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Identifying the essential nodes in network pharmacology based on multilayer network combined with random walk

Xianlai Chen1, Mingyue Xu1, Ying An1

  • 1Big Data Institute, Central South University, Changsha, Hunan, China.

Journal of Biomedical Informatics
|December 22, 2020
PubMed
Summary

This study introduces a multilayer network and random walk algorithm approach to identify key drug target proteins. This method effectively screens vital proteins for prescription-based treatments, offering a novel network pharmacology tool.

Keywords:
Betweenness centralityMultilayer networkNetwork pharmacologyRandom walk algorithm

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Area of Science:

  • Network pharmacology
  • Computational biology
  • Systems pharmacology

Background:

  • Multilayer networks offer a more realistic representation of complex biological systems compared to traditional complex networks.
  • Network pharmacology utilizes network analysis to understand drug mechanisms from a holistic perspective.

Purpose of the Study:

  • To develop and validate a method for identifying crucial target proteins involved in the action of traditional prescriptions.
  • To leverage multilayer network analysis combined with random walk algorithms for enhanced drug target discovery.

Main Methods:

  • Construction of a four-layer network integrating ingredients, target proteins, metabolic pathways, and diseases.
  • Application of the random walk algorithm to calculate betweenness centrality for ranking protein node importance within the multilayer network.
  • Screening of the top 10% most important proteins based on their centrality scores.

Main Results:

  • The developed method successfully identified key proteins for the prescriptions Xiaochaihu Decoction and Yupingfeng Decoction.
  • The accuracy of the multilayer network approach was comparable to single-layer network topology-based methods.
  • The identified proteins showed significant association with the treated diseases, validating the method's efficacy.

Conclusions:

  • The combination of multilayer networks and random walk algorithms provides an effective strategy for pre-screening vital target proteins related to prescriptions.
  • This approach enhances the application of network pharmacology in understanding and discovering drug mechanisms.