YaTCM: Yet another Traditional Chinese Medicine Database for Drug Discovery

Abstract

Traditional Chinese Medicine (TCM) has a long history of widespread clinical applications, especially in East Asia, and is becoming frequently used in Western countries. However, owing to extreme complicacy in both chemical ingredients and mechanism of action, a deep understanding of TCM is still difficult. To accelerate the modernization and popularization of TCM, a single comprehensive database is required, containing a wealth of TCM-related information and equipped with complete analytical tools. Here we present YaTCM (Yet another Traditional Chinese Medicine database), a free web-based toolkit, which provides comprehensive TCM information and is furnished with analysis tools. YaTCM allows a user to (1) identify the potential ingredients that are crucial to TCM herbs through similarity search and substructure search, (2) investigate the mechanism of action for TCM or prescription through pathway analysis and network pharmacology analysis, (3) predict potential targets for TCM molecules by multi-voting chemical similarity ensemble approach, and (4) explore functionally similar herb pairs. All these functions can lead to one systematic network for visualization of TCM recipes, herbs, ingredients, definite or putative protein targets, pathways, and diseases. This web service would help in uncovering the mechanism of action of TCM, revealing the essence of TCM theory and then promoting the drug discovery process. YaTCM is freely available at http://cadd.pharmacy.nankai.edu.cn/yatcm/home.

Keywords: AM, Astragalus Membranaceus.; Drug discovery; HHN, Herb-herb network.; MV-SEA, Multi-voting similarity ensemble approach.; Pathway analysis; RA, Atractylodes Macrocephala.; SD, Saposhnikovia Divaricata.; Systems pharmacology; TCM; TCM, Traditional Chinese medicine..

Fig. 1

The main database schema for YaTCM. Each record contains six data fields, for prescription, herbs, ingredients, diseases, targets, pathways. There are two analysis modules—network analysis and pathway analysis. It includes one target prediction function, similarity ensemble approach.

Fig. 2

Pathway analysis. To obtain the comprehensive pathway analysis of TCM, YaTCM maps related ingredients and TTD targets to one specific pathway. Corresponding compounds and protein targets were highlighted in red point and blue rectangle respectively. These can be clicked to reveal the corresponding relationship between YaTCM and KEGG data.

Fig. 3

Herb-herb network. User can obtain functionally similar herb pairs by adjusting the number of shared TTD target (A) or diseases (B). Double clicking the edge between two nodes will all lead to comprehensive pathway analysis and network analysis page between the two herbs.

Fig. 4

Prescription exploration. Clicking the edge between any two herbs reveals three function links, a list of shared therapeutic targets (arrow D-1), a list of common KEGG pathways (arrow D-2), and a list of therapeutic targets that were present only in the common KEGG pathway (arrow D-3).

Fig. 5

The search page for compounds that involves drawing a molecule in JSME sketcher. When drawing the molecule Ephedrine, various information is displayed. Users can specify the preferred information to be displayed. They can explore the mechanism of action through MV-SEA, pathway analysis and network pharmacology analysis.

Fig. 6

The search page of prescription category as seen by submitting different names. When Yu Ping Feng is queried, a variety of information is presented. Users can select their preferred information to display and further explore the mechanism of action through variable tools, such as pathway analysis and network pharmacology analysis.

Fig. 7

The mechanism of Yu Ping Feng. The mapping relationships generated are consistent with the experimental results and provide novel insights into the mechanism of pulmonary fibrosis.

Supplementary Fig. S1

The shared targets between any two or any more herbs in Yu Ping Feng. Clicking "View" button will lead to a list of shared TTD targets (red arrow).

Supplementary Fig. S2

The shared targets and pathways in Yu Ping Feng. Clicking the edge between any two herbs will lead to three function links: a list of shared therapeutic targets (arrow 1), a list of common KEGG pathways (arrow 2), and a list of therapeutic targets that were appeared only in common KEGG pathway (arrow 3)

Supplementary Fig. S3

The shared diseases between any two or any more herbs in Yu Ping Feng. Clicking "View" button will lead to a list of shared diseases (red arrow).

Supplementary Fig. S4

The shared diseases between any two herbs in Yu Ping Feng. Clicking the edge between any two herbs or clicking "View" button will lead to a list of shared diseases (red arrow)