Journal: Acta Pharmaceutica Sinica. B

Article Title: Corilagin inhibits SARS-CoV-2 replication by targeting viral RNA-dependent RNA polymerase

doi: 10.1016/j.apsb.2021.02.011

Figure Lengend Snippet: Structure-based virtual screening of the Drugbank database and TargetMol active compound library against SARS-CoV-2 RdRp. (A) Flowchart outlining the steps of the virtual screening and the selection of candidate molecules to be tested. (B) Results of virtual screening using AutoDock Vina (ADV) of the small molecule compound database against SARS-CoV-2 nsp12. Bars represent numbers of compounds with predicted free energies of binding in the indicated 1 kcal/mol bins.

Article Snippet: Figure 1 Structure-based virtual screening of the Drugbank database and TargetMol active compound library against SARS-CoV-2 RdRp. (A) Flowchart outlining the steps of the virtual screening and the selection of candidate molecules to be tested. (B) Results of virtual screening using AutoDock Vina (ADV) of the small molecule compound database against SARS-CoV-2 nsp12.

Techniques: Selection, Binding Assay

Journal: Acta Pharmaceutica Sinica. B

Article Title: Corilagin inhibits SARS-CoV-2 replication by targeting viral RNA-dependent RNA polymerase

doi: 10.1016/j.apsb.2021.02.011

Figure Lengend Snippet: A plot of BLI responses with SARS-CoV-2 nsp12 for 50 compounds. The His-tagged SARS-CoV-2 RdRp captured onto NTA biosensors were applied to solutions containing compounds at a single concentration of 50 μmol/L. Double reference subtraction method was used to subtract the effect of baseline drift and non-specific binding. The data shown are a representative result of three independent experiments.

Article Snippet: Figure 1 Structure-based virtual screening of the Drugbank database and TargetMol active compound library against SARS-CoV-2 RdRp. (A) Flowchart outlining the steps of the virtual screening and the selection of candidate molecules to be tested. (B) Results of virtual screening using AutoDock Vina (ADV) of the small molecule compound database against SARS-CoV-2 nsp12.

Techniques: Concentration Assay, Binding Assay

Journal: Acta Pharmaceutica Sinica. B

Article Title: Corilagin inhibits SARS-CoV-2 replication by targeting viral RNA-dependent RNA polymerase

doi: 10.1016/j.apsb.2021.02.011

Figure Lengend Snippet: Binding of RAI-S-37 to SARS-CoV-2 RdRp using cell-free BLI binding assay. (A) BLI binding kinetics of the interaction of RAI-S-37 with SARS-CoV-2 nsp12. The His-tagged SARS-CoV-2 RdRp captured onto NTA biosensors were applied to solutions containing RAI-S-37 from 3.125 to 100 μmol/L. Double reference subtraction method was used to subtract the effect of baseline drift and non-specific binding. K D was acquired from fitting into 1:1 binding model by global fitting of multiple kinetic traces and analyzed by Data Analysis 9.0 software. Date are expressed as mean ± SD. The data shown are a representative result of three independent experiments. (B) The chemical structure, molecule name, CAS number, and molecular weight of RAI-S-37.

Article Snippet: Figure 1 Structure-based virtual screening of the Drugbank database and TargetMol active compound library against SARS-CoV-2 RdRp. (A) Flowchart outlining the steps of the virtual screening and the selection of candidate molecules to be tested. (B) Results of virtual screening using AutoDock Vina (ADV) of the small molecule compound database against SARS-CoV-2 nsp12.

Techniques: Binding Assay, Software, Molecular Weight

Journal: Acta Pharmaceutica Sinica. B

Article Title: Corilagin inhibits SARS-CoV-2 replication by targeting viral RNA-dependent RNA polymerase

doi: 10.1016/j.apsb.2021.02.011

Figure Lengend Snippet: RAI-S-37 inhibits SARS-CoV-2 RdRp in the cell-free viral RNA synthesis assay. (A) SDS-PAGE analysis of purified SARS-CoV-2 RdRp subunits nsp12, nsp8, nsp7, and nsp7–6His–nsp8. Standard protein markers are shown in the last lane. (B) and (C) Cell-free polymerase activity of nsp7, nsp8, nsp7–6His–nsp8, nsp12 in various combinations. A 40 nt template RNA mimics the 3ʹ UTR of SARS-CoV-2 RNA genome without the polyA tail, was used together with a 20 nt primer labeled with FAM to monitor the polymerase activity, which was determined by measuring the 40 nt FAM RNA product. In addition to the 40 nt fully elongated RNA product, some prematurely terminated products (shorter than 40 nt) were also observed. (D)–(I) Inhibitory effects of RAI-S-11, RAI-S-35, RAI-S-36, RAI-S-37, RAI-S-45, and RAI-S-47 on SARS-CoV-2 RdRp at the concentration of 40, 10, and 2.5 μmol/L, respectively. Polymerase activity was determined by quantifying the intensity of the fully elongated 40 nt RNA product bands. Data are expressed as mean ± SD ( n = 3). ∗ P < 0.05, ∗∗ P < 0.01, ∗∗∗ P < 0.001. n.s. indicates non-significant.

Article Snippet: Figure 1 Structure-based virtual screening of the Drugbank database and TargetMol active compound library against SARS-CoV-2 RdRp. (A) Flowchart outlining the steps of the virtual screening and the selection of candidate molecules to be tested. (B) Results of virtual screening using AutoDock Vina (ADV) of the small molecule compound database against SARS-CoV-2 nsp12.

Techniques: SDS Page, Purification, Activity Assay, Labeling, Concentration Assay

Journal: Acta Pharmaceutica Sinica. B

Article Title: Corilagin inhibits SARS-CoV-2 replication by targeting viral RNA-dependent RNA polymerase

doi: 10.1016/j.apsb.2021.02.011

Figure Lengend Snippet: Inhibitory effect of remdesivir provided in combination with RAIS-S-37 on SARS-CoV-2 RdRp activity. (A) HEK293T cells were transfected with CoV-Gluc, nsp12, nsp7, and nsp8 plasmid DNA at the ratio of 1:10:30:30. (B) HEK293T cells were transfected with CoV-Gluc, nsp12, nsp7, nsp8, nsp10, and nsp14 plasmid DNA at the ratio of 1:20:60:60:50:50. At 12 h post transfection, cells were re-seeded in 96-well plates (10 4 /well) and treated with serially diluted remdesivir and RAI-S-37. After 24 h incubation, Gluc activity in supernatants was determined. EC 50 values were obtained by non-linear regression analysis using GraphPad Prism 8.0. The Data are expressed as mean ± SD ( n = 3).

Article Snippet: Figure 1 Structure-based virtual screening of the Drugbank database and TargetMol active compound library against SARS-CoV-2 RdRp. (A) Flowchart outlining the steps of the virtual screening and the selection of candidate molecules to be tested. (B) Results of virtual screening using AutoDock Vina (ADV) of the small molecule compound database against SARS-CoV-2 nsp12.

Techniques: Activity Assay, Transfection, Plasmid Preparation, Incubation

Journal: Acta Pharmaceutica Sinica. B

Article Title: Corilagin inhibits SARS-CoV-2 replication by targeting viral RNA-dependent RNA polymerase

doi: 10.1016/j.apsb.2021.02.011

Figure Lengend Snippet: The antiviral activities of RAI-S-37 against SARS-CoV-2 and HCoV-OC43. (A) Vero E6 cells were infected with SARS-CoV-2 at the MOI of 0.05 with the treatment of different doses of the indicated drugs for 48 h. Levels of SARS-CoV-2 in the cell supernatant was determined by qRT-PCR. Data of the graphs represent mean % inhibition of virus yield. The experiments were performed in triplicates. (B) Huh-7 cells were infected with HCoV-OC43 at the MOI of 0.1 in the presence of increasing concentrations of the tested compounds. DMSO was used as vehicle control. The Data are expressed as mean ± SD ( n = 3).

Article Snippet: Figure 1 Structure-based virtual screening of the Drugbank database and TargetMol active compound library against SARS-CoV-2 RdRp. (A) Flowchart outlining the steps of the virtual screening and the selection of candidate molecules to be tested. (B) Results of virtual screening using AutoDock Vina (ADV) of the small molecule compound database against SARS-CoV-2 nsp12.

Techniques: Infection, Quantitative RT-PCR, Inhibition

Journal: Acta Pharmaceutica Sinica. B

Article Title: Corilagin inhibits SARS-CoV-2 replication by targeting viral RNA-dependent RNA polymerase

doi: 10.1016/j.apsb.2021.02.011

Figure Lengend Snippet: Predicted binding sites for RAI-S-37 in SARS-CoV-2 RdRp. (A) Predicted structure of SARS-CoV-2 RdRp in complex with RAI-S-37. (B) Superimposition of the structures of SARS-CoV-2 RdRp/RAI-S-37 and SARS-CoV-2 RdRp/template-RTP. RAI-S-37 and RTP are shown as cyan dots and magenta stick, respectively. (C) The polymerases are shown in cartoon representation with the backbone atoms depicted in purple. RAI-S-37 and the amino acid residues involved the polymerase–ligand interactions are shown as sticks. (D) The 2D ligand–polymerase interaction diagrams. Residues within 4 Å of RAI-S-37 are displayed. Hydrogen bond is represented by the arrows with the distance between the donor and the acceptor. Dark blue indicates positive charge, red indicates negative charge, light blue for polar, green for hydrophobic, and white for glycine. (E) Superposition of the SARS-CoV-2-nsp12/RAI-S-37 and HCoV-OC43-nsp9/RAI-S-37 complexes. SARS-CoV-2-nsp12 and HCoV-OC43-nsp9 are shown as slate and yellow cartoons, and the bound RAI-S-37 is shown as cyan and salmon sticks, respectively. (F) Comparisons of protein–ligand interactions of complexes SARS-CoV-2-nsp12/RAI-S-37 and HCoV-OC43-nsp9/RAI-S-37.

Article Snippet: Figure 1 Structure-based virtual screening of the Drugbank database and TargetMol active compound library against SARS-CoV-2 RdRp. (A) Flowchart outlining the steps of the virtual screening and the selection of candidate molecules to be tested. (B) Results of virtual screening using AutoDock Vina (ADV) of the small molecule compound database against SARS-CoV-2 nsp12.

Techniques: Binding Assay