GC-MS- and NMR-Based Metabolomics and Molecular Docking Reveal the Potential Alpha-Glucosidase Inhibitors from Psychotria malayana Jack Leaves

Abstract

Psychotria malayana Jack leaf, known in Indonesia as “daun salung”, is traditionally used for the treatment of diabetes and other diseases. Despite its potential, the phytochemical study related to its anti-diabetic activity is still lacking. Thus, this study aimed to identify putative inhibitors of α-glucosidase, a prominent enzyme contributing to diabetes type 2 in P. malayana leaf extract using gas chromatography-mass spectrometry (GC-MS)- and nuclear magnetic resonance (NMR)-based metabolomics, and to investigate the molecular interaction between those inhibitors and the enzyme through in silico approach. Twenty samples were extracted with different solvent ratios of methanol–water (0, 25, 50, 75, and 100% v/v). All extracts were tested on the alpha-glucosidase inhibition (AGI) assay and analyzed using GC-MS and NMR. Multivariate data analysis through a partial least square (PLS) and orthogonal partial square (OPLS) models were developed in order to correlate the metabolite profile and the bioactivity leading to the annotation of the putative bioactive compounds in the plant extracts. A total of ten putative bioactive compounds were identified and some of them reported in this plant for the first time, namely 1,3,5-benzenetriol (1); palmitic acid (2); cholesta-7,9(11)-diene-3-ol (3); 1-monopalmitin (4); β-tocopherol (5); α-tocopherol (6); 24-epicampesterol (7); stigmast-5-ene (8); 4-hydroxyphenylpyruvic acid (10); and glutamine (11). For the evaluation of the potential binding modes between the inhibitors and protein, the in silico study via molecular docking was performed where the crystal structure of Saccharomyces cerevisiae isomaltase (PDB code: 3A4A) was used. Ten amino acid residues, namely ASP352, HIE351, GLN182, ARG442, ASH215, SER311, ARG213, GLH277, GLN279, and PRO312 established hydrogen bond in the docked complex, as well as hydrophobic interaction of other amino acid residues with the putative compounds. The α-glucosidase inhibitors showed moderate to high binding affinities (−5.5 to −9.4 kcal/mol) towards the active site of the enzymatic protein, where compounds 3, 5, and 8 showed higher binding affinity compared to both quercetin and control ligand.

Preliminary Phytochemical Screening, In Vitro Antidiabetic, Antioxidant Activities, and Toxicity of Leaf Extracts of Psychotria malayana Jack

“…Palmitic acid, 1,3,5-benzenetriol, 1-monopalmitin, beta-tocopherol, 24-epicampesterol, alpha-tocopherol, and stigmast-5-ene were detected as alpha-glucosidase inhibitors in our previous research [6]. On the other hand, palmitic acid, isolated from the methanolic fraction of Syzygium littorale stem bark, was reported as an antioxidant (IC 50 189.9 µg/mL) [40].…”

“…Despite its long history of traditional use as a therapeutic herb, the research on this plant's glucose uptake and antioxidant activity is limited. This plant has been reported to possess alpha-glucosidase inhibitory activity, a key enzyme corresponding to type 2 diabetes [5,6]. In addition, the water extract of this plant reported to have the antidiabetic activity on the type 1 diabetic adult zebrafish model [7].…”

In vitro and molecular docking of α-Glucosidase inhibitor potency from Artabotrys suaveolens leaf and stem bark

“…The ligand structures were obtained from ZINC (https://zinc.docking.org) and PubChem (https://pubchem.ncbi.nlm.nih.gov/) databases. The software for preparing the ligand and receptor was AutoDock Tools version 1.5.7 and the docking simulation was done using AutoDock version 4.2.6 [18]. The grid size was 0.55 Å and the grid was arranged in rectangular shape of size 126 x 126 x 126 with the center coordinate x=21.301; y=-0.833; z=18.662 which covered the whole receptor.…”

“…Using these parameters, GLC as the native ligand of α-glucosidase structure was docked to the αglucosidase and resulted RMSD value of 0.66 Å. This value was good enough, because it was still below 1.5 Å [18].…”

Metabolomics and Network Pharmacology in the Exploration of the Multi-Targeted Therapeutic Approach of Traditional Medicinal Plants

“… [ 44 ] 2 Aerva javanica (Leaf) GC-MS (Qualitative) Column: HP-5MS (30 m × 0.025 mm) Medium: Helium as a carrier gas, flow rate of 13 mL/min 3-allyl-6-methoxyphenol, dodecanal, (E)-6,10-dimethyl-5,9-undecadien-2-one, trans-β-ionone, β-panasinsene [ 45 , 46 ] 3 Aerva lanata (Aerial parts and roots) LC-ESI-MS/MS (Qualitative and quantitative) Column: (30 m × 0.25 mm I.D., × 1 EMdf) Medium: Helium as carrier gas, flow rate of 1 mL/min. Quercetin, kaempferol, and myricetin, Gallic acid, p -coumaric, Vanillic, Caffeic acid, Rutin, Ferulic acid, Astragalin [ 47 ] 4 Allamanda cathartica (Leaf) GC-MS (Qualitative) Column: 30 mm in length, 0.25 mm I.D., and 1 µm Medium: Helium as a carrier gas, flow rate of 1 mL/min Glycerin, n-hexadecanoic acid, Phytol, Thymine, Tetradecanoic acid, Dodecanoic acid, Octanoic acid, ethyl ester, [ 48 , 49 ] 5 Artemisia absinthium (Aerial part) GC/MS HS-SPME analysis (Qualitative and quantitative) Colum: DB-5(30 × 0.2 mm, film thickness 0.32 µm) Medium: helium gas, flow rate of 1.7 mL/min Camphor, p-cymene, Isoledene, Caryophyllene, Isopulegol Acetate, Hysterol, Isocaryophillene, Diisoamylene, β-farnesene, and Cyclohexane,2,4-diisopropyl-1,1-dimethyl [ 50 ] 6 Aurantii fructus (Dry who...…”