Mechanistic and thermodynamic characterization of antivirals targeting druggable pocket of SARS-CoV-2 nucleocapsid
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
The N-terminal (NTD) and the C-terminal (CTD) domains comprises the structure of the SARS-CoV-2 Nucleocapsid (N) protein. Crystal structure of the SARS-CoV-2 N protein determined by Kang et al, 2020, reveals the N-terminal RNA binding domain as a unique drug binding site. The present study targets this unique pocket with identified antivirals using structure-based drug repurposing approach. The high-affinity binding of potential molecules was characterised thermodynamically using Isothermal titration calorimetry. The selected molecules showed an inhibitory RNA binding potential between 8.8 μM and 15.7 μM IC 50 when evaluated with a fluorescent-based assay. Furthermore, in an in vitro cell-based antiviral assay, these ten antiviral molecules demonstrated high effectiveness in halting SARS-CoV-2 replication. Telmisartan and BMS-189453, the two highly potent antivirals, have ∼0.98μM and 1.02 μM EC 50 values with the selective index of >102, and >98, respectively. For the first time, this study presents drug molecules specifically targeting the NTD of SARS-CoV-2, offering essential insights for the development of therapeutic interventions against this virus, which is still a potential global threat to public health.
Article activity feed
-
-
-
-
SciScore for 10.1101/2022.03.12.484092: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: All studies on infectious SARS-CoV-2 were performed in Biosafety level 3 facility at Indian Veterinary Research Institute (IVRI), Izatnagar Bareilly, after obtaining necessary approvals from Biosafety Committees. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources For this purpose, Vero cells were seeded in a 96-well cell culture plate and were incubated at 37 ºC and 5% CO2 tension overnight. Verosuggested: NoneRecombinant DNA Sentences Resources The PCR product was digested with NheI and SalI enzymes and … SciScore for 10.1101/2022.03.12.484092: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: All studies on infectious SARS-CoV-2 were performed in Biosafety level 3 facility at Indian Veterinary Research Institute (IVRI), Izatnagar Bareilly, after obtaining necessary approvals from Biosafety Committees. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources For this purpose, Vero cells were seeded in a 96-well cell culture plate and were incubated at 37 ºC and 5% CO2 tension overnight. Verosuggested: NoneRecombinant DNA Sentences Resources The PCR product was digested with NheI and SalI enzymes and subsequently ligated into the pET28c vector using DNA ligase. pET28csuggested: RRID:Addgene_161936)Software and Algorithms Sentences Resources For molecular docking study, the atomic structure of SARS-CoV-2 NTD (PDB ID: 6M3M)25 was retrieved from RCSB-PDB and three-dimensional structure of GMP was extracted from the PubChem database. PubChemsuggested: (PubChem, RRID:SCR_004284)Virtual screening and molecular docking of compound libraries: For structure-based virtual screening of small molecules against NTD, PyRx 0.840, and AutoDock tools/Vina37,38 platforms were used. AutoDocksuggested: (AutoDock, RRID:SCR_012746)Cell viability was calculated as a percentage against the untreated control, and the data were plotted using GraphPad prism to calculate the 50% cytotoxic concentration (CC50) of identified compounds. 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: 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.
Results from scite Reference Check: We found no unreliable references.
-