PMC:7441777 / 8804-13859 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7441777","sourcedb":"PMC","sourceid":"7441777","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7441777","text":"2.1. Molecular docking studies\n\n2.1.1. Protein preparations\nThe crystal structure of SARS-CoV-2 RdRp (PDB ID: 6M71) (Yan et al., 2020) was retrieved from the protein databank (www.rcsb.org) (Berman et al., 2000). The crystal structure was prepared individually by adding hydrogen atoms and computing the Gasteiger charge using the AutoDock v4.2 program (Morris et al., 2009). Subsequently, the file was saved as .pdbqt format in preparation for molecular docking. Schematic representation of the work-flow for selecting potential natural polyphenolic inhibitors for the SARS-CoV-2 RdRp is shown in Figure 2.\nFigure 2. Flow chart of the methodology for shortlisting the best natural polyphenolic inhibitor of the SARS-CoV-2 RdRp.\n\n2.1.2. Ligand preparations\nThe SDF structures of GTP, remdesivir, and selected hundred polyphenols (see Table S1 in Supplementary Information) were retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) (Kim et al., 2019). The compounds were converted into PDB format, and conformational energies of all the compounds were minimized by using UCSF Chimera (Pettersen et al., 2004).\nTable 1. Binding energy (kcal/mol) of the natural polyphenols along with the control compounds (GTP and remdesivir) against RdRp of the SARS-CoV-2 (PDB ID: 6M71) by molecular docking study.\nS. No. Compound Name Binding energy (kcal/mol) S. No. Compound Name Binding energy (kcal/mol)\n1 TF3 −9.9 52 Cyanidin −6.3\n2 TF2b −9.6 53 Daidzein −6.3\n3 TF1 −9.6 54 Glycitein −6.3\n4 TF2a −9.3 55 Wogonin −6.3\n5 Hesperidin −8.8 56 Phloretin −6.3\n6 EGCG −7.3 57 Catechin −6.2\n7 Myricetin −7.2 58 Urolithin B −6.2\n8 Quercetagetin −7.0 59 Angolensin −6.2\n9 Quercetin −6.9 60 Pinosylvin −6.2\n10 Curcumin −6.9 61 Formononetin −6.2\n11 Dihydrorobinetin −6.8 62 Liquiritigenin −6.2\n12 Peonidin −6.8 63 Prunetin −6.2\n13 Fisetin −6.8 64 Alpinetin −6.2\n14 Robinetin −6.7 65 Biochanin A −6.2\n15 5-Deoxygalangin −6.7 66 Rhapontigenin −6.1\n16 Kaempferol −6.7 67 Genistein −6.1\n17 Scutellarein −6.7 68 Chrysin −6.1\n18 (-)-Epicatechin −6.7 69 6-Hydroxyflavone −6.1\n19 Purpurin −6.7 70 Equol −6.1\n20 Isorhamnetin −6.7 71 Piceatannol −6.1\n21 Tricetin −6.6 72 Isorhapontigenin −6.0\n22 Gossypetin −6.6 73 Resveratrol −5.8\n23 Norathyriol −6.6 74 Danshensu −5.7\n24 Coumestrol −6.6 75 Eugenin −5.6\n25 Isosakuranetin −6.6 76 Sinapic acid −5.5\n26 Pectolinarigenin −6.6 77 Pterostilbene −5.5\n27 Tangeritin −6.6 78 Ferulic acid −5.4\n28 Nobiletin −6.6 79 Caffeic acid −5.4\n29 Pratensein −6.6 80 Isoferulic acid −5.4\n30 Hispidulin −6.6 81 Dihydrocaffeic acid −5.4\n31 Baicalein −6.5 82 Gentisic acid −5.3\n32 Apigenin −6.5 83 Pyrogallol −5.3\n33 Morin −6.5 84 4-Hydroxycinnamic acid −5.2\n34 Urolithin A −6.5 85 Resacetophenone −5.2\n35 Acacetin −6.5 86 Salicyclic acid −5.1\n36 Pelargonidin −6.5 87 Syringic acid −5.1\n37 Irilone −6.5 88 2-Hydroxybenzoic acid −5.1\n38 Naringenin −6.5 89 Gallic acid −5.0\n39 Pinocembrin −6.5 90 3-Hydroxybenzoic acid −5.0\n40 Kaempferide −6.5 91 4-Hydroxybenzoic acid −5.0\n41 Malvidin −6.5 92 Vanillin −5.0\n42 Luteolin −6.4 93 p-Coumeric acid −4.9\n43 Dalbergin −6.4 94 Vanillic acid −4.8\n44 Butein −6.4 95 Paeonol −4.8\n45 Biochanin A (1-) −6.4 96 Cinnamic acid −4.7\n46 Fustin −6.4 97 Protocatechuic acid −4.6\n47 5-Hydroxyflavone −6.4 98 4-Ethylphenol −4.5\n48 Pinostrobin −6.4 99 Catechol −4.5\n49 Pinobanksin −6.4 100 Tyrosol −4.5\n50 Datiscetin −6.3 101 GTP −7.9\n51 Galangin −6.3 102 Remdesivir −7.7\n\n2.1.3. Docking studies using AutoDock Vina\nThe energy-minimized structure of all the natural polyphenols, remdesivir, and GTP were docked with the receptor (RdRp of SARS-CoV-2) using AutoDock Vina 1.1.2 (Trott \u0026 Olson, 2010). The ligand files were further saved in PDBQT file format, a modified PDB format containing atomic charges, atom type definitions for ligands, and topological information (rotatable bonds). A grid box (30 Å × 30 Å × 30 Å) centered at (121, 120, 125) Å for the SARS-CoV-2 RdRp, was used in the docking experiments. After the receptor-ligand preparation, docking runs were started from the command prompt. The lowest binding energy and best-docked conformation were considered as the ligand molecule with maximum binding affinity.\n\n2.1.4. Protein-ligand interactions\nLigPlot+ was used to investigate protein-ligand interactions for a given .pdb file containing the docked conformation and also the final simulated conformation (Wallace et al., 1995). The LigPlot+ program self-generated schematic 2D representations of protein-ligand interaction. The output file represents the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic contacts, and atom accessibilities. H-bonds are shown in green dotted lines, whereas residues involved in hydrophobic interaction are represented in the red 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