Identification of Plitidepsin as Potent Inhibitor of SARS-CoV-2-Induced Cytopathic Effect after a Drug Repurposing Screen

  1. Jordi Rodon
  2. Jordana Muñoz-Basagoiti
  3. Daniel Perez-Zsolt
  4. Marc Noguera-Julian
  5. Roger Paredes
  6. Lourdes Mateu
  7. Carles Quiñones
  8. Itziar Erkizia
  9. Ignacio Blanco
  10. Alfonso Valencia
  11. Víctor Guallar
  12. Jorge Carrillo
  13. Julià Blanco
  14. Joaquim Segalés
  15. Bonaventura Clotet
  16. Júlia Vergara-Alert
  17. Nuria Izquierdo-Useros

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Abstract

There is an urgent need to identify therapeutics for the treatment of Coronavirus diseases 2019 (COVID-19). Although different antivirals are given for the clinical management of SARS-CoV-2 infection, their efficacy is still under evaluation. Here, we have screened existing drugs approved for human use in a variety of diseases, to compare how they counteract SARS-CoV-2-induced cytopathic effect and viral replication in vitro. Among the potential 72 antivirals tested herein that were previously proposed to inhibit SARS-CoV-2 infection, only 18% had an IC 50 below 25 μM or 10 2 IU/mL. These included plitidepsin, novel cathepsin inhibitors, nelfinavir mesylate hydrate, interferon 2-alpha, interferon-gamma, fenofibrate, camostat along the well-known remdesivir and chloroquine derivatives. Plitidepsin was the only clinically approved drug displaying nanomolar efficacy. Four of these families, including novel cathepsin inhibitors, blocked viral entry in a cell-type specific manner. Since the most effective antivirals usually combine therapies that tackle the virus at different steps of infection, we also assessed several drug combinations. Although no particular synergy was found, inhibitory combinations did not reduce their antiviral activity. Thus, these combinations could decrease the potential emergence of resistant viruses. Antivirals prioritized herein identify novel compounds and their mode of action, while independently replicating the activity of a reduced proportion of drugs which are mostly approved for clinical use. Combinations of these drugs should be tested in animal models to inform the design of fast track clinical trials.

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  1. Version published to 10.1101/2020.04.23.055756v3 on bioRxiv
  2. Version published to 10.1101/2020.04.23.055756v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.04.23.055756: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics statement: The institutional review board on biomedical research from Hospital Germans Trias i Pujol (HUGTiP) approved this study.
    Consent: The individual who provided the sample to isolate virus gave a written informed consent to participate.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableVirus isolation, titration and sequencing: SARS-CoV-2 was isolated from a nasopharyngeal swab collected from an 89-year-old male patient giving informed consent and treated with Betaferon and hydroxychloroquine for 2 days before sample collection.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Vero E6 cells were cultured on a cell culture flask (25 cm2) at 1.5 x 106 cells overnight prior to inoculation with 1 mL of the processed sample, for 1 h at 37°C and 5% CO2.
    Vero E6
    suggested: None
    Spike plasmid was transfected with X-tremeGENE HP Transfection Reagent (Merck) into HEK-293T cells, and 24 hours post-transfection, cells were transfected with pNL4-3.Luc.R-.E-.
    HEK-293T
    suggested: None
    Pseudovirus assay: HEK-293T overexpressing the human ACE2 and TMPRSS2 were used to test antivirals at the concentrations found to be effective for SARS-CoV-2 without toxicity, which were the following: 5 μM for niclosamide; 10 μM for chloroquine, chlorpromazine, ciclesonide, MDL 28170 and fenofibrate; 20 μM for hydroxychloroquine, CA-074-Me and arbidol HCl; 25 μM for E-64d; 50 μM for Baricitinib; 100 μM for Amantadine, NB-DNJ,
    MDL 28170
    suggested: None
    Software and Algorithms
    SentencesResources
    Sequence reads were quality filtered and adapter primer sequences were trimmed using trimmomatic.
    trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Amplification primer sequences were removed using cutadapt12 Sequencing reads were then mapped against coronavirus reference (NC_045512.2) using bowtie2 tool13.
    bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    All analyses and figures were generated with the GraphPad Prism v8.0b Software.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.04.23.055756v1 on bioRxiv