Network pharmacology prediction and molecular docking-based strategy to discover the potential pharmacological mechanism of action of Wang Bu Liu Xing (Semen vaccariae) for colorectal cancer

Yongquan Shi; Yunshu Zhang; Jifeng Liu; Yanping Zhao; Wei Liu

doi:10.21037/jgo-23-83

Network pharmacology prediction and molecular docking-based strategy to discover the potential pharmacological mechanism of action of Wang Bu Liu Xing (Semen vaccariae) for colorectal cancer

J Gastrointest Oncol. 2023 Apr 29;14(2):504-515. doi: 10.21037/jgo-23-83. Epub 2023 Apr 24.

Authors

Yongquan Shi^#¹, Yunshu Zhang^#², Jifeng Liu^#³, Yanping Zhao¹, Wei Liu²

Affiliations

¹ Department of Clinical Laboratory Center, Shandong Second Provincial General Hospital, Jinan, China.
² Department of Traditional Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China.
³ Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, China.

^# Contributed equally.

Abstract

Background: Colorectal cancer (CRC) is the leading cause of cancer-related death worldwide. Wang Bu Liu Xing [Semen vaccariae (SV)] is a traditional Chinese medicine (TCM) ingredient with anti-angiogenic and anti-tumor effects. However, little research has been done on the ingredients found in SV or the putative process by which SV fights CRC, and this paper aims to reveal the components of SV that are effective in treating CRC.

Methods: The open database and online platform were used in this study, Symptom Mapping (SymMap) and Traditional Chinese Medicine Systems Pharmacology (TCMSP) for SV ingredient and targets, Gene Expression Omnibus (GEO) for differentially expressed genes (DEGs) of CRC, Database for Annotation Visualization and Integrated Discovery (DAVID) for Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, STRING-Cytoscape for protein-protein interaction (PPI), AutoDockTools for Molecular docking and others. were conducted to determine how SV affects CRC and what are the most important components, potential targets, and signaling pathways.

Results: The findings of the network pharmacology study indicated that swerchirin and CDK2 potential target gene for SV was connected to anti-CRC actions. SV may inhibit CRC by interacting with crucial targets like BCL2L1, CDK2, and SERPINE1. Additionally, KEGG analysis revealed that the p53 signaling pathway may be a driver of the anti-CRC impact of SV. Molecular docking showed that swerchirin can bind with its target protein in a good bond by intermolecular force.

Conclusions: In this study, the pharmacological effects of SV were examined, along with its potential therapeutic impact on CRC. These effects of SV appear to be mediated via a variety of substances, targets, and pathways. SV exerts pharmacological effects in CRC, p53 signaling pathway is great value. The main molecular docking is CDK2 and swerchirin. Moreover, our research offers a promising method for characterizing therapeutic pathways and identifying molecules in TCM.

Keywords: Colorectal cancer (CRC); Semen vaccariae; molecular docking; network pharmacology; p53 signaling pathway.