Journal: Molecules

Article Title: Computational Docking as a Tool in Guiding the Drug Design of Rutaecarpine Derivatives as Potential SARS-CoV-2 Inhibitors

doi: 10.3390/molecules29112636

Figure Lengend Snippet: Docking studies to show the interaction of rutaecarpine or its derivatives (RU-75 and RU-184) with the 3CL protease. The protein structure was downloaded from the Protein Data Bank ( https://www.rcsb.org/ , PDB ID: 6WNP, accessed on 28 March 2024), and the chemical structures were obtained from the Pubchem database ( https://pubchem.ncbi.nlm.nih.gov/ , accessed on 28 March 2024) and Chemdraw (Version 20.0).

Article Snippet: Samples were tested for their ability to bind to 3CL protease on a fluorogenic substrate using the SensoLyte SARS-CoV-2 3CL protease assay kit (AnaSpec, San Jose, CA, USA), according to the manufacturer’s instructions.

Techniques:

Journal: Molecules

Article Title: Computational Docking as a Tool in Guiding the Drug Design of Rutaecarpine Derivatives as Potential SARS-CoV-2 Inhibitors

doi: 10.3390/molecules29112636

Figure Lengend Snippet: RU-75 and RU-184 suppress 3CL protease activity. GC376 (100 µM) was used as a positive control. RU-75 and RU-184 both inhibited the 3CL protease in a dose-dependent manner. The IC 50 values are shown. The data indicate the mean ± SD percentage of inhibition, compared to a no drug control ( n = 4).

Article Snippet: Samples were tested for their ability to bind to 3CL protease on a fluorogenic substrate using the SensoLyte SARS-CoV-2 3CL protease assay kit (AnaSpec, San Jose, CA, USA), according to the manufacturer’s instructions.

Techniques: Activity Assay, Positive Control, Inhibition, Control

Journal: Journal of Chemical Information and Modeling

Article Title: Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease

doi: 10.1021/acs.jcim.1c00994

Figure Lengend Snippet: (a) Activity of compounds 9 and 6 represent strong efficacy against the coronavirus 3CL proteases from SARS-CoV-2. The combination of compounds 9 and 6 was used at 100 and 50 μM concentrations. (b) GC376 at 100 μM was used as an internal control. Data are shown as mean ± S.D. for three technical replicates.

Article Snippet: A SARS-CoV-2 3CL protease assay kit was purchased from BPS Biosciences (San Diego, CA, USA), which includes recombinant 3CL protease enzyme, 3CL protease substrate, 3CL protease assay buffer, GC376 as an inhibitor control, and a black, low binding microtiter plate for assay performance.

Techniques: Activity Assay

Journal: Journal of Chemical Information and Modeling

Article Title: Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease

doi: 10.1021/acs.jcim.1c00994

Figure Lengend Snippet: (a) Efficacy of the compound was calculated by the percentage inhibition of SARS-CoV-2 3CL protease by the specified concentrations of compounds 6 and 9 in combination ranged from 0.1 to 100 μM. Data are shown as mean ± S.D. for three technical replicates. Binding kinetics of (b) compound 6 , (c) compound 9 , and (d) combination of compounds 6 and 9 to the 3CL Protease. Kinetic analysis of 3CL Protease binding was performed by injecting different known concentrations of aggregates (from 0.31 to 5 μM) onto the immobilized carboxymethyl dextran-coated CM5 sensor chip was used with amine-coupling chemistry. All measurements were performed at 25 °C with a flow rate of 30 μL/min using HBS-EP buffer with association time 60 s, followed by 60 s dissociation phase. Kinetic constants (KDs) were calculated from the sensorgrams using the 1:1 fit model using BIA Evaluation 2.0.1 (Cytiva) software. The blue line indicates the actual curve, and the black line indicates the fitted curve of the sensorgram.

Article Snippet: A SARS-CoV-2 3CL protease assay kit was purchased from BPS Biosciences (San Diego, CA, USA), which includes recombinant 3CL protease enzyme, 3CL protease substrate, 3CL protease assay buffer, GC376 as an inhibitor control, and a black, low binding microtiter plate for assay performance.

Techniques: Inhibition, Binding Assay, Software

Journal: Archives of Virology

Article Title: Anti-SARS-CoV-2 activity of various PET-bottled Japanese green teas and tea compounds in vitro

doi: 10.1007/s00705-022-05483-x

Figure Lengend Snippet: Antiviral activity of GTB-A to -F (a) the tea compounds EGCG and ECG, and remdesivir (b) against SARS-CoV-2 at 2 days p.i. (MOI 0.02) and their cytotoxicity in Vero E6 cells. The blue and red lines represent the CC 50 and IC 50 , respectively; the blue circles represent cell viability (%), and the red squares represent % inhibition of SARS-CoV-2 infection. The values are the mean ± SD (N = 3).

Article Snippet: Inhibition of SARS-CoV-2 3CL pro (main protease, M pro ) by the GTBs, ECG, and EGCG was measured using a fluorogenic 3CL Protease, MBP-tagged (SARS-CoV-2) Assay Kit (BPS Bioscience, CA, USA).

Techniques: Activity Assay, Inhibition, Infection

Journal: Archives of Virology

Article Title: Anti-SARS-CoV-2 activity of various PET-bottled Japanese green teas and tea compounds in vitro

doi: 10.1007/s00705-022-05483-x

Figure Lengend Snippet: Immunofluorescence assay of SARS-CoV-2 (MOI 0.02) infection of Vero E6 cells treated with GTB-A to -F (a) and the tea compounds EGCG and ECG (b) at 2 days p.i. The confocal microscope images show cell nuclei (blue) and the SARS-CoV-2 nucleocapsid protein N (green). The mean ± SD was calculated from triplicate experiments.

Article Snippet: Inhibition of SARS-CoV-2 3CL pro (main protease, M pro ) by the GTBs, ECG, and EGCG was measured using a fluorogenic 3CL Protease, MBP-tagged (SARS-CoV-2) Assay Kit (BPS Bioscience, CA, USA).

Techniques: Immunofluorescence, Infection, Microscopy

Journal: Archives of Virology

Article Title: Anti-SARS-CoV-2 activity of various PET-bottled Japanese green teas and tea compounds in vitro

doi: 10.1007/s00705-022-05483-x

Figure Lengend Snippet: Time-of-addition assay. SARS-CoV-2 viral protein was analyzed after addition of 50-fold dilutions of GTB-B, GTB-C, and GTB-E (a), 50 µM EGCG or ECG (b), or DMSO at different time points. N protein expression in cell lysates was analyzed by western blot at 16 h p.i. Band intensities were quantitated using ImageJ and are graphically displayed for GTB-B, GTB-C, and GTB-E (c), EGCG and ECG (d), and DMSO. The relative intensities of c and d were normalized to the DMSO control, which was set to 1.0.

Article Snippet: Inhibition of SARS-CoV-2 3CL pro (main protease, M pro ) by the GTBs, ECG, and EGCG was measured using a fluorogenic 3CL Protease, MBP-tagged (SARS-CoV-2) Assay Kit (BPS Bioscience, CA, USA).

Techniques: Expressing, Western Blot

Journal: Archives of Virology

Article Title: Anti-SARS-CoV-2 activity of various PET-bottled Japanese green teas and tea compounds in vitro

doi: 10.1007/s00705-022-05483-x

Figure Lengend Snippet: Time-of-addition assay for quantification of SARS-CoV-2 inhibition (%) after addition of 50-fold dilutions of GTB-B, GTB-C, and GTB-E (a) and 50 µM EGCG and ECG (b) at different time points. Viral RNA in cell supernatants was measured by qRT-PCR at 16 h p.i. The mean ± SD was calculated from triplicate experiments. *, p < 0.05; **, p < 0.01; **, p < 0.001. Student’s t -test was used to compare the different treatments after normalization to the virus control.

Article Snippet: Inhibition of SARS-CoV-2 3CL pro (main protease, M pro ) by the GTBs, ECG, and EGCG was measured using a fluorogenic 3CL Protease, MBP-tagged (SARS-CoV-2) Assay Kit (BPS Bioscience, CA, USA).

Techniques: Inhibition, Quantitative RT-PCR

Journal: Phytotherapy Research

Article Title: Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS‐CoV‐2

doi: 10.1002/ptr.7486

Figure Lengend Snippet: Schematic representation for the rational selection of flavonoids with potential activity against SARS‐CoV‐2

Article Snippet: SARS‐CoV‐2 S protein inhibition assay was performed using SARS‐CoV‐2 Spike: ACE‐2 inhibitor Screening Assay Kit (CAT # 79331, BPS Bioscience, San Diego, CA, USA) following the supplier protocol.

Techniques: Selection, Activity Assay

Journal: Phytotherapy Research

Article Title: Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS‐CoV‐2

doi: 10.1002/ptr.7486

Figure Lengend Snippet: Heatmap representing the levels of binding affinity of flavonoids against vital SARS‐CoV‐2 protein targets. Relative binding affinity levels were displayed as colors ranging from red to green as shown in the key

Article Snippet: SARS‐CoV‐2 S protein inhibition assay was performed using SARS‐CoV‐2 Spike: ACE‐2 inhibitor Screening Assay Kit (CAT # 79331, BPS Bioscience, San Diego, CA, USA) following the supplier protocol.

Techniques: Binding Assay

Journal: Phytotherapy Research

Article Title: Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS‐CoV‐2

doi: 10.1002/ptr.7486

Figure Lengend Snippet: In vitro antiviral activity of flavonoids under study. The antiviral activity of the compounds was screened on SARS‐CoV‐2 co‐cultured with Vero‐E6 cells. Values of inhibitory concentration 50% (IC 50 ) on viral cells and cytotoxic concentration 50% (CC 50 ) on Vero cells were calculated using nonlinear regression analysis. The data display the mean of cell viability percentage ± SEM of 4 replicates

Article Snippet: SARS‐CoV‐2 S protein inhibition assay was performed using SARS‐CoV‐2 Spike: ACE‐2 inhibitor Screening Assay Kit (CAT # 79331, BPS Bioscience, San Diego, CA, USA) following the supplier protocol.

Techniques: In Vitro, Activity Assay, Cell Culture, Concentration Assay

Journal: Phytotherapy Research

Article Title: Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS‐CoV‐2

doi: 10.1002/ptr.7486

Figure Lengend Snippet: Pharmacophore features of flavonoids required for the anti‐SARS‐CoV‐2 activity. (a) Common pharmacophore generation sites with distance in Å with two acceptors [pink sphere with two arrows], two aromatic rings [dark yellow circle], and one donor [blue sphere with arrow]. (b) Alignment of all active flavonoids including silibinin, myricetin and eriodictyol to the pharmacophore. (c) The good alignment of the active silibinin to the pharmacophore. (d) The bad alignment of inactive daidzein to the pharmacophore

Article Snippet: SARS‐CoV‐2 S protein inhibition assay was performed using SARS‐CoV‐2 Spike: ACE‐2 inhibitor Screening Assay Kit (CAT # 79331, BPS Bioscience, San Diego, CA, USA) following the supplier protocol.

Techniques: Activity Assay

Journal: Phytotherapy Research

Article Title: Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS‐CoV‐2

doi: 10.1002/ptr.7486

Figure Lengend Snippet: Inhibition percentage of selected flavonoids against SARS‐CoV‐2 S protein compared to remdesivir. The inhibition percentage of eriodictyol, myricetin, and silibinin flavonoids to the binding of S protein to ACE‐2 receptor was screened at 15 μg/ml compared to remdesivir at its IC 50 (2.5 μg/ml). The data was analyzed using one‐way ANOVA and statistical significance was calculated with Dunnett's multiple comparisons test and significance level indicated by asterisks (* p < 0.05; ** p < 0.01: *** p < 0.001; **** p < 0.0001). The data display the mean ± SEM of three independent replicates. p ‐value <0.05 was considered as significant

Article Snippet: SARS‐CoV‐2 S protein inhibition assay was performed using SARS‐CoV‐2 Spike: ACE‐2 inhibitor Screening Assay Kit (CAT # 79331, BPS Bioscience, San Diego, CA, USA) following the supplier protocol.

Techniques: Inhibition, Binding Assay

Journal: Phytotherapy Research

Article Title: Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS‐CoV‐2

doi: 10.1002/ptr.7486

Figure Lengend Snippet: Inhibition percentage of silibinin against selected critical SARS‐CoV‐2 targets. (a) IC 50 calculation of silibinin against SARS‐CoV‐2 S protein. (b) IC 50 calculation of silibinin against SARS‐CoV‐2 M pro enzyme. (c) IC 50 calculation of silibinin against SARS‐CoV‐2 RdRp. (d) Inhibition percentage of silibinin on SARS‐CoV‐2 RdRp compared to remdesivir. The data was analyzed using Unpaired t test with Welch's correction and significance level indicated by asterisks. The data display the mean of the percentage of the enzyme inhibition ± SEM of 3 replicates

Article Snippet: SARS‐CoV‐2 S protein inhibition assay was performed using SARS‐CoV‐2 Spike: ACE‐2 inhibitor Screening Assay Kit (CAT # 79331, BPS Bioscience, San Diego, CA, USA) following the supplier protocol.

Techniques: Inhibition, Enzyme Inhibition Assay

Journal: Phytotherapy Research

Article Title: Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS‐CoV‐2

doi: 10.1002/ptr.7486

Figure Lengend Snippet: Silibinin exhibited strong virucidal effect on SARS‐CoV‐2 strain NRC‐03‐nhCoV. The diluted pre‐incubated control virus and silibinin‐treated virus were cultured with Vero E6 cells using plaque infectivity assay. (a) Viral titer of virus control (untreated) and silibinin‐treated virus. (b) Plaque reduction by treatment with silibinin. The data was analyzed using Unpaired t test with Welch's correction and significance level indicated by asterisks. The data display the mean of the percentage of virucidal activity of silibinin ± SEM of 4 replicates

Article Snippet: SARS‐CoV‐2 S protein inhibition assay was performed using SARS‐CoV‐2 Spike: ACE‐2 inhibitor Screening Assay Kit (CAT # 79331, BPS Bioscience, San Diego, CA, USA) following the supplier protocol.

Techniques: Incubation, Cell Culture, Infection, Activity Assay

Journal: Phytotherapy Research

Article Title: Comparative evaluation of flavonoids reveals the superiority and promising inhibition activity of silibinin against SARS‐CoV‐2

doi: 10.1002/ptr.7486

Figure Lengend Snippet: Interaction of silibinin with SARS‐CoV‐2 target proteins. (a–d) Interaction of silibinin within the active site of viral proteins. (a) Interaction of silibinin with SARS‐CoV‐2 S protein (PDB:6VSB). (b) Interaction of silibinin with SARS‐CoV‐2 M pro enzyme (PDB: 6LU7). (c) Interaction of silibinin with SARS‐CoV‐2 RdRp enzyme (PDB:7BV2). (d) Interaction of silibinin with TMPRSS2 enzyme (PDB:2OQ5)

Article Snippet: SARS‐CoV‐2 S protein inhibition assay was performed using SARS‐CoV‐2 Spike: ACE‐2 inhibitor Screening Assay Kit (CAT # 79331, BPS Bioscience, San Diego, CA, USA) following the supplier protocol.

Techniques: