Integrative GC-MS, network pharmacology, and molecular dynamics elucidate synergistic anti-diabetic mechanisms of Chongqing Citrus reticulata ‘Dahongpao’ volatile oil via multi-target stabilization
Wanting Zhong, YaYi Xiong, Jie Luo, Shujaat Ahmad, Jian Wang
TL;DR
This study uses chemical analysis and computer modeling to show how a citrus oil from Chongqing may help treat diabetes by affecting multiple biological targets.
Contribution
The novel integration of GC-MS, network pharmacology, and molecular dynamics reveals synergistic anti-diabetic mechanisms of a citrus volatile oil.
Findings
GC-MS identified 82 compounds in the citrus oil, with D-limonene as the main component.
Molecular docking and MD simulations confirmed strong binding of thymol and n-hexadecanoic acid to diabetes-related proteins.
Pathway analysis linked the oil's effects to PPAR signaling and insulin resistance pathways.
Abstract
Diabetes mellitus involves complex pathogenesis requiring multi-target interventions. Citrus reticulata ‘Dahongpao’ from Chongqing exhibits anti-diabetic potential, but its mechanisms remain elusive. We employed an integrative strategy: GC-MS identified 82 compounds (96.61% coverage), dominated by D-limonene (62.48%). Network pharmacology revealed 36 diabetes-related targets. Molecular docking prioritized ligands (thymol: −6.8 kcal/mol with FABP1; n-hexadecanoic acid: −6.7 kcal/mol with PTGS2). Critical validation was achieved via 100-ns molecular dynamics (MD) simulations and MM-GBSA binding free energy calculations. MD simulations demonstrated structural stability (RMSD < 2.5 Å) for core complexes (e.g., CYP19A1/thymol). MM-GBSA quantified robust binding for FABP1/dodecanoic acid (−43.26 kcal/mol) and PTGS2/n-hexadecanoic acid (−43.93 kcal/mol), driven by van der Waals forces.…
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Taxonomy
TopicsComputational Drug Discovery Methods · Phytochemicals and Antioxidant Activities · Protein Interaction Studies and Fluorescence Analysis