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1.
Commun Biol ; 5(1): 483, 2022 05 19.
Article in English | MEDLINE | ID: covidwho-1852521

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF6 is an antagonist of interferon (IFN)-mediated antiviral signaling, achieved through the prevention of STAT1 nuclear localization. However, the exact mechanism through which ORF6 prevents STAT1 nuclear trafficking remains unclear. Herein, we demonstrate that ORF6 directly binds to STAT1 with or without IFN stimulation, resulting in the nuclear exclusion of STAT1. ORF6 also recognizes importin α subtypes with different modes, in particular, high affinity to importin α1 but a low affinity to importin α5. Although ORF6 potentially disrupts the importin α/importin ß1-mediated nuclear transport, thereby suppressing the nuclear translocation of the other classical nuclear localization signal-containing cargo proteins, the inhibitory effect of ORF6 is modest when compared with that of STAT1. The results indicate that the drastic nuclear exclusion of STAT1 is attributed to the specific binding with ORF6, which is a distinct strategy for the importin α1-mediated pathway. Combined with the results from a newly-produced replicon system and a hamster model, we conclude that SARS-CoV-2 ORF6 acts as a virulence factor via regulation of nucleocytoplasmic trafficking to accelerate viral replication, resulting in disease progression.


Subject(s)
COVID-19 , SARS-CoV-2 , Viral Proteins/metabolism , Animals , Antiviral Agents , Biological Transport , Cricetinae , Viral Proteins/genetics , Virus Replication , alpha Karyopherins/genetics , alpha Karyopherins/metabolism
2.
J Virol ; 96(9): e0040022, 2022 05 11.
Article in English | MEDLINE | ID: covidwho-1807320

ABSTRACT

Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic enteric coronavirus that causes high mortality in piglets. Interferon (IFN) responses are the primary defense mechanism against viral infection; however, viruses always evolve elaborate strategies to antagonize the antiviral action of IFN. Previous study showed that PEDV nonstructural protein 7 (nsp7), a component of the viral replicase polyprotein, can antagonize ploy(I:C)-induced type I IFN production. Here, we found that PEDV nsp7 also antagonized IFN-α-induced JAK-STAT signaling and the production of IFN-stimulated genes. PEDV nsp7 did not affect the protein and phosphorylation levels of JAK1, Tyk2, STAT1, and STAT2 or the formation of the interferon-stimulated gene factor 3 (ISGF3) complex. However, PEDV nsp7 prevented the nuclear translocation of STAT1 and STAT2. Mechanistically, PEDV nsp7 interacted with the DNA binding domain of STAT1/STAT2, which sequestered the interaction between karyopherin α1 (KPNA1) and STAT1, thereby blocking the nuclear transport of ISGF3. Collectively, these data reveal a new mechanism developed by PEDV to inhibit type I IFN signaling pathway. IMPORTANCE In recent years, an emerging porcine epidemic diarrhea virus (PEDV) variant has gained attention because of serious outbreaks of piglet diarrhea in China and the United States. Coronavirus nonstructural protein 7 (nsp7) has been proposed to act with nsp8 as part of an RNA primase to generate RNA primers for viral RNA synthesis. However, accumulating evidence indicates that coronavirus nsp7 can also antagonize type I IFN production. Our present study extends previous findings and demonstrates that PEDV nsp7 also antagonizes IFN-α-induced IFN signaling by competing with KPNA1 for binding to STAT1, thereby enriching the immune regulation function of coronavirus nsp7.


Subject(s)
Janus Kinase 1 , Porcine epidemic diarrhea virus , STAT1 Transcription Factor , Signal Transduction , Viral Nonstructural Proteins , alpha Karyopherins , Animals , Cell Line , Interferons/metabolism , Janus Kinase 1/metabolism , Porcine epidemic diarrhea virus/genetics , STAT1 Transcription Factor/metabolism , Swine , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism , alpha Karyopherins/metabolism
3.
Cells ; 11(7)2022 04 02.
Article in English | MEDLINE | ID: covidwho-1785537

ABSTRACT

The global burden of malaria and toxoplasmosis has been limited by the use of efficacious anti-parasitic agents, however, emerging resistance in Plasmodium species and Toxoplasma gondii threatens disease control worldwide, implying that new agents/therapeutic targets are urgently needed. Nuclear localization signal (NLS)-dependent transport into the nucleus, mediated by members of the importin (IMP) superfamily of nuclear transporters, has shown potential as a target for intervention to limit viral infection. Here, we show for the first time that IMPα from P. falciparum and T. gondii have promise as targets for small molecule inhibitors. We use high-throughput screening to identify agents able to inhibit P. falciparum IMPα binding to a P. falciparum NLS, identifying a number of compounds that inhibit binding in the µM-nM range, through direct binding to P. falciparum IMPα, as shown in thermostability assays. Of these, BAY 11-7085 is shown to be a specific inhibitor of P. falciparum IMPα-NLS recognition. Importantly, a number of the inhibitors limited growth by both P. falciparum and T. gondii. The results strengthen the hypothesis that apicomplexan IMPα proteins have potential as therapeutic targets to aid in identifying novel agents for two important, yet neglected, parasitic diseases.


Subject(s)
Plasmodium falciparum , alpha Karyopherins , High-Throughput Screening Assays , Nuclear Localization Signals/metabolism , Plasmodium falciparum/drug effects , Plasmodium falciparum/metabolism , Protein Binding , alpha Karyopherins/antagonists & inhibitors
4.
Viruses ; 13(10)2021 10 15.
Article in English | MEDLINE | ID: covidwho-1470998

ABSTRACT

Nuclear transport and vesicle trafficking are key cellular functions involved in the pathogenesis of RNA viruses. Among other pleiotropic effects on virus-infected host cells, ivermectin (IVM) inhibits nuclear transport mechanisms mediated by importins and atorvastatin (ATV) affects actin cytoskeleton-dependent trafficking controlled by Rho GTPases signaling. In this work, we first analyzed the response to infection in nasopharyngeal swabs from SARS-CoV-2-positive and -negative patients by assessing the gene expression of the respective host cell drug targets importins and Rho GTPases. COVID-19 patients showed alterations in KPNA3, KPNA5, KPNA7, KPNB1, RHOA, and CDC42 expression compared with non-COVID-19 patients. An in vitro model of infection with Poly(I:C), a synthetic analog of viral double-stranded RNA, triggered NF-κB activation, an effect that was halted by IVM and ATV treatment. Importin and Rho GTPases gene expression was also impaired by these drugs. Furthermore, through confocal microscopy, we analyzed the effects of IVM and ATV on nuclear to cytoplasmic importin α distribution, alone or in combination. Results showed a significant inhibition of importin α nuclear accumulation under IVM and ATV treatments. These findings confirm transcriptional alterations in importins and Rho GTPases upon SARS-CoV-2 infection and point to IVM and ATV as valid drugs to impair nuclear localization of importin α when used at clinically-relevant concentrations.


Subject(s)
Active Transport, Cell Nucleus/drug effects , Atorvastatin/pharmacology , COVID-19 Drug Treatment , Ivermectin/pharmacology , SARS-CoV-2/drug effects , alpha Karyopherins/metabolism , A549 Cells , Actin Cytoskeleton/drug effects , Animals , Antiviral Agents/pharmacology , Cell Line, Tumor , Chlorocebus aethiops , Drug Repositioning , HeLa Cells , Humans , NF-kappa B/metabolism , Vero Cells , rho GTP-Binding Proteins/metabolism
5.
Biophys Chem ; 278: 106677, 2021 11.
Article in English | MEDLINE | ID: covidwho-1363894

ABSTRACT

The SARS-CoV-2 pandemic has accelerated the study of existing drugs. The mixture of homologs called ivermectin (avermectin-B1a [HB1a] + avermectin-B1b [HB1b]) has shown antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the behavior of each homolog. We investigated the interaction of each homolog with promising targets of interest associated with SARS-CoV-2 infection from a biophysical and computational-chemistry perspective using docking and molecular dynamics. We observed a differential behavior for each homolog, with an affinity of HB1b for viral structures, and of HB1a for host structures considered. The induced disturbances were differential and influenced by the hydrophobicity of each homolog and of the binding pockets. We present the first comparative analysis of the potential theoretical inhibitory effect of both avermectins on biomolecules associated with COVID-19, and suggest that ivermectin through its homologs, has a multiobjective behavior.


Subject(s)
Antiviral Agents/chemistry , Coronavirus 3C Proteases/antagonists & inhibitors , DNA Helicases/antagonists & inhibitors , Ivermectin/analogs & derivatives , alpha Karyopherins/antagonists & inhibitors , beta Karyopherins/antagonists & inhibitors , Animals , Antiviral Agents/pharmacology , Binding Sites , COVID-19/virology , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/metabolism , DNA Helicases/chemistry , DNA Helicases/metabolism , Humans , Ivermectin/chemistry , Ivermectin/pharmacology , Kinetics , Mice , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Conformation , Protein Interaction Domains and Motifs , SARS-CoV-2/chemistry , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Thermodynamics , alpha Karyopherins/chemistry , alpha Karyopherins/metabolism , beta Karyopherins/chemistry , beta Karyopherins/metabolism , COVID-19 Drug Treatment
6.
J Biomol Struct Dyn ; 40(5): 2217-2226, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1214172

ABSTRACT

While an FDA approved drug Ivermectin was reported to dramatically reduce the cell line of SARS-CoV-2 by ∼5000 folds within 48 h, the precise mechanism of action and the COVID-19 molecular target involved in interaction with this in-vitro effective drug are unknown yet. Among 12 different COVID-19 targets along with Importin-α studied here, the RNA dependent RNA polymerase (RdRp) with RNA and Helicase NCB site show the strongest affinity to Ivermectin amounting -10.4 kcal/mol and -9.6 kcal/mol, respectively, followed by Importin-α with -9.0 kcal/mol. Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-α, with MM/PBSA free energy of -187.3 kJ/mol, almost twice that of Helicase (-94.6 kJ/mol) and even lower than that of Importin-α (-156.7 kJ/mol). The selectivity of Ivermectin to RdRp is triggered by a cooperative interaction of RNA-RdRp by ternary complex formation. Identification of the target and its interaction profile with Ivermectin can lead to more powerful drug designs for COVID-19 and experimental exploration.


Subject(s)
COVID-19 Drug Treatment , Pharmaceutical Preparations , Antiviral Agents/chemistry , Humans , Ivermectin/pharmacology , Molecular Docking Simulation , SARS-CoV-2 , alpha Karyopherins
7.
Front Immunol ; 12: 663586, 2021.
Article in English | MEDLINE | ID: covidwho-1190318

ABSTRACT

As of January 2021, SARS-CoV-2 has killed over 2 million individuals across the world. As such, there is an urgent need for vaccines and therapeutics to reduce the burden of COVID-19. Several vaccines, including mRNA, vector-based vaccines, and inactivated vaccines, have been approved for emergency use in various countries. However, the slow roll-out of vaccines and insufficient global supply remains a challenge to turn the tide of the pandemic. Moreover, vaccines are important tools for preventing the disease but therapeutic tools to treat patients are also needed. As such, since the beginning of the pandemic, repurposed FDA-approved drugs have been sought as potential therapeutic options for COVID-19 due to their known safety profiles and potential anti-viral effects. One of these drugs is ivermectin (IVM), an antiparasitic drug created in the 1970s. IVM later exerted antiviral activity against various viruses including SARS-CoV-2. In this review, we delineate the story of how this antiparasitic drug was eventually identified as a potential treatment option for COVID-19. We review SARS-CoV-2 lifecycle, the role of the nucleocapsid protein, the turning points in past research that provided initial 'hints' for IVM's antiviral activity and its molecular mechanism of action- and finally, we culminate with the current clinical findings.


Subject(s)
Active Transport, Cell Nucleus/drug effects , Antiviral Agents/therapeutic use , COVID-19 Drug Treatment , Ivermectin/therapeutic use , SARS-CoV-2/drug effects , Animals , Cell Line , Chlorocebus aethiops , Coronavirus Nucleocapsid Proteins/antagonists & inhibitors , Coronavirus Nucleocapsid Proteins/metabolism , Drug Repositioning , Humans , Phosphoproteins/antagonists & inhibitors , Phosphoproteins/metabolism , Protein Transport/drug effects , SARS-CoV-2/growth & development , Vero Cells , Virus Replication/drug effects , alpha Karyopherins/antagonists & inhibitors , beta Karyopherins/antagonists & inhibitors
8.
J Biomol Struct Dyn ; 40(18): 8375-8383, 2022 11.
Article in English | MEDLINE | ID: covidwho-1180369

ABSTRACT

Ivermectin (IVM) is an FDA-approved drug that has shown antiviral activity against a wide variety of viruses in recent years. IVM inhibits the formation of the importin-α/ß1 heterodimeric complex responsible for the translocation and replication of various viral species proteins. Also, IVM hampers SARS-CoV-2 replication in vitro; however, the molecular mechanism through which IVM inhibits SARS-CoV-2 is not well understood. Previous studies have explored the molecular mechanism through which IVM inhibits importin-α and several potential targets associated with COVID-19 by using docking approaches and MD simulations to corroborate the docked complexes. This study explores the energetic and structural properties through which IVM inhibits importin-α and five targets associated with COVID-19 by using docking and MD simulations combined with the molecular mechanics generalized Born surface area (MMGBSA) approach. Energetic and structural analysis showed that the main protease 3CLpro reached the most favorable affinity, followed by importin-α and Nsp9, which shared a similar relationship. Therefore, in vitro activity of IVM can be explained by acting as an inhibitor of importin-α, dimeric 3CLpro, and Nsp9, but mainly over dimeric 3CLpro.Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Humans , Ivermectin/pharmacology , Molecular Docking Simulation , Molecular Dynamics Simulation , Peptide Hydrolases/metabolism , Protease Inhibitors/chemistry , Viral Proteins , alpha Karyopherins
9.
Biochem Biophys Res Commun ; 538: 163-172, 2021 01 29.
Article in English | MEDLINE | ID: covidwho-1125081

ABSTRACT

FDA approved for parasitic indications, the small molecule ivermectin has been the focus of growing attention in the last 8 years due to its potential as an antiviral. We first identified ivermectin in a high throughput compound library screen as an agent potently able to inhibit recognition of the nuclear localizing Human Immunodeficiency Virus-1 (HIV-1) integrase protein by the host importin (IMP) α/ß1 heterodimer, and recently demonstrated its ability to bind directly to IMPα to cause conformational changes that prevent its function in nuclear import of key viral as well as host proteins. Cell culture experiments have shown robust antiviral action towards a whole range of viruses, including HIV-1, dengue, Zika and West Nile Virus, Venezuelan equine encephalitis virus, Chikungunya, pseudorabies virus, adenovirus, and SARS-CoV-2 (COVID-19). Close to 70 clinical trials are currently in progress worldwide for SARS-CoV-2. Although few of these studies have been completed, the results that are available, as well as those from observational/retrospective studies, indicate clinical benefit. Here we discuss the case for ivermectin as a host-directed broad-spectrum antiviral agent, including for SARS-CoV-2.


Subject(s)
Antiparasitic Agents/pharmacology , Antiviral Agents/pharmacology , COVID-19 Drug Treatment , Ivermectin/pharmacology , SARS-CoV-2/drug effects , Antiparasitic Agents/therapeutic use , Antiviral Agents/therapeutic use , Humans , Ivermectin/therapeutic use , alpha Karyopherins/antagonists & inhibitors
10.
Biochem Soc Trans ; 49(1): 281-295, 2021 02 26.
Article in English | MEDLINE | ID: covidwho-1065978

ABSTRACT

Although transport into the nucleus mediated by the importin (IMP) α/ß1-heterodimer is central to viral infection, small molecule inhibitors of IMPα/ß1-dependent nuclear import have only been described and shown to have antiviral activity in the last decade. Their robust antiviral activity is due to the strong reliance of many different viruses, including RNA viruses such as human immunodeficiency virus-1 (HIV-1), dengue (DENV), and Zika (ZIKV), on the IMPα/ß1-virus interface. High-throughput compound screens have identified many agents that specifically target this interface. Of these, agents targeting IMPα/ß1 directly include the FDA-approved macrocyclic lactone ivermectin, which has documented broad-spectrum activity against a whole range of viruses, including HIV-1, DENV1-4, ZIKV, West Nile virus (WNV), Venezuelan equine encephalitis virus, chikungunya, and most recently, SARS-CoV-2 (COVID-19). Ivermectin has thus far been tested in Phase III human clinical trials for DENV, while there are currently close to 80 trials in progress worldwide for SARS-CoV-2; preliminary results for randomised clinical trials (RCTs) as well as observational/retrospective studies are consistent with ivermectin affording clinical benefit. Agents that target the viral component of the IMPα/ß1-virus interface include N-(4-hydroxyphenyl) retinamide (4-HPR), which specifically targets DENV/ZIKV/WNV non-structural protein 5 (NS5). 4-HPR has been shown to be a potent inhibitor of infection by DENV1-4, including in an antibody-dependent enhanced animal challenge model, as well as ZIKV, with Phase II clinical challenge trials planned. The results from rigorous RCTs will help determine the therapeutic potential of the IMPα/ß1-virus interface as a target for antiviral development.


Subject(s)
Ivermectin/pharmacology , Viral Nonstructural Proteins/metabolism , Virus Diseases/prevention & control , Viruses/metabolism , alpha Karyopherins/metabolism , beta Karyopherins/metabolism , Animals , Antiviral Agents/pharmacology , Humans , Protein Binding/drug effects , Virus Diseases/metabolism , Virus Diseases/virology , Viruses/pathogenicity
11.
J Biomol Struct Dyn ; 40(6): 2851-2864, 2022 04.
Article in English | MEDLINE | ID: covidwho-1026871

ABSTRACT

Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IMP)α directly and averts interaction with IMPß1, leading to the prevention of nuclear localization signal (NLS) recognition. Therefore, the current study seeks to employ molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) analysis and molecular dynamics simulation studies for decrypting the binding mode, key interacting residues as well as mechanistic insights on IVM interaction with 15 potential drug targets associated with COVID-19 as well as IMPα. Among all COVID-19 targets, the non-structural protein 9 (Nsp9) exhibited the strongest affinity to IVM showing -5.30 kcal/mol and -84.85 kcal/mol binding energies estimated by AutoDock Vina and MM-GBSA, respectively. However, moderate affinity was accounted for IMPα amounting -6.9 kcal/mol and -66.04 kcal/mol. Stability of the protein-ligand complexes of Nsp9-IVM and IMPα-IVM was ascertained by 100 ns trajectory of all-atom molecular dynamics simulation. Structural conformation of protein in complex with docked IVM exhibited stable root mean square deviation while root mean square fluctuations were also found to be consistent. In silico exploration of the potential targets and their interaction profile with IVM can assist experimental studies as well as designing of COVID-19 drugs. Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 Drug Treatment , Ivermectin , Antiviral Agents/chemistry , Humans , Ivermectin/pharmacology , Ivermectin/therapeutic use , Molecular Docking Simulation , SARS-CoV-2 , alpha Karyopherins
12.
Cell Rep ; 33(1): 108234, 2020 10 06.
Article in English | MEDLINE | ID: covidwho-778591

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and host immune response determine coronavirus disease 2019 (COVID-19), but studies evaluating viral evasion of immune response are lacking. Here, we use unbiased screening to identify SARS-CoV-2 proteins that antagonize type I interferon (IFN-I) response. We found three proteins that antagonize IFN-I production via distinct mechanisms: nonstructural protein 6 (nsp6) binds TANK binding kinase 1 (TBK1) to suppress interferon regulatory factor 3 (IRF3) phosphorylation, nsp13 binds and blocks TBK1 phosphorylation, and open reading frame 6 (ORF6) binds importin Karyopherin α 2 (KPNA2) to inhibit IRF3 nuclear translocation. We identify two sets of viral proteins that antagonize IFN-I signaling through blocking signal transducer and activator of transcription 1 (STAT1)/STAT2 phosphorylation or nuclear translocation. Remarkably, SARS-CoV-2 nsp1 and nsp6 suppress IFN-I signaling more efficiently than SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Thus, when treated with IFN-I, a SARS-CoV-2 replicon replicates to a higher level than chimeric replicons containing nsp1 or nsp6 from SARS-CoV or MERS-CoV. Altogether, the study provides insights on SARS-CoV-2 evasion of IFN-I response and its potential impact on viral transmission and pathogenesis.


Subject(s)
Capsid Proteins/metabolism , Coronavirus Infections/immunology , Immune Evasion , Interferon Type I/metabolism , Methyltransferases/metabolism , Pneumonia, Viral/immunology , RNA Helicases/metabolism , Viral Nonstructural Proteins/metabolism , Viral Proteins/metabolism , A549 Cells , Animals , Betacoronavirus/immunology , Betacoronavirus/pathogenicity , COVID-19 , Coronavirus Infections/virology , Coronavirus Nucleocapsid Proteins , Cricetinae , Cricetulus , HEK293 Cells , Humans , Interferon Regulatory Factor-3/metabolism , Interferon Type I/genetics , Pandemics , Pneumonia, Viral/virology , Protein Binding , Protein Serine-Threonine Kinases/metabolism , SARS-CoV-2 , STAT Transcription Factors/metabolism , alpha Karyopherins/metabolism
13.
Cell Rep ; 31(3): 107549, 2020 04 21.
Article in English | MEDLINE | ID: covidwho-100496

ABSTRACT

Importin-α adaptor proteins orchestrate dynamic nuclear transport processes involved in cellular homeostasis. Here, we show that importin-α3, one of the main NF-κB transporters, is the most abundantly expressed classical nuclear transport factor in the mammalian respiratory tract. Importin-α3 promoter activity is regulated by TNF-α-induced NF-κB in a concentration-dependent manner. High-level TNF-α-inducing highly pathogenic avian influenza A viruses (HPAIVs) isolated from fatal human cases harboring human-type polymerase signatures (PB2 627K, 701N) significantly downregulate importin-α3 mRNA expression in primary lung cells. Importin-α3 depletion is restored upon back-mutating the HPAIV polymerase into an avian-type signature (PB2 627E, 701D) that can no longer induce high TNF-α levels. Importin-α3-deficient mice show reduced NF-κB-activated antiviral gene expression and increased influenza lethality. Thus, importin-α3 plays a key role in antiviral immunity against influenza. Lifting the bottleneck in importin-α3 availability in the lung might provide a new strategy to combat respiratory virus infections.


Subject(s)
Influenza A virus/immunology , Influenza, Human/immunology , Orthomyxoviridae Infections/immunology , alpha Karyopherins/biosynthesis , A549 Cells , Animals , Cell Line, Tumor , Chlorocebus aethiops , Down-Regulation , Female , HEK293 Cells , Humans , Influenza, Human/genetics , Influenza, Human/virology , Mice , Mice, Inbred C57BL , Mice, Knockout , Middle Aged , Orthomyxoviridae Infections/genetics , Orthomyxoviridae Infections/virology , RNA, Messenger/genetics , RNA, Messenger/metabolism , Vero Cells , alpha Karyopherins/genetics , alpha Karyopherins/immunology
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