CETSA ® MS profiling for a comparative assessment of FDA approved antivirals repurposed for COVID-19 therapy identifies Trip13 as a Remdesivir off-target

  1. Tomas Friman
  2. Alexey Chernobrovkin
  3. Daniel Martinez Molina
  4. Laurence Arnold

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Abstract

The reuse of pre-existing small molecules for a novel emerging disease threat is a rapid measure to discover unknown applications for previously validated therapies. A pertinent and recent example where such strategy could be employed is in the fight against COVID-19. Therapies designed or discovered to target viral proteins also have off-target effects on the host proteome when employed in a complex physiological environment. This study aims to assess these host cell targets for a panel of FDA approved antiviral compounds including Remdesivir, using the cellular thermal shift assay (CETSA ® ) coupled to mass spectrometry (CETSA MS) in non-infected cells. CETSA MS is a powerful method to delineate direct and indirect interactions between small molecules and protein targets in intact cells. Biologically active compounds can induce changes in thermal stability, in their primary binding partners as well as in proteins that in turn interact with the direct targets. Such engagement of host targets by antiviral drugs may contribute to the clinical effect against the virus but can also constitute a liability. We present here a comparative study of CETSA molecular target engagement fingerprints of antiviral drugs to better understand the link between off-targets and efficacy.

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  1. ScreenIT

    SciScore for 10.1101/2020.07.19.210492: (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: The human cell line HepG2 was procured from ATCC and cultured until 70% confluency in collagen-coated flasks.
    HepG2
    suggested: None
    Software and Algorithms
    SentencesResources
    For protein identification, validation was done at the peptide-spectrum-match (PSM) level using the following acceptance criteria; 1 % FDR determined by Percolator scoring based on Q-value, rank 1 peptides only.
    Percolator
    suggested: (OMSSAPercolator, RRID:SCR_000287)
    Data analysis: Quantitative results were exported from Proteome Discoverer as tab-separated files and analyzed using R version 4.0.2 software.
    Proteome Discoverer
    suggested: (Proteome Discoverer, RRID:SCR_014477)
    For each protein and each compound, thermal stability changes were assessed by comparing normalized log2-transformed intensities to DMSO treated control using moderated t-test implemented in “limma” R-package version 3.44.120.
    R-package
    suggested: None

    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.
    • No funding statement was detected.
    • 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 10.1101/2020.07.19.210492 on bioRxiv