Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures

  1. Zhengnan Shen
  2. Kiira Ratia
  3. Laura Cooper
  4. Deyu Kong
  5. Hyun Lee
  6. Youngjin Kwon
  7. Yangfeng Li
  8. Saad Alqarni
  9. Fei Huang
  10. Oleksii Dubrovskyi
  11. Lijun Rong
  12. Gregory Thatcher
  13. Rui Xiong

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Abstract

Antiviral agents blocking SARS-CoV-2 viral replication are desperately needed to complement vaccination to end the COVID-19 pandemic. Viral replication and assembly are entirely dependent on two viral cysteine proteases: 3C-like protease (3CLpro) and the papain-like protease (PLpro). PLpro also has deubiquitinase (DUB) activity, removing ubiquitin (Ub) and Ub-like modifications from host proteins, disrupting the host immune response. 3CLpro is inhibited by many known cysteine protease inhibitors, whereas PLpro is a relatively unusual cysteine protease, being resistant to blockade by such inhibitors. A high-throughput screen of biased and unbiased libraries gave a low hit rate, identifying only CPI-169 and the positive control, GRL0617, as inhibitors with good potency (IC 50 < 10 µM). Analogues of both inhibitors were designed to develop structure-activity relationships; however, without a co-crystal structure of the CPI-169 series, we focused on GRL0617 as a starting point for structure-based drug design, obtaining several co-crystal structures to guide optimization. A series of novel 2-phenylthiophene-based non-covalent SARS-CoV-2 PLpro inhibitors were obtained, culminating in low nanomolar potency. The high potency and slow inhibitor off-rate were rationalized by newly identified ligand interactions with a “BL2 groove” that is distal from the active site cysteine. Trapping of the conformationally flexible BL2 loop by these inhibitors blocks binding of viral and host protein substrates; however, until now it has not been demonstrated that this mechanism can induce potent and efficacious antiviral activity. In this study, we report that novel PLpro inhibitors have excellent antiviral efficacy and potency against infectious SARS-CoV-2 replication in cell cultures. Together, our data provide structural insights into the design of potent PLpro inhibitors and the first validation that non-covalent inhibitors of SARS-CoV-2 PLpro can block infection of human cells with low micromolar potency.

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  1. ScreenIT

    SciScore for 10.1101/2021.02.13.431008: (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
    Cell Culture and cytotoxicity: African green monkey kidney epithelial cells Vero E6 (ATCC# CRL-1586) were cultured in DMEM supplemented with 10% fetal bovine serum (Gibco), 100 units of penicillin and 100 µg/mL streptomycin (Invitrogen).
    Vero E6
    suggested: RRID:CVCL_XD71)
    Human alveolar epithelial cell line (A549) that stably express hACE2 are from BEI Resources (NR-53821).
    A549
    suggested: None
    A549-hACE2 cells were seeded 1.5×105 cells/well in DMEM complete into 24-well plates (0.5 mL/well) then incubated for 16 hours at 37 °C and 5% CO2.
    A549-hACE2
    suggested: None
    Software and Algorithms
    SentencesResources
    Bioactive Library) and ChemDiv (a 10,000-compound SMART library subset)
    SMART
    suggested: (SMART, RRID:SCR_005026)
    Rigid body refinement followed by iterative rounds of restrained refinement and model building were performed with CCP4i modules Refmac559 and Coot.
    Coot
    suggested: (Coot, RRID:SCR_014222)
    EC50 values were determined by fitting the dose-response curves with four-parameter logistic regression in Prism GraphPad (version 8.1.2).
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Statistical analysis: GraphPad Prism 8 software package (GraphPad Software, USA) was used to perform statistical analysis.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: Thank you for sharing your data.

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.

  2. Version published to 10.1101/2021.02.13.431008 on bioRxiv