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. 2024 Mar 22;19(1):50.
doi: 10.1186/s13020-024-00924-y.

TCMNPAS: a comprehensive analysis platform integrating network formulaology and network pharmacology for exploring traditional Chinese medicine

Yishu Liu  1 , Xue Li  1 , Chao Chen  1 , Nan Ding  1 , Peiyong Zheng  1 , Xiaoyun Chen  1 , Shiyu Ma  2 , Ming Yang  3
Affiliations

TCMNPAS: a comprehensive analysis platform integrating network formulaology and network pharmacology for exploring traditional Chinese medicine

Yishu Liu et al. Chin Med. .

Abstract

The application of network formulaology and network pharmacology has significantly advanced the scientific understanding of traditional Chinese medicine (TCM) treatment mechanisms in disease. The field of herbal biology is experiencing a surge in data generation. However, researchers are encountering challenges due to the fragmented nature of the data and the reliance on programming tools for data analysis. We have developed TCMNPAS, a comprehensive analysis platform that integrates network formularology and network pharmacology. This platform is designed to investigate in-depth the compatibility characteristics of TCM formulas and their potential molecular mechanisms. TCMNPAS incorporates multiple resources and offers a range of functions designed for automated analysis implementation, including prescription mining, molecular docking, network pharmacology analysis, and visualization. These functions enable researchers to analyze and obtain core herbs and core formulas from herbal prescription data through prescription mining. Additionally, TCMNPAS facilitates virtual screening of active compounds in TCM and its formulas through batch molecular docking, allowing for the rapid construction and analysis of networks associated with "herb-compound-target-pathway" and disease targets. Built upon the integrated analysis concept of network formulaology and network pharmacology, TCMNPAS enables quick point-and-click completion of network-based association analysis, spanning from core formula mining from clinical data to the exploration of therapeutic targets for disease treatment. TCMNPAS serves as a powerful platform for uncovering the combinatorial rules and mechanism of TCM formulas holistically. We distribute TCMNPAS within an open-source R package at GitHub ( https://github.com/yangpluszhu/tcmnpas ), and the project is freely available at http://54.223.75.62:3838/ .

Keywords: Core formula mining; Molecular docking; Molecular mechanism; Network pharmacology analysis system; TCMNPAS; Traditional Chinese medicine.

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Conflict of interest statement

There is no competing interests involved in this paper.

Figures

Fig. 1
Fig. 1
Schematic diagram of the main information architecture
Fig. 2
Fig. 2
Analysis workflow diagram (A) and schematic diagram of the main interface of TCMNPAS (B)
Fig. 3
Fig. 3
Databases included in TCMNPAS v1.0 for searching herbs, components and targets (A), Setting the threshold of QED value for drug-likeness and setting the threshold of drug-target score (B), Setting the significance P-value of drug-target (C), Herb-Compound-Target (D), Setting the violation count of Lipinski Rule and Veber Rule for drug-likeness (E), KEGG Enrichment (F), Shared-KEGG-Enrichment-Curve (G), Network Distance Score (H), KATZ Score (I)
Fig. 4
Fig. 4
Prescription mining algorithm (A), parameter setting area for prescription mining analysis (B), Summary of results (C), Core formulas (D), Herb compatibility network (under optimized threshold) (E), Optimized herb compatibility network (F)
Fig. 5
Fig. 5
Molecular docking principle diagram (A), Parameter setting and result example page for single molecule docking (B), Cross batch docking mode (C), Parallel batch docking mode (D), Molecular docking results (E), Extraction of standard ligands from PDB (F), Batch retrieval of PDB docking parameters (G), RMSD calculation (H)
Fig. 6
Fig. 6
Overview of the main functions of TCMNPAS v1.0 (including usage frequency and number of users)
See this image and copyright information in PMC

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