1
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Pan R, Li P, Meyerholz DK, Perlman S. Mutations in nonstructural proteins essential for pathogenicity in SARS-CoV-2-infected mice. J Virol 2024:e0058424. [PMID: 38888344 DOI: 10.1128/jvi.00584-24] [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: 03/31/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in substantial morbidity and mortality. The basis of severe disease in humans is difficult to determine without the use of experimental animal models. Mice are resistant to infection with ancestral strains of SARS-CoV-2, although many variants that arose later in the pandemic were able to directly infect mice. In almost all cases, viruses that naturally infected mice or were engineered to enable mouse infection required mouse passage to become virulent. In most cases, changes in structural and nonstructural changes occurred during mouse adaptation. However, the mechanism of increased virulence in mice is not understood. Here, using a recently described strain of mouse-adapted SARS-CoV-2 (rSARS2-MA30N501Y), we engineered a series of recombinant viruses that expressed a subset of the mutations present in rSARS2-MA30N501Y. Mutations were detected in the spike protein and in three nonstructural proteins (nsp4, nsp8, and nsp9). We found that infection of mice with recombinant SARS-CoV-2 expressing only the S protein mutations caused very mild infection. Addition of the mutations in nsp4 and nsp8 was required for complete virulence. Of note, all these recombinant viruses replicated equivalently in cultured cells. The innate immune response was delayed after infection with virulent compared to attenuated viruses. Further, using a lineage tracking system, we found that attenuated virus was highly inhibited in the ability to infect the parenchyma, but not the airway after infection. Together, these results indicate that mutations in both the S protein and nonstructural proteins are required for maximal virulence during mouse adaptation.IMPORTANCEUnderstanding the pathogenesis of coronavirus disease 2019 (COVID-19) requires the study of experimental animals after infection with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). For this purpose, several mouse-adapted SARS-CoV-2 strains have been developed. Here, using a strain of mouse-adapted virus that causes a range of diseases ranging from mild to severe, we show that mutations in both a structural protein [spike (S) protein] and nonstructural proteins are required for maximal virulence. Thus, changes in the S protein, the most widely studied viral protein, while required for mouse adaptation, are not sufficient to result in a virulent virus.
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Affiliation(s)
- Ruangang Pan
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Pengfei Li
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
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2
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Su HH, Lin ES, Huang YH, Lien Y, Huang CY. Inhibition of SARS-CoV-2 Nsp9 ssDNA-Binding Activity and Cytotoxic Effects on H838, H1975, and A549 Human Non-Small Cell Lung Cancer Cells: Exploring the Potential of Nepenthes miranda Leaf Extract for Pulmonary Disease Treatment. Int J Mol Sci 2024; 25:6120. [PMID: 38892307 PMCID: PMC11173125 DOI: 10.3390/ijms25116120] [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: 05/10/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Carnivorous pitcher plants from the genus Nepenthes are renowned for their ethnobotanical uses. This research explores the therapeutic potential of Nepenthes miranda leaf extract against nonstructural protein 9 (Nsp9) of SARS-CoV-2 and in treating human non-small cell lung carcinoma (NSCLC) cell lines. Nsp9, essential for SARS-CoV-2 RNA replication, was expressed and purified, and its interaction with ssDNA was assessed. Initial tests with myricetin and oridonin, known for targeting ssDNA-binding proteins and Nsp9, respectively, did not inhibit the ssDNA-binding activity of Nsp9. Subsequent screenings of various N. miranda extracts identified those using acetone, methanol, and ethanol as particularly effective in disrupting Nsp9's ssDNA-binding activity, as evidenced by electrophoretic mobility shift assays. Molecular docking studies highlighted stigmast-5-en-3-ol and lupenone, major components in the leaf extract of N. miranda, as potential inhibitors. The cytotoxic properties of N. miranda leaf extract were examined across NSCLC lines H1975, A549, and H838, focusing on cell survival, apoptosis, and migration. Results showed a dose-dependent cytotoxic effect in the following order: H1975 > A549 > H838 cells, indicating specificity. Enhanced anticancer effects were observed when the extract was combined with afatinib, suggesting synergistic interactions. Flow cytometry indicated that N. miranda leaf extract could induce G2 cell cycle arrest in H1975 cells, potentially inhibiting cancer cell proliferation. Gas chromatography-mass spectrometry (GC-MS) enabled the tentative identification of the 19 most abundant compounds in the leaf extract of N. miranda. These outcomes underscore the dual utility of N. miranda leaf extract in potentially managing SARS-CoV-2 infection through Nsp9 inhibition and offering anticancer benefits against lung carcinoma. These results significantly broaden the potential medical applications of N. miranda leaf extract, suggesting its use not only in traditional remedies but also as a prospective treatment for pulmonary diseases. Overall, our findings position the leaf extract of N. miranda as a promising source of natural compounds for anticancer therapeutics and antiviral therapies, warranting further investigation into its molecular mechanisms and potential clinical applications.
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Affiliation(s)
- Hsin-Hui Su
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City 717, Taiwan
| | - En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, Taichung City 403, Taiwan
| | - Yen-Hua Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Yi Lien
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung City 402, Taiwan
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3
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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.
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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.
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4
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Aydin J, Gabel A, Zielinski S, Ganskih S, Schmidt N, Hartigan C, Schenone M, Carr S, Munschauer M. SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells. Nucleic Acids Res 2024; 52:e26. [PMID: 38281241 PMCID: PMC10954451 DOI: 10.1093/nar/gkae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNase H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures minimal background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with sequentially mapping interactomes for multiple target RNAs in a single experiment. Using SHIFTR, we comprehensively identify interactions of cis-regulatory elements located at the 5' and 3'-terminal regions of authentic SARS-CoV-2 RNAs in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type and has the potential to revolutionize our understanding of transcriptomes and their regulation.
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Affiliation(s)
- Jens Aydin
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Alexander Gabel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sebastian Zielinski
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Nora Schmidt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | | | - Monica Schenone
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
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5
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Podadera A, Campo L, Rehman F, Kolobaric N, Zutic A, Ng KKS. Optimized Recombinant Expression and Purification of the SARS-CoV-2 Polymerase Complex. Curr Protoc 2024; 4:e1007. [PMID: 38511495 DOI: 10.1002/cpz1.1007] [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] [Indexed: 03/22/2024]
Abstract
An optimized protocol has been developed to express and purify the core RNA-dependent RNA polymerase (RdRP) complex from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The expression and purification of active core SARS-CoV-2 RdRp complex is challenging due to the complex multidomain fold of nsp12, and the assembly of the multimeric complex involving nsp7, nsp8, and nsp12. Our approach adapts a previously published method to express the core SARS-CoV-2 RdRP complex in Escherichia coli and combines it with a procedure to express the nsp12 fusion with maltose-binding protein in insect cells to promote the efficient assembly and purification of an enzymatically active core polymerase complex. The resulting method provides a reliable platform to produce milligram amounts of the polymerase complex with the expected 1:2:1 stoichiometry for nsp7, nsp8, and nsp12, respectively, following the removal of all affinity tags. This approach addresses some of the limitations of previously reported methods to provide a reliable source of the active polymerase complex for structure, function, and inhibition studies of the SARS-CoV-2 RdRP complex using recombinant plasmid constructs that have been deposited in the widely accessible Addgene repository. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Expression and production of SARS-CoV-2 nsp7, nsp8, and nsp12 in E. coli cells Support Protocol: Establishment and maintenance of insect cell cultures Basic Protocol 2: Generation of recombinant baculovirus in Sf9 cells and production of nsp12 fusion protein in T. ni cells Basic Protocol 3: Purification of the SARS-CoV-2 core polymerase complex.
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Affiliation(s)
- Ana Podadera
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Lucas Campo
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Fasih Rehman
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Nikola Kolobaric
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Adriana Zutic
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Kenneth K-S Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
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6
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Korn SM, Sharma S, Steckelberg AL. The ART of RNAylation: covalent RNA-protein linkage in bacteriophage infection. Trends Biochem Sci 2024; 49:97-98. [PMID: 37980188 PMCID: PMC10872422 DOI: 10.1016/j.tibs.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/20/2023]
Abstract
Bacteriophages have been a treasure trove for the discovery of fundamental biological principles and the expansion of our enzymatic toolkit since the dawn of molecular biology. In a recent study by Wolfram-Schauerte et al. these ubiquitous bacteria-infecting viruses reveal yet another new biological concept: post-translational modification through covalent RNA-protein linkages.
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Affiliation(s)
- Sophie M Korn
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sunny Sharma
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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7
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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.
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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
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8
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Mol Cell 2023; 83:3921-3930.e7. [PMID: 37890482 PMCID: PMC10843261 DOI: 10.1016/j.molcel.2023.10.001] [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: 06/07/2023] [Revised: 08/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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9
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Osinski A, Tagliabracci VS. A domain of all trades: The enzymatic versatility of the NiRAN domain. Mol Cell 2023; 83:3758-3760. [PMID: 37922868 DOI: 10.1016/j.molcel.2023.10.009] [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: 10/11/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
The SARS-CoV-2 NiRAN domain is essential for viral replication. Despite adopting a pseudokinase fold, it catalyzes three distinct biochemical reactions from a single active site. In this issue of Molecular Cell, Small et al.1 elucidate the structural intricacies of the NiRAN domain shedding light on the factors that underlie its remarkable versatility.
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Affiliation(s)
- Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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10
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Schmidt N, Ganskih S, Wei Y, Gabel A, Zielinski S, Keshishian H, Lareau CA, Zimmermann L, Makroczyova J, Pearce C, Krey K, Hennig T, Stegmaier S, Moyon L, Horlacher M, Werner S, Aydin J, Olguin-Nava M, Potabattula R, Kibe A, Dölken L, Smyth RP, Caliskan N, Marsico A, Krempl C, Bodem J, Pichlmair A, Carr SA, Chlanda P, Erhard F, Munschauer M. SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9. Cell 2023; 186:4834-4850.e23. [PMID: 37794589 PMCID: PMC10617981 DOI: 10.1016/j.cell.2023.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 07/13/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Regulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection. To characterize host RNA-binding proteins (RBPs) involved in this process, we biochemically identified proteins bound to genomic and subgenomic SARS-CoV-2 RNAs. We find that the host protein SND1 binds the 5' end of negative-sense viral RNA and is required for SARS-CoV-2 RNA synthesis. SND1-depleted cells form smaller replication organelles and display diminished virus growth kinetics. We discover that NSP9, a viral RBP and direct SND1 interaction partner, is covalently linked to the 5' ends of positive- and negative-sense RNAs produced during infection. These linkages occur at replication-transcription initiation sites, consistent with NSP9 priming viral RNA synthesis. Mechanistically, SND1 remodels NSP9 occupancy and alters the covalent linkage of NSP9 to initiating nucleotides in viral RNA. Our findings implicate NSP9 in the initiation of SARS-CoV-2 RNA synthesis and unravel an unsuspected role of a cellular protein in orchestrating viral RNA production.
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Affiliation(s)
- Nora Schmidt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Alexander Gabel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Sebastian Zielinski
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | | | - Caleb A Lareau
- Program in Computational and System Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liv Zimmermann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Karsten Krey
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Sebastian Stegmaier
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lambert Moyon
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Simone Werner
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jens Aydin
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Marco Olguin-Nava
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Ramya Potabattula
- Institute of Human Genetics, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Christine Krempl
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Jochen Bodem
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Andreas Pichlmair
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany; Faculty for Computer and Data Science, University of Regensburg, Regensburg, Germany
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany; Faculty of Medicine, Julius-Maximilians-University Würzburg, Würzburg, Germany.
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11
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait B, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558837. [PMID: 37808858 PMCID: PMC10557602 DOI: 10.1101/2023.09.25.558837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N-terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5'-cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here we determine high-resolution cryo-electron microscopy structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Chemistry and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Present address: University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Lead contact:
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12
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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.
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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
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13
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Gratteri C, Ambrosio FA, Lupia A, Moraca F, Catalanotti B, Costa G, Bellocchi M, Carioti L, Salpini R, Ceccherini-Silberstein F, Frazia SL, Malagnino V, Sarmati L, Svicher V, Bryant S, Artese A, Alcaro S. Molecular and Structural Aspects of Clinically Relevant Mutations of SARS-CoV-2 RNA-Dependent RNA Polymerase in Remdesivir-Treated Patients. Pharmaceuticals (Basel) 2023; 16:1143. [PMID: 37631058 PMCID: PMC10459223 DOI: 10.3390/ph16081143] [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: 07/13/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Background: SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target to fight COVID-19, and many RdRp inhibitors nucleotide/nucleoside analogs, such as remdesivir, have been identified or are in clinical studies. However, the appearance of resistant mutations could reduce their efficacy. In the present work, we structurally evaluated the impact of RdRp mutations found at baseline in 39 patients treated with remdesivir and associated with a different degree of antiviral response in vivo. (2) Methods: A refined bioinformatics approach was applied to assign SARS-CoV-2 clade and lineage, and to define RdRp mutational profiles. In line with such a method, the same mutations were built and analyzed by combining docking and thermodynamics evaluations with both molecular dynamics and representative pharmacophore models. (3) Results: Clinical studies revealed that patients bearing the most prevalent triple mutant P323L+671S+M899I, which was present in 41% of patients, or the more complex mutational profile P323L+G671S+L838I+D738Y+K91E, which was found with a prevalence of 2.6%, showed a delayed reduced response to remdesivir, as confirmed by the increase in SARS-CoV-2 viral load and by a reduced theoretical binding affinity versus RdRp (ΔGbindWT = -122.70 kcal/mol; ΔGbindP323L+671S+M899I = -84.78 kcal/mol; ΔGbindP323L+G671S+L838I+D738Y+K91E = -96.74 kcal/mol). Combined computational approaches helped to rationalize such clinical observations, offering a mechanistic understanding of the allosteric effects of mutants on the global motions of the viral RNA synthesis machine and in the changes of the interactions patterns of remdesivir during its binding.
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Affiliation(s)
- Carmen Gratteri
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
| | - Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy;
| | - Antonio Lupia
- Dipartimento di Scienze della vita e dell’ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy;
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Federica Moraca
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Bruno Catalanotti
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Maria Bellocchi
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Luca Carioti
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Romina Salpini
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Francesca Ceccherini-Silberstein
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Simone La Frazia
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Vincenzo Malagnino
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Loredana Sarmati
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Valentina Svicher
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Sharon Bryant
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, 1070 Vienna, Austria;
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
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14
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Štefek M, Chalupská D, Chalupský K, Zgarbová M, Dvořáková A, Krafčíková P, Li ASM, Šála M, Dejmek M, Otava T, Chaloupecká E, Kozák J, Kozic J, Vedadi M, Weber J, Mertlíková-Kaiserová H, Nencka R. Rational Design of Highly Potent SARS-CoV-2 nsp14 Methyltransferase Inhibitors. ACS OMEGA 2023; 8:27410-27418. [PMID: 37546609 PMCID: PMC10398685 DOI: 10.1021/acsomega.3c02815] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023]
Abstract
The search for new drugs against COVID-19 and its causative agent, SARS-CoV-2, is one of the major trends in the current medicinal chemistry. Targeting capping machinery could be one of the therapeutic concepts based on a unique mechanism of action. Viral RNA cap synthesis involves two methylation steps, the first of which is mediated by the nsp14 protein. Here, we rationally designed and synthesized a series of compounds capable of binding to both the S-adenosyl-l-methionine and the RNA-binding site of SARS-CoV-2 nsp14 N7-methyltransferase. These hybrid molecules showed excellent potency, high selectivity toward various human methyltransferases, nontoxicity, and high cell permeability. Despite the outstanding activity against the enzyme, our compounds showed poor antiviral performance in vitro. This suggests that the activity of this viral methyltransferase has no significant effect on virus transcription and replication at the cellular level. Therefore, our compounds represent unique tools to further explore the role of the SARS-CoV-2 nsp14 methyltransferase in the viral life cycle and the pathogenesis of COVID-19.
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Affiliation(s)
- Milan Štefek
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Dominika Chalupská
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Karel Chalupský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Michala Zgarbová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Alexandra Dvořáková
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Petra Krafčíková
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Alice Shi Ming Li
- Department
of Pharmacology and Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Milan Dejmek
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Tomáš Otava
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Ema Chaloupecká
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Jaroslav Kozák
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Ján Kozic
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Masoud Vedadi
- Department
of Pharmacology and Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
- QBI
COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
| | - Jan Weber
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
| | - Radim Nencka
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí
2, Prague 6 166 10, Czech Republic
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15
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Slanina H, Madhugiri R, Wenk K, Reinke T, Schultheiß K, Schultheis J, Karl N, Linne U, Ziebuhr J. Conserved Characteristics of NMPylation Activities of Alpha- and Betacoronavirus NiRAN Domains. J Virol 2023; 97:e0046523. [PMID: 37199624 PMCID: PMC10308930 DOI: 10.1128/jvi.00465-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Coronavirus genome replication and expression are mediated by the viral replication-transcription complex (RTC) which is assembled from multiple nonstructural proteins (nsp). Among these, nsp12 represents the central functional subunit. It harbors the RNA-directed RNA polymerase (RdRp) domain and contains, at its N terminus, an additional domain called NiRAN which is widely conserved in coronaviruses and other nidoviruses. In this study, we produced bacterially expressed coronavirus nsp12s to investigate and compare NiRAN-mediated NMPylation activities from representative alpha- and betacoronaviruses. We found that the four coronavirus NiRAN domains characterized to date have a number of conserved properties, including (i) robust nsp9-specific NMPylation activities that appear to operate largely independently of the C-terminal RdRp domain, (ii) nucleotide substrate preference for UTP followed by ATP and other nucleotides, (iii) dependence on divalent metal ions, with Mn2+ being preferred over Mg2+, and (iv) a key role of N-terminal residues (particularly Asn2) of nsp9 for efficient formation of a covalent phosphoramidate bond between NMP and the N-terminal amino group of nsp9. In this context, a mutational analysis confirmed the conservation and critical role of Asn2 across different subfamilies of the family Coronaviridae, as shown by studies using chimeric coronavirus nsp9 variants in which six N-terminal residues were replaced with those from other corona-, pito- and letovirus nsp9 homologs. The combined data of this and previous studies reveal a remarkable degree of conservation among coronavirus NiRAN-mediated NMPylation activities, supporting a key role of this enzymatic activity in viral RNA synthesis and processing. IMPORTANCE There is strong evidence that coronaviruses and other large nidoviruses evolved a number of unique enzymatic activities, including an additional RdRp-associated NiRAN domain, that are conserved in nidoviruses but not in most other RNA viruses. Previous studies of the NiRAN domain mainly focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and suggested different functions for this domain, such as NMPylation/RNAylation of nsp9, RNA guanylyltransferase activities involved in canonical and/or unconventional RNA capping pathways, and other functions. To help resolve partly conflicting information on substrate specificities and metal ion requirements reported previously for the SARS-CoV-2 NiRAN NMPylation activity, we extended these earlier studies by characterizing representative alpha- and betacoronavirus NiRAN domains. The study revealed that key features of NiRAN-mediated NMPylation activities, such as protein and nucleotide specificity and metal ion requirements, are very well conserved among genetically divergent coronaviruses, suggesting potential avenues for future antiviral drug development targeting this essential viral enzyme.
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Affiliation(s)
- Heiko Slanina
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | | | - Kai Wenk
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Tess Reinke
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Karin Schultheiß
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Julia Schultheis
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Nadja Karl
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility, Department of Chemistry, Philipps University, Marburg, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
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16
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Li G, Hilgenfeld R, Whitley R, De Clercq E. Therapeutic strategies for COVID-19: progress and lessons learned. Nat Rev Drug Discov 2023; 22:449-475. [PMID: 37076602 PMCID: PMC10113999 DOI: 10.1038/s41573-023-00672-y] [Citation(s) in RCA: 127] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2023] [Indexed: 04/21/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has stimulated tremendous efforts to develop therapeutic strategies that target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or human proteins to control viral infection, encompassing hundreds of potential drugs and thousands of patients in clinical trials. So far, a few small-molecule antiviral drugs (nirmatrelvir-ritonavir, remdesivir and molnupiravir) and 11 monoclonal antibodies have been marketed for the treatment of COVID-19, mostly requiring administration within 10 days of symptom onset. In addition, hospitalized patients with severe or critical COVID-19 may benefit from treatment with previously approved immunomodulatory drugs, including glucocorticoids such as dexamethasone, cytokine antagonists such as tocilizumab and Janus kinase inhibitors such as baricitinib. Here, we summarize progress with COVID-19 drug discovery, based on accumulated findings since the pandemic began and a comprehensive list of clinical and preclinical inhibitors with anti-coronavirus activities. We also discuss the lessons learned from COVID-19 and other infectious diseases with regard to drug repurposing strategies, pan-coronavirus drug targets, in vitro assays and animal models, and platform trial design for the development of therapeutics to tackle COVID-19, long COVID and pathogenic coronaviruses in future outbreaks.
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Affiliation(s)
- Guangdi Li
- Xiangya School of Public Health, Central South University; Hunan Children's Hospital, Changsha, China.
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine & German Center for Infection Research (DZIF), University of Lübeck, Lübeck, Germany.
| | - Richard Whitley
- Department of Paediatrics, Microbiology, Medicine and Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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17
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Pon A, Osinski A, Sreelatha A. Redefining pseudokinases: A look at the untapped enzymatic potential of pseudokinases. IUBMB Life 2023; 75:370-376. [PMID: 36602414 PMCID: PMC10050101 DOI: 10.1002/iub.2698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/19/2022] [Indexed: 01/06/2023]
Abstract
Catalytically inactive kinases, known as pseudokinases, are conserved in all three domains of life. Due to the lack of catalytic residues, pseudokinases are considered to act as allosteric regulators and scaffolding proteins with no enzymatic function. However, since these "dead" kinases are conserved along with their active counterparts, a role for pseudokinases may have been overlooked. In this review, we will discuss the recently characterized pseudokinases Selenoprotein O, Legionella effector SidJ, and the SARS-CoV2 protein nsp12 which catalyze AMPylation, glutamylation, and RNAylation, respectively. These studies provide structural and mechanistic insight into the versatility and diversity of the kinase fold.
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Affiliation(s)
- Alex Pon
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Anju Sreelatha
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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18
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Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
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19
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Severe acute respiratory syndrome coronaviruses contributing to mitochondrial dysfunction: Implications for post-COVID complications. Mitochondrion 2023; 69:43-56. [PMID: 36690315 PMCID: PMC9854144 DOI: 10.1016/j.mito.2023.01.005] [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: 07/09/2022] [Revised: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/21/2023]
Abstract
Mitochondria play a central role in oxidative phosphorylation (OXPHOS), bioenergetics linked with ATP production, fatty acids biosynthesis, calcium signaling, cell cycle regulation, apoptosis, and innate immune response. Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection manipulates the host cellular machinery for its survival and replication in the host cell. The infectiaon causes perturbed the cellular metabolism that favours viral replication leading to mitochondrial dysfunction and chronic inflammation. By localizing to the mitochondria, SARS CoV proteins increase reactive oxygen species (ROS) levels, perturbation of Ca2+ signaling, changes in mtDNA copy number, mitochondrial membrane potential (MMP), mitochondrial mass, and induction of mitophagy. These proteins also influence the fusion and fission kinetics, size, structure, and distribution of mitochondria in the infected host cells. This results in compromised bioenergetics, altered metabolism, and innate immune signaling, and hence can be a key player in determining the outcome of SARS-CoV infection. SARS-CoV infection contributes to stress and activates apoptotic pathways. This review summarizes how mitochondrial function and dynamics are affected by SARS-CoV and how the mitochondria-SARS-CoV interaction benefits viral survival and growth by evading innate host immunity. We also highlight how the SARS-CoV-mediated mitochondrial dysfunction contributes to post-COVID complications. Besides, a discussion on targeting virus-mitochondria interactions as a therapeutic strategy is presented.
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20
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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.
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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
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21
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Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 PMCID: PMC9957694 DOI: 10.1186/s12985-023-01998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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22
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Shannon A, Canard B. Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2. Antiviral Res 2023; 210:105501. [PMID: 36567022 PMCID: PMC9773703 DOI: 10.1016/j.antiviral.2022.105501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase for incorporation into the viral RNA genome. Incorporated analogues can either 'kill' (terminate) synthesis, or 'corrupt' (genetically or chemically) the RNA. Against coronaviruses, the use of NAs has been further complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities. Here, we describe the mechanism of action of four promising anti-COVID-19 NAs; remdesivir, molnupiravir, favipiravir and bemnifosbuvir. Their distinct mechanisms of action best exemplify the concept of 'killers' and 'corruptors'. We review available data regarding their ability to be incorporated and excised, and discuss the specific structural features that dictate their overall potency, toxicity, and mutagenic potential. This should guide the synthesis of novel analogues, lend insight into the potential for resistance mutations, and provide a rational basis for upcoming combinations therapies.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.
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23
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Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Götte M, Chait BT, Campbell EA, Darst SA. Structural basis for substrate selection by the SARS-CoV-2 replicase. Nature 2023; 614:781-787. [PMID: 36725929 PMCID: PMC9891196 DOI: 10.1038/s41586-022-05664-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/15/2022] [Indexed: 02/03/2023]
Abstract
The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC)1. Accordingly, the RTC is a target for clinically approved antiviral nucleoside analogues, including remdesivir2. Faithful synthesis of viral RNAs by the RTC requires recognition of the correct nucleotide triphosphate (NTP) for incorporation into the nascent RNA. To be effective inhibitors, antiviral nucleoside analogues must compete with the natural NTPs for incorporation. How the SARS-CoV-2 RTC discriminates between the natural NTPs, and how antiviral nucleoside analogues compete, has not been discerned in detail. Here, we use cryogenic-electron microscopy to visualize the RTC bound to each of the natural NTPs in states poised for incorporation. Furthermore, we investigate the RTC with the active metabolite of remdesivir, remdesivir triphosphate (RDV-TP), highlighting the structural basis for the selective incorporation of RDV-TP over its natural counterpart adenosine triphosphate3,4. Our results explain the suite of interactions required for NTP recognition, informing the rational design of antivirals. Our analysis also yields insights into nucleotide recognition by the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase), an enigmatic catalytic domain essential for viral propagation5. The NiRAN selectively binds guanosine triphosphate, strengthening proposals for the role of this domain in the formation of the 5' RNA cap6.
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Affiliation(s)
- Brandon F Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | | | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Hery W Lee
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | | | - Joy Y Feng
- Gilead Sciences, Inc., Foster City, CA, USA
| | | | - Honkit Ng
- The Evelyn Gruss Lipper Cryo-Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Johanna Sotiris
- The Evelyn Gruss Lipper Cryo-Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Mark Ebrahim
- The Evelyn Gruss Lipper Cryo-Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Eugene Y D Chua
- National Center for Cryo-EM Access and Training, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H Mendez
- National Center for Cryo-EM Access and Training, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Ed T Eng
- National Center for Cryo-EM Access and Training, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
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24
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Nitin S, Srinivasa R. B, Monica MS, Thyago H. C. Incursions by severe acute respiratory syndrome coronavirus-2 on the host anti-viral immunity during mild, moderate, and severe coronavirus disease 2019 disease. EXPLORATION OF MEDICINE 2022. [DOI: 10.37349/ei.2022.00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in the human host can lead to various clinical manifestations, from symptomless carriers to mild to moderate to severe/critical illness. Therefore, the clinical classification of SARS-CoV-2 disease, based on severity, is a reliable way to predict disease states in SARS-CoV-2 infection. Recent studies on genomics, transcriptomics, epigenomics, and immunogenomics, along with spatial analysis of immune cells have delineated and defined the categorization of these disease groups using these high throughout technologies. These technologies hold the promise of providing not only a detailed but a holistic view of SARS-CoV-2-led pathogenesis. The main genomic, cellular, and immunologic features of each disease category, and what separates them spatially and molecularly are discussed in this brief review to provide a foundational spatial understanding of SARS-CoV-2 immunopathogenesis.
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Affiliation(s)
- Saksena Nitin
- Institute for Health and Sport, Victoria University, Footscray Campus, Melbourne VIC. 3011, Australia; Aegros Therapeutics Pty Ltd, Macquarie Park, Sydney 2019, Australia
| | - Bonam Srinivasa R.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Miranda-Saksena Monica
- Westmead Institute of Medical Research (WIMR), Herpes Virus Laboratory, Sydney 2145, Australia
| | - Cardoso Thyago H.
- OMICS Centre of Excellence, G42 Healthcare, Mazdar City, Abu Dhabi 3079, United Arab Emirates
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25
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Anderson ML, McDonald Esstman S. In vitro particle-associated uridyltransferase activity of the rotavirus VP1 polymerase. Virology 2022; 577:24-31. [PMID: 36257129 PMCID: PMC10728782 DOI: 10.1016/j.virol.2022.09.015] [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: 08/29/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
Rotaviruses are 11-segmented, double-stranded RNA (dsRNA) viruses with a unique intra-particle RNA synthesis mechanism. During genome replication, the RNA-dependent RNA polymerase (VP1) performs minus-strand RNA (-ssRNA) synthesis on positive-strand RNA (+ssRNA) templates to create dsRNA segments. Recombinant VP1 catalyzes -ssRNA synthesis using substrate NTPs in vitro, but only when the VP2 core shell protein or virus-like particles made of VP2 and VP6 (2/6-VLPs) are included in the reaction. The dsRNA product can be labeled using [α32P]-UTP and separated from the input +ssRNA template by polyacrylamide gel electrophoresis. Here, we report the generation of [α32P]-labeled rotavirus +ssRNA templates in reactions that lacked non-radiolabeled NTPs but contained catalytically-active VP1, 2/6-VLPs, and [α32P]-UTP. Non-radiolabeled UTP competed with [α32P]-UTP to decrease product levels, whereas CTP and GTP had little effect. Interesting, ATP stimulated [α32P]-labeled product production. These results suggest that rotavirus VP1 transferred [α32P]-UMP onto viral + ssRNA in vitro via a particle-associated uridyltransferase activity.
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26
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Focus on Marine Animal Safety and Marine Bioresources in Response to the SARS-CoV-2 Crisis. Int J Mol Sci 2022; 23:ijms232315136. [PMID: 36499463 PMCID: PMC9737530 DOI: 10.3390/ijms232315136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2 as a zoonotic virus has significantly affected daily life and social behavior since its outbreak in late 2019. The concerns over its transmission through different media directly or indirectly have evoked great attention about the survival of SARS-CoV-2 virions in the environment and its potential infection of other animals. To evaluate the risk of infection by SARS-CoV-2 and to counteract the COVID-19 disease, extensive studies have been performed to understand SARS-CoV-2 biogenesis and its pathogenesis. This review mainly focuses on the molecular architecture of SARS-CoV-2, its potential for infecting marine animals, and the prospect of drug discovery using marine natural products to combat SARS-CoV-2. The main purposes of this review are to piece together progress in SARS-CoV-2 functional genomic studies and antiviral drug development, and to raise our awareness of marine animal safety on exposure to SARS-CoV-2.
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27
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A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors. Cell 2022; 185:4347-4360.e17. [PMID: 36335936 PMCID: PMC9531661 DOI: 10.1016/j.cell.2022.09.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/01/2022] [Accepted: 09/27/2022] [Indexed: 01/26/2023]
Abstract
Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs.
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28
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Sheetz JB, Lemmon MA. Looking lively: emerging principles of pseudokinase signaling. Trends Biochem Sci 2022; 47:875-891. [PMID: 35585008 PMCID: PMC9464697 DOI: 10.1016/j.tibs.2022.04.011] [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: 01/28/2022] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
Progress towards understanding catalytically 'dead' protein kinases - pseudokinases - in biology and disease has hastened over the past decade. An especially lively area for structural biology, pseudokinases appear to be strikingly similar to their kinase relatives, despite lacking key catalytic residues. Distinct active- and inactive-like conformation states, which are crucial for regulating bona fide protein kinases, are conserved in pseudokinases and appear to be essential for function. We discuss recent structural data on conformational transitions and nucleotide binding by pseudokinases, from which some common principles emerge. In both pseudokinases and bona fide kinases, a conformational toggle appears to control the ability to interact with signaling effectors. We also discuss how biasing this conformational toggle may provide opportunities to target pseudokinases pharmacologically in disease.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
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29
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Low ZY, Zabidi NZ, Yip AJW, Puniyamurti A, Chow VTK, Lal SK. SARS-CoV-2 Non-Structural Proteins and Their Roles in Host Immune Evasion. Viruses 2022; 14:v14091991. [PMID: 36146796 PMCID: PMC9506350 DOI: 10.3390/v14091991] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 12/02/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has caused an unprecedented global crisis and continues to threaten public health. The etiological agent of this devastating pandemic outbreak is the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). COVID-19 is characterized by delayed immune responses, followed by exaggerated inflammatory responses. It is well-established that the interferon (IFN) and JAK/STAT signaling pathways constitute the first line of defense against viral and bacterial infections. To achieve viral replication, numerous viruses are able to antagonize or hijack these signaling pathways to attain productive infection, including SARS-CoV-2. Multiple studies document the roles of several non-structural proteins (NSPs) of SARS-CoV-2 that facilitate the establishment of viral replication in host cells via immune escape. In this review, we summarize and highlight the functions and characteristics of SARS-CoV-2 NSPs that confer host immune evasion. The molecular mechanisms mediating immune evasion and the related potential therapeutic strategies for controlling the COVID-19 pandemic are also discussed.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Nur Zawanah Zabidi
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Ashwini Puniyamurti
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Vincent T. K. Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore 117545, Singapore
- Correspondence: (V.T.K.C.); (S.K.L.)
| | - Sunil K. Lal
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Malaysia
- Correspondence: (V.T.K.C.); (S.K.L.)
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30
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Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. The mechanism of RNA capping by SARS-CoV-2. Nature 2022; 609:793-800. [PMID: 35944563 PMCID: PMC9492545 DOI: 10.1038/s41586-022-05185-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
The RNA genome of SARS-CoV-2 contains a 5′ cap that facilitates the translation of viral proteins, protection from exonucleases and evasion of the host immune response1–4. How this cap is made in SARS-CoV-2 is not completely understood. Here we reconstitute the N7- and 2′-O-methylated SARS-CoV-2 RNA cap (7MeGpppA2′-O-Me) using virally encoded non-structural proteins (nsps). We show that the kinase-like nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain5 of nsp12 transfers the RNA to the amino terminus of nsp9, forming a covalent RNA–protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers the RNA to GDP, forming the core cap structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication–transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N terminus of nsp9 and the kinase-like active-site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19. Reconstitution of the SARS-CoV-2 RNA 5′ cap reveals the unconventional mechanism by which SARS-CoV-2 caps its RNA genome, providing a new target in the development of antiviral agents to treat COVID-19.
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Affiliation(s)
- Gina J Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abir Majumdar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA. .,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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31
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Proteolytic Processing of the Coronavirus Replicase Nonstructural Protein 14 Exonuclease Is Not Required for Virus Replication but Alters RNA Synthesis and Viral Fitness. J Virol 2022; 96:e0084122. [PMID: 35924922 PMCID: PMC9400476 DOI: 10.1128/jvi.00841-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coronaviruses (CoVs) initiate replication by translation of the positive-sense RNA genome into the replicase polyproteins connecting 16 nonstructural protein domains (nsp1-16), which are subsequently processed by viral proteases to yield mature nsp. For the betacoronavirus murine hepatitis virus (MHV), total inhibition of translation or proteolytic processing of replicase polyproteins results in rapid cessation of RNA synthesis. The nsp5-3CLpro (Mpro) processes nsps7-16, which assemble into functional replication-transcription complexes (RTCs), including the enzymatic nsp12-RdRp and nsp14-exoribonuclease (ExoN)/N7-methyltransferase. The nsp14-ExoN activity mediates RNA-dependent RNA proofreading, high-fidelity RNA synthesis, and replication. To date, the solved partial RTC structures, biochemistry, and models use or assume completely processed, mature nsp. Here, we demonstrate that in MHV, engineered deletion of the cleavage sites between nsp13-14 and nsp14-15 allowed recovery of replication-competent virus. Compared to wild-type (WT) MHV, the nsp13-14 and nsp14-15 cleavage deletion mutants demonstrated delayed replication kinetics, impaired genome production, altered abundance and patterns of recombination, and impaired competitive fitness. Further, the nsp13-14 and nsp14-15 mutant viruses demonstrated mutation frequencies that were significantly higher than with the WT. The results demonstrate that cleavage of nsp13-14 or nsp14-15 is not required for MHV viability and that functions of the RTC/nsp14-ExoN are impaired when assembled with noncleaved intermediates. These data will inform future genetic, structural, biochemical, and modeling studies of coronavirus RTCs and nsp 13, 14, and 15 and may reveal new approaches for inhibition or attenuation of CoV infection. IMPORTANCE Coronavirus replication requires proteolytic maturation of the nonstructural replicase proteins to form the replication-transcription complex. Coronavirus replication-transcription complex models assume mature subunits; however, mechanisms of coronavirus maturation and replicase complex formation have yet to be defined. Here, we show that for the coronavirus murine hepatitis virus, cleavage between the nonstructural replicase proteins nsp13-14 and nsp14-15 is not required for replication but does alter RNA synthesis and recombination. These results shed new light on the requirements for coronavirus maturation and replication-transcription complex assembly, and they may reveal novel therapeutic targets and strategies for attenuation.
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Jin Y, Ouyang M, Yu T, Zhuang J, Wang W, Liu X, Duan F, Guo D, Peng X, Pan JA. Genome-Wide Analysis of the Indispensable Role of Non-structural Proteins in the Replication of SARS-CoV-2. Front Microbiol 2022; 13:907422. [PMID: 35722274 PMCID: PMC9198553 DOI: 10.3389/fmicb.2022.907422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022] Open
Abstract
Understanding the process of replication and transcription of SARS-CoV-2 is essential for antiviral strategy development. The replicase polyprotein is indispensable for viral replication. However, whether all nsps derived from the replicase polyprotein of SARS-CoV-2 are indispensable is not fully understood. In this study, we utilized the SARS-CoV-2 replicon as the system to investigate the role of each nsp in viral replication. We found that except for nsp16, all the nsp deletions drastically impair the replication of the replicon, and nsp14 could recover the replication deficiency caused by its deletion in the viral replicon. Due to the unsuccessful expressions of nsp1, nsp3, and nsp16, we could not draw a conclusion about their in trans-rescue functions. Our study provided a new angle to understand the role of each nsp in viral replication and transcription, helping the evaluation of nsps as the target for antiviral drug development.
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Affiliation(s)
- Yunyun Jin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Muzi Ouyang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ting Yu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Jiaxin Zhuang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Wenhao Wang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xue Liu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Fangfang Duan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Deyin Guo
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xiaoxue Peng
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
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Lou Z, Rao Z. The Life of SARS-CoV-2 Inside Cells: Replication-Transcription Complex Assembly and Function. Annu Rev Biochem 2022; 91:381-401. [PMID: 35729072 DOI: 10.1146/annurev-biochem-052521-115653] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The persistence of the coronavirus disease 2019 (COVID-19) pandemic has resulted in increasingly disruptive impacts, and it has become the most devastating challenge to global health in a century. The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants challenges the currently available therapeutics for clinical application. Nonstructural proteins (also known as replicase proteins) with versatile biological functions play central roles in viral replication and transcription inside the host cells, and they are the most conserved target proteins among the SARS-CoV-2 variants. Specifically, they constitute the replication-transcription complexes (RTCs) dominating the synthesis of viral RNA. Knowledge of themolecular mechanisms of nonstructural proteins and their assembly into RTCs will benefit the development of antivirals targeting them against existing or potentially emerging variants. In this review, we summarize current knowledge of the structures and functions of coronavirus nonstructural proteins as well as the assembly and functions of RTCs in the life cycle of the virus.
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Affiliation(s)
- Zhiyong Lou
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; ,
| | - Zihe Rao
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; , .,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,School of Life Sciences, Tsinghua University, Beijing, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Guangzhou Laboratory, Guangzhou, China
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Herbert A, Poptsova M. Z-RNA and the Flipside of the SARS Nsp13 Helicase: Is There a Role for Flipons in Coronavirus-Induced Pathology? Front Immunol 2022; 13:912717. [PMID: 35784331 PMCID: PMC9247175 DOI: 10.3389/fimmu.2022.912717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022] Open
Abstract
We present evidence suggesting that the severe acute respiratory syndrome (SARS) coronavirus non-structural protein 13 (Nsp13) modulates the Z-RNA dependent regulated cell death pathways . We show that Z-prone sequences [called flipons] exist in coronavirus and provide a signature (Z-sig) that enables identification of the animal viruses from which the human pathogens arose. We also identify a potential RIP Homology Interaction Motif (RHIM) in the helicase Nsp13 that resembles those present in proteins that initiate Z-RNA-dependent cell death through interactions with the Z-RNA sensor protein ZBP1. These two observations allow us to suggest a model in which Nsp13 down regulates Z-RNA activated innate immunity by two distinct mechanisms. The first involves a novel ATP-independent Z-flipon helicase (flipase) activity in Nsp13 that differs from that of canonical A-RNA helicases. This flipase prevents formation of Z-RNAs that would otherwise activate cell death pathways. The second mechanism likely inhibits the interactions between ZBP1 and the Receptor Interacting Proteins Kinases RIPK1 and RIPK3 by targeting their RHIM domains. Together the described Nsp13 RHIM and flipase activities have the potential to alter the host response to coronaviruses and impact the design of drugs targeting the Nsp13 protein. The Z-sig and RHIM domains may provide a way of identifying previously uncharacterized viruses that are potentially pathogenic for humans.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, Discovery, Charlestown, MA, United States
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
- *Correspondence: Alan Herbert,
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
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Kung YA, Lee KM, Chiang HJ, Huang SY, Wu CJ, Shih SR. Molecular Virology of SARS-CoV-2 and Related Coronaviruses. Microbiol Mol Biol Rev 2022; 86:e0002621. [PMID: 35343760 PMCID: PMC9199417 DOI: 10.1128/mmbr.00026-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. Although several COVID-19 vaccines are currently being administered, none of them is 100% effective. Moreover, SARS-CoV-2 variants remain an important worldwide public health issue. Hence, the accelerated development of efficacious antiviral agents is urgently needed. Coronavirus depends on various host cell factors for replication. An ongoing research objective is the identification of host factors that could be exploited as targets for drugs and compounds effective against SARS-CoV-2. In the present review, we discuss the molecular mechanisms of SARS-CoV-2 and related coronaviruses, focusing on the host factors or pathways involved in SARS-CoV-2 replication that have been identified by genome-wide CRISPR screening.
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Affiliation(s)
- Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Huan-Jung Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sheng-Yu Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Jung Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
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Wang B, Svetlov D, Bartikofsky D, Wobus CE, Artsimovitch I. Going Retro, Going Viral: Experiences and Lessons in Drug Discovery from COVID-19. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123815. [PMID: 35744940 PMCID: PMC9228142 DOI: 10.3390/molecules27123815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
The severity of the COVID-19 pandemic and the pace of its global spread have motivated researchers to opt for repurposing existing drugs against SARS-CoV-2 rather than discover or develop novel ones. For reasons of speed, throughput, and cost-effectiveness, virtual screening campaigns, relying heavily on in silico docking, have dominated published reports. A particular focus as a drug target has been the principal active site (i.e., RNA synthesis) of RNA-dependent RNA polymerase (RdRp), despite the existence of a second, and also indispensable, active site in the same enzyme. Here we report the results of our experimental interrogation of several small-molecule inhibitors, including natural products proposed to be effective by in silico studies. Notably, we find that two antibiotics in clinical use, fidaxomicin and rifabutin, inhibit RNA synthesis by SARS-CoV-2 RdRp in vitro and inhibit viral replication in cell culture. However, our mutagenesis studies contradict the binding sites predicted computationally. We discuss the implications of these and other findings for computational studies predicting the binding of ligands to large and flexible protein complexes and therefore for drug discovery or repurposing efforts utilizing such studies. Finally, we suggest several improvements on such efforts ongoing against SARS-CoV-2 and future pathogens as they arise.
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Affiliation(s)
- Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | | | - Dylan Bartikofsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; (D.B.); (C.E.W.)
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; (D.B.); (C.E.W.)
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
- Correspondence:
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Newly Emerged Antiviral Strategies for SARS-CoV-2: From Deciphering Viral Protein Structural Function to the Development of Vaccines, Antibodies, and Small Molecules. Int J Mol Sci 2022; 23:ijms23116083. [PMID: 35682761 PMCID: PMC9181103 DOI: 10.3390/ijms23116083] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 01/09/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become the most severe health crisis, causing extraordinary economic disruption worldwide. SARS-CoV-2 is a single-stranded RNA-enveloped virus. The process of viral replication and particle packaging is finished in host cells. Viral proteins, including both structural and nonstructural proteins, play important roles in the viral life cycle, which also provides the targets of treatment. Therefore, a better understanding of the structural function of virus proteins is crucial to speed up the development of vaccines and therapeutic strategies. Currently, the structure and function of proteins encoded by the SARS-CoV-2 genome are reviewed by several studies. However, most of them are based on the analysis of SARS-CoV-1 particles, lacking a systematic review update for SARS-CoV-2. Here, we specifically focus on the structure and function of proteins encoded by SARS-CoV-2. Viral proteins that contribute to COVID-19 infection and disease pathogenesis are reviewed according to the most recent research findings. The structure-function correlation of viral proteins provides a fundamental rationale for vaccine development and targeted therapy. Then, current antiviral vaccines are updated, such as inactive viral vaccines and protein-based vaccines and DNA, mRNA, and circular RNA vaccines. A summary of other therapeutic options is also reviewed, including monoclonal antibodies such as a cross-neutralizer antibody, a constructed cobinding antibody, a dual functional monoclonal antibody, an antibody cocktail, and an engineered bispecific antibody, as well as peptide-based inhibitors, chemical compounds, and clustered regularly interspaced short palindromic repeats (CRISPR) exploration. Overall, viral proteins and their functions provide the basis for targeted therapy and vaccine development.
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Grellet E, L'Hôte I, Goulet A, Imbert I. Replication of the coronavirus genome: A paradox among positive-strand RNA viruses. J Biol Chem 2022; 298:101923. [PMID: 35413290 PMCID: PMC8994683 DOI: 10.1016/j.jbc.2022.101923] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/18/2023] Open
Abstract
Coronavirus (CoV) genomes consist of positive-sense single-stranded RNA and are among the largest viral RNAs known to date (∼30 kb). As a result, CoVs deploy sophisticated mechanisms to replicate these extraordinarily large genomes as well as to transcribe subgenomic messenger RNAs. Since 2003, with the emergence of three highly pathogenic CoVs (SARS-CoV, MERS-CoV, and SARS-CoV-2), significant progress has been made in the molecular characterization of the viral proteins and key mechanisms involved in CoV RNA genome replication. For example, to allow for the maintenance and integrity of their large RNA genomes, CoVs have acquired RNA proofreading 3'-5' exoribonuclease activity (in nonstructural protein nsp14). In order to replicate the large genome, the viral-RNA-dependent RNA polymerase (RdRp; in nsp12) is supplemented by a processivity factor (made of the viral complex nsp7/nsp8), making it the fastest known RdRp. Lastly, a viral structural protein, the nucleocapsid (N) protein, which is primarily involved in genome encapsidation, is required for efficient viral replication and transcription. Therefore, CoVs are a paradox among positive-strand RNA viruses in the sense that they use both a processivity factor and have proofreading activity reminiscent of DNA organisms in addition to structural proteins that mediate efficient RNA synthesis, commonly used by negative-strand RNA viruses. In this review, we present a historical perspective of these unsuspected discoveries and detail the current knowledge on the core replicative machinery deployed by CoVs.
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Affiliation(s)
- Emeline Grellet
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - India L'Hôte
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - Adeline Goulet
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - Isabelle Imbert
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France.
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Wang J, Shi Y, Reiss K, Allen B, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Insights into Binding of Single-Stranded Viral RNA Template to the Replication-Transcription Complex of SARS-CoV-2 for the Priming Reaction from Molecular Dynamics Simulations. Biochemistry 2022; 61:424-432. [PMID: 35199520 PMCID: PMC8887646 DOI: 10.1021/acs.biochem.1c00755] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/09/2022] [Indexed: 01/18/2023]
Abstract
A minimal replication-transcription complex (RTC) of SARS-CoV-2 for synthesis of viral RNAs includes the nsp12 RNA-dependent RNA polymerase and two nsp8 RNA primase subunits for de novo primer synthesis, one nsp8 in complex with its accessory nsp7 subunit and the other without it. The RTC is responsible for faithfully copying the entire (+) sense viral genome from its first 5'-end to the last 3'-end nucleotides through a replication-intermediate (RI) template. The single-stranded (ss) RNA template for the RI is its 33-nucleotide 3'-poly(A) tail adjacent to a well-characterized secondary structure. The ssRNA template for viral transcription is a 5'-UUUAU-3' next to stem-loop (SL) 1'. We analyze the electrostatic potential distribution of the nsp8 subunit within the RTC around the template strand of the primer/template (P/T) RNA duplex in recently published cryo-EM structures to address the priming reaction using the viral poly(A) template. We carried out molecular dynamics (MD) simulations with a P/T RNA duplex, the viral poly(A) template, or a generic ssRNA template. We find evidence that the viral poly(A) template binds similarly to the template strand of the P/T RNA duplex within the RTC, mainly through electrostatic interactions, providing new insights into the priming reaction by the nsp8 subunit within the RTC, which differs significantly from the existing proposal of the nsp7/nsp8 oligomer formed outside the RTC. High-order oligomerization of nsp8 and nsp7 for SARS-CoV observed outside the RTC of SARS-CoV-2 is not found in the RTC and not likely to be relevant to the priming reaction.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry,
Yale University, New Haven, Connecticut 06520-8114,
United States
| | - Yuanjun Shi
- Department of Chemistry, Yale
University, New Haven, Connecticut 06511-8499, United
States
| | - Krystle Reiss
- Department of Chemistry, Yale
University, New Haven, Connecticut 06511-8499, United
States
| | - Brandon Allen
- Department of Chemistry, Yale
University, New Haven, Connecticut 06511-8499, United
States
| | - Federica Maschietto
- Department of Chemistry, Yale
University, New Haven, Connecticut 06511-8499, United
States
| | - Elias Lolis
- Department of Pharmacology, Yale
University, New Haven, Connecticut 06520-8066, United
States
| | - William H. Konigsberg
- Department of Molecular Biophysics and Biochemistry,
Yale University, New Haven, Connecticut 06520-8114,
United States
| | - George P. Lisi
- Department of Molecular and Cell Biology and
Biochemistry, Brown University, Providence, Rhode Island 02912,
United States
| | - Victor S. Batista
- Department of Chemistry, Yale
University, New Haven, Connecticut 06511-8499, United
States
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Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. The mechanism of RNA capping by SARS-CoV-2. RESEARCH SQUARE 2022:rs.3.rs-1336910. [PMID: 35194601 PMCID: PMC8863163 DOI: 10.21203/rs.3.rs-1336910/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The SARS-CoV-2 RNA genome contains a 5'-cap that facilitates translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made is not completely understood. Here, we reconstitute the SARS-CoV-2 7MeGpppA2'-O-Me-RNA cap using virally encoded non-structural proteins (nsps). We show that the kinase-like NiRAN domain5 of nsp12 transfers RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers RNA to GDP, forming the cap core structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N-terminus of nsp9 and the kinase-like active site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19.
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Affiliation(s)
- Gina J. Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer L. Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Abir Majumdar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-776, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John W. Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S. Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase. Nat Commun 2022; 13:621. [PMID: 35110538 PMCID: PMC8810794 DOI: 10.1038/s41467-022-28113-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/09/2022] [Indexed: 01/21/2023] Open
Abstract
The guanosine analog AT-527 represents a promising candidate against Severe Acute Respiratory Syndrome coronavirus type 2 (SARS-CoV-2). AT-527 recently entered phase III clinical trials for the treatment of COVID-19. Once in cells, AT-527 is converted into its triphosphate form, AT-9010, that presumably targets the viral RNA-dependent RNA polymerase (RdRp, nsp12), for incorporation into viral RNA. Here we report a 2.98 Å cryo-EM structure of the SARS-CoV-2 nsp12-nsp7-nsp82-RNA complex, showing AT-9010 bound at three sites of nsp12. In the RdRp active-site, one AT-9010 is incorporated at the 3′ end of the RNA product strand. Its modified ribose group (2′-fluoro, 2′-methyl) prevents correct alignment of the incoming NTP, in this case a second AT-9010, causing immediate termination of RNA synthesis. The third AT-9010 is bound to the N-terminal domain of nsp12 - known as the NiRAN. In contrast to native NTPs, AT-9010 is in a flipped orientation in the active-site, with its guanine base unexpectedly occupying a previously unnoticed cavity. AT-9010 outcompetes all native nucleotides for NiRAN binding, inhibiting its nucleotidyltransferase activity. The dual mechanism of action of AT-527 at both RdRp and NiRAN active sites represents a promising research avenue against COVID-19. The drug AT-527 targets the SARS-CoV-2 replication machinery. Here the authors use Cryo-EM to show how AT-527 inhibits SARS-CoV-2 polymerase by acting as an immediate RNA chain terminator and stably binding in a NiRAN active-site pocket; impeding an essential nucleotide-transfer activity.
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Barros FR, Leite DC, Guimarães LJ, Lopes JM, Vasconcelos MW, Ferreira LX, Gonçalves S, Pastre VG, Pereira G, Trentin AB, Gabiatti NC, Kuhn BC, Perseguini JM, Wendt SN, Ghisi NC. Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene Allplex TM 2019-nCoV protocol. J Virol Methods 2022; 300:114429. [PMID: 34919975 PMCID: PMC8668600 DOI: 10.1016/j.jviromet.2021.114429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022]
Abstract
The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led the world to a pandemic. Therefore, rapid, sensitive, and reproducible diagnostic tests are essential to indicate which measures should be taken during pandemics. We retrospectively tested unextracted nasopharyngeal samples from consecutive patients with suspected SARS-CoV-2 infection (n = 334), and compared two different Ct cut-off values for interpretation of results using a modified Allplex protocol. Its performance was evaluated using the USA Centers for Disease Control and Prevention (CDC) as reference. The reduction on Ct cut-off to 35 increased the test NPA from 79.65 to 88.00 %, reducing the number of false positives, from 10.48 to 6.29 %, resulting in an almost perfect agreement between the Allplex and the CDC protocol (Cohen's Kappa coefficient = 0.830 ± 0.032). This study demonstrates that the Seegene Allplex™ 2019-nCoV protocol skipping the viral RNA extraction step using the Ct cut-off of 35 is a rapid and efficient method to detect SARS-CoV-2 in nasopharyngeal samples.
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Affiliation(s)
- Flavia R.O. Barros
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
| | - Deborah C.A. Leite
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | - Nédia C. Ghisi
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
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43
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Nencka R, Silhan J, Klima M, Otava T, Kocek H, Krafcikova P, Boura E. Coronaviral RNA-methyltransferases: function, structure and inhibition. Nucleic Acids Res 2022; 50:635-650. [PMID: 35018474 PMCID: PMC8789044 DOI: 10.1093/nar/gkab1279] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/08/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023] Open
Abstract
Coronaviral methyltransferases (MTases), nsp10/16 and nsp14, catalyze the last two steps of viral RNA-cap creation that takes place in cytoplasm. This cap is essential for the stability of viral RNA and, most importantly, for the evasion of innate immune system. Non-capped RNA is recognized by innate immunity which leads to its degradation and the activation of antiviral immunity. As a result, both coronaviral MTases are in the center of scientific scrutiny. Recently, X-ray and cryo-EM structures of both enzymes were solved even in complex with other parts of the viral replication complex. High-throughput screening as well as structure-guided inhibitor design have led to the discovery of their potent inhibitors. Here, we critically summarize the tremendous advancement of the coronaviral MTase field since the beginning of COVID pandemic.
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Affiliation(s)
- Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Tomas Otava
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Hugo Kocek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
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44
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Malone B, Urakova N, Snijder EJ, Campbell EA. Structures and functions of coronavirus replication-transcription complexes and their relevance for SARS-CoV-2 drug design. Nat Rev Mol Cell Biol 2022; 23:21-39. [PMID: 34824452 PMCID: PMC8613731 DOI: 10.1038/s41580-021-00432-z] [Citation(s) in RCA: 183] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to cause massive global upheaval. Coronaviruses are positive-strand RNA viruses with an unusually large genome of ~30 kb. They express an RNA-dependent RNA polymerase and a cohort of other replication enzymes and supporting factors to transcribe and replicate their genomes. The proteins performing these essential processes are prime antiviral drug targets, but drug discovery is hindered by our incomplete understanding of coronavirus RNA synthesis and processing. In infected cells, the RNA-dependent RNA polymerase must coordinate with other viral and host factors to produce both viral mRNAs and new genomes. Recent research aiming to decipher and contextualize the structures, functions and interplay of the subunits of the SARS-CoV-2 replication and transcription complex proteins has burgeoned. In this Review, we discuss recent advancements in our understanding of the molecular basis and complexity of the coronavirus RNA-synthesizing machinery. Specifically, we outline the mechanisms and regulation of RNA translation, replication and transcription. We also discuss the composition of the replication and transcription complexes and their suitability as targets for antiviral therapy.
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Affiliation(s)
- Brandon Malone
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY USA
| | - Nadya Urakova
- grid.10419.3d0000000089452978Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric J. Snijder
- grid.10419.3d0000000089452978Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Elizabeth A. Campbell
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY USA
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45
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Copper complex of a thienyl-hydrazone rhodamine derivative is a highly selective colorimetric sensor for pyrophosphate. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2021.153606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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46
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IMTIAZ F, PASHA MK. A systematic review of RdRp of SARS-CoV-2 through artificial intelligence and machine learning utilizing structure-based drug design strategy. Turk J Chem 2021; 46:583-594. [PMID: 37720604 PMCID: PMC10503974 DOI: 10.55730/1300-0527.3355] [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: 09/10/2021] [Revised: 06/16/2022] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Since the coronavirus disease has been declared a global pandemic, it had posed a challenge among researchers and raised common awareness and collaborative efforts towards finding the solution. Caused by severe acute respiratory coronavirus syndrome-2 (SARS-CoV-2), coronavirus drug design strategy needs to be optimized. It is understandable that cognizance of the pathobiology of COVID-19 can help scientists in the development and discovery of therapeutically effective antiviral drugs by elucidating the unknown viral pathways and structures. Considering the role of artificial intelligence and machine learning with its advancements in the field of science, it is rational to use these methods which can aid in the discovery of new potent candidates in silico. Our review utilizes similar methodologies and focuses on RNA-dependent RNA polymerase (RdRp), based on its importance as an essential element for virus replication and also a promising target for COVID-19 therapeutics. Artificial neural network technique was used to shortlist articles with the support of PRISMA, from different research platforms including Scopus, PubMed, PubChem, and Web of Science, through a combination of keywords. "English language", from the year "2000" and "published articles in journals" were selected to carry out this research. We summarized that structural details of the RdRp reviewed in this analysis will have the potential to be taken into consideration when developing therapeutic solutions and if further multidisciplinary efforts are taken in this domain then potential clinical candidates for RdRp of SARS-CoV-2 could be successfully delivered for experimental validations.
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Affiliation(s)
- Fariha IMTIAZ
- Punjab University College of Pharmacy, University of the Punjab, Lahore,
Pakistan
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47
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Larsen JC. Dynamical Aspects of Corona Virus Infection. INT J BIOMATH 2021. [DOI: 10.1142/s1793524522500115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, we consider five mathematical models of corona virus infection. The first model is a mathematical model of corona virus entry. The second model is a mathematical model for interactions of virus N-protein and viral RNA. Here, we prove that phosphorylated N protein increases the affinity of viral RNA. The third model is a mathematical model of virion assembly. It is a six-dimensional model. But there is an invariant three-dimensional submodel, which we can prove has a positive stable equilibrium. The fourth model is a model of an enzyme inhibitor that blocks viral replication. The fifth model is a model of a virus and a vaccine.
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Affiliation(s)
- Jens Christian Larsen
- The Royal Veterinary and Agricultural University of Denmark, Vanløse Alle 50 2. mf. tv., Vanløse, 2720 Copenhagen, Denmark
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48
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Walker AP, Fan H, Keown JR, Knight ML, Grimes J, Fodor E. The SARS-CoV-2 RNA polymerase is a viral RNA capping enzyme. Nucleic Acids Res 2021; 49:13019-13030. [PMID: 34850141 PMCID: PMC8682786 DOI: 10.1093/nar/gkab1160] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/01/2021] [Accepted: 11/08/2021] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2 is a positive-sense RNA virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic, which continues to cause significant morbidity, mortality and economic strain. SARS-CoV-2 can cause severe respiratory disease and death in humans, highlighting the need for effective antiviral therapies. The RNA synthesis machinery of SARS-CoV-2 is an ideal drug target and consists of non-structural protein 12 (nsp12), which is directly responsible for RNA synthesis, and numerous co-factors involved in RNA proofreading and 5' capping of viral RNAs. The formation of the 5' 7-methylguanosine (m7G) cap structure is known to require a guanylyltransferase (GTase) as well as a 5' triphosphatase and methyltransferases; however, the mechanism of SARS-CoV-2 RNA capping remains poorly understood. Here we find that SARS-CoV-2 nsp12 is involved in viral RNA capping as a GTase, carrying out the addition of a GTP nucleotide to the 5' end of viral RNA via a 5' to 5' triphosphate linkage. We further show that the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase) domain performs this reaction, and can be inhibited by remdesivir triphosphate, the active form of the antiviral drug remdesivir. These findings improve understanding of coronavirus RNA synthesis and highlight a new target for novel or repurposed antiviral drugs against SARS-CoV-2.
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Affiliation(s)
- Alexander P Walker
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jeremy R Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Michael L Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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49
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Esposito G, Hunashal Y, Percipalle M, Venit T, Dieng MM, Fogolari F, Hassanzadeh G, Piano F, Gunsalus KC, Idaghdour Y, Percipalle P. NMR-Based Analysis of Nanobodies to SARS-CoV-2 Nsp9 Reveals a Possible Antiviral Strategy Against COVID-19. Adv Biol (Weinh) 2021; 5:e2101113. [PMID: 34705339 PMCID: PMC8646926 DOI: 10.1002/adbi.202101113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/16/2021] [Indexed: 11/17/2022]
Abstract
Following the entry into the host cell, SARS-CoV-2 replication is mediated by the replication transcription complex (RTC) assembled through a number of nonstructural proteins (Nsps). A monomeric form of Nsp9 is particularly important for RTC assembly and function. In the present study, 136 unique nanobodies targeting Nsp9 are generated. Several nanobodies belonging to different B-cell lineages are expressed, purified, and characterized. Results from immunoassays applied to purified Nsp9 and neat saliva from coronavirus disease (COVID-19) patients show that these nanobodies effectively and specifically recognize both recombinant and endogenous Nsp9. Nuclear magnetic resonance analyses supported by molecular dynamics reveal a composite Nsp9 oligomerization pattern and demonstrate that both nanobodies stabilize the tetrameric form of wild-type Nsp9 also identifying the epitopes on the tetrameric assembly. These results can have important implications in the potential use of these nanobodies to combat viral replication.
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Affiliation(s)
- Gennaro Esposito
- Chemistry Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Istituto Nazionale Biostrutture e BiosistemiRoma00136Italy
| | - Yamanappa Hunashal
- Chemistry Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Mathias Percipalle
- Chemistry Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Department of Chemistry and Magnetic Resonance CenterUniversity of FlorenceFlorence50019Italy
| | - Tomas Venit
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Mame Massar Dieng
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Federico Fogolari
- Istituto Nazionale Biostrutture e BiosistemiRoma00136Italy
- Dipartimento di Scienze Matematiche, Informatiche, e FisicheUdine UniversityUdine33100Italy
| | | | - Fabio Piano
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Public Health Research CenterNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Kristin C. Gunsalus
- Center for Genomics and Systems BiologyNew York University Abu Dhabi (NYUAD)P.O. Box 129188Abu DhabiUnited Arab Emirates
- Department of BiologyCenter for Genomics and Systems Biology New York UniversityNew YorkNY10003USA
| | - Youssef Idaghdour
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Public Health Research CenterNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
| | - Piergiorgio Percipalle
- Biology Program, Science DivisionNew York University Abu DhabiAbu Dhabi129188United Arab Emirates
- Department of Molecular BioscienceThe Wenner Gren InstituteStockholm UniversityStockholmS‐106 91Sweden
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50
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Svetlov D, Artsimovitch I. Reductionism Ad Absurdum: The Misadventures of Structural Biology in the Time of Coronavirus. ACS Infect Dis 2021; 7:2948-2952. [PMID: 34613689 PMCID: PMC8507565 DOI: 10.1021/acsinfecdis.1c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 01/18/2023]
Abstract
The tragic consequences of the COVID-19 pandemic have led to admirable responses by the global scientific community, including a profound acceleration in the pace of research and exchange of findings. However, this has had considerable costs of its own, as erroneous conclusions have propagated faster than researchers have been able to detect and correct them. We illustrate the specific misunderstandings that have resulted from reductionist approaches to the study of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), which are but one instance of a regrettably growing trend in structural biology. Far from merely being cautionary tales about the conduct of scientific research, these errors have had significant practical impact, by hampering a correct understanding of RdRp structure and mechanism, its inhibition by nucleoside analogues such as remdesivir, and the discovery and characterization of such analogues. After correcting these misunderstandings, we close with several recommendations for a broader correction of the course of scientific research.
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Affiliation(s)
- Dmitri Svetlov
- Svetlov Scientific
Software, Pasadena, California 91106, United States
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA
Biology, The Ohio State University, Columbus, Ohio 43210,
United States
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