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11 results for “Graptopetalum paraguayense”
Molecular docking and quantum-chemical characterization of inhibitory activity of procyanidins and flavonol glucosides from Graptopetalum paraguayense E. Walther against nonstructural proteins of SARS-Cov-2
<p>The dataset includes:</p> <ol> <li><span>Optimized geometries of all ligands, NSPs and their complexes in gas phase</span></li> <li><span>Total energies (a.u.) and interaction energies (a.u. and kcal mol-1) of the complexes, ligands and NSPs in gas phase and in argon</span></li> <li><span>Mass spectra (full ms) and product ion spectra (ms2) of standards and identified components from GP. </span></li> <li><span>Output files from quantum-chemical calculations.</span></li> <li><span>pdb files of NSPs</span></li> <li><span>mol files of all complexes</span></li> </ol>
Effects of Graptopetalum Paraguayense E. Walther on the Oxidative Stress, Antioxidant Enzyme Activity and Inflammation in Subjects With Metabolic Syndrome
ClinicalTrials.gov study NCT01463748. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Figure 6 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 6 Structures of amino acids from GP phenolic fraction "C", optimized at B3LYP/6-31+G(d,p) level.
Figure 3 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 3 Acyclovir triphosphate and its vicinity in the DNA polymerase pocket after docking procedure: a) 3D plane of view and b) 2D plane of view. The interactions of the ligand in the active site cavity are represented as follows: the proximity contour is depicted with a black dotted line; solvent accessibility, as blue clouds around atoms or blue shadows around amino acid residues; polar amino acids are displayed with pink, while the lipophilic ones are in green. Basic amino acids are outlined with blue and the acidic – with red. Hydrogen bond interactions are depicted with dotted arrows, while the ionic ones are depicted with dotted lines.
Figure 2 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 2 Phenolic (trans-ferulic) acid and its vicinity after docking procedure. The amino acid residues of HSV-1 DNA polymerase active site, mostly involved in interaction with ligands, are represented as follows: Lis928 is basic amino acid right from the ligand, Glu 927 is above it, basic amino acid on the left is Lis 939 and Asp 886 is in its right.
Supplementary material 1 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Tables S1–S3 and Figures S1–S4
Figure 8 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 8 Complex of acyclovir triphosphate and amino acids from DNA polymerase active site, optimized at B3LYP/6-31+G(d,p) level.
Figure 7 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 7 Complexes of phenolic acids from GP phenolic fraction "C" and amino acids from DNA polymerase active site, optimized at B3LYP/6-31+G(d,p) level.
Figure 5 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 5 Structures of hydroxybenzoic acids from GP phenolic fraction "C", optimized at B3LYP/6-31+G(d,p) level.
Figure 1 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 1 Graptopetalum paraguayense E. Walther.
Figure 4 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 4 Fitting of phenolic acids in the DNA polymerase pocket.
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