Life (Basel, Switzerland) · 2025
Computational Investigation Identifies mTOR as a Primary Binding Target of Medicarpin in Cholangiocarcinoma: Insights from Network Pharmacology and Molecular Docking.
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Sitthirak Sirinya, Tedasen Aman, Rattanapan Yanisa, Duangchan Thitinat, Dokduang Hasaya, Pattaranggoon Nawanwat C, Saisuwan Krittamate, Loilome Watcharin, Namwat Nisana
Аннотация
BACKGROUND: Cholangiocarcinoma (CCA) is an aggressive cancer of biliary tract with poor prognosis and limited therapeutic alternatives. While targeted medicines only benefit a small subset of patients with specific genetic modifications, conventional chemotherapy offers negligible survival advantages. There is an urgent need for novel medicines with multi-target action to combat the diverse and treatment-resistant characteristics of CCA.
METHODS: An integrative computational strategy combining drug-likeness evaluation, target prediction, network pharmacology, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses, and molecular docking was employed to elucidate the pharmacological profile of medicarpin, a natural pterocarpan derived from Dalbergia species. Overlapping targets between medicarpin and CCA-related genes were analysed to construct a protein-protein interaction (PPI) network and identify hub genes.
RESULTS: Forty-four overlapping targets were identified, with mTOR, SRC, PIK3CA, and CCND1 emerging as central nodes within the network. Enrichment analyses revealed significant involvement in carcinogenic pathways, including PI3K-Akt/mTOR, ErbB signalling, apoptosis regulation, and drug resistance. Molecular docking demonstrated a stable binding of medicarpin within the catalytic pocket of mTOR (binding energy -9.6 kcal/mol), supported by multiple hydrogen bonds and hydrophobic interactions with key residues essential for kinase activation.
CONCLUSIONS: This study provides systems-level evidence that medicarpin exerts polypharmacological activity against CCA, with mTOR indicated as a possible mechanistic hub. These findings highlight medicarpin's potential as a promising multi-target therapeutic candidate and underscore the value of natural compounds in expanding treatment strategies for cholangiocarcinoma.
METHODS: An integrative computational strategy combining drug-likeness evaluation, target prediction, network pharmacology, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses, and molecular docking was employed to elucidate the pharmacological profile of medicarpin, a natural pterocarpan derived from Dalbergia species. Overlapping targets between medicarpin and CCA-related genes were analysed to construct a protein-protein interaction (PPI) network and identify hub genes.
RESULTS: Forty-four overlapping targets were identified, with mTOR, SRC, PIK3CA, and CCND1 emerging as central nodes within the network. Enrichment analyses revealed significant involvement in carcinogenic pathways, including PI3K-Akt/mTOR, ErbB signalling, apoptosis regulation, and drug resistance. Molecular docking demonstrated a stable binding of medicarpin within the catalytic pocket of mTOR (binding energy -9.6 kcal/mol), supported by multiple hydrogen bonds and hydrophobic interactions with key residues essential for kinase activation.
CONCLUSIONS: This study provides systems-level evidence that medicarpin exerts polypharmacological activity against CCA, with mTOR indicated as a possible mechanistic hub. These findings highlight medicarpin's potential as a promising multi-target therapeutic candidate and underscore the value of natural compounds in expanding treatment strategies for cholangiocarcinoma.