Efficient incorporation and template-dependent polymerase inhibition are major determinants for the broad-spectrum antiviral activity of remdesivir
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SciScore for 10.1101/2021.10.14.464416: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources The protein identities of the purified HCV nsp5b RdRp and NiV RdRp P/L complex were confirmed by mass spectrometry (MS) analysis (Alberta Proteomics and Mass Spectrometry, Edmonton, AB, Canada). ABsuggested: RRID:BDSC_203)Recombinant DNA Sentences Resources The pFastBac-1 (Invitrogen, Burlington, ON, Canada) plasmid with the codon-optimized synthetic DNA sequences (GenScript, Piscataway, NJ, USA) coding for HCV nsp5b RdRp (CAB46677.1 polyprotein, residues 2420 to 3010) minus the 21 C-terminus … SciScore for 10.1101/2021.10.14.464416: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources The protein identities of the purified HCV nsp5b RdRp and NiV RdRp P/L complex were confirmed by mass spectrometry (MS) analysis (Alberta Proteomics and Mass Spectrometry, Edmonton, AB, Canada). ABsuggested: RRID:BDSC_203)Recombinant DNA Sentences Resources The pFastBac-1 (Invitrogen, Burlington, ON, Canada) plasmid with the codon-optimized synthetic DNA sequences (GenScript, Piscataway, NJ, USA) coding for HCV nsp5b RdRp (CAB46677.1 polyprotein, residues 2420 to 3010) minus the 21 C-terminus residues was used as a starting material for protein expression in insect cells (Sf9, Invitrogen, Burlington, ON, Canada). pFastBac-1suggested: NoneSoftware and Algorithms Sentences Resources Data were analyzed using GraphPad Prism 7.0 (GraphPad Software, Inc GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)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:Structures of EBOV, NiV, CCHFV RdRp enzymes are not available, and structure of RSV and LASV RdRp lack the RNA substrate, which is a limitation of our modeling approach. Clear evidence for delayed chain-termination following a single incorporation of RDV-TP has so far only been demonstrated for SARS-CoV, MERS-CoV, and SARS-CoV-2 RdRp complexes. In these cases, a conserved serine clashes with the 1’-cyano group of the incorporated RDV-MP at position “i+3”(26,27,29,31,32). However, NTP concentrations > 10 μM are often sufficient to overcome the inhibition(26,27,29,31). The clash between the 1’-cyano group of RDV-MP and S861 in SARS-CoV-2 occurs in a region of the RdRp away from the active site. Indeed, tested polymerases of other viruses did not show any significant inhibition in primer extension reactions, although previous studies have shown that multiple consecutive incorporations of the inhibitor can also lead to delayed chain-termination at positions “i+3” and “i+5” with EBOV, RSV, and NiV RdRp complexes(11,16). In this work, we have also shown a subtle inhibitory effect at position “i” with HCV RdRp. Overall, this analysis suggests that the inhibitory effect in primer extension reactions is heterogeneous and generally weak. In contrast, the template-dependent inhibition of RNA synthesis seems to provide a unifying mechanism that shows strong inhibition of UTP incorporation opposite RDV-MP. The template nucleotide that base-pairs with the incoming nucleotide substrate is p...
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.
Results from scite Reference Check: We found no unreliable references.
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