Clinacanthus nutans fractions exert anti-nasopharyngeal carcinoma effects: integrating untargeted metabolomics, network pharmacology, molecular docking and experimental validation

Background: Clinacanthus nutans (C. nutans), a Southeast Asian medicinal herb, has ethnopharmacological potential against nasopharyngeal carcinoma (NPC). This study aimed to elucidate the bioactive compounds, potential molecular targets, and regulatory pathways responsible for the anticancer activity of the Clinacanthus nutans leaves ethanol extract (E-CNL) fractions against NPC.
Methods: HPLC-Q-TOF/MS/MS and GC-MS analyses, combined with chemometric modeling, were employed to comprehensively profile the phytochemical composition of E-CNL fractions. NPC-related targets were retrieved from GEO, GeneCards, and DisGeNET, and integrated into a PPI network constructed via Cytoscape. GO and KEGG enrichment analyses were performed to characterize key targets and pathways. Molecular docking (AutoDockTools, PyMOL) was used to assess compound–target binding. Pharmacological validation was conducted using NPC cell lines (HK-1, C666-1, and CNE2).
Results: Sixty-one compounds and 794 potential targets were identified with 175 overlapping NPC-associated targets. PPI analysis highlighted ten hub genes, including TP53, STAT3, BCL2, CASP3, BCL2L1, MTOR, TNF, AKT1, ALB, and HIF1A. GO terms indicated roles in oxidative stress response, kinase regulation, phosphorylation, and MAPK cascade modulation, while KEGG analysis revealed significant associations with the PI3K–Akt, p53, TNF, FoxO, and VEGF signaling pathways. Molecular docking revealed strong affinities of the key compounds with PIK3CA, AKT1, TP53, and CDK1. In vitro assays confirmed that E-CNL fractions significantly inhibited NPC cell proliferation and migration, supporting their potential therapeutic relevance.
Conclusion: E-CNL fractions exert their anti-NPC effects through multicomponent, multi-target, and multi-pathway mechanisms. These findings provide a scientific foundation for the further exploration of E-CNL fractions as promising treatment agents for NPC.