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Systematic analysis on the mechanism of Zhizi-Bopi decoction against hepatitis B via network pharmacology and molecular docking

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Abstract

Purpose: Zhizi-Bopi decoction (ZZBPD) is a classic herbal formula with wide clinical applications in treating liver diseases including hepatitis B. However, the mechanism needs to be elucidated.

Methods: Chemical components of ZZBPD were identified by ultra-high-performance liquid chromatography coupled with time-of-flight mass spectrometry (UHPLC-TOF-MS). Then we used network pharmacology to identify their potential targets. Network construction, coupled with protein–protein interaction and enrichment analysis was used to identify representative components and core targets. Finally, molecular docking simulation was conducted to further refine the drug-target interaction.

Results: One hundred and forty-eight active compounds were identified in ZZBPD, targeting 779 genes/proteins, among which 174 were related to hepatitis B. ZZBPD mainly influences the progression of hepatitis B through the hepatitis B pathway (hsa05161) via core anti-HBV targets (AKT1, PIK3CA, PIK3R1, SRC, TNF, MAPK1, and MAPK3). Enrichment analysis indicated that ZZBPD can also potentially regulate lipid metabolism and enhance cell survival. Molecular docking suggested that the representative active compounds can bind to the core anti-HBV targets with high affinity.

Conclusion: The potential molecular mechanisms of ZZBPD in hepatitis B treatment were identified using network pharmacology and molecular docking approaches. The results serve as an important basis for the modernization of ZZBPD.

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Data availability

The intermediate data supporting this paper’s findings are available from the authors upon reasonable request.

Abbreviations

AKT1:

AKT Serine/Threonine Kinase 1

BP:

Biological process

CC:

Cell component;

cccDNA:

Covalently closed circular DNA

ERK:

Extracellular signal-regulated kinase

FDR:

False discovery rate

Gancao:

Dry rhizome of Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat. or Glycyrrhiza glabra L.

GO:

Gene ontology

Huangbo:

Dry bark of Phellodendron chinense Schneid

HBV:

Hepatitis B virus

HCC:

Hepatocellular carcinoma

HPLC:

High performance liquid chromatography

IDA:

Information-dependent acquisition

KEGG:

Kyoto encyclopedia of genes and genomes

MAPK:

Mitogen-activated protein kinase

MCODE:

Molecular complex detection

MF:

Molecular function

OMIM:

Online Mendelian Inheritance in Man database

PIK3CA:

Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

PIK3R1:

Phosphatidylinositol 3-kinase regulatory subunit alpha

SRC:

Proto-oncogene tyrosine-protein kinase Src

PPI:

Protein–protein interaction

RCSB:

Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

STAT3:

Signal Transducer and Activator of Transcription 3

STRING:

Search Tool for the Retrieval of Interacting Genes/Proteins

TCM:

Traditional Chinese medicine

TCMSP:

Traditional Chinese Medicine System Pharmacology Database

TNF:

Tumor necrosis factor

TTD:

Terapeutic Target Database

UHPLC-TOF-MS:

Ultra-high performance liquid chromatography coupled with time-of-flight mass spectrometry

Zhizi:

Dry fruit of Gardenia jasminoides Ellis

ZZBPD:

Zhizi-Bopi decoction

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Acknowledgements

We appreciate Dr. Sujun Chen for her generous help with draft modification advice. We also acknowledge OriginLab Corporation and Axure Software Solutions Inc. for their offer of software for educational use.

Funding

This research was supported by the P.R.C State Administration of Traditional Chinese Medicine Project [No. LPGZS2012-34].

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Contributions

HZ: conceptualization, methodology, investigation, visualization, and original draft writing. ZX: investigation. HG: writing—reviewing and editing. QZ: supervision and project administration. All authors have read and approved the final version manuscript. The authors declare that all data were generated in-house and that no paper mill was used.

Corresponding author

Correspondence to Qinyuan Zhang.

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The authors declare that they have no conflict of interest.

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Zhang, H., Xu, Z., Gao, H. et al. Systematic analysis on the mechanism of Zhizi-Bopi decoction against hepatitis B via network pharmacology and molecular docking. Biotechnol Lett 45, 463–478 (2023). https://doi.org/10.1007/s10529-023-03359-x

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  • DOI: https://doi.org/10.1007/s10529-023-03359-x

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