledge of the aggregation behaviour of viral proteins, however, is still rather limited. Here, we investigated this behaviour in the SARS-CoV and SARS-CoV-2 proteomes. An initial analysis using a panel of sequence-based predictors suggested the presence of multiple aggregation-prone regions (APRs) in these proteomes and revealed a strong aggregation propensity in some SARS-CoV-2 proteins. We then studied the in vitro aggregation of predicted aggregation-prone SARS-CoV and SARS-CoV-2 proteins and protein regions, including the signal sequence peptide and fusion peptides 1 and 2 of the spike protein, a peptide from the NSP6 protein, and the ORF10 and NSP11 proteins. Our results show that these peptides and proteins can form amyloid aggregates. We used circular dichroism spectroscopy to reveal the presence of β-sheet rich cores in aggregates and X-ray diffraction and Raman spectroscopy to confirm the formation of amyloid structures. Furthermore, we demonstrated that SARS-CoV-2 NSP11 aggregates are toxic to mammalian cell cultures. These results motivate further studies about the possible role of aggregation of SARS proteins in protein misfolding diseases and other human conditions.
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22
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Pedenko B, Sulbaran G, Guilligay D, Effantin G, Weissenhorn W. SARS-CoV-2 S Glycoprotein Stabilization Strategies. Viruses 2023; 15:v15020558. [PMID: 36851772 PMCID: PMC9960574 DOI: 10.3390/v15020558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The SARS-CoV-2 pandemic has again shown that structural biology plays an important role in understanding biological mechanisms and exploiting structural data for therapeutic interventions. Notably, previous work on SARS-related glycoproteins has paved the way for the rapid structural determination of the SARS-CoV-2 S glycoprotein, which is the main target for neutralizing antibodies. Therefore, all vaccine approaches aimed to employ S as an immunogen to induce neutralizing antibodies. Like all enveloped virus glycoproteins, SARS-CoV-2 S native prefusion trimers are in a metastable conformation, which primes the glycoprotein for the entry process via membrane fusion. S-mediated entry is associated with major conformational changes in S, which can expose many off-target epitopes that deviate vaccination approaches from the major aim of inducing neutralizing antibodies, which mainly target the native prefusion trimer conformation. Here, we review the viral glycoprotein stabilization methods developed prior to SARS-CoV-2, and applied to SARS-CoV-2 S, in order to stabilize S in the prefusion conformation. The importance of structure-based approaches is highlighted by the benefits of employing stabilized S trimers versus non-stabilized S in vaccines with respect to their protective efficacy.
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23
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Essalmani R, Andréo U, Evagelidis A, Le Dévéhat M, Pereira Ramos OH, Fruchart Gaillard C, Susan-Resiga D, Cohen ÉA, Seidah NG. SKI-1/S1P Facilitates SARS-CoV-2 Spike Induced Cell-to-Cell Fusion via Activation of SREBP-2 and Metalloproteases, Whereas PCSK9 Enhances the Degradation of ACE2. Viruses 2023; 15:v15020360. [PMID: 36851576 PMCID: PMC9959508 DOI: 10.3390/v15020360] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Proprotein convertases activate various envelope glycoproteins and participate in cellular entry of many viruses. We recently showed that the convertase furin is critical for the infectivity of SARS-CoV-2, which requires cleavage of its spike protein (S) at two sites: S1/S2 and S2'. This study investigates the implication of the two cholesterol-regulating convertases SKI-1 and PCSK9 in SARS-CoV-2 entry. The assays used were cell-to-cell fusion in HeLa cells and pseudoparticle entry into Calu-3 cells. SKI-1 increased cell-to-cell fusion by enhancing the activation of SREBP-2, whereas PCSK9 reduced cell-to-cell fusion by promoting the cellular degradation of ACE2. SKI-1 activity led to enhanced S2' formation, which was attributed to increased metalloprotease activity as a response to enhanced cholesterol levels via activated SREBP-2. However, high metalloprotease activity resulted in the shedding of S2' into a new C-terminal fragment (S2″), leading to reduced cell-to-cell fusion. Indeed, S-mutants that increase S2″ formation abolished S2' and cell-to-cell fusion, as well as pseudoparticle entry, indicating that the formation of S2″ prevents SARS-CoV-2 cell-to-cell fusion and entry. We next demonstrated that PCSK9 enhanced the cellular degradation of ACE2, thereby reducing cell-to-cell fusion. However, different from the LDLR, a canonical target of PCSK9, the C-terminal CHRD domain of PCSK9 is dispensable for the PCSK9-induced degradation of ACE2. Molecular modeling suggested the binding of ACE2 to the Pro/Catalytic domains of mature PCSK9. Thus, both cholesterol-regulating convertases SKI-1 and PCSK9 can modulate SARS-CoV-2 entry via two independent mechanisms.
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Affiliation(s)
- Rachid Essalmani
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), Université de Montréal, Montreal, QC H2W 1R7, Canada
| | - Ursula Andréo
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), Université de Montréal, Montreal, QC H2W 1R7, Canada
| | - Alexandra Evagelidis
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), Université de Montréal, Montreal, QC H2W 1R7, Canada
| | - Maïlys Le Dévéhat
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), Université de Montréal, Montreal, QC H2W 1R7, Canada
| | - Oscar Henrique Pereira Ramos
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SI-MoS, 91191 Gif-sur-Yvette, France
| | - Carole Fruchart Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SI-MoS, 91191 Gif-sur-Yvette, France
| | - Delia Susan-Resiga
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), Université de Montréal, Montreal, QC H2W 1R7, Canada
| | - Éric A. Cohen
- Laboratory of Human Retrovirology, Montreal Clinical Research Institute (IRCM), Université de Montréal, 110 Pine Ave West, Montreal, QC H2W 1R7, Canada
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nabil G. Seidah
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), Université de Montréal, Montreal, QC H2W 1R7, Canada
- Correspondence: ; Tel.: +1-514-987-5609
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24
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Díez JJ, Iglesias P, García A, Martín-Casasempere I, Bernabéu-Andréu FA. Serum Calcium, Magnesium, and Phosphorus Levels in Patients with COVID-19: Relationships with Poor Outcome and Mortality. Horm Metab Res 2023; 55:31-39. [PMID: 35998676 DOI: 10.1055/a-1899-8862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this retrospective study to assess the impact of serum corrected calcium (CorrCa), magnesium (Mg) and phosphorus (P) levels, all adult patients with laboratory-confirmed COVID-19 hospitalized during 2020 were included. Poor outcome was considered in patients who presented need for mechanical ventilation, intensive care unit (ICU) admission, or in-hospital mortality. We analyzed 2473 patients (956 females) aged (mean±SD) 63.4±15.9 years. During admission, 169 patients (6.8%) required mechanical ventilation, 205 (8.3%) were admitted to the ICU, and 270 (10.9%) died. Composite variable of poor outcome, defined as need for mechanical ventilation, ICU admission or death, was present in 434 (17.5%) patients. In univariate analysis, the need for mechanical ventilation was positively related to Mg levels (OR 8.37, 95% CI 3.62-19.33; p<0.001); ICU admission was related to CorrCa (OR 0.49, 95% CI 0.25-0.99; p=0.049) and Mg levels (OR 5.81, 95% CI 2.74-12.35; p<0.001); and in-hospital mortality was related to CorrCa (OR 1.73, 95% CI 1.14-2.64; p=0.011). The composite variable of poor outcome was only related to Mg (OR 2.68, 95% CI 1.54-4.68; p=0.001). However, in multivariate analysis only CorrCa was significantly related to the need for mechanical ventilation (OR 0.19, 95% CI 0.05-0.72; p=0.014) and ICU admission (OR 0.25; 95% CI 0.09-0.66; p=0.005), but not with in-hospital mortality or the composite variable. In conclusion, CorrCa can be used as a simple and reliable marker of poor outcome in patients with COVID-19, although not to predict the risk of in-hospital mortality.
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Affiliation(s)
- Juan J Díez
- Department of Endocrinology, Hospital Universitario Puerta de Hierro Majadahonda, Instituto de Investigación Sanitaria Puerta de Hierro Segovia de Arana, Majadahonda, Spain
| | - Pedro Iglesias
- Department of Endocrinology, Hospital Universitario Puerta de Hierro Majadahonda, Instituto de Investigación Sanitaria Puerta de Hierro Segovia de Arana, Majadahonda, Spain
| | - Agustín García
- Department of Admission and Clinical Documentation, Hospital Universitario Puerta de Hierro Majadahonda, Majadahonda, Spain
| | - Ignacio Martín-Casasempere
- Subdirección General de Farmacia y Productos Sanitarios, Consejería de Sanidad de la Comunidad de Madrid, Madrid, Spain
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25
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Iamartino L, Brandi ML. The calcium-sensing receptor in inflammation: Recent updates. Front Physiol 2022; 13:1059369. [PMID: 36467702 PMCID: PMC9716066 DOI: 10.3389/fphys.2022.1059369] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023] Open
Abstract
The Calcium-Sensing Receptor (CaSR) is a member of the class C of G-proteins coupled receptors (GPCRs), it plays a pivotal role in calcium homeostasis by directly controlling calcium excretion in the kidneys and indirectly by regulating parathyroid hormone (PTH) release from the parathyroid glands. The CaSR is found to be ubiquitously expressed in the body, playing a plethora of additional functions spanning from fluid secretion, insulin release, neuronal development, vessel tone to cell proliferation and apoptosis, to name but a few. The present review aims to elucidate and clarify the emerging regulatory effects that the CaSR plays in inflammation in several tissues, where it mostly promotes pro-inflammatory responses, with the exception of the large intestine, where contradictory roles have been recently reported. The CaSR has been found to be expressed even in immune cells, where it stimulates immune response and chemokinesis. On the other hand, CaSR expression seems to be boosted under inflammatory stimulus, in particular, by pro-inflammatory cytokines. Because of this, the CaSR has been addressed as a key factor responsible for hypocalcemia and low levels of PTH that are commonly found in critically ill patients under sepsis or after burn injury. Moreover, the CaSR has been found to be implicated in autoimmune-hypoparathyroidism, recently found also in patients treated with immune-checkpoint inhibitors. Given the tight bound between the CaSR, calcium and vitamin D metabolism, we also speculate about their roles in the pathogenesis of severe acute respiratory syndrome coronavirus-19 (SARS-COVID-19) infection and their impact on patients' prognosis. We will further explore the therapeutic potential of pharmacological targeting of the CaSR for the treatment and management of aberrant inflammatory responses.
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Affiliation(s)
- Luca Iamartino
- Department of Experimental Clinical and Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Maria Luisa Brandi
- F.I.R.M.O. (Italian Foundation for the Research on Bone Diseases), Florence, Italy
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26
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Chan SW. Fusion assays for screening of fusion inhibitors targeting SARS-CoV-2 entry and syncytia formation. Front Pharmacol 2022; 13:1007527. [PMID: 36438831 PMCID: PMC9691968 DOI: 10.3389/fphar.2022.1007527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/19/2022] [Indexed: 08/30/2023] Open
Abstract
Virus fusion process is evolutionarily conserved and provides a promising pan-viral target. Cell-cell fusion leads to syncytial formation and has implications in pathogenesis, virus spread and immune evasion. Drugs that target these processes can be developed into anti-virals. Here, we have developed sensitive, rapid, adaptable fusion reporter gene assays as models for plasma membrane and alternative fusion pathways as well as syncytial fusion in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have confirmed their specificity using neutralizing antibodies and specific protease inhibitors. The fusion report gene assays are more sensitive and unbiased than morphological fusion assay. The fusion assays can differentiate between transmembrane serine protease 2 (TMPRSS2)-dependency in TMPRSS2(+) cells and trypsin-dependency in angiotensin-converting enzyme 2 (ACE2)(+)TMPRSS2(-) cells. Moreover, we have identified putative novel fusion processes that are triggered by an acidic pH with and without trypsin. Coupled with morphological fusion criteria, we have found that syncytia formation is enhanced by TMPRSS2 or trypsin. By testing against our top drug hits previously shown to inhibit SARS-CoV-2 pseudovirus infection, we have identified several fusion inhibitors including structurally related lopsided kite-shaped molecules. Our results have important implications in the development of universal blockers and synergistic therapeutics and the small molecule inhibitors can provide important tools in elucidating the fusion process.
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Affiliation(s)
- Shiu-Wan Chan
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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27
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Patidar BS, Mukhopadhyay T, Subramanian A, Aggarwal R, Soni KD, Nischal N, Sahoo D, Surbhi S, Wig N, Pandey RM, Malhotra R, Trikha A. Association between Hypocalcemia and Outcome in COVID-19 Patients: A Retrospective Study. J Lab Physicians 2022. [DOI: 10.1055/s-0042-1757415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Abstract
Background Calcium has been shown to play a vital role in the pathophysiology of severe acute respiratory syndrome-coronavirus-2 and middle east respiratory syndrome coronavirus diseases, but less is known about hypocalcemia in coronavirus disease 2019 (COVID-19) patients and its association with the disease severity and the final outcome. Therefore, this study was conducted with an aim to assess clinical features in COVID-19 patients having hypocalcemia and to observe its impact on COVID-19 disease severity and the final outcome.
Methods In this retrospective study, consecutive COVID-19 patients of all age groups were enrolled. Demographical, clinical, and laboratory details were collected and analyzed. On the basis of albumin-corrected calcium levels, patients were classified into normocalcemic (n = 51) and hypocalcemic (n = 110) groups. Death was the primary outcome.
Results The mean age of patients in the hypocalcemic group was significantly lower (p < 0.05). A significantly higher number of hypocalcemic patients had severe COVID-19 infection (92.73%; p < 0.01), had comorbidities (82.73%, p < 0.05), and required ventilator support (39.09%; p < 0.01) compared with normocalcemic patients. The mortality rate was significantly higher in the hypocalcemic patients (33.63%; p < 0.05). Hemoglobin (p < 0.01), hematocrit (p < 0.01), and red cell count (p < 0.01) were significantly lower with higher levels of absolute neutrophil count (ANC; p < 0.05) and neutrophil-to-lymphocyte ratio (NLR; p < 0.01) in the hypocalcemic patients.Albumin-corrected calcium levels had a significant positive correlation with hemoglobin levels, hematocrit, red cell count, total protein, albumin, and albumin-to-globulin ratio and a significant negative correlation with ANC and NLR.
Conclusion The disease severity, ventilator requirement, and mortality were considerably higher in hypocalcemic COVID-19 patients.
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Affiliation(s)
- Bhagwan Singh Patidar
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Tapasyapreeti Mukhopadhyay
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Arulselvi Subramanian
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Richa Aggarwal
- Department of Anaesthesia, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Kapil Dev Soni
- Department of Anaesthesia, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Neeraj Nischal
- Department of Medicine, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Debasis Sahoo
- Department of Anaesthesia, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Surbhi Surbhi
- Department of Anaesthesia, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Naveet Wig
- Department of Medicine, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Ravindra Mohan Pandey
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Malhotra
- Department of Orthopedics, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
| | - Anjan Trikha
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences, New Delhi, India
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Lee SJ, Kim YJ, Ahn DG. Distinct Molecular Mechanisms Characterizing Pathogenesis of SARS-CoV-2. J Microbiol Biotechnol 2022; 32:1073-1085. [PMID: 36039385 PMCID: PMC9628960 DOI: 10.4014/jmb.2206.06064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has continued for over 2 years, following the outbreak of coronavirus-19 (COVID-19) in 2019. It has resulted in enormous casualties and severe economic crises. The rapid development of vaccines and therapeutics against SARS-CoV-2 has helped slow the spread. In the meantime, various mutations in the SARS-CoV-2 have emerged to evade current vaccines and therapeutics. A better understanding of SARS-CoV-2 pathogenesis is a prerequisite for developing efficient, advanced vaccines and therapeutics. Since the outbreak of COVID-19, a tremendous amount of research has been conducted to unveil SARSCoV-2 pathogenesis, from clinical observations to biochemical analysis at the molecular level upon viral infection. In this review, we discuss the molecular mechanisms of SARS-CoV-2 propagation and pathogenesis, with an update on recent advances.
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Affiliation(s)
- Su Jin Lee
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Yu-Jin Kim
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Dae-Gyun Ahn
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
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Nogueira GM, Silva NLOR, Moura AF, Duarte Silveira MA, Moura-Neto JA. Acute kidney injury and electrolyte disorders in COVID-19. World J Virol 2022; 11:283-292. [PMID: 36188735 PMCID: PMC9523327 DOI: 10.5501/wjv.v11.i5.283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 02/05/2023] Open
Abstract
Acute kidney injury (AKI) and electrolyte disorders are important complications of hospitalized coronavirus disease 2019 (COVID-19) patients. AKI is thought to occur due to multiple pathophysiological mechanisms, such as multiple organ dysfunction (mainly cardiac and respiratory), direct viral entry in the renal tubules, and cytokine release syndrome. AKI is present in approximately one in every ten hospitalized COVID-19 patients. The incidence rates of AKI increase in patients who are admitted to the intensive care unit (ICU), with levels higher than 50%. Additionally, renal replacement therapy (RRT) is used in 7% of all AKI cases, but in nearly 20% of patients admitted to an ICU. COVID-19 patients with AKI are considered moderate-to-severe cases and are managed with multiple interdisciplinary conducts. AKI acts as a risk factor for mortality in severe acute respiratory syndrome coronavirus 2 infection, especially when RRT is needed. Electrolyte disorders are also common manifestations in hospitalized COVID-19 patients, mainly hyponatremia, hypokalemia, and hypocalcemia. Hyponatremia occurs due to a combination of syndrome of inappropriate secretion of antidiuretic hormone and gastrointestinal fluid loss from vomiting and diarrhea. When it comes to hypokalemia, its mechanism is not fully understood but may derive from hyperaldosteronism due to renin angiotensin aldosterone system overstimulation and gastrointestinal fluid loss as well. The clinical features of hypokalemia in COVID-19 are similar to those in other conditions. Hypocalcemia is the most common electrolyte disorder in COVID-19 and seems to occur because of vitamin D deficiency and parathyroid imbalance. It is also highly associated with longer hospital and ICU stay.
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Affiliation(s)
- Gabriel Martins Nogueira
- Department of Medicine, Bahiana School of Medicine and Public Health, Salvador 40290-000, Bahia, Brazil
| | | | - Ana Flávia Moura
- Department of Medicine, Bahiana School of Medicine and Public Health, Salvador 40290-000, Bahia, Brazil
| | | | - José A Moura-Neto
- Department of Medicine, Bahiana School of Medicine and Public Health, Salvador 40290-000, Bahia, Brazil
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Saini J, Kaur P, Malik N, Lakhawat SS, Sharma PK. Antimicrobial peptides: A promising tool to combat multidrug resistance in SARS CoV2 era. Microbiol Res 2022; 265:127206. [PMID: 36162150 PMCID: PMC9491010 DOI: 10.1016/j.micres.2022.127206] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/26/2022] [Accepted: 09/16/2022] [Indexed: 10/25/2022]
Abstract
COVID-19 (Coronavirus Disease 2019), a life-threatening viral infection, is caused by a highly pathogenic virus named SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). Currently, no treatment is available for COVID-19; hence there is an urgent need to find effective therapeutic drugs to combat COVID-19 pandemic. Considering the fact that the world is facing a major issue of antimicrobial drug resistance, naturally occurring compounds have the potential to achieve this goal. Antimicrobial peptides (AMPs) are naturally occurring antimicrobial agents which are effective against a wide variety of microbial infections. Therefore, the use of AMPs is an attractive therapeutic strategy for the treatment of SARS-CoV-2 infection. This review sheds light on the potential of antimicrobial peptides as antiviral agents followed by a comprehensive description of effective antiviral peptides derived from various natural sources found to be effective against SARS-CoV and other respiratory viruses. It also highlights the mechanisms of action of antiviral peptides with special emphasis on their effectiveness against SARS-CoV-2 infection.
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Affiliation(s)
- Jasleen Saini
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Pritpal Kaur
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Naveen Malik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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Wettstein L, Immenschuh P, Weil T, Conzelmann C, Almeida‐Hernández Y, Hoffmann M, Kempf A, Nehlmeier I, Lotke R, Petersen M, Stenger S, Kirchhoff F, Sauter D, Pöhlmann S, Sanchez‐Garcia E, Münch J. Native and activated antithrombin inhibits TMPRSS2 activity and SARS-CoV-2 infection. J Med Virol 2022; 95:e28124. [PMID: 36056630 PMCID: PMC9538173 DOI: 10.1002/jmv.28124] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 01/11/2023]
Abstract
Host cell proteases such as TMPRSS2 are critical determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tropism and pathogenesis. Here, we show that antithrombin (AT), an endogenous serine protease inhibitor regulating coagulation, is a broad-spectrum inhibitor of coronavirus infection. Molecular docking and enzyme activity assays demonstrate that AT binds and inhibits TMPRSS2, a serine protease that primes the Spike proteins of coronaviruses for subsequent fusion. Consequently, AT blocks entry driven by the Spikes of SARS-CoV, MERS-CoV, hCoV-229E, SARS-CoV-2 and its variants of concern including Omicron, and suppresses lung cell infection with genuine SARS-CoV-2. Thus, AT is an endogenous inhibitor of SARS-CoV-2 that may be involved in COVID-19 pathogenesis. We further demonstrate that activation of AT by anticoagulants, such as heparin or fondaparinux, increases the anti-TMPRSS2 and anti-SARS-CoV-2 activity of AT, suggesting that repurposing of native and activated AT for COVID-19 treatment should be explored.
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Affiliation(s)
- Lukas Wettstein
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
| | | | - Tatjana Weil
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
| | - Carina Conzelmann
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
| | - Yasser Almeida‐Hernández
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg‐EssenEssenGermany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate ResearchGöttingenGermany,Faculty of Biology and PsychologyGeorg‐August‐UniversityGöttingenGermany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate ResearchGöttingenGermany,Faculty of Biology and PsychologyGeorg‐August‐UniversityGöttingenGermany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate ResearchGöttingenGermany
| | - Rishikesh Lotke
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TübingenTübingenGermany
| | - Moritz Petersen
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TübingenTübingenGermany
| | - Steffen Stenger
- Institute for Microbiology and HygieneUlm University Medical CenterUlmGermany
| | - Frank Kirchhoff
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TübingenTübingenGermany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate ResearchGöttingenGermany,Faculty of Biology and PsychologyGeorg‐August‐UniversityGöttingenGermany
| | - Elsa Sanchez‐Garcia
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg‐EssenEssenGermany
| | - Jan Münch
- Institute of Molecular VirologyUlm University Medical CenterUlmGermany
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Kim J, Jo S, Choi Y, Kim TW, Park JE. Chestnut inner shell extract inhibits viral entry of porcine epidemic diarrhea virus and other coronaviruses in vitro. Front Vet Sci 2022; 9:930608. [PMID: 36118328 PMCID: PMC9478750 DOI: 10.3389/fvets.2022.930608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a coronavirus that causes acute diarrhea in suckling piglets. Although vaccines are able to reduce the incidence of PEDV infection, outbreaks of PEDV continue to be reported worldwide and cause serious economic losses in the swine industry. To identify novel antiviral sources, we identified the chestnut (Castanea crenata) inner shell (CIS) as a natural material with activity against PEDV infection in vitro. The ethanol fractions of CIS extracts potently inhibited PEDV infection with an IC90 of 30 μg/ml. Further investigation of the virus lifecycle demonstrated that CIS extract particularly targeted the early stages of PEDV infection by blocking viral attachment and membrane fusion at rates of 80~90%. In addition, CIS extract addition reduced the viral entry of other members of the Coronaviridae family. Our data demonstrated that CIS extract inhibited PEDV infection by blocking cell entry in vitro and suggest that CIS extract is a new prophylactic and therapeutic agent against PEDV and other coronavirus infections.
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Affiliation(s)
- Jinman Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Sohee Jo
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Yeojin Choi
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Tae-Won Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
- Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
- Tae-Won Kim
| | - Jung-Eun Park
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
- Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
- *Correspondence: Jung-Eun Park
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33
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Qiao S, Zhang S, Ge J, Wang X. The spike glycoprotein of highly pathogenic human coronaviruses: structural insights for understanding infection, evolution and inhibition. FEBS Open Bio 2022; 12:1602-1622. [PMID: 35689514 PMCID: PMC9433818 DOI: 10.1002/2211-5463.13454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 12/29/2022] Open
Abstract
Highly pathogenic human coronaviruses (CoV) including SARS-CoV, MERS-CoV and SARS-CoV-2 have emerged over the past two decades, resulting in infectious disease outbreaks that have greatly affected public health. The CoV surface spike (S) glycoprotein mediates receptor binding and membrane fusion for cell entry, playing critical roles in CoV infection and evolution. The S glycoprotein is also the major target molecule for prophylactic and therapeutic interventions, including neutralizing antibodies and vaccines. In this review, we summarize key studies that have revealed the structural basis of S-mediated cell entry of SARS-CoV, MERS-CoV and SARS-CoV-2. Additionally, we discuss the evolution of the S glycoprotein to realize cross-species transmission from the viewpoint of structural biology. Lastly, we describe the recent progress in developing antibodies, nanobodies and peptide inhibitors that target the SARS-CoV-2 S glycoprotein for therapeutic purposes.
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Affiliation(s)
- Shuyuan Qiao
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life SciencesTsinghua UniversityBeijingChina
| | - Shuyuan Zhang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life SciencesTsinghua UniversityBeijingChina
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life SciencesTsinghua UniversityBeijingChina
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life SciencesTsinghua UniversityBeijingChina
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34
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Karsten H, Cords L, Westphal T, Knapp M, Brehm TT, Hermanussen L, Omansen TF, Schmiedel S, Woost R, Ditt V, Peine S, Lütgehetmann M, Huber S, Ackermann C, Wittner M, Addo MM, Sette A, Sidney J, Schulze zur Wiesch J. High-resolution analysis of individual spike peptide-specific CD4 + T-cell responses in vaccine recipients and COVID-19 patients. Clin Transl Immunology 2022; 11:e1410. [PMID: 35957961 PMCID: PMC9363231 DOI: 10.1002/cti2.1410] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/06/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
Objectives Potential differences in the breadth, distribution and magnitude of CD4+ T-cell responses directed against the SARS-CoV-2 spike glycoprotein between vaccinees, COVID-19 patients and subjects who experienced both ways of immunisation have not been comprehensively compared on a peptide level. Methods Following virus-specific in vitro cultivation, we determined the T-cell responses directed against 253 individual overlapping 15-mer peptides covering the entire SARS-CoV-2 spike glycoprotein using IFN-γ ELISpot and intracellular cytokine staining. In vitro HLA binding was determined for selected peptides. Results We mapped 955 single peptide-specific CD4+ T-cell responses in a cohort of COVID-19 patients (n = 8), uninfected vaccinees (n = 16) and individuals who experienced both infection and vaccination (n = 11). Patients and vaccinees (two-time and three-time vaccinees alike) had a comparable number of CD4+ T-cell responses (median 26 vs. 29, P = 0.7289). Most of these specificities were conserved in B.1.1.529 and the BA.4 and BA.5 sublineages. The highest magnitude of these in vitro IFN-γ CD4+ T-cell responses was observed in COVID-19 patients (median 0.35%), and three-time vaccinees showed a higher magnitude than two-time vaccinees (median 0.091% vs. 0.175%, P < 0.0001). Twelve peptide specificities were each detected in at least 40% of subjects. In vitro HLA binding showed promiscuous presentation by DRB1 molecules for several peptides. Conclusion Both SARS-CoV-2 infection and vaccination prime broadly directed T-cell responses directed against the SARS-CoV-2 spike glycoprotein. This comprehensive high-resolution analysis of spike peptide specificities will be a useful resource for further investigation of spike-specific T-cell responses.
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Affiliation(s)
- Hendrik Karsten
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Leon Cords
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Tim Westphal
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- German Center for Infection Research (DZIF)Partner Site Hamburg‐Lübeck‐Borstel‐RiemsHamburgGermany
| | - Maximilian Knapp
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Thomas Theo Brehm
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- German Center for Infection Research (DZIF)Partner Site Hamburg‐Lübeck‐Borstel‐RiemsHamburgGermany
| | - Lennart Hermanussen
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Till Frederik Omansen
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- Department of Tropical MedicineBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Stefan Schmiedel
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Robin Woost
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Vanessa Ditt
- Institute of Transfusion MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Sven Peine
- Institute of Transfusion MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Marc Lütgehetmann
- German Center for Infection Research (DZIF)Partner Site Hamburg‐Lübeck‐Borstel‐RiemsHamburgGermany
- Institute of Medical Microbiology, Virology and HygieneUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Samuel Huber
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Christin Ackermann
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Melanie Wittner
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- German Center for Infection Research (DZIF)Partner Site Hamburg‐Lübeck‐Borstel‐RiemsHamburgGermany
| | - Marylyn Martina Addo
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- German Center for Infection Research (DZIF)Partner Site Hamburg‐Lübeck‐Borstel‐RiemsHamburgGermany
- Department of Tropical MedicineBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine ResearchLa Jolla Institute for Immunology (LJI)La JollaCAUSA
| | - John Sidney
- Center for Infectious Disease and Vaccine ResearchLa Jolla Institute for Immunology (LJI)La JollaCAUSA
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit, 1. Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- German Center for Infection Research (DZIF)Partner Site Hamburg‐Lübeck‐Borstel‐RiemsHamburgGermany
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Hsu CH, Chen WL, Hsieh MF, Gu Y, C.-W. Wu K. Construction of magnetic Fe3O4@NH2-MIL-100(Fe)-C18 with excellent hydrophobicity for effective protein separation and purification. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Krisanova N, Pozdnyakova N, Pastukhov A, Dudarenko M, Shatursky O, Gnatyuk O, Afonina U, Pyrshev K, Dovbeshko G, Yesylevskyy S, Borisova T. Amphiphilic anti-SARS-CoV-2 drug remdesivir incorporates into the lipid bilayer and nerve terminal membranes influencing excitatory and inhibitory neurotransmission. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - BIOMEMBRANES 2022; 1864:183945. [PMID: 35461828 PMCID: PMC9023372 DOI: 10.1016/j.bbamem.2022.183945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/03/2022] [Accepted: 04/17/2022] [Indexed: 12/05/2022]
Abstract
Remdesivir is a novel antiviral drug, which is active against the SARS-CoV-2 virus. Remdesivir is known to accumulate in the brain but it is not clear whether it influences the neurotransmission. Here we report diverse and pronounced effects of remdesivir on transportation and release of excitatory and inhibitory neurotransmitters in rat cortex nerve terminals (synaptosomes) in vitro. Direct incorporation of remdesivir molecules into the cellular membranes was shown by FTIR spectroscopy, planar phospholipid bilayer membranes and computational techniques. Remdesivir decreases depolarization-induced exocytotic release of L-[14C] glutamate and [3H] GABA, and also [3H] GABA uptake and extracellular level in synaptosomes in a dose-dependent manner. Fluorimetric studies confirmed remdesivir-induced impairment of exocytosis in nerve terminals and revealed a decrease in synaptic vesicle acidification. Our data suggest that remdesivir dosing during antiviral therapy should be precisely controlled to prevent possible neuromodulatory action at the presynaptic level. Further studies of neurotropic and membranotropic effects of remdesivir are necessary.
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37
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Atik N, Wirawan F, Amalia R, Khairani AF, Pradini GW. Differences in endosomal Rab gene expression between positive and negative COVID-19 patients. BMC Res Notes 2022; 15:252. [PMID: 35840993 PMCID: PMC9284097 DOI: 10.1186/s13104-022-06144-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/03/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE SARS CoV-2, the etiologic agent of coronavirus disease-2019 (COVID-19) is well-known to use ACE2 to begin internalization. Some viruses enter the host cell through the endocytosis process and involve some endocytosis proteins, such as the Rab family. However, the relationship between SARS CoV-2 infection with endocytic mRNA RAB5, RAB7, and RAB11B is unknown. This study aims to compare the expression of RAB5, RAB7, and RAB11B between positive and negative COVID-19 patient groups. RESULTS Both viral and human epithelial RNA Isolation and RT-PCR were performed from 249 samples. The genes expression was analysed using appropriate statistical tests. We found the Median (inter-quartile range/IQR) of RAB5, RAB7, and RAB11B expression among the COVID-19 patient group was 2.99 (1.88), 0.17 (0.47), 0.47 (1.49), and 1.60 (2.88), 1.05 (2.49), 1.10 (3.96) among control group respectively. We proceeded with Mann Whitney U Test and found that RAB5 expression was significantly increased (P < 0.001), and RAB7 and RAB11B expression was significantly decreased (P < 0.001 and P = 0.036) in the COVID-19 patient group compared to the control group. This first report showed significant differences in RAB5, RAB7, and RAB11B exist between COVID-19 positive and negative patients.
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Affiliation(s)
- Nur Atik
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, 40161, Indonesia.
| | - Farruqi Wirawan
- Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Riezki Amalia
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Astrid Feinisa Khairani
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, 40161, Indonesia
| | - Gita Widya Pradini
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, 40161, Indonesia
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Krut' VG, Chuvpilo SA, Astrakhantseva IV, Kozlovskaya LI, Efimov GA, Kruglov AA, Drutskaya MS, Nedospasov SA. Will Peptides Help to Stop COVID-19? BIOCHEMISTRY (MOSCOW) 2022; 87:590-604. [PMID: 36154880 PMCID: PMC9282900 DOI: 10.1134/s0006297922070021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Peptides are widely used for the diagnostics, prevention, and therapy of certain human diseases. How useful can they be for the disease caused by the SARS-CoV-2 coronavirus? In this review, we discuss the possibility of using synthetic and recombinant peptides and polypeptides for prevention of COVID-19 via blocking the interaction between the virus and its main receptor ACE2, as well as components of antiviral vaccines, in particular, against new emerging virus variants.
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Affiliation(s)
- Viktoriya G Krut'
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Sergei A Chuvpilo
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Irina V Astrakhantseva
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Liubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia
| | - Grigory A Efimov
- National Medical Research Center of Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Andrei A Kruglov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- German Rheumatism Research Center (DRFZ), Leibniz Institute, Berlin, 10117, Germany
| | - Marina S Drutskaya
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Sergei A Nedospasov
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
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Fujioka Y, Kashiwagi S, Yoshida A, Satoh AO, Fujioka M, Amano M, Yamauchi Y, Ohba Y. A method for the generation of pseudovirus particles bearing SARS coronavirus spike protein in high yields. Cell Struct Funct 2022; 47:43-53. [PMID: 35491102 PMCID: PMC10511058 DOI: 10.1247/csf.21047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/19/2022] [Indexed: 12/17/2023] Open
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has threatened human health and the global economy. Development of additional vaccines and therapeutics is urgently required, but such development with live virus must be conducted with biosafety level 3 confinement. Pseudotyped viruses have been widely adopted for studies of virus entry and pharmaceutical development to overcome this restriction. Here we describe a modified protocol to generate vesicular stomatitis virus (VSV) pseudotyped with SARS-CoV or SARS-CoV-2 spike protein in high yield. We found that a large proportion of pseudovirions produced with the conventional transient expression system lacked coronavirus spike protein at their surface as a result of inhibition of parental VSV infection by overexpression of this protein. Establishment of stable cell lines with an optimal expression level of coronavirus spike protein allowed the efficient production of progeny pseudoviruses decorated with spike protein. This improved VSV pseudovirus production method should facilitate studies of coronavirus entry and development of antiviral agents.Key words: severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, pseudovirus, vesicular stomatitis virus (VSV), spike protein.
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Affiliation(s)
- Yoichiro Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Sayaka Kashiwagi
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Aiko Yoshida
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Aya O. Satoh
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Mari Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Maho Amano
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Yohei Yamauchi
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yusuke Ohba
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, N12W6, Kita-ku, Sapporo 060-8612, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, N15W7, Kita-ku, Sapporo 060-8638, Japan
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40
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Kung YA, Lee KM, Chiang HJ, Huang SY, Wu CJ, Shih SR. Molecular Virology of SARS-CoV-2 and Related Coronaviruses. Microbiol Mol Biol Rev 2022; 86:e0002621. [PMID: 35343760 PMCID: PMC9199417 DOI: 10.1128/mmbr.00026-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. Although several COVID-19 vaccines are currently being administered, none of them is 100% effective. Moreover, SARS-CoV-2 variants remain an important worldwide public health issue. Hence, the accelerated development of efficacious antiviral agents is urgently needed. Coronavirus depends on various host cell factors for replication. An ongoing research objective is the identification of host factors that could be exploited as targets for drugs and compounds effective against SARS-CoV-2. In the present review, we discuss the molecular mechanisms of SARS-CoV-2 and related coronaviruses, focusing on the host factors or pathways involved in SARS-CoV-2 replication that have been identified by genome-wide CRISPR screening.
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Affiliation(s)
- Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Huan-Jung Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sheng-Yu Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Jung Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
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41
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Jocher G, Grass V, Tschirner SK, Riepler L, Breimann S, Kaya T, Oelsner M, Hamad MS, Hofmann LI, Blobel CP, Schmidt-Weber CB, Gokce O, Jakwerth CA, Trimpert J, Kimpel J, Pichlmair A, Lichtenthaler SF. ADAM10 and ADAM17 promote SARS-CoV-2 cell entry and spike protein-mediated lung cell fusion. EMBO Rep 2022; 23:e54305. [PMID: 35527514 PMCID: PMC9171409 DOI: 10.15252/embr.202154305] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 12/17/2022] Open
Abstract
The severe‐acute‐respiratory‐syndrome‐coronavirus‐2 (SARS‐CoV‐2) is the causative agent of COVID‐19, but host cell factors contributing to COVID‐19 pathogenesis remain only partly understood. We identify the host metalloprotease ADAM17 as a facilitator of SARS‐CoV‐2 cell entry and the metalloprotease ADAM10 as a host factor required for lung cell syncytia formation, a hallmark of COVID‐19 pathology. ADAM10 and ADAM17, which are broadly expressed in the human lung, cleave the SARS‐CoV‐2 spike protein (S) in vitro, indicating that ADAM10 and ADAM17 contribute to the priming of S, an essential step for viral entry and cell fusion. ADAM protease‐targeted inhibitors severely impair lung cell infection by the SARS‐CoV‐2 variants of concern alpha, beta, delta, and omicron and also reduce SARS‐CoV‐2 infection of primary human lung cells in a TMPRSS2 protease‐independent manner. Our study establishes ADAM10 and ADAM17 as host cell factors for viral entry and syncytia formation and defines both proteases as potential targets for antiviral drug development.
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Affiliation(s)
- Georg Jocher
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Vincent Grass
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Sarah K Tschirner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Lydia Riepler
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Breimann
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, Freising, Germany
| | - Tuğberk Kaya
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.,Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Madlen Oelsner
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, German Center for Lung Research (DZL), Munich, Germany
| | - M Sabri Hamad
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Laura I Hofmann
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carl P Blobel
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA.,Departments of Medicine and of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Carsten B Schmidt-Weber
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, German Center for Lung Research (DZL), Munich, Germany
| | - Ozgun Gokce
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Constanze A Jakwerth
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, German Center for Lung Research (DZL), Munich, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Janine Kimpel
- Department of Hygiene, Microbiology and Public Health, Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Pichlmair
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Munich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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42
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Lousada CM. Interactions between glucosides of the tip of the S1 subunit of SARS-CoV-2 spike protein and dry and wet surfaces of CuO and Cu-A model for the surfaces of coinage metals. Colloids Surf B Biointerfaces 2022; 214:112465. [PMID: 35334309 PMCID: PMC8940556 DOI: 10.1016/j.colsurfb.2022.112465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022]
Abstract
Despite their importance there is little knowledge at the atomic scale on the interactions between fragments of SARS-CoV-2 and inorganic materials. Such knowledge is important to understand the survival of the virus at surfaces and for the development of antiviral materials. Here is reported a study of the interactions between glucoside monomers of the tip of the S1 subunit of SARS-CoV-2 spike protein with dry and wet surfaces of CuO and Cu, performed with dispersion corrected density functional theory—DFT. The three glucoside monomers that constitute the tip of S1: 6VSB, 6VXX and 6X6P, were adsorbed onto dry and wet CuO(111) and Cu(110) with different orientations and surface alignments. There are large differences—of up to 1.3 eV—in binding energies between these monomers and the surfaces. These differences depend on: the type of surface; if the surface is wet or dry; if the glucosidic O-atom points towards or away from the surfaces; and to a smaller extent on the surface alignment of the monomers. All monomers bind strongly to the surfaces via molecular adsorption that does not involve bond breaking in the monomers at this stage. 6VSB has the larger adsorption energies—that reach 2.2 eV—due to its larger dipole moment. Both materials bind the monomers more strongly when their surfaces are dry. At Cu(110) the bonds are on average 1 eV stronger when the surface is dry when compared to wet. The difference between dry and wet CuO(111) is smaller, in the order of 0.2 eV. Overall, it is here shown that the stability of the monomers of the tip of the spike protein of the virus is very different at different surfaces. For a given surface the larger binding energies in dry conditions could explain the differences in the surface stability of the spike protein depending on the presence of moisture.
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Affiliation(s)
- Cláudio M Lousada
- Department of Materials Science and Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
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43
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Souza PF, Mesquita FP, Amaral JL, Landim PG, Lima KR, Costa MB, Farias IR, Belém MO, Pinto YO, Moreira HH, Magalhaes IC, Castelo-Branco DS, Montenegro RC, de Andrade CR. The spike glycoprotein of SARS-CoV-2: A review of how mutations of spike glycoproteins have driven the emergence of variants with high transmissibility and immune escape. Int J Biol Macromol 2022; 208:105-125. [PMID: 35300999 PMCID: PMC8920968 DOI: 10.1016/j.ijbiomac.2022.03.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/23/2022]
Abstract
Late in 2019, SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) emerged, causing an unknown type of pneumonia today called coronaviruses disease 2019 (COVID-19). COVID-19 is still an ongoing global outbreak that has claimed and threatened many lives worldwide. Along with the fastest vaccine developed in history to fight SARS-CoV-2 came a critical problem, SARS-CoV-2. These new variants are a result of the accumulation of mutations in the sequence and structure of spike (S) glycoprotein, which is by far the most critical protein for SARS-CoV-2 to recognize cells and escape the immune system, in addition to playing a role in SARS-CoV-2 infection, pathogenicity, transmission, and evolution. In this review, we discuss mutation of S protein and how these mutations have led to new variants that are usually more transmissible and can thus mitigate the immunity produced by vaccination. Here, analysis of S protein sequences and structures from variants point out the mutations among them, how they emerge, and the behavior of S protein from each variant. This review brings details in an understandable way about how the variants of SARS-CoV-2 are a result of mutations in S protein, making them more transmissible and even more aggressive than their relatives.
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Affiliation(s)
- Pedro F.N. Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil,Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil,Corresponding author at: Drug research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Brazil, Rua Coronel Nunes de Melo 100, Caixa 60430-275 Fortaleza, CE, Brazil
| | - Felipe P. Mesquita
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Jackson L. Amaral
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Patrícia G.C. Landim
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Karollyny R.P. Lima
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Marília B. Costa
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Izabelle R. Farias
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Mônica O. Belém
- Laboratory of Translational Research, Christus University Center, Fortaleza, Ceará 60192, Brazil
| | - Yago O. Pinto
- Medical Education Institution-Idomed, Canindé, Ceará, Brazil
| | | | | | - Débora S.C.M. Castelo-Branco
- Department of Pathology and Legal Medicine, Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Raquel C. Montenegro
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Claudia R. de Andrade
- Laboratory of Translational Research, Christus University Center, Fortaleza, Ceará 60192, Brazil
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44
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Gorący A, Rosik J, Szostak B, Ustianowski Ł, Ustianowska K, Gorący J. Human Cell Organelles in SARS-CoV-2 Infection: An Up-to-Date Overview. Viruses 2022; 14:v14051092. [PMID: 35632833 PMCID: PMC9144443 DOI: 10.3390/v14051092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
Since the end of 2019, the whole world has been struggling with the life-threatening pandemic amongst all age groups and geographic areas caused by Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). The Coronavirus Disease 2019 (COVID-19) pandemic, which has led to more than 468 million cases and over 6 million deaths reported worldwide (as of 20 March 2022), is one of the greatest threats to human health in history. Meanwhile, the lack of specific and irresistible treatment modalities provoked concentrated efforts in scientists around the world. Various mechanisms of cell entry and cellular dysfunction were initially proclaimed. Especially, mitochondria and cell membrane are crucial for the course of infection. The SARS-CoV-2 invasion depends on angiotensin converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2), and cluster of differentiation 147 (CD147), expressed on host cells. Moreover, in this narrative review, we aim to discuss other cell organelles targeted by SARS-CoV-2. Lastly, we briefly summarize the studies on various drugs.
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Affiliation(s)
- Anna Gorący
- Independent Laboratory of Invasive Cardiology, Pomeranian Medical University, 70-204 Szczecin, Poland; (A.G.); (J.G.)
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-204 Szczecin, Poland
| | - Jakub Rosik
- Independent Laboratory of Invasive Cardiology, Pomeranian Medical University, 70-204 Szczecin, Poland; (A.G.); (J.G.)
- Department of Physiology, Pomeranian Medical University, 70-204 Szczecin, Poland; (B.S.); (Ł.U.); (K.U.)
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Correspondence:
| | - Bartosz Szostak
- Department of Physiology, Pomeranian Medical University, 70-204 Szczecin, Poland; (B.S.); (Ł.U.); (K.U.)
| | - Łukasz Ustianowski
- Department of Physiology, Pomeranian Medical University, 70-204 Szczecin, Poland; (B.S.); (Ł.U.); (K.U.)
| | - Klaudia Ustianowska
- Department of Physiology, Pomeranian Medical University, 70-204 Szczecin, Poland; (B.S.); (Ł.U.); (K.U.)
| | - Jarosław Gorący
- Independent Laboratory of Invasive Cardiology, Pomeranian Medical University, 70-204 Szczecin, Poland; (A.G.); (J.G.)
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45
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Kianpour M, Akbarian M, Uversky VN. Nanoparticles for Coronavirus Control. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1602. [PMID: 35564311 PMCID: PMC9104235 DOI: 10.3390/nano12091602] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 01/18/2023]
Abstract
More than 2 years have passed since the SARS-CoV-2 outbreak began, and many challenges that existed at the beginning of this pandemic have been solved. Some countries have been able to overcome this global challenge by relying on vaccines against the virus, and vaccination has begun in many countries. Many of the proposed vaccines have nanoparticles as carriers, and there are different nano-based diagnostic approaches for rapid detection of the virus. In this review article, we briefly examine the biology of SARS-CoV-2, including the structure of the virus and what makes it pathogenic, as well as describe biotechnological methods of vaccine production, and types of the available and published nano-based ideas for overcoming the virus pandemic. Among these issues, various physical and chemical properties of nanoparticles are discussed to evaluate the optimal conditions for the production of the nano-mediated vaccines. At the end, challenges facing the international community and biotechnological answers for future viral attacks are reviewed.
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Affiliation(s)
- Maryam Kianpour
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan;
| | - Mohsen Akbarian
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Health Byrd Alzheimer’s Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center ‘‘Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences’’, 142290 Pushchino, Moscow Region, Russia
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46
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Qing E, Li P, Cooper L, Schulz S, Jäck HM, Rong L, Perlman S, Gallagher T. Inter-domain communication in SARS-CoV-2 spike proteins controls protease-triggered cell entry. Cell Rep 2022; 39:110786. [PMID: 35477024 PMCID: PMC9015963 DOI: 10.1016/j.celrep.2022.110786] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 01/29/2023] Open
Abstract
SARS-CoV-2 continues to evolve into variants of concern (VOC), with greatest variability in the multidomain, entry-facilitating spike proteins. To recognize the significance of adaptive spike protein changes, we compare variant SARS-CoV-2 virus particles in several assays reflecting authentic virus-cell entry. Virus particles with adaptive changes in spike amino-terminal domains (NTDs) are hypersensitive to proteolytic activation of membrane fusion, an essential step in virus-cell entry. Proteolysis is within fusion domains (FDs), at sites over 10 nm from the VOC-specific NTD changes, indicating allosteric inter-domain control of fusion activation. In addition, NTD-specific antibodies block FD cleavage, membrane fusion, and virus-cell entry, suggesting restriction of inter-domain communication as a neutralization mechanism. Finally, using structure-guided mutagenesis, we identify an inter-monomer β sheet structure that facilitates NTD-to-FD transmissions and subsequent fusion activation. This NTD-to-FD axis that sensitizes viruses to infection and to NTD-specific antibody neutralization provides new context for understanding selective forces driving SARS-CoV-2 evolution.
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Affiliation(s)
- Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Pengfei Li
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Laura Cooper
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Sebastian Schulz
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nuremberg and University Hospital Erlangen, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nuremberg and University Hospital Erlangen, 91054 Erlangen, Germany
| | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA,Corresponding author
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47
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Al-Hakeim HK, Al-Jassas HK, Morris G, Maes M. Increased ACE2, sRAGE, and Immune Activation, but Lowered Calcium and Magnesium in COVID-19. RECENT ADVANCES IN INFLAMMATION & ALLERGY DRUG DISCOVERY 2022; 16:32-43. [PMID: 35307003 DOI: 10.2174/2772270816666220318103929] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND The characterization of new biomarkers that could help externally validate the diagnosis of COVID-19 and optimize treatments is extremely important. Many studies have established changes in immune-inflammatory and antibody levels, but few studies measured the soluble receptor for the advanced glycation end product (sRAGE), angiotensin-converting enzyme 2 (ACE2), calcium, and magnesium in COVID-19. OBJECTIVE To evaluate serum advanced glycation end-product receptor (sRAGE) and angiotensin converting enzyme (ACE)2 and peripheral oxygen saturation (SpO2) and chest CT scan abnormalities (CCTA) in COVID-19. METHODS sRAGE, ACE2, interleukin (IL)-6, IL-10, C-reactive protein (CRP), calcium, magnesium, and albumin were measured in 60 COVID-19 patients and 30 healthy controls. RESULTS COVID-19 is characterized by significantly increased IL-6, CRP, IL-10, sRAGE, ACE2, and lowered SpO2, albumin, magnesium, and calcium. COVID-19 with CCTAs showed lower SpO2 and albumin. SpO2 was significantly inversely correlated with IL-6, IL-10, CRP, sRAGE, and ACE2, and positively with albumin, magnesium, and calcium. Neural networks showed that a combination of calcium, IL-6, CRP, and sRAGE yielded an accuracy of 100% in detecting COVID-19 patients, with calcium being the most important predictor followed by IL-6 and CRP. Patients with positive IgG results showed a significant elevation in the serum level of IL-6, sRAGE, and ACE2 compared to the negatively IgG patient subgroup. CONCLUSION The results show that immune-inflammatory and RAGE pathways biomarkers may be used as an external validating criterion for the diagnosis of COVID-19. Those pathways coupled with lowered SpO2, calcium, and magnesium are drug targets that may help reduce the consequences of COVID-19.
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Affiliation(s)
| | | | - Gerwyn Morris
- School of Medicine, IMPACT-the Institute for Mental and Physical Health and Clinical Translation, Deakin University, Barwon Health, Geelong, Australia
| | - Michael Maes
- School of Medicine, IMPACT-the Institute for Mental and Physical Health and Clinical Translation, Deakin University, Barwon Health, Geelong, Australia.,Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria.,Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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48
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Färber I, Krüger J, Rocha C, Armando F, von Köckritz-Blickwede M, Pöhlmann S, Braun A, Baumgärtner W, Runft S, Krüger N. Investigations on SARS-CoV-2 Susceptibility of Domestic and Wild Animals Using Primary Cell Culture Models Derived from the Upper and Lower Respiratory Tract. Viruses 2022; 14:v14040828. [PMID: 35458558 PMCID: PMC9032458 DOI: 10.3390/v14040828] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 02/04/2023] Open
Abstract
Several animal species are susceptible to SARS-CoV-2 infection, as documented by case reports and serological and in vivo infection studies. However, the susceptibility of many animal species remains unknown. Furthermore, the expression patterns of SARS-CoV-2 entry factors, such as the receptor angiotensin-converting enzyme 2 (ACE2), as well as transmembrane protease serine subtype 2 (TMPRSS2) and cathepsin L (CTSL), cellular proteases involved in SARS-CoV-2 spike protein activation, are largely unexplored in most species. Here, we generated primary cell cultures from the respiratory tract of domestic and wildlife animals to assess their susceptibility to SARS-CoV-2 infection. Additionally, the presence of ACE2, TMPRSS2 and CTSL within respiratory tract compartments was investigated in a range of animals, some with unknown susceptibility to SARS-CoV-2. Productive viral replication was observed in the nasal mucosa explants and precision-cut lung slices from dogs and hamsters, whereas culture models from ferrets and multiple ungulate species were non-permissive to infection. Overall, whereas TMPRSS2 and CTSL were equally expressed in the respiratory tract, the expression levels of ACE2 were more variable, suggesting that a restricted availability of ACE2 may contribute to reduced susceptibility. Summarized, the experimental infection of primary respiratory tract cell cultures, as well as an analysis of entry-factor distribution, enable screening for SARS-CoV-2 animal reservoirs.
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Affiliation(s)
- Iris Färber
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
| | - Johannes Krüger
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
| | - Cheila Rocha
- Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (C.R.); (S.P.); (N.K.)
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
| | - Maren von Köckritz-Blickwede
- Department of Biochemistry, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (C.R.); (S.P.); (N.K.)
- Faculty of Biology and Psychology, Georg-August-University, 37073 Göttingen, Germany
| | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, 30625 Hannover, Germany;
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
- Correspondence: ; Tel.: +49-511-953-8620; Fax: +49-511-953-8675
| | - Sandra Runft
- Department of Pathology, University of Veterinary Medicine, Foundation, 30559 Hannover, Germany; (I.F.); (J.K.); (F.A.); (S.R.)
| | - Nadine Krüger
- Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; (C.R.); (S.P.); (N.K.)
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49
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Liu X, Wei L, Xu F, Zhao F, Huang Y, Fan Z, Mei S, Hu Y, Zhai L, Guo J, Zheng A, Cen S, Liang C, Guo F. SARS-CoV-2 spike protein-induced cell fusion activates the cGAS-STING pathway and the interferon response. Sci Signal 2022; 15:eabg8744. [PMID: 35412852 DOI: 10.1126/scisignal.abg8744] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the unprecedented coronavirus disease 2019 (COVID-19) pandemic. Critical cases of COVID-19 are characterized by the production of excessive amounts of cytokines and extensive lung damage, which is partially caused by the fusion of SARS-CoV-2-infected pneumocytes. Here, we found that cell fusion caused by the SARS-CoV-2 spike (S) protein induced a type I interferon (IFN) response. This function of the S protein required its cleavage by proteases at the S1/S2 and the S2' sites. We further showed that cell fusion damaged nuclei and resulted in the formation of micronuclei that were sensed by the cytosolic DNA sensor cGAS and led to the activation of its downstream effector STING. Phosphorylation of the transcriptional regulator IRF3 and the expression of IFNB, which encodes a type I IFN, were abrogated in cGAS-deficient fused cells. Moreover, infection with VSV-SARS-CoV-2 also induced cell fusion, DNA damage, and cGAS-STING-dependent expression of IFNB. Together, these results uncover a pathway underlying the IFN response to SARS-CoV-2 infection. Our data suggest a mechanism by which fused pneumocytes in the lungs of patients with COVID-19 may enhance the production of IFNs and other cytokines, thus exacerbating disease severity.
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Affiliation(s)
- Xiaoman Liu
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Liang Wei
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Fengwen Xu
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Fei Zhao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yu Huang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zhangling Fan
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Shan Mei
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yamei Hu
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Linxuan Zhai
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Justin Guo
- International Division, High School Affiliated to Renmin University of China, Beijing 100080, China
| | - Aihua Zheng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100730, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Chen Liang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal H3T 1E2, Canada
| | - Fei Guo
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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50
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di Filippo L, Doga M, Frara S, Giustina A. Hypocalcemia in COVID-19: Prevalence, clinical significance and therapeutic implications. Rev Endocr Metab Disord 2022; 23:299-308. [PMID: 33846867 PMCID: PMC8041474 DOI: 10.1007/s11154-021-09655-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 01/08/2023]
Abstract
COVID-19 extra-pulmonary features include several endocrine manifestations and these are becoming strongly clinically relevant in patients affected influencing disease severity and outcomes.At the beginning of COVID-19 pandemic no population data on calcium levels in patients affected were available and in April 2020 a first case of severe acute hypocalcemia in an Italian patient with SARS-CoV-2 infection was reported. Subsequently, several studies reported hypocalcemia as a highly prevalent biochemical abnormality in COVID-19 patients with a marked negative influence on disease severity, biochemical inflammation and thrombotic markers, and mortality. Also a high prevalence of vertebral fractures with worse respiratory impairment in patients affected and a widespread vitamin D deficiency have been frequently observed, suggesting an emerging "Osteo-Metabolic Phenotype" in COVID-19.To date, several potential pathophysiological factors have been hypothesized to play a role in determining hypocalcemia in COVID-19 including calcium dependent viral mechanisms of action, high prevalence of hypovitaminosis D in general population, chronic and acute malnutrition during critical illness and high levels of unbound and unsaturated fatty acids in inflammatory responses.Since hypocalcemia is a frequent biochemical finding in hospitalized COVID-19 patients possibly predicting worse outcomes and leading to acute cardiovascular and neurological complications if severe, it is reasonable to assess, monitor and, if indicated, replace calcium at first patient hospital evaluation and during hospitalization.
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Affiliation(s)
- Luigi di Filippo
- Institute of Endocrine and Metabolic Sciences, Università Vita-Salute San Raffaele, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Mauro Doga
- Institute of Endocrine and Metabolic Sciences, Università Vita-Salute San Raffaele, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Stefano Frara
- Institute of Endocrine and Metabolic Sciences, Università Vita-Salute San Raffaele, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Andrea Giustina
- Institute of Endocrine and Metabolic Sciences, Università Vita-Salute San Raffaele, IRCCS Ospedale San Raffaele, Milan, Italy
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