4.1. Spike (S) protein

Spike is a trimeric glycoprotein that mediates the binding of the virus to host cell surface-specific receptors and virus-cell membrane fusion [122]. It plays a vital role in determining host tropism and the diversity of coronaviruses (CoVs). SARS-CoV-2 is more contagious than SARS-CoV as SARS-CoV-2 spike protein interacts with ACE2 with 10–20 folds higher affinity than SARS-CoV. The receptor-binding motif (RBM) (437–508 amino acids) present in the RBD (319–541 amino acids) of the S1 subunit (13–685 amino acids) of the spike protein is majorly responsible for the binding of the virus to ACE2 [7,8,89] ( Figure-5 ). In-silico docking results showed that the phytocompounds enlisted under the spike section in Table-1 interact well with the hot-spot residues of the RBD of spike glycoprotein of SARS-CoV-2.

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Fig. 5

Molecular structure of spike protein of SARS-CoV-2 and interactions with plant-based drugs. A furin cleavage site is present at the interface between S1 and S2 subunits of the spike protein. Amino acid positions of spike protein that can be interacted by different groups of plant-based inhibitors (steroids, quinones, terpenoids, flavonoids, and tannins) are also shown. Please refer Table-1 for precise details. SP- signal peptide; RBD- Receptor binding domain; RBM- Receptor binding motif; TM-transmembrane motif; FP- fusion peptide; HR1-Heptad repeat-1, HR2-heptad repeat-2; NTD- N-terminal domain, CP- cytoplasmic domain(adapted from Joshi et al., 2020[40] with some modifications).

Table 1

Interactions of plant-based small molecules with targeted SARS-CoV-2 or host proteins.

Spike Glycoprotein (viral protein)
Class	Small molecule inhibitors	Interacting amino acids with different classes of phytocompounds	References
Tannins	Punicalin (3-IR and −7.406 BE), punicalagin (6-IR and −7.312 BE), Pedunculagin (4-HB, 6 NBI and −7.7 BE), punigluconin (7-HB, 5-NBI and −7.9 BE), chebulagic acid (5-HB, 5-NBI and −7.5 BE), chebulinic acid (5-HB, 7-NBI and −6.5 BE), cinnamtannin-B1 (3-HB, 3-HP and −10.2 BE), 6-Glucopyranosyl procyanidin-B1 (8-HB, 1-EI and −9.9 BE), Procyanidin-B7 (2-HB, 3-HP, 2-EI and −9.6 BE), proanthocyanidin-A2 (5-HxB, 1-HP, 2-EI and −9.4 BE), ellagic acid (3 IR and −6.114 BE), gallic acid (2 IR and −4.808 BE), gallotannins (6 HB, 7-NBI, −7.4 BE).	Phe40, Leu95, Gln102, Asn103, Lys187, Asp206, Val209, Asn210, Leu335, Phe342, Asn343, Pro346, Thr347, Trp349, Val367, Leu368, Tyr369, Asn370, Ser371, Ala372, Phe374, Phe377, Asp382, Phe390, Arg393, Asn394, Glu398, Gln493, Ala396, His401, Glu402, Arg403, Glu406, Gln409, Lys417, Tyr449, Tyr453, Leu455, Phe456, Tyr489, Phe490, Leu492, Gln493, Ser494, Tyr495, Gln496, Asn501, Tyr505, Asp509, Arg514, Tyr515, Lys562, Lys562, Pro565	[56,66,79].
Terpenoids	Geraniol (2-HB and-5.0 BE), L-4-terpineol (2-HB and −5.1 BE), carvacrol (1-HB and −5.2 BE), limonene (12-HPI and −5.1 BE), thymol (-5.4 BE), tinosporide (2HB, 6-NBI and −6.4 BE), taraxerol (7-NBI and −7.9 BE), daturaolone (8 NBI and −7.5 BE), glycyrrhizin (7-HB, 3-NBI, −7.1 BE), friedelin (1-HB, 2-IR and −7.3 BE), tenuifolin (4-HB, 2-HP and −8.7 BE), -terpinene (−4.8 BE), α-terpinene (−5.0 BE), camphene (2-HPI and −5.2 BE), camphor (2-HPI and −4.8 BE).	Leu73, Asp350, Tyr385, Phe390, Asn394, Arg403, Asp405, Glu406, Arg408, Gln409, Gly416, Lys417, Tyr449, Tyr451, Leu452, Tyr453, Leu455, Phe-456, Lys458, Ser-459, Leu461, Ile468, Thr470, Ile472, Glu484, Tyr489, Phe490, Pro491, Leu492, Gln493, Ser494, Tyr495, Gly496, Asn501, Tyr505	[47,56,66]
Flavonoids	Pavetannin-C1 (9-HB, 4-HP, 1-EI and −11.1 BE), hesperidin (5 IR and −8.99), chrysin (9 IR and −6.87), querceitin 3-O-robinobioside (5-HB, 6-NBI, −7.9 BE), kaempferol 3 - alpha-l-arabinofuranoside 7-rhamnoside (7-HB, 2-HP and −8.7 BE), catechin gallate (5 HB, 3 HP and −6.1 BE), cinnamaldehyde (2-HB and −5.0 BE), Anthranol (1 HB, 2 HP and-9.08 BE),Apigenin (5 HB, 2 HP and -10.09 BE)Derrisin (2 HB, 2 HP and -11.04 BE)Jaceidin (2 HB, 2 HP and -10.54 BE),Lupiwighteone (1 HB, 3 HP and -9.92 BE), Luteolin (2 HB, 2 HP and -10.92 BE), Mundulinol (2 HB, 1 HP and -11.08 BE), Naringenin (2 HB, 2 HP and -10.12 BE), Rhamnetin (2 HB, 2 HP and -10.15 BE), Tamarixetin (2 HB, 1 HP and -10.33 BE), Cannflavin (1 HB, 2 HP and -9.11 BE), Methylglovanon (1 HB, 1 HP and -9.43 BE)	Ser44, Leu48, Ala292,Cys301, Leu303, Ile312, Tyr313, Thr315, Asn317, Phe318, Arg319, His345, Thr347, Ala348, Trp349, Asp350, His374, Glu375, His378, Asp382, Tyr385, Gly395, Asn397, Glu398, His401, Arg403, Glu406, Tyr410, Lys417, Arg443, Ser448, Asn449, Tyr453, Arg454, Leu455, Phe456, Ser459, Glu471, Val472, Glu473, Gly474, Phe475, Phe486, Tyr484, Thr487, Asn488, Ser494, Tyr495, Gly496, Phe497, Tyr505, Tyr510, Arg514, Tyr515, Gln516, Leu517, His519, Ala520, Ala522, Asn544, Gly545, Leu546, Val595, Pro665, Ser730, Met731, Lys733, Gln762, Arg765, Ala766, Asn856, Val860, Pro863, Asp867, Asp867, Lys964, Leu966, Ser967, Phe970, Asn969, His1058.	[12,47,56,57,[25], [66]]
Steroids	Withametelin (8 NBI and −8.0 BE), withanolide-A (1-HB, 7-NBI and −7.7 BE), echinacin (2-HB, 6-NBI and −7.9 BE), stigmasterol (2-IR and −7.2 BE), withanolide G (4 HB, 2 HP and −8.4 BE)	Asp66, Arg67, Gln85, Val367, Asn370, Phe374, Tyr449, Leu452, Leu455, Phe456, Glu484, Tyr489, Phe490, Leu492, Gln493, Ser494.	[41,56,57]
Quinone	Emodin (4 IR and −6.19), rhein (5 IR and −8.73)	Asn332, Thr333, Asn353, Ser388, Val401, Asn448, Ala464, Val472, Gly474,	[12]
Steroidal saponins	Asparoside-C (5 HB and −7.54 BE), asparoside-D (6 HB and −7.06 BE), shatavarin-I (Asparoside-B) (5 HB and −6.52 BE), shatavarin-X (6 HB and −6.43 BE), racemoside-A (3 HB and −6.23)	Arg403, Glu406, Gln409, Gln414, Thr415, Lys417, Asp420, Lys444, Gly447, Tyr449, Tyr453, Glu484, Ser494, Gly496, Gly496, Gln498, Gly502	[16]
Alkaloid	Chelidimerine (2 HB, 3 HP and −8.2 BE), Withanone (1 HB, 5 HP and −7.8 BE), Norsanguinarine (3 HB, 3 HP and −7.0 BE), Sanguinarine (1 HB, 4 HP and −6.8 BE), Adlumidine (3 HB, 4 HP and −6.8 BE), Somniferine (2 HB, 4 HP and −6.7 BE), Fumariline (1 HB, 3 HP and −6.4 BE)	Asp66, Arg67, Leu335, Phe338, Gly339, Phe342, Asn343, Asp364, Val367, Leu368, Leu368, Asn370, Ser371, Phe374, Trp436	[57]
Sesquiterpene	Badrakemin acetate (3 HB, 5 HP, and −8.0 BE), Samarcandin (2 HB, 3 HP, and −7.4 BE)	Leu335, Phe338, Gly339, Glu340, Asn343, Asp364, Val367, Leu368	[57]
Plant lignans	Pinoresinol-4-O-b-d- glucopyranoside (4 HB, 3 HP, and −4.9 BE)	Cys336, Phe338, Asn343, Asp364, Val367, Leu368, Ser371	[57]
Anthocyanin	Pelargonidin 3-glucoside (4 HB, 3 HP and −6.2 BE)	Cys336, Phe338, Asn343, Asn364, Val367, Leu368, Ser371	[57]
Other compounds	Cinnamyl acetate (3-HB and −5.2 BE), barlerinoside (7-HB, 9-NBI and −7.4 BE), deoxytubulosine (1-HB, 8-NBI and −7.2 BE)	Arg403, Asp405, Glu406, Gln409, Lys417, Tyr449, Tyr453, Arg454, Leu455, Phe456, Ser469, Glu471, Glu484, Gly485, Tyr489, Phe490, Leu492, Gln493, Ser494, Gly496, Asn501, Tyr505	[47,56]
Standards	Remidesvir (3 IR and −5.94 BE), chloroquine (3 IR and −8.98), hydroxychloroquine (4 IR and −7.82 BE)	Arg403, Glu406, Tyr453, Thr467, Pro468, Cys469, Gly471, Val472	[12,16,41] [16]
ACE2 (host protein acting as CoV-2 receptor)
Class	Small molecule inhibitors	Interacting residues with different classes of phytocompounds	References
Organo-sulfur	Allyl disulfide (3 IR and −12.84 BE), allyl trisulfide (2 IR and −12.76 BE), allyl (E)-1-propenyl disulfide (2 IR and −9.07 BE), allyl methyl trisulfide (2 IR and −12.50 BE), diallyl tetrasulfide (4 IR and −14.06 BE), 1,2-dithiole (2 IR and −13.21 BE), 1,2-dithiole (1 IR and −7.89), allyl (Z)-1-propenyl disulfide (T7) (2 IR and −9.04 BE), 2-vinyl-4H-1,3-dithiine (3 IR and −11.83 BE), 3-vinyl-1,2-dithiacyclohex-4-ene (3 IR and −10.57 BE), carvone (2 IR and −8.58 BE), trisulfide, 2-propenyl propyl (4 IR and −14.01 BE), methyl allyl disulfide (3 IR and −10.32 BE), diacetonalcohol (2 IR and −9.71 BE), trisulfide, (1E)-1-propenyl 2- propenyl (2 IR and −9.57 BE), allyl sulfide (3 IR and −9.38 BE), 1-propenyl methyl disulfide (2 IR and −8.06 BE), trisulfide, (1Z)-1-propenyl 2- propenyl (2 IR and −8.06 BE).	Lys94, Gln98, Gln101, Gln102, Asn103, Gly205, Asp206, Glu208, Val209, Asn210, Ala396, Lys562, Ser563, Pro565, Trp566	[82]
Tannins	Punicalin (5 IR and −7.353 BE), punicalagin (4 IR and −7.144 BE), ellagic acid (4 IR and −6.85 BE), gallic acid (4 IR and −5.24 BE), pedunculagin (4 HB, 4 HPI and −7.2 BE), punigluconin (5 HB, 5 HPI and −6.6 BE), chebulagic acid (1 HB, 6 HPI and −6.6 BE), chebulinic acid (4 HB, 3 HPI and −6.8 BE), gallotannins (4 HB, 7 HPI and −7.1 BE).	Asp30, Asn33, His34, Glu35, Glu37, Asp38, Tyr41, Ser280, Pro289, Asn290, Ile291, Asp292, Arg393, Lys353, Asp367, Ala386, Ala387, Gln388, Pro389, Arg393, Phe428, Lys441, Gln442, Thr445.	[79]
Flavonoid	Hesperidin (4 IR and −9.167 BE), chrysin (3 IR and −7.146 BE), rutin (6 IR and −3.41 BE), vitexin (7 IR and −5.71 BE), apigenin (5 IR and −3.75 BE), quercetin (5 IR and −4.11 BE)	Thr27, Lys31, His34, Glu35, Glu37, Asp38, Gln42, Asn63, Thr125, Ile126, Thr129, Asn137, Pro138, Gly139, Lys353	[[12], [100]]
Quinone	Emodin (3 IR and −9.83 BE), Rhein (- 7.423 BE)	Asp67, Ala71, Lys74	[12]
Terpenoid	Thymol and iso-thymol (1 H-donor and −4.74 BE), m-eugenol (4 IR and −2.53 BE), p-thymol (3 IR and −2.75 BE), carvacrol (7 IR and −3.31 BE), costunolide (4 IR and −4.0 BE), cynaropicrin (5 IR and −3.06 BE), bharangin (4 IR and −4.36 BE), andrographolide (6 IR and −4.53 BE), beta-pinene (5 IR and −5.22 BE), spathulenol (6 IR and −4.98 BE), vetiverol (6 IR and - 4.96 BE), cucurbitacin B (6 IR and −5.36 BE), alpha-bisabolol (7 IR and −5.69 BE), 6-shogaol (6 IR and −3.33 BE), 6-gingerol (6 IR and −3.49 BE), beta-sitosterol (7 IR and −4.88 BE), linoleic acid (6 IR and −2.07 BE), glycyrrhizinic acid (4 HB, 2 Pi-Alkyl, 1CHB, 9 VDW and −9.5 BE), maslinic acid (4 HB, 3 Pi-Alkyl, 5 VDW and −8.5 BE), obacunone (1 HB, 1 Pi-sigma, 1 Pi-Pi T shaped, 2 Pi-Alkyl, 8 VSW and −8.1 BE), epoxyazadiradione (2 Alkyl/Pi-Alkyl, 1 Pi-Sigma, 7 VDW and −8.0 BE), azadiradionolide (3 HB, 3 Alkyl/Pi-Alkyl, 6 VDW and −8.0 BE), Ursolic acid (3 HB, 3 Pi-Alkyl, 7 VDW and −7.4 BE), gedunin (1 HB, 3 Alkyl/Pi-Alkyl, 1 Pi-Sigma, 1 CHB, 7 VDW and −7.3 BE).	Lys26, Thr27, Asp30, Lys31, Asn33, His34, Glu35, Asp38, Glu37, Leu39, Phe40, Gln42, Asn90, Thr92, Val93, Gln96, Tyr127, Ser128, Glu145, Asn 149, Trp271, Arg273, Phe274, His345, Pro346, Thr347, Ala348, Trp349, Asp350, Lys353, Asp367, Lue370, Thr371, His373, His374, Glu375, Asp382, Tyr385, Ala387, Gln388, Pro389, Phe390, Arg393, Asn394, His401, Glu402, Glu406, Ser409, Gln442, Thr445, Leu503, Phe504, His505, Asn508, Arg514, Tyr515, Lys562	[[1], [87], [100]]
Alkaloids	Pellitorine (5 IR and −3.4 BE), vasicine (5 IR and −6.21 BE), piperidine (9 IR and −4.31 BE), piperine (5 IR and −4.1 BE)	Asp30, Lys31, Asn33, His34, Glu35, Glu37, Asp38, Phe40, Asp350, Lys353, Pro389, Phe390, Arg393, Asn394,	[100]
Standards	Lopinavir (9 IR and −7.5 BE), umifenovir (7 IR and −6.5 BE), Hydroxychloroquine (10 IR and −7.1 BE)	His34, Glu37, Thr276, Asn290, Ile291, Met366, Asp367, Leu370, Gln388, Pro389, Arg393, Lys403, Glu406, Ser409, Leu410, Ala413, Lys441, Thr445, Ser494, Tyr495, Gly496, Tyr505	[10,79]
TMPRSS2 (host protease)
Class	Small molecule inhibitors	Interacting residues with different classes of phytocompounds	References
Tannins	Punicalin (5 IR and −8.168 BE), punicalagin (6 IR and −7.358 BE), ellagic acid (2 IR and −6.829 BE), gallic acid (5 IR and −5.709 BE)	Arg87, Ala88, Arg91, Asp92, Asn97, Asp129, Tyr401, Met404, Arg405, Gly408	[79]
Steroidal lactone	Withaferin-A (2 HB, 19 IR and −5.60 BE), Withanone (1 HB; 18 HP and −4.30 BE)	His296, Glu299, Tyr337, Lys342, Glu389, Asp435, Ser436, Cys437, Gln438, Asp440, Ser441, Thr459, Ser460, Trp461, Gly462, Ser463. Gly464, Cys465, Ala466, Gly472, Val473	[49]
Caffeate ester	Caffeic acid phenethyl ester (2 HB; 17 HP and −6.20 BE)	Cys281, Val280, His296, Cys297, Glu299, Leu302, Asp435, Ser436, Cys437, Gln438, Gly439, Asp440, Ser441, Thr459, Ser460, Trp461, Gly462, Gly464, Cys465	[49]
Standards	Camostat (5 IR and −7.069 BE), Camostat mesylate (1 HB and 20 HPI and -5.9 BE)	Arg87, Asn97, Phe99, Met404, Arg405, Val275, Gln276, Val278, Val 280, His296, Cys297, Leu302, Asp435, Ser436, Cys437, Gln438, Gly439, Ser441, Thr459, Trp461, Gly462, Cys465, Ala466, Gly472, Val473	[79] [49]
Furin (host protein)
Class	Small molecule inhibitors		References
Tannins	Punicalin (7 IR and −9.725 BE), punicalagin (4 IR and −9.385 BE), ellagic acid (5 IR and −7.801 BE	His194, Gly255, Pro256, Pro256, Glu257, Asp258, Asp259, Thr262, Arg298, Cys303, Asp306, Gly307, Ser311, Gly366, Ser368, Thr365, Arg 490, Trp531, Ala532,	[79]
Standards	Sulcanozole (4 IR and −6.923 BE)	Val263, Phe528, Trp531, Ala532	[79]
Papain-like protease/nsp3 (viral protease)
Class	Small molecule inhibitors	Interacting residues with different classes of phytocompounds	References
Terpenoid, Flavonoid	Oleonolic acid (4 IR and −10 BE), ursolic acid (5 IR and −9.7 BE), 3β-acetoxyolean-12-en-27-ioc acid (3 IR and −9.5 BE), Isovitexin (5 IR and −9.3 BE)	His89, Trp106, Ala107, Asp108, Asn109, Val159, Gly160, Gu161, Leu162, Pro248, Tyr264	[55]
3 Chymotrypsin-like protease/nsp5 (viral protease)
Class	Small molecule inhibitors	Interacting residues with different classes of phytocompounds	References
Flavonoid	Epigallocatechin (6 IR and −7.0 BE), gallocatechin (6 IR and −7.1 BE) catechin (6 IR and −7.1 BE), epicatechin (6 IR and −7.2 BE), catechin gallate (6 IR and −7.2 BE), epigallocatechin gallate (9 IR and −7.6 BE), epicatechin gallate (10 IR and −8.2 BE), gallocatechin-3-gallate (9 IR and −9.0 BE), kaempferol (4 HB, 6 HPI and −8.58 BE), quercetin (8 IR and −6.58), luteolin-7- glucoside (10 IR and −8.17 BE), myricetin (4 IR and −6.15 BE), scutellarin (2 IR and −7.13 BE), isoflavone (2 IR and −5.69 BE), Quercetin-3-O-rutinose (6 HB, 1 PS and −9.2 BE), Quercetin-7-O-glucuronide (6 HB, 1 PC, 1 PS, 1 PP, 1 Pal and −8.4 BE), quercetin-3′-O-glucuronide (6 HB, 1 PS, 2 Pal and −8.5 BE), quercetin-3-O-glucuronide (3 HB, 1 PS, 1 PC, 1 Pal and −8.5 BE), quercetin-7-O-sulfate (6 HB, 1 PS, 1 Pal and −8.4 BE), quercetin-3-O-sulfate (4 HB, 1 PS, 1 Pal and −7.6 BE), quercetin-3′-O-sulfate (6 HB, 1 PC, 3 PS and −8.1 BE), quercetin (4 HB; 1 PS, 2 Pal and −7.5 BE), kaempferol-3-O-rutinose (nicotiflorin) (4 HB, 1 PS, 1 Psi, 1 PP and −8.9 BE), kaempferol-4′-O-glucuronide (4 HB, 3 Pal and −8.0 BE), kaempferol-3-O-glucuronide (6 HB, 1 PS, 1 PP, 1 Psi and −8.3 BE), kaempferol-7-O- glucuronide (4 HB, 2 PS, 1 Psi, 2 Pal and −8.3 BE), kaempferol-7-O-sulfate (3 HB, 1 PS, 1 PP, 2 Pal and −8.3 BE), kaempferol-4′-O-sulfate (4 HB, 1 Pal and −8.2 BE), kaempferol-3-O-sulfate (3 HB, 1 PS, 1 Pal and −7.3 BE), kaempferol (1 HB, 2 PS, 2 Pal and −7.2 BE), 5,7,3′4’ - tetrahydroxy2’-(3,3- dimethylallyl) isoflavone (14 IR and −16.35 BE), myricitrin (16 IR and −15.64 BE), methyl rosmarinate (16 IR and −15.44 BE), 3,5,7,3′,4′,5′- hexahydroxy flavanone – 3 – O – beta – D glucopyranoside (13 IR and −14.42 BE), (2S)-eriodictyol 7-O-(6″-Ogalloyl)-beta-d-glucopyranoside, (15 IR and −14.41 BE), calceolarioside B (16 IR and −19.87 BE), myricetin 3-Obeta-d-glucopyranoside (17 IR and −13.70 BE); licoleafol (13 IR and −13.63 BE), amaranthin (16 IR and −12.67 BE), peonidin 3-O-glucoside (5 HB, 7 HP and −9.4 BE), kaempferol 3-O-β –rutinoside (4 HB, 6 HP and −9.3 BE), rutin (2 HB, 6 HP and −9.2 BE), 4 - (3, 4 - Dihydroxyphenyl) – 7 – methoxy - 5 - [(6 – O – b –d– xylopyranosyl – b –d- glucopyranosyl) oxy] - 2H-1-benzopyran – 2 - one (5 HB and 7 HP), quercetin-3-D-xyloside (7 HB, 5 HP and −9.1 BE), quercetin 3-O-a-l-arabinopyranoside (4 HB, 6 IR and −9.0 BE), kaempferol 3-rutinoside 40-glucoside (9 HB, 6 HP and −8.9 BE), quercetin 3-O-(6″-O-malonyl)-b-D-glucoside (3 HB, 8 HP and −8.8 BE), idaein (2 HB and 8 HP), callistephin (3 HB and 8 HP); malvin (4 HB, 8 HP and −8.7 BE), luteolin 7-rutinoside (2 HB; 9 HP; −8.6 BE), cyanin (4 HB; 4 HP; −8.5 BE), kaempferol 7-O-neohesperidoside (5HB, 7 HP and −8.4 BE), rhamnetin 3 sophoroside (5 HB, 4 HP and −8.3 BE), myricetin 3-O-b-d-galactopyranoside (5 HB, 2 HP and −8.2 BE), 2″-O-alpha-l-rhamnopyranosyl-isovitexin (3 HB, 10 HP and −8.2 BE), hesperidin methylchalcone (5 HB, 4 HP and −8.0 BE), procyanidin-B7 (4 HB, 1 HP, 1 EI and −8.2 BE), kaempferol 3-alpha-l-arabinofuranoside-7-rhamnoside (3 HB, 1 HP, 1 EI and −8.1 BE), proanthocyanidin-A2 (1 HB, 1 HP, 1 EI and −8.0 BE), 6-glucopyranosyl procyanidin B1 (5 HB, 1 HP, and −7.6 BE), pavetannin-C1 (4 HB, 1 HP, 1 EI and −7.3 BE), querceitin 3-O-robinobioside (6 HB, 8 NBI and −8.8 BE).	Lys5, Thr24, Thr25, Thr26, Leu27, His41, Cys44, Thr45, Ser46, Met49, Tyr53, Tyr54, Pro108, Lys137, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu-166, Leu-167, Pro168, His172, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192, Gly195, Asp197, Thr199, Asn238, Tyr239, His246, Leu271, Leu272, Leu286, Leu287, Glu288, Asp289.	[[20], [57], [66], [67], [73], [109]]
Organosulfur	Allyl disulfide (6 IR and −15.32 BE), allyl trisulfide (4 IR and −15.02 BE), allyl (E)-1-propenyl disulfide (2 IR and −13.25 BE), allyl methyl trisulfide (4 IR and −14.36 BE), diallyl tetrasulfide (4 IR and −14.47 BE), 1,2-dithiole (T6-ACE2) (2 IR and -13.21 BE), allyl (Z)-1-propenyl disulfide (2 IR and −12.60 BE), 2-vinyl-4H-1,3-dithiine (4 IR and −14.04 BE), 3-vinyl-1,2-dithiacyclohex-4-ene (3 IR and −13.83 BE), carvone (1 IR and −12.36 BE), trisulfide, 2-propenyl propyl (5 IR and −14.36 BE), methyl allyl disulfide (3 IR and −13.56 BE), diacetonalcohol (2 IR and −13.26 BE); trisulfide, (1E)-1-propenyl 2- propenyl (2 IR and −12.00 BE); (1Z)-1-propenyl 2- propenyl (1 IR and −11.68 BE)	Leu141, Asn142, Gly143, Ser144, Cys145, His163, Met165, Glu166	[82]
Terpenoids	Glycyrrhizic acid (4 HB, 3 CHB, 12 VDW and −8.7 BE), 6-oxoisoiguesterin (5 IR and −9.1 BE), daturaolone (10 NBI and −7.3 BE), glycyrrhizin (7 HB; 7 NBI and −8.2 BE), calendulaglycoside B (16 IR and −8.2 BE), calenduloside (15 IR and −7.9), tenuifolin (6 HB, HP-2 and 8.8 BE), 7-Deacetyl-7-benzoylgedunin L (1 CHB, 2 HB, 10 VDW, 1 Pi-Pi T shaped, 1 alkyl, 1 Pi-alkyl, −9.1), glycyrrhizic acid (4 HB, 3 CHB, 12 VDW, −8.7), limonin: 3 HB, 1 pi-donor, 1 CHB, 4 VDW, −8.7), Obacunone (3 HB, 1 pi-donor, 1 pi-alkyl, 5 VDW, −7.5), Dihydroartemisinin (2 HB, 2A, 1 PA and −7.0 BE)	Thr24, Thr25, Thr26, Leu27, His41, Cys44, Thr45, Ser46, Met49 Leu50, Tyr118, Arg131, Lys137, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, His172, Asp187, Arg188, Gln189, Thr190, Ala191, Tyr239, Leu275, Leu286, Leu287	[21,31,51,56,87]
Sesquiterpene	Badrakemin acetate (2 HB, 5 HP and −8.6 BE), Samarcandin (3 HB, 2 HP and −8.5 BE)	His41, Gly143, Cys145, His163, Glu166, Leu167, Pro168, Gln192	[57]
Iridoid glycoside	Harpagoside (3 HB, 3 HP and −6.1 BE)	His41, Met49, Leu141, Asn142, Met165, Glu166	[57]
Beta-diketone	demethoxycurcumin (1 IR and −7.02 BE), curcumin (2 IR and −6.04 BE); bisdemethoxycurcumin (5 IR and −7.3 BE)	His41, Asn119, Phe140, Cys145, His163	[73]
Beta-hydroxy ketone	Zingerol (5 IR and −5.40 BE) and gingerol (5 IR and −5.38 BE)	Met49, His163, Met165, Glu166, Pro168, Asp187, Arg188, Gln189, Thr190	[43]
Furanocoumarin	Bergapten (5-methoxypsoralens) (2 IR and −5.98 BE)	Phe140, His163	[73]
Anthocyanins	Delphinidin 3-Sambubioside-5-Glucoside (27 IR and −12.37 BE); Delphinidin 3,3′-Di-Glucoside-5-(6-P-Coumarylglucoside) (28 IR and −11.59 BE), 2-(3,4,5-Trihydroxyphenyl)-3-[6-[(E)-3-(4-hydroxyphenyl) acryloyl]-beta-D-galactopyranosyloxy]-5,7-dihydroxy-1-benzopyrylium 2-(3,4,5- Trihydroxyphenyl)-3-[6-[(Z)-3-(4-hydroxyphenyl) acryloyl]-beta-D-galactopyranosyloxy]-5,7-dihydroxy-1-benzopyrylium (27 IR and −10.94 BE), 3-O-[b-d-Glucopyranosyl-(1->2)-[4-hydroxycinnamoyl-(->6)]-b-d-glucopyranoside](E-), 5-O-(6-O-malonyl-b-d-glucopyranoside) Pelargonidin 3-O-[b-d-Glucopyranosyl-(1->2)-[4-hydroxycinnamoyl-(->6)]-b-d-glucopyranoside](E-) 5-O-(6-O-malonyl-b-d-glucopyranoside (25 IR and −10.30 BE), 3-< [4,5-dihydroxy-6-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-< [hydroxy(4-oxocyclohexa-2,5-dien-1-ylidene)methoxy]methyl > oxan-2- yl)oxy]oxan-2-yl]oxy>-2-(3,4-dihydroxyphenyl)-7-hydroxy-5-< [3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy>-1lambda-chromen-1-ylium (25 IR and −13.59 BE), Cyanidin 3-(60 ‘-p-coumarylsambubioside) (22 and −9.58 BE), Pelargonidin 3-glucoside (4 HB, 5 HP and −8.1 BE), Cyanidin 3,5-di-O-glucoside (4 HB, 6 HP and −6.9 BE), Cyanidin 3-O-rutinoside (7 HB, 4 HP and −6.9 BE)	Thr24, Thr25, Thr26, Leu27, His41, Cys44, Met49, Leu50, Pro52, Tyr54, Gly138, Ser139, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, Thr169, Gly170, His 172, Val186, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192	[27,57]
Steroidal lactone	Withanoside-II (20 IR and −11.30 BE), withanoside IV (20 IR and 11.02 BE), withanoside-V (27 IR and −8.96 BE), sitoindoside IX (24 IR and −8.37 BE), Withanolide G (4 HB, 4 HP and −8.6 BE)	Thr24, Thr25, Thr26, Leu27, His41, Cys44, Thr45, Ser46, Met49, Leu50, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, Arg188, Gln189, Thr190, Ala191, Gln192	[57,84]
Alkaloid	10-Hydroxyusambarensine ( 10 IR and −10.1 BE), cryptoquindoline (3 IR and −9.7 BE); 6-Oxoisoiguesterin (1 HB, 4 IR and −9.1 BE), N-[(5-methylisoxazole - 3-yl) carbonyl] alanyl-l-valyl-n1- ((1r,2z)-4-(benzyloxy) – 4 – oxo -1- [(3r)-2-oxopyrrolidin-3-yl] methyl] but-2-enyl)-l-leucinamide (3 HB, 3 HPI, −7.4 BE), 22-hydroxyhopan-3-one (1 HB, 4 IR and −8.6 BE), Chelidimerine (2 HB, 6 HP and −10.2 BE), Somniferine (3 HB, 3 HP and −8.3 BE), Adlumidine (5 HB, 2 HP and −8.2 BE), Withanone (4 HB, 3 HP and −8.2 BE), Fumariline (3 HB, 5HP and −7.8 BE), Sanguinarine (5 HB, 3 HP and −7.7 BE), Norsanguinarine (3 HB, 5 HP and −7.5 BE)	His41, Met49, Tyr54, Lys137, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, Cys148, Met49, His163, Met165, Glu166, Leu167, Pro168, Asp187, Gln189, Gln192, Thr199, Tyr239, Tyr273, Leu275 Leu286, Leu287	[31,57]
Tannins Phenylpropanoids Aromatic alcohol	Pedunculagin (5 HB, 9 NBI and −8.9 BE), punigluconin (6 HB, 12 NBI and −8.5 BE), taraxerol (11 NBI and −7.2 BE), withametelin (8 NBI and −7.9 BE), tinosporide (2 HB, 12 NBI and −8.5 BE), chebulagic acid (6 HB, 3 NBI and −6.5 BE), chebulinic acid (9 HB, 9 NBI and −8.6 BE), gallotannins (5 HB, 10 NBI and −8.3 BE), cinnamtannin-B1 (3 HB, 4 HP and −8.4 BE), barlerinoside (7 HB, 10 NBI and −7.5 BE) Hydroxycinnamic acid (3 HB, 2A, 1 PA, and −7.5 BE) Phenethyl alcohol (6 HB, 2 PA, −7.3 BE)	Thr24, Thr25, Thr26, His41, Cys44, Thr45, Ser46, Tyr54, Cys145, His163, Thr25, Met49, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His164, Met165, Glu166, His172, Ala285, Asp187, Arg188, Gln189, Asp197, Thr199, Tyr239, Met276, Leu287, Leu286 His41, His164, Gln192, Thr190, Pro168, Met165, Arg188, Arg187, Val186, Thr190, Gln192, Met49, Met165, Pro168	[[41], [56], [66]] [51] [51]
Standards	N3 inhibitor (native cocrystal ligand) (8 HB, 6 HPI and −7.9 BE/28 IR and −9.47 BE/23 IR and −8.12 BE), nelfinavir (9 IR and −12.20 BE); prulifloxacin (10 IR and −11.32 BE) and colistin (18 IR and −13.73 BE), x77 (4 HB, 2 PS, 1 Pal, 1 Pam, 1 PP and −8.4 BE), ribavirin (5 IR and −5.43 BE), lopinavir (3 HB, 3 HP and −9.41 BE), ritonavir (2 HB, 3 IR and −6.8 BE), l X77 (4 HB, 2 PS, 1 PA1, 1 Pam, 1 PP and −8.4 BE)	Thr24, Thr25, Thr26, Leu27, His41, Cys44, Thr45, Ser46, Glua47, Met49, Leu50, Pro52, Tyr54, Val104, Gln110, Ile106, Asp153, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, Ser158, His163, His164, Met165, Glu166, Leu167, Pro168, Gly170, Hie172, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192, Val202, Ile249, Pro293, Phe294 Val297.	[[20], [27], [31], [67], [73], [84], [109]]
RNA dependent RNA polymerase/nsp12 (viral replicase)
Class	Small molecule inhibitors	Interacting residues with different classes of phytocompounds	References
Flavonoid	Theaflavin (8 HB, 2 PA and −9.1 BE), quercetin-3-O- (rutin) (9 HB, 1 Psi and −8.5 BE), quercetin-7-O-glucuronide (6 HB, 1 PA and −8.2 BE), quercetin-3′-O-glucuronide (5 HB; 1 PAm; −8.2 BE), quercetin-3-O-glucuronide (6 HB; 2 PA; 1 Pal; −8.0 BE), quercetin-7-O-sulfate (6 HB, 1 PC, 1 Pal, and −8.0 BE), quercetin-3-O-sulfate (2 HB, 2 PA and −7.1 BE), quercetin-3′-O-sulfate (6 HB, 1 PC, 1 Pal and −8.1 BE), quercetin (3 HB, 2 Psi and −7.4 BE), kaempferol-3-O-rutinose (4 HB, 2 PA and −9.2 BE), kaempferol -4′-O-glucuronide (6 HB, 1 PC and −8.3 BE), kaempferol-3-O-glucuronide (6 HB, 2 PA, 2 Pal and −7.9 BE), kaempferol-7-O-glucuronide (8 HB, 1 PC and −7.9 BE), kaempferol-7-O-sulfate (4 HB, 1 PC, 2 PA, 2 Pal and −7.3 BE), kaempferol-4′-O-sulfate (1 HB, 2 PA and −6.7 BE), kaempferol-3-O-sulfate (1 HB, 2 PA and −6.7 BE), kaempferol (2 HB, 2 Psi and −7.2 BE)	Asp452, Lys545, Arg553, Ala554, Arg555, Thr556, Met615, Trp617, Asp618, Tyr619, Pro620, Lys621, Cys622, Asp623, Arg624, Thr687, Asn691, Ser759, Asp760, Asp761, Ser778, Ile779, Glu796, Lys798, Cys799, Trp800, Thr801, Glu811, Cys813, Ser814	[20]
Terpenoids	Glycyrrhizic acid (7 HB, 1 CHB, 1 pi-alkyl, 16 VDW and −9.9 BE), limonin (2 HB, 2 pi-alkyl, 1 pi-pi T shaped, 10 VDW and −8.2 BE), 7-Deacetyl-7-benzoylgedunin (1 HB, 1 Alkyl/pi-alkyl, 2 CHB, 1 pi-anion, 3 pi-cation, 6 VDW and −8.2 BE), limonin glucoside (3 HB, 1 CHB, 4 Alkyl/Pi-Alkyl, 9 VDW and −8.2 BE), 7- -deacetylgedunin (1 HB, 2 CHB, 1 Pi-Alkyl, 1 Pi-sigma, 1 Pi-anion, 5 VDW and −8.1 BE), obacunone (2 HB, 1 Alkyl, 1 Pi-Anion, 8 VDW and −7.8 BE)	His439, Asp452, Tyr456, Met542, Lys545, Ala547, Ile548, Ser 549, Ala550, Lys551, Arg553, Ala554, Arg555, Thr556, Val557, Ala558, Gly616, Trp617, Asp618, Tyr619, Pro620, Cys622, Asp623, Arg624, Ser682, Asp760, Asp761, Ala762, Val763, Ala797, Lys798, Trp800, His810, Glu 811, Phe812, Ser814, Arg836	[87]
Standards	Remdesivir (3 IR and −6.3 BE), favipiravir (3 IR and −3.6 BE)	Lys551, Arg553, Arg555, Asp623, Ser682	[41]
Helicase/nsp13 (viral protein)
Class	Small molecule inhibitors	Interacting residues with different classes of phytocompounds	References
Flavonoids	Tomentodiplacone B (9 IR and −8.4 BE), osajin (4 IR and −8.2 BE), sesquiterpene glycoside (9 IR and −8.2 BE), rhamnetin (9 IR and −8.1 BE), silydianin (6 IR and −8.1 BE)	Val6, Asn9, Arg21, Arg22, Pro23, Phe24, Glu128, Arg129, Leu132, Phe133, Glu136, Arg178, Asn179, Pro234, Pro238, Ser310, Pro406, Ala407, Pro408, Asp534, Arg560	[46]
Standards	Nelfinavir (6 IR and −6.2 BE), remdesivir (8 IR and −6.8 BE), prulifloxacin (7 IR and −8.1 BE)	Val6, Arg21, Arg129, Leu132, Glu136, Lys139, Glu142, Asn177, Asn179, Tyr180, Pro234, Pro238, Cys309, Met378, Asp383, Pro406, Ala407, Pro408, Arg409, Thr410, Leu412, Leu417, Arg560	[46]
Endoribonuclease/nsp15 (viral protein)
Class	Small molecule inhibitors	Interacting residues with different classes of phytocompounds	References
Flavonoid	Naringin (5 IR and −7.8 BE), taxifolin (6 IR and −7.2 BE), luteolin (5 IR and −7.2 BE), apigenin (4 IR and −7.2 BE), myricetin (4 IR and −7.0 BE), wogonin (3 IR and −6.9 BE), epigallocatechin (3 IR and −6.8 BE), chlorogenic acid (6 IR and −6.8 BE), afromosin (4 IR and −6.7 BE), rutin (5 IR and −7.8 BE), silymarin (IR and −8.0 BE).	His235, ASP240, Gln245, Gly248, His250, Lys290, Val292, Ser294, Val339, Glu 340, Thr341, Tyr343, Pro344, Leu346	[106]
Beta-diketone	Demethoxycurcumin (5 IR and −7.51 BE), quercetin (4 IR and −6.49 BE), bisdemethoxycurcumin (1 IR and −6.56 BE), curcumin (1 IR and −6.48 BE), myricetin (4 IR and −6.52 BE), bergapten (4 IR and −5.92 BE), scutellarin (4 IR and −6.97 BE), isoflavone (2 IR and −5.47 BE)	His235, Glu340, Thr341, His250, Lys290; Ser294, Gly248	[73]
Terpenoid	Saikosaponin-V (8 HB, 9 HP and −8.35 BE), saikosaponin-U (8 HB, 8 HP and −7.27 BE), saikosaponin-C (6 HB, 9 HP and −6.98 BE), saikosaponin-K (5 HB, 10 HP and −6.79 BE), saikosaponin-1b (4 HB, 8 HP and −6.36 BE), alpha-amyrin (1 IR and −8.1 BE), pomolic acid (2 IR and −7.9 BE), carnosol (2 IR and −7.8 BE), arjunolic acid (1 IR and −7.6), asiatic acid (5 IR and −7.4 BE), betulinic acid (1 IR and −7.3 BE), platanic acid (5 IR and −7.3 BE), alphitolic acid (1 IR and −7.2), Asiatic acid (5 IR and −7.4), ursonic acid (5 IR and −8.4 BE).	Gly230, Ala232, Glu234, Hip235, Asp240, Gly245, Leu246, Gly247, Gly248, His250, Asn278, Lys290, Cys291, Val292, Cys293, Met331, Ala232, Trp333, Val339, Glu340, Thr341, Tyr343, Pro344, Leu346	[[75], [106]]
Coumarin	Beta sitosterol (1 IR and −8.1 BE), gliotoxin (3 IR and −6.7 BE), psoralen (5 IR and −6.7 BE), carinatine (4 IR and −6.6 BE), rhinacanthin (6 IR and −6.5 BE), caffeic acid (4 IR and −6.3 BE), coriandrin (3 IR and −6.2 BE), scopoletin (5 IR and −6.1 BE), cordycepin (4 IR and −5.6 BE), ricinoleic acid (3 IR and −5.0 BE), alpha asarone (1 IR and −4.9 BE), valproic acid (4 IR and −4.6 BE)	His235, Gly248, His250, Lys290, Val292, Cys293, Ser294, Thr341, Tyr343.	[106]
Organosulfur	allicin (3 IR and −3.8 BE)	His235, Thr341, His250	[106]
Alkaloid	Taspine (4 IR and −7.3 BE), ajmalicine (5 IR and −8.1 BE), reserpine (4 IR and −7.4)	His235, Thr341, Gly248, His250, Lys290, Glu340	[106]
Steroids	Asparoside-C (5 HB and −7.16 BE), asparoside-F (7 HB and −6.6 BE), asparoside-D (6 HB and −6.4 BE), rutin (5 HB), racemoside-A (4 HB and −5.99)	Gly230, Ala232, Glu234, Hip235, Val339, Asp240, His243, Gln245, His250, Asn278, Val292, Glu340, Thr341, Leu346	[16]
Standards	Hydroxychloroquine (4 IR and −5.8 BE), Nelfinavir (4 IR and −7.3 BE), ribavirin (9 IR and −5.84)	Thr26, His235, His250, Gly248, Lys290, Val-292, Ser294, Thr341, Tyr 343, Pro344,	[[73], [106]]
2′-O- methyl transferase/nsp16 (viral protein)
Class	Small molecule inhibitors	Interacting residues with different classes of phytocompounds	References
Flavonoids, Alkaloids, others	Eryvarin-M (9 IR and −8.6 BE), silydianin (9 IR and −8.5), osajin (6 IR and −8.2 BE), raddeanine (8 IR and −8.2 BE)	Asp6873, Asn6899, Asp6897, Amet6929, Leu6898, Asn6841, Lys6844, Cys6913, Lys6968, Phe6947, Lys6944, Asn6899, Asp6928, Cys6913, Gly6911, Leu6898, Met6929, Asp6897, Asp6928, Met6929, Cys6913, Leu6898, Gly6869, Cys6898, Asp6928, Asp6897, Asp6912, Cys6913, Leu6898, Asp6897, Gly6871, Asn6811, Met6929, Phe6947.	[46]
Standards	Nelfinavir (9 IR and −8.2 BE), remdesivir (9 IR and −7.0 BE), prulifloxacin (12 IR and −7.6 BE)	Leu6898, Tyr6930, Gly6871, Pro6932, Lys6968, Lys6844, Gly6911, Met6929, GLy6969, Pro6932, Lys6968, Lys6844, Leu6898, Lys6996, Glu7001, Lys6844, Lys6844, Lys6968, Asp6928, Met6929, Cys6913, Asp6897, Asn6841, Gly6871, Leu6898, Phe6947, Tyr6930, Asp6897, Asn6899, Pro6932, Asp6931	[46]

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Note: BE - binding energy, HB - hydrogen bond, HP/HPI - hydrophobic interactions, NBI = non-bonding interactions, IR-interacting residues, EI- electrostatic interactions, CHB –carbon-hydrogen bond, VDW – van der Waals interactions. PS: π-sulfur; Pal: π-alkyl; PP: π-π; PA: π-anion; PC: π-cation; Psi: π-sigma; Pam: π-amide; Pi-H = π-hydrogen bond, PA- π-alkyl; A-alkyl.

4.2. Angiotensin-Converting Enzyme 2 (ACE2)

ACE2 is a single-pass type-1 transmembrane protein of 805 amino acids with an extracellular N-terminal peptidase domain and an intracellular C-terminus collectrin-like domain (CLD) [23]. The N- terminus has a zinc metallopeptidase binding motif (374–378 amino acids, HEMGH) essential for the interaction with SARS-CoV-2 S-protein ( Figure - 6 ). Histochemical and single-cell RNA sequencing techniques revealed that ACE2 is primarily expressed in type-II lung alveolar epithelial cells [33,95].

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Fig. 6

Molecular organization of host ACE-2 monomer showing the interaction sites of different classes of phytocompounds (quinones, alkaloids, flavonoids, tannins, terpenoids, and organosulphur compounds) on the HEMGH/SARS CoV-2 spike protein binding domain and the collectrin domain (adapted from Bian and Li, 2021[118]).

A recent study, using bioinformatics, cheminformatics, and molecular docking, has demonstrated that tea flavonoids (epigallocatechin gallate, EGCG, and theaflavin gallate) have higher atomic contact energy value, dissociation constant (Ki)-value, surface area, ligand efficiency, and higher number of amino acid interactions with spike protein than synthetic hydroxychloroquine [53]). Another study showed that daturaolone, gallotannins, taraxerol, tinosporide, withanolide-A, deoxytubulosine, withametelin form strong hydrogen and non-bonding interactions with the amino acids of spike protein (between Arg 403 to Tyr 505) and have drug-likeliness properties based on Lipinski's rule of five. Moreover, these bioactive compounds have lower toxic effects and better gastrointestinal absorption than standards [56]. A simulation study using the crystal structure of SARS-CoV-2 S protein demonstrated that saikosaponin-U and saikosaponin-V, oleanane derivatives found in Chinese medicinal plants, can also interact with the spike glycoprotein via their octadecahydropicene and oxane rings [75]. Using molecular docking and conceptual density functional theory approaches, Kulkarni et al. showed that components of essential oils (monoterpenes, terpenoid phenols and phenyl propanoids) have the potential to interact with the RBD [47]. The phytocompounds punicalagin and punicalin (from Pomegranate), tenufolin, cinnamtannin-B1, pavetannin-C1, 6-glucopyranosyl procyanidin B1, procyanidin-B7, proanthocyanidin-A2 and Kaempferol-3-alpha-l-arabinoside-7-rhamnoside (from Cinnamon), frieldlin, and stigmasterol (from Clerodendrum spp) were also found to be effective candidates exhibiting important interactions with the targeted S protein [41,66,79], suggesting that they could serve as possible candidates for further in-vitro and in-vivo evaluations. Additionally, a molecular dynamics simulation study of the complex of RBD of S-protein with taraxerol for a time scale of 40 ns revealed its potent anti-SARS-CoV-2 activity [41]. Tellimagrandin-II and O-demethyl-deoxy curcumin isolated from plants used in Indian traditional medicine demonstrated stable intramolecular interactions with Asn343, which could be an important hit to affect host-immune evasion by inhibiting S-protein glycosylation [85].

The complex between viral S protein and human ACE2 has also been explored to identify antiviral phytochemicals. Using molecular dynamics, hesperidin, a major flavonoid present in citrus fruits, has been demonstrated to interact with this complex noncompetitively at a site different from that of S-protein. Further, the antiviral activity of hesperidin was validated by a quantitative structure-activity relationship study [12]. Another study, using virtual screening followed by protein-ligand interaction approach, showed that phytochemicals like glycyrrhizinic acid, maslinic acid, ursolic acid, corosolic acid, 2-hydroxyseneganolide, gedunin, and oleanane can bind firmly with the active site and other important amino residues of S protein and ACE2 through multiple noncovalent interactions [87]. Of particular interest, His-34 is an important amino acid of ACE2 receptor as it lies on the surface and exhibits crucial interactions with the S protein. One of the molecular dynamic studies revealed that the andrographolide and pterostilbene could negatively affect SARS-CoV-2 by interacting with the His-34 [10]. Rilapladib, a quinoline, can interrupt the spike-ACE2 complex [11]. Natural compounds such as isothymol, thymol, p-cymene, limonene, and gamma-terpinene (from Ammoides verticillata), and 17- organosulfur compounds (from garlic) were also found to be potential inhibitors of ACE2 receptor [1,82]. Further, xanthones, proanthocyanidins, secoiridoids, naringenin, hesperetin, baicalin and neohesperidin, scutellarin, nicotinamin, and glycyrinodin could exhibit ACE2 inhibition activity [58]. Hesperidin can modulate the binding energy of ACE2-spike protein complex and affects the stability of viral-host interaction [12]. At the binding contact of the spike-ACE2 complex, the di-hydroflavone moiety of hesperidin has been predicted to be parallel to the β-6 sheet of RBD [92]. Apart from this, punicalin and punicalagin from pomegranate peel are predicted to interact with ACE2 and block entry of SARS-CoV-2 into host cells [79]. Several bioactive compounds shown in research article by Mondal et al can interact with hot-spot binding residues (Lys31 and Lys353) of the ACE2 receptor through hydrogen bond or non-bonded interactions [56]. Besides these, geranium and lemon essential oils downregulate the expression of ACE2 in human colon adenocarcinoma cells as observed by western blot experiments [48]. More details of in-silico studies, including types of interactions, binding energy values, as well as identity and position of interacting amino acids with different phytocompounds are presented in Table-1.

4.3. Transmembrane Serine Protease-2

Human TMPRSS2 is a 492 amino acid type-II transmembrane protein that belongs to the serine protease family. The N-terminal half consists of a predicted transmembrane domain (84–106 amino acids), a low-density lipoprotein receptor class A domain (LDLRA, 113–148 amino acids), and a scavenger receptor cysteine-rich domain (SRCR, 149–242 amino acids), whereas the C-terminus half contains a serine protease domain (255–492 amino acids) [63] ( Figure-7). For priming of the viral spike protein, TMPRSS2 cleaves off the spike protein at two sites, Arg-685/Ser-686 and Arg-815/Ser-816. The catalytic site of TMPRSS2 consists of amino acid residues Ser-441, His-296, and Asp-345, whereas the substrate-binding sites include Asp-435, Ser-460, and Gly-462 [34]. Molecular docking studies showed that the bioactive constituents of different plants enlisted under the TMPRSS2 section in Table-1 and presented in Figure-7 display significant interactions with the amino acid residues of the serine protease domain (255–492), particularly with the amino acids of catalytic and substrate binding sites.

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Fig. 7

Molecular structure of transmembrane protease serine-2 (TMPRSS2) and the interaction sites of tannins, steroidal lactone, and caffeate ester in its domains. H-296, D-345 and S-441 are the catalytic residues present in the serine protease domain (adapted from Paoloni-Giacobino et al, 1997 [63] and Mahmoud and Jarrar, 2021[119])

The phytocompounds withaferin-A, withanolide-N, punicalin, punicalagin, ellagic acid and gallic acid could interact well with the important amino acid residues of TMPRSS2 [49,79]. Withanolide-N not only showed stronger interactions compared to withaferin-A, but it could also downregulate the expression of TMPRSS2 mRNA in human breast cancer cell line. This observation led authors to predict its dual role in inhibiting SARS-CoV-2 entry. The disruption of substrate binding was most likely due to interactions of withanolide-N with the Ser-441 [49].

5.1. Papain-like protease (PLpro)/nsp3

Papain-like protease (PLpro)/nsp3 is a multidomain transmembrane protein with an active site containing catalytic triad residues (Cys-111, His-272 and Asp-286) in between thumb and palm protein domains ( Figure-8 ). This protein is autocleaved from nsp3 protein via its intrinsic proteolytic activity. PLpro can also perform deISGylation of host proteins which could lead to inhibition of host innate immune response [18,40]. Due to its key role in viral replication and disease pathogenesis, it represents a promising drug target [52]. The docking score and the prediction of the molecular interactions showed that phytochemicals oleanolic acid, 3β-acetoxyolean-12-en-27-oic, and isovitexin could efficiently interact with the PLpro mainly by hydrogen bond [55]. Another study showed that catechins from green tea can interact to the S1 ubiquitin-binding site of PLpro which might lead to inhibition of its protease enzymatic function as well as abrogation of SARS-CoV-2 inhibitory role on interferon-stimulated gene system [18]( Table 1 ).

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Fig. 8

Location of amino acid interaction site (89–264) of tannins and flavonoids on SARS-CoV-2 nsp3 papain-like protease monomer(adapted from Joshi et al., 2020 [40]).

5.2. 3-chymotrypsin-like protease (3-CL pro)/nsp5

The 3CLpro, also called as viral main protease (or nsp5), consists of N-terminal finger domain (1–9 amino acids), domain-1 (10–99 amino acids), domain-2 (100–182 amino acids) and the C-terminal domain-3 (amino acid residues 198–303) [40,94]. The catalytic dyad consists of His-41 and Cys-145 (Fig. 9 ). The dimerization of 3-CLpro is required for its proteolytic activity.

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Fig. 9

The interaction sites of several classes of phytocompounds on different domains of SARS-CoV-2 3-chymotrypsin like protease (3CLpro) including the catalytic dyad residues (His-41 and Cys-145; shown in purple). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.) (3CLpro domain organization is adapted from Joshi et al., 2020 [40])

In-silico screening followed by molecular docking analyses suggested that the phytochemicals bisdemethoxycurcumin, scutellarin, desmethoxycurcumin, quercetin, myricetin, luteolin and mundulinol could potentially inhibit 3-CL pro as these compounds exhibit low binding energy [25,73]. Another study recommended certain compounds such as catechin, naringenin, kaempferol, glucosides, quercetin, and epicatechin-gallate as potential inhibitors of 3CLpro [43]. The phytocompounds like melitric acid-A, salvianolic acid-A, withanoside-V, and a few bioactive compounds from Calendula officinalis showed higher binding affinities with 3-CLpro than the N3 and lopinavir (standards). Also, they could have important interactions with the amino acid residues of the catalytic dyad [20,21,24,56,84]. In another study, a database of medicinal plants consisting of more than 30,000 potential anti-viral phytochemicals was screened, and the top hits that could inhibit SARS-CoV-2 3CLpro function and viral RNA replication were selected. These hits include myricitrin, 5,7,3′,4′-tetrahydroxy2’-(3,3- dimethylallyl) isoflavone, methyl rosmarinate, (2S)-eriodictyol 7-O-(6″-O-galloyl)-beta-d-glucopyranoside, calceolarioside B, 3,5,7,3′,4′,5′-hexahydroxy flavanone-3-O-beta-d-glucopyranoside, myricetin 3-O-beta-d-glucopyranoside, licoleafol, amaranthine, colistin, nelfinavir, and prulifloxacin [67]. Terpenoids (6-Oxoisoiguesterin and 22-hydroxyhopan-3-one) and some anthocyanin derivatives could stably interact with catalytic dyad and other crucial residues via hydrogen and hydrophobic interactions [27,31].Epigallocatechin, gallocatechin, and epicatechin from green tea also showed the potential to restrict the activity of 3-CL pro (Ghosh et al., 2020[101]). Similarly, several phytocompounds bind firmly at the catalytic dyad (Cys-145 and His-41) and other crucial amino acid residues (Phe-140, Leu-141, Asn-142, Gly-143, Ser-144, Glu-166, His-163, His-164, Met-165, Leu-167, Pro-168, His-172, Asp-187, Arg-188) of 3-CL pro via making hydrogen bonds, hydrophobic bonds and other interactions (like Pi-alkyl and Pi-Pi T-shaped, van der Waals etc). Phytocompounds extracted from Avincennia officinalis and Iranian medicinal plants have also been proposed as inhibitors of 3-CLpro [51,57]. Tanshinones, a class of natural phytocompounds have been found to inhibit 3-CLpro activity of SARS-CoV in-vitro enzymatic assay studies (Park et al., 2012[115]). Likewise, as listed in Table-1 and shown in Figure-9, several phytocompounds have ability to block 3-CLpro preferentially by interacting with its domain-1 and domain-2.

5.3. RNA dependent RNA polymerase/nsp12

With the help of accessory subunits nsp7 and nsp8, the catalytic subunit nsp12 of RdRp plays a crucial role in the transcription cycle of SARS-CoV-2 [88]. Its structure is highly similar to SARS-CoV. The nucleotide triphosphate (NTP) entry channel comprises positively charged amino acid residues Lys-545, Arg-553, and Arg-555. The right hand-like structure of the RdRp domain is further divided into a finger-domain (398–581 and 628–687 amino acids), a palm-domain (582–627 amino acids and 688–815 amino acids), and a thumb domain (816–919 amino acids). Two Zn ions are also required to stabilize three-dimensional structure of the RdRp [3,45] ( Figure-10 ). Tyr-618, Asn-691, Met-755, Ile-756, Leu-757, Ser-759, Asp-760, Asp-761, Val-763, Phe-812, Cys-813 and Ser-814 are some of the amino acids residues that are crucial in interacting with the nsp7/8 complex. In addition, Asp-761 and Asp-762 are active site residues [3].

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Fig. 10

Molecular structure of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and the interaction sites of flavonoids and and terpenoids on its different domains(protein domain organization is adapted from Zhang et al., 2020[120])

Several compounds have been analyzed in-silico against these important sites to investigate their possible antiviral viral targets for the SARS-CoV-2. Green tea polyphenols EGCG and theaflavin gallates including theaflavin-3-O-gallate (TF2a), theaflavin-3′-digallate (TF2b) and theaflavin 3,3′-digallate (TF3) have the ability to form stable bound conformations with the RdRp protein and could interact with the catalytic site indicating their potential to serve as inhibitors [81].

Several alkaloids from Argemone mexicana and Clerodendrum spp. could be a potential inhibitory candidates against the SARS-CoV-2 RdRp protein [41,62] ( Table-1 ).

5.4. RNA helicase (nsp13)

It is a multi-functional magnesium ion-dependent protein that belongs to the helicase superfamily-1 (SF-1) and has 5′ to 3’ based RNA and DNA unwinding activities [121]. Compounds such as tomentodiplacone-B, sesquiterpene glycoside, rhamnetin, osajin, and silydianin have been shown to exhibit better docking results than those of remdesivir, nelfinavir, and prulifloxacin (standards) [46] ( Table-1 ).

5.5. Endoribonuclease/nsp15

Endoribonuclease/nsp15 cleaves RNA genome into multiple subgenomic RNAs (sgRNAs). Based on the docking score, phytocompounds asparoside-C, asparoside-D, asparoside-F, racemoside-A, and rutin (from Asparagus racemosus) were found to be effective against nsp15 endoribonuclease [16]. The 100 nano-second based molecular dynamic simulation study and molecular mechanics-generalized born solvent accessibility calculations demonstrated that some phytoconstituents such as withanolide-N, ashwagandanolide, withanoside-X, and dihydrowithaferin-A from Withania somnifera could potentially suppress the nsp15 endoribonuclease activity of SARS-CoV-2 [17]. Another study revealed the binding capacity of silymarin, sarsasapogenin, ursonic acid, rosmarinic acid, curcumin, ajmalicine, novobiocin, aranotin, gingerol, and alpha terpinyl acetate to nsp15 protein [106].

6.1. Envelope protein

E protein (8–12 kDa) is involved in host cell binding, penetration, virion assembly, and budding. It is a transmembrane ion channel protein with an N-terminal ectodomain and an endodomain at C-terminus. Structural insights revealed that compounds from Withania somnifera could block the ion channel activity of E protein by binding to the pore region [5].

We thank Mayra Segura for proofreading and language editing.