Journal: Nature Communications

Article Title: Tubeimosides are pan-coronavirus and filovirus inhibitors that can block their fusion protein binding to Niemann-Pick C1

doi: 10.1038/s41467-023-44504-4

Figure Lengend Snippet: A Docking of indicated compounds to NPC1-C and EBOV-GP complex (PDB: 5F1B) was analyzed via Webina. B SNB-19 cells were treated overnight with indicated compounds. After being fixed, cells were stained with filipin (50 µg/mL) and visualized by confocal microscopy (scale bar, 40 μm). Experiments were repeated 3 times independently, and representative results are shown. C Vero-E6 cells were treated with Tubs I/II/III at 0.5 μM and infected with HIV-1 Luc-pseudovirus expressing MARV-GP. Viral infection was determined as previously. D Vero-E6 cells were treated with indicated compounds and infected with HIV-1 Luc-pseudovirus expressing EBOV-GP. Tor, Tam, and Tubs I/II/III were used at 2.5 μM, 5.0 μM, or 0.5 μM, respectively. DMSO was used as a control (Ctr). E Vero-E6 cells were pretreated for 1 h with EIPA and Tubs I/II/III and spinoculated with GFP-labeled EBOV-VLPs expressing EBOV-GP or VSV-G. After removal of VLPs and culture for another 3 h, GFP-positive cells were quantified by flow cytometry. EIPA [5-(N-ethyl-N-isopropyl) amiloride] and Tubs I/II/III were used at 25 μM, or 0.5 μM, respectively. F CTS-B or CTS-L substrates were incubated with cell lysate from A549 cells treated with Tubs I/II/III, and their activity was determined. E-64-d ethyl ester (EST) was used at 10 μM and Tubs I/II/III were used at indicated concentrations. G A549 cells were treated with NH 4 Cl at 100 µM and Tubs I/II/III at 0.5 μM. After being stained with LysoTracker Red, cells were visualized by fluorescence microscope (EVOS FL Auto Imaging System) (scale bar, 200 μm). Experiments were repeated 3 times independently, and representative results are shown. Error bars in C and D indicate SEMs ( n = 3 biologically independent experiments). One-way ANOVA was applied. *** P < 0.001, **** P < 0.0001; n.s. not significant.

Article Snippet: Initially, we performed molecular docking and structural analysis via Webina ( https://durrantlab.pitt.edu/webina/ ), a web server based on Autodock vina , .

Techniques: Staining, Confocal Microscopy, Infection, Expressing, Control, Labeling, Flow Cytometry, Incubation, Activity Assay, Fluorescence, Microscopy, Imaging

Journal: Nature Communications

Article Title: Tubeimosides are pan-coronavirus and filovirus inhibitors that can block their fusion protein binding to Niemann-Pick C1

doi: 10.1038/s41467-023-44504-4

Figure Lengend Snippet: A Huh-7-A-T cells were treated with indicated compounds at 1 µM and infected with HIV-1 Luc-pseudoviruses expressing SARS1-S or MERS-S and viral inhibition was determined as previously. DMSO was used as a control (Ctr). B Caco2, Vero-E6, and their NPC1 -KO cells were infected with HIV-1 Luc-pseudoviruses expressing SARS1-S or MERS-S, and viral infection was determined. C NPC1 was expressed with SARS1-S, MERS-S, and influenza virus A/WSN/1933 (H1N1) HA in HEK293T cells. After immunoprecipitation (IP), proteins in cell lysate (input) and pulldown samples were analyzed by WB. (*) indicates non-specific bands. D Caco2 WT and NPC1 -KO cells were infected with HIV-1 Luc-pseudoviruses expressing indicated S proteins and viral infection was determined. E Huh-7-A-T cells were treated with Tubs I/II/III at 0.5 µM and infected with HIV-1 Luc-pseudovirions expressing indicated S proteins from SARS variants. Viral inhibition was determined as previously. DMSO was used as a control (Ctr). F Predicted NPC1-C and Omicron-S complex. The Omicron-S structure is shown in cyan, while the NPC1-C is depicted in lime yellow. The binding interface of Omicron-S in RBD, predicted to directly bind NPC1-C, is highlighted in red. G Docking of Tubs I/II/III to the interphase of NPC1-C and Omicron-S protein complex was obtained via Webina. H A549 cells were treated with 0.5 μM Tubs I/II/III for 1 h and infected with influenza virus A/WSN/1933 (H1N1). After 24 h, viral nucleoprotein (NP) genes were quantified by RT-PCR. Results are shown as relative values, with those from cells treated with DMSO set as 1. DMSO was used as a control (Ctr). Error bars indicate SEMs ( n = 3 biologically independent experiments). one-way ANOVA was applied. ** P < 0.01, *** P < 0.001. I A549 WT and NPC1 -KO clones were infected with H1N1, and NP genes were quantified the same as in H at indicated time points.

Article Snippet: Initially, we performed molecular docking and structural analysis via Webina ( https://durrantlab.pitt.edu/webina/ ), a web server based on Autodock vina , .

Techniques: Infection, Expressing, Inhibition, Control, Virus, Immunoprecipitation, Binding Assay, Reverse Transcription Polymerase Chain Reaction, Clone Assay

Journal: Frontiers in Molecular Biosciences

Article Title: ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina

doi: 10.3389/fmolb.2023.1243970

Figure Lengend Snippet: Cross-docking results are obtained by docking each ligand from the indicated PDB structure to all other PDB structures using ReverseDock. The ranking of the target PDB and the ligand RMSD of the first docking pose compared to the crystal structure is provided.

Article Snippet: To bring the full power of docking to the experimental community, we developed ReverseDock, an AutoDock Vina-based, easy-to-use blind docking web server allowing users to freely select multiple protein targets for docking their ligand of interest.

Techniques: