Network pharmacology integrated with molecular docking technology to reveal the potential mechanism of Shuganfang against drug-induced liver injury.

Ying Wang, Xueying Chen, Yan Wang, Hong Zhong, Liqin Liu, Yang Ye
Author Information
  1. Ying Wang: Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, China. ORCID
  2. Xueying Chen: The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
  3. Yan Wang: Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, China.
  4. Hong Zhong: Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, China.
  5. Liqin Liu: Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, China.
  6. Yang Ye: Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, China.

Abstract

This study aimed to investigate the active composition and mechanism of the Shuganfang (SGF) in treating drug-induced liver injury (DILI) using network pharmacology and molecular docking. The potential active ingredients and targets of SGF were obtained from the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) database. DILI-related targets were queried from various databases including GEO, GeneCards, OMIM, NCBI, and DisGeNET. The STRING database was used to establish a protein-protein interaction (PPI) network. DAVID was utilized for conducting gene ontology (GO) function enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses. The data visualization and analysis of herb-ingredient-target and disease-pathway-target-ingredient networks were conducted using Cytoscape software (version 3.7.2). PyMoL and AutoDock software was used to select the best binding target for molecular docking. A total of 177 active ingredients,126 targets and 10112 disease targets were obtained, including 122 intersection targets. The identified potential active ingredients consisted of quercetin, kaempferol, luteolin, tanshinone IIa, nobiletin, isorhamnetin, beta-sitosterol and naringenin. The core targets implicated in the study were IL6, estrogen receptor 1 (ESR1), hypoxia-inducible factor alpha subunit 1 (HIF1A), MYC and vascular endothelial growth factor A (VEGFA). KEGG analysis revealed that the treatment of DILI with SGF mainly acted through apoptosis, the PI3K-Akt signaling pathway, and the tumor necrosis factor (TNF) signaling pathway. Furthermore, the binding affinities between the potential ingredients and the core targets were subsequently confirmed through molecular docking experiments. The findings indicated that the docking outcomes remained consistent and demonstrated a favorable capacity for binding. SGF exerts a therapeutic effect on DILI through multiple active ingredients, multiple targets and multiple pathways. Our findings contribute to a positive investigation and establish a theoretical basis for further extensive exploration of SGF as a potential treatment for DILI in future research.

References

  1. Hepatology. 2020 Jun;71(6):2105-2117 [PMID: 31529728]
  2. Sci Rep. 2018 Nov 26;8(1):17362 [PMID: 30478434]
  3. Nucleic Acids Res. 2021 Jan 8;49(D1):D1388-D1395 [PMID: 33151290]
  4. Nat Rev Drug Discov. 2020 Feb;19(2):131-148 [PMID: 31748707]
  5. Int J Biol Sci. 2020 Jan 14;16(5):752-765 [PMID: 32071546]
  6. Phytomedicine. 2018 Dec 1;51:128-138 [PMID: 30466610]
  7. Genome Biol. 2003;4(5):P3 [PMID: 12734009]
  8. Phytother Res. 2018 Nov;32(11):2235-2246 [PMID: 30039882]
  9. J Comput Chem. 2010 Jan 30;31(2):455-61 [PMID: 19499576]
  10. Pharmacol Ther. 2007 Feb;113(2):229-46 [PMID: 17046066]
  11. Database (Oxford). 2016 Feb 20;2016: [PMID: 26896845]
  12. J Healthc Eng. 2021 Nov 2;2021:1142638 [PMID: 34900173]
  13. J Gastroenterol Hepatol. 2008 Jul;23(7 Pt 2):e207-11 [PMID: 17784864]
  14. BMC Syst Biol. 2014;8 Suppl 4:S11 [PMID: 25521941]
  15. Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52 [PMID: 25352553]
  16. Comput Biol Med. 2022 Jun;145:105454 [PMID: 35367781]
  17. Int J Mol Sci. 2017 May 09;18(5): [PMID: 28486401]
  18. Food Funct. 2018 Aug 15;9(8):4184-4193 [PMID: 29993075]
  19. Nucleic Acids Res. 2015 Jan;43(Database issue):D789-98 [PMID: 25428349]
  20. Int Immunopharmacol. 2015 Jul;27(1):164-70 [PMID: 26002582]
  21. Drug Res (Stuttg). 2022 Jun;72(5):245-254 [PMID: 35359022]
  22. Comput Biol Med. 2022 May;144:105389 [PMID: 35303581]
  23. Biomed Pharmacother. 2019 Mar;111:468-475 [PMID: 30594786]
  24. Front Pharmacol. 2021 Jun 28;12:683707 [PMID: 34262454]
  25. Nat Chem Biol. 2008 Nov;4(11):682-90 [PMID: 18936753]
  26. Nucleic Acids Res. 2000 Jan 1;28(1):235-42 [PMID: 10592235]
  27. Trends Genet. 1997 Apr;13(4):163 [PMID: 9097728]
  28. Evid Based Complement Alternat Med. 2020 Jan 07;2020:6219432 [PMID: 31998398]
  29. Evid Based Complement Alternat Med. 2022 Oct 5;2022:1672670 [PMID: 36248427]
  30. J Hepatol. 2019 Jun;70(6):1222-1261 [PMID: 30926241]
  31. Curr Drug Metab. 2018;19(10):830-838 [PMID: 29788883]
  32. Nat Rev Gastroenterol Hepatol. 2011 Apr;8(4):202-11 [PMID: 21386809]
  33. J Cell Physiol. 2007 Nov;213(2):286-300 [PMID: 17559071]
  34. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5 [PMID: 23193258]
  35. BMC Med Genet. 2012 Jun 24;13:49 [PMID: 22727021]
  36. Genome Res. 2003 Nov;13(11):2498-504 [PMID: 14597658]
  37. Pharm Biol. 2021 Dec;59(1):1378-1387 [PMID: 34629029]
  38. Mol Med Rep. 2017 Oct;16(4):4583-4592 [PMID: 28791364]
  39. Nucleic Acids Res. 2021 Jan 8;49(D1):D10-D17 [PMID: 33095870]
  40. Ann N Y Acad Sci. 2006 Nov;1089:228-36 [PMID: 17261770]
  41. Nucleic Acids Res. 2020 Jan 8;48(D1):D845-D855 [PMID: 31680165]
  42. G Chir. 2004 Mar;25(3):61-4 [PMID: 15219100]
  43. CMAJ. 2021 Mar 1;193(9):E310 [PMID: 33649170]
  44. Bioorg Chem. 2022 Jan;118:105476 [PMID: 34788696]
  45. N Engl J Med. 2019 Jul 18;381(3):264-273 [PMID: 31314970]
  46. Gut. 2017 Jun;66(6):1154-1164 [PMID: 28341748]
  47. Acta Pharmacol Sin. 2021 Oct;42(10):1610-1619 [PMID: 33495514]
  48. Crit Care Med. 2013 Nov;41(11):2543-50 [PMID: 23949472]
  49. Biomed Res Int. 2022 Sep 26;2022:4758189 [PMID: 36237735]
  50. J Pharmacol Exp Ther. 2011 Aug;338(2):492-502 [PMID: 21576378]
  51. Int Immunopharmacol. 2023 Jul;120:110375 [PMID: 37267857]
  52. Nat Biotechnol. 2012 Jan 15;30(2):179-83 [PMID: 22252509]
  53. Evid Based Complement Alternat Med. 2022 Jan 21;2022:3968494 [PMID: 35096111]
  54. Handb Exp Pharmacol. 2010;(196):267-310 [PMID: 20020266]
  55. Biomed Pharmacother. 2017 Aug;92:544-553 [PMID: 28577493]
  56. J Clin Invest. 2003 Oct;112(7):978-80 [PMID: 14523032]
  57. Minerva Gastroenterol (Torino). 2021 Mar;67(1):50-64 [PMID: 33222432]
  58. Phytomedicine. 2016 Jun 1;23(6):589-96 [PMID: 27161400]
  59. Eur J Intern Med. 2022 Mar;97:26-31 [PMID: 34772600]
  60. Med Sci Monit. 2019 Nov 08;25:8403-8411 [PMID: 31699960]

MeSH Term

Humans
Molecular Docking Simulation
Network Pharmacology
Vascular Endothelial Growth Factor A
Phosphatidylinositol 3-Kinases
Chemical and Drug Induced Liver Injury
Drugs, Chinese Herbal

Chemicals

Vascular Endothelial Growth Factor A
Phosphatidylinositol 3-Kinases
Drugs, Chinese Herbal

Word Cloud

Created with Highcharts 10.0.0targetsactiveSGFdockingpotentialingredientsDILImolecularpathwaybindingfactormultiplestudymechanismShuganfangdrug-inducedliverinjuryusingnetworkpharmacologyobtaineddatabaseincludingusedestablishenrichmentKEGGanalysissoftwarecore1treatmentsignalingfindingsaimedinvestigatecompositiontreatingTraditionalChineseMedicineSystemsPharmacologyDatabaseTCMSPDILI-relatedqueriedvariousdatabasesGEOGeneCardsOMIMNCBIDisGeNETSTRINGprotein-proteininteractionPPIDAVIDutilizedconductinggeneontologyGOfunctionKyotoencyclopediagenesgenomesanalysesdatavisualizationherb-ingredient-targetdisease-pathway-target-ingredientnetworksconductedCytoscapeversion372PyMoLAutoDockselectbesttargettotal17712610112disease122intersectionidentifiedconsistedquercetinkaempferolluteolintanshinoneIIanobiletinisorhamnetinbeta-sitosterolnaringeninimplicatedIL6estrogenreceptorESR1hypoxia-induciblealphasubunitHIF1AMYCvascularendothelialgrowthVEGFArevealedmainlyactedapoptosisPI3K-AkttumornecrosisTNFFurthermoreaffinitiessubsequentlyconfirmedexperimentsindicatedoutcomesremainedconsistentdemonstratedfavorablecapacityexertstherapeuticeffectpathwayscontributepositiveinvestigationtheoreticalbasisextensiveexplorationfutureresearchNetworkintegratedtechnologyreveal

Similar Articles

Cited By