Table 3.
Docking score and type of interaction of standard inhibitor and top three Azadirachta indica and Aloe barbadensis phytochemicals against SARS-CoV-2 Mpro, spike, and RdRp proteins.
| Target | PMID of ligand | Ligand name | Hydrogen-forming residues | Residues with hydrophobic interaction |
|---|---|---|---|---|
| Mpro | ||||
| Standard | ||||
| 92727 | Lopinavir | Asn142, Ser46, Thr45, Cys44, Thr25, Thr24, Leu27, Gly143, Thr26, Met49, Arg188, His41, Asp187, Val186, His164, Met165, Ser144, Phe140, Leu141, Cys145, His163, Glu166, Gln189, | ||
| Aloe | ||||
| 14889736 | 10-Hydroxyaloin A | His41, Leu141, Gly143, Cys145, Leu27, Arg188, Thr26, Glu166, Ser144, His164, Asn142, His163, Thr25, Thr45, Cys44, Ser46, Met49, Gln189, Met165 | ||
| 158096 | 7-Hydroxyaloin B | Leu141, His41, Gln189, Glu166, Thr190, Met49, Asn142, His163, Pro168, Met165, Arg188, | ||
| 10648253 | 10-Hydroxyaloin B 6’-catate | Gly143, His164, Cys145, Phe140, Ser46, Thr45, His41, Thr25, Cys44, Met49, Gln189, Met165, Leu141, Glu166, His163 | ||
| Neem | ||||
| 10813969 | Isoquercetin | Glu166, Asn146, His41, Gly143, Leu27, Thr25, Cys44, Val42, Met49, Cys145, Met165, Arg188, Gln189, Thr190, Pro168, Leu167, Leu141, Ser144, His163, Phe140 | ||
| 97343-95-8 | VEPAOL | Thr26, Asn142, Gly143, Ser46, Gln189, Met49, His41, Leu27, His164, Met165, Glu166, His163, Ser144, Leu141, Phe140, HSI172, Cys145, Thr24, Thr25 | ||
| 29803-85-8 | Nimbidiol | Gly143, Thr26, Met49, Gln189, Ser46, Asn142, Thr24, Thr25, Leu27, Ser144, Cys145, His164, His41, Met165, Glu166 | ||
| Spike | ||||
| Standard | ||||
| VE607 | – | Asp422, Arg346, Thr345, Phe347, Arg509, Ser494, Lys417, Tyr421, Pro491, Leu492, Tyr351, Gln493, Ile418, Val350, Tyr495, Ile402, Ser349, Ala348, Phe497, Asp442 | ||
| Aloe | ||||
| 100450 | MS 3 | Ser494, Gln493, Leu492, Pro491, Tyr421, Asn422, Lys417, Ile418, Tyr495, Val350, Gly496, Ser349 | ||
| – | BB | Phe497, Asp442, Phe347, Tyr495, Ser349, Val401, Ser443 | ||
| 12305761 | Barbaloin | Tyr495, Ser494, Val401, Gln493, Val350, Ser349 | ||
| 158096 | 7-Hydroxyaloin B | Phe347, Asp442, Arg346, Val401, Tyr495, Val350, Ser494, Ser349, Phe497 | ||
| Neem | ||||
| 10813969 | Isoquercitin | Phe347, Val350, Asp442, Phe497, Arg509, Arg346, Ala348, Val401, Ser349, Gln493, Tyr495, Tyr351, Ser494, Gln498, Pro499, Ser443 | ||
| 97343-95-8 | Vepaol | Val350, Asn422, Pro491, Tyr351, Gln493, Leu492, Lys417, Ile418, Tyr495, Ser349 | ||
| RdRp | ||||
| Standard | ||||
| 37542 | Ribavirin | Trp617, Asp618, Lys798, Glu811, Tyr619, Ser814, Phe812, Asp761, Asp760, Ala762, Gly616, Trp800, Cys799, | ||
| Aloe | ||||
| 158096 | 7-Hydroxyaloin B |
Asp618, Tyr619, Lys621, Asp760, Lys798, Glu811, Asp761, Asp623, Cys622, Pro620, Lys551, Arg553, Ser814 |
||
| 6857486 | CHEBI:35671 | Asp760, Asp761, Ala762, His810, Glu811, Asp618, Tyr619, Lys798, Cys799, Trp800, Gly616, Trp617, Val763, Phe812, Ser759, Ser814 | ||
| 5317657 | UNII-73899319HU | Arg553, Ser759, Asp760, Ser814, Lys798, Lys545, Glu811, Phe812, Trp800, Cys799, Trp617, Tyr619, Trp617, Cys813, Asp618, Asp761, Leu758, | ||
| Neem | ||||
| 10813969 | Isoquercetin | Trp617, Asp618, Tyr619, Asp760, Lys798, Pro620, Lys621, Cys622, Cys799, Trp800, Gly616, Ala762, Asp761, Glu811, Ser814, Ser759 | ||
| 184310 | Isonimocinolide | Tyr619, Lys621, Asp761, Ser814, Asp618, Lys798, Asp623, Cys622, Pro620, Leu758, Asp760, Ser759, Cys813, Ala762, Phe812, Glu811, Trp617, Gly616, Trp800 | ||
BB- (10R)‐2,8‐dihydroxy‐6‐(hydroxymethyl)‐1‐methoxy‐10‐[(2R,3R,4R,5R,6R)‐3,4,5‐trihydroxy‐6‐(hydroxymethyl)oxan‐2‐yl]‐9,10‐dihydroanthracen‐9‐one.
The amino acids shown in bold were involved in hydrogen bond formation with their respective protein.