A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy

  1. Anastassia L. Kantsadi
  2. Emma Cattermole
  3. Minos-Timotheos Matsoukas
  4. Georgios A. Spyroulias
  5. Ioannis Vakonakis

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological cause of the coronavirus disease 2019, for which no effective antiviral therapeutics are available. The SARS-CoV-2 main protease (M pro ) is essential for viral replication and constitutes a promising therapeutic target. Many efforts aimed at deriving effective M pro inhibitors are currently underway, including an international open-science discovery project, codenamed COVID Moonshot. As part of COVID Moonshot, we used saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy to assess the binding of putative M pro ligands to the viral protease, including molecules identified by crystallographic fragment screening and novel compounds designed as M pro inhibitors. In this manner, we aimed to complement enzymatic activity assays of M pro performed by other groups with information on ligand affinity. We have made the M pro STD-NMR data publicly available. Here, we provide detailed information on the NMR protocols used and challenges faced, thereby placing these data into context. Our goal is to assist the interpretation of M pro STD-NMR data, thereby accelerating ongoing drug design efforts.

Article activity feed

  1. Version published to 10.1007/s10858-021-00365-x
  2. Version published to 10.1101/2020.06.17.156679v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.17.156679: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Experiments were performed and data processed using TopSpin (Bruker).
    TopSpin
    suggested: (TopSpin, RRID:SCR_014227)
    Data fitting to extract Kd values were performed in OriginPro (OriginLab).
    OriginPro
    suggested: None
    Molecular dynamics (MD) simulations: The monomeric complexes of Mpro bound to chemical fragments were obtained from the RCSB Protein Data Bank entries 5R81 (ligand x0195), 5REB (x0387), 5RGI (x0397), 5RGK (x0426), 5R83 (x0434) and 5REH (x0540) for MD simulations with GROMACS version 2018 (25) and the AMBER99SB-ILDN force field (26).
    GROMACS
    suggested: (GROMACS, RRID:SCR_014565)
    Structures were visualised using PyMOL (32).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    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: We detected the following sentences addressing limitations in the study:
    Although this metric has limitations due to its dependency on magnetisation transfer between protein and ligand, and on relatively rapid exchange between the ligand-free and -bound states, we demonstrated that it can nevertheless be informative. Specifically, the relative STDratio values of chemical fragments bound to the Mpro active site provided insight on fragment affinity (Fig. 2A), as crosschecked by quantitative titrations (Fig. S2) and MD simulations (Fig. S3). Furthermore, STDratio values of COVID Moonshot compounds held a weak correlation to enzymatic IC50 parameters (Fig. 3B), although false-negative and -positive results from both methods contribute to multiple outliers. Thus, in our view the biggest limitation of using the single-concentration STDratio value as metric relates to its supra-linear sensitivity to ligand concentration (Fig. S1), which as demonstrated here can vary substantially across ligands in a large project (Fig. 3A). How then should the STD data recorded as part of COVID Moonshot be used? Firstly, we showed that at least for some bespoke Mpro ligands the STDratio value obtained is a better proxy for compound affinity compared to IC50 parameters from enzymatic assays (Fig. S5). This, inherently, is the value of employing orthogonal methods thereby minimizing the number of potential false results. Thus, when one is considering existing Mpro ligands to base the design of future inhibitors, a high STDratio value as well as low IC50 parameters are bot...

    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 10.1101/2020.06.17.156679v1 on bioRxiv