full length untagged 3clpro  (BPS Bioscience)

Journal: Frontiers in Pharmacology

Article Title: Identification of novel SARS-CoV-2 3CLpro inhibitors by molecular docking, in vitro assays, molecular dynamics simulations and DFT analyses

doi: 10.3389/fphar.2024.1494953

Figure Lengend Snippet: Structure-based virtual screening scheme of potent 3CLpro inhibitor.

Article Snippet: The molecular docking of 3CLpro was performed on 5 million compounds obtained by preliminary screening using Lipinski’s rule from the Topscience database.

Techniques:

Journal: Frontiers in Pharmacology

Article Title: Identification of novel SARS-CoV-2 3CLpro inhibitors by molecular docking, in vitro assays, molecular dynamics simulations and DFT analyses

doi: 10.3389/fphar.2024.1494953

Figure Lengend Snippet: (A) Structure and IC 50 value of compounds 1, 5, 10, 34, 36 and 43. (B) Concentration response curve of compounds 1, 5, 10, 34, 36, 43 and S-217622 against 3CLpro activity.

Article Snippet: The molecular docking of 3CLpro was performed on 5 million compounds obtained by preliminary screening using Lipinski’s rule from the Topscience database.

Techniques: Concentration Assay, Activity Assay

Journal: Frontiers in Pharmacology

Article Title: Identification of novel SARS-CoV-2 3CLpro inhibitors by molecular docking, in vitro assays, molecular dynamics simulations and DFT analyses

doi: 10.3389/fphar.2024.1494953

Figure Lengend Snippet: (A) RMSD for apo-3CLpro, compound 34 and 36 complexes over 200 ns along with their respective distributions. (B) SASA for apo-3CLpro, compound 34 and 36 complexes over 200 ns along with their respective distributions. (C) Rg for apo-3CLpro, compound 34 and 36 complexes over 200 ns along with their respective distributions. (D) RMSF for apo-3CLpro, compound 34 and 36 complexes over last 50 ns, along with their respective distributions.

Article Snippet: The molecular docking of 3CLpro was performed on 5 million compounds obtained by preliminary screening using Lipinski’s rule from the Topscience database.

Techniques:

Journal: Frontiers in Pharmacology

Article Title: Identification of novel SARS-CoV-2 3CLpro inhibitors by molecular docking, in vitro assays, molecular dynamics simulations and DFT analyses

doi: 10.3389/fphar.2024.1494953

Figure Lengend Snippet: (A) Dotted line plots representing the first 50 eigenvectors and corresponding eigenvalues of apo-3CLpro, compound 34 and 36 complexes. (B) Projection of the first principal component onto the protein structure to visualize the motion direction of each residue. (C) Representation of the 2D projections of apo-3CLpro, compound 34 and 36 complexes conformational changes during the simulation.

Article Snippet: The molecular docking of 3CLpro was performed on 5 million compounds obtained by preliminary screening using Lipinski’s rule from the Topscience database.

Techniques: Residue

Journal: Frontiers in Pharmacology

Article Title: Identification of novel SARS-CoV-2 3CLpro inhibitors by molecular docking, in vitro assays, molecular dynamics simulations and DFT analyses

doi: 10.3389/fphar.2024.1494953

Figure Lengend Snippet: (A) Free energy landscapes for apo-3CLpro, compound 34 and 36 systems. (B) Dynamic cross-correlation map of the Cα atoms of apo-3CLpro, compound 34 and 36 systems.

Article Snippet: The molecular docking of 3CLpro was performed on 5 million compounds obtained by preliminary screening using Lipinski’s rule from the Topscience database.

Techniques:

Journal: Frontiers in Pharmacology

Article Title: Identification of novel SARS-CoV-2 3CLpro inhibitors by molecular docking, in vitro assays, molecular dynamics simulations and DFT analyses

doi: 10.3389/fphar.2024.1494953

Figure Lengend Snippet: (A) Percentage of the top 10 conformational clusters to the total conformational clusters. (B) Protein-ligand interactions of compound 34 and 36 with 3CLpro (3D). (C) Protein-ligand interactions of compound 34 and 36 with 3CLpro (2D).

Article Snippet: The molecular docking of 3CLpro was performed on 5 million compounds obtained by preliminary screening using Lipinski’s rule from the Topscience database.

Techniques:

Journal: Scientific Reports

Article Title: 9-aminominocycline potentiates the efficacy of EIDD-1931 and PF-332 by targeting the papain like protease enzyme of SARS-CoV-2

doi: 10.1038/s41598-025-89717-3

Figure Lengend Snippet: Inhibition of SARS-CoV-2 PLpro enzyme activities by 9-AMN. The enzymatic inhibitory effects of 9-AMN and minocycline (each at 50 µM) on the SARS-CoV-2 PLpro enzyme were evaluated as detailed in the materials and methods. ( A ) Inhibition of proteolytic activity. ( B ) Inhibition of DUB activity. ( C ) Gradual reduction of proteolytic activity with increasing 9-AMN concentration. ( D ) Gradual decline of DUB activity with increasing 9-AMN concentration. ( E ) Inhibition of 3CLpro enzyme activity ( F ) Inhibition of RdRp enzyme activity. The enzymatic activity of control samples treated with DMSO (0.1%) is taken as 100% for calculating relative enzymatic activity. GRL-0617 (50 µM) treated wells were used as a specificity control. The graph is representative of three independent experiments (n = 3). The P value < 0.05 is denoted as "*" indicating statistical significance, while “ns” refers to statistically not significant.

Article Snippet: The recombinant full-length untagged 3CLpro (cat#100823) and His-tagged PLpro (cat#100735), assay buffers (cat#79956 and cat#78039-1 for 3CLpro and PLpro, respectively), GC-367 (cat#78013), and fluorescently labeled substrates (cat#79952 for 3CLpro, cat#79997 for PLpro protease activity, and cat#82200 for DUB activity) were purchased from BPS Biosciences (San Diego, CA, USA).

Techniques: Inhibition, Activity Assay, Concentration Assay, Control