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Zhang Y, Wu F, Han Y, Wu Y, Huang L, Huang Y, Yan D, Jiang X, Ma J, Xu W. Unraveling the assembly mechanism of SADS-CoV virus nucleocapsid protein: insights from RNA binding, dimerization, and epitope diversity profiling. J Virol 2024; 98:e0092624. [PMID: 39082816 PMCID: PMC11334509 DOI: 10.1128/jvi.00926-24] [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: 05/27/2024] [Accepted: 07/02/2024] [Indexed: 08/21/2024] Open
Abstract
The swine acute diarrhea syndrome coronavirus (SADS-CoV) has caused significant disruptions in porcine breeding and raised concerns about potential human infection. The nucleocapsid (N) protein of SADS-CoV plays a vital role in viral assembly and replication, but its structure and functions remain poorly understood. This study utilized biochemistry, X-ray crystallography, and immunization techniques to investigate the N protein's structure and function in SADS-CoV. Our findings revealed distinct domains within the N protein, including an RNA-binding domain, two disordered domains, and a dimerization domain. Through biochemical assays, we confirmed that the N-terminal domain functions as an RNA-binding domain, and the C-terminal domain is involved in dimerization, with the crystal structure analysis providing visual evidence of dimer formation. Immunization experiments demonstrated that the disordered domain 2 elicited a significant antibody response. These identified domains and their interactions are crucial for viral assembly. This comprehensive understanding of the N protein in SADS-CoV enhances our knowledge of its assembly and replication mechanisms, enabling the development of targeted interventions and therapeutic strategies. IMPORTANCE SADS-CoV is a porcine coronavirus that originated from a bat HKU2-related coronavirus. It causes devastating swine diseases and poses a high risk of spillover to humans. The coronavirus N protein, as the most abundant viral protein in infected cells, likely plays a key role in viral assembly and replication. However, the structure and function of this protein remain unclear. Therefore, this study employed a combination of biochemistry and X-ray crystallography to uncover distinct structural domains in the N protein, including RNA-binding domains, two disordered domains, and dimerization domains. Additionally, we made the novel discovery that the disordered domain elicited a significant antibody response. These findings provide new insights into the structure and functions of the SADS-CoV N protein, which have important implications for future studies on SADS-CoV diagnosis, as well as the development of vaccines and anti-viral drugs.
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Affiliation(s)
- Ying Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening & NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Fang Wu
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Yongyue Han
- Guangdong Provincial Key Laboratory of New Drug Screening & NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yuzhe Wu
- Guangdong Provincial Key Laboratory of New Drug Screening & NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Liqiu Huang
- Guangdong Provincial Key Laboratory of New Drug Screening & NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yuanwei Huang
- Guangdong Provincial Key Laboratory of New Drug Screening & NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Di Yan
- Guangdong Provincial Key Laboratory of New Drug Screening & NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Xiwen Jiang
- School of Life Sciences and Biopharmaceuticals, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jingyun Ma
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wei Xu
- Guangdong Provincial Key Laboratory of New Drug Screening & NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
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2
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Zhou Z, Ali A, Walelign E, Demissie GF, El Masry I, Abayneh T, Getachew B, Krishnan P, Ng DY, Gardner E, Makonnen Y, Miguel E, Chevalier V, Chu DK, So RTY, Von Dobschuetz S, Mamo G, Poon LLM, Peiris M. Genetic diversity and molecular epidemiology of Middle East Respiratory Syndrome Coronavirus in dromedaries in Ethiopia, 2017-2020. Emerg Microbes Infect 2023; 12:e2164218. [PMID: 36620913 PMCID: PMC9888459 DOI: 10.1080/22221751.2022.2164218] [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] [Indexed: 01/10/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels and causes zoonotic infection and disease in humans. Although over 80% of the global population of infected dromedary camels are found in Africa, zoonotic disease had only been reported in the Arabia Peninsula and travel-associated disease has been reported elsewhere. In this study, genetic diversity and molecular epidemiology of MERS-CoV in dromedary camels in Ethiopia were investigated during 2017-2020. Of 1766 nasal swab samples collected, 61 (3.5%) were detected positive for MERS-CoV RNA. Of 484 turbinate swab samples collected, 10 (2.1%) were detected positive for MERS-CoV RNA. Twenty-five whole genome sequences were obtained from these MERS-CoV positive samples. Phylogenetically, these Ethiopian camel-originated MERS-CoV belonged to clade C2, clustering with other East African camel strains. Virus sequences from camel herds clustered geographically while in an abattoir, two distinct phylogenetic clusters of MERS-CoVs were observed in two sequential sampling collections, which indicates the greater genetic diversity of MERS-CoV in abattoirs. In contrast to clade A and B viruses from the Arabian Peninsula, clade C camel-originated MERS-CoV from Ethiopia had various nucleotide insertions and deletions in non-structural gene nsp3, accessory genes ORF3 and ORF5 and structural gene N. This study demonstrates the genetic instability of MERS-CoV in dromedaries in East Africa, which indicates that the virus is still actively adapting to its camel host. The impact of the observed nucleotide insertions and deletions on virus evolution, viral fitness, and zoonotic potential deserves further study.
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Affiliation(s)
- Ziqi Zhou
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Abraham Ali
- Bacterial, Parasitic and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia,Department of Veterinary Microbiology, Immunology and Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Elias Walelign
- Food and Agriculture Organization, Emergency Centre for Transboundary Animal Diseases, Addis Ababa, Ethiopia
| | - Getnet F. Demissie
- College of Veterinary Medicine, Department of Veterinary Epidemiology, Microbiology and Public Health, Haramaya University, Haramaya, Ethiopia
| | - Ihab El Masry
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | | | | | - Pavithra Krishnan
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Daisy Y.M. Ng
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Emma Gardner
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Yilma Makonnen
- Food and Agriculture Organization, Subregional Office for Eastern Africa, Addis Ababa, Ethiopia
| | - Eve Miguel
- Animal, Santé, Territoires, Risques et Ecosystèmes, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Université de Montpellier, Montpellier, France,Maladies Infectieuses et Vecteurs: Ecologie Genetique, Evolution et Controle, L’Institut de Recherche pour le Developpment, CNRS, Montpellier, France
| | - Véronique Chevalier
- International Center of Research in Agriculture for Development (CIRAD), UMR ASTRE, Montpellier, France,CIRAD, UMR ASTRE, Antananarivo, Madagascar,Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Daniel K. Chu
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,UK Health Security Agency, London, UK
| | - Ray T. Y. So
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | | | - Gezahegne Mamo
- Department of Veterinary Microbiology, Immunology and Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Leo L. M. Poon
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China, Malik Peiris
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3
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Boniardi I, Corona A, Basquin J, Basquin C, Milia J, Nagy I, Tramontano E, Zinzula L. Suramin inhibits SARS-CoV-2 nucleocapsid phosphoprotein genome packaging function. Virus Res 2023; 336:199221. [PMID: 37704176 PMCID: PMC10514558 DOI: 10.1016/j.virusres.2023.199221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is fading, however its etiologic agent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues posing - despite the availability of licensed vaccines - a global health threat, due to the potential emergence of vaccine-resistant SARS-CoV-2 variants. This makes the development of new drugs against COVID-19 a persistent urgency and sets as research priority the validation of novel therapeutic targets within the SARS-CoV-2 proteome. Among these, a promising one is the SARS-CoV-2 nucleocapsid (N) phosphoprotein, a major structural component of the virion with indispensable role in packaging the viral genome into a ribonucleoprotein (RNP) complex, which also contributes to SARS-CoV-2 innate immune evasion by inhibiting the host cell type-I interferon (IFN-I) response. By combining miniaturized differential scanning fluorimetry with microscale thermophoresis, we found that the 100-year-old drug Suramin interacts with SARS-CoV-2 N-terminal domain (NTD) and C-terminal domain (CTD), thereby inhibiting their single-stranded RNA (ssRNA) binding function with low-micromolar Kd and IC50 values. Molecular docking suggests that Suramin interacts with basic NTD cleft and CTD dimer interface groove, highlighting three potentially druggable ssRNA binding sites. Electron microscopy shows that Suramin inhibits the formation in vitro of RNP complex-like condensates by SARS-CoV-2 N with a synthetic ssRNA. In a dose-dependent manner, Suramin also reduced SARS-CoV-2-induced cytopathic effect on Vero E6 and Calu-3 cells, partially reverting the SARS-CoV-2 N-inhibited IFN-I production in 293T cells. Our findings indicate that Suramin inhibits SARS-CoV-2 replication by hampering viral genome packaging, thereby representing a starting model for design of new COVID-19 antivirals.
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Affiliation(s)
- Irene Boniardi
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - Jerome Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jessica Milia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - István Nagy
- Center of Research and Development, Eszterházy Károly Catholic University, Eger 3300, Hungary
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy.
| | - Luca Zinzula
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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4
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Castillo G, Mora-Díaz JC, Breuer M, Singh P, Nelli RK, Giménez-Lirola LG. Molecular mechanisms of human coronavirus NL63 infection and replication. Virus Res 2023; 327:199078. [PMID: 36813239 PMCID: PMC9944649 DOI: 10.1016/j.virusres.2023.199078] [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: 12/20/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Human coronavirus NL63 (HCoV-NL63) is spread globally, causing upper and lower respiratory tract infections mainly in young children. HCoV-NL63 shares a host receptor (ACE2) with severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 but, unlike them, HCoV-NL63 primarily develops into self-limiting mild to moderate respiratory disease. Although with different efficiency, both HCoV-NL63 and SARS-like CoVs infect ciliated respiratory cells using ACE2 as receptor for binding and cell entry. Working with SARS-like CoVs require access to BSL-3 facilities, while HCoV-NL63 research can be performed at BSL-2 laboratories. Thus, HCoV-NL63 could be used as a safer surrogate for comparative studies on receptor dynamics, infectivity and virus replication, disease mechanism, and potential therapeutic interventions against SARS-like CoVs. This prompted us to review the current knowledge on the infection mechanism and replication of HCoV-NL63. Specifically, after a brief overview on the taxonomy, genomic organization and virus structure, this review compiles the current HCoV-NL63-related research in virus entry and replication mechanism, including virus attachment, endocytosis, genome translation, and replication and transcription. Furthermore, we reviewed cumulative knowledge on the susceptibility of different cells to HCoV-NL63 infection in vitro, which is essential for successful virus isolation and propagation, and contribute to address different scientific questions from basic science to the development and assessment of diagnostic tools, and antiviral therapies. Finally, we discussed different antiviral strategies that have been explored to suppress replication of HCoV-NL63, and other related human coronaviruses, by either targeting the virus or enhancing host antiviral mechanisms.
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Affiliation(s)
- Gino Castillo
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Juan Carlos Mora-Díaz
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Mary Breuer
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Pallavi Singh
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.
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5
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Chechetkin VR, Lobzin VV. Evolving ribonucleocapsid assembly/packaging signals in the genomes of the human and animal coronaviruses: targeting, transmission and evolution. J Biomol Struct Dyn 2022; 40:11239-11263. [PMID: 34338591 DOI: 10.1080/07391102.2021.1958061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A world-wide COVID-19 pandemic intensified strongly the studies of molecular mechanisms related to the coronaviruses. The origin of coronaviruses and the risks of human-to-human, animal-to-human and human-to-animal transmission of coronaviral infections can be understood only on a broader evolutionary level by detailed comparative studies. In this paper, we studied ribonucleocapsid assembly-packaging signals (RNAPS) in the genomes of all seven known pathogenic human coronaviruses, SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-229E and HCoV-NL63 and compared them with RNAPS in the genomes of the related animal coronaviruses including SARS-Bat-CoV, MERS-Camel-CoV, MHV, Bat-CoV MOP1, TGEV and one of camel alphacoronaviruses. RNAPS in the genomes of coronaviruses were evolved due to weakly specific interactions between genomic RNA and N proteins in helical nucleocapsids. Combining transitional genome mapping and Jaccard correlation coefficients allows us to perform the analysis directly in terms of underlying motifs distributed over the genome. In all coronaviruses, RNAPS were distributed quasi-periodically over the genome with the period about 54 nt biased to 57 nt and to 51 nt for the genomes longer and shorter than that of SARS-CoV, respectively. The comparison with the experimentally verified packaging signals for MERS-CoV, MHV and TGEV proved that the distribution of particular motifs is strongly correlated with the packaging signals. We also found that many motifs were highly conserved in both characters and positioning on the genomes throughout the lineages that make them promising therapeutic targets. The mechanisms of encapsidation can affect the recombination and co-infection as well.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladimir R Chechetkin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - Vasily V Lobzin
- School of Physics, University of Sydney, Sydney, NSW, Australia
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6
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Montesinos-Guevara C, Buitrago-Garcia D, Felix ML, Guerra CV, Hidalgo R, Martinez-Zapata MJ, Simancas-Racines D. Vaccines for the common cold. Cochrane Database Syst Rev 2022; 12:CD002190. [PMID: 36515550 PMCID: PMC9749450 DOI: 10.1002/14651858.cd002190.pub6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND The common cold is a spontaneously remitting infection of the upper respiratory tract, characterised by a runny nose, nasal congestion, sneezing, cough, malaise, sore throat, and fever (usually < 37.8 ºC). Whilst the common cold is generally not harmful, it is a cause of economic burden due to school and work absenteeism. In the United States, economic loss due to the common cold is estimated at more than USD 40 billion per year, including an estimate of 70 million workdays missed by employees, 189 million school days missed by children, and 126 million workdays missed by parents caring for children with a cold. Additionally, data from Europe show that the total cost per episode may be up to EUR 1102. There is also a large expenditure due to inappropriate antimicrobial prescription. Vaccine development for the common cold has been difficult due to antigenic variability of the common cold viruses; even bacteria can act as infective agents. Uncertainty remains regarding the efficacy and safety of interventions for preventing the common cold in healthy people, thus we performed an update of this Cochrane Review, which was first published in 2011 and updated in 2013 and 2017. OBJECTIVES To assess the clinical effectiveness and safety of vaccines for preventing the common cold in healthy people. SEARCH METHODS We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (April 2022), MEDLINE (1948 to April 2022), Embase (1974 to April 2022), CINAHL (1981 to April 2022), and LILACS (1982 to April 2022). We also searched three trials registers for ongoing studies, and four websites for additional trials (April 2022). We did not impose any language or date restrictions. SELECTION CRITERIA Randomised controlled trials (RCTs) of any virus vaccine compared with placebo to prevent the common cold in healthy people. DATA COLLECTION AND ANALYSIS We used Cochrane's Screen4Me workflow to assess the initial search results. Four review authors independently performed title and abstract screening to identify potentially relevant studies. We retrieved the full-text articles for those studies deemed potentially relevant, and the review authors independently screened the full-text reports for inclusion in the review, recording reasons for exclusion of the excluded studies. Any disagreements were resolved by discussion or by consulting a third review author when needed. Two review authors independently collected data on a data extraction form, resolving any disagreements by consensus or by involving a third review author. We double-checked data transferred into Review Manager 5 software. Three review authors independently assessed risk of bias using RoB 1 tool as outlined in the Cochrane Handbook for Systematic Reviews of Interventions. We carried out statistical analysis using Review Manager 5. We did not conduct a meta-analysis, and we did not assess publication bias. We used GRADEpro GDT software to assess the certainty of the evidence and to create a summary of findings table. MAIN RESULTS: We did not identify any new RCTs for inclusion in this update. This review includes one RCT conducted in 1965 with an overall high risk of bias. The RCT included 2307 healthy young men in a military facility, all of whom were included in the analyses, and compared the effect of three adenovirus vaccines (live, inactivated type 4, and inactivated type 4 and 7) against a placebo (injection of physiological saline or gelatin capsule). There were 13 (1.14%) events in 1139 participants in the vaccine group, and 14 (1.19%) events in 1168 participants in the placebo group. Overall, we do not know if there is a difference between the adenovirus vaccine and placebo in reducing the incidence of the common cold (risk ratio 0.95, 95% confidence interval 0.45 to 2.02; very low-certainty evidence). Furthermore, no difference in adverse events when comparing live vaccine preparation with placebo was reported. We downgraded the certainty of the evidence to very low due to unclear risk of bias, indirectness because the population of this study was only young men, and imprecision because confidence intervals were wide and the number of events was low. The included study did not assess vaccine-related or all-cause mortality. AUTHORS' CONCLUSIONS: This Cochrane Review was based on one study with very low-certainty evidence, which showed that there may be no difference between the adenovirus vaccine and placebo in reducing the incidence of the common cold. We identified a need for well-designed, adequately powered RCTs to investigate vaccines for the common cold in healthy people. Future trials on interventions for preventing the common cold should assess a variety of virus vaccines for this condition, and should measure such outcomes as common cold incidence, vaccine safety, and mortality (all-cause and related to the vaccine).
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Affiliation(s)
- Camila Montesinos-Guevara
- Cochrane Ecuador, Centro de Investigación en Salud Pública y Epidemiología Clínica (CISPEC), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Diana Buitrago-Garcia
- Institute of Social and Preventive Medicine (ISPM), Graduate School of Health Sciences, University of Bern, Bern, Switzerland
| | - Maria L Felix
- Departamento de Neonatología, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Claudia V Guerra
- Cochrane Ecuador, Centro de Investigación en Salud Pública y Epidemiología Clínica (CISPEC), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Ricardo Hidalgo
- Cochrane Ecuador, Centro de Investigación en Salud Pública y Epidemiología Clínica (CISPEC), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Maria José Martinez-Zapata
- Cochrane Ecuador, Centro de Investigación en Salud Pública y Epidemiología Clínica (CISPEC), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
- Iberoamerican Cochrane Centre, Biomedical Research Institute Sant Pau (IIB Sant Pau), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Daniel Simancas-Racines
- Cochrane Ecuador, Centro de Investigación en Salud Pública y Epidemiología Clínica (CISPEC), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
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Pohler A, Abdelfatah S, Riedl M, Meesters C, Hildebrandt A, Efferth T. Potential Coronaviral Inhibitors of the Nucleocapsid Protein Identified In Silico and In Vitro from a Large Natural Product Library. Pharmaceuticals (Basel) 2022; 15:ph15091046. [PMID: 36145267 PMCID: PMC9503946 DOI: 10.3390/ph15091046] [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: 07/06/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022] Open
Abstract
The nucleocapsid protein (NP) is one of the main proteins out of four structural proteins of coronaviruses including the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, discovered in 2019. NP packages the viral RNA during virus assembly and is, therefore, indispensable for virus reproduction. NP consists of two domains, i.e., the N- and C-terminal domains. RNA-binding is mainly performed by a binding pocket within the N-terminal domain (NTD). NP represents an important target for drug discovery to treat COVID-19. In this project, we used the Vina LC virtual drug screening software and a ZINC-based database with 210,541 natural and naturally derived compounds that specifically target the binding pocket of NTD of NP. Our aim was to identify coronaviral inhibitors that target NP not only of SARS-CoV-2 but also of other diverse human pathogenic coronaviruses. Virtual drug screening and molecular docking procedures resulted in 73 candidate compounds with a binding affinity below −9 kcal/mol with NP NTD of SARS-CoV-1, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-NL63, HoC-229E, and HCoV-HKU1. The top five compounds that met the applied drug-likeness criteria were then tested for their binding in vitro to the NTD of the full-length recombinant NP proteins using microscale thermophoresis. Compounds (1), (2), and (4), which belong to the same scaffold family of 4-oxo-substituted-6-[2-(4a-hydroxy-decahydroisoquinolin-2-yl)2H-chromen-2-ones and which are derivates of coumarin, were bound with good affinity to NP. Compounds (1) and (4) were bound to the full-length NP of SARS-CoV-2 (aa 1–419) with Kd values of 0.798 (±0.02) µM and 8.07 (±0.36) µM, respectively. Then, these coumarin derivatives were tested with the SARS-CoV-2 NP NTD (aa 48–174). Compounds (1) and (4) revealed Kd-values of 0.95 (±0.32) µM and 7.77 (±6.39) µM, respectively. Compounds (1) and (4) caused low toxicity in human A549 and MRC-5 cell lines. These compounds may represent possible drug candidates, which need further optimization to be used against COVID-19 and other coronaviral infections.
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Affiliation(s)
- Alexandra Pohler
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Sara Abdelfatah
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Max Riedl
- High Performance Computing Group, University of Mainz, 55131 Mainz, Germany
| | - Christian Meesters
- High Performance Computing Group, University of Mainz, 55131 Mainz, Germany
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
- Correspondence: ; Tel.: +49-6131-3925751; Fax: +49-6131-3923752
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8
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Agarwal A, Beck KL, Capponi S, Kunitomi M, Nayar G, Seabolt E, Mahadeshwar G, Bianco S, Mukherjee V, Kaufman JH. Predicting Epitope Candidates for SARS-CoV-2. Viruses 2022; 14:v14081837. [PMID: 36016459 PMCID: PMC9416013 DOI: 10.3390/v14081837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Epitopes are short amino acid sequences that define the antigen signature to which an antibody or T cell receptor binds. In light of the current pandemic, epitope analysis and prediction are paramount to improving serological testing and developing vaccines. In this paper, known epitope sequences from SARS-CoV, SARS-CoV-2, and other Coronaviridae were leveraged to identify additional antigen regions in 62K SARS-CoV-2 genomes. Additionally, we present epitope distribution across SARS-CoV-2 genomes, locate the most commonly found epitopes, and discuss where epitopes are located on proteins and how epitopes can be grouped into classes. The mutation density of different protein regions is presented using a big data approach. It was observed that there are 112 B cell and 279 T cell conserved epitopes between SARS-CoV-2 and SARS-CoV, with more diverse sequences found in Nucleoprotein and Spike glycoprotein.
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Affiliation(s)
- Akshay Agarwal
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
- Correspondence: (A.A.); (K.L.B.)
| | - Kristen L. Beck
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
- Correspondence: (A.A.); (K.L.B.)
| | - Sara Capponi
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
- NSF Center for Cellular Construction, San Francisco, CA 94158, USA
| | - Mark Kunitomi
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Gowri Nayar
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Edward Seabolt
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Gandhar Mahadeshwar
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Simone Bianco
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
- NSF Center for Cellular Construction, San Francisco, CA 94158, USA
| | - Vandana Mukherjee
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - James H. Kaufman
- AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
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9
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Rafael Ciges-Tomas J, Franco ML, Vilar M. Identification of a guanine-specific pocket in the protein N of SARS-CoV-2. Commun Biol 2022; 5:711. [PMID: 35842466 PMCID: PMC9288159 DOI: 10.1038/s42003-022-03647-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/28/2022] [Indexed: 01/14/2023] Open
Abstract
The SARS-CoV-2 nucleocapsid protein (N) is responsible for RNA binding. Here we report the crystal structure of the C-terminal domain (NCTD) in open and closed conformations and in complex with guanine triphosphate, GTP. The crystal structure and biochemical studies reveal a specific interaction between the guanine, a nucleotide enriched in the packaging signals regions of coronaviruses, and a highly conserved tryptophan residue (W330). In addition, EMSA assays with SARS-CoV-2 derived RNA hairpin loops from a putative viral packaging sequence showed the preference interaction of the N-CTD to RNA oligonucleotides containing G and the loss of the specificity in the mutant W330A. Here we propose that this interaction may facilitate the viral assembly process. In summary, we have identified a specific guanine-binding pocket in the N protein that may be used to design viral assembly inhibitors. The molecular basis of GTP binding to the N protein from SARS-CoV-2 is presented, providing a framework for drug design and disruption of the RNA packing function in the N protein.
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Affiliation(s)
- J Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia-CSIC Spanish National Research Council, C/Jaime Roig, 11, 46010, Valencia, Spain. .,Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200, Copenhagen, Denmark.
| | - María Luisa Franco
- Instituto de Biomedicina de Valencia-CSIC Spanish National Research Council, C/Jaime Roig, 11, 46010, Valencia, Spain
| | - Marçal Vilar
- Instituto de Biomedicina de Valencia-CSIC Spanish National Research Council, C/Jaime Roig, 11, 46010, Valencia, Spain.
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10
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Dang S, Ren L, Wang J. Functional mutations of SARS-CoV-2: implications to viral transmission, pathogenicity and immune escape. Chin Med J (Engl) 2022; 135:1213-1222. [PMID: 35788093 PMCID: PMC9337262 DOI: 10.1097/cm9.0000000000002158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT The pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to major public health challenges globally. The increasing viral lineages identified indicate that the SARS-CoV-2 genome is evolving at a rapid rate. Viral genomic mutations may cause antigenic drift or shift, which are important ways by which SARS-CoV-2 escapes the human immune system and changes its transmissibility and virulence. Herein, we summarize the functional mutations in SARS-CoV-2 genomes to characterize its adaptive evolution to inform the development of vaccination, treatment as well as control and intervention measures.
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Affiliation(s)
- Shengyuan Dang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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11
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Zhang B, Tian J, Zhang Q, Xie Y, Wang K, Qiu S, Lu K, Liu Y. Comparing the Nucleocapsid Proteins of Human Coronaviruses: Structure, Immunoregulation, Vaccine, and Targeted Drug. Front Mol Biosci 2022; 9:761173. [PMID: 35573742 PMCID: PMC9099148 DOI: 10.3389/fmolb.2022.761173] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/28/2022] [Indexed: 01/08/2023] Open
Abstract
The seven pathogenic human coronaviruses (HCoVs) include HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1, which usually cause mild upper respiratory tract diseases, and SARS-CoV, MERS-CoV, and SARS-CoV-2, which cause a severe acute respiratory syndrome. The nucleocapsid (N) protein, as the dominant structural protein from coronaviruses that bind to the genomic RNA, participates in various vital activities after virus invasion and will probably become a promising target of antiviral drug design. Therefore, a comprehensive literature review of human coronavirus’ pathogenic mechanism and therapeutic strategies is necessary for the control of the pandemic. Here, we give a systematic summary of the structures, immunoregulation, and potential vaccines and targeted drugs of the HCoVs N protein. First, we provide a general introduction to the fundamental structures and molecular function of N protein. Next, we outline the N protein mediated immune regulation and pathogenesis mechanism. Finally, we comprehensively summarize the development of potential N protein-targeted drugs and candidate vaccines to treat coronavirus disease 2019 (COVID-19). We believe this review provides insight into the virulence and transmission of SARS-CoV-2 as well as support for further study on epidemic control of COVID-19.
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Affiliation(s)
- Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
| | - Junjie Tian
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Qintao Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Yan Xie
- School of Public Health, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Shuyi Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Keyu Lu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
| | - Yang Liu
- School of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
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12
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Taborska P, Lastovicka J, Stakheev D, Strizova Z, Bartunkova J, Smrz D. SARS-CoV-2 spike glycoprotein-reactive T cells can be readily expanded from COVID-19 vaccinated donors. IMMUNITY INFLAMMATION AND DISEASE 2021; 9:1452-1467. [PMID: 34314576 PMCID: PMC8427053 DOI: 10.1002/iid3.496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 12/16/2022]
Abstract
Introduction The COVID‐19 vaccine was designed to provide protection against infection by the severe respiratory coronavirus 2 (SARS‐CoV‐2) and coronavirus disease 2019 (COVID‐19). However, the vaccine's efficacy can be compromised in patients with immunodeficiencies or the vaccine‐induced immunoprotection suppressed by other comorbidity treatments, such as chemotherapy or immunotherapy. To enhance the protective role of the COVID‐19 vaccine, we have investigated a combination of the COVID‐19 vaccination with ex vivo enrichment and large‐scale expansion of SARS‐CoV‐2 spike glycoprotein‐reactive CD4+ and CD8+ T cells. Methods SARS‐CoV‐2‐unexposed donors were vaccinated with two doses of the BNT162b2 SARS‐CoV‐2 vaccine. The peripheral blood mononuclear cells of the vaccinated donors were cell culture‐enriched with T cells reactive to peptides derived from SARS‐CoV‐2 spike glycoprotein. The enriched cell cultures were large‐scale expanded using the rapid expansion protocol (REP) and the peptide‐reactive T cells were evaluated. Results We show that vaccination with the SARS‐CoV‐2 spike glycoprotein‐based mRNA COVID‐19 vaccine‐induced humoral response against SARS‐CoV‐2 spike glycoprotein in all tested healthy SARS‐CoV‐2‐unexposed donors. This humoral response was found to correlate with the ability of the donors' PBMCs to become enriched with SARS‐CoV‐2 spike glycoprotein‐reactive CD4+ and CD8+ T cells. Using an 11‐day REP, the enriched cell cultures were expanded nearly 1000‐fold, and the proportions of the SARS‐CoV‐2 spike glycoprotein‐reactive T cells increased. Conclusion These findings show for the first time that the combination of the COVID‐19 vaccination and ex vivo T cell large‐scale expansion of SARS‐CoV‐2‐reactive T cells could be a powerful tool for developing T cell‐based adoptive cellular immunotherapy of COVID‐19.
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Affiliation(s)
- Pavla Taborska
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Lastovicka
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Dmitry Stakheev
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Zuzana Strizova
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jirina Bartunkova
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Daniel Smrz
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
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13
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Liu Y, Liang QZ, Lu W, Yang YL, Chen R, Huang YW, Wang B. A Comparative Analysis of Coronavirus Nucleocapsid (N) Proteins Reveals the SADS-CoV N Protein Antagonizes IFN-β Production by Inducing Ubiquitination of RIG-I. Front Immunol 2021; 12:688758. [PMID: 34220846 PMCID: PMC8242249 DOI: 10.3389/fimmu.2021.688758] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 12/23/2022] Open
Abstract
Coronaviruses (CoVs) are a known global threat, and most recently the ongoing COVID-19 pandemic has claimed more than 2 million human lives. Delays and interference with IFN responses are closely associated with the severity of disease caused by CoV infection. As the most abundant viral protein in infected cells just after the entry step, the CoV nucleocapsid (N) protein likely plays a key role in IFN interruption. We have conducted a comprehensive comparative analysis and report herein that the N proteins of representative human and animal CoVs from four different genera [swine acute diarrhea syndrome CoV (SADS-CoV), porcine epidemic diarrhea virus (PEDV), severe acute respiratory syndrome CoV (SARS-CoV), SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), infectious bronchitis virus (IBV) and porcine deltacoronavirus (PDCoV)] suppress IFN responses by multiple strategies. In particular, we found that the N protein of SADS-CoV interacted with RIG-I independent of its RNA binding activity, mediating K27-, K48- and K63-linked ubiquitination of RIG-I and its subsequent proteasome-dependent degradation, thus inhibiting the host IFN response. These data provide insight into the interaction between CoVs and host, and offer new clues for the development of therapies against these important viruses.
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Affiliation(s)
- Yan Liu
- Department of Veterinary Medicine, Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China
| | - Qi-Zhang Liang
- Department of Veterinary Medicine, Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China
| | - Wan Lu
- Department of Veterinary Medicine, Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China
| | - Yong-Le Yang
- Department of Veterinary Medicine, Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China
| | - Ruiai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Bin Wang
- Department of Veterinary Medicine, Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China
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14
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Sherwood LJ, Hayhurst A. Toolkit for Quickly Generating and Characterizing Molecular Probes Specific for SARS-CoV-2 Nucleocapsid as a Primer for Future Coronavirus Pandemic Preparedness. ACS Synth Biol 2021; 10:379-390. [PMID: 33534552 PMCID: PMC7875338 DOI: 10.1021/acssynbio.0c00566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 12/31/2022]
Abstract
Generating and characterizing immunoreagents to enable studies of novel emerging viruses is an area where ensembles of synthetic genes, recombinant antibody pipelines, and modular antibody-reporter fusion proteins can respond rapidly. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread through the global population causing widespread morbidity, mortality, and socioeconomic chaos. Using SARS-CoV-2 as our model and starting with a gBlocks encoded nucleocapsid (N) gene, we purified recombinant protein from E. coli, to serve as bait for selecting semisynthetic nanobodies from our Nomad single-pot library. Clones were isolated in days and first fused to Gaussia luciferase to determine EC50 in the tens of nM range, and second fused to the ascorbate peroxidase derivative APEX2 for sensitive detection of SARS-CoV-2 infected cells. To generate inherently fluorescent immunoreagents, we introduce novel periplasmic sdAb fusions made with mNeonGreen and mScarlet-I, which were produced at milligram amounts. The fluorescent fusion proteins enabled concise visualization of SARS-CoV-2 N in the cytoplasm but not in the nucleus 24 h post infection, akin to the distribution of SARS-CoV N, thereby validating these useful imaging tools. SdAb reactivity appeared specific to SARS-CoV-2 with very much weaker binding to SARS-CoV, and no noticeable cross-reactivity to a panel of overexpressed human codon optimized N proteins from other CoV. High periplasmic expression levels and in silico immortalization of the nanobody constructs guarantees a cost-effective and reliable source of SARS-CoV-2 immunoreagents. Our proof-of-principle study should be applicable to known and newly emerging CoV to broaden the tools available for their analysis and help safeguard human health in a more proactive than reactive manner.
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Affiliation(s)
- Laura Jo Sherwood
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Andrew Hayhurst
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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15
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Zinzula L, Basquin J, Bohn S, Beck F, Klumpe S, Pfeifer G, Nagy I, Bracher A, Hartl FU, Baumeister W. High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2. Biochem Biophys Res Commun 2021; 538:54-62. [PMID: 33039147 PMCID: PMC7532810 DOI: 10.1016/j.bbrc.2020.09.131] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022]
Abstract
Unprecedented by number of casualties and socio-economic burden occurring worldwide, the coronavirus disease 2019 (Covid-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the worst health crisis of this century. In order to develop adequate countermeasures against Covid-19, identification and structural characterization of suitable antiviral targets within the SARS-CoV-2 protein repertoire is urgently needed. The nucleocapsid phosphoprotein (N) is a multifunctional and highly immunogenic determinant of virulence and pathogenicity, whose main functions consist in oligomerizing and packaging the single-stranded RNA (ssRNA) viral genome. Here we report the structural and biophysical characterization of the SARS-CoV-2 N C-terminal domain (CTD), on which both N homo-oligomerization and ssRNA binding depend. Crystal structures solved at 1.44 Å and 1.36 Å resolution describe a rhombus-shape N CTD dimer, which stably exists in solution as validated by size-exclusion chromatography coupled to multi-angle light scattering and analytical ultracentrifugation. Differential scanning fluorimetry revealed moderate thermal stability and a tendency towards conformational change. Microscale thermophoresis demonstrated binding to a 7-bp SARS-CoV-2 genomic ssRNA fragment at micromolar affinity. Furthermore, a low-resolution preliminary model of the full-length SARS-CoV N in complex with ssRNA, obtained by cryo-electron microscopy, provides an initial understanding of self-associating and RNA binding functions exerted by the SARS-CoV-2 N.
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Affiliation(s)
- Luca Zinzula
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany,Corresponding authors
| | - Jerome Basquin
- The Max-Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Stefan Bohn
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany,The Max-Planck Institute of Biochemistry, Department of Cellular Machines and Signaling, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Florian Beck
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Sven Klumpe
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Günter Pfeifer
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - István Nagy
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Andreas Bracher
- The Max-Planck Institute of Biochemistry, Department of Cellular Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - F. Ulrich Hartl
- The Max-Planck Institute of Biochemistry, Department of Cellular Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Baumeister
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
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16
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Yang M, He S, Chen X, Huang Z, Zhou Z, Zhou Z, Chen Q, Chen S, Kang S. Structural Insight Into the SARS-CoV-2 Nucleocapsid Protein C-Terminal Domain Reveals a Novel Recognition Mechanism for Viral Transcriptional Regulatory Sequences. Front Chem 2021; 8:624765. [PMID: 33511102 PMCID: PMC7835709 DOI: 10.3389/fchem.2020.624765] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has caused massive disruptions to society and the economy, and the transcriptional regulatory mechanisms behind the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are poorly understood. Herein, we determined the crystal structure of the SARS-CoV-2 nucleocapsid protein C-terminal domain (CTD) at a resolution of 2.0 Å, and demonstrated that the CTD has a comparable distinct electrostatic potential surface to equivalent domains of other reported CoVs, suggesting that the CTD has novel roles in viral RNA binding and transcriptional regulation. Further in vitro biochemical assays demonstrated that the viral genomic intergenic transcriptional regulatory sequences (TRSs) interact with the SARS-CoV-2 nucleocapsid protein CTD with a flanking region. The unpaired adeno dinucleotide in the TRS stem-loop structure is a major determining factor for their interactions. Taken together, these results suggested that the nucleocapsid protein CTD is responsible for the discontinuous viral transcription mechanism by recognizing the different patterns of viral TRS during transcription.
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Affiliation(s)
- Mei Yang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Suhua He
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Xiaoxue Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhaoxia Huang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Ziliang Zhou
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhechong Zhou
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Qiuyue Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Shoudeng Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Sisi Kang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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17
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Qi M, Zambrano-Moreno C, Pineda P, Calderón C, Rincón-Monroy MA, Diaz A, Marthaler DG. Several lineages of porcine epidemic diarrhea virus in Colombia during the 2014 and 2016 epidemic. Transbound Emerg Dis 2020; 68:2465-2476. [PMID: 33155439 DOI: 10.1111/tbed.13914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/16/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is a significant global, enteric coronavirus in pigs and was first reported in Colombia in 2014. However, the epidemiology, genetic and antigenic characteristics of the virus have yet to be investigated. In this study, we investigated the dissemination of PEDV by testing 536 samples by RT-PCR over a 33-month period. The 35.8% of positive samples (n = 192) was significantly different (p < .01) between months over time, with a higher number of positives samples occurring at the beginning of the epidemic and during the second epidemic wave within the main pork producing region. The complete PEDV genomes were generated for 21 strains, which shared a high nucleotide and amino acid sequence identity, except for the spike (S) gene. Recombinant regions were identified within the Colombian strains and between Colombian and Asian PEDV strains. Phylogenetic analysis of the 21 Colombian strains demonstrated the presence of 7 lineages that shared common ancestors with PEDV strains from the United States. Moreover, the antigenic analysis demonstrated residue differences in the neutralizing epitopes in the spike and nucleocapsid proteins. Our results illustrated the simultaneous introduction of the two PEDV genotypes (GIIa American pandemic and S-INDEL) into the Colombian swine industry during the 2014 PEDV epidemic and enhanced our understanding of the epidemiology and molecular diversity of PEDV in Colombia.
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Affiliation(s)
- Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | | | - Pilar Pineda
- Asociación Colombiana de Porcicultores - PorkColombia, Bogotá, Colombia
| | - Claudia Calderón
- Laboratorio Nacional de Diagnóstico Veterinario, Instituto Colombiano Agropecuario ICA, Bogotá, Colombia
| | - María A Rincón-Monroy
- Laboratorio Nacional de Diagnóstico Veterinario, Instituto Colombiano Agropecuario ICA, Bogotá, Colombia
| | - Andres Diaz
- Asociación Colombiana de Porcicultores - PorkColombia, Bogotá, Colombia.,Pig Improvement Company LATAM, Santiago de Querétaro, Querétaro, Mexico
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.,Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
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18
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Dinesh DC, Chalupska D, Silhan J, Koutna E, Nencka R, Veverka V, Boura E. Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein. PLoS Pathog 2020; 16:e1009100. [PMID: 33264373 PMCID: PMC7735635 DOI: 10.1371/journal.ppat.1009100] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/14/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 is a single-stranded positive-sense RNA virus. Like other coronaviruses, SARS-CoV-2 has an unusually large genome that encodes four structural proteins and sixteen nonstructural proteins. The structural nucleocapsid phosphoprotein N is essential for linking the viral genome to the viral membrane. Both N-terminal RNA binding (N-NTD) and C-terminal dimerization domains are involved in capturing the RNA genome and, the intrinsically disordered region between these domains anchors the ribonucleoprotein complex to the viral membrane. Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy. We observed a positively charged canyon on the surface of the N-NTD that might serve as a putative RNA binding site similarly to other coronaviruses. The subsequent NMR titrations using single-stranded and double-stranded RNA revealed a much more extensive U-shaped RNA-binding cleft lined with regularly distributed arginines and lysines. The NMR data supported by mutational analysis allowed us to construct hybrid atomic models of the N-NTD/RNA complex that provided detailed insight into RNA recognition.
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Affiliation(s)
| | - Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eliska Koutna
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vaclav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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19
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Dinesh DC, Chalupska D, Silhan J, Koutna E, Nencka R, Veverka V, Boura E. Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein. PLoS Pathog 2020. [PMID: 33264373 DOI: 10.1101/2020.04.02.022194] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 is a single-stranded positive-sense RNA virus. Like other coronaviruses, SARS-CoV-2 has an unusually large genome that encodes four structural proteins and sixteen nonstructural proteins. The structural nucleocapsid phosphoprotein N is essential for linking the viral genome to the viral membrane. Both N-terminal RNA binding (N-NTD) and C-terminal dimerization domains are involved in capturing the RNA genome and, the intrinsically disordered region between these domains anchors the ribonucleoprotein complex to the viral membrane. Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy. We observed a positively charged canyon on the surface of the N-NTD that might serve as a putative RNA binding site similarly to other coronaviruses. The subsequent NMR titrations using single-stranded and double-stranded RNA revealed a much more extensive U-shaped RNA-binding cleft lined with regularly distributed arginines and lysines. The NMR data supported by mutational analysis allowed us to construct hybrid atomic models of the N-NTD/RNA complex that provided detailed insight into RNA recognition.
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Affiliation(s)
| | - Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eliska Koutna
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vaclav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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20
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Peng Y, Du N, Lei Y, Dorje S, Qi J, Luo T, Gao GF, Song H. Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design. EMBO J 2020; 39:e105938. [PMID: 32914439 PMCID: PMC7560215 DOI: 10.15252/embj.2020105938] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
COVID-19, caused by SARS-CoV-2, has resulted in severe and unprecedented economic and social disruptions in the world. Nucleocapsid (N) protein, which is the major structural component of the virion and is involved in viral replication, assembly and immune regulation, plays key roles in the viral life cycle. Here, we solved the crystal structures of the N- and C-terminal domains (N-NTD and N-CTD) of SARS-CoV-2 N protein, at 1.8 and 1.5 Å resolution, respectively. Both structures show conserved features from other CoV N proteins. The binding sites targeted by small molecules against HCoV-OC43 and MERS-CoV, which inhibit viral infection by blocking the RNA-binding activity or normal oligomerization of N protein, are relatively conserved in our structure, indicating N protein is a promising drug target. In addition, certain areas of N-NTD and N-CTD display distinct charge distribution patterns in SARS-CoV-2, which may alter the RNA-binding modes. The specific antigenic characteristics are critical for developing specific immune-based rapid diagnostic tests. Our structural information can aid in the discovery and development of antiviral inhibitors against SARS-CoV-2 in the future.
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Affiliation(s)
- Ya Peng
- Laboratory of Animal Infectious DiseasesCollege of Animal Sciences and Veterinary MedicineGuangxi UniversityNanningChina
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ning Du
- Research Network of Immunity and Health (RNIH)Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
| | - Yuqing Lei
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Sonam Dorje
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tingrong Luo
- Laboratory of Animal Infectious DiseasesCollege of Animal Sciences and Veterinary MedicineGuangxi UniversityNanningChina
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Research Network of Immunity and Health (RNIH)Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hao Song
- Research Network of Immunity and Health (RNIH)Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
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21
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Ye Q, West AMV, Silletti S, Corbett KD. Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. Protein Sci 2020; 29:1890-1901. [PMID: 32654247 PMCID: PMC7405475 DOI: 10.1002/pro.3909] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 01/18/2023]
Abstract
The COVID-2019 pandemic is the most severe acute public health threat of the twenty-first century. To properly address this crisis with both robust testing and novel treatments, we require a deep understanding of the life cycle of the causative agent, the SARS-CoV-2 coronavirus. Here, we examine the architecture and self-assembly properties of the SARS-CoV-2 nucleocapsid protein, which packages viral RNA into new virions. We determined a 1.4 Å resolution crystal structure of this protein's N2b domain, revealing a compact, intertwined dimer similar to that of related coronaviruses including SARS-CoV. While the N2b domain forms a dimer in solution, addition of the C-terminal spacer B/N3 domain mediates formation of a homotetramer. Using hydrogen-deuterium exchange mass spectrometry, we find evidence that at least part of this putatively disordered domain is structured, potentially forming an α-helix that self-associates and cooperates with the N2b domain to mediate tetramer formation. Finally, we map the locations of amino acid substitutions in the N protein from over 38,000 SARS-CoV-2 genome sequences. We find that these substitutions are strongly clustered in the protein's N2a linker domain, and that substitutions within the N1b and N2b domains cluster away from their functional RNA binding and dimerization interfaces. Overall, this work reveals the architecture and self-assembly properties of a key protein in the SARS-CoV-2 life cycle, with implications for both drug design and antibody-based testing.
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Affiliation(s)
- Qiaozhen Ye
- Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Alan M. V. West
- Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Steve Silletti
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kevin D. Corbett
- Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCaliforniaUSA
- Ludwig Institute for Cancer ResearchLa JollaCaliforniaUSA
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22
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Zhou R, Zeng R, von Brunn A, Lei J. Structural characterization of the C-terminal domain of SARS-CoV-2 nucleocapsid protein. MOLECULAR BIOMEDICINE 2020; 1:2. [PMID: 34765991 PMCID: PMC7406681 DOI: 10.1186/s43556-020-00001-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/12/2020] [Indexed: 12/18/2022] Open
Abstract
The newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a global human health crisis. The CoV nucleocapsid (N) protein plays essential roles both in the viral genomic RNA packaging and the regulation of host cellular machinery. Here, to contribute to the structural information of the N protein, we describe the 2.0 Å crystal structure of the SARS-CoV-2 N protein C-terminal domain (N-CTD). The structure indicates an extensive interaction dimer in a domain-swapped manner. The interface of this dimer was first thoroughly illustrated. Also, the SARS-CoV-2 N-CTD dimerization form was verified in solution using size-exclusion chromatography. Based on the structural comparison of the N-CTDs from alpha-, beta-, and gamma-CoVs, we demonstrate the common and specific characteristics of the SARS-CoV-2 N-CTD. Furthermore, we provide evidence that the SARS-CoV-2 N-CTD possesses the binding ability to single-stranded RNA, single-stranded DNA as well as double-stranded DNA in vitro. In conclusion, this study could potentially accelerate research to understand the complete biological functions of the new CoV N protein.
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23
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Ye Q, West AM, Silletti S, Corbett KD. Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.17.100685. [PMID: 32511359 PMCID: PMC7263487 DOI: 10.1101/2020.05.17.100685] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The COVID-2019 pandemic is the most severe acute public health threat of the twenty-first century. To properly address this crisis with both robust testing and novel treatments, we require a deep understanding of the life cycle of the causative agent, the SARS-CoV-2 coronavirus. Here, we examine the architecture and self-assembly properties of the SARS-CoV-2 nucleocapsid protein, which packages viral RNA into new virions. We determined a 1.4 Å resolution crystal structure of this protein's N2b domain, revealing a compact, intertwined dimer similar to that of related coronaviruses including SARS-CoV. While the N2b domain forms a dimer in solution, addition of the C-terminal spacer B/N3 domain mediates formation of a homotetramer. Using hydrogen-deuterium exchange mass spectrometry, we find evidence that at least part of this putatively disordered domain is structured, potentially forming an α-helix that self-associates and cooperates with the N2b domain to mediate tetramer formation. Finally, we map the locations of amino acid substitutions in the N protein from over 38,000 SARS-CoV-2 genome sequences. We find that these substitutions are strongly clustered in the protein's N2a linker domain, and that substitutions within the N1b and N2b domains cluster away from their functional RNA binding and dimerization interfaces. Overall, this work reveals the architecture and self-assembly properties of a key protein in the SARS-CoV-2 life cycle, with implications for both drug design and antibody-based testing.
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Affiliation(s)
- Qiaozhen Ye
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Alan M.V. West
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Steve Silletti
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Kevin D. Corbett
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA
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24
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Kronbichler A, Effenberger M, Eisenhut M, Lee KH, Shin JI. Seven recommendations to rescue the patients and reduce the mortality from COVID-19 infection: An immunological point of view. Autoimmun Rev 2020; 19:102570. [PMID: 32376397 PMCID: PMC7252097 DOI: 10.1016/j.autrev.2020.102570] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/28/2022]
Abstract
Now COVID-19 is causing a severe public health emergency and the mortality is rapidly increasing all over the world. In the current pandemic era, although there have been many efforts to diagnose a number of patients with symptoms or close contacts, there is no definite guideline for the initial therapeutic approach for them and therefore, many patients have been dying due to a hyperinflammatory immunological reaction labeled as “cytokine storm”. Severe patients are hospitalized and the treatment is done, though they have not been established yet. Currently, however, no treatment is provided for those who are isolated at home or shelter until they get severe symptoms, which will increase the harms to the patients. In this review, we discuss some important points dedicated to the management of patients with COVID-19, which should help reducing morbidity and mortality. In this era, we suggest 7 recommendations to rescue the patients and to reduce the morbidity and mortality due to COVID-19 based on the immunological point of view.
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Affiliation(s)
- Andreas Kronbichler
- Department of Internal Medicine IV Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Maria Effenberger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University Innsbruck, Innsbruck, Austria
| | - Michael Eisenhut
- Luton & Dunstable University Hospital NHS Foundation Trust, Luton, United Kingdom
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea.
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25
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Li YH, Hu CY, Wu NP, Yao HP, Li LJ. Molecular Characteristics, Functions, and Related Pathogenicity of MERS-CoV Proteins. ENGINEERING (BEIJING, CHINA) 2019; 5:940-947. [PMID: 32288963 PMCID: PMC7104727 DOI: 10.1016/j.eng.2018.11.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/24/2018] [Accepted: 11/12/2018] [Indexed: 05/02/2023]
Abstract
Middle East respiratory syndrome (MERS) is a viral respiratory disease caused by a de novo coronavirus-MERS-CoV-that is associated with high mortality. However, the mechanism by which MERS-CoV infects humans remains unclear. To date, there is no effective vaccine or antibody for human immunity and treatment, other than the safety and tolerability of the fully human polyclonal Immunoglobulin G (IgG) antibody (SAB-301) as a putative therapeutic agent specific for MERS. Although rapid diagnostic and public health measures are currently being implemented, new cases of MERS-CoV infection are still being reported. Therefore, various effective measures should be taken to prevent the serious impact of similar epidemics in the future. Further investigation of the epidemiology and pathogenesis of the virus, as well as the development of effective therapeutic and prophylactic anti-MERS-CoV infections, is necessary. For this purpose, detailed information on MERS-CoV proteins is needed. In this review, we describe the major structural and nonstructural proteins of MERS-CoV and summarize different potential strategies for limiting the outbreak of MERS-CoV. The combination of computational biology and virology can accelerate the advanced design and development of effective peptide therapeutics against MERS-CoV. In summary, this review provides important information about the progress of the elimination of MERS, from prevention to treatment.
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Affiliation(s)
- Yan-Hua Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
| | - Chen-Yu Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
| | - Nan-Ping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
| | - Lan-Juan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
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26
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Xie W, Ao C, Yang Y, Liu Y, Liang R, Zeng Z, Ye G, Xiao S, Fu ZF, Dong W, Peng G. Two critical N-terminal epitopes of the nucleocapsid protein contribute to the cross-reactivity between porcine epidemic diarrhea virus and porcine transmissible gastroenteritis virus. J Gen Virol 2019; 100:206-216. [PMID: 30652967 DOI: 10.1099/jgv.0.001216] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both porcine epidemic diarrhoea virus (PEDV) and porcine transmissible gastroenteritis virus (TGEV), which cause high mortality in piglets and produce similar clinical symptoms and histopathological morphology, belong to the genus Alphacoronavirus. Serological diagnosis plays an important role in distinguishing pathogen species. Together with the spike (S) protein, the nucleocapsid (N) protein is one of the immunodominant regions among coronaviruses. In this study, two-way antigenic cross-reactivity between the N proteins of PEDV and TGEV was observed by indirect immunofluorescence assay (IFA) and Western blot analysis. Furthermore, the PEDV N protein harbouring truncations of amino acids (aa) 1 to 170 or aa 125 to 301 was demonstrated to cross-react with the anti-TGEV N polyclonal antibody (PAb), whereas the truncation-expressing aa 302 to 401 resulted in a specific reaction with the anti-PEDV N PAb but not with the anti-TGEV N PAb. Mutants of the PEDV N protein were generated based on sequence alignment and structural analysis; we then confirmed that the N-terminal residues 58-RWRMRRGERIE-68 and 78-LGTGPHAD-85 contributed to the cross-reactivity. All the results provide vital clues for the development of precise diagnostic assays for porcine coronaviruses.
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Affiliation(s)
- Wenting Xie
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 3The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Chaojie Ao
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Yilin Yang
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 3The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Yinan Liu
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 3The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Rui Liang
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 3The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Zhe Zeng
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 3The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Gang Ye
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 3The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Shaobo Xiao
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Zhen F Fu
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 4Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Wanyu Dong
- 5National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
- 3The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Guiqing Peng
- 3The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 2College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, PR China
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, PR China
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27
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Nguyen THV, Lichière J, Canard B, Papageorgiou N, Attoumani S, Ferron F, Coutard B. Structure and oligomerization state of the C-terminal region of the Middle East respiratory syndrome coronavirus nucleoprotein. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:8-15. [PMID: 30644840 PMCID: PMC7159728 DOI: 10.1107/s2059798318014948] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a human pathogen responsible for a severe respiratory illness that emerged in 2012. Structural information about the proteins that constitute the viral particle is scarce. In order to contribute to a better understanding of the nucleoprotein (N) in charge of RNA genome encapsidation, the structure of the C-terminal domain of N from MERS-CoV obtained using single-crystal X-ray diffraction is reported here at 1.97 Å resolution. The molecule is present as a dimer in the crystal structure and this oligomerization state is confirmed in solution, as measured by additional methods including small-angle X-ray scattering measurements. Comparisons with the structures of the C-terminal domains of N from other coronaviruses reveals a high degree of structural conservation despite low sequence conservation, and differences in electrostatic potential at the surface of the protein.
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Affiliation(s)
| | - Julie Lichière
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| | - Bruno Canard
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| | | | - Sarah Attoumani
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| | - François Ferron
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| | - Bruno Coutard
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
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