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1.
STAR Protoc ; 3(1): 101067, 2022 03 18.
Article in English | MEDLINE | ID: covidwho-1595326

ABSTRACT

N 6 -methylation of adenosine (m6A) is the most abundant internal mRNA modification and is an important post-transcriptional regulator of gene expression. Here, we describe a protocol for methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to detect and quantify m6A modifications in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. The protocol is optimized for low viral RNA levels and is readily adaptable for other applications. For complete details on the use and execution of this protocol, please refer to Li et al. (2021).


Subject(s)
Adenosine/analogs & derivatives , Immunoprecipitation/methods , Sequence Analysis, RNA/methods , Adenosine/analysis , Adenosine/genetics , Animals , COVID-19/genetics , Caco-2 Cells , Chlorocebus aethiops , Gene Expression/genetics , Gene Expression Regulation/genetics , Genetic Techniques , HEK293 Cells , Humans , Methylation , RNA/chemistry , RNA/genetics , RNA Processing, Post-Transcriptional , RNA, Viral/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Vero Cells
2.
J Med Chem ; 65(4): 2866-2879, 2022 02 24.
Article in English | MEDLINE | ID: covidwho-1440451

ABSTRACT

The emergence of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents an urgent public health crisis. Without available targeted therapies, treatment options remain limited for COVID-19 patients. Using medicinal chemistry and rational drug design strategies, we identify a 2-phenyl-1,2-benzoselenazol-3-one class of compounds targeting the SARS-CoV-2 main protease (Mpro). FRET-based screening against recombinant SARS-CoV-2 Mpro identified six compounds that inhibit proteolysis with nanomolar IC50 values. Preincubation dilution experiments and molecular docking determined that the inhibition of SARS-CoV-2 Mpro can occur by either covalent or noncovalent mechanisms, and lead E04 was determined to inhibit Mpro competitively. Lead E24 inhibited viral replication with a nanomolar EC50 value (844 nM) in SARS-CoV-2-infected Vero E6 cells and was further confirmed to impair SARS-CoV-2 replication in human lung epithelial cells and human-induced pluripotent stem cell-derived 3D lung organoids. Altogether, these studies provide a structural framework and mechanism of Mpro inhibition that should facilitate the design of future COVID-19 treatments.


Subject(s)
Antiviral Agents/pharmacology , Benzothiazoles/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , Cysteine Proteinase Inhibitors/pharmacology , Drug Discovery , SARS-CoV-2/drug effects , Animals , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Benzothiazoles/chemistry , COVID-19/drug therapy , COVID-19/metabolism , Chlorocebus aethiops , Coronavirus 3C Proteases/isolation & purification , Coronavirus 3C Proteases/metabolism , Crystallography, X-Ray , Cysteine Proteinase Inhibitors/chemical synthesis , Cysteine Proteinase Inhibitors/chemistry , Dose-Response Relationship, Drug , Fluorescence Resonance Energy Transfer , Humans , Microbial Sensitivity Tests , Molecular Docking Simulation , Molecular Structure , SARS-CoV-2/enzymology , Vero Cells , Virus Replication/drug effects
3.
Cell Rep ; 35(6): 109091, 2021 05 11.
Article in English | MEDLINE | ID: covidwho-1213072

ABSTRACT

It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlining molecular mechanism. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. Here, we investigate m6A modification of the SARS-CoV-2 gene in regulating the host cell innate immune response. Our data show that the SARS-CoV-2 virus has m6A modifications that are enriched in the 3' end of the viral genome. We find that depletion of the host cell m6A methyltransferase METTL3 decreases m6A levels in SARS-CoV-2 and host genes, and m6A reduction in viral RNA increases RIG-I binding and subsequently enhances the downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in patients with severe coronavirus disease 2019 (COVID-19). These findings will aid in the understanding of COVID-19 pathogenesis and the design of future studies regulating innate immunity for COVID-19 treatment.


Subject(s)
COVID-19/genetics , Methyltransferases/metabolism , SARS-CoV-2/genetics , Adenosine/metabolism , COVID-19/metabolism , Cell Line , DEAD Box Protein 58/genetics , DEAD Box Protein 58/metabolism , Humans , Immunity, Innate/genetics , Methylation , Methyltransferases/genetics , RNA, Viral/genetics , Receptors, Immunologic/genetics , Receptors, Immunologic/metabolism , SARS-CoV-2/pathogenicity , Signal Transduction
4.
Stem Cell Reports ; 16(3): 437-445, 2021 03 09.
Article in English | MEDLINE | ID: covidwho-1084274

ABSTRACT

COVID-19 is a transmissible respiratory disease caused by a novel coronavirus, SARS-CoV-2, and has become a global health emergency. There is an urgent need for robust and practical in vitro model systems to investigate viral pathogenesis. Here, we generated human induced pluripotent stem cell (iPSC)-derived lung organoids (LORGs), cerebral organoids (CORGs), neural progenitor cells (NPCs), neurons, and astrocytes. LORGs containing epithelial cells, alveolar types 1 and 2, highly express ACE2 and TMPRSS2 and are permissive to SARS-CoV-2 infection. SARS-CoV-2 infection induces interferons, cytokines, and chemokines and activates critical inflammasome pathway genes. Spike protein inhibitor, EK1 peptide, and TMPRSS2 inhibitors (camostat/nafamostat) block viral entry in LORGs. Conversely, CORGs, NPCs, astrocytes, and neurons express low levels of ACE2 and TMPRSS2 and correspondingly are not highly permissive to SARS-CoV-2 infection. Infection in neuronal cells activates TLR3/7, OAS2, complement system, and apoptotic genes. These findings will aid in understanding COVID-19 pathogenesis and facilitate drug discovery.


Subject(s)
Brain/virology , COVID-19/virology , Induced Pluripotent Stem Cells/virology , Lung/virology , Neural Stem Cells/virology , Organoids/virology , SARS-CoV-2/pathogenicity , Apoptosis/physiology , Brain/metabolism , COVID-19/metabolism , Cells, Cultured , Complement System Proteins/metabolism , Epithelial Cells/metabolism , Epithelial Cells/virology , Humans , Induced Pluripotent Stem Cells/metabolism , Inflammation/metabolism , Inflammation/virology , Lung/metabolism , Neural Stem Cells/metabolism , Neurons/metabolism , Neurons/virology , Organoids/metabolism , Serine Endopeptidases/metabolism , Signal Transduction/physiology , Stem Cells/metabolism , Stem Cells/virology
5.
EMBO J ; 39(21): e106057, 2020 11 02.
Article in English | MEDLINE | ID: covidwho-846583

ABSTRACT

Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 and has spread across the globe. SARS-CoV-2 is a highly infectious virus with no vaccine or antiviral therapy available to control the pandemic; therefore, it is crucial to understand the mechanisms of viral pathogenesis and the host immune responses to SARS-CoV-2. SARS-CoV-2 is a new member of the betacoronavirus genus like other closely related viruses including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Both SARS-CoV and MERS-CoV have caused serious outbreaks and epidemics in the past eighteen years. Here, we report that one of the interferon-stimulated genes (ISGs), cholesterol 25-hydroxylase (CH25H), is induced by SARS-CoV-2 infection in vitro and in COVID-19-infected patients. CH25H converts cholesterol to 25-hydrocholesterol (25HC) and 25HC shows broad anti-coronavirus activity by blocking membrane fusion. Furthermore, 25HC inhibits USA-WA1/2020 SARS-CoV-2 infection in lung epithelial cells and viral entry in human lung organoids. Mechanistically, 25HC inhibits viral membrane fusion by activating the ER-localized acyl-CoA:cholesterol acyltransferase (ACAT) which leads to the depletion of accessible cholesterol from the plasma membrane. Altogether, our results shed light on a potentially broad antiviral mechanism by 25HC through depleting accessible cholesterol on the plasma membrane to suppress virus-cell fusion. Since 25HC is a natural product with no known toxicity at effective concentrations, it provides a potential therapeutic candidate for COVID-19 and emerging viral diseases in the future.


Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Cholesterol/metabolism , Coronavirus Infections/drug therapy , Pneumonia, Viral/drug therapy , Respiratory Mucosa/virology , Steroid Hydroxylases/pharmacology , Virus Internalization/drug effects , Acetyl-CoA C-Acetyltransferase/metabolism , Animals , COVID-19 , Cell Line , Cell Membrane/drug effects , Cell Membrane/metabolism , Chlorocebus aethiops , Enzyme Activation/drug effects , Humans , Middle East Respiratory Syndrome Coronavirus/drug effects , Organoids/virology , Pandemics , Respiratory Mucosa/drug effects , SARS Virus/drug effects , SARS-CoV-2 , Vero Cells
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