TABLE 5.
Details of shortlisted top 10 natural compounds/small molecules screened against various targets of coronaviruses.
| Protein name | Binding affinity kcal/mol | Compound name | Puchem ID | Chemical structure | Bioavailability score | Solubility score/Class | Plant name |
|---|---|---|---|---|---|---|---|
| SARS COV main protease (PDB ID: 2GZ9) | −9.0 | Rutin (ZINC4096846) | 5,280,805 |
|
0.17 | 0.29/Soluble | Terminalia chebula, Azadirachta indica and Ocimum basilicum |
| −8.7 | Quercetin 3 gentiobioside (ZINC49783852) | 5,320,834 |
|
0.17 | 0.29/Soluble | Solanum nigrum | |
| −8.6 | 3-O-trans-caffeoyltormentic acid | 44,584,640 |
|
0.56 | -5.99/moderately soluble | Antiviral compounds | |
| −8.5 | (-)Epicatechin 3 o gallate (epicatechin) | 107,905 |
|
0.55 | -3.09/soluble | Camellia sinensis | |
| −8.5 | Corilagin (ZINC4098612) | 73,568 |
|
0.17 | -0.51/soluble | Terminalia bellirica, Terminalia chebula | |
| −8.4 | Quercetin galactoside (ZINC3973253) | 5,281,643 |
|
0.17 | -1.51/soluble | Antiviral compounds | |
| −8.3 | Quercetrin (ZINC4175638) | 5,280,459 |
|
0.17 | -2.08/soluble | Azadirachta indica | |
| −8.3 | Isoquercetin (ZINC4096845) | 5,280,804 |
|
0.17 | -1.51/soluble | Ocimum basilicum, Terminalia chebula | |
| −8.3 | Acetoside (ZINC8234351) | 5,281,800 |
|
0.17 | -0.22/soluble | Clerodendrum serratum | |
| −8.2 | Cyanin (ZINC4097727) | 441,688 |
|
0.17 | 0.86/soluble | Zingiber officinale | |
| SARS-COV-2 main protease (PDB ID: 5R81) | −8.2 | Agathisflavone (ZINC4098505) | 5,281,599 |
|
0.17 | -8.7/Poorly soluble | Anacardium occidentale |
| −8.1 | Rubusic acid | 101,297,651 |
|
0.56 | -5.3/moderately soluble | Pedalium murex | |
| −7.9 | Solanocapsine | 73,419 |
|
0.55 | -4.2/moderately soluble | Solanum nigrum | |
| −7.7 | Chlorogenin (ZINC84668707) | 12,303,065 |
|
0.55 | -3.69/soluble | Solanum torvum | |
| −7.7 | Lupeol (ZINC4081455) | 259,846 |
|
0.55 | -6.74/poorly soluble | Carica papaya and Azadirachta indica | |
| −7.7 | Cyanin (ZINC4097727) | 441,688 |
|
0.17 | 0.86/soluble | Zingiber officinale | |
| −7.7 | 3-O-trans-caffeoyltormentic acid | 44,584,640 |
|
0.56 | -5.99/moderately soluble | Antiviral compound | |
| −7.7 | Luteolin 7-O-(6''-malonylglucoside) | 5,281,669 |
|
0.11 | -2.05/soluble | Vitex negundo | |
| −7.6 | Agnuside (ZINC4098330) | 442,416 |
|
0.17 | 0.66/soluble | Vitex negundo | |
| −7.6 | Luteolin 7-O-beta-D-glucoside (ZINC4096258) | 5,280,637 |
|
0.17 | -2.1/soluble | Vitex negundo | |
| MERS main protease (MERS) (PDB ID: 5C3N) | −8.6 | Amentoflavone (ZINC3984030) | 5,281,600 |
|
0.17 | -8./poorly soluble | Mangifera indica |
| −8.4 | Corilagin (ZINC4098612) | 73,568 |
|
0.17 | -0.51/soluble | Terminalia bellirica, Terminalia chebula | |
| −8.3 | Cyanin (ZINC4097727) | 441,688 |
|
0.17 | 0.86/soluble | Zingiber officinale | |
| −8.2 | Rutin (ZINC4096846) | 5,280,805 |
|
0.17 | -0.29/soluble | Terminalia chebula, Azadirachta indica and Ocimum basilicum | |
| −8.2 | Betulinic acid (ZINC4097714) | 64,971 |
|
0.85 | -5.7/moderately soluble | Vitex negundo | |
| −8.1 | 3.8'-biapigenin (ZINC17545581) | 10,414,856 |
|
0.17 | -8.7/poorly soluble | antiviral compound | |
| −8.0 | (-)-Epicatechin-3-o-gallate (ZINC3978503) | 107,905 |
|
0.55 | -3.09/soluble | Camellia sinensis | |
| −8.0 | Chrysanthemin (ZINC4097706) | 441,667 |
|
0.17 | -0.93/soluble | Zingiber officinale | |
| −8.0 | Vicenin-2 (ZINC4098604) | 442,664 |
|
0.17 | -0.27/soluble | Ocimum basilicum | |
| −8.0 | Quercetin 3 gentiobioside (ZINC49783852) | 5,320,834 |
|
0.17 | 0.29/soluble | Solanum nigrum | |
| RNA-dependent RNA polymerase (PDB ID: 6M71) | −9.4 | Ivermectin (ZINC238808778) (DB00602) | 6,427,057 |
|
0.17 | -3.89/soluble | FDA approved drug |
| −9.3 | Amentoflavone (ZINC3984030) | 5,281,600 |
|
0.17 | -8.7/poorly soluble | Mangiferaindica | |
| −9.0 | Corilagin (ZINC4098612) | 73,568 |
|
0.17 | -0.51/soluble | Terminalia bellirica, Terminalia chebula | |
| −8.9 | Agathisflavone (ZINC4098505) | 5,281,599 |
|
0.17 | -8.7/poorly soluble | Anacardium occidentale | |
| −8.6 | 3-O-trans-caffeoyltormentic acid | 44,584,640 |
|
0.56 | -5.99/moderately soluble | Antiviral compound | |
| −8.2 | Arjungenin (ZINC38143755) | 6,321,424 |
|
0.17 | -3.89/soluble | Terminalia chebula | |
| −8.2 | Crateogolic acid (ZINC4273446) | 12,444,386 |
|
0.56 | -3.9/soluble | Syzygium aromaticum | |
| −8.1 | Maslinic acid (ZINC4273446) | 73,659 |
|
0.56 | -5.3/moderately soluble | Antiviral compound | |
| −8.0 | 3.8'-biapigenin (ZINC17545,581)) | 10,414,856 |
|
0.17 | -8.7/Poorly soluble | Zingiber officinale | |
| −7.9 | Cyanin | 441,688 |
|
0.17 | 0.86/soluble | Camellia sinensis | |
| NSP9 (PDB ID: 6W4B) | −9.6 | Friedelin (ZINC4097720) | 91,472 |
|
0.55 | -7.88/poorly soluble | Vitex negundo, Acoruscalamus |
| −9.3 | N-methylsolasodine | 21,573,751 |
|
0.55 | -4.46/moderately soluble | Solanum nigrum | |
| −8.9 | Solasodine (ZINC8214722) | 442,985 |
|
0.55 | -4.8/moderately soluble | Solanum nigrum, Solanum torvum | |
| −8.9 | Diosgenin (ZINC6857614) | 99,474 |
|
0.55 | -4.49/moderately soluble | Solanum nigrum, Pedalium murex | |
| −8.6 | Spirostan-3-ol (ZINC253504500) | 3,035,446 |
|
0.55 | -4.51/Moderately soluble | Solanum nigrum | |
| −8.6 | Solanocapsine | 73,419 |
|
0.55 | -4.22/moderately soluble | Solanum nigrum | |
| −8.5 | Taraxerol (ZINC4082498) | 92,097 |
|
0.55 | -7.16/Poorly soluble | Cissus quadrangularis | |
| −8.3 | Amentoflavone (ZINC3984030) | 5,281,600 |
|
0.17 | -8.7/Poorly soluble | Mangifera indica | |
| −8.2 | Chlorogenin (ZINC84668707) | 12,303,065 |
|
0.55 | -3.69/soluble | Solanum torvum | |
| −8.1 | Agathisflavone (ZINC4098505) | 5,281,599 |
|
0.17 | -8.7/poorly soluble | Anacardium occidentale | |
| NSP15 (PDB ID: 6W01) | −9.2 | Oleanolic acid (ZINC3785416) | 10,494 |
|
0.85 | -6.12/poorly soluble | Ocimum basilicum, Cyprus rotundus, Clerodendrum serratum, Ocimum tenuiflorum |
| −9.2 | Ursolic-acid (ZINC3978827) | 64,945 |
|
0.85 | -5.67/moderately soluble | Ocimum basilicum, Pedalium murex, Malus domestica, Ocimum tenuiflorum | |
| −8.9 | Crategolic acid (ZINC4273446) | 73,659 |
|
0.56 | -5.3/Moderately soluble | Syzygium aromaticum | |
| −8.8 | Arjungenin (ZINC38143755) | 12,444,386 |
|
0.56 | -3.9/soluble | Terminalia chebula | |
| −8.7 | Hederagenin (ZINC3946009) | 73,299 |
|
0.56 | -5.55/moderately soluble | Nigella sativa | |
| −8.6 | Triterpenoid (ZINC40164454) | 451,674 |
|
0.56 | -5.12/moderately solule | Abutilon indicum | |
| −8.6 | Beta-amyrin (ZINC3978270) | 73,145 |
|
0.55 | -7.16/poorly solube | Cissus quadrangularis | |
| −8.6 | Friedelin (ZINC4097720) | 91,472 |
|
0.55 | -7.88/poorly soluble | Vitex negundo, Acorus calamus | |
| −8.5 | Catechin 7-O-gallate | 471,393 |
|
0.55 | -3.09/soluble | Camellia sinensis | |
| −8.5 | Arjunolic acid (ZINC31158038) | 73,641 |
|
0.56 | -4.72/moderately soluble | Terminalia chebula | |
| NSP3 (PDB ID: 6W02) | −7.4 | Amentoflavone (ZINC3984030) | 5,281,600 |
|
0.17 | -8.7/poorly soluble | Mangifera indica |
| −7.1 | Luteolin 7-O-(6''-malonylglucoside) | 5,281,669 |
|
0.11 | -2.05/soluble | Vitex negundo | |
| −6.8 | Rubusic acid | 101,297,651 |
|
0.56 | -5.3/moderately soluble | Pedalium murex | |
| −6.7 | Acteoside (ZINC8234351) | 5,281,800 |
|
0.17 | -0.22/soluble | Clerodendrum serratum | |
| −6.7 | Ivermectin (ZINC238808778) (DB00602) | 6,427,057 |
|
0.17 | -3.89/soluble | FDA approved drug | |
| −6.7 | Taraxerol acetate (ZINC31334747) | 94,225 |
|
0.55 | -7.77/poorly soluble | Cissus quadrangularis | |
| −6.6 | Catechin 7-O-gallate | 471,393 |
|
0.55 | -3.09/soluble | Antiviral compound | |
| −6.6 | Luteolin 7-O-beta-D-glucoside (ZINC4096258) | 5,280,637 |
|
0.17 | -2.1/soluble | Vitex negundo | |
| −6.6 | Agathisflavone (ZINC4098505) | 5,281,599 |
|
0.17 | -8.7/poorly soluble | Anacardium occidentale | |
| −6.6 | Luteolin-7-o-beta-d-glucopyranoside | 5,291,488 |
|
0.17 | -2.1/soluble | Vitex negundo | |
| NSP10-NSP16 (PDB ID: 6W4H) | −8.5 | Amentoflavone (ZINC3984030) | 5,281,600 |
|
0.17 | -8.7/poorly solbule | Mangifera indica |
| −8.3 | 10-Methoxycamptothecin (ZINC4823972) | 97,283 |
|
0.55 | -5.93/moderately soluble | Antiviral compound | |
| −8.2 | 3.8'-biapigenin (ZINC17545581) | 10,414,856 |
|
0.17 | -8.7/poorly soluble | Antiviral compound | |
| −8.0 | Taraxerol acetate (ZINC31334747) | 94,225 |
|
0.55 | -7.77/poorly soluble | Cissus quadrangularis | |
| −7.8 | Corilagin (ZINC4098612) | 73,568 |
|
0.17 | -0.15/soluble | Terminalia bellirica, Terminalia chebula | |
| −7.8 | Lupeol acetate (ZINC4097722) | 92,157 |
|
0.55 | -7.35/poorly soluble | Pedalium murex | |
| −7.6 | Emetine (ZINC000003830747) (DB13393) | 10,219 |
|
0.55 | -7.7/poorly soluble | FDA approved drug | |
| −7.6 | Chlorogenin (ZINC84668707) | 12,303,065 |
|
0.55 | -3.69/soluble | Solanum torvum | |
| −7.6 | Spirostan-3-ol (ZINC253504500) | 14,492,795 |
|
0.55 | -6.56/poorly soluble | Solanum nigrum | |
| −7.6 | 5,7-Dihydroxy-4'-methoxy-8.3'-di-C-prenylflavanone | 3,035,446 |
|
0.55 | -4.51/moderately soluble | Azadirachta indica | |
| Spike glycoprotein (PDB ID: 6M0J) | −8.2 | 1,8-Dichloro-9,10-diphenylanthracene-9,10-diol (ZINC5438671) | 320,066 |
|
0.55 | -10.45/insoluble | Carica papaya |
| −8.2 | Agathisflavone (ZINC4098505) | 5,281,599 |
|
0.17 | -8.7/poorly soluble | Anacardium occidentale | |
| −8.2 | Amentoflavone (ZINC3984030) | 5,281,600 |
|
0.17 | -8.7/poorly soluble | Mangifera indica | |
| −8.2 | Ivermectin (ZINC238808778) (DB00602) | 6,427,057 |
|
0.17 | -3.89/soluble | FDA approved drug | |
| −8.1 | 3 o caffeoyltormentic acid | 44,584,640 |
|
0.56 | -5.99/moderately soluble | Antiviral compound | |
| −7.5 | Agnuside (ZINC4098330) | 442,416 |
|
0.17 | 0.66/soluble | Vitex negundo | |
| −7.4 | 1,8-Dichloro-9,10-diphenylanthracene-9,10-diol (ZINC5438671) | 320,066 |
|
0.55 | -10.45/insoluble | Cissus quadrangularis | |
| −7.3 | Taraxerol (ZINC4082498) | 92,097 |
|
0.55 | -7.16/poorly soluble | Azadirachta indica | |
| −7.3 | Nimbinene | 44,715,635 |
|
0.55 | -5.66/moderately soluble | Antiviral compound | |
| −7.3 | β-amyrin (ZINC13298265) | 92,156 |
|
0.55 | -7.77/poorly soluble | Cissus quadrangularis |