1
|
Baker DL, Wang B, Wilkinson-White LE, El-Kamand S, Allport TA, Ataide SF, Kwan AH, Artsimovitch I, Cubeddu L, Gamsjaeger R. A Biochemical and Biophysical Analysis of the Interaction of nsp9 with nsp12 from SARS-CoV-2-Implications for Future Drug Discovery Efforts. Proteins 2024. [PMID: 38958516 DOI: 10.1002/prot.26725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/27/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
Abstract
The ongoing global pandemic of the coronavirus 2019 (COVID-19) disease is caused by the virus SARS-CoV-2, with very few highly effective antiviral treatments currently available. The machinery responsible for the replication and transcription of viral RNA during infection is made up of several important proteins. Two of these are nsp12, the catalytic subunit of the viral polymerase, and nsp9, a cofactor of nsp12 involved in the capping and priming of viral RNA. While several recent studies have determined the structural details of the interaction of nsp9 with nsp12 in the context of RNA capping, very few biochemical or biophysical details are currently available. In this study, we have used a combination of surface plasmon resonance (SPR) experiments, size exclusion chromatography (SEC) experiments, and biochemical assays to identify specific nsp9 residues that are critical for nsp12 binding as well as RNAylation, both of which are essential for the RNA capping process. Our data indicate that nsp9 dimerization is unlikely to play a significant functional role in the virus. We confirm that a set of recently discovered antiviral peptides inhibit nsp9-nsp12 interaction by specifically binding to nsp9; however, we find that these peptides do not impact RNAylation. In summary, our results have important implications for future drug discovery efforts to combat SARS-CoV-2 and any newly emerging coronaviruses.
Collapse
Affiliation(s)
- David L Baker
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lorna E Wilkinson-White
- Sydney Analytical, Core Research Facilities, University of Sydney, Camperdown, New South Wales, Australia
| | - Serene El-Kamand
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Thomas A Allport
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Sandro F Ataide
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Liza Cubeddu
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Roland Gamsjaeger
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
Collapse
Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Mani G, El-Kamand S, Wang B, Baker DL, Ataide SF, Artsimovitch I, Cubeddu L, Gamsjaeger R. A structural analysis of the nsp9 protein from the coronavirus MERS CoV reveals a conserved RNA binding interface. Proteins 2024; 92:418-426. [PMID: 37929701 PMCID: PMC10872591 DOI: 10.1002/prot.26630] [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: 06/02/2023] [Revised: 08/29/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS CoV) and severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) are RNA viruses from the Betacoronavirus family that cause serious respiratory illness in humans. One of the conserved non-structural proteins encoded for by the coronavirus family is non-structural protein 9 (nsp9). Nsp9 plays an important role in the RNA capping process of the viral genome, where it is covalently linked to viral RNA (known as RNAylation) by the conserved viral polymerase, nsp12. Nsp9 also directly binds to RNA; we have recently revealed a distinct RNA recognition interface in the SARS CoV-2 nsp9 by using a combination of nuclear magnetic resonance spectroscopy and biolayer interferometry. In this study, we have utilized a similar methodology to determine a structural model of RNA binding of the related MERS CoV. Based on these data, we uncover important similarities and differences to SARS CoV-2 nsp9 and other coronavirus nsp9 proteins. Our findings that replacing key RNA binding residues in MERS CoV nsp9 affects RNAylation efficiency indicate that recognition of RNA may play a role in the capping process of the virus.
Collapse
Affiliation(s)
- Gayathri Mani
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Serene El-Kamand
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - David L. Baker
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Sandro F. Ataide
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Liza Cubeddu
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Roland Gamsjaeger
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
Collapse
Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| |
Collapse
|
9
|
Arya R, Tripathi P, Nayak K, Ganesh J, Bihani SC, Ghosh B, Prashar V, Kumar M. Insights into the evolution of mutations in SARS-CoV-2 non-spike proteins. Microb Pathog 2023; 185:106460. [PMID: 37995880 DOI: 10.1016/j.micpath.2023.106460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
The COVID-19 pandemic has been driven by the emergence of SARS-CoV-2 variants with mutations across all the viral proteins. Although mutations in the spike protein have received significant attention, understanding the prevalence and potential impact of mutations in other viral proteins is essential for comprehending the evolution of SARS-CoV-2. Here, we conducted a comprehensive analysis of approximately 14 million sequences of SARS-CoV-2 deposited in the GISAID database until December 2022 to identify prevalent mutations in the non-spike proteins at the global and country levels. Additionally, we evaluated the energetics of each mutation to better understand their impact on protein stability. While the consequences of many mutations remain unclear, we discuss potential structural and functional significance of some mutations. Our study highlights the ongoing evolutionary process of SARS-CoV-2 and underscores the importance of understanding changes in non-spike proteins.
Collapse
Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Preeti Tripathi
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Karthik Nayak
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; School of Chemical Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, 400098, India
| | - Janani Ganesh
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Biplab Ghosh
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India; Beamline Development & Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Vishal Prashar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| | - Mukesh Kumar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Inniss NL, Kozic J, Li F, Rosas-Lemus M, Minasov G, Rybáček J, Zhu Y, Pohl R, Shuvalova L, Rulíšek L, Brunzelle JS, Bednárová L, Štefek M, Kormaník JM, Andris E, Šebestík J, Li ASM, Brown PJ, Schmitz U, Saikatendu K, Chang E, Nencka R, Vedadi M, Satchell KJ. Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. ACS Infect Dis 2023; 9:1918-1931. [PMID: 37728236 PMCID: PMC10961098 DOI: 10.1021/acsinfecdis.3c00203] [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] [Indexed: 09/21/2023]
Abstract
A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.
Collapse
Affiliation(s)
- Nicole L. Inniss
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Ján Kozic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - George Minasov
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Yingjie Zhu
- WuXi AppTec Co., Ltd, China (Shanghai) Pilot Free Trade Zone, Shanghai, 201308, China
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ludmilla Shuvalova
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Joseph S. Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL, 60439, United States
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Milan Štefek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ján Michael Kormaník
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Alice Shi Ming Li
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Uli Schmitz
- Structural Chemistry, Gilead Pharmaceuticals, San Mateo, CA, 94404, United States
| | - Kumar Saikatendu
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Masoud Vedadi
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Karla J.F. Satchell
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| |
Collapse
|
13
|
Tam D, Lorenzo-Leal AC, Hernández LR, Bach H. Targeting SARS-CoV-2 Non-Structural Proteins. Int J Mol Sci 2023; 24:13002. [PMID: 37629182 PMCID: PMC10455537 DOI: 10.3390/ijms241613002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped respiratory β coronavirus that causes coronavirus disease (COVID-19), leading to a deadly pandemic that has claimed millions of lives worldwide. Like other coronaviruses, the SARS-CoV-2 genome also codes for non-structural proteins (NSPs). These NSPs are found within open reading frame 1a (ORF1a) and open reading frame 1ab (ORF1ab) of the SARS-CoV-2 genome and encode NSP1 to NSP11 and NSP12 to NSP16, respectively. This study aimed to collect the available literature regarding NSP inhibitors. In addition, we searched the natural product database looking for similar structures. The results showed that similar structures could be tested as potential inhibitors of the NSPs.
Collapse
Affiliation(s)
- Donald Tam
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| | - Ana C. Lorenzo-Leal
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| | - Luis Ricardo Hernández
- Laboratorio de Investigación Fitoquímica, Departamento de Ciencias Químico Biológicas, Universidad de las Américas Puebla, Ex Hacienda Sta. Catarina Mártir S/N, San Andrés Cholula 72810, Mexico;
| | - Horacio Bach
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
Collapse
Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
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.
Collapse
|
19
|
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.
Collapse
|
20
|
Cellier MFM. Nramp: Deprive and conquer? Front Cell Dev Biol 2022; 10:988866. [PMID: 36313567 PMCID: PMC9606685 DOI: 10.3389/fcell.2022.988866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.
Collapse
|
21
|
Shi FS, Yu Y, Li YL, Cui L, Zhao Z, Wang M, Wang B, Zhang R, Huang YW. Expression Profile and Localization of SARS-CoV-2 Nonstructural Replicase Proteins in Infected Cells. Microbiol Spectr 2022; 10:e0074422. [PMID: 35730969 PMCID: PMC9431475 DOI: 10.1128/spectrum.00744-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is responsible for the COVID-19 pandemic that has caused unprecedented loss of life and economic trouble all over the world, though the mechanism of its replication remains poorly understood. In this study, antibodies were generated and used to systematically determine the expression profile and subcellular distribution of 11 SARS-CoV-2 nonstructural replicase proteins (nsp1, nsp2, nsp3, nsp5, nsp7, nsp8, nsp9, nsp10, nsp13, nsp14, and nsp15) by Western blot and immunofluorescence assay. Nsp3, nsp5, and nsp8 were detected in perinuclear foci at different time points, with diffusion and stronger fluorescence observed over time. In particular, colocalization of nsp8 and nsp13 with different replicase proteins suggested viral protein-protein interaction, which may be key to understanding their functions and potential molecular mechanisms. Viral intermediate dsRNA was detected in perinuclear foci as early as 2-h postinfection, indicating the initiation of virus replication. With the passage of time, these perinuclear dsRNA foci became larger and brighter, and nearly all colocalized with N protein, consistent with viral growth over time. Thus, the development of these anti-nsp antibodies provides basic tools for the further study of replication and diagnosis of SARS-CoV-2. IMPORTANCE The intracellular localization of SARS-CoV-2 replicase nonstructural proteins (nsp) during infection has not been fully elucidated. In this study, we systematically analyzed the expression and subcellular localization of 11 distinct viral nsp and dsRNA over time in SARS-CoV-2-infected cells by using individual antibody against these replicase proteins. The data indicated that nsp gene expression is highly regulated in space and time, which could be useful to understand the function of viral replicases and future development of diagnostics and potential antiviral strategies against SARS-CoV-2.
Collapse
Affiliation(s)
- Fang-Shu Shi
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Yin Yu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, China
| | - Ya-Li Li
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Lilan Cui
- Novoprotein Scientific Inc., Shanghai, China
| | - Zhuangzhuang Zhao
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Mi Wang
- Novoprotein Scientific Inc., Shanghai, China
| | - Bin Wang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Rong Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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.
Collapse
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:
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein. J Biol Chem 2021; 297:101362. [PMID: 34756886 PMCID: PMC8553373 DOI: 10.1016/j.jbc.2021.101362] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 01/18/2023] Open
Abstract
The Nsp9 replicase is a conserved coronaviral protein that acts as an essential accessory component of the multi-subunit viral replication/transcription complex. Nsp9 is the predominant substrate for the essential nucleotidylation activity of Nsp12. Compounds specifically interfering with this viral activity would facilitate its study. Using a native mass-spectrometry-based approach to screen a natural product library for Nsp9 binders, we identified an ent-kaurane natural product, oridonin, capable of binding to purified SARS-CoV-2 Nsp9 with micromolar affinities. By determining the crystal structure of the Nsp9-oridonin complex, we showed that oridonin binds through a conserved site near Nsp9’s C-terminal GxxxG-helix. In enzymatic assays, oridonin’s binding to Nsp9 reduces its potential to act as substrate for Nsp12’s Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain. We also showed using in vitro cellular assays oridonin, while cytotoxic at higher doses has broad antiviral activity, reducing viral titer following infection with either SARS-CoV-2 or, to a lesser extent, MERS-CoV. Accordingly, these preliminary findings suggest that the oridonin molecular scaffold may have the potential to be developed into an antiviral compound to inhibit the function of Nsp9 during coronaviral replication.
Collapse
|