2. Academic Validation
  3. Integration of Untargeted Metabolomics, Network Pharmacology, Single-Cell RNA Sequencing, and Molecular Dynamics Simulation Reveals GOT1, CYP1A2, and CA2 as Potential Targets of Huang Qin Decoction Preventing Colorectal Cancer Liver Metastasis

Integration of Untargeted Metabolomics, Network Pharmacology, Single-Cell RNA Sequencing, and Molecular Dynamics Simulation Reveals GOT1, CYP1A2, and CA2 as Potential Targets of Huang Qin Decoction Preventing Colorectal Cancer Liver Metastasis

  • Pharmaceuticals (Basel). 2025 Jul 17;18(7):1052. doi: 10.3390/ph18071052.
Tiegang Li 1 2,  Zheng Yan 1 2,  Mingxuan Zhou 1 2,  Wenyi Zhao 1 2,  Fang Zhang 1 2,  Silin Lv 1 2,  Yufang Hou 1 2,  Zifan Zeng 1 2,  Liu Yang 1 2,  Yixin Zhou 1 2,  Zengni Zhu 1 2,  Xinyi Ren 1 2 3,  Min Yang 1 2
Affiliations

Affiliations

  • 1 State Key Laboratory of Digestive Health, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
  • 2 State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
  • 3 School of Pharmacy, Minzu University of China, Beijing 100081, China.
PMID: 40732339 DOI: 10.3390/ph18071052
Abstract

Background: Huang Qin Decoction (HQD) is a well-established Traditional Chinese Medicine (TCM) formulation recognized for its application in the treatment of colorectal Cancer (CRC). However, the precise therapeutic mechanisms remain inadequately defined. Methods: This study integrates metabolomics from a mouse model and network pharmacology to screen potential targets and bio-active ingredients of HQD. The pharmacological activity of HQD for CRC was evidenced via single-cell RNA Sequencing (scRNA-seq), molecular docking, and molecular dynamics simulations. Atomic force microscopy (AFM) assays and cellular experimental validation were used to confirm the relative mechanisms. Results: The metabolite profile undergoes significant alterations, with metabolic reprogramming evident during the malignant progression of CRC liver metastasis. Network pharmacology analysis identified that HQD regulates several metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism, nitrogen metabolism, phenylalanine metabolism, and linoleic acid metabolism, by targeting key proteins such as aspartate aminotransferase (GOT1), Cytochrome P450 1A2 (CYP1A2), and Carbonic Anhydrase 2 (CA2). ScRNA-seq analysis indicated that HQD may enhance the functionality of cytotoxic T cells, thereby reversing the immunosuppressive microenvironment. Virtual verification revealed a strong binding affinity between the identified hub targets and active constituents of HQD, a finding subsequently corroborated by AFM assays. Cellular experiments confirmed that naringenin treatment inhibits the proliferation, migration, and invasion of CRC cells by downregulating GOT1 expression and disrupting glutamine metabolism. Conclusions: Computational prediction and in vitro validation reveal the active ingredients, potential targets, and molecular mechanisms of HQD against CRC liver metastasis, thereby providing a scientific foundation for the application of TCM in CRC treatment.

Keywords

Huang Qin Decoction; colorectal cancer; metabolomics; molecular dynamics simulation; network pharmacology; single-cell RNA sequencing.

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