Table 2 Docking energy scores and amino acids involved in binding for XX5 ligand, chloroquine, and the reported inhibitors docked with the ACE2 receptor
From: A study on the effect of natural products against the transmission of B.1.1.529 Omicron
Name | Compound | Docking score (kcal/mol) |
|---|---|---|
Cocrystalized ligand (XX5 ligand) |  − 16.82 | Arg273, His374, Glu402, His505, and Zn2+ ion |
Chloroquine (Standard) |  − 10.33 | Thr445 |
Flavonoids | ||
Caflanone |  − 15.35 | His374, Thr445, and Pro346 |
Hesperetin |  − 15.63 | Thr347 and Zn2+ ion |
Myricetin |  − 18.02 | Glu406 and Pro346 |
Pectolinarin |  − 22.56 | Arg518, His378, His374, Glu402, His505, and Zn2+ ion |
Quercetin |  − 16.51 | Glu406 and Pro346 |
Baicalin |  − 18.64 | His374, Glu375, and Zn2+ ion |
Diosgenin |  − 16.20 | Tyr515, Asp367, and Zn2+ ion |
Baicalein |  − 14.94 | Arg273 |
Luteolin |  − 16.73 | Glu375 and Asp367 |
Cyanidin |  − 16.36 | Asp367 |
Kaempferol |  − 14.87 | Arg273 and Thr445 |
Rutin |  − 24.22 | Arg518, Glu375, Tyr515, His345, His374, Glu402, and Zn2+ ion |
Narcissoside |  − 21.40 | Asp269, Asn149, Thr371, Glu375, His505, Tyr515, Met270, His345, His374, Glu402, and Zn2+ ion |
Isorhamnetin-3-O-B-D-Glucoside (IRG) |  − 17.39 | His374 and Thr371 |
Calendoflaside |  − 21.42 | Asn149, Asp368, and Glu406 |
Procyanidin |  − 21.75 | Asp367 and Pro346 |
Nicotiflorin |  − 20.91 | Pro346, Arg518, Ala348, His345, and His505 |
Broussochalcone A |  − 17.94 | Pro346 |
Broussoflavan A |  − 16.96 | Asp368, Phe274, Glu375, and Zn2+ ion |
Fisetin |  − 14.49 | Glu406 |
Licoisoflavone B |  − 15.90 | Thr347, Glu375, and Zn2+ ion |
Isolicoflavonol |  − 16.65 | Zn2+ ion |
Limonene |  − 6.94 | Tyr510 |
b-Carophyllene |  − 8.977 | Zn2+ ion |
Ascorbic acid |  − 12.55 | His345 and Zn2+ ion |
Terpenoids | ||
Crocin |  − 23.85 | Glu406, Leu120, Thr445, Gln442, Lys441, and Trp349 |
Sarsasapogenin |  − 15.16 | Asp367, Tyr515, and Zn2+ ion |
Ursonic Acid |  − 13.44 | Arg273 and His374 |
Carvacrol |  − 10.19 | Glu375 |
Alkaloids | ||
Quinadoline B |  − 13.50 | His374 |
Scedapin C |  − 15.68 | Thr371 |
Berberine |  − 16.52 | His378 and Ala348 |
Nigellidine |  − 11.73 | Glu402 |
Noscapine |  − 15.35 | Arg518 |
Oxoturkiyenine |  − 13.97 | Arg518 |
3α,17α-Cinchophylline |  − 15.22 | Arg273 |
Speciophylline |  − 13.47 | Arg518, Phe274, and Zn2+ ion |
Cadambine |  − 20.04 | Arg518, Glu375, Tyr510, His505, His345, and Zn2+ ion |
Glycosides | ||
Delphinidin 3,3′-Di-Glucoside-5-(6-P-Coumarylglucoside) (DGCG) |  − 34.03 | Glu406, Phe274, His345, Tyr127, Asn149, Lys363, Asp367, and Asp368 |
Pelargonidin |  − 15.47 | Asp367 |
Digitoxigenin |  − 14.35 | Glu375, Thr445, Phe274, and Zn2+ ion |
Carotenoids | ||
Astaxanthin |  − 17.48 | Ser47 and Gln442 |
Emodin |  − 14.08 | Arg518 |
Monolignols | ||
Anethole |  − 8.967 | Thr347 |
Cinnamaldehyde |  − 9.208 | Zn2+ ion |
Phenolic and polyphenolic compounds | ||
Curcumin |  − 13.5 | Asp269, His345, and Zn2+ ion |
Gallocatechin gallate |  − 21.94 | Glu375, Asp367, and Asp368 |
Ararobinol |  − 16.00 | Asp368 and Tyr127 |
Gingerol |  − 12.86 | Glu375 and His345 |
Miscellaneous compounds | ||
Isochaetochromin D1 |  − 20.96 | Asn149, Asn277, Thr371, and Asp368 |
Bisindigotin |  − 14.66 | Glu406 and Phe274 |
Edgeworoside C |  − 17.07 | Glu375, Tyr515, Phe274, His345, and Zn2+ ion |
Adlumidine |  − 12.79 | Thr371 |
Asparagoside-C |  − 21.66 | Glu406, Tyr127, Arg518, and Thr519 |
Asparagoside-D |  − 24.66 | Thr445, Thr276, His345, Asp367, Asp368, and Arg518 |
Asparagoside-F |  − 29.62 | Arg518, Thr445, Asp367, Thr371, and Zn2+ ion |
3-(3-Methylbut-2-enyl)-3,4,7-trihydroxyflavane (MTHF) |  − 14.87 | Glu375 and Zn2+ ion |
Kazinol F |  − 17.11 | Pro346 |
Kazinol J |  − 18.08 | Asp368, Thr371, and His374 |
Cinnamyl acetate |  − 8.858 | Arg518, Glu375, and Zn2+ ion |
L-4-terpineol |  − 9.345 | Zn2+ ion |
Allicin |  − 8.180 | Glu402, His505, His345, and Zn2+ ion |
Anthraquinone |  − 9.508 | Arg518 |
Gallocatechin gallate |  − 21.94 | Glu375, Asp367, and Asp368 |
Ararobinol |  − 16.00 | Asp368 and Tyr127 |
Gingerol |  − 12.86 | Glu375 and His345 |
Miscellaneous compounds | ||
Isochaetochromin D1 |  − 20.96 | Asn149, Asn277, Thr371, and Asp368 |
Bisindigotin |  − 14.66 | Glu406 and Phe274 |
Edgeworoside C |  − 17.07 | Glu375, Tyr515, Phe274, His345, and Zn2+ ion |
Adlumidine |  − 12.79 | Thr371 |
Asparagoside-C |  − 21.66 | Glu406, Tyr127, Arg518, and Thr519 |
Asparagoside-D |  − 24.66 | Thr445, Thr276, His345, Asp367, Asp368, and Arg518 |
Asparagoside-F |  − 29.62 | Arg518, Thr445, Asp367, Thr371, and Zn2+ ion |
3-(3-Methylbut-2-enyl)-3,4,7-trihydroxyflavane (MTHF) |  − 14.87 | Glu375 and Zn2+ ion |
Kazinol F |  − 17.11 | Pro346 |
Kazinol J |  − 18.08 | Asp368, Thr371, and His374 |
Cinnamyl acetate |  − 8.858 | Arg518, Glu375, and Zn2+ ion |
L-4-terpineol |  − 9.345 | Zn2+ ion |
Allicin |  − 8.180 | Glu402, His505, His345, and Zn2+ ion |
Anthraquinone |  − 9.508 | Arg518 |