Identification of Antidiabetic Metabolites from Paederia foetida L. Twigs by Gas Chromatography-Mass Spectrometry-Based Metabolomics and Molecular Docking Study

Abstract

Paederia foetida L. (Rubiaceae) is a climber which is widely distributed in Asian countries including Malaysia. The plant is traditionally used to treat various diseases including diabetes. This study is to evaluate the enzymatic inhibition activity of Paederia foetida twigs extracts and to identify the metabolites responsible for the bioactivity by gas chromatography-mass spectrometry (GC-MS) metabolomics profiling. Three different twig extracts, namely, hexane (PFH), chloroform (PFC), and methanol (PFM), were submerged for their α-amylase and α-glucosidase inhibition potential in 5 replicates for each. Results obtained from the loading column scatter plot of orthogonal partial least square (OPLS) model revealed the presence of 12 bioactive compounds, namely, dl-α-tocopherol, n-hexadecanoic acid, 2-hexyl-1-decanol, stigmastanol, 2-nonadecanone, cholest-8(14)-en-3-ol, 4,4-dimethyl-, (3β,5α)-, stigmast-4-en-3-one, stigmasterol, 1-ethyl-1-tetradecyloxy-1-silacyclohexane, ɣ-sitosterol, stigmast-7-en-3-ol, (3β,5α,24S)-, and α-monostearin. In silico molecular docking was carried out using the crystal structure α-amylase (PDB ID: 4W93) and α-glucosidase (PDB ID: 3WY1). α-Amylase-n-hexadecanoic acid exhibited the lowest binding energy of -2.28 kcal/mol with two hydrogen bonds residue, namely, LYS178 and TYR174, along with hydrophobic interactions involving PRO140, TRP134, SER132, ASP135, and LYS172. The binding interactions of α-glucosidase-n-hexadecanoic acid complex ligand also showed the lowest binding energy among 5 major compounds with the energy value of -4.04 kcal/mol. The complex consists of one hydrogen bond interacting residue, ARG437, and hydrophobic interactions with ALA444, ASP141, GLN438, GLU432, GLY374, LEU373, LEU433, LYS352, PRO347, THR445, HIS348, and PRO351. The study provides informative data on the potential antidiabetic inhibitors identified in Paederia foetida twigs, indicating the plant has the therapeutic effect properties to manage diabetes.

Figure 1

PCA score plot of plant extracts based on GC-MS spectra. PFH, PFC, and PFM are hexane, chloroform, and methanol extracts, respectively.

Figure 2

PLS score plot of plant extracts based on GC-MS spectra. PFH, PFC, and PFM are hexane, chloroform, and methanol extracts, respectively.

Figure 3

(a) The permutation test for the two components of the PLS model with R²Y = 0.439 and Q²Y = -0.0958 for α-amylase. (b) The permutation test for the two components of the PLS model with R²Y = 0.477 and Q²Y = -0.038 for α-glucosidase.

Figure 4

OPLS score plot of plant extracts based on GC-MS spectra. PFH, PFC, and PFM are hexane, chloroform, and methanol extracts, respectively.

Figure 5

(a) The permutation test for the one component of the OPLS model with R²Y = 0.433 and Q²Y = -0.601 for α-amylase. (b) The permutation test for the one component of the OPLS model with R²Y = 0.47 and Q²Y = -0.496 for α-glucosidase.

Figure 6

OPLS loading scatters plot of active extract in the range -0.1 to -0.02. (a) All the peak numbers on GC-MS chromatogram. (b) Selected peak numbers on GC-MS chromatogram.

Figure 7

VIP plot of active extract of P. foetida twigs. Metabolites identification (Var ID): (C29H50O: 1, 96, 379, 383); (C16H32O2: 14, 17, 64); (C16H34O: 21); (C29H52O: 26, 27, 135); (C19H38O: 95); (C29H48O: 233, 247); (C21H44OSi: 372,392) and (C21H42O4: 384).

Figure 8

The 2D diagram showing the interaction between the protein residues of α-amylase and the inhibitors. (a) n-hexadecanoic acid, (b) cholest-8(14)-en-3-ol, 4,4-dimethyl-, (3β,5α)-, (c) ɣ-sitosterol, (d) stigmast-7-en-3-ol, (3β,5α,24S)-, (e) stigmasterol, (f) acarbose.

Figure 9

The 2D diagram showing the interaction between the protein residues of α-glucosidase and the inhibitors. (a) n-hexadecanoic acid, (b) cholest-8(14)-en-3-ol, 4,4-dimethyl-, (3β,5α)-, (c) ɣ-sitosterol, (d) stigmast-7-en-3-ol, (3β,5α,24S)-, (e) stigmasterol, (f) acarbose.