Network Pharmacological Studies in Biological Interactions of Thymoquinone

Abstract

Thymoquinone, a bioactive phytochemical compound belonging to the class of benzoquinones, is prominently present in the plant Nigella sativa. Despite its widespread use, the precise molecular mechanisms underlying its beneficial effects remain elusive. To address this gap, we employed network pharmacology to investigate the actions of Thymoquinone (TQ). Our methodology encompassed the utilization of diverse bioinformatic tools to scrutinize this molecule of interest comprehensively. Initially, we retrieved the chemical structure, formula, and CAS (Chemical Abstracts Service) of Thymoquinone (TQ) from the PubChem database. Subsequently, we employed ADMET lab 2.0 to dissect the pharmacokinetics of Thymoquinone (TQ), while the Comparative Toxicogenomic Database (CTD) aided in identifying potential targets of Thymoquinone (TQ). To delve deeper into the biological implications, we conducted GO enrichment analysis and KEGG pathway enrichment of target genes using the web-based gene set analysis toolkit, Webgestalt. The resultant data were then utilized to construct an interaction network through String 11.0, which was further visualized using Cytoscape to delineate protein-protein interaction (PPI) networks and molecule-target-pathway networks for comprehensive analysis. Additionally, molecular docking studies were performed to elucidate the interaction between targets and Thymoquinone (TQ). Our investigation unveiled the profound drug utilization and biological activity of Thymoquinone (TQ), with a total of 47 gene targets identified. These findings underscore the close association of these selected genes with TQ, indicating its multi-faceted interactions with various pathways and proteins. Ultimately, our study highlights the potential of TQ in shaping a structured pharmacological network, thereby offering significant implications for drug development, design, and utilization.