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(A) Molecular docking of hydroxychloroquine (ball and stick), (B) chloroquine (ball and stick), and (C) nelfinavir (ball and stick) with active site of coronavirus disease 2019 main protease (PDB: 6LU7).

(A) Molecular docking of hydroxychloroquine (ball and stick), (B) chloroquine (ball and stick), and (C) nelfinavir (ball and stick) with active site of coronavirus disease 2019 main protease (PDB: 6LU7).

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Figure 1 (A) Molecular docking of hydroxychloroquine (ball and stick),...
Potential drugs of coronavirus disease 2019 main protease inhibitors
Medicinal plant-based saponins targeting COVID-19 M pro in silico
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  • Mar 2021
Background: Recently, the Chinese scientists Liu et al. demonstrated a crystallized form of severe acute respiratory syndrome coronavirus-2 main protease (Mpro), the best target of the drug, which was published in Nature in June 2020. Many components of herbs are determined as the potential inhibitors of coronavirus disease 2019 (COVID-19) Mpro suc...
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Context 1
... studies of hydroxychloroquine drug with 6LU7 show binding energy of −4.6 kcal/mol. Hydrogen and pi-alkyl hydrophobic binding is displayed with amino acids Gly-302 and Phe-305 ( Figure 1(1); Table 1, entry 1). Chloroquine forms hydrogen and hydrophobic interaction with amino acids Ser-139, Ala-116, and Lys-137 and shows binding energy of −5.6 kcal/mol ( Figure 1 (2); Table 1, entry 2). ...
Context 2
... and pi-alkyl hydrophobic binding is displayed with amino acids Gly-302 and Phe-305 ( Figure 1(1); Table 1, entry 1). Chloroquine forms hydrogen and hydrophobic interaction with amino acids Ser-139, Ala-116, and Lys-137 and shows binding energy of −5.6 kcal/mol ( Figure 1 (2); Table 1, entry 2). Nelfinavir forms pi-anion, hydrogen, and alkyl/pi-alkyl hydrophobic interaction with amino acids Glu-14, Gly-11, Lys-12, Lys-97, and Pro-99 and shows binding energy of −6.4 kcal/mol ( Figure 1 (3); Table 1, entry 3). ...
Context 3
... forms hydrogen and hydrophobic interaction with amino acids Ser-139, Ala-116, and Lys-137 and shows binding energy of −5.6 kcal/mol ( Figure 1 (2); Table 1, entry 2). Nelfinavir forms pi-anion, hydrogen, and alkyl/pi-alkyl hydrophobic interaction with amino acids Glu-14, Gly-11, Lys-12, Lys-97, and Pro-99 and shows binding energy of −6.4 kcal/mol ( Figure 1 (3); Table 1, entry 3). These three drugs are used as a positive control. ...
Context 4
... Interaction of structure with 4LU7 Docking affinity (kcal/mol) Amino acid residue Molecular docking analysis of 27 saponins with COVID-19 M pro exhibits binding energies in the range from −6.7 to −9.8 kcal/mol. Gypenoside LVII forms two hydrogen bonds with Val-125 and Val-125 and an alkyl/pi-alkyl hydrophobic bond with Lys-5, Trp-207, and Phe-291 ( Figure 3 (1); Table 3, entry 1). Smilscobinoside F is found in the rhizome of Smilax scobinicaulis plant which forms two hydrogen bonds with Trp-218 and Leu-220 and a hydrophobic bond with Leu-220 ( Figure 3 (2); Table 3, entry 2). ...
Context 5
... -binoxoside is a cycloartane-type saponin which exhibits binding energy of −8.8 kcal/mol ( Figure 3 (8); Table 3, entry 8). 3-O-α-L-Arabinopyranosyl-(1S,24R) -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 6
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 7
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 8
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 9
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 10
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 11
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 12
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 13
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 14
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 15
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 16
... studies of hydroxychloroquine drug with 6LU7 show binding energy of −4.6 kcal/mol. Hydrogen and pi-alkyl hydrophobic binding is displayed with amino acids Gly-302 and Phe-305 ( Figure 1(1); Table 1, entry 1). Chloroquine forms hydrogen and hydrophobic interaction with amino acids Ser-139, Ala-116, and Lys-137 and shows binding energy of −5.6 kcal/mol ( Figure 1 (2); Table 1, entry 2). ...
Context 17
... and pi-alkyl hydrophobic binding is displayed with amino acids Gly-302 and Phe-305 ( Figure 1(1); Table 1, entry 1). Chloroquine forms hydrogen and hydrophobic interaction with amino acids Ser-139, Ala-116, and Lys-137 and shows binding energy of −5.6 kcal/mol ( Figure 1 (2); Table 1, entry 2). Nelfinavir forms pi-anion, hydrogen, and alkyl/pi-alkyl hydrophobic interaction with amino acids Glu-14, Gly-11, Lys-12, Lys-97, and Pro-99 and shows binding energy of −6.4 kcal/mol ( Figure 1 (3); Table 1, entry 3). ...
Context 18
... forms hydrogen and hydrophobic interaction with amino acids Ser-139, Ala-116, and Lys-137 and shows binding energy of −5.6 kcal/mol ( Figure 1 (2); Table 1, entry 2). Nelfinavir forms pi-anion, hydrogen, and alkyl/pi-alkyl hydrophobic interaction with amino acids Glu-14, Gly-11, Lys-12, Lys-97, and Pro-99 and shows binding energy of −6.4 kcal/mol ( Figure 1 (3); Table 1, entry 3). These three drugs are used as a positive control. ...
Context 19
... Interaction of structure with 4LU7 Docking affinity (kcal/mol) Amino acid residue Molecular docking analysis of 27 saponins with COVID-19 M pro exhibits binding energies in the range from −6.7 to −9.8 kcal/mol. Gypenoside LVII forms two hydrogen bonds with Val-125 and Val-125 and an alkyl/pi-alkyl hydrophobic bond with Lys-5, Trp-207, and Phe-291 ( Figure 3 (1); Table 3, entry 1). Smilscobinoside F is found in the rhizome of Smilax scobinicaulis plant which forms two hydrogen bonds with Trp-218 and Leu-220 and a hydrophobic bond with Leu-220 ( Figure 3 (2); Table 3, entry 2). ...
Context 20
... -binoxoside is a cycloartane-type saponin which exhibits binding energy of −8.8 kcal/mol ( Figure 3 (8); Table 3, entry 8). 3-O-α-L-Arabinopyranosyl-(1S,24R) -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 21
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 22
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 23
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 24
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 25
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 26
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 27
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 28
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 29
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...
Context 30
... -1,24,25-trihydroxy-15-oxo-acta-(16R,23R)-16,23-mo noxoside exhibits binding energy of −8.8 kcal/mol ( Figure 3 (9); Table 3, entry 9). 9 (R), 19, 22 (S), 24 (R) Dicyclolanost-3β, 12α, 16β, 17α tetrol-25-one 3-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranoside is found in aerial parts of Mussaenda luteola plant which exhibits binding energy of −8.6 kcal/mol ( Figure 3 (10); Table 3, entry 10). TPG3 ( Figure 3 (11); Table 3, entry 11), cimiheraclein G ( Figure 3 (12); Table 3, entry 12), (20R)-16,21-O-di-(β-D-fucopyrano syl)-24-methyl-cholesta-5,24(28)-diene-3β,7α,16α,21-t etraol ( Figure 3 (13); Table 3, entry 13), calendustellatoside D (Figure 3 (14); Table 3, entry 14), 2α,3β,23-trihydroxylup-20(29)-en-28-oic acid 3-O-α-L -arabinopyranoside ( Figure 3 (15); Table 3, entry 15), yesanchinoside R3 ( Figure 3 (16); Table 3, entry 16), anemarsaponin B (Figure 3 (17); Table 3, entry 17), actein ( Figure 3 (18); Table 3, entry 18), glinusopposide M ( Figure 3 (19); Table 3, entry 19), schekwanglupaside B (Figure 3 (20); Table 3, entry 20), 3-O-β-D-glucopyranosyl 3α, 11α-dihydroxylup-20(2 -en-28-oic acid ( Figure 3 (21); Table 3, entry 21), t ( Table 3, entry 22), 3β,6β-dihydroxy-7β-((4-hydroxybenzoyl)oxy)-21αH-2 4-norhopa-4(23),22(29)-diene ( Figure 3 (23); Table 3, entry 23), 6β,11α-dihydroxy-7β-((4-hydroxybenzoyl)o xy)-3-oxo-24-norhopa-4(23),17(21)-diene ( Figure 3 (24); Table 3, entry 24), 3-oxo-olean-12-ene-28,30-dioic acid ( Figure 3 (25); Table 3, entry 25), β-amyrin ( Figure 3 (26); Table 3 ...

Citations

... 48 and PYMOL software (https://pymol.org/). 60 ...
Search for Novel Antagonist/S of HIF-1α from Selected Synthetic Analgesics/ Bioactive Flavonoids: An In-Silico Approach: Pharmaceutical Science-Drug Design and Development
Article
Full-text available
  • Sep 2023
Computer aided drug designing as well as drug repurposing implies the usage of molecular modelling techniques like analysis of the structures of receptor and ligand, molecular docking, pharmacokinetics and toxicity prediction, to explain the bioactivity of the synthetic molecules or plant secondary metabolites to design more efficient drug candidates or to repurpose an old drug in new diseases. Numerous studies have demonstrated that the low oxygen environment inside the cell is a key factor in developing breast cancer metastasis. To gain insight into the spread of breast cancer, hypoxia-inducible factor 1 (HIF-1), one of the master regulators of the hypoxic response, has been intensively explored. Our current research focuses on the insilico analysis and comparative study to evaluate the effects of different cancer drugs, analgesics, and plant-derived flavonoid compounds on HIF-1α regulation of breast cancer metastasis. According to the study, Quercetin shows the maximum binding affinity, i.e., -8.2 kcal/ mol. followed by Letrozole (-7.3 kcal/mol.), Naringenin (-7.11 kcal/mol), Tamoxifen (-7.07 kcal/mol), Phenacetin (-6.16 kcal/mol), and Aspirin (-5.7 kcal/mol). The study highlighted that Quercetin has the strongest binding affinity whereas Aspirin has the least binding affinity with HIF-1α protein. Hence the least toxic compound Quercetin can be a good candidate to control breast cancer metastasis by modulating the HIF-1 pathway.
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... To generate affinity potentials the autogrid has been applied. The visualization of the results was carried out by PyMOl and Biovia Discovery Studio [28,29]. ...
Virtual Screening through Molecular Docking Analysis to Identify Potential Natural Inhibitor(s) of Lyn Tyrosine Kinase- An In-silico Approach
Article
Full-text available
  • Nov 2021
Breast cancer on becoming one of the leading cancer types, emerged as an important barrier in increasing life expectancy of the overall population. In the current study, some compounds were screened based on literature survey for the identification of natural bioactive compounds as potential inhibitors of Lyn tyrosine kinase. Therefore, a multi-step molecular docking was carried out using AutoDock embedded in the MGL Tools. After initial screening, molecules having a higher docking score and binding free energy compared to Tamoxifen were considered for further assessment. Some already known synthetic lyn tyrosine kinase inhibitor have been used for better understanding of the comparative study. Based on in silico Lipinski filter analysis, toxicity prediction, pharmacokinetic analysis, four compounds were proposed to be promising inhibitors of Lyn tyrosine kinase. Furthermore, the binding interactions of all proposed inhibitors of Lyn showed strong ligand efficiency in terms of energy score obtained with the help of molecular modelling analyses. Hence, the proposed compounds out of which three are bioactive compounds might be taken forward as potential next-generation Lyn kinase inhibitors for managing Lyn associated breast cancer after experimental authentication.
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... Main protease (M pro ) of SARS-2 is the best target of several drugs. In current, many potential bioactive natural products as saponins, avonoids, steroids, terpenes, are used on COVID-19 M pro in silico [12][13][14]. In this study, we used diverse types of iradoides on this target using molecular docking. ...
Discovery of Potential Plant-derived Iradoides with COVID-19 Mpro in silico
Preprint
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  • May 2021
Iradoides are a small class of plant derived natural products, which used in traditional system of medicine such as Unani, Tibetan, Ayurveda, Siddha, and Chinese medicine. The several diverse types of iradoides have been isolated from many parts of the plant such as root, leaves, flowers, stem, rhizomes, bark, and seed. Here, we used bioactive iradoides to know the potency against COVID-19 M pro . The COVID-19 M pro is a potential target of the drug, which identified by Chinese scientist (published manuscript in Nature on June 2020). From several studies, we found that many natural products such as flavonoids, saponins, steroids, terpenoids, and synthesized compounds have been used on this target (COVID-19 M pro ). We screened a series of iradoides against COVID-19 M pro (PDB ID: 6LU7) by using many docking software as BIOVIA Discovery Studio 2017 R2, Chimera 1.13.1, Auto Dock Tools-1.5.6, AutoDock Vina to known best inhibitor against COVID-19 M pro . According to obtained results, 6′-O-trans-feruloylnegundoside, p-hydroxybenzoyl-6′-O-trans-caffeoylgardoside, 2′-O-p-hydroxybenzoyl gardoside, 6-deoxyharpagide, reptoside show binding energies -8.1, -8.3, -8.2, -7.0, and -7.1 Kcal/mol, respectively. From this study, we found that all iradoides show more potency on COVID-19 M pro when compared with Chloroquine and hydroxychloroquine. The Chloroquine and hydroxychloroquine used as standards for comparison. From the results of this study, we found that iradoides may be useful in the treatment of COVID-19 patients.
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ORIENTAL JOURNAL OF CHEMISTRY Search for New Inhibitors of Human Aromatase Enzyme (Cyp450) from Bioactive Compounds of Citrus species
Article
Full-text available
  • Sep 2023
Oestrogen synthesis pathway is one of the bottom line steps for breast cancer advancement; involving, aromatase enzyme (Cyp450), which transform androgens to oestrogens. Thus endocrine-based therapies comprising of human aromatase blockage is the most necessary way in order to decrease the oestrogen levels and thereafter prohibiting the chances of breast cancer commencement. In recent years, limelight on drug discovery from green sources has been growing for their less toxicity and cost effectiveness. Our present course of study aims at searching of new antagonist/s from a common dietary source "Citrus species". Molecular docking along with In-silico evaluation their pharmacokinetics (ADME) properties and toxicity were employed to fulfill the aim. Result shows that, all the five Citrus compounds have reasonable affinity towards cytochrome p450. However, Hesperidin shows highest affinity towards its target receptor protein i.e.-9.7 kcal/ mol, followed by Chalcone that shows the lowest affinity towards its target protein i.e.-7.4 kcal/ mol. Hence, bioactive components of Citrus species can be green alternatives for breast cancer therapy.
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Traditional soap plants used in hand hygiene, can play an important role in curbing infectious diseases including COVID-19. So why is there so little research?
Preprint
Full-text available
  • Jun 2023
The standard recommendations for reducing the risk of transmission of COVID-19 include the use of hand sanitisers, and regular handwashing. However, worldwide few have access to soap and water, let alone hand sanitiser. Kunwinjku relatives in western Arnhem Land, NT, Australia believed they had no protection except prayer. Yet soap plants are found on every inhabited continent, including Australia and were used widely by Aboriginal peoples. Soap plants contain saponins, phytochemicals that display a range of pharmacological properties. Given the plethora of research on the anti-viral, anti-bacterial and anti-fungal properties of plant-based saponins, and the number of people at risk from COVID-19 there should be much literature on their topical use. However, in 2020 I found none and even now little exists. Research institutions must begin “think outside the box”, to see the world through the eyes of others and act accordingly.
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