Table 3.
Natural compounds against α-glucosidase and α-amylase enzymes discovered via in silico approaches, listing the docking package and scoring function used in the studies.
| In Silico Modeling | ||||
|---|---|---|---|---|
| Natural Compound | Plant Family | Binding Energy (Kcal/mol) |
PDB ID | Hydrophobic & Hydrogen-Bond Interaction |
| Quercetin | Euphorbiaceae | −7.6 | 2ZJ3; Homo sapiens, AutoDock Vina [211], VMD Quantum Chemistry Visualization [228,244] | Ser420, Lys675, Gln421, Thr375, Ser422 |
| Quercitrin | −9.0 | |||
| Quercetin-3-O-galactoside | −9.1 | |||
| Cosmosiin | −9.9 | |||
| Kaempferol | −7.6 | |||
| 2-(4 methyl-3-cyclohexene-1-yl)-2-propanol | −5.4 | Val677, Ala674, Thr375 | ||
| Β-amyrine | −9.0 | |||
| Β-Sitosterol | −7.8 | |||
| Campesterol | −8.2 | |||
| Caryophyllene | −7.1 | |||
| Limonene | −4.8 | |||
| Phytol | −5.2 | |||
| Piperitenone | −5.4 | |||
| Safranal | −5.5 | |||
| Stigmasterol | −8.5 | |||
| Taraxerol | −8.9 | |||
| Euphorbol | −8.3 | |||
| 24 methylene cycloartenol | −7.9 | |||
| 1-O-Galloyl-beta-D-glucose | −8.0 | |||
| Corilagin | −8.9 | Ser420, Lys675, Gln421, Thr375, Ser422 | ||
| Baicalein | Bignoniaceae | −6.98 | 3TOP; Homo sapiens, Schrodinger Maestro [116] | Pro1327, Glu1284, Pro1405, Leu1401 |
| Catechin | −7.70 | His1584, Asp1279, Asp1526, Arg1510, Asp1157 | ||
| Luteolin | −7.52 | |||
| Quercetin | −7.19 | |||
| Quinoline | Rubiaceae | −8.6 | 3AJ7; Saccharomyces cerevisiae, MOE-docking 2010.11software [140] | Phe177, Asp214, His279, Phe157 |
| Benzothiazole | Ericaceae | −8.08 | No mentioned for PDB code, 3D structure: α-glucosidase of Saccharomyces cerevisiae, AutodockTools 1.5.6 package [161], PyMol 1.7.6 software (http://www.pymol.org/, accessed on 19 February 2020) | Phe157, Phe310, Phe311 |
| β-Sitosterol | Dryopteridaceae | −16.097 | The three-dimensional structure for α-glucosidase of Saccharomyces cerevisiae has not yet been solved, MOE-Dock (MOE 2010.11) software [165] | Asp215, Asp352, Arg442, Gln182 |
| β-Sitosterol3-O-β-D-glucopyranoside | −7.756 | Asn415 | ||
| 2, 3, 5, 7-trihydroxy-2-(p-tolyl) chorman-4-one | −22.480 | Arg315, Asp307, His280, Lys156, Ser240, Thr310, Tyr158 | ||
| Quercetin-3-0-β-D-glucopyranoside (3/→0-3///)-β-D-Quercetin-3-0-β-D-galactopyranoside | −12.931 | Arg442, Tyr158 | ||
| 5, 7, 4/-Trihydroxyflavon-3-glucopyranoid | −15.752 | Asp242, Lys156, Pro312, Tyr158 | ||
| 2,6-diethylpiiperidine-3,4,5-triol | Campanulaceae | −6.1790 | 3A47; Saccharomyces cerevisiae, MOE-Dock module (v.2011.10), Model Scoring of GB/VI test, The force field AMBER99 [143] | Lys155, Glu304, Arg312, Asn153 |
| 2-ethyl-6-methylpiperidine-3,4,5-triol | −8.8493 | |||
| 6-ethyl-2-(hydroxymethyl)piperidine-3,4-diol | −6.9539 | |||
| 1,2,4-tri-O-gal-loyl-β-D-glucopyranose | Geraniaceae | −8.7 | 3AHX; Clostridium cellulovorans, The SCM model, SiteMap (Schrodinger Release 2018-1: SiteMap, Schrodinger, LLC, New York, NY, 2018) [163] | Asp232, Ser235, Asn314, Glu426 |
| Kaempferol-3-O-α-rhamnopyranoside | −9.4 | Asp214, Asn241, Val277 | ||
| Kaempferol-3-O-α-arabinofuranoside | −9.2 | Asp68, Asp214, Thr215, Glu276, Asp408 | ||
| Quercetin-3-O-β-glucuronopyranoside | −9.8 | Asp68, Asp214, Arg312, Asp349, Gln350 | ||
| Quercetin-3-O-α-arabinofuranoside | −5.4 | Asp232, Asp429 | ||
| Kuwanon L | Moraceae | −8.4412 | 3A4A; Saccharomyces cerevisiae, Agilent Masshunter software Ver. B.04.00, The Molecular Operating Environment (MOE.2009.10) software [131] | Asp 69, Asp215, Asp352, Asp307 |
| Mulberrofuran G | −8.4634 | |||
| Sanggenon C | −8.4291 | Asp69, Asp352, Asp215, Glu277 | ||
| Moracenin D | −8.3188 | Asp 69, Asp215, Asp352, Asp307 | ||
| Mortatarin C | −5.4358 | No interaction | ||
| Sanggenon G | −9.2855 | Asp69, Asp352, Asp215, Glu277, Phe178 | ||
| Sanggenon O | −8.9427 | Asp69, Asp352, Asp215, Glu277 | ||
| Sanggenol A | −7.7639 | No interaction | ||
| Sanggenon W | −8.4194 | Asp 69, Asp215, Asp352, Asp307 | ||
| 5′-Geranyl-5,7,2′,4′-tetraphydroxy flavone | −8.2431 | No interaction | ||
| Nigrasin F | −8.0232 | Asp 69, Asp215, Asp352, Asp307 | ||
| Sanggenol G | −8.7875 | Asp69, Asp352, Asp215, Glu277 | ||
| Mortatarin B | −5.9508 | Asp 69, Asp215, Asp352, Asp307 | ||
| 4,6,8-Megastigmatrien-3-one | Acanthaceae | −7.47 | 3A4A; Saccharomyces cerevisiae, 2PQR; Saccharomyces cerevisiae, AutoDock Tools, Biovia Discovery Studio (San Diego, CA, USA, USA), PyMOLTM 1.7.4.5 (Schrodinger, LLC, New York, NY, USA) [245] | Asn259, Hid295 |
| N-Isobutyl-2-nonen-6,8-diynamide | −5.54 | Lys156 | ||
| 1′,2′-bis(acetyloxy)-3′,4′-didehydro-2′-hydro-β,ψ-carotene | −10.19 | Arg335 | ||
| 22-acetate-3-hydroxy21(6-methyl-2,4-octadienoate)-olean-12-en-28-oic acid. | −8.31 | Gly209 | ||
| Polyhydroxy pyrrolidines | Rutaceeae | −2.4 | 3CZJ; Escherichia coli, Pardock (http://scfbio-iitd.res.in/dock/paradock.jsp, accessed on 19 February 2020), Accelrys and AutoDock software (AutoDock v.4.2.6, San Diego, CA, USA) [246,247] | No interaction |
| Tosyl | −3.1 | Asp229, Asp231 | ||