LitCovid-sentences  

PMC:7441777 / 8804-13859 JSONTXT 8 Projects

Annnotations TAB TSV DIC JSON TextAE Lectin_function

Id Subject Object Predicate Lexical cue
T62 0-4 Sentence denotes 2.1.
T63 6-31 Sentence denotes Molecular docking studies
T64 33-39 Sentence denotes 2.1.1.
T65 41-61 Sentence denotes Protein preparations
T66 62-111 Sentence denotes The crystal structure of SARS-CoV-2 RdRp (PDB ID:
T67 112-214 Sentence denotes 6M71) (Yan et al., 2020) was retrieved from the protein databank (www.rcsb.org) (Berman et al., 2000).
T68 215-377 Sentence denotes 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).
T69 378-465 Sentence denotes Subsequently, the file was saved as .pdbqt format in preparation for molecular docking.
T70 466-609 Sentence denotes Schematic representation of the work-flow for selecting potential natural polyphenolic inhibitors for the SARS-CoV-2 RdRp is shown in Figure 2.
T71 610-619 Sentence denotes Figure 2.
T72 621-731 Sentence denotes Flow chart of the methodology for shortlisting the best natural polyphenolic inhibitor of the SARS-CoV-2 RdRp.
T73 733-739 Sentence denotes 2.1.2.
T74 741-760 Sentence denotes Ligand preparations
T75 761-973 Sentence denotes The 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).
T76 974-1131 Sentence denotes The compounds were converted into PDB format, and conformational energies of all the compounds were minimized by using UCSF Chimera (Pettersen et al., 2004).
T77 1132-1140 Sentence denotes Table 1.
T78 1142-1288 Sentence denotes 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:
T79 1289-1322 Sentence denotes 6M71) by molecular docking study.
T80 1323-1325 Sentence denotes S.
T81 1326-1329 Sentence denotes No.
T82 1331-1375 Sentence denotes Compound Name Binding energy (kcal/mol) S.
T83 1376-1379 Sentence denotes No.
T84 1381-1421 Sentence denotes Compound Name Binding energy (kcal/mol)
T85 1422-1456 Sentence denotes 1 TF3 −9.9 52 Cyanidin −6.3
T86 1457-1492 Sentence denotes 2 TF2b −9.6 53 Daidzein −6.3
T87 1493-1528 Sentence denotes 3 TF1 −9.6 54 Glycitein −6.3
T88 1529-1563 Sentence denotes 4 TF2a −9.3 55 Wogonin −6.3
T89 1564-1606 Sentence denotes 5 Hesperidin −8.8 56 Phloretin −6.3
T90 1607-1642 Sentence denotes 6 EGCG −7.3 57 Catechin −6.2
T91 1643-1686 Sentence denotes 7 Myricetin −7.2 58 Urolithin B −6.2
T92 1687-1733 Sentence denotes 8 Quercetagetin −7.0 59 Angolensin −6.2
T93 1734-1774 Sentence denotes 9 Quercetin −6.9 60 Pinosylvin −6.2
T94 1775-1817 Sentence denotes 10 Curcumin −6.9 61 Formononetin −6.2
T95 1818-1870 Sentence denotes 11 Dihydrorobinetin −6.8 62 Liquiritigenin −6.2
T96 1871-1909 Sentence denotes 12 Peonidin −6.8 63 Prunetin −6.2
T97 1910-1948 Sentence denotes 13 Fisetin −6.8 64 Alpinetin −6.2
T98 1949-1991 Sentence denotes 14 Robinetin −6.7 65 Biochanin A −6.2
T99 1992-2042 Sentence denotes 15 5-Deoxygalangin −6.7 66 Rhapontigenin −6.1
T100 2043-2084 Sentence denotes 16 Kaempferol −6.7 67 Genistein −6.1
T101 2085-2126 Sentence denotes 17 Scutellarein −6.7 68 Chrysin −6.1
T102 2127-2180 Sentence denotes 18 (-)-Epicatechin −6.7 69 6-Hydroxyflavone −6.1
T103 2181-2216 Sentence denotes 19 Purpurin −6.7 70 Equol −6.1
T104 2217-2262 Sentence denotes 20 Isorhamnetin −6.7 71 Piceatannol −6.1
T105 2263-2309 Sentence denotes 21 Tricetin −6.6 72 Isorhapontigenin −6.0
T106 2310-2353 Sentence denotes 22 Gossypetin −6.6 73 Resveratrol −5.8
T107 2354-2396 Sentence denotes 23 Norathyriol −6.6 74 Danshensu −5.7
T108 2397-2436 Sentence denotes 24 Coumestrol −6.6 75 Eugenin −5.6
T109 2437-2485 Sentence denotes 25 Isosakuranetin −6.6 76 Sinapic acid −5.5
T110 2486-2537 Sentence denotes 26 Pectolinarigenin −6.6 77 Pterostilbene −5.5
T111 2538-2582 Sentence denotes 27 Tangeritin −6.6 78 Ferulic acid −5.4
T112 2583-2626 Sentence denotes 28 Nobiletin −6.6 79 Caffeic acid −5.4
T113 2627-2674 Sentence denotes 29 Pratensein −6.6 80 Isoferulic acid −5.4
T114 2675-2726 Sentence denotes 30 Hispidulin −6.6 81 Dihydrocaffeic acid −5.4
T115 2727-2771 Sentence denotes 31 Baicalein −6.5 82 Gentisic acid −5.3
T116 2772-2812 Sentence denotes 32 Apigenin −6.5 83 Pyrogallol −5.3
T117 2813-2862 Sentence denotes 33 Morin −6.5 84 4-Hydroxycinnamic acid −5.2
T118 2863-2911 Sentence denotes 34 Urolithin A −6.5 85 Resacetophenone −5.2
T119 2912-2957 Sentence denotes 35 Acacetin −6.5 86 Salicyclic acid −5.1
T120 2958-3005 Sentence denotes 36 Pelargonidin −6.5 87 Syringic acid −5.1
T121 3006-3056 Sentence denotes 37 Irilone −6.5 88 2-Hydroxybenzoic acid −5.1
T122 3057-3100 Sentence denotes 38 Naringenin −6.5 89 Gallic acid −5.0
T123 3101-3155 Sentence denotes 39 Pinocembrin −6.5 90 3-Hydroxybenzoic acid −5.0
T124 3156-3210 Sentence denotes 40 Kaempferide −6.5 91 4-Hydroxybenzoic acid −5.0
T125 3211-3249 Sentence denotes 41 Malvidin −6.5 92 Vanillin −5.0
T126 3250-3295 Sentence denotes 42 Luteolin −6.4 93 p-Coumeric acid −4.9
T127 3296-3340 Sentence denotes 43 Dalbergin −6.4 94 Vanillic acid −4.8
T128 3341-3376 Sentence denotes 44 Butein −6.4 95 Paeonol −4.8
T129 3377-3428 Sentence denotes 45 Biochanin A (1-) −6.4 96 Cinnamic acid −4.7
T130 3429-3476 Sentence denotes 46 Fustin −6.4 97 Protocatechuic acid −4.6
T131 3477-3528 Sentence denotes 47 5-Hydroxyflavone −6.4 98 4-Ethylphenol −4.5
T132 3529-3570 Sentence denotes 48 Pinostrobin −6.4 99 Catechol −4.5
T133 3571-3612 Sentence denotes 49 Pinobanksin −6.4 100 Tyrosol −4.5
T134 3613-3651 Sentence denotes 50 Datiscetin −6.3 101 GTP −7.9
T135 3652-3695 Sentence denotes 51 Galangin −6.3 102 Remdesivir −7.7
T136 3697-3703 Sentence denotes 2.1.3.
T137 3705-3740 Sentence denotes Docking studies using AutoDock Vina
T138 3741-3923 Sentence denotes The 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 & Olson, 2010).
T139 3924-4112 Sentence denotes 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).
T140 4113-4236 Sentence denotes 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.
T141 4237-4326 Sentence denotes After the receptor-ligand preparation, docking runs were started from the command prompt.
T142 4327-4451 Sentence denotes The lowest binding energy and best-docked conformation were considered as the ligand molecule with maximum binding affinity.
T143 4453-4459 Sentence denotes 2.1.4.
T144 4461-4488 Sentence denotes Protein-ligand interactions
T145 4489-4672 Sentence denotes LigPlot+ 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).
T146 4673-4768 Sentence denotes The LigPlot+ program self-generated schematic 2D representations of protein-ligand interaction.
T147 4769-4922 Sentence denotes The output file represents the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic contacts, and atom accessibilities.
T148 4923-5055 Sentence denotes H-bonds are shown in green dotted lines, whereas residues involved in hydrophobic interaction are represented in the red semicircle.