1
|
Parihar A, Vishwakarma P, Khan R. Miniaturized MXene-based electrochemical biosensors for virus detection. Bioelectrochemistry 2024; 158:108700. [PMID: 38582009 DOI: 10.1016/j.bioelechem.2024.108700] [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: 04/04/2023] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
The timely control of infectious diseases can prevent the spread of infections and mitigate the significant socio-economic damage witnessed during recent pandemics. Diagnostic methods play a significant role in detecting highly contagious agents, such as viruses, to prevent further transmission. The emergence of advanced point-of-care techniques offers several advantages over conventional approaches for detecting infectious agents. These techniques are highly sensitive, rapid, can be miniaturized, and are cost-effective. Recently, MXene-based 2D nanocomposites have proven beneficial for fabricating electrochemical biosensors due to their suitable electrical, optical, and mechanical properties. This article covers electrochemical biosensors based on MXene nanocomposite for the detection of viruses, along with the associated challenges and future possibilities. Additionally, we highlight various conventional techniques for the detection of infectious agents, discussing their pros and cons. We delve into the challenges faced during the fabrication of MXene-based biosensors and explore future endeavors. It is anticipated that the information presented in this work will pave the way for the development of Point-of-Care (POC) devices capable of sensitive and selective virus detection, enhancing preparedness for ongoing and future pandemics.
Collapse
Affiliation(s)
- Arpana Parihar
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal- 462026, MP, India
| | - Preeti Vishwakarma
- Department of Microbiology, Barkatullah University, Hoshangabad Road, Bhopal- 462026, MP, India
| | - Raju Khan
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal- 462026, MP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
| |
Collapse
|
2
|
Leekha A, Saeedi A, Sefat KMSR, Kumar M, Martinez-Paniagua M, Damian A, Kulkarni R, Reichel K, Rezvan A, Masoumi S, Liu X, Cooper LJN, Sebastian M, Sands CM, Das VE, Patel NB, Hurst B, Varadarajan N. Multi-antigen intranasal vaccine protects against challenge with sarbecoviruses and prevents transmission in hamsters. Nat Commun 2024; 15:6193. [PMID: 39043645 PMCID: PMC11266618 DOI: 10.1038/s41467-024-50133-2] [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: 08/01/2023] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
Immunization programs against SARS-CoV-2 with commercial intramuscular vaccines prevent disease but are less efficient in preventing infections. Mucosal vaccines can provide improved protection against transmission, ideally for different variants of concern (VOCs) and related sarbecoviruses. Here, we report a multi-antigen, intranasal vaccine, NanoSTING-SN (NanoSTING-Spike-Nucleocapsid), eliminates virus replication in both the lungs and the nostrils upon challenge with the pathogenic SARS-CoV-2 Delta VOC. We further demonstrate that NanoSTING-SN prevents transmission of the SARS-CoV-2 Omicron VOC (BA.5) to vaccine-naïve hamsters. To evaluate protection against other sarbecoviruses, we immunized mice with NanoSTING-SN. We showed that immunization affords protection against SARS-CoV, leading to protection from weight loss and 100% survival in mice. In non-human primates, animals immunized with NanoSTING-SN show durable serum IgG responses (6 months) and nasal wash IgA responses cross-reactive to SARS-CoV-2 (XBB1.5), SARS-CoV and MERS-CoV antigens. These observations have two implications: (1) mucosal multi-antigen vaccines present a pathway to reducing transmission of respiratory viruses, and (2) eliciting immunity against multiple antigens can be advantageous in engineering pan-sarbecovirus vaccines.
Collapse
Affiliation(s)
- Ankita Leekha
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Arash Saeedi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - K M Samiur Rahman Sefat
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Monish Kumar
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Melisa Martinez-Paniagua
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Adrian Damian
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Rohan Kulkarni
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Kate Reichel
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Ali Rezvan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Shalaleh Masoumi
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Xinli Liu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | | | | | | | - Vallabh E Das
- College of Optometry, University of Houston, Houston, TX, USA
| | - Nimesh B Patel
- College of Optometry, University of Houston, Houston, TX, USA
| | - Brett Hurst
- Institute of Antiviral Research, Utah State University, UT, Logan, USA
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
| |
Collapse
|
3
|
Kumari S, Mistry H, Bihani SC, Mukherjee SP, Gupta GD. Unveiling potential inhibitors targeting the nucleocapsid protein of SARS-CoV-2: Structural insights into their binding sites. Int J Biol Macromol 2024; 273:133167. [PMID: 38885868 DOI: 10.1016/j.ijbiomac.2024.133167] [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: 04/05/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
The Nucleocapsid (N) protein of SARS-CoV-2 plays a crucial role in viral replication and pathogenesis, making it an attractive target for developing antiviral therapeutics. In this study, we used differential scanning fluorimetry to establish a high-throughput screening method for identifying high-affinity ligands of N-terminal domain of the N protein (N-NTD). We screened an FDA-approved drug library of 1813 compounds and identified 102 compounds interacting with N-NTD. The screened compounds were further investigated for their ability to inhibit the nucleic-acid binding activity of the N protein using electrophoretic mobility-shift assays. We have identified three inhibitors, Ceftazidime, Sennoside A, and Tannic acid, that disrupt the N protein's interaction with RNA probe. Ceftazidime and Sennoside A exhibited nano-molar range binding affinities with N protein, determined through surface plasmon resonance. The binding sites of Ceftazidime and Sennoside A were investigated using [1H, 15N]-heteronuclear single quantum coherence (HSQC) NMR spectroscopy. Ceftazidime and Sennoside A bind to the putative RNA binding site of the N protein, thus providing insights into the inhibitory mechanism of these compounds. These findings will contribute to the development of novel antiviral agents targeting the N protein of SARS-CoV-2.
Collapse
Affiliation(s)
- Shweta Kumari
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Hiral Mistry
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Subhash C Bihani
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Sulakshana P Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha 760003, India
| | - Gagan D Gupta
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
| |
Collapse
|
4
|
Stuwe H, Reardon PN, Yu Z, Shah S, Hughes K, Barbar EJ. Phosphorylation in the Ser/Arg-rich region of the nucleocapsid of SARS-CoV-2 regulates phase separation by inhibiting self-association of a distant helix. J Biol Chem 2024; 300:107354. [PMID: 38718862 PMCID: PMC11180338 DOI: 10.1016/j.jbc.2024.107354] [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: 04/01/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
The nucleocapsid protein (N) of SARS-CoV-2 is essential for virus replication, genome packaging, evading host immunity, and virus maturation. N is a multidomain protein composed of an independently folded monomeric N-terminal domain that is the primary site for RNA binding and a dimeric C-terminal domain that is essential for efficient phase separation and condensate formation with RNA. The domains are separated by a disordered Ser/Arg-rich region preceding a self-associating Leu-rich helix. Phosphorylation in the Ser/Arg region in infected cells decreases the viscosity of N:RNA condensates promoting viral replication and host immune evasion. The molecular level effect of phosphorylation, however, is missing from our current understanding. Using NMR spectroscopy and analytical ultracentrifugation, we show that phosphorylation destabilizes the self-associating Leu-rich helix 30 amino-acids distant from the phosphorylation site. NMR and gel shift assays demonstrate that RNA binding by the linker is dampened by phosphorylation, whereas RNA binding to the full-length protein is not significantly affected presumably due to retained strong interactions with the primary RNA-binding domain. Introducing a switchable self-associating domain to replace the Leu-rich helix confirms the importance of linker self-association to droplet formation and suggests that phosphorylation not only increases solubility of the positively charged elongated Ser/Arg region as observed in other RNA-binding proteins but can also inhibit self-association of the Leu-rich helix. These data highlight the effect of phosphorylation both at local sites and at a distant self-associating hydrophobic helix in regulating liquid-liquid phase separation of the entire protein.
Collapse
Affiliation(s)
- Hannah Stuwe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | | | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Sahana Shah
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Kaitlyn Hughes
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA.
| |
Collapse
|
5
|
Tian X, Tang Y, Gan J, Ye J. A novel linear B cell epitope of the canine coronavirus nucleocapsid protein identified by a monoclonal antibody. Vet Microbiol 2024; 293:110098. [PMID: 38677126 DOI: 10.1016/j.vetmic.2024.110098] [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: 12/27/2023] [Revised: 03/24/2024] [Accepted: 04/20/2024] [Indexed: 04/29/2024]
Abstract
The infection of canine coronavirus (CCoV) causes a highly contagious disease in dogs with acute gastroenteritis. The efficient serological diagnostics is critical for controlling the disease caused by CCoV. Nucleocapsid (N) protein of CCoV is an important target for developing serological approaches. However, little is known about the antigenic sites in the N protein of CCoV. In this study, we generated a monoclonal antibody (mAb) against the N protein of CCoV, designated as 13E8, through the fusion of the sp2/0 cells with the spleen cells from a mouse immunized with the purified recombinant GST-N protein. Epitope mapping revealed that mAb 13E8 recognized a novel linear B cell epitope in N protein at 294-314aa (named as EP-13E8) by using a serial of truncated N protein through Western blot and ELISA. Sequence analysis showed that the sequence of EP-13E8 was highly conserved (100 %) among different CCoV strains analyzed, but exhibited a low similarity (31.8-63.6 %) with the responding sequence in other coronaviruses of the same genus such as FCoV, PEDV and HCoV except for TGEV (95.5 % identity). Structural assay suggested that the epitope of EP-13E8 were located in the close proximity on the surface of the N protein. Overall, the mAb 13E8 against N protein generated and its epitope EP-13E8 identified here paid the way for further developing epitope-based serological diagnostics for CCoV.
Collapse
Affiliation(s)
- Xiaoyan Tian
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ye Tang
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Junji Gan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Jianqiang Ye
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| |
Collapse
|
6
|
Mendoza-Ramírez NJ, García-Cordero J, Shrivastava G, Cedillo-Barrón L. The Key to Increase Immunogenicity of Next-Generation COVID-19 Vaccines Lies in the Inclusion of the SARS-CoV-2 Nucleocapsid Protein. J Immunol Res 2024; 2024:9313267. [PMID: 38939745 PMCID: PMC11208798 DOI: 10.1155/2024/9313267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 06/29/2024] Open
Abstract
Vaccination is one of the most effective prophylactic public health interventions for the prevention of infectious diseases such as coronavirus disease (COVID-19). Considering the ongoing need for new COVID-19 vaccines, it is crucial to modify our approach and incorporate more conserved regions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to effectively address emerging viral variants. The nucleocapsid protein is a structural protein of SARS-CoV-2 that is involved in replication and immune responses. Furthermore, this protein offers significant advantages owing to the minimal accumulation of mutations over time and the inclusion of key T-cell epitopes critical for SARS-CoV-2 immunity. A novel strategy that may be suitable for the new generation of vaccines against COVID-19 is to use a combination of antigens, including the spike and nucleocapsid proteins, to elicit robust humoral and potent cellular immune responses, along with long-lasting immunity. The strategic use of multiple antigens aims to enhance vaccine efficacy and broaden protection against viruses, including their variants. The immune response against the nucleocapsid protein from other coronavirus is long-lasting, and it can persist up to 11 years post-infection. Thus, the incorporation of nucleocapsids (N) into vaccine design adds an important dimension to vaccination efforts and holds promise for bolstering the ability to combat COVID-19 effectively. In this review, we summarize the preclinical studies that evaluated the use of the nucleocapsid protein as antigen. This study discusses the use of nucleocapsid alone and its combination with spike protein or other proteins of SARS-CoV-2.
Collapse
Affiliation(s)
- Noe Juvenal Mendoza-Ramírez
- Departamento de Biomedicina MolecularCINVESTAV IPN, Av. IPN # 2508 Col, San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Julio García-Cordero
- Departamento de Biomedicina MolecularCINVESTAV IPN, Av. IPN # 2508 Col, San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Gaurav Shrivastava
- Laboratory of Malaria and Vector ResearchNational Institute of Allergy and Infectious DiseasesNational Institutes of Health, Rockville, MD, USA
| | - Leticia Cedillo-Barrón
- Departamento de Biomedicina MolecularCINVESTAV IPN, Av. IPN # 2508 Col, San Pedro Zacatenco, Mexico City 07360, Mexico
| |
Collapse
|
7
|
Huang Y, Chen J, Chen S, Huang C, Li B, Li J, Jin Z, Zhang Q, Pan P, Du W, Liu L, Liu Z. Molecular characterization of SARS-CoV-2 nucleocapsid protein. Front Cell Infect Microbiol 2024; 14:1415885. [PMID: 38846351 PMCID: PMC11153676 DOI: 10.3389/fcimb.2024.1415885] [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: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 06/09/2024] Open
Abstract
Corona Virus Disease 2019 (COVID-19) is a highly prevalent and potent infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Until now, the world is still endeavoring to develop new ways to diagnose and treat COVID-19. At present, the clinical prevention and treatment of COVID-19 mainly targets the spike protein on the surface of SRAS-CoV-2. However, with the continuous emergence of SARS-CoV-2 Variants of concern (VOC), targeting the spike protein therapy shows a high degree of limitation. The Nucleocapsid Protein (N protein) of SARS-CoV-2 is highly conserved in virus evolution and is involved in the key process of viral infection and assembly. It is the most expressed viral structural protein after SARS-CoV-2 infection in humans and has high immunogenicity. Therefore, N protein as the key factor of virus infection and replication in basic research and clinical application has great potential research value. This article reviews the research progress on the structure and biological function of SARS-CoV-2 N protein, the diagnosis and drug research of targeting N protein, in order to promote researchers' further understanding of SARS-CoV-2 N protein, and lay a theoretical foundation for the possible outbreak of new and sudden coronavirus infectious diseases in the future.
Collapse
Affiliation(s)
- Yanping Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Junkai Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Siwei Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Bei Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixiong Jin
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Central Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Pan Pan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| |
Collapse
|
8
|
Lugo-Trampe A, López-Cifuentes D, Mendoza-Pérez P, Tafurt-Cardona Y, Joo-Domínguez ADJ, Rios-Ibarra CP, Espinoza-Ruiz M, Chang-Rueda C, Rodriguez-Sanchez IP, Martinez-Fierro ML, Delgado-Enciso I, Trujillo-Murillo KDC. Nine-Month Trend of IgG Antibody Persistence and Associated Symptoms Post-SARS-CoV-2 Infection. Healthcare (Basel) 2024; 12:948. [PMID: 38727505 PMCID: PMC11083704 DOI: 10.3390/healthcare12090948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Between 2 and 8.5% of patients who recover from COVID-19 do not develop antibodies, and the durability of IgG antibodies is under scrutiny. Therefore, the presence and persistence of IgM and IgG antibodies were evaluated in a group of patients diagnosed with SARS-CoV-2 from May to August 2020. Out of 2199 suspected COVID-19 cases, 1264 were confirmed for SARS-CoV-2 by rRT-PCR; 328 consented to participate in the study, with 220 participants followed for 9 months, including 124 men (56%) and 96 women (44%). The primary symptoms were headache, dry cough, and fever. IgG antibodies developed in 95% of patients within 4 weeks post-diagnosis, and a second evaluation at 9 months showed that 72.7% still had detectable IgG antibodies. The presence of IgM in one individual (0.45%) suggested the possibility of reinfection.
Collapse
Affiliation(s)
- Angel Lugo-Trampe
- Faculty of Human Medicine, Campus IV, Universidad Autónoma de Chiapas, Tapachula 30700, Mexico
- Genodiagnóstica SA de CV, Tapachula, Chiapas 30700, Mexico
| | - Daniel López-Cifuentes
- Faculty of Chemistry Sciences, Campus IV, Universidad Autónoma de Chiapas, Tapachula 30700, Mexico
| | - Paúl Mendoza-Pérez
- Faculty of Human Medicine, Campus IV, Universidad Autónoma de Chiapas, Tapachula 30700, Mexico
| | - Yaliana Tafurt-Cardona
- Faculty of Human Medicine, Campus IV, Universidad Autónoma de Chiapas, Tapachula 30700, Mexico
| | | | - Clara Patricia Rios-Ibarra
- Medical and Pharmaceutical Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco (CIATEJ), Guadalajara 44270, Mexico
| | - Marisol Espinoza-Ruiz
- Faculty of Chemistry Sciences, Campus IV, Universidad Autónoma de Chiapas, Tapachula 30700, Mexico
| | - Consuelo Chang-Rueda
- Faculty of Chemistry Sciences, Campus IV, Universidad Autónoma de Chiapas, Tapachula 30700, Mexico
| | - Iram Pablo Rodriguez-Sanchez
- Molecular and Structural Physiology Laboratory, School of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Unidad de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - Iván Delgado-Enciso
- School of Medicine, University of Colima, Colima 28040, Mexico
- Colima Cancerology State Institute, IMSS-Bienestar, Colima 28085, Mexico
| | | |
Collapse
|
9
|
Wang TH, Shao HP, Zhao BQ, Zhai HL. Molecular Insights into the Variability in Infection and Immune Evasion Capabilities of SARS-CoV-2 Variants: A Sequence and Structural Investigation of the RBD Domain. J Chem Inf Model 2024; 64:3503-3523. [PMID: 38517012 DOI: 10.1021/acs.jcim.3c01730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continuously emerge, an increasing number of mutations are accumulating in the Spike protein receptor-binding domain (RBD) region. Through sequence analysis of various Variants of Concern (VOC), we identified that they predominantly fall within the ο lineage although recent variants introduce any novel mutations in the RBD. Molecular dynamics simulations were employed to compute the binding free energy of these variants with human Angiotensin-converting enzyme 2 (ACE2). Structurally, the binding interface of the ο RBD displays a strong positive charge, complementing the negatively charged binding interface of ACE2, resulting in a significant enhancement in the electrostatic potential energy for the ο variants. Although the increased potential energy is partially offset by the rise in polar solvation free energy, enhanced electrostatic potential contributes to the long-range recognition between the ο variant's RBD and ACE2. We also conducted simulations of glycosylated ACE2-RBD proteins. The newly emerged ο (JN.1) variant has added a glycosylation site at N-354@RBD, which significantly weakened its binding affinity with ACE2. Further, our interaction studies with three monoclonal antibodies across multiple SARS-CoV-2 strains revealed a diminished neutralization efficacy against the ο variants, primarily attributed to the electrostatic repulsion between the antibodies and RBD interface. Considering the characteristics of the ο variant and the trajectory of emerging strains, we propose that newly developed antibodies against SARS-CoV-2 RBD should have surfaces rich in negative potential and, postbinding, exhibit strong van der Waals interactions. These findings provide invaluable guidance for the formulation of future therapeutic strategies.
Collapse
Affiliation(s)
- Tian Hua Wang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hai Ping Shao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Bing Qiang Zhao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| |
Collapse
|
10
|
Song J. Adenosine Triphosphate: The Primordial Molecule That Controls Protein Homeostasis and Shapes the Genome-Proteome Interface. Biomolecules 2024; 14:500. [PMID: 38672516 PMCID: PMC11048592 DOI: 10.3390/biom14040500] [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: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Adenosine triphosphate (ATP) acts as the universal energy currency that drives various biological processes, while nucleic acids function to store and transmit genetic information for all living organisms. Liquid-liquid phase separation (LLPS) represents the common principle for the formation of membrane-less organelles (MLOs) composed of proteins rich in intrinsically disordered regions (IDRs) and nucleic acids. Currently, while IDRs are well recognized to facilitate LLPS through dynamic and multivalent interactions, the precise mechanisms by which ATP and nucleic acids affect LLPS still remain elusive. This review summarizes recent NMR results on the LLPS of human FUS, TDP-43, and the viral nucleocapsid (N) protein of SARS-CoV-2, as modulated by ATP and nucleic acids, revealing the following: (1) ATP binds to folded domains overlapping with nucleic-acid-binding interfaces; (2) ATP and nucleic acids interplay to biphasically modulate LLPS by competitively binding to overlapping pockets of folded domains and Arg/Lys within IDRs; (3) ATP energy-independently induces protein folding with the highest efficiency known so far. As ATP likely emerged in the prebiotic monomeric world, while LLPS represents a pivotal mechanism to concentrate and compartmentalize rare molecules for forming primordial cells, ATP appears to control protein homeostasis and shape genome-proteome interfaces throughout the evolutionary trajectory, from prebiotic origins to modern cells.
Collapse
Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
| |
Collapse
|
11
|
Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
Collapse
Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
| |
Collapse
|
12
|
Hussein HAM, Thabet AA, Wardany AA, El-Adly AM, Ali M, Hassan MEA, Abdeldayem MAB, Mohamed ARMA, Sobhy A, El-Mokhtar MA, Afifi MM, Fathy SM, Sultan S. SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression. Virol J 2024; 21:75. [PMID: 38539202 PMCID: PMC10967059 DOI: 10.1186/s12985-024-02342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 03/12/2024] [Indexed: 05/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.
Collapse
Affiliation(s)
- Hosni A M Hussein
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt.
| | - Ali A Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed A Wardany
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed M El-Adly
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed Ali
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed E A Hassan
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A B Abdeldayem
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | | | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos Campus, Lebanon
| | - Magdy M Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Samah M Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum, Egypt.
| | - Serageldeen Sultan
- Department of Microbiology, Virology Division, Faculty of Veterinary medicine, South Valley University, 83523, Qena, Egypt.
| |
Collapse
|
13
|
Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar E, Abu Zeid IM, Bouback TA, Bamagoos A, Aljohny BO, Uversky VN, Redwan EM. Overview of the SARS-CoV-2 nucleocapsid protein. Int J Biol Macromol 2024; 260:129523. [PMID: 38232879 DOI: 10.1016/j.ijbiomac.2024.129523] [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: 06/04/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/19/2024]
Abstract
Since the emergence of SARS-CoV in 2003, researchers worldwide have been toiling away at deciphering this virus's biological intricacies. In line with other known coronaviruses, the nucleocapsid (N) protein is an important structural component of SARS-CoV. As a result, much emphasis has been placed on characterizing this protein. Independent research conducted by a variety of laboratories has clearly demonstrated the primary function of this protein, which is to encapsidate the viral genome. Furthermore, various accounts indicate that this particular protein disrupts diverse intracellular pathways. Such observations imply its vital role in regulating the virus as well. The opening segment of this review will expound upon these distinct characteristics succinctly exhibited by the N protein. Additionally, it has been suggested that the N protein possesses diagnostic and vaccine capabilities when dealing with SARS-CoV. In light of this fact, we will be reviewing some recent headway in the use cases for N protein toward clinical purposes within this article's concluding segments. This forward movement pertains to both developments of COVID-19-oriented therapeutic targets as well as diagnostic measures. The strides made by medical researchers offer encouragement, knowing they are heading toward a brighter future combating global pandemic situations such as these.
Collapse
Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab Mattar
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Bassam O Aljohny
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Elrashdy M Redwan
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, 21934 Alexandria, Egypt.
| |
Collapse
|
14
|
Valadan R, Alizadeh-Navaei R, Lagzian M, Saeedi M, Roozbeh F, Hedayatizadeh-Omran A, Amanlou M. Repurposing naproxen as a potential nucleocapsid antagonist of beta-coronaviruses: targeting a conserved protein in the search for a broad-spectrum treatment option. J Biomol Struct Dyn 2024:1-16. [PMID: 38407203 DOI: 10.1080/07391102.2024.2321245] [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: 06/06/2023] [Accepted: 02/14/2024] [Indexed: 02/27/2024]
Abstract
Ongoing mutations in the coronavirus family, especially beta-coronaviruses, raise new concerns about the possibility of new unexpected outbreaks. Therefore, it is crucial to explore new alternative treatments to reduce the impact of potential future strains until new vaccines can be developed. A promising approach to combat the virus is to target its conserved parts such as the nucleocapsid, especially via repurposing of existing drugs. The possibility of this approach is explored here to find a potential anti-nucleocapsid compound to target these viruses. 3D models of the N- and C-terminal domains (CTDs) of the nucleocapsid consensus sequence were constructed. Each domain was then screened against an FDA-approved drug database, and the most promising candidate was selected for further analysis. A 100 ns molecular dynamics (MD) simulation was conducted to analyze the final candidate in more detail. Naproxen was selected and found to interact with the N-terminal domain via conserved salt bridges and hydrogen bonds which are completely conserved among all Coronaviridae members. MD analysis also revealed that all relevant coordinates of naproxen with N terminal domain were kept during 100 ns of simulation time. This study also provides insights into the specific interaction of naproxen with conserved RNA binding pocket of the nucleocapsid that could interfere with the packaging of the viral genome into capsid and virus assembly. Additionally, the in-vitro binding assay demonstrated direct interaction between naproxen and recombinant nucleocapsid protein, further supporting the computational predictions.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Reza Valadan
- Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Center, Non-Communicable Disease Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Milad Lagzian
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Majid Saeedi
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
- Pharmaceutical Sciences Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Roozbeh
- Infectious Specialist, Mazandaran University of Medical Sciences, Sari, Iran
| | - Akbar Hedayatizadeh-Omran
- Gastrointestinal Cancer Research Center, Non-Communicable Disease Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
15
|
Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [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: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
Collapse
Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| |
Collapse
|
16
|
Drobysh M, Liustrovaite V, Kanetski Y, Brasiunas B, Zvirbliene A, Rimkute A, Gudas D, Kucinskaite-Kodze I, Simanavicius M, Ramanavicius S, Slibinskas R, Ciplys E, Plikusiene I, Ramanavicius A. Electrochemical biosensing based comparative study of monoclonal antibodies against SARS-CoV-2 nucleocapsid protein. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168154. [PMID: 37923263 DOI: 10.1016/j.scitotenv.2023.168154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
In this study, we are reporting an electrochemical biosensor for the determination of three different clones of monoclonal antibodies (mAbs) against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recombinant nucleocapsid protein (rN). The nucleocapsid protein was chosen as a system component identifying and discriminating antibodies that occur after virus infection instead of S protein used in serological tests to measure antibodies raised after vaccination and infection. The sensing platform was based on a screen-printed carbon electrode (SPCE) covered with gold nanoparticles (AuNP) and subsequently modified with a self-assembled monolayer (SAM) to ensure the covalent immobilization of the rN. The interaction between the protein and three clones of mAbs against SARS-CoV-2 rN with clone numbers 4G6, 7F10, and 1A6, were electrochemically registered in the range of concentrations. Three techniques, cyclic voltammetry (CV), differential pulse voltammetry (DPV), and pulse amperometric detection (PAD) were used for the detection. A gradual change in the responses with an increase in mAbs concentration for all techniques was observed. To assess the performance of the developed electrochemical biosensor, 'complexation constant' (KC), limit of detection (LOD), and limit of quantification (LOQ) were calculated for all assessed clones of mAbs and all used techniques. Our results indicated that DPV possessing higher fitting accuracy illustrated more significant differences in KC constants and LOD/LOQ values. According to the DPV results, 7F10 clone was characterized with the highest KC value of 1.47 ± 0.07 μg/mL while the lowest LOD and LOQ values belonged to the 4G6 clone and equaled 0.08 ± 0.01 and 0.25 ± 0.01 μg/mL, respectively. Overall, these results demonstrate the potential of electrochemical techniques for the detection and distinguishing of different clones of mAbs against SARS-CoV-2 nucleocapsid protein.
Collapse
Affiliation(s)
- Maryia Drobysh
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, Vilnius, Lithuania; Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Viktorija Liustrovaite
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Yahor Kanetski
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Benediktas Brasiunas
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Aurelija Zvirbliene
- Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | - Agne Rimkute
- Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | - Dainius Gudas
- Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | | | | | - Simonas Ramanavicius
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, Vilnius, Lithuania; Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Rimantas Slibinskas
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania; Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | - Evaldas Ciplys
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania; Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | - Ieva Plikusiene
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Arunas Ramanavicius
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, Vilnius, Lithuania; Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania.
| |
Collapse
|
17
|
Abram QH, Landry BN, Wang AB, Kothe RF, Hauch HC, Sagan SM. The myriad roles of RNA structure in the flavivirus life cycle. RNA Biol 2024; 21:14-30. [PMID: 38797925 PMCID: PMC11135854 DOI: 10.1080/15476286.2024.2357857] [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] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
As positive-sense RNA viruses, the genomes of flaviviruses serve as the template for all stages of the viral life cycle, including translation, replication, and infectious particle production. Yet, they encode just 10 proteins, suggesting that the structure and dynamics of the viral RNA itself helps shepherd the viral genome through these stages. Herein, we highlight advances in our understanding of flavivirus RNA structural elements through the lens of their impact on the viral life cycle. We highlight how RNA structures impact translation, the switch from translation to replication, negative- and positive-strand RNA synthesis, and virion assembly. Consequently, we describe three major themes regarding the roles of RNA structure in flavivirus infections: 1) providing a layer of specificity; 2) increasing the functional capacity; and 3) providing a mechanism to support genome compaction. While the interactions described herein are specific to flaviviruses, these themes appear to extend more broadly across RNA viruses.
Collapse
Affiliation(s)
- Quinn H. Abram
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Breanna N. Landry
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B. Wang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ronja F. Kothe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Hannah C.H. Hauch
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M. Sagan
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| |
Collapse
|
18
|
Liu X, Xiong W, Ye M, Lu T, Yuan K, Chang S, Han Y, Wang Y, Lu L, Bao Y. Non-coding RNAs expression in SARS-CoV-2 infection: pathogenesis, clinical significance, and therapeutic targets. Signal Transduct Target Ther 2023; 8:441. [PMID: 38057315 PMCID: PMC10700414 DOI: 10.1038/s41392-023-01669-0] [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: 12/09/2022] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 12/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has been looming globally for three years, yet the diagnostic and treatment methods for COVID-19 are still undergoing extensive exploration, which holds paramount importance in mitigating future epidemics. Host non-coding RNAs (ncRNAs) display aberrations in the context of COVID-19. Specifically, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) exhibit a close association with viral infection and disease progression. In this comprehensive review, an overview was presented of the expression profiles of host ncRNAs following SARS-CoV-2 invasion and of the potential functions in COVID-19 development, encompassing viral invasion, replication, immune response, and multiorgan deficits which include respiratory system, cardiac system, central nervous system, peripheral nervous system as well as long COVID. Furthermore, we provide an overview of several promising host ncRNA biomarkers for diverse clinical scenarios related to COVID-19, such as stratification biomarkers, prognostic biomarkers, and predictive biomarkers for treatment response. In addition, we also discuss the therapeutic potential of ncRNAs for COVID-19, presenting ncRNA-based strategies to facilitate the development of novel treatments. Through an in-depth analysis of the interplay between ncRNA and COVID-19 combined with our bioinformatic analysis, we hope to offer valuable insights into the stratification, prognosis, and treatment of COVID-19.
Collapse
Affiliation(s)
- Xiaoxing Liu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Wandi Xiong
- Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, 570228, Haikou, China
| | - Maosen Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, 650204, Kunming, Yunnan, China
| | - Tangsheng Lu
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China
| | - Kai Yuan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Suhua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Ying Han
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China
| | - Yongxiang Wang
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, China.
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
| | - Lin Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China.
- Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China.
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China.
| | - Yanping Bao
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China.
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, China.
- School of Public Health, Peking University, 100191, Beijing, China.
| |
Collapse
|
19
|
Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO. Assembly of SARS-CoV-2 ribonucleosomes by truncated N ∗ variant of the nucleocapsid protein. J Biol Chem 2023; 299:105362. [PMID: 37863261 PMCID: PMC10665939 DOI: 10.1016/j.jbc.2023.105362] [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: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein serine/arginine (SR) region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N∗ or Δ(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we use mass photometry and negative stain electron microscopy to show that purified Δ(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1-209) vRNPs requires the leucine-rich helix of the central disordered region and that this helix promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by phosphorylation.
Collapse
Affiliation(s)
- Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | | | - Abdullah M Syed
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Alison Ciling
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA; Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
| |
Collapse
|
20
|
He S, Gou H, Zhou Y, Wu C, Ren X, Wu X, Guan G, Jin B, Huang J, Jin Z, Zhao T. The SARS-CoV-2 nucleocapsid protein suppresses innate immunity by remodeling stress granules to atypical foci. FASEB J 2023; 37:e23269. [PMID: 37889852 DOI: 10.1096/fj.202201973rr] [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: 11/25/2022] [Revised: 08/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023]
Abstract
Viruses deploy multiple strategies to suppress the host innate immune response to facilitate viral replication and pathogenesis. Typical G3BP1+ stress granules (SGs) are usually formed in host cells after virus infection to restrain viral translation and to stimulate innate immunity. Thus, viruses have evolved various mechanisms to inhibit SGs or to repurpose SG components such as G3BP1. Previous studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection inhibited host immunity during the early stage of COVID-19. However, the precise mechanism is not yet well understood. Here we showed that the SARS-CoV-2 nucleocapsid (SARS2-N) protein suppressed the double-stranded RNA (dsRNA)-induced innate immune response, concomitant with inhibition of SGs and the induction of atypical SARS2-N+ /G3BP1+ foci (N+ foci). The SARS2-N protein-induced formation of N+ foci was dependent on the ability of its ITFG motif to hijack G3BP1, which contributed to suppress the innate immune response. Importantly, SARS2-N protein facilitated viral replication by inducing the formation of N+ foci. Viral mutations within SARS2-N protein that impair the formation of N+ foci are associated with the inability of the SARS2-N protein to suppress the immune response. Taken together, our study has revealed a novel mechanism by which SARS-CoV-2 suppresses the innate immune response via induction of atypical N+ foci. We think that this is a critical strategy for viral pathogenesis and has potential therapeutic implications.
Collapse
Affiliation(s)
- Su He
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Hongwei Gou
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yulin Zhou
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Chunxiu Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Xinxin Ren
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Xiajunpeng Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Guanwen Guan
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Boxing Jin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jinhua Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Zhigang Jin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Tiejun Zhao
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| |
Collapse
|
21
|
Haque S, Kumar P, Mathkor DM, Bantun F, Jalal NA, Mufti AH, Prakash A, Kumar V. In silico evaluation of the inhibitory potential of nucleocapsid inhibitors of SARS-CoV-2: a binding and energetic perspective. J Biomol Struct Dyn 2023; 41:9797-9807. [PMID: 36379684 DOI: 10.1080/07391102.2022.2146752] [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: 08/17/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022]
Abstract
The COVID-19 outbreak brought on by the SARS-CoV-2 virus continued to infect a sizable population worldwide. The SARS-CoV-2 nucleocapsid (N) protein is the most conserved RNA-binding structural protein and is a desirable target because of its involvement in viral transcription and replication. Based on this aspect, this study focused to repurpose antiviral compounds approved or in development for treating COVID-19. The inhibitors chosen are either FDA-approved or are currently being studied in clinical trials against COVID-19. Initially, they were designed to target stress granules and other RNA biology. We have utilized structure-based molecular docking and all-atom molecular dynamics (MD) simulation approach to investigate in detail the binding energy and binding modes of the different anti-N inhibitors to N protein. The result showed that five drugs including Silmitasterib, Ninetanidinb, Ternatin, Luteolin, Fedratinib, PJ34, and Zotatafin were found interacting with RNA binding sites as well as to predicted protein interface with higher binding energy. Overall, drug binding increases the stability of the complex with maximum stability found in the order, Silmitasertib > PJ34 > Zotatatafin. In addition, the frustration changes due to drug binding brings a decrease in local frustration and this decrease is mainly observed in α-helix, β3, β5, and β6 strands and are important for drug binding. Our in-silico data suggest that an effective interaction occurs for some of the tested drugs and prompt their further validation to reduce the rapid outspreading of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Pawan Kumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ahmad Hasan Mufti
- Medical Genetics Department, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, India
| |
Collapse
|
22
|
Estelle AB, Forsythe HM, Yu Z, Hughes K, Lasher B, Allen P, Reardon PN, Hendrix DA, Barbar EJ. RNA structure and multiple weak interactions balance the interplay between RNA binding and phase separation of SARS-CoV-2 nucleocapsid. PNAS NEXUS 2023; 2:pgad333. [PMID: 37901441 PMCID: PMC10605006 DOI: 10.1093/pnasnexus/pgad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023]
Abstract
The nucleocapsid (N) protein of SARS-CoV-2 binds viral RNA, condensing it inside the virion, and phase separating with RNA to form liquid-liquid condensates. There is little consensus on what differentiates sequence-independent N-RNA interactions in the virion or in liquid droplets from those with specific genomic RNA (gRNA) motifs necessary for viral function inside infected cells. To identify the RNA structures and the N domains responsible for specific interactions and phase separation, we use the first 1,000 nt of viral RNA and short RNA segments designed as models for single-stranded and paired RNA. Binding affinities estimated from fluorescence anisotropy of these RNAs to the two-folded domains of N (the NTD and CTD) and comparison to full-length N demonstrate that the NTD binds preferentially to single-stranded RNA, and while it is the primary RNA-binding site, it is not essential to phase separation. Nuclear magnetic resonance spectroscopy identifies two RNA-binding sites on the NTD: a previously characterized site and an additional although weaker RNA-binding face that becomes prominent when binding to the primary site is weak, such as with dsRNA or a binding-impaired mutant. Phase separation assays of nucleocapsid domains with double-stranded and single-stranded RNA structures support a model where multiple weak interactions, such as with the CTD or the NTD's secondary face promote phase separation, while strong, specific interactions do not. These studies indicate that both strong and multivalent weak N-RNA interactions underlie the multifunctional abilities of N.
Collapse
Affiliation(s)
- Aidan B Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Heather M Forsythe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Kaitlyn Hughes
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Brittany Lasher
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick Allen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick N Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, OR 97331, USA
| | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| |
Collapse
|
23
|
Lao T, Avalos I, Rodríguez EM, Zamora Y, Rodriguez A, Ramón A, Alvarez Y, Cabrales A, Andújar I, González LJ, Puente P, García C, Gómez L, Valdés R, Estrada MP, Carpio Y. Production and characterization of a chimeric antigen, based on nucleocapsid of SARS-CoV-2 fused to the extracellular domain of human CD154 in HEK-293 cells as a vaccine candidate against COVID-19. PLoS One 2023; 18:e0288006. [PMID: 37751460 PMCID: PMC10522030 DOI: 10.1371/journal.pone.0288006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/16/2023] [Indexed: 09/28/2023] Open
Abstract
Despite that more than one hundred vaccines against SARS-CoV-2 have been developed and that some of them were evaluated in clinical trials, the latest results revealed that these vaccines still face great challenges. Among the components of the virus, the N-protein constitutes an attractive target for a subunit vaccine because it is the most abundant, highly conserved and immunogenic protein. In the present work, a chimeric protein (N-CD protein) was constructed by the fusion of the N-protein to the extracellular domain of human CD154 as the molecular adjuvant. HEK-293 cells were transduced with lentiviral vector bearing the N-CD gene and polyclonal cell populations were obtained. The N-CD protein was purified from cell culture supernatant and further characterized by several techniques. Immunogenicity studies in mice and non-human primates showed the N-CD protein induced high IgG titers in both models after two doses. Moreover, overall health monitoring of non-human primates demonstrated that animals were healthy during 228 days after first immunization. Data obtained support further investigation in order to develop this chimeric protein as vaccine candidate against COVID-19 and other coronavirus diseases.
Collapse
Affiliation(s)
- Thailin Lao
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana, Cuba
| | - Ileanet Avalos
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana, Cuba
| | - Elsa María Rodríguez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana, Cuba
| | - Yasser Zamora
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana, Cuba
| | - Alianet Rodriguez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana, Cuba
| | - Ailyn Ramón
- Center for Genetic Engineering and Biotechnology, Laboratory of Molecular Oncology, Havana, Cuba
| | - Yanitza Alvarez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana, Cuba
| | - Ania Cabrales
- Center for Genetic Engineering and Biotechnology, Systems Biology, Havana, Cuba
| | - Ivan Andújar
- Center for Genetic Engineering and Biotechnology, Systems Biology, Havana, Cuba
| | | | - Pedro Puente
- Center for Genetic Engineering and Biotechnology, Animal housing, Havana, Cuba
| | - Cristina García
- Center for Genetic Engineering and Biotechnology, Production Division, Havana, Cuba
| | - Leonardo Gómez
- Center for Genetic Engineering and Biotechnology, Production Division, Havana, Cuba
| | - Rodolfo Valdés
- Center for Genetic Engineering and Biotechnology, Production Division, Havana, Cuba
| | - Mario Pablo Estrada
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana, Cuba
| | - Yamila Carpio
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana, Cuba
| |
Collapse
|
24
|
Justo Arevalo S, Castillo-Chávez A, Uribe Calampa CS, Zapata Sifuentes D, Huallpa CJ, Landa Bianchi G, Garavito-Salini Casas R, Quiñones Aguilar M, Pineda Chavarría R. What do we know about the function of SARS-CoV-2 proteins? Front Immunol 2023; 14:1249607. [PMID: 37790934 PMCID: PMC10544941 DOI: 10.3389/fimmu.2023.1249607] [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: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
The COVID-19 pandemic has highlighted the importance in the understanding of the biology of SARS-CoV-2. After more than two years since the first report of COVID-19, it remains crucial to continue studying how SARS-CoV-2 proteins interact with the host metabolism to cause COVID-19. In this review, we summarize the findings regarding the functions of the 16 non-structural, 6 accessory and 4 structural SARS-CoV-2 proteins. We place less emphasis on the spike protein, which has been the subject of several recent reviews. Furthermore, comprehensive reviews about COVID-19 therapeutic have been also published. Therefore, we do not delve into details on these topics; instead we direct the readers to those other reviews. To avoid confusions with what we know about proteins from other coronaviruses, we exclusively report findings that have been experimentally confirmed in SARS-CoV-2. We have identified host mechanisms that appear to be the primary targets of SARS-CoV-2 proteins, including gene expression and immune response pathways such as ribosome translation, JAK/STAT, RIG-1/MDA5 and NF-kβ pathways. Additionally, we emphasize the multiple functions exhibited by SARS-CoV-2 proteins, along with the limited information available for some of these proteins. Our aim with this review is to assist researchers and contribute to the ongoing comprehension of SARS-CoV-2's pathogenesis.
Collapse
Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Daniela Zapata Sifuentes
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - César J. Huallpa
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | | | | | | | | |
Collapse
|
25
|
Coelho GM, Cataneo AHD, Raboni SM, Nogueira MB, de Paula CBV, Almeida ACSF, Rogerio VZ, Zanchin NT, de Noronha L, Zanluca C, Duarte Dos Santos CN. Development of an anti-SARS-CoV-2 monoclonal antibody panel and its applicability as a reagent in high-throughput fluorescence reduction neutralization and immunohistochemistry assays. J Med Virol 2023; 95:e29111. [PMID: 37750235 DOI: 10.1002/jmv.29111] [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: 05/31/2023] [Revised: 09/01/2023] [Accepted: 09/10/2023] [Indexed: 09/27/2023]
Abstract
Since its emergence in late 2019, coronavirus disease 2019 (COVID-19) has caused millions of deaths and socioeconomic losses. Although vaccination significantly reduced disease mortality, it has been shown that protection wanes over time, and that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) may escape vaccine-derived immunity. Therefore, serological studies are necessary to assess protection in the population and guide vaccine regimens. A common measure of protective immunity is the presence of neutralizing antibodies (nAbs). However, the gold standard for measuring nAbs (plaque reduction neutralization test, or PRNT) is laborious and time-consuming, limiting its large-scale applicability. We developed a high-throughput fluorescence reduction neutralization assay (FRNA) to detect SARS-CoV-2 nAbs. Because the assay relies on immunostaining, we developed and characterized monoclonal antibodies (mAbs) to lower costs and reduce the assay's vulnerability to reagent shortages. Using samples of individuals vaccinated with COVID-19 and unvaccinated/pre-pandemic samples, we showed that FRNA results using commercial and in-house mAbs strongly correlated with those of the PRNT method while providing results in 70% less time. In addition to providing a fast, reliable, and high-throughput alternative for measuring nAbs, the FRNA can be easily customized to assess SARS-CoV-2 VOCs. Additionally, the mAb we produced was able to detect SARS-CoV-2 in pulmonary tissues by immunohistochemistry assays.
Collapse
Affiliation(s)
- Gabriela M Coelho
- Laboratório de Virologia Molecular, Instituto Carlos Chagas (ICC/Fiocruz), Curitiba, Paraná, Brasil
| | - Allan H D Cataneo
- Laboratório de Virologia Molecular, Instituto Carlos Chagas (ICC/Fiocruz), Curitiba, Paraná, Brasil
| | - Sonia M Raboni
- Complexo Hospital de Clínicas, Universidade Federal Do Paraná, Curitiba, Paraná, Brasil
| | - Meri B Nogueira
- Complexo Hospital de Clínicas, Universidade Federal Do Paraná, Curitiba, Paraná, Brasil
| | - Caroline B Vaz de Paula
- Laboratório de Patologia Experimental, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brasil
| | - Ana C S F Almeida
- Laboratório de Patologia Experimental, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brasil
| | - Vanessa Z Rogerio
- Laboratório de Biologia Estrutural e Engenharia de Proteínas, Instituto Carlos Chagas (ICC/Fiocruz), Curitiba, Paraná, Brasil
| | - Nilson T Zanchin
- Laboratório de Biologia Estrutural e Engenharia de Proteínas, Instituto Carlos Chagas (ICC/Fiocruz), Curitiba, Paraná, Brasil
| | - Lucia de Noronha
- Laboratório de Patologia Experimental, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brasil
| | - Camila Zanluca
- Laboratório de Virologia Molecular, Instituto Carlos Chagas (ICC/Fiocruz), Curitiba, Paraná, Brasil
| | | |
Collapse
|
26
|
Li P, Xue B, Schnicker NJ, Wong LYR, Meyerholz DK, Perlman S. Nsp3-N interactions are critical for SARS-CoV-2 fitness and virulence. Proc Natl Acad Sci U S A 2023; 120:e2305674120. [PMID: 37487098 PMCID: PMC10400999 DOI: 10.1073/pnas.2305674120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/22/2023] [Indexed: 07/26/2023] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19 encodes at least 16 nonstructural proteins of variably understood function. Nsp3, the largest nonstructural protein contains several domains, including a SARS-unique domain (SUD), which occurs only in Sarbecovirus. The SUD has a role in preferentially enhancing viral translation. During isolation of mouse-adapted SARS-CoV-2, we isolated an attenuated virus that contained a single mutation in a linker region of nsp3 (nsp3-S676T). The S676T mutation decreased virus replication in cultured cells and primary human cells and in mice. Nsp3-S676T alleviated the SUD translational enhancing ability by decreasing the interaction between two translation factors, Paip1 and PABP1. We also identified a compensatory mutation in the nucleocapsid (N) protein (N-S194L) that restored the virulent phenotype, without directly binding to SUD. Together, these results reveal an aspect of nsp3-N interactions, which impact both SARS-CoV-2 replication and, consequently, pathogenesis.
Collapse
Affiliation(s)
- Pengfei Li
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Biyun Xue
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242
| | | | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242
| |
Collapse
|
27
|
Segovia-de los Santos P, Padula-Roca C, Simon X, Echaides C, Lassabe G, Gonzalez-Sapienza G. A highly sensitive nanobody-based immunoassay detecting SARS-CoV-2 nucleocapsid protein using all-recombinant reagents. Front Immunol 2023; 14:1220477. [PMID: 37497229 PMCID: PMC10367427 DOI: 10.3389/fimmu.2023.1220477] [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: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Antigen tests have been crucial for managing the COVID-19 pandemic by identifying individuals infected with SARS-CoV-2. This remains true even after immunity has been widely attained through natural infection and vaccination, since it only provides moderate protection against transmission and is highly permeable to the emergence of new virus variants. For this reason, the widespread availability of diagnostic methods is essential for health systems to manage outbreaks effectively. In this work, we generated nanobodies to the virus nucleocapsid protein (NP) and after an affinity-guided selection identified a nanobody pair that allowed the detection of NP at sub-ng/mL levels in a colorimetric two-site ELISA, demonstrating high diagnostic value with clinical samples. We further modified the assay by using a nanobody-NanoLuc luciferase chimeric tracer, resulting in increased sensitivity (detection limit = 61 pg/mL) and remarkable improvement in diagnostic performance. The luminescent assay was finally evaluated using 115 nasopharyngeal swab samples. Receiver Operating Characteristic (ROC) curve analysis revealed a sensitivity of 78.7% (95% confidence interval: 64.3%-89.3%) and specificity of 100.0% (95% confidence interval: 94.7%-100.0%). The test allows the parallel analysis of a large number of untreated samples, and fulfills our goal of producing a recombinant reagent-based test that can be reproduced at low cost by other laboratories with recombinant expression capabilities, aiding to build diagnostic capacity.
Collapse
Affiliation(s)
- Paula Segovia-de los Santos
- Cátedra de Inmunología, Departamento de Biociencias (DEPBIO), Facultad de Química, Instituto de Higiene, Montevideo, Uruguay
| | - Carolina Padula-Roca
- Cátedra de Inmunología, Departamento de Biociencias (DEPBIO), Facultad de Química, Instituto de Higiene, Montevideo, Uruguay
| | | | - Cesar Echaides
- Parque Lecocq, Intendencia Municipal de Montevideo (IMM), Montevideo, Uruguay
| | - Gabriel Lassabe
- Cátedra de Inmunología, Departamento de Biociencias (DEPBIO), Facultad de Química, Instituto de Higiene, Montevideo, Uruguay
| | - Gualberto Gonzalez-Sapienza
- Cátedra de Inmunología, Departamento de Biociencias (DEPBIO), Facultad de Química, Instituto de Higiene, Montevideo, Uruguay
| |
Collapse
|
28
|
Zhang X, Qian C, Yang L, Gao H, Jiang P, Dai M, Wang Y, Kang H, Xu Y, Hu Q, Feng F, Cheng B, Dai E. Diagnostic value and characteristic analysis of serum nucleocapsid antigen in COVID-19 patients. PeerJ 2023; 11:e15515. [PMID: 37304882 PMCID: PMC10257392 DOI: 10.7717/peerj.15515] [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: 03/09/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
Background To date, several types of laboratory tests for coronavirus disease 2019 (COVID-19) diagnosis have been developed. However, the clinical importance of serum severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen (N-Ag) remains to be fully elucidated. In this study, we sought to investigate the value of serum SARS-CoV-2 N-Ag for COVID-19 diagnosis and to analyze N-Ag characteristics in COVID-19 individuals. Methods Serum samples collected from 215 COVID-19 patients and 65 non-COVID-19 individuals were used to quantitatively detect N-Ag via chemiluminescent immunoassay according to the manufacturer's instructions. Results The sensitivity and specificity of the N-Ag assay were 64.75% (95% confidence interval (95% CI) [55.94-72.66%]) and 100% (95% CI [93.05-100.00%]), respectively, according to the cut-off value recommended by the manufacturer. The receiver operating characteristic (ROC) curve showed a sensitivity of 100.00% (95% CI [94.42-100.00%]) and a specificity of 71.31% (95% CI [62.73-78.59%]). The positive rates and levels of serum SARS-CoV-2 N-Ag were not related to sex, comorbidity status or disease severity of COVID-19 (all P < 0.001). Compared with RT‒PCR, there was a lower positive rate of serum N-Ag for acute COVID-19 patients (P < 0.001). The positive rate and levels of serum SARS-CoV-2 N-Ag in acute patients were significantly higher than those in convalescent patients (all P < 0.001). In addition, the positive rate of serum SARS-CoV-2 N-Ag in acute COVID-19 patients was higher than that of serum antibodies (IgM, IgG, IgA and neutralizing antibodies (Nab)) against SARS-CoV-2 (all P < 0.001). However, the positive rate of serum SARS-CoV-2 N-Ag in convalescent COVID-19 patients was significantly lower than that of antibodies (all P < 0.001). Conclusion Serum N-Ag can be used as a biomarker for early COVID-19 diagnosis based on appropriate cut-off values. In addition, our study also demonstrated the relationship between serum N-Ag and clinical characteristics.
Collapse
Affiliation(s)
- Xihong Zhang
- School of Public Health, North China University of Science and Technology, Tangshan, Hebei, China
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| | - Chungen Qian
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Yang
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| | - Ping Jiang
- Department of Tuberculosis, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| | - Muwei Dai
- Orthopaedic Department, The Fourth Hospital of Hebei Medical University and Hebei Cancer Hospital, Shijiazhuang, Hebei, China
| | - Yuling Wang
- Department of Tuberculosis, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| | - Haiyan Kang
- Department of Tuberculosis, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| | - Yi Xu
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| | - Qian Hu
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| | - Fumin Feng
- School of Public Health, North China University of Science and Technology, Tangshan, Hebei, China
| | - Bangning Cheng
- Shenzhen YHLO Biotech Co., Ltd, Shenzhen, Guangdong, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, Hebei, China
| |
Collapse
|
29
|
Wang Y, Ling X, Zhang C, Zou J, Luo B, Luo Y, Jia X, Jia G, Zhang M, Hu J, Liu T, Wang Y, Lu K, Li D, Ma J, Liu C, Su Z. Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly. MOLECULAR BIOMEDICINE 2023; 4:16. [PMID: 37211575 DOI: 10.1186/s43556-023-00129-z] [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: 01/13/2023] [Accepted: 04/09/2023] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the NIDR, the serine/arginine rich motif (SRIDR), and the CIDR. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (NFL) assembles into ring-like architecture whereas the truncated SRIDR-CTD-CIDR (N182-419) promotes filamentous assembly. Moreover, LLPS droplets of NFL and N182-419 are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N182-419 droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.
Collapse
Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Minghua Zhang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Junchao Hu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Ting Liu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yuanfeiyi Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Kefeng Lu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cong Liu
- Interdisciplinary Research Center On Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China.
| |
Collapse
|
30
|
Sutton WJH, Branham PJ, Williamson YM, Cooper HC, Najjar FN, Pierce-Ruiz CL, Barr JR, Williams TL. Quantification of SARS-CoV-2 spike protein expression from mRNA vaccines using isotope dilution mass spectrometry. Vaccine 2023:S0264-410X(23)00458-9. [PMID: 37202272 DOI: 10.1016/j.vaccine.2023.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/03/2023] [Accepted: 04/17/2023] [Indexed: 05/20/2023]
Abstract
The advent of mRNA vaccine technology has been vital in rapidly creating and manufacturing COVID-19 vaccines at an industrial scale. To continue to accelerate this leading vaccine technology, an accurate method is needed to quantify antigens produced by the transfection of cells with a mRNA vaccine product. This will allow monitoring of protein expression during mRNA vaccine development and provide information on how changes to vaccine components affects the expression of the desired antigen. Developing novel approaches that allow for high-throughput screening of vaccines to detect changes in antigen production in cell culture prior to in vivo studies could aid vaccine development. We have developed and optimized an isotope dilution mass spectrometry method to detect and quantify the spike protein expressed after transfection of baby hamster kidney cells with expired COVID-19 mRNA vaccines. Five peptides of the spike protein are simultaneously quantified and provide assurance that protein digestion in the region of the target peptides is complete since results between the five peptides had a relative standard deviation of less than 15 %. In addition, two housekeeping proteins, actin and GAPDH, are quantified in the same analytical run to account for any variation in cell growth within the experiment. IDMS allows a precise and accurate means to quantify protein expression by mammalian cells transfected with an mRNA vaccine.
Collapse
Affiliation(s)
- William J H Sutton
- Oak Ridge Institute for Science and Education, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - Paul J Branham
- Oak Ridge Institute for Science and Education, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - Yulanda M Williamson
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - Hans C Cooper
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - Fabio N Najjar
- Oak Ridge Institute for Science and Education, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - Carrie L Pierce-Ruiz
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - John R Barr
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - Tracie L Williams
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA.
| |
Collapse
|
31
|
Bonam SR, Hu H. Next-Generation Vaccines Against COVID-19 Variants: Beyond the Spike Protein. ZOONOSES (BURLINGTON, MASS.) 2023; 3:10.15212/zoonoses-2023-0003. [PMID: 38031548 PMCID: PMC10686570 DOI: 10.15212/zoonoses-2023-0003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Vaccines are among the most effective medical countermeasures against infectious diseases. The current Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spurred the scientific strategies to fight against the disease. Since 2020, a great number of vaccines based on different platforms have been in development in response to the pandemic, among which mRNA, adenoviral vector, and subunit vaccines have been clinically approved for use in humans. These first-generation COVID-19 vaccines largely target the viral spike (S) protein and aim for eliciting potent neutralizing antibodies. With the emergence of SARS-CoV-2 variants, especially the highly transmissible Omicron strains, the S-based vaccine strategies have been faced constant challenges due to strong immune escape by the variants. The coronavirus nucleocapsid (N) is one of the viral proteins that induces strong T-cell immunity and is more conserved across different SARS-CoV-2 variants. Inclusion of N in the development of COVID-19 vaccines has been reported. Here, we briefly reviewed and discussed COVID-19 disease, current S-based vaccine strategies, and focused on the immunobiology of N protein in SARS-CoV-2 host immunity, as well as the next-generation vaccine strategies involving N protein, to combat current and emerging SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Srinivasa Reddy Bonam
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA 77555
| | - Haitao Hu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA 77555
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA 77555
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA 77555
| |
Collapse
|
32
|
Cao L, Kong X, Zhang Y, Suo X, Li X, Duan Y, Yuan C, Zheng H, Wang Q. Development of a novel double-antibody sandwich quantitative ELISA for detecting SADS-CoV infection. Appl Microbiol Biotechnol 2023; 107:2413-2422. [PMID: 36809389 PMCID: PMC9942060 DOI: 10.1007/s00253-023-12432-4] [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: 11/01/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/23/2023]
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is an emerging swine enteric alphacoronavirus that can cause acute diarrhea, vomiting, dehydration, and death of newborn piglets. In this study, we developed a double-antibody sandwich quantitative enzyme-linked immunosorbent assay (DAS-qELISA) for detection of SADS-CoV by using an anti-SADS-CoV N protein rabbit polyclonal antibody (PAb) and a specific monoclonal antibody (MAb) 6E8 against the SADS-CoV N protein. The PAb was used as the capture antibodies and HRP-labeled 6E8 as the detector antibody. The detection limit of the developed DAS-qELISA assay was 1 ng/mL of purified antigen and 101.08TCID50/mL of SADS-CoV, respectively. Specificity assays showed that the developed DAS-qELISA has no cross-reactivity with other swine enteric coronaviruses, such as porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV). Three-day-old piglets were challenged with SADS-CoV and collected anal swab samples which were screened for the presence of SADS-CoV by using DAS-qELISA and reverse transcriptase PCR (RT-PCR). The coincidence rate of the DAS-qELISA and RT-PCR was 93.93%, and the kappa value was 0.85, indicating that DAS-qELISA is a reliable method for applying antigen detection of clinical samples. KEY POINTS: • The first double-antibody sandwich quantitative enzyme-linked immunosorbent assay for detection SADS-CoV infection. • The custom ELISA is useful for controlling the SADS-CoV spread.
Collapse
Affiliation(s)
- Liyan Cao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Xiangyu Kong
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Yu Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Xuepeng Suo
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Xiangtong Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Yueyue Duan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Cong Yuan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Qi Wang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China.
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Chengdu National Agricultural Science and Technology Center, Chengdu, China.
| |
Collapse
|
33
|
Soares SR, da Silva Torres MK, Lima SS, de Sarges KML, Santos EFD, de Brito MTFM, da Silva ALS, de Meira Leite M, da Costa FP, Cantanhede MHD, da Silva R, de Oliveira Lameira Veríssimo A, Vallinoto IMVC, Feitosa RNM, Quaresma JAS, Chaves TDSS, Viana GMR, Falcão LFM, Santos EJMD, Vallinoto ACR, da Silva ANMR. Antibody Response to the SARS-CoV-2 Spike and Nucleocapsid Proteins in Patients with Different COVID-19 Clinical Profiles. Viruses 2023; 15:v15040898. [PMID: 37112878 PMCID: PMC10141342 DOI: 10.3390/v15040898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
The first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in Brazil was diagnosed on February 26, 2020. Due to the important epidemiological impact of COVID-19, the present study aimed to analyze the specificity of IgG antibody responses to the S1, S2 and N proteins of SARS-CoV-2 in different COVID-19 clinical profiles. This study enrolled 136 individuals who were diagnosed with or without COVID-19 based on clinical findings and laboratory results and classified as asymptomatic or as having mild, moderate or severe disease. Data collection was performed through a semistructured questionnaire to obtain demographic information and main clinical manifestations. IgG antibody responses to the S1 and S2 subunits of the spike (S) protein and the nucleocapsid (N) protein were evaluated using an enzyme-linked immunosorbent assay (ELISA) according to the manufacturer’s instructions. The results showed that among the participants, 87.5% (119/136) exhibited IgG responses to the S1 subunit and 88.25% (120/136) to N. Conversely, only 14.44% of the subjects (21/136) displayed S2 subunit responses. When analyzing the IgG antibody response while considering the different proteins of the virus, patients with severe disease had significantly higher antibody responses to N and S1 than asymptomatic individuals (p ≤ 0.0001), whereas most of the participants had low antibody titers against the S2 subunit. In addition, individuals with long COVID-19 showed a greater IgG response profile than those with symptomatology of a short duration. Based on the results of this study, it is concluded that levels of IgG antibodies may be related to the clinical evolution of COVID-19, with high levels of IgG antibodies against S1 and N in severe cases and in individuals with long COVID-19.
Collapse
Affiliation(s)
- Sinei Ramos Soares
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Maria Karoliny da Silva Torres
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
- Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Sandra Souza Lima
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Kevin Matheus Lima de Sarges
- Laboratório de Genética de Doenças Complexas, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Erika Ferreira dos Santos
- Laboratório de Genética de Doenças Complexas, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | | | - Andréa Luciana Soares da Silva
- Laboratório de Genética de Doenças Complexas, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Mauro de Meira Leite
- Laboratório de Genética de Doenças Complexas, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Flávia Póvoa da Costa
- Laboratório de Genética de Doenças Complexas, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | | | - Rosilene da Silva
- Laboratório de Genética de Doenças Complexas, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | | | - Izaura Maria Vieira Cayres Vallinoto
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
- Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Rosimar Neris Martins Feitosa
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
- Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Juarez Antônio Simões Quaresma
- Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Universidade Federal do Pará, Belém 66075-110, Brazil
- Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém 66050-540, Brazil
| | - Tânia do Socorro Souza Chaves
- Laboratório de Pesquisas Básicas em Malária em Malária, Seção de Parasitologia, Instituto Evandro Chagas, Secretaria de Ciência, Tecnologia e Insumos Estratégicos, Ministério da Saúde do Brasil, Ananindeua 70068-900, Brazil
| | - Giselle Maria Rachid Viana
- Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Universidade Federal do Pará, Belém 66075-110, Brazil
- Laboratório de Pesquisas Básicas em Malária em Malária, Seção de Parasitologia, Instituto Evandro Chagas, Secretaria de Ciência, Tecnologia e Insumos Estratégicos, Ministério da Saúde do Brasil, Ananindeua 70068-900, Brazil
| | - Luiz Fábio Magno Falcão
- Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém 66050-540, Brazil
| | - Eduardo José Melo dos Santos
- Laboratório de Genética de Doenças Complexas, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
| | | | - Andréa Nazaré Monteiro Rangel da Silva
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil
- Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Universidade Federal do Pará, Belém 66075-110, Brazil
| |
Collapse
|
34
|
Wang X, Liu Y, Li K, Hao Z. Roles of p53-Mediated Host–Virus Interaction in Coronavirus Infection. Int J Mol Sci 2023; 24:ijms24076371. [PMID: 37047343 PMCID: PMC10094438 DOI: 10.3390/ijms24076371] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
The emergence of the SARS-CoV-2 coronavirus has garnered global attention due to its highly pathogenic nature and the resulting health crisis and economic burden. Although drugs such as Remdesivir have been considered a potential cure by targeting the virus on its RNA polymerase, the high mutation rate and unique 3’ to 5’ exonuclease with proofreading function make it challenging to develop effective anti-coronavirus drugs. As a result, there is an increasing focus on host–virus interactions because coronaviruses trigger stress responses, cell cycle changes, apoptosis, autophagy, and the dysregulation of immune function and inflammation in host cells. The p53 tumor suppressor molecule is a critical regulator of cell signaling pathways, cellular stress responses, DNA repair, and apoptosis. However, viruses can activate or inhibit p53 during viral infections to enhance viral replication and spread. Given its pivotal role in cell physiology, p53 represents a potential target for anti-coronavirus drugs. This review aims to summarize the relationship between p53 and coronaviruses from various perspectives, to shed light on potential targets for antiviral drug development and vaccine design.
Collapse
Affiliation(s)
| | | | | | - Zhihui Hao
- Correspondence: ; Tel./Fax: +86-010-6273-1192
| |
Collapse
|
35
|
Quek RT, Hardy KS, Walker SG, Nguyen DT, de Almeida
Magalhães T, Salic A, Gopalakrishnan SM, Silver PA, Mitchison TJ. Screen for Modulation of Nucleocapsid Protein Condensation Identifies Small Molecules with Anti-Coronavirus Activity. ACS Chem Biol 2023; 18:583-594. [PMID: 36795767 PMCID: PMC9942534 DOI: 10.1021/acschembio.2c00908] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023]
Abstract
Biomolecular condensates formed by liquid-liquid phase separation have been implicated in multiple diseases. Modulation of condensate dynamics by small molecules has therapeutic potential, but so far, few condensate modulators have been disclosed. The SARS-CoV-2 nucleocapsid (N) protein forms phase-separated condensates that are hypothesized to play critical roles in viral replication, transcription, and packaging, suggesting that N condensation modulators might have anti-coronavirus activity across multiple strains and species. Here, we show that N proteins from all seven human coronaviruses (HCoVs) vary in their tendency to undergo phase separation when expressed in human lung epithelial cells. We developed a cell-based high-content screening platform and identified small molecules that both promote and inhibit condensation of SARS-CoV-2 N. Interestingly, these host-targeted small molecules exhibited condensate-modulatory effects across all HCoV Ns. Some have also been reported to exhibit antiviral activity against SARS-CoV-2, HCoV-OC43, and HCoV-229E viral infections in cell culture. Our work reveals that the assembly dynamics of N condensates can be regulated by small molecules with therapeutic potential. Our approach allows for screening based on viral genome sequences alone and might enable rapid paths to drug discovery with value for confronting future pandemics.
Collapse
Affiliation(s)
- Rui Tong Quek
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, Massachusetts 02115,
United States
| | - Kierra S. Hardy
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, Massachusetts 02115,
United States
| | - Stephen G. Walker
- Drug Discovery Science and Technology,
AbbVie Inc., North Chicago, Illinois 60064, United
States
| | - Dan T. Nguyen
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, Massachusetts 02115,
United States
| | | | - Adrian Salic
- Department of Cell Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
| | | | - Pamela A. Silver
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, Massachusetts 02115,
United States
| | - Timothy J. Mitchison
- Department of Systems Biology, Harvard
Medical School, Boston, Massachusetts 02115, United
States
| |
Collapse
|
36
|
Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA. Molecules 2023; 28:molecules28062534. [PMID: 36985506 PMCID: PMC10051649 DOI: 10.3390/molecules28062534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Suramin was originally used as an antiparasitic drug in clinics. Here, we demonstrate that suramin can bind to the N-terminal domain of SARS-CoV-2 nucleocapsid protein (N-NTD) and disturb its interaction with RNA. The BLI experiments showed that N-NTD interacts suramin with a dissociate constant (Kd = 2.74 μM) stronger than that of N-NTD with ssRNA-16 (Kd = 8.37 μM). Furthermore, both NMR titration experiments and molecular docking analysis suggested that suramin mainly binds to the positively charged cavity between the finger and the palm subdomains of N-NTD, and residues R88, R92, R93, I94, R95, K102 and A156 are crucial for N-NTD capturing suramin. Besides, NMR dynamics experiments showed that suramin-bound N-NTD adopts a more rigid structure, and the loop between β2-β3 exhibits fast motion on the ps-ns timescale, potentially facilitating suramin binding. Our findings not only reveal the molecular basis of suramin disturbing the association of SARS-CoV-2 N-NTD with RNA but also provide valuable structural information for the development of drugs against SARS-CoV-2.
Collapse
|
37
|
Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [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: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
Collapse
Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
38
|
Merino VF, Yan Y, Ordonez AA, Bullen CK, Lee A, Saeki H, Ray K, Huang T, Jain SK, Pomper MG. Nucleolin mediates SARS-CoV-2 replication and viral-induced apoptosis of host cells. Antiviral Res 2023; 211:105550. [PMID: 36740097 PMCID: PMC9896859 DOI: 10.1016/j.antiviral.2023.105550] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Host-oriented antiviral therapeutics are promising treatment options to combat COVID-19 and its emerging variants. However, relatively little is known about the cellular proteins hijacked by SARS-CoV-2 for its replication. Here we show that SARS-CoV-2 induces expression and cytoplasmic translocation of the nucleolar protein, nucleolin (NCL). NCL interacts with SARS-CoV-2 viral proteins and co-localizes with N-protein in the nucleolus and in stress granules. Knockdown of NCL decreases the stress granule component G3BP1, viral replication and improved survival of infected host cells. NCL mediates viral-induced apoptosis and stress response via p53. SARS-CoV-2 increases NCL expression and nucleolar size and number in lungs of infected hamsters. Inhibition of NCL with the aptamer AS-1411 decreases viral replication and apoptosis of infected cells. These results suggest nucleolin as a suitable target for anti-COVID therapies.
Collapse
Affiliation(s)
- Vanessa F Merino
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Yu Yan
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Alvaro A Ordonez
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - C Korin Bullen
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Albert Lee
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harumi Saeki
- Department of Human Pathology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sanjay K Jain
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin G Pomper
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
39
|
Ni X, Han Y, Zhou R, Zhou Y, Lei J. Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2. Commun Biol 2023; 6:193. [PMID: 36806252 PMCID: PMC9938351 DOI: 10.1038/s42003-023-04570-2] [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: 03/10/2022] [Accepted: 02/09/2023] [Indexed: 02/20/2023] Open
Abstract
The coronavirus nucleocapsid (N) protein interacts with non-structural protein 3 (Nsp3) to facilitate viral RNA synthesis and stabilization. However, structural information on the N-Nsp3 complex is limited. Here, we report a 2.6 Å crystal structure of the N-terminal domain (NTD) of the N protein in complex with the ubiquitin-like domain 1 (Ubl1) of Nsp3 in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One NTD and two Ubl1s formed a stable heterotrimer. We performed mutational analysis to reveal the key residues for this interaction. We confirmed the colocalization of SARS-CoV-2 N and Nsp3 in Huh-7 cells. N-Ubl1 interaction also exists in SARS-CoV and Middle East respiratory syndrome coronavirus. We found that SARS-CoV-2 Ubl1 competes with RNA to bind N protein in a dose-dependent manner. Based on our results, we propose a model for viral ribonucleoprotein dissociation through N protein binding to Ubl1 of Nsp3.
Collapse
Affiliation(s)
- Xincheng Ni
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yinze Han
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Renjie Zhou
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yanmei Zhou
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Jian Lei
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| |
Collapse
|
40
|
Islam MA, Shahi S, Marzan AA, Amin MR, Hasan MN, Hoque MN, Ghosh A, Barua A, Khan A, Dhama K, Chakraborty C, Bhattacharya P, Wei DQ. Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development. Front Pharmacol 2023; 14:1090717. [PMID: 36825152 PMCID: PMC9941545 DOI: 10.3389/fphar.2023.1090717] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates. Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to assess the spread and emergence of the mutations in the SARS-CoV-2 genome. The available data sources of NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) and NextStrain (https://nextstrain.org/) were searched for tracking SARS-CoV-2 mutations, analysed using the PROVEAN, Polyphen-2, and Predict SNP mutational analysis tools and validated by Machine Learning models. Result: Compared to the Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 mutations in the SARS-CoV-2 genome. We determined that the Omicron variant had 6,307 mutations (retrieved sequence:1947), including 67.8% unique mutations, more than any other variant evaluated in this study. The spike protein of the Omicron variant harboured 876 mutations, including 443 deleterious mutations. Among these deleterious mutations, 187 were common and 256 were unique non-synonymous mutations. In contrast, after analysing 1,884 sequences of the Delta variant, we discovered 4,468 mutations, of which 66% were unique, and not previously reported in other variants. Mutations affecting spike proteins are mostly found in RBD regions for Omicron, whereas most of the Delta variant mutations drawn to focus on amino acid regions ranging from 911 to 924 in the context of epitope prediction (B cell & T cell) and mutational stability impact analysis protruding that Omicron is more transmissible. Discussion: The pathogenesis of the Omicron variant could be prevented if the deleterious and persistent unique immunosuppressive mutations can be targeted for vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor and track the continuously evolving nature of SARS-CoV-2 strains, the associated genetic variants, and their implications for developing effective control and prophylaxis strategies.
Collapse
Affiliation(s)
- Md. Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Bangladesh,COVID-19 Diagnostic lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh,*Correspondence: Md. Aminul Islam, , ; Prosun Bhattacharya,
| | - Shatila Shahi
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Abdullah Al Marzan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Mohammad Ruhul Amin
- COVID-19 Diagnostic lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mohammad Nayeem Hasan
- Department of Statistics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Abanti Barua
- COVID-19 Diagnostic lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nayang, Henan, China
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
| | - Prosun Bhattacharya
- COVID-19 Research @KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Stockholm, Sweden,*Correspondence: Md. Aminul Islam, , ; Prosun Bhattacharya,
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nayang, Henan, China,Peng Cheng Laboratory, Shenzhen, Guangdong, China
| |
Collapse
|
41
|
Ali Z, Cardoza JV, Basak S, Narsaria U, Singh VP, Isaac SP, França TCC, LaPlante SR, George SS. Computational design of candidate multi-epitope vaccine against SARS-CoV-2 targeting structural (S and N) and non-structural (NSP3 and NSP12) proteins. J Biomol Struct Dyn 2023; 41:13348-13367. [PMID: 36744449 DOI: 10.1080/07391102.2023.2173297] [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: 04/15/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 virus has created a global damage and has exposed the vulnerable side of scientific research towards novel diseases. The intensity of the pandemic is huge, with mortality rates of more than 6 million people worldwide in a span of 2 years. Considering the gravity of the situation, scientists all across the world are continuously attempting to create successful therapeutic solutions to combat the virus. Various vaccination strategies are being devised to ensure effective immunization against SARS-CoV-2 infection. SARS-CoV-2 spreads very rapidly, and the infection rate is remarkably high than other respiratory tract viruses. The viral entry and recognition of the host cell is facilitated by S protein of the virus. N protein along with NSP3 is majorly responsible for viral genome assembly and NSP12 performs polymerase activity for RNA synthesis. In this study, we have designed a multi-epitope, chimeric vaccine considering the two structural (S and N protein) and two non-structural proteins (NSP3 and NSP12) of SARS-CoV-2 virus. The aim is to induce immune response by generating antibodies against these proteins to target the viral entry and viral replication in the host cell. In this study, computational tools were used, and the reliability of the vaccine was verified using molecular docking, molecular dynamics simulation and immune simulation studies in silico. These studies demonstrate that the vaccine designed shows steady interaction with Toll like receptors with good stability and will be effective in inducing a strong and specific immune response in the body.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Zeeshan Ali
- Krupanidhi College of Physiotherapy, Bangalore, India
| | | | | | | | - Vijay Pratap Singh
- Department of Physiotherapy, Kasturba Medical College, Mangalore, Manipal academy of higher education, Mangalore, Manipal, India
| | | | - Tanos C C França
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | | |
Collapse
|
42
|
Zheng Y, Gao C. Phase Separation: The Robust Modulator of Innate Antiviral Signaling and SARS-CoV-2 Infection. Pathogens 2023; 12:pathogens12020243. [PMID: 36839515 PMCID: PMC9962166 DOI: 10.3390/pathogens12020243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 has been a pandemic threat to human health and the worldwide economy, but efficient treatments are still lacking. Type I and III interferons are essential for controlling viral infection, indicating that antiviral innate immune signaling is critical for defense against viral infection. Phase separation, one of the basic molecular processes, governs multiple cellular activities, such as cancer progression, microbial infection, and signaling transduction. Notably, recent studies suggest that phase separation regulates antiviral signaling such as the RLR and cGAS-STING pathways. Moreover, proper phase separation of viral proteins is essential for viral replication and pathogenesis. These observations indicate that phase separation is a critical checkpoint for virus and host interaction. In this study, we summarize the recent advances concerning the regulation of antiviral innate immune signaling and SARS-CoV-2 infection by phase separation. Our review highlights the emerging notion that phase separation is the robust modulator of innate antiviral signaling and viral infection.
Collapse
|
43
|
Chau BA, Chen V, Cochrane AW, Parent LJ, Mouland AJ. Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication. Cell Rep 2023; 42:111968. [PMID: 36640305 PMCID: PMC9790868 DOI: 10.1016/j.celrep.2022.111968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due to their central roles in virus replication, among which is their capacity to bind their respective genomic RNAs for packaging into nascent virions. This review focuses on fundamental studies of these nucleocapsid proteins and how their intrinsic abilities to condense through liquid-liquid phase separation (LLPS) contribute to viral replication. Therapeutic targeting of these condensates and methodological advances are also described to address future questions on how phase separation contributes to viral replication.
Collapse
Affiliation(s)
- Bao-An Chau
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Venessa Chen
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alan W Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leslie J Parent
- Division of Infectious Diseases and Epidemiology, Departments of Medicine and Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
| |
Collapse
|
44
|
Wang F, Zhang Q, Zhang F, Zhang E, Li M, Ma S, Guo J, Yang Z, Zhu J. Adenovirus vector-mediated single chain variable fragments target the nucleocapsid protein of porcine epidemic diarrhea virus and protect against viral infection in piglets. Front Immunol 2023; 14:1058327. [PMID: 36761768 PMCID: PMC9902916 DOI: 10.3389/fimmu.2023.1058327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) mainly infects the intestinal epithelial cells of pigs, causing porcine epidemic diarrhea (PED). In particular, the virus causes severe diarrhea, dehydration, and death in neonatal piglets. Maternal immunity effectively protects neonatal piglets from PEDV infection; however, maternal antibodies can only prevent PEDV attachment and entry into target cells, but have no effects on intracellular viruses. Intracellular antibodies targeting virus-encoded proteins are effective in preventing viral infection. We previously identified four single chain variable fragments (scFvs), ZW1-16, ZW3-21, ZW1-41, and ZW4-16, which specifically targeted the PEDV N protein and significantly inhibited PEDV replication and up-regulated interferon-λ1 (IFN-λ1) expression in host cells. In our current study, the four scFvs were subcloned into replication-defective adenovirus vectors to generate recombinant adenoviruses rAdV-ZW1-16, rAdV-ZW3-21, rAdV-ZW1-41, and rAdV-ZW4-16. ScFvs were successfully expressed in Human Embryonic Kidney 293 (HEK293) cells and intestinal porcine epithelial cell line J2 (IPEC-J2) and were biosafe for piglets as indicated by body temperature and weight, scFv excretion in feces, IFN-γ and interleukin-4 (IL-4) expression in jejunum, and pathological changes in porcine tissue after oral administration. Western blotting, immunofluorescence, and immunohistochemical analyses showed that scFvs were expressed in porcine jejunum. The prophylactic effects of rAdV-ZW, a cocktail of the four rAdV-scFvs, on piglet diarrhea caused by PEDV was investigated. Clinical symptoms in piglets orally challenged with PEDV, following a two-time treatment with rAdV-ZW, were significantly reduced when compared with PEDV-infected piglets treated with phosphate buffered saline (PBS) or rAdV-wild-type. Also, no death and jejunal lesions were observed. ScFv co-localization with the PEDV N protein in vivo was also observed. Next, the expression of pro-inflammatory serum cytokines such as tumor necrosis factor-α (TNF-α), IL-6, IL-8, IL-12, and IFN-λ was assessed by enzyme-linked immunosorbent assay (ELISA), which showed that scFvs significantly suppressed PEDV-induced pro-inflammatory cytokine expression and restored PEDV-inhibited IFN-λ expression. Therefore, our study supported a promising role for intracellular scFvs targeting the PEDV N protein to prevent and treat diarrhea in PEDV-infected piglets.
Collapse
Affiliation(s)
- Fengqing Wang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Zhang
- State Key Laboratory of Advanced Optical Communication Systems and Networks, Key Laboratory for Laser Plasmas (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Qing Zhang, ; Jianguo Zhu,
| | - Fanqing Zhang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - En Zhang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Mei Li
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiwei Ma
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianming Guo
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhibiao Yang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianguo Zhu
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Qing Zhang, ; Jianguo Zhu,
| |
Collapse
|
45
|
Dang M, Li T, Song J. ATP and nucleic acids competitively modulate LLPS of the SARS-CoV2 nucleocapsid protein. Commun Biol 2023; 6:80. [PMID: 36681763 PMCID: PMC9862227 DOI: 10.1038/s42003-023-04480-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/13/2023] [Indexed: 01/22/2023] Open
Abstract
SARS-CoV-2 nucleocapsid (N) protein with very low mutation rates is the only structural protein which not only functions to package viral genomic RNA, but also manipulates host-cell machineries, thus representing a key target for drug development. Recent discovery of its liquid-liquid phase separation (LLPS) opens up a new direction for developing anti-SARS-CoV-2 strategies/drugs. However, so far the high-resolution mechanism of its LLPS still remains unknown. Here by DIC and NMR characterization, we have demonstrated: 1) nucleic acids modulate LLPS by dynamic and multivalent interactions over both folded NTD/CTD and Arg/Lys residues within IDRs; 2) ATP with concentrations > mM in all living cells but absent in viruses not only binds NTD/CTD, but also Arg residues within IDRs with a Kd of 2.8 mM; and 3) ATP dissolves nucleic-acid-induced LLPS by competitively displacing nucleic acid from binding the protein. Our study deciphers that the essential binding of N protein with nucleic acid and its LLPS are targetable by small molecules including ATP, which is emerging as a cellular factor controlling the host-SARS-CoV-2 interaction. Fundamentally, our results imply that the mechanisms of LLPS of IDR-containing proteins mediated by ATP and nucleic acids appear to be highly conserved from human to virus.
Collapse
Affiliation(s)
- Mei Dang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore, Singapore
| | - Tongyang Li
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore, Singapore.
| |
Collapse
|
46
|
Monteiro FP, Tavares VDS, Souza RDSO, Venâncio LPR, Fabres-Klein MH, do Carmo RF, Klein RC, Lima JB, Araújo-Santos T. Coagulopathy and the humoral response against viral proteins in patients at different stages of COVID-19. Mem Inst Oswaldo Cruz 2023; 117:e220072. [PMID: 36700578 PMCID: PMC9870257 DOI: 10.1590/0074-02760220072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/17/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Patients with severe coronavirus disease 2019 (COVID-19) often present with coagulopathies and have high titres of circulating antibodies against viral proteins. OBJECTIVES Herein, we evaluated the association between D-dimer and circulating immunoglobulin levels against viral proteins in patients at different clinical stages of COVID-19. METHODS For this, we performed a cross-sectional study involving patients of the first wave of COVID-19 clinically classified as oligosymptomatic (n = 22), severe (n = 30), cured (n = 27) and non-infected (n = 9). Next, we measured in the plasma samples the total and fraction of immunoglobulins against the nucleoprotein (NP) and the receptor-binding domain (RBD) of the spike proteins by enzyme-linked immunosorbent assay (ELISA) assays. FINDINGS Patients with severe disease had a coagulation disorder with high levels of D-dimer as well as circulating IgG against the NP but not the RBD compared to other groups of patients. In addition, high levels of D-dimer and IgG against the NP and RBD were associated with disease severity among the patients in this study. MAIN CONCLUSIONS Our data suggest that IgG against NP and RBD participates in the worsening of COVID-19. Although the humoral response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is partially understood, and more efforts are needed to clarify gaps in the knowledge of this process.
Collapse
Affiliation(s)
- Fernanda Pereira Monteiro
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Victor de Souza Tavares
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Rayane da Silva Oliveira Souza
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Larissa Paola Rodrigues Venâncio
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Mary Hellen Fabres-Klein
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Rodrigo Feliciano do Carmo
- Universidade Federal do Vale do São Francisco, Colegiado de Ciências Farmacêuticas, Petrolina, PE, Brasil
| | - Raphael Contelli Klein
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Jonilson Berlink Lima
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Théo Araújo-Santos
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil,+ Corresponding author:
| |
Collapse
|
47
|
Solo-Gabriele HM, Kumar S, Abelson S, Penso J, Contreras J, Babler KM, Sharkey ME, Mantero AMA, Lamar WE, Tallon JJ, Kobetz E, Solle NS, Shukla BS, Kenney RJ, Mason CE, Schürer SC, Vidovic D, Williams SL, Grills GS, Jayaweera DT, Mirsaeidi M, Kumar N. Predicting COVID-19 cases using SARS-CoV-2 RNA in air, surface swab and wastewater samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159188. [PMID: 36202365 PMCID: PMC9529341 DOI: 10.1016/j.scitotenv.2022.159188] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 05/08/2023]
Abstract
Genomic footprints of pathogens shed by infected individuals can be traced in environmental samples, which can serve as a noninvasive method of infectious disease surveillance. The research evaluates the efficacy of environmental monitoring of SARS-CoV-2 RNA in air, surface swabs and wastewater to predict COVID-19 cases. Using a prospective experimental design, air, surface swabs, and wastewater samples were collected from a college dormitory housing roughly 500 students from March to May 2021 at the University of Miami, Coral Gables, FL. Students were randomly screened for COVID-19 during the study period. SARS-CoV-2 concentration in environmental samples was quantified using Volcano 2nd Generation-qPCR. Descriptive analyses were conducted to examine the associations between time-lagged SARS-CoV-2 in environmental samples and COVID-19 cases. SARS-CoV-2 was detected in air, surface swab and wastewater samples on 52 (63.4 %), 40 (50.0 %) and 57 (68.6 %) days, respectively. On 19 (24 %) of 78 days SARS-CoV-2 was detected in all three sample types. COVID-19 cases were reported on 11 days during the study period and SARS-CoV-2 was also detected two days before the case diagnosis on all 11 (100 %), 9 (81.8 %) and 8 (72.7 %) days in air, surface swab and wastewater samples, respectively. SARS-CoV-2 detection in environmental samples was an indicator of the presence of local COVID-19 cases and a 3-day lead indicator for a potential outbreak at the dormitory building scale. Proactive environmental surveillance of SARS-CoV-2 or other pathogens in multiple environmental media has potential to guide targeted measures to contain and/or mitigate infectious disease outbreaks within communities.
Collapse
Affiliation(s)
- Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, FL, United States of America
| | - Shelja Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Samantha Abelson
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Johnathon Penso
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Julio Contreras
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, FL, United States of America
| | - Mark E Sharkey
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Alejandro M A Mantero
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Walter E Lamar
- Facilities Safety & Compliance, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - John J Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL, United States of America
| | - Erin Kobetz
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Natasha Schaefer Solle
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Bhavarth S Shukla
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Richard J Kenney
- Department of Housing & Residential Life, University of Miami, Coral Gables, FL, United States of America
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, United States of America
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, United States of America; Department of Molecular & Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Dusica Vidovic
- Department of Molecular & Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Sion L Williams
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - George S Grills
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Dushyantha T Jayaweera
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, FL, United States of America
| | - Naresh Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America.
| |
Collapse
|
48
|
Jin X, Liu X, Shen C. A systemic review of T-cell epitopes defined from the proteome of SARS-CoV-2. Virus Res 2023; 324:199024. [PMID: 36526016 PMCID: PMC9757803 DOI: 10.1016/j.virusres.2022.199024] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection remains in a global pandemic, and no eradicative therapy is currently available. Host T cells have been shown to play a crucial role in the antiviral immune protection and pathology in Coronavirus disease 2019 (COVID-19) patients; thus, identifying sufficient T-cell epitopes from the SARS-CoV-2 proteome can contribute greatly to the development of T-cell epitope vaccines and the precise evaluation of host SARS-CoV-2-specific cellular immunity. This review presents a comprehensive map of T-cell epitopes functionally validated from SARS-CoV-2 antigens, the human leukocyte antigen (HLA) supertypes to present these epitopes, and the strategies to screen and identify T-cell epitopes. To the best of our knowledge, a total of 1349 CD8+ T-cell epitopes and 790 CD4+ T-cell epitopes have been defined by functional experiments thus far, but most are presented by approximately twenty common HLA supertypes, such as HLA-A0201, A2402, B0702, DR15, DR7 and DR11 molecules, and 74-80% of the T-cell epitopes are derived from S protein and nonstructural protein. These data provide useful insight into the development of vaccines and specific T-cell detection systems. However, the currently defined T-cell epitope repertoire cannot cover the HLA polymorphism of major populations in an indicated geographic region. More research is needed to depict an overall landscape of T-cell epitopes, which covers the overall SARS-CoV-2 proteome and global patients.
Collapse
Affiliation(s)
- Xiaoxiao Jin
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China 225002; Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009.
| |
Collapse
|
49
|
Wu W, Cheng Y, Zhou H, Sun C, Zhang S. The SARS-CoV-2 nucleocapsid protein: its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics. Virol J 2023; 20:6. [PMID: 36627683 PMCID: PMC9831023 DOI: 10.1186/s12985-023-01968-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) continues to take a heavy toll on personal health, healthcare systems, and economies around the globe. Scientists are expending tremendous effort to develop diagnostic technologies for detecting positive infections within the shortest possible time, and vaccines and drugs specifically for the prevention and treatment of COVID-19 disease. At the same time, emerging novel variants have raised serious concerns about vaccine efficacy. The SARS-CoV-2 nucleocapsid (N) protein plays an important role in the coronavirus life cycle, and participates in various vital activities after virus invasion. It has attracted a large amount of attention for vaccine and drug development. Here, we summarize the latest research of the N protein, including its role in the SARS-CoV-2 life cycle, structure and function, and post-translational modifications in addition to its involvement in liquid-liquid phase separation (LLPS) and use as a basis for the development of vaccines and diagnostic techniques.
Collapse
Affiliation(s)
- Wenbing Wu
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Ying Cheng
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Hong Zhou
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Changzhen Sun
- grid.410578.f0000 0001 1114 4286Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000 China
| | - Shujun Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
| |
Collapse
|
50
|
Mahmoudvand S, Esmaeili Gouvarchin Ghaleh H, Jalilian FA, Farzanehpour M, Dorostkar R. Design of a multi-epitope-based vaccine consisted of immunodominant epitopes of structural proteins of SARS-CoV-2 using immunoinformatics approach. Biotechnol Appl Biochem 2023:10.1002/bab.2431. [PMID: 36577011 PMCID: PMC9880719 DOI: 10.1002/bab.2431] [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: 02/25/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown rapid global spread and has resulted in a significant death toll worldwide. In this study, we aimed to design a multi-epitope vaccine against SARS-CoV-2 based on structural proteins S, M, N, and E. We identified B- and T-cell epitopes and then the antigenicity, toxicity, allergenicity, and similarity of predicted epitopes were analyzed. T-cell epitopes were docked with corresponding HLA alleles. Consequently, the selected T- and B-cell epitopes were included in the final construct. All selected epitopes were connected with different linkers and flagellin and pan-HLA DR binding epitopes (PADRE) as an adjuvant were used in the vaccine construct. Furthermore, molecular docking was used to evaluate the complex between the final vaccine construct and two alleles, HLA-A*02:01 and HLA-DRB1*01:01. Finally, codons were optimized for in silico cloning into pET28a(+) vector using SnapGene. The final vaccine construct comprised 11 CTL, HTL, and B-cell epitopes corresponding to 394 amino acid residues. In silico evaluation showed that the designed vaccine might potentially promote an immune response. Further in vivo preclinical and clinical testing is required to determine the safety and efficacy of the designed vaccine.
Collapse
Affiliation(s)
- Shahab Mahmoudvand
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Farid Azizi Jalilian
- Department of Medical VirologyFaculty of MedicineHamadan University of Medical SciencesHamadanIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| |
Collapse
|