Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking
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Abstract
Massive fragment screening effort provides a foundation for the development of macrodomain inhibitors as novel antiviral agents.
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SciScore for 10.1101/2020.11.24.393405: (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
Antibodies Sentences Resources Assay: Fragment inhibitory activity on Mac1 was assessed by the displacement of an ADP-ribose-conjugated biotin peptide from the His6-tagged Nsp3 Mac1 domain using HTRF with a Eu3+-conjugated anti-His6 antibody donor and streptavidin-conjugated acceptor. anti-His6suggested: NoneExperimental Models: Organisms/Strains Sentences Resources Purity and structure determination of initial fragment samples ZINC901381520, ZINC82473428 and ZINC89254160 provided by Enamine: Samples of ZINC901391520, ZINC82473428 and ZINC89254160 obtained from Enamine were expected to be N9-alkylated isomers but electron density of … SciScore for 10.1101/2020.11.24.393405: (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
Antibodies Sentences Resources Assay: Fragment inhibitory activity on Mac1 was assessed by the displacement of an ADP-ribose-conjugated biotin peptide from the His6-tagged Nsp3 Mac1 domain using HTRF with a Eu3+-conjugated anti-His6 antibody donor and streptavidin-conjugated acceptor. anti-His6suggested: NoneExperimental Models: Organisms/Strains Sentences Resources Purity and structure determination of initial fragment samples ZINC901381520, ZINC82473428 and ZINC89254160 provided by Enamine: Samples of ZINC901391520, ZINC82473428 and ZINC89254160 obtained from Enamine were expected to be N9-alkylated isomers but electron density of compounds in X-ray co-crystal structures indicated these samples were N3-alkylated isomers instead (ZINC901391520_N3, ZINC82473428_N3 and ZINC89254160_N3, see Fig. S7I-L). ZINC89254160suggested: NoneSoftware and Algorithms Sentences Resources The fragment library at XChem combined molecules from multiple fragment libraries: the Diamond, SGC and iNEXT (DSI)-poised Library (768 molecules, (34)), the Edelris fragment collection (280 molecules, (75)), the MiniFrags Probing Library (80 molecules, (76)), the FragLites collection (31 compounds, (77)), the PepLite library (25 molecules, (38)), the SpotFinder (~100 compounds, (78)), and the York3D (106 molecules, (79)) and the EU Open screen (969 molecules, (52)). SpotFindersuggested: (Spotfinder, RRID:SCR_000085)Pyrimidines were identified using RDKit (http://www.rdkit.org) (82) and molecular charges at pH 7.4 were approximated using ChemAxon Jchem version 2019.15 (http://www.chemaxon.com) to identify anionic fragments (83). http://www.rdkit.orgsuggested: (RDKit: Open-Source Cheminformatics Software, RRID:SCR_014274)ChemAxonsuggested: (ChemAxon, RRID:SCR_004111)Compounds with DOCK scores < −20 (top 500,000 compounds from the entire fragment screen), were subsequently filtered for those with strained conformations, and inspected for their ability to form hydrogen bonds to residues Asp22, Ile23, Gly48, Val49, Gly130 or Phe156. DOCKsuggested: (DOCK, RRID:SCR_000128)Raw data were processed to give an HTRF ratio (channel A/B × 10,000), which was used to generate IC50 curves by nonlinear regression using GraphPad Prism v8 (GraphPad Software, CA, USA). GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Admittedly, weaknesses also emerged from the docking. Intriguingly, the oxyanion site that featured so prominently among the crystallographic screening hits were not to be found among the docking predictions. This gap reflects both a failure of the docking scoring function to prioritize anions binding to this site (as they were at least sampled), and to some extent a failure of the docking group to pick the few molecules that did dock well to this site as likely candidates. More broadly, as we docked against a single rigid structure of the protein, the subsequent conformational changes that the protein underwent, and the changes in the water network, were not captured in the docking predictions, and this was sometimes reflected in the larger RMSD differences between predicted and observed fragment poses. These caveats, important as they are, should not obscure a central observation from this study: the docking hit rate was not only high, but the hits were typically right for the right reasons; this may be something to build on for the field. From the docked compounds, the most promising hits identified by in-solution binding experiments were also crystallographically confirmed. However, as expected, the majority of soaking hits did not show appreciable activity in the orthogonal biophysical assays within the tested concentration range (up to 10 mM in ITC, Supplementary Table 1). The macrodomain ADPr-peptide displacement assay also identified two docking hits not previously ob...
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.
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- No protocol registration statement was detected.
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