TCMNPAS: a Comprehensive Analysis Platform Integrating Network Formulaology and Network Pharmacology for Exploring Traditional Chinese Medicine

Overview

Journal Chin Med

Publisher Biomed Central

Specialty Biomedical Engineering

Date 2024 Mar 23

PMID 38519956

Authors

Yishu Liu

Xue Li

Chao Chen

Nan Ding

Peiyong Zheng

Xiaoyun Chen

Shiyu Ma

Ming Yang

Affiliations

Soon will be listed here.

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/ .

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References

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S . PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res. 2020; 49(D1):D1388-D1395. PMC: 7778930. DOI: 10.1093/nar/gkaa971. View

Veber D, Johnson S, Cheng H, Smith B, Ward K, Kopple K . Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem. 2002; 45(12):2615-23. DOI: 10.1021/jm020017n. View

Yu G, Wang L, Han Y, He Q . clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16(5):284-7. PMC: 3339379. DOI: 10.1089/omi.2011.0118. View

Singh-Blom U, Natarajan N, Tewari A, Woods J, Dhillon I, Marcotte E . Prediction and validation of gene-disease associations using methods inspired by social network analyses. PLoS One. 2013; 8(5):e58977. PMC: 3641094. DOI: 10.1371/journal.pone.0058977. View

Gao L, Cao M, Li J, Qin X, Fang J . Traditional Chinese Medicine Network Pharmacology in Cardiovascular Precision Medicine. Curr Pharm Des. 2020; 27(26):2925-2933. DOI: 10.2174/1381612826666201112142408. View

Zhang Y, Li X, Shi Y, Chen T, Xu Z, Wang P . ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine. Acta Pharm Sin B. 2023; 13(6):2559-2571. PMC: 10326295. DOI: 10.1016/j.apsb.2023.03.012. View

Luo W, Brouwer C . Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics. 2013; 29(14):1830-1. PMC: 3702256. DOI: 10.1093/bioinformatics/btt285. View

Xu Q, Guo Q, Wang C, Zhang S, Wen C, Sun T . Network differentiation: A computational method of pathogenesis diagnosis in traditional Chinese medicine based on systems science. Artif Intell Med. 2021; 118:102134. DOI: 10.1016/j.artmed.2021.102134. View

Huang L, Xie D, Yu Y, Liu H, Shi Y, Shi T . TCMID 2.0: a comprehensive resource for TCM. Nucleic Acids Res. 2017; 46(D1):D1117-D1120. PMC: 5753259. DOI: 10.1093/nar/gkx1028. View

10.

Wu Y, Zhou S, Pi D, Dong Y, Wang W, Ye H . Deciphering the Molecular Mechanism of Yifei-Sanjie Pill in Cancer-Related Fatigue. J Oncol. 2023; 2023:5486017. PMC: 9940949. DOI: 10.1155/2023/5486017. View

11.

Wang J, Lu Y, Zhang C, Tian S, Xiang H, Ding P . Qinggan Huoxue Recipe attenuates Alcoholic Liver Disease by suppressing PI3K/AKT signaling pathway based on network pharmacology. Int J Med Sci. 2023; 20(3):346-358. PMC: 9969510. DOI: 10.7150/ijms.80329. View

12.

Yang M, Li J, Jiao L, Chen P, Xu L . [Effective core formulae for lung cancer based on complex network and survival analysis]. Zhongguo Zhong Yao Za Zhi. 2016; 40(22):4482-90. View

13.

Szklarczyk D, Santos A, von Mering C, Jensen L, Bork P, Kuhn M . STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 2015; 44(D1):D380-4. PMC: 4702904. DOI: 10.1093/nar/gkv1277. View

14.

Kong X, Liu C, Zhang Z, Cheng M, Mei Z, Li X . BATMAN-TCM 2.0: an enhanced integrative database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins. Nucleic Acids Res. 2023; 52(D1):D1110-D1120. PMC: 10767940. DOI: 10.1093/nar/gkad926. View

15.

Tai H, Jusoh S, Siu S . Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening. J Cheminform. 2018; 10(1):62. PMC: 6755579. DOI: 10.1186/s13321-018-0320-9. View

16.

Jupe S, Akkerman J, Soranzo N, Ouwehand W . Reactome - a curated knowledgebase of biological pathways: megakaryocytes and platelets. J Thromb Haemost. 2012; 10(11):2399-402. PMC: 3578965. DOI: 10.1111/j.1538-7836.2012.04930.x. View

17.

Long S, Xu J, Huang H . Analysis of differential gene immune infiltration and clinical characteristics of skin cutaneous melanoma based on systems biology and drug repositioning methods to identify drug candidates for skin cutaneous melanoma. Naunyn Schmiedebergs Arch Pharmacol. 2023; 396(10):2427-2447. PMC: 10122093. DOI: 10.1007/s00210-023-02461-1. View

18.

Zhang T, Xue R, Wang X, Zhao S, An L, Li Y . Network-based drug repositioning: A novel strategy for discovering potential antidepressants and their mode of action. Eur Neuropsychopharmacol. 2018; 28(10):1137-1150. DOI: 10.1016/j.euroneuro.2018.07.096. View

19.

Ma S, Zheng L, Zheng L, Bian X . Data Mining, Network Pharmacology, and Molecular Docking Explore the Effects of Core Traditional Chinese Medicine Prescriptions in Patients with Rectal Cancer and Qi and Blood Deficiency Syndrome. Evid Based Complement Alternat Med. 2021; 2021:1353674. PMC: 8360715. DOI: 10.1155/2021/1353674. View

20.

Carbon S, Ireland A, Mungall C, Shu S, Marshall B, Lewis S . AmiGO: online access to ontology and annotation data. Bioinformatics. 2008; 25(2):288-9. PMC: 2639003. DOI: 10.1093/bioinformatics/btn615. View