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1.
Cells ; 10(3)2021 03 02.
Article in English | MEDLINE | ID: covidwho-1125490

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) that has resulted in the current pandemic. The lack of highly efficacious antiviral drugs that can manage this ongoing global emergency gives urgency to establishing a comprehensive understanding of the molecular pathogenesis of SARS-CoV-2. We characterized the role of the nucleocapsid protein (N) of SARS-CoV-2 in modulating antiviral immunity. Overexpression of SARS-CoV-2 N resulted in the attenuation of retinoic acid inducible gene-I (RIG-I)-like receptor-mediated interferon (IFN) production and IFN-induced gene expression. Similar to the SARS-CoV-1 N protein, SARS-CoV-2 N suppressed the interaction between tripartate motif protein 25 (TRIM25) and RIG-I. Furthermore, SARS-CoV-2 N inhibited polyinosinic: polycytidylic acid [poly(I:C)]-mediated IFN signaling at the level of Tank-binding kinase 1 (TBK1) and interfered with the association between TBK1 and interferon regulatory factor 3 (IRF3), subsequently preventing the nuclear translocation of IRF3. We further found that both type I and III IFN production induced by either the influenza virus lacking the nonstructural protein 1 or the Zika virus were suppressed by the SARS-CoV-2 N protein. Our findings provide insights into the molecular function of the SARS-CoV-2 N protein with respect to counteracting the host antiviral immune response.


Subject(s)
Coronavirus Nucleocapsid Proteins/metabolism , DEAD Box Protein 58/metabolism , Interferons/metabolism , Receptors, Immunologic/metabolism , SARS-CoV-2/metabolism , DEAD Box Protein 58/genetics , Host-Pathogen Interactions/genetics , Humans , Interferon Regulatory Factor-3/genetics , Interferon Regulatory Factor-3/metabolism , Interferon Type I/genetics , Interferon Type I/metabolism , Interferon-gamma/genetics , Interferon-gamma/metabolism , Interferons/genetics , Orthomyxoviridae/genetics , Orthomyxoviridae/metabolism , Phosphoproteins/metabolism , Poly C/pharmacology , Poly I/pharmacology , Promoter Regions, Genetic , /metabolism , Receptors, Immunologic/genetics , SARS-CoV-2/genetics , Signal Transduction/drug effects , Signal Transduction/genetics , Transcription Factors/metabolism , Tripartite Motif Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Up-Regulation , Zika Virus/genetics , Zika Virus/metabolism
2.
Cells ; 10(2)2021 02 02.
Article in English | MEDLINE | ID: covidwho-1060037

ABSTRACT

Many viruses disrupt host gene expression by degrading host mRNAs and/or manipulating translation activities to create a cellular environment favorable for viral replication. Often, virus-induced suppression of host gene expression, including those involved in antiviral responses, contributes to viral pathogenicity. Accordingly, clarifying the mechanisms of virus-induced disruption of host gene expression is important for understanding virus-host cell interactions and virus pathogenesis. Three highly pathogenic human coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome (MERS)-CoV, and SARS-CoV-2, have emerged in the past two decades. All of them encode nonstructural protein 1 (nsp1) in their genomes. Nsp1 of SARS-CoV and MERS-CoV exhibit common biological functions for inducing endonucleolytic cleavage of host mRNAs and inhibition of host translation, while viral mRNAs evade the nsp1-induced mRNA cleavage. SARS-CoV nsp1 is a major pathogenic determinant for this virus, supporting the notion that a viral protein that suppresses host gene expression can be a virulence factor, and further suggesting the possibility that SARS-CoV-2 nsp1, which has high amino acid identity with SARS-CoV nsp1, may serve as a major virulence factor. This review summarizes the gene expression suppression functions of nsp1 of CoVs, with a primary focus on SARS-CoV nsp1 and MERS-CoV nsp1.


Subject(s)
Betacoronavirus , Coronavirus Infections/virology , RNA-Dependent RNA Polymerase/physiology , Viral Nonstructural Proteins/physiology , Animals , Betacoronavirus/pathogenicity , Betacoronavirus/physiology , Gene Expression Regulation , Host Microbial Interactions , Humans , Mice , RNA, Messenger/genetics , Virus Replication
3.
Comb Chem High Throughput Screen ; 24(9): 1482-1491, 2021.
Article in English | MEDLINE | ID: covidwho-914342

ABSTRACT

AIM AND OBJECTIVE: A recent study has revealed that non-structural protein 1 (Nsp1) of the SARS-CoV-2 is one of the novel targets for developing new antiviral drugs. To date, there is no significant exact medication available to treat Covid-19. As a result, both the death toll and the number of people affecting by this disease are increasing with each passing day. 35 phytochemicals having antiviral properties were taken to get the best compounds against Nsp1 Materials and Methods: As no PDB structure of this protein is available, homology modeling was done to predict the probable structure. After homology modeling, the best model was taken according to C-score and TM- score and then validated using different web servers. After validation, docking of these compounds was done using AutoDock vina, vega zz, and PyRx, and consensus docking score was considered to select molecules after docking. Finally, the orbitals energy calculation of these compounds was done to check their activity and the binding interactions of these molecules also analyzed. RESULTS: Molecules having a consensus score of -8kcal/mol or more negative were kept for further study and it was seen that 16 molecules had the given criteria. Then, drug-likeness filtration was done according to Lipinski's rule of five and 11 molecules remained. Out of these 11 molecules, 5 molecules had satisfactory ADMET properties. Calculation of orbital energy revealed their activity. CONCLUSION: It is expected that this research might be helpful for the development of new antiviral drugs active against SARS-CoV-2 targeting Nsp1.


Subject(s)
COVID-19/drug therapy , Computational Biology , Phytotherapy/methods , Plants, Medicinal/chemistry , Algorithms , Antiviral Agents , Binding Sites , Drug Development , Drug Evaluation, Preclinical , Humans , Ligands , Models, Theoretical , Molecular Docking Simulation , Predictive Value of Tests , Reproducibility of Results
4.
J Gen Virol ; 102(1)2021 01.
Article in English | MEDLINE | ID: covidwho-910383

ABSTRACT

The emerging pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused social and economic disruption worldwide, infecting over 9.0 million people and killing over 469 000 by 24 June 2020. Unfortunately, no vaccine or antiviral drug that completely eliminates the transmissible disease coronavirus disease 2019 (COVID-19) has been developed to date. Given that coronavirus nonstructural protein 1 (nsp1) is a good target for attenuated vaccines, it is of great significance to explore the detailed characteristics of SARS-CoV-2 nsp1. Here, we first confirmed that SARS-CoV-2 nsp1 had a conserved function similar to that of SARS-CoV nsp1 in inhibiting host-protein synthesis and showed greater inhibition efficiency, as revealed by ribopuromycylation and Renilla luciferase (Rluc) reporter assays. Specifically, bioinformatics and biochemical experiments showed that by interacting with 40S ribosomal subunit, the lysine located at amino acid 164 (K164) was the key residue that enabled SARS-CoV-2 nsp1 to suppress host gene expression. Furthermore, as an inhibitor of host-protein expression, SARS-CoV-2 nsp1 contributed to cell-cycle arrest in G0/G1 phase, which might provide a favourable environment for virus production. Taken together, this research uncovered the detailed mechanism by which SARS-CoV-2 nsp1 K164 inhibited host gene expression, laying the foundation for the development of attenuated vaccines based on nsp1 modification.


Subject(s)
Host-Pathogen Interactions/genetics , Lysine/genetics , Ribosomal Proteins/genetics , Ribosome Subunits, Small, Eukaryotic/genetics , SARS-CoV-2/genetics , Viral Nonstructural Proteins/genetics , Amino Acid Sequence , Amino Acid Substitution , Computational Biology/methods , G1 Phase Cell Cycle Checkpoints/genetics , Gene Expression Regulation , Genes, Reporter , HEK293 Cells , Humans , Luciferases/genetics , Luciferases/metabolism , Lysine/metabolism , Mutation , Ribosomal Proteins/antagonists & inhibitors , Ribosomal Proteins/metabolism , Ribosome Subunits, Small, Eukaryotic/metabolism , Ribosome Subunits, Small, Eukaryotic/virology , SARS Virus/genetics , SARS Virus/metabolism , SARS-CoV-2/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Signal Transduction , Viral Nonstructural Proteins/metabolism
5.
Front Microbiol ; 11: 587317, 2020.
Article in English | MEDLINE | ID: covidwho-883856

ABSTRACT

The emerging coronavirus disease (COVID-19) caused by SARS-CoV-2 has led to social and economic disruption globally. It is urgently needed to understand the structure and function of the viral proteins for understanding of the viral infection and pathogenesis and development of prophylaxis and treatment strategies. Coronavirus non-structural protein 1 (nsp1) is a notable virulence factor with versatile roles in virus-host interactions and exhibits unique characteristics on sequence, structure, and function mode. However, the roles and characteristics of SARS-CoV-2 nsp1 are currently unclear. Here, we analyze the nsp1 of SARS-CoV-2 from the following perspectives: (1) bioinformatics analysis reveals that the novel nsp1 is conserved among SARS-CoV-2 strains and shares significant sequence identity with SARS-CoV nsp1; (2) structure modeling shows a 3D α/ß-fold of SARS-CoV-2 nsp1 highly similar to that of the SARS-CoV homolog; (3) by detailed, functional review of nsp1 proteins from other coronaviruses (especially SARS-CoV) and comparison of the protein sequence and structure, we further analyzed the potential roles of SARS-CoV-2 nsp1 in manipulating host mRNA translation, antiviral innate immunity and inflammation response and thus likely promoting viral infection and pathogenesis, which are merited to be tested in the future. Finally, we discussed how understanding of the novel nsp1 may provide valuable insights into the designs of drugs and vaccines against the unprecedented coronavirus pandemic.

6.
Nat Struct Mol Biol ; 27(10): 959-966, 2020 10.
Article in English | MEDLINE | ID: covidwho-752470

ABSTRACT

The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes, including the 43S pre-initiation complex and the non-translating 80S ribosome. The protein inserts its C-terminal domain into the mRNA channel, where it interferes with mRNA binding. We observe translation inhibition in the presence of Nsp1 in an in vitro translation system and in human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5' untranslated region of the genomic viral mRNA stimulates translation in vitro, suggesting that SARS-CoV-2 combines global inhibition of translation by Nsp1 with efficient translation of the viral mRNA to allow expression of viral genes.


Subject(s)
Betacoronavirus/chemistry , Betacoronavirus/metabolism , Protein Biosynthesis , RNA, Messenger/genetics , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , 5' Untranslated Regions , Betacoronavirus/genetics , Cryoelectron Microscopy , HEK293 Cells , HeLa Cells , Host-Pathogen Interactions/physiology , Humans , Models, Molecular , Mutation , Protein Conformation , Protein Domains , RNA, Messenger/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Ribosome Subunits, Small, Eukaryotic/genetics , Ribosome Subunits, Small, Eukaryotic/metabolism , SARS-CoV-2 , Viral Nonstructural Proteins/genetics
7.
J Transl Med ; 18(1): 329, 2020 08 31.
Article in English | MEDLINE | ID: covidwho-736398

ABSTRACT

BACKGROUND: The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic. Phylogenetic analysis revealed that it is similar to other betacoronaviruses, such as SARS-CoV and Middle-Eastern Respiratory Syndrome, MERS-CoV. Its genome is ∼ 30 kb in length and contains two large overlapping polyproteins, ORF1a and ORF1ab that encode for several structural and non-structural proteins. The non-structural protein 1 (nsp1) is arguably the most important pathogenic determinant, and previous studies on SARS-CoV indicate that it is both involved in viral replication and hampering the innate immune system response. Detailed experiments of site-specific mutagenesis and in vitro reconstitution studies determined that the mechanisms of action are mediated by (a) the presence of specific amino acid residues of nsp1 and (b) the interaction between the protein and the host's small ribosomal unit. In fact, substitution of certain amino acids resulted in reduction of its negative effects. METHODS: A total of 17,928 genome sequences were obtained from the GISAID database (December 2019 to July 2020) from patients infected by SARS-CoV-2 from different areas around the world. Genomes alignment was performed using MAFFT (REFF) and the nsp1 genomic regions were identified using BioEdit and verified using BLAST. Nsp1 protein of SARS-CoV-2 with and without deletion have been subsequently modelled using I-TASSER. RESULTS: We identified SARS-CoV-2 genome sequences, from several Countries, carrying a previously unknown deletion of 9 nucleotides in position 686-694, corresponding to the AA position 241-243 (KSF). This deletion was found in different geographical areas. Structural prediction modelling suggests an effect on the C-terminal tail structure. CONCLUSIONS: Modelling analysis of a newly identified deletion of 3 amino acids (KSF) of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host's gene expression. In addition, substitution of the two amino acids (KS) from nsp1 of SARS-CoV was previously reported to revert loss of interferon-alpha expression. The deletion that we describe indicates that SARS-CoV-2 is undergoing profound genomic changes. It is important to: (i) confirm the spreading of this particular viral strain, and potentially of strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and (ii) correlate these changes in nsp1 with potential decreased viral pathogenicity.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/virology , Pneumonia, Viral/virology , Sequence Deletion , Viral Nonstructural Proteins/genetics , Amino Acid Sequence , Base Sequence , Betacoronavirus/pathogenicity , COVID-19 , Communicable Diseases, Emerging/virology , Coronavirus Infections/epidemiology , Gene Frequency , Genome, Viral , Geography , Humans , Lysine/genetics , Models, Molecular , Pandemics/statistics & numerical data , Phenylalanine/genetics , Pneumonia, Viral/epidemiology , Protein Domains/genetics , SARS-CoV-2 , Serine/genetics , Viral Nonstructural Proteins/chemistry , Virulence/genetics , Virus Replication/genetics
8.
Science ; 369(6508): 1249-1255, 2020 09 04.
Article in English | MEDLINE | ID: covidwho-654484

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1), which suppresses host gene expression by ribosome association. Here, we show that Nsp1 from SARS-CoV-2 binds to the 40S ribosomal subunit, resulting in shutdown of messenger RNA (mRNA) translation both in vitro and in cells. Structural analysis by cryo-electron microscopy of in vitro-reconstituted Nsp1-40S and various native Nsp1-40S and -80S complexes revealed that the Nsp1 C terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks retinoic acid-inducible gene I-dependent innate immune responses that would otherwise facilitate clearance of the infection. Thus, the structural characterization of the inhibitory mechanism of Nsp1 may aid structure-based drug design against SARS-CoV-2.


Subject(s)
Betacoronavirus/chemistry , Immune Evasion , Immunity, Innate , Protein Biosynthesis , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Betacoronavirus/immunology , Betacoronavirus/metabolism , Betacoronavirus/physiology , Binding Sites , COVID-19 , Coronavirus Infections/immunology , Coronavirus Infections/virology , Cryoelectron Microscopy , DEAD Box Protein 58/genetics , DEAD Box Protein 58/metabolism , Humans , Interferon-beta/genetics , Interferon-beta/metabolism , Models, Molecular , Pandemics , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Protein Binding , Protein Domains , Protein Interaction Domains and Motifs , Protein Structure, Secondary , RNA, Messenger/metabolism , Receptors, Immunologic , Ribosome Subunits, Small, Eukaryotic/chemistry , Ribosome Subunits, Small, Eukaryotic/metabolism , SARS-CoV-2
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