Table 2.
Molecular docking of Tricholoma giganteum AGDR1 and products obtained from organic synthesis (Table 1) with their docking energy and interacted amino acid residues
| No | Product name | Binding energy (KJ/mol) ‡ | Binding residues (distance#; interaction type*) |
|---|---|---|---|
| 1 | 1,4-naphthoquinone | − 7.0 ± 0.1 | Y126 (3.45; B), R131 (3.11; A), L140 (4.89; D), S192 (2.84; A), I373 (5.16; C) |
| 2a | 4-(2-Amino-1,4-naphthoquinone) benzoic acid | − 9.1 ± 0.2 | W117 (3.82; E), Y126 (4.80; F), R131 (3.15; E), R131 (5.21; G), L140 (4.80; D), L251 (2.53; A), L251 (4.88; D), P316 (4.79; D), H372 (2.66; A), I373 (3.70; H) |
| 2b | 4-(1,4-dihydro-1,4-dioxonaphthalen-2-ylamino)-3-chlorobenzoic acid | − 9.3 ± 0.1 | W117 (3.76; E), Y126 (4.76; A), R131 (3.32; G), Q133 (3.31; A), L140 (4.92; D), D141 (4.99; I), L251 (4.85; D), P316 (5.22; D), H372 (2.43; A), I373 (3.49; H) |
| 2c | 4-(1,4-dihydro-1,4-dioxonaphthalen-2-ylamino)-3-methylbenzoic acid | − 9.8 ± 0.1 | W117 (5.18; D), Y126 (2.77; A), Q133 (3.24; A), L140 (4.92; D), D141 (4.84; I), L251 (4.98; D), P316 (5.23; D), H372 (2.44; A), I373 (5.23; H) |
| 2e | 4-(1,4-dihydro-2-methyl-1,4-dioxonaphthalen-3-ylamino)-3-chlorobenzoic acid | − 9.5 ± 0.2 | W117 (3.98; E), Y126 (4.58; A), R131 (3.27; G), L140 (4.50; D), D141 (4.15; I), L251 (4.04; D), P316 (5.05; D), H372 (2.58; A), I373 (3.21; H) |
| 2f | 4-(1,4-dihydro-2-methyl-1,4-dioxonaphthalen-3-ylamino)-3-methylbenzoic acid | − 9.6 ± 0.2 | W117 (3.65; E), Y126 (4.36; A), R131 (3.25; G), L140 (4.59; D), D141 (4.31; I), L251 (4.57; D), P316 (5.57; D), H372 (2.67; A), I373 (3.79; H) |
| 2 h | 4-(2-bromo-1,4-dihydro-1,4-dioxonaphthalen-3-ylamino)-3-chlorobenzoic acid | − 9.1 ± 0.3 | W117 (3.38 E), Y126 (4.23; A), R131 (3.06; G), L140 (4.70; D), D141 (4.64; I), P316 (5.25; D), H372 (2.32; A), I373 (3.56; H) |
| 3 | 2,5-bis(phenyl-sulfonyl)cyclohexa-2,5-diene-1,4-dione | − 8.6 ± 0.1 | Y126 (3.60; B), L140 (4.80; D), S192 (2.99; A), P314 (4.34; D), P316 (4.74; D), Q345 (3.21; A), H372 (3.15; A) |
| 4 | trans-resveratrol dimer | − 9.4 ± 0.3 | T121 (2.66; A), P266 (4.88; D), F368 (3.75; C) |
#Distance is shown for each residue in parenthesis, and it is expressed in Å
*Type of interactions between ligand and enzyme: A: Conventional H-bond, B: π-donor H-bond; C: π-π T shaped, D: π-alkyl, E: attractive charge, F: C–H bond, G: π-anion, H: π-Sigma, I: Salt bridge
‡Molecular docking study of individual compounds is performed in triplicates and displayed values of binding energy is mean of triplicates with SD shown