Table 1.
Binding energy of top ranked plant secondary metabolites against four targets of SARS-CoV-2 pathogenesis and their physicochemical properties.
| Code | Name | BE | MW | RB | HA | HD | TPSA | MLogP | PGP | GI | LV | BAS |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SARS-CoV-2 Spike protein | ||||||||||||
| B0162-10327320 | Bismahanine | − 9.1 | 692.8 | 7 | 4 | 4 | 90.50 | 6.18 | Yes | Low | 2 | 0.17 |
| C0572-100920596 | Coagulin N | − 9.1 | 648.7 | 4 | 12 | 6 | 192.44 | − 0.36 | Yes | Low | 3 | 0.17 |
| A0297-16162334 | Arecatannin A3 | − 8.9 | 1443.2 | 9 | 30 | 25 | 551.90 | − 3.21 | Yes | Low | 3 | 0.17 |
| C0563-15970528 | Coagulin K | − 8.9 | 616.7 | 4 | 10 | 4 | 151.98 | 1.16 | Yes | Low | 1 | 0.55 |
| G0134-16129878 | Tannic acid | − 8.9 | 1701.2 | 31 | 46 | 25 | 777.98 | − 4.24 | Yes | Low | 3 | 0.17 |
| K0070-101721039 | Kamalachalcone C | − 8.8 | 530.5 | 4 | 8 | 4 | 147.14 | 1.92 | No | Low | 1 | 0.55 |
| A0155-5281600 | Amentoflavone | − 8.7 | 538.4 | 3 | 10 | 6 | 181.80 | 0.25 | No | Low | 2 | 0.17 |
| P0479-16398499 | Pseudojervine | − 8.7 | 587.7 | 3 | 9 | 5 | 137.71 | 1.02 | Yes | High | 1 | 0.55 |
| F0096-643975 | Flavin adenine dinucleotide | − 8.6 | 785.5 | 13 | 20 | 9 | 382.55 | − 3.77 | Yes | Low | 3 | 0.11 |
| G0075-156783 | Graecunin E | − 8.6 | 1047.1 | 11 | 22 | 12 | 335.06 | − 3.68 | Yes | Low | 3 | 0.17 |
| SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) | ||||||||||||
| E0189-3564542 | Eriodictyol-7-O-rutinoside | − 9.9 | 596.5 | 6 | 15 | 9 | 245.29 | − 3.24 | Yes | Low | 3 | 0.17 |
| N0007-442431 | Narirutin | − 9.7 | 580.5 | 6 | 14 | 8 | 225.06 | − 2.77 | Yes | Low | 3 | 0.17 |
| H0135-191266 | Hippomannin A | − 9.6 | 634.4 | 6 | 18 | 11 | 318.50 | − 2.90 | Yes | Low | 3 | 0.17 |
| I0135-5318569 | Isoginkgetin | − 9.5 | 566.5 | 5 | 10 | 14 | 159.80 | 0.63 | No | Low | 1 | 0.55 |
| K0010-5491813 | *Kaempferol | − 9.5 | 600.4 | 7 | 15 | 9 | 257.04 | − 2.30 | No | Low | 3 | 0.17 |
| M0284-44259428 | Myricetin 3-rutinoside | − 9.5 | 626.5 | 6 | 17 | 11 | 289.66 | − 4.35 | Yes | Low | 3 | 0.17 |
| R0047-441943 | Rotundioside B | − 9.5 | 1184.3 | 15 | 26 | 13 | 428.71 | − 3.89 | Yes | Low | 3 | 0.11 |
| T0047-73179 | Tellimagradin I | − 9.5 | 786.5 | 9 | 22 | 13 | 385.26 | − 3.08 | Yes | Low | 3 | 0.17 |
| A0245-5281599 | Agathisflavone | − 9.4 | 538.4 | 3 | 10 | 6 | 181.80 | 0.25 | No | Low | 2 | 0.17 |
| E0140-119058016 | Emblicanin A | − 9.4 | 782.5 | 6 | 22 | 12 | 374.26 | − 2.33 | Yes | Low | 3 | 0.11 |
| Human transmembrane serine protease (TMPRSS2) | ||||||||||||
| G0154-14982 | Glycyrrhizic acid | − 9.5 | 822.9 | 7 | 16 | 8 | 267.04 | 0.02 | Yes | Low | 3 | 0.11 |
| C0387-366355 | cis-Miyabenol C | − 9.4 | 680.7 | 6 | 9 | 7 | 160.07 | 3.43 | No | Low | 2 | 0.17 |
| P0126-124025 | Proanthocyanidin A2 | − 9.2 | 576.5 | 2 | 12 | 9 | 209.76 | 0.14 | No | Low | 3 | 0.17 |
| G0038-131752181 | Granatin B | − 9.1 | 952.6 | 3 | 27 | 14 | 450.25 | − 3.45 | Yes | Low | 3 | 0.17 |
| H0134-101601938 | Hippophaenin B | − 9.1 | 1104.7 | 7 | 31 | 19 | 542.17 | − 3.90 | Yes | Low | 3 | 0.11 |
| C0126-101710863 | 3-Caffeoyl-5-Feruloylquinic Acid | − 9 | 530.4 | 10 | 12 | 16 | 200.28 | − 0.15 | Yes | Low | 3 | 0.11 |
| B0138-183757 | 3,3′-Biplumbagin | − 8.9 | 374.3 | 1 | 6 | 2 | 108.74 | 0.62 | No | High | 0 | 0.55 |
| A0245-5281599 | Agathisflavone | − 8.9 | 538.4 | 3 | 10 | 6 | 181.80 | 0.25 | No | Low | 2 | 0.17 |
| A0156-362574 | Aromoline | − 8.9 | 594.7 | 2 | 8 | 2 | 83.86 | 3.37 | No | High | 1 | 0.55 |
| C0453-6324923 | Chrysophanein | − 8.9 | 416.3 | 3 | 9 | 5 | 153.75 | − 1.26 | Yes | Low | 0 | 0.55 |
| SARS-CoV-2 Main protease (Mpro) | ||||||||||||
| H0349-3663 | Hypericin | − 10.4 | 504.4 | 0 | 8 | 6 | 155.52 | 1.36 | No | Low | 2 | 0.17 |
| A0155-5281600 | Amentoflavone | − 9.7 | 538.4 | 3 | 10 | 6 | 181.80 | 0.25 | No | Low | 2 | 0.17 |
| T0163-44584734 | Terflavin B | − 9.7 | 784.5 | 8 | 22 | 13 | 385.24 | − 2.83 | Yes | Low | 3 | 0.17 |
| M0522-21593828 | Mudanpioside J | − 9.6 | 630.5 | 11 | 14 | 5 | 199.90 | − 0.04 | Yes | Low | 2 | 0.17 |
| Q0019-44259101 | Quercetin 3,5-digalactoside | − 9.6 | 626.5 | 7 | 17 | 11 | 289.66 | − 4.62 | No | Low | 3 | 0.17 |
| V0041-168165 | Vescalagin | − 9.6 | 934.6 | 0 | 26 | 16 | 455.18 | − 3.23 | Yes | Low | 3 | 0.17 |
| G0227-5271805 | Ginkgetin | − 9.5 | 566.5 | 5 | 10 | 4 | 159.80 | 0.63 | No | Low | 1 | 0.55 |
| I0135-5318569 | Isoginkgetin | − 9.5 | 566.5 | 5 | 10 | 14 | 159.80 | 0.63 | No | Low | 1 | 0.55 |
| C0163-44256718 | Cyanidin 3,5-diglucoside | − 9.4 | 611.5 | 7 | 16 | 11 | 272.59 | − 3.82 | No | Low | 3 | 0.17 |
| D0307-15922818 | *Delphinidin | − 9.4 | 611.5 | 8 | 14 | 9 | 239.97 | − 1.18 | No | Low | 3 | 0.17 |
Only top 10 ranked molecules against each target are represented here. Details of all the plants secondary metabolites studied are available in Supplementary Files 2 and 3.
BE, binding energy (Kcal/mol); MW, molecular weight (g/mol); RB, number of rotatable bonds; HA, number of H-bond acceptors; HD, Number of H-bond donors; TPSA, total polar surface area (Å2); MLogP, predicted octanol/water partition coefficient; PGP-S, pgp substrate; GI, GI tract crossing, LV, Number of Lipinski’s rule violation; BAS: bioavailability score.
*Kaempferol 3-O-(6′'-galloyl)-beta-D-glucopyranoside; *Delphinidin-3-O-(6-p-coumaroyl) glucoside.