2.1.2.  Ligand preparations
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). The compounds were converted into PDB format, and conformational energies of all the compounds were minimized by using UCSF Chimera (Pettersen et al., 2004).
Table 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.
S. No.  Compound Name  Binding energy (kcal/mol)  S. No.  Compound Name  Binding energy (kcal/mol)
1   TF3   −9.9  52  Cyanidin  −6.3
2   TF2b   −9.6  53  Daidzein  −6.3
3   TF1   −9.6  54  Glycitein  −6.3
4   TF2a   −9.3  55  Wogonin  −6.3
5   Hesperidin   −8.8  56  Phloretin  −6.3
6   EGCG   −7.3  57  Catechin  −6.2
7   Myricetin   −7.2  58  Urolithin B  −6.2
8   Quercetagetin   −7.0  59  Angolensin  −6.2
9  Quercetin  −6.9  60  Pinosylvin  −6.2
10  Curcumin  −6.9  61  Formononetin  −6.2
11  Dihydrorobinetin  −6.8  62  Liquiritigenin  −6.2
12  Peonidin  −6.8  63  Prunetin  −6.2
13  Fisetin  −6.8  64  Alpinetin  −6.2
14  Robinetin  −6.7  65  Biochanin A  −6.2
15  5-Deoxygalangin  −6.7  66  Rhapontigenin  −6.1
16  Kaempferol  −6.7  67  Genistein  −6.1
17  Scutellarein  −6.7  68  Chrysin  −6.1
18  (-)-Epicatechin  −6.7  69  6-Hydroxyflavone  −6.1
19  Purpurin  −6.7  70  Equol  −6.1
20  Isorhamnetin  −6.7  71  Piceatannol  −6.1
21  Tricetin  −6.6  72  Isorhapontigenin  −6.0
22  Gossypetin  −6.6  73  Resveratrol  −5.8
23  Norathyriol  −6.6  74  Danshensu  −5.7
24  Coumestrol  −6.6  75  Eugenin  −5.6
25  Isosakuranetin  −6.6  76  Sinapic acid  −5.5
26  Pectolinarigenin  −6.6  77  Pterostilbene  −5.5
27  Tangeritin  −6.6  78  Ferulic acid  −5.4
28  Nobiletin  −6.6  79  Caffeic acid  −5.4
29  Pratensein  −6.6  80  Isoferulic acid  −5.4
30  Hispidulin  −6.6  81  Dihydrocaffeic acid  −5.4
31  Baicalein  −6.5  82  Gentisic acid  −5.3
32  Apigenin  −6.5  83  Pyrogallol  −5.3
33  Morin  −6.5  84  4-Hydroxycinnamic acid  −5.2
34  Urolithin A  −6.5  85  Resacetophenone  −5.2
35  Acacetin  −6.5  86  Salicyclic acid  −5.1
36  Pelargonidin  −6.5  87  Syringic acid  −5.1
37  Irilone  −6.5  88  2-Hydroxybenzoic acid  −5.1
38  Naringenin  −6.5  89  Gallic acid  −5.0
39  Pinocembrin  −6.5  90  3-Hydroxybenzoic acid  −5.0
40  Kaempferide  −6.5  91  4-Hydroxybenzoic acid  −5.0
41  Malvidin  −6.5  92  Vanillin  −5.0
42  Luteolin  −6.4  93  p-Coumeric acid  −4.9
43  Dalbergin  −6.4  94  Vanillic acid  −4.8
44  Butein  −6.4  95  Paeonol  −4.8
45  Biochanin A (1-)  −6.4  96  Cinnamic acid  −4.7
46  Fustin  −6.4  97  Protocatechuic acid  −4.6
47  5-Hydroxyflavone  −6.4  98  4-Ethylphenol  −4.5
48  Pinostrobin  −6.4  99  Catechol  −4.5
49  Pinobanksin  −6.4  100  Tyrosol  −4.5
50  Datiscetin  −6.3  101   GTP   −7.9
51  Galangin  −6.3  102   Remdesivir   −7.7