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Rak A, Gorbunov N, Kostevich V, Sokolov A, Prokopenko P, Rudenko L, Isakova-Sivak I. Assessment of Immunogenic and Antigenic Properties of Recombinant Nucleocapsid Proteins of Five SARS-CoV-2 Variants in a Mouse Model. Viruses 2023; 15:230. [PMID: 36680269 PMCID: PMC9861333 DOI: 10.3390/v15010230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
COVID-19 cases caused by new variants of highly mutable SARS-CoV-2 continue to be identified worldwide. Effective control of the spread of new variants can be achieved through targeting of conserved viral epitopes. In this regard, the SARS-CoV-2 nucleocapsid (N) protein, which is much more conserved than the evolutionarily influenced spike protein (S), is a suitable antigen. The recombinant N protein can be considered not only as a screening antigen but also as a basis for the development of next-generation COVID-19 vaccines, but little is known about induction of antibodies against the N protein via different SARS-CoV-2 variants. In addition, it is important to understand how antibodies produced against the antigen of one variant can react with the N proteins of other variants. Here, we used recombinant N proteins from five SARS-CoV-2 strains to investigate their immunogenicity and antigenicity in a mouse model and to obtain and characterize a panel of hybridoma-derived monoclonal anti-N antibodies. We also analyzed the variable epitopes of the N protein that are potentially involved in differential recognition of antiviral antibodies. These results will further deepen our knowledge of the cross-reactivity of the humoral immune response in COVID-19.
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Affiliation(s)
- Alexandra Rak
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Nikolay Gorbunov
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Valeria Kostevich
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Alexey Sokolov
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Polina Prokopenko
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Larisa Rudenko
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Irina Isakova-Sivak
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
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2
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Liu B, Wu Z, Liang C, Lu J, Li J, Zhang L, Li T, Zhao W, Fu Y, Hou S, Tang X, Li C. Development of a Smartphone-Based Nanozyme-Linked Immunosorbent Assay for Quantitative Detection of SARS-CoV-2 Nucleocapsid Phosphoprotein in Blood. Front Microbiol 2021; 12:692831. [PMID: 34497592 PMCID: PMC8420716 DOI: 10.3389/fmicb.2021.692831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/23/2021] [Indexed: 12/28/2022] Open
Abstract
Since December 2019, a novel coronavirus (SARS-CoV-2) has resulted in a global pandemic of coronavirus disease (COVID-19). Although viral nucleic acid test (NAT) has been applied predominantly to detect SARS-CoV-2 RNA for confirmation diagnosis of COVID-19, an urgent need for alternative, rapid, and sensitive immunoassays is required for primary screening of virus. In this study, we developed a smartphone-based nanozyme-linked immunosorbent assay (SP-NLISA) for detecting the specific nucleocapsid phosphoprotein (NP) of SARS-CoV-2 in 37 serum samples from 20 COVID-19 patients who were diagnosed by NAT previously. By using SP-NLISA, 28/37 (75.7%) serum samples were detected for NP antigens and no cross-reactivity with blood donors' control samples collected from different areas of China. In a control assay using the conventional enzyme-linked immunosorbent assay (ELISA), only 7/37 (18.91%) serum samples were detected for NP antigens and no cross-reactivity with control samples. SP-NLISA could be used for rapid detection of SARS-CoV-2 NP antigen in primary screening of SARS-CoV-2 infected individuals.
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Affiliation(s)
- Bochao Liu
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Guangzhou Blood Center, Guangzhou, China
| | - Ze Wu
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Chaolan Liang
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Jinhui Lu
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Jinfeng Li
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Shenzhen Key Laboratory of Molecular Epidemiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ling Zhang
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Tingting Li
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Wei Zhao
- Laboratory of Biosafety, School of Public Health, Southern Medical University, Guangzhou, China
| | | | - Shuiping Hou
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Microbiological Laboratory, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Xi Tang
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Department of Infection, The First People's Hospital of Foshan, Foshan, China
| | - Chengyao Li
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
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Yadav R, Imran M, Dhamija P, Suchal K, Handu S. Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2. J Biomol Struct Dyn 2021; 39:4433-4448. [PMID: 32568013 PMCID: PMC7332875 DOI: 10.1080/07391102.2020.1778536] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/29/2020] [Indexed: 12/23/2022]
Abstract
The emergence of the coronavirus disease-2019 pandemic has led to an outbreak in the world. The SARS-CoV-2 is seventh and latest in coronavirus family with unique exonucleases for repairing any mismatches in newly transcribed genetic material. Therefore, drugs with novel additional mechanisms are required to simultaneously target and eliminate the virus. Thus, a newly deciphered N protein is taken as a target that belongs to SARS-CoV-2. They play a vital role in RNA transcription, viral replication and new virion formation. This study used virtual screening, molecular modeling and docking of the 8987 ligands from Asinex and PubChem databases against this novel target protein. Three hotspot sites having DScore ≥1 (Site 1, Site 2 and Site 3) for ligand binding were selected. Subsequently, high throughput screening, standard precision and extra precision docking process and molecular dynamics concluded three best drugs from two libraries. Two antiviral moieties from Asinex databases (5817 and 6799) have docking scores of -10.29 and -10.156; along with their respective free binding energies (ΔG bind) of -51.96 and -64.36 on Site 3. The third drug, Zidovudine, is from PubChem database with docking scores of -9.75 with its binding free energies (ΔG bind) of -59.43 on Site 3. The RMSD and RMSF were calculated for all the three drugs through molecular dynamics simulation studies for 50 ns. Zidovudine shows a very stable interaction with fluctuation starting at 2.4 Å on 2 ns and remained stable at 3 Å from 13 to 50 ns. Thus, paving the way for further biological validation as a potential treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
| | - Mohammed Imran
- Department of Pharmacology, College of Medicine, Shaqra University, Shaqra, Kingdom of Saudi Arabia
| | - Puneet Dhamija
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
| | - Kapil Suchal
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Shailendra Handu
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
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Xu Y, Chen C, Lai H, He Y, Guo G, Feng J, Li L. Determination of human COVID-19 total antibodies in serum using a time-resolved fluorescence immunoassay. Biotechnol Appl Biochem 2021; 69:1474-1481. [PMID: 34245473 PMCID: PMC8426795 DOI: 10.1002/bab.2219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/04/2021] [Indexed: 01/23/2023]
Abstract
Coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is spreading rapidly around the world. Antibody detection plays an important role in the diagnosis of COVID‐19. Here, we established a new time‐resolved fluorescence immunoassay (TRFIA) to determine COVID‐19 total antibodies. A double‐antigen sandwich TRFIA was optimized and established: recombinant nucleocapsid phosphoprotein (N protein) and spike protein (S protein) of COVID‐19 immobilized on 96‐well plates captured human COVID‐19 antibodies and then banded together with the N/S proteins labeled with europium(III) (Eu3+) chelates, and finally, time‐resolved fluorometry was used to measure the fluorescence values. We successfully established a TRFIA method for the detection of human COVID‐19 total antibodies, and the cutoff value was 2.02. There was no cross‐reactivity with the negative reference of the National Reference Panel for IgM and IgG antibodies to COVID‐19. The CV of the precision assay was 3.19%, and the assay could be stored stably for 15 days at 37°C. Compared with that of the colloidal gold method and chemiluminescence method, the sensitivity of the TRFIA method was higher, and the false positive/negative rate was lower. This established TRFIA has high sensitivity, accuracy, and specificity, which indicates that this method provides a new detection method for the high‐throughput routine diagnosis of COVID‐19.
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Affiliation(s)
- Yunjian Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Cuicui Chen
- Guangzhou Youdi Biotechnology Co., Ltd., Guangzhou, China
| | - Hongrui Lai
- Guangzhou Youdi Biotechnology Co., Ltd., Guangzhou, China
| | - Ying He
- Guangzhou Youdi Biotechnology Co., Ltd., Guangzhou, China
| | - Guiling Guo
- Guangzhou Youdi Biotechnology Co., Ltd., Guangzhou, China
| | - Jianming Feng
- Guangzhou Fenghua Bioengineering Co., Ltd., Guangzhou, China
| | - Laiqing Li
- Guangzhou Youdi Biotechnology Co., Ltd., Guangzhou, China
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Muthumanickam S, Kamaladevi A, Boomi P, Gowrishankar S, Pandian SK. Indian Ethnomedicinal Phytochemicals as Promising Inhibitors of RNA-Binding Domain of SARS-CoV-2 Nucleocapsid Phosphoprotein: An In Silico Study. Front Mol Biosci 2021; 8:637329. [PMID: 34277698 PMCID: PMC8283196 DOI: 10.3389/fmolb.2021.637329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2, an etiological agent of COVID-19, has been the reason for the unexpected global pandemic, causing severe mortality and imposing devastative effects on public health. Despite extensive research work put forward by scientist around globe, so far, no suitable drug or vaccine (safe, affordable, and efficacious) has been identified to treat SARS-CoV-2. As an alternative way of improvising the COVID-19 treatment strategy, that is, strengthening of host immune system, a great deal of attention has been given to phytocompounds from medicinal herbs worldwide. In a similar fashion, the present study deliberately focuses on the phytochemicals of three Indian herbal medicinal plants viz., Mentha arvensis, Coriandrum sativum, and Ocimum sanctum for their efficacy to target well-recognized viral receptor protein through molecular docking and dynamic analyses. Nucleocapsid phosphoprotein (N) of SARS-CoV-2, being a pivotal player in replication, transcription, and viral genome assembly, has been recognized as one of the most attractive viral receptor protein targets for controlling the viral multiplication in the host. Out of 127 phytochemicals screened, nine (linarin, eudesmol, cadinene, geranyl acetate, alpha-thujene, germacrene A, kaempferol-3-O-glucuronide, kaempferide, and baicalin) were found to be phenomenal in terms of exhibiting high binding affinity toward the catalytic pocket of target N-protein. Further, the ADMET prediction analysis unveiled the non-tumorigenic, noncarcinogenic, nontoxic, non-mutagenic, and nonreproductive nature of the identified bioactive molecules. Furthermore, the data of molecular dynamic simulation validated the conformational and dynamic stability of the docked complexes. Concomitantly, the data of the present study validated the anti-COVID efficacy of the bioactives from selected medicinal plants of Indian origin.
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Affiliation(s)
| | - Arumugam Kamaladevi
- Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - Pandi Boomi
- Department of Bioinformatics, Alagappa University, Karaikudi, India
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Azeez SA, Alhashim ZG, Al Otaibi WM, Alsuwat HS, Ibrahim AM, Almandil NB, Borgio JF. State-of-the-art tools to identify druggable protein ligand of SARS-CoV-2. Arch Med Sci 2020; 16:497-507. [PMID: 32399095 PMCID: PMC7212236 DOI: 10.5114/aoms.2020.94046] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The SARS-CoV-2 (previously 2019-nCoV) outbreak in Wuhan, China and other parts of the world affects people and spreads coronavirus disease 2019 (COVID-19) through human-to-human contact, with a mortality rate of > 2%. There are no approved drugs or vaccines yet available against SARS-CoV-2. MATERIAL AND METHODS State-of-the-art tools based on in-silico methods are a cost-effective initial approach for identifying appropriate ligands against SARS-CoV-2. The present study developed the 3D structure of the envelope and nucleocapsid phosphoprotein of SARS-CoV-2, and molecular docking analysis was done against various ligands. RESULTS The highest log octanol/water partition coefficient, high number of hydrogen bond donors and acceptors, lowest non-bonded interaction energy between the receptor and the ligand, and high binding affinity were considered for the best ligand for the envelope (mycophenolic acid: log P = 3.00; DG = -10.2567 kcal/mol; pKi = 7.713 µM) and nucleocapsid phosphoprotein (1-[(2,4-dichlorophenyl)methyl]pyrazole-3,5-dicarboxylic acid: log P = 2.901; DG = -12.2112 kcal/mol; pKi = 7.885 µM) of SARS-CoV-2. CONCLUSIONS The study identifies the most potent compounds against the SARS-CoV-2 envelope and nucleocapsid phosphoprotein through state-of-the-art tools based on an in-silico approach. A combination of these two ligands could be the best option to consider for further detailed studies to develop a drug for treating patients infected with SARS-CoV-2, COVID-19.
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Affiliation(s)
- Sayed Abdul Azeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Zahra Ghalib Alhashim
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Waad Mohammed Al Otaibi
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Hind Saleh Alsuwat
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdallah M. Ibrahim
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Department of Fundamentals of Nursing, College of Nursing, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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