Table 1.
Estimated docking scores, 2D chemical structures, and binding features for lopinavir and the top 27 potent marine natural products (MNPs) towards SARS-CoV-2 main protease (Mpro).
| MNP Name | Plant Source | 2D Chemical Structure | Docking Score (kcal/mol) |
Binding Features a |
|---|---|---|---|---|
| Lopinavir | --- b |
|
−9.8 | HIS164 (2.62 Å), GLY143 (2.01 Å), LEU141 (1.96 Å), SER144 (3.09 Å) |
| Depresosterol (190) |
L. depressum |
|
−12.3 | THR26 (2.15, 2.66 Å), HIS41 (2.17 Å), CYS145 (2.70 Å), ASN142 (1.96, 2.04, 2.24 Å), GLU166 (1.99, 2.55 Å) |
| 3β-25-Dihydroxy-4-methyl-5α,8α-epidioxy-2-ketoergost-9-ene (178) |
Sinularia candidula |
|
−12.2 | LEU141 (2.08 Å), SER144 (1.97, 2.28, 2.66 Å), HIS163 (2.08 Å), CYS145 (2.49 Å), GLN192 (2.26 Å), THR190 (1.80 Å) |
| Erylosides B (226) |
E. lendenfeldi |
|
−12.1 | HIS41 (1.96 Å), TYR54 (3.05 Å), AS142 (1.75, 2.96 Å), GLY143 (2.82 Å), CYS145 (2.04 Å), HIS163 (1.93 Å), GLU166 (2.37 Å), GLN189 (1.91 Å) |
| Sipholenol H (157) |
S. siphonella |
|
−12.0 | GLY143 (1.74 Å), CYS145 (2.88 Å), HIS163 (2.56 Å), HIS164 (2.85 Å), MET165 (2.74 Å), THR190 (1.74, 2.17 Å), GLN192 (2.11 Å) |
| Dahabinone A (162) |
S. siphonella |
|
−11.9 | CYS145 (2.34 Å), HIS41 (2.43 Å), GLU166 (2.01, 2.23, 2.38 Å), GLY143 (2.12 Å), GLN189 (2.03 Å) |
| Sipholenol I (174) |
S. siphonella |
|
−11.8 | GLY143 (2.04 Å), CYS145 (2.89 Å), HIS163 (2.89 Å), HIS164 (2.01 Å), GLU166 (1.62, 2.03, 2.52 Å) |
| Lobophytosterol (188) |
L. depressum |
|
−11.5 | TYR54 (2.24, 2.55 Å), ASN142 (1.91, 2.75 Å), GLU166 (1.86, 2.66 Å), ASP187 (2.94 Å) |
| (22R,24E,28E)-5β,6β-Epoxy-22,28-oxido-24-methyl-5αcholestan-3β,25,28-triol (191) |
L. depressum |
|
−11.4 | THR26 (2.69 Å), HIS41 (2.14 Å), CYS145 (2.45 Å), ARG188 (2.03 Å), THR190 (2.06, 2.55 Å), GLN192 (2.26 Å) |
| Tasnemoxide A (144) |
D. erythraeanus |
|
−11.4 | CYS44 (2.10 Å), TYR54 (2.54, 2.97 Å), GLU166 (1.91, 1.97 Å) |
| Siphonellinol C (172) |
S. siphonella |
|
−11.3 | GLY143 (1.95 Å), GLN189 (2.09 Å), THR190 (1.73, 2.41 Å), GLN192 (2.10 Å) |
| Siphonellinol-C-23-hydroperoxide (171) |
S. siphonella |
|
−11.2 | GLY143 (2.00 Å), GLN189 (1.97 Å), THR190 (2.03, 2.43 Å), GLN192 (2.46 Å) |
| Erylosides K (224) |
Erylus lendenfeldi |
|
−11.1 | GLU166 (3.03 Å), HIS163 (2.18 Å), HIS164 (2.26, 2.10 Å) |
| Sipholenol D (176) |
S. siphonella |
|
−11.0 | THR190 (2.08 Å), HIS163 (2.48 Å), GLU166 (2.98 Å), GLN189 (1.91 Å) |
| Sipholenone A (175) |
S. siphonella |
|
−11.0 | GLY143 (1.93 Å), HIS163 (2.41 Å), HIS164 (2.54 Å), GLU166 (2.36 Å) |
| Neviotine B (158) |
S. siphonella |
|
−10.9 | ASN142 (2.26 Å), GLU166 (1.95 Å), GLN189 (1.80 Å), THR190 (2.57 Å) |
| Eryloside A (197) |
Genus Erylus |
|
−10.7 | ASN142 (2.32 Å), GLU166 (1.95 Å), THR190 (1.87 Å) |
| Sipholenone D (155) |
S. siphonella |
|
−10.7 | GLN189 (1.77 Å), THR190 (1.83 Å), GLN192 (2.23 Å) |
| 24-Methylcholestane-5-en-3β,25-diol (187) |
S. polydactyla |
|
−10.6 | MET49 (2.16 Å), PHE140 (1.87 Å), GLN189 (2.97 Å) |
| SipholenolA-4-O-3′,4′-dichlorobenzoate (151) |
S. siphonella |
|
−10.5 | HIS163 (2.30 Å), GLN189 (1.78 Å) |
| Stigmasterol (220) |
D. coccinea |
|
−10.5 | MET49 (2.18 Å), GLN189 (2.97 Å) |
| Cholest-5-en-3β,7β-diol (206) |
A. dichotoma |
|
−10.3 | MET49 (2.17 Å), GLN189 (1.94 Å) |
| Campesterol (221) |
D. coccinea |
|
−10.3 | MET49 (2.17 Å), GLN189 (3.01 Å) |
| Cholesterol (184) |
Dendronephthya |
|
−10.3 | MET49 (2.10 Å), GLN189 (2.97 Å) |
| Clionasterol (219) |
Dragmacidon coccinea |
|
−10.3 | MET49 (2.16 Å), GLN189 (2.95 Å) |
| Brassicasterol (222) |
D. coccinea |
|
−10.1 | MET49 (2.17 Å) |
| 3β-Hexadecanoylcholest-5-en-7-one (202) |
A. dichotoma |
|
−10.0 | GLY143 (1.95 Å) |
| Sipholenone E (163) |
S. siphonella |
|
−9.9 | GLN189 (1.83 Å) |
a Only hydrogen bonds (in Å) were listed. b No plant source was noticed.