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Alruwaili M, Armstrong S, Prince T, Erdmann M, Matthews DA, Luu L, Davidson A, Aljabr W, Hiscox JA. SARS-CoV-2 NSP12 associates with TRiC and the P323L substitution acts as a host adaption. J Virol 2023; 97:e0042423. [PMID: 37929963 PMCID: PMC10688337 DOI: 10.1128/jvi.00424-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/29/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE SARS-CoV-2 has caused a worldwide health and economic crisis. During the course of the pandemic, genetic changes occurred in the virus, which have resulted in new properties of the virus-particularly around gains in transmission and the ability to partially evade either natural or vaccine-acquired immunity. Some of these viruses have been labeled Variants of Concern (VoCs). At the root of all VoCs are two mutations, one in the viral spike protein that has been very well characterized and the other in the virus polymerase (NSP12). This is the viral protein responsible for replicating the genome. We show that NSP12 associates with host cell proteins that act as a scaffold to facilitate the function of this protein. Furthermore, we found that different variants of NSP12 interact with host cell proteins in subtle and different ways, which affect function.
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Affiliation(s)
- Muhannad Alruwaili
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Medical Laboratory Technology Department, Northern Border University, Arar City, Saudi Arabia
| | - Stuart Armstrong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Maximillian Erdmann
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - David A. Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Lisa Luu
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
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Westphal T, Mader M, Karsten H, Cords L, Knapp M, Schulte S, Hermanussen L, Peine S, Ditt V, Grifoni A, Addo MM, Huber S, Sette A, Lütgehetmann M, Pischke S, Kwok WW, Sidney J, Schulze zur Wiesch J. Evidence for broad cross-reactivity of the SARS-CoV-2 NSP12-directed CD4 + T-cell response with pre-primed responses directed against common cold coronaviruses. Front Immunol 2023; 14:1182504. [PMID: 37215095 PMCID: PMC10196118 DOI: 10.3389/fimmu.2023.1182504] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction The nonstructural protein 12 (NSP12) of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has a high sequence identity with common cold coronaviruses (CCC). Methods Here, we comprehensively assessed the breadth and specificity of the NSP12-specific T-cell response after in vitro T-cell expansion with 185 overlapping 15-mer peptides covering the entire SARS-CoV-2 NSP12 at single-peptide resolution in a cohort of 27 coronavirus disease 2019 (COVID-19) patients. Samples of nine uninfected seronegative individuals, as well as five pre-pandemic controls, were also examined to assess potential cross-reactivity with CCCs. Results Surprisingly, there was a comparable breadth of individual NSP12 peptide-specific CD4+ T-cell responses between COVID-19 patients (mean: 12.82 responses; range: 0-25) and seronegative controls including pre-pandemic samples (mean: 12.71 responses; range: 0-21). However, the NSP12-specific T-cell responses detected in acute COVID-19 patients were on average of a higher magnitude. The most frequently detected CD4+ T-cell peptide specificities in COVID-19 patients were aa236-250 (37%) and aa246-260 (44%), whereas the peptide specificities aa686-700 (50%) and aa741-755 (36%), were the most frequently detected in seronegative controls. In CCC-specific peptide-expanded T-cell cultures of seronegative individuals, the corresponding SARS-CoV-2 NSP12 peptide specificities also elicited responses in vitro. However, the NSP12 peptide-specific CD4+ T-cell response repertoire only partially overlapped in patients analyzed longitudinally before and after a SARS-CoV-2 infection. Discussion The results of the current study indicate the presence of pre-primed, cross-reactive CCC-specific T-cell responses targeting conserved regions of SARS-CoV-2, but they also underline the complexity of the analysis and the limited understanding of the role of the SARS-CoV-2 specific T-cell response and cross-reactivity with the CCCs.
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Affiliation(s)
- Tim Westphal
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Maria Mader
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hendrik Karsten
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leon Cords
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Knapp
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sophia Schulte
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lennart Hermanussen
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vanessa Ditt
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marylyn Martina Addo
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Institute of Infection Research and Vaccine Development, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marc Lütgehetmann
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Pischke
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
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3
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Goldswain H, Dong X, Penrice-Randal R, Alruwaili M, Shawli GT, Prince T, Williamson MK, Raghwani J, Randle N, Jones B, Donovan-Banfield I, Salguero FJ, Tree JA, Hall Y, Hartley C, Erdmann M, Bazire J, Jearanaiwitayakul T, Semple MG, Openshaw PJM, Baillie JK, Emmett SR, Digard P, Matthews DA, Turtle L, Darby AC, Davidson AD, Carroll MW, Hiscox JA; ISARIC4C Investigators. The P323L substitution in the SARS-CoV-2 polymerase ( NSP12) confers a selective advantage during infection. Genome Biol 2023; 24:47. [PMID: 36915185 DOI: 10.1186/s13059-023-02881-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change in the spike protein, associated with an increase in transmissibility. Genomes with D614G are accompanied by a P323L substitution in the viral polymerase (NSP12). However, P323L is not thought to be under strong selective pressure. RESULTS Investigation of P323L/D614G substitutions in the population shows rapid emergence during the containment phase and early surge phase during the first wave. These substitutions emerge from minor genomic variants which become dominant viral genome sequence. This is investigated in vivo and in vitro using SARS-CoV-2 with P323 and D614 in the dominant genome sequence and L323 and G614 in the minor variant population. During infection, there is rapid selection of L323 into the dominant viral genome sequence but not G614. Reverse genetics is used to create two viruses (either P323 or L323) with the same genetic background. L323 shows greater abundance of viral RNA and proteins and a smaller plaque morphology than P323. CONCLUSIONS These data suggest that P323L is an important contribution in the emergence of variants with transmission advantages. Sequence analysis of viral populations suggests it may be possible to predict the emergence of a new variant based on tracking the frequency of minor variant genomes. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.
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Meng W, Guo S, Cao S, Shuda M, Robinson‐McCarthy LR, McCarthy KR, Shuda Y, Paniz Mondolfi AE, Bryce C, Grimes Z, Sordillo EM, Cordon‐Cardo C, Li P, Zhang H, Perlman S, Guo H, Gao S, Chang Y, Moore PS. Development and characterization of a new monoclonal antibody against SARS-CoV-2 NSP12 (RdRp). J Med Virol 2023; 95:e28246. [PMID: 36271490 PMCID: PMC9874566 DOI: 10.1002/jmv.28246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 01/29/2023]
Abstract
SARS-CoV-2 NSP12, the viral RNA-dependent RNA polymerase (RdRp), is required for viral replication and is a therapeutic target to treat COVID-19. To facilitate research on SARS-CoV-2 NSP12 protein, we developed a rat monoclonal antibody (CM12.1) against the NSP12 N-terminus that can facilitate functional studies. Immunoblotting and immunofluorescence assay (IFA) confirmed the specific detection of NSP12 protein by this antibody for cells overexpressing the protein. Although NSP12 is generated from the ORF1ab polyprotein, IFA of human autopsy COVID-19 lung samples revealed NSP12 expression in only a small fraction of lung cells including goblet, club-like, vascular endothelial cells, and a range of immune cells, despite wide-spread tissue expression of spike protein antigen. Similar studies using in vitro infection also generated scant protein detection in cells with established virus replication. These results suggest that NSP12 may have diminished steady-state expression or extensive posttranslation modifications that limit antibody reactivity during SARS-CoV-2 replication.
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Affiliation(s)
- Wen Meng
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Siying Guo
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- School of MedicineTsinghua UniversityBeijingChina
| | - Simon Cao
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Masahiro Shuda
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Lindsey R. Robinson‐McCarthy
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Kevin R. McCarthy
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Center for Vaccine ResearchUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Yoko Shuda
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
| | - Alberto E. Paniz Mondolfi
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Clare Bryce
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Zachary Grimes
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Emilia M. Sordillo
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Carlos Cordon‐Cardo
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Pengfei Li
- Department of Microbiology and ImmunologyUniversity of IowaIowa CityIowaUSA
| | - Hu Zhang
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Stanley Perlman
- Department of Microbiology and ImmunologyUniversity of IowaIowa CityIowaUSA
| | - Haitao Guo
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Shou‐Jiang Gao
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Yuan Chang
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Patrick S. Moore
- Cancer Virology ProgramUniversity of Pittsburgh Medical Center Hillman Cancer CenterPittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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5
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Li A, Zhao K, Zhang B, Hua R, Fang Y, Jiang W, Zhang J, Hui L, Zheng Y, Li Y, Zhu C, Wang PH, Peng K, Xia Y. SARS-CoV-2 NSP12 Protein Is Not an Interferon-β Antagonist. J Virol 2021. [PMID: 34133897 DOI: 10.1128/jvi.00747-21:jvi0074721] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is bringing an unprecedented health crisis to the world. To date, our understanding of the interaction between SARS-CoV-2 and host innate immunity is still limited. Previous studies reported that SARS-CoV-2 nonstructural protein 12 (NSP12) was able to suppress interferon-β (IFN-β) activation in IFN-β promoter luciferase reporter assays, which provided insights into the pathogenesis of COVID-19. In this study, we demonstrated that IFN-β promoter-mediated luciferase activity was reduced during coexpression of NSP12. However, we could show NSP12 did not affect IRF3 or NF-κB activation. Moreover, IFN-β production induced by Sendai virus (SeV) infection or other stimulus was not affected by NSP12 at mRNA or protein level. Additionally, the type I IFN signaling pathway was not affected by NSP12, as demonstrated by the expression of interferon-stimulated genes (ISGs). Further experiments revealed that different experiment systems, including protein tags and plasmid backbones, could affect the readouts of IFN-β promoter luciferase assays. In conclusion, unlike as previously reported, our study showed SARS-CoV-2 NSP12 protein is not an IFN-β antagonist. It also rings the alarm on the general usage of luciferase reporter assays in studying SARS-CoV-2. IMPORTANCE Previous studies investigated the interaction between SARS-CoV-2 viral proteins and interferon signaling and proposed that several SARS-CoV-2 viral proteins, including NSP12, could suppress IFN-β activation. However, most of these results were generated from IFN-β promoter luciferase reporter assay and have not been validated functionally. In our study, we found that, although NSP12 could suppress IFN-β promoter luciferase activity, it showed no inhibitory effect on IFN-β production or its downstream signaling. Further study revealed that contradictory results could be generated from different experiment systems. On one hand, we demonstrated that SARS-CoV-2 NSP12 could not suppress IFN-β signaling. On the other hand, our study suggests that caution needs to be taken with the interpretation of SARS-CoV-2-related luciferase assays.
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Affiliation(s)
- Aixin Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan Universitygrid.49470.3e, Wuhan, Hubei, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan Universitygrid.49470.3e, Wuhan, Hubei, China
| | - Bei Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan Universitygrid.49470.3e, Wuhan, Hubei, China
| | - Rong Hua
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan Universitygrid.49470.3e, Wuhan, Hubei, China
| | - Yujie Fang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wuhui Jiang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan Universitygrid.49470.3e, Wuhan, Hubei, China
| | - Jing Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong Universitygrid.27255.37, Jinan, China
| | - Lixia Hui
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan Universitygrid.49470.3e, Wuhan, Hubei, China
| | - Yingcheng Zheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan Universitygrid.49470.3e, Wuhan, Hubei, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Tongji-Rongcheng Center for Biomedicine, Huazhong University of Science and Technology, Wuhan, China
| | - Chengliang Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan Universitygrid.49470.3e, Wuhan, China
| | - Pei-Hui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong Universitygrid.27255.37, Jinan, China
| | - Ke Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan Universitygrid.49470.3e, Wuhan, Hubei, China
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Li A, Zhao K, Zhang B, Hua R, Fang Y, Jiang W, Zhang J, Hui L, Zheng Y, Li Y, Zhu C, Wang PH, Peng K, Xia Y. SARS-CoV-2 NSP12 Protein Is Not an Interferon-β Antagonist. J Virol 2021; 95:e0074721. [PMID: 34133897 DOI: 10.1128/JVI.00747-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is bringing an unprecedented health crisis to the world. To date, our understanding of the interaction between SARS-CoV-2 and host innate immunity is still limited. Previous studies reported that SARS-CoV-2 nonstructural protein 12 (NSP12) was able to suppress interferon-β (IFN-β) activation in IFN-β promoter luciferase reporter assays, which provided insights into the pathogenesis of COVID-19. In this study, we demonstrated that IFN-β promoter-mediated luciferase activity was reduced during coexpression of NSP12. However, we could show NSP12 did not affect IRF3 or NF-κB activation. Moreover, IFN-β production induced by Sendai virus (SeV) infection or other stimulus was not affected by NSP12 at mRNA or protein level. Additionally, the type I IFN signaling pathway was not affected by NSP12, as demonstrated by the expression of interferon-stimulated genes (ISGs). Further experiments revealed that different experiment systems, including protein tags and plasmid backbones, could affect the readouts of IFN-β promoter luciferase assays. In conclusion, unlike as previously reported, our study showed SARS-CoV-2 NSP12 protein is not an IFN-β antagonist. It also rings the alarm on the general usage of luciferase reporter assays in studying SARS-CoV-2. IMPORTANCE Previous studies investigated the interaction between SARS-CoV-2 viral proteins and interferon signaling and proposed that several SARS-CoV-2 viral proteins, including NSP12, could suppress IFN-β activation. However, most of these results were generated from IFN-β promoter luciferase reporter assay and have not been validated functionally. In our study, we found that, although NSP12 could suppress IFN-β promoter luciferase activity, it showed no inhibitory effect on IFN-β production or its downstream signaling. Further study revealed that contradictory results could be generated from different experiment systems. On one hand, we demonstrated that SARS-CoV-2 NSP12 could not suppress IFN-β signaling. On the other hand, our study suggests that caution needs to be taken with the interpretation of SARS-CoV-2-related luciferase assays.
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7
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Begum F, Srivastava AK, Ray U. Repurposing nonnucleoside antivirals against SARS-CoV2 NSP12 (RNA dependent RNA polymerase): In silico-molecular insight. Biochem Biophys Res Commun 2021; 571:26-31. [PMID: 34303192 PMCID: PMC8282484 DOI: 10.1016/j.bbrc.2021.07.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/24/2021] [Revised: 07/08/2021] [Accepted: 07/14/2021] [Indexed: 01/23/2023]
Abstract
The pandemic of SARS-CoV-2 has necessitated expedited research efforts towards finding potential antiviral targets and drug development measures. While new drug discovery is time consuming, drug repurposing has been a promising area for elaborate virtual screening and identification of existing FDA approved drugs that could possibly be used for targeting against functions of various proteins of SARS-CoV-2 virus. RNA dependent RNA polymerase (RdRp) is an important enzyme for the virus that mediates replication of the viral RNA. Inhibition of RdRp could inhibit viral RNA replication and thus new virus particle production. Here, we screened non-nucleoside antivirals and found three out of them to be strongest in binding to RdRp out of which two retained binding even using molecular dynamic simulations. We propose these two drugs as potential RdRp inhibitors which need further in-depth testing.
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Affiliation(s)
- Feroza Begum
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amit Kumar Srivastava
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Upasana Ray
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C., Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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8
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Srikanth L, Sarma PVGK. Andrographolide binds to spike glycoprotein and RNA-dependent RNA polymerase ( NSP12) of SARS-CoV-2 by in silico approach: a probable molecule in the development of anti-coronaviral drug. J Genet Eng Biotechnol 2021; 19:101. [PMID: 34255214 PMCID: PMC8276218 DOI: 10.1186/s43141-021-00201-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/12/2021] [Accepted: 06/19/2021] [Indexed: 01/03/2023]
Abstract
The SARS-CoV-2 belongs to Coronaviridae family infects host cells by the interaction of its spike glycoprotein and angiotensin-converting enzyme 2 (ACE 2) of host cells. Upon entry, the virus uses its RNA dependent RNA polymerase (NSP12) for transcribing its genome to survive in the cell and spread its infection. The protein sequences of receptor-binding domain (RBD) of spike glycoprotein, and NSP12 exhibits high homology in the family of Coronoviridae and are ideal candidates for the development of anti-coronaviral drugs. In the quest to identify inhibitory molecules against these proteins, we searched several molecules that are present in naturally occurring medicinal plants database. Andrographolide which is largely present in the leaf extracts of Andrographis paniculata (AP) and is known to exhibit antiviral, antibacterial, and stabilizes Th1/Th2/Th17 responses; taking this clue, we used in silico approaches to see the binding of andrographolide to RBD and NSP12 molecules. Our docking results showed very strong affinity of andrographolide to RBD and NSP12 of the SARS-CoV-2 virus with dock scores of -10.3460 for RBD and -10.7313 for NSP12 indicating andrographolide acts as an inhibitor of RBD and NSP12. These unique properties of andrographolide, AP extract, can be tested as anti-coronaviral drug.
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Affiliation(s)
- Lokanathan Srikanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences and University, Tirupati, Andhra Pradesh, 517507, India
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Barakat K, Ahmed M, Tabana Y, Ha M. A 'deep dive' into the SARS-Cov-2 polymerase assembly: identifying novel allosteric sites and analyzing the hydrogen bond networks and correlated dynamics. J Biomol Struct Dyn 2021; 40:9443-9463. [PMID: 34034620 DOI: 10.1080/07391102.2021.1930162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Replication of the SARS-CoV-2 genome is a fundamental step in the virus life cycle and inhibiting the SARS-CoV2 replicase machinery has been proven recently as a promising approach in combating the virus. Despite this recent success, there are still several aspects related to the structure, function and dynamics of the CoV-2 polymerase that still need to be addressed. This includes understanding the dynamicity of the various polymerase subdomains, analyzing the hydrogen bond networks at the active site and at the template entry in the presence of water, studying the binding modes of the nucleotides at the active site, highlighting positions for acceptable nucleotides' substitutions that can be tolerated at different positions within the nascent RNA strand, identifying possible allosteric sites within the polymerase structure and studying their correlated dynamics relative to the catalytic site. Here, we combined various cutting-edge modelling tools with the recently resolved SARS-CoV-2 cryo-EM polymerase structures to fill this gap in knowledge. Our findings provide a detailed analysis of the hydrogen bond networks at various parts of the polymerase structure and suggest possible nucleotides' substitutions that can be tolerated by the polymerase complex. We also report here three 'druggable' allosteric sites within the NSP12 RdRp that can be targeted by small molecule inhibitors. Our correlated motion analysis shows that the dynamics within one of the newly identified sites are linked to the active site, indicating that targeting this site can significantly impact the catalytic activity of the SARS-CoV-2 polymerase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.,Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, Canada
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Minwoo Ha
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
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Singh SK, Upadhyay AK, Reddy MS. Screening of potent drug inhibitors against SARS-CoV-2 RNA polymerase: an in silico approach. 3 Biotech 2021; 11:93. [PMID: 33520579 PMCID: PMC7826501 DOI: 10.1007/s13205-020-02610-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022] Open
Abstract
COVID-19 has emerged as a rapidly escalating serious global health issue, affecting every section of population in a detrimental way. Present situation invigorated researchers to look for potent targets, development as well as repurposing of conventional therapeutic drugs. NSP12, a RNA polymerase, is key player in viral RNA replication and, hence, viral multiplication. In our study, we have screened a battery of FDA-approved drugs against SARS-CoV-2 RNA polymerase using in silico molecular docking approach. Identification of potent inhibitors against SARS-CoV-2 NSP12 (RNA polymerase) were screeened from FDA approved drugs by virtual screening for therapeutic applications in treatment of COVID-19. In this study, virtual screening of 1749 antiviral drugs was executed using AutoDock Vina in PyRx software. Binding affinities between NSP12 and drug molecules were determined using Ligplot+ and PyMOL was used for visualization of docking between interacting residues. Screening of 1749 compounds resulted in 14 compounds that rendered high binding affinity for NSP12 target molecule. Out of 14 compounds, 5 compounds which include 3a (Paritaprevir), 3d (Glecaprevir), 3h (Velpatasvir), 3j (Remdesivir) and 3l (Ribavirin) had a binding affinity of − 10.2 kcal/mol, −9.6 kcal/mol, − 8.5 kcal/mol, − 8.0 kcal/mol and − 6.8 kcal/mol, respectively. Moreover, a number of hydrophobic interactions and hydrogen bonding between these 5 compounds and NSP12 active site were observed. Further, 3l (Ribavirin) was docked with 6M71 and molecular dynamic simulation of the complex was also performed to check the stability of the conformation. In silico analysis postulated the potential of conventional antiviral drugs in treatment of COVID-19. However, these finding may be further supported by experimental data for its possible clinical application in present scenario.
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