Blockade of SARS-CoV-2 infection in vitro by highly potent PI3K-α/mTOR/BRD4 inhibitor

  1. Arpan Acharya
  2. Kabita Pandey
  3. Michellie Thurman
  4. Kishore B. Challagundala
  5. Kendra R. Vann
  6. Tatiana G. Kutateladze
  7. Guillermo A Morales
  8. Donald L. Durden
  9. Siddappa N. Byrareddy

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Abstract

Pathogenic viruses like SARS-CoV-2 and HIV hijack the host molecular machinery to establish infection and survival in infected cells. This has led the scientific community to explore the molecular mechanisms by which SARS-CoV-2 infects host cells, establishes productive infection, and causes life-threatening pathophysiology. Very few targeted therapeutics for COVID-19 currently exist, such as remdesivir. Recently, a proteomic approach explored the interactions of 26 of 29 SARS-CoV-2 proteins with cellular targets in human cells and identified 67 interactions as potential targets for drug development. Two of the critical targets, the bromodomain and extra-terminal domain proteins (BETs): BRD2/BRD4 and mTOR, are inhibited by the dual inhibitory small molecule SF2523 at nanomolar potency. SF2523 is the only known mTOR PI3K-α/(BRD2/BRD4) inhibitor with potential to block two orthogonal pathways necessary for SARS-CoV-2 pathogenesis in human cells. Our results demonstrate that SF2523 effectively blocks SARS-CoV-2 replication in lung bronchial epithelial cells in vitro , showing an IC 50 value of 1.5 µM, comparable to IC 50 value of remdesivir (1.1 µM). Further, we demonstrated that the combination of doses of SF2523 and remdesivir is highly synergistic: it allows for the reduction of doses of SF2523 and remdesivir by 25-fold and 4-fold, respectively, to achieve the same potency observed for a single inhibitor. Because SF2523 inhibits two SARS-CoV-2 driven pathogenesis mechanisms involving BRD2/BRD4 and mTOR signaling, our data suggest that SF2523 alone or in combination with remdesivir could be a novel and efficient therapeutic strategy to block SARS-CoV-2 infection and hence be beneficial in preventing severe COVID-19 disease evolution.

One Sentence Summary

Evidence of in silico designed chemotype (SF2523) targeting PI3K-α/mTOR/BRD4 inhibits SARS-CoV-2 infection and is highly synergistic with remdesivir.

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  1. ScreenIT

    SciScore for 10.1101/2021.03.02.433604: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIACUC: BSL-3 core laboratory setting and approved by the University of Nebraska Medical Center institutional Biosafety Committee (IBC) with the approval number 20-05-029-BL3.
    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
    UNCN1T cells (a human bronchial epithelial cell line; Kerafast; cat# ENC011) were cultured using BEGM media (Bronchial Epithelial Cell Growth Medium; Lonza: cat# CC-3170) in FNC (Athena Enzyme Systems; cat# 0407) coated plates.
    UNCN1T
    suggested: RRID:CVCL_ZC91)
    In brief, Vero E6 cells were seeded in 6-well plates.
    Vero E6
    suggested: None
    Dose-response percent inhibition matrix of single and combined treatment of remdesivir and SF2523 in SARS-CoV-2 infected UNCN1T and Vero-STAT1 knockout cells 24 hrs post infection and 3-D interaction landscape between remdesivir and SF2523 were calculated based on Loewe additive model using SynergyFinder v.
    Vero-STAT1
    suggested: ATCC Cat# CCL-81-VHG, RRID:CVCL_YZ45)
    Software and Algorithms
    SentencesResources
    In silico docking of SF2523 against BRD4-BD1 was performed using AutoDock Vina (40) and rDock (41).
    AutoDock
    suggested: (AutoDock, RRID:SCR_012746)
    Dose-response percent inhibition matrix of single and combined treatment of remdesivir and SF2523 in SARS-CoV-2 infected UNCN1T and Vero-STAT1 knockout cells 24 hrs post infection and 3-D interaction landscape between remdesivir and SF2523 were calculated based on Loewe additive model using SynergyFinder v.
    SynergyFinder
    suggested: (SynergyFinder, RRID:SCR_019318)

    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: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04280705CompletedAdaptive COVID-19 Treatment Trial (ACTT)
    NCT04315948Active, not recruitingTrial of Treatments for COVID-19 in Hospitalized Adults

    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

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  2. Version published to 10.1101/2021.03.02.433604v2 on bioRxiv
  3. Version published to 10.1101/2021.03.02.433604v1 on bioRxiv