Identification of SARS-CoV-2 3CL Protease Inhibitors by a Quantitative High-Throughput Screening

  1. Wei Zhu
  2. Miao Xu
  3. Catherine Z. Chen
  4. Hui Guo
  5. Min Shen
  6. Xin Hu
  7. Paul Shinn
  8. Carleen Klumpp-Thomas
  9. Samuel G. Michael
  10. Wei Zheng

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Abstract

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emphasized the urgency to develop effective therapeutics. Drug repurposing screening is regarded as one of the most practical and rapid approaches for the discovery of such therapeutics. The 3C-like protease (3CLpro), or main protease (Mpro) of SARS-CoV-2 is a valid drug target as it is a specific viral enzyme and plays an essential role in viral replication. We performed a quantitative high-throughput screening (qHTS) of 10?755 compounds consisting of approved and investigational drugs, and bioactive compounds using a SARS-CoV-2 3CLpro assay. Twenty-three small molecule inhibitors of SARS-CoV-2 3CLpro have been identified with IC50s ranging from 0.26 to 28.85 ?M. Walrycin B (IC50 = 0.26 ?M), hydroxocobalamin (IC50 = 3.29 ?M), suramin sodium (IC50 = 6.5 ?M), Z-DEVD-FMK (IC50 = 6.81 ?M), LLL-12 (IC50 = 9.84 ?M), and Z-FA-FMK (IC50 = 11.39 ?M) are the most potent 3CLpro inhibitors. The activity of the anti-SARS-CoV-2 viral infection was confirmed in 7 of 23 compounds using a SARS-CoV-2 cytopathic effect assay. The results demonstrated a set of SARS-CoV-2 3CLpro inhibitors that may have potential for further clinical evaluation as part of drug combination therapies to treating COVID-19 patients and as starting points for chemistry optimization for new drug development.

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  1. Version published to 10.1021/acsptsci.0c00108
  2. ScreenIT

    SciScore for 10.1101/2020.07.17.207019: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    In brief, high ACE2 expressing Vero E6 cells were inoculated with SARS-CoV-2 (USA_WA1/2020) at 0.002 M.O.I.
    Vero E6
    suggested: None
    Software and Algorithms
    SentencesResources
    MIPE 5.0 library includes 2480 compounds that are mixed with approved and investigational compounds, and mechanistic based compounds focusing on oncology
    MIPE
    suggested: (MIPE, RRID:SCR_003065)
    Concentration-response curves were fitted and IC50 values of confirmed compounds were calculated using the GraphPad Prism software (San Diego, CA, USA).
    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.

  3. Version published to 10.1101/2020.07.17.207019 on bioRxiv