Systems pharmacology approaches in herbal medicine research: a brief review

Abstract

Herbal medicine, a multi-component treatment, has been extensively practiced for treating various symptoms and diseases. However, its molecular mechanism of action on the human body is unknown, which impedes the development and application of herbal medicine. To address this, recent studies are increasingly adopting systems pharmacology, which interprets pharmacological effects of drugs from consequences of the interaction networks that drugs might have. Most conventional network-based approaches collect associations of herb-compound, compound-target, and target-disease from individual databases, respectively, and construct an integrated network of herb-compound-target-disease to study the complex mechanisms underlying herbal treatment. More recently, rapid advances in highthroughput omics technology have led numerous studies to exploring gene expression profiles induced by herbal treatments to elicit information on direct associations between herbs and genes at the genome-wide scale. In this review, we summarize key databases and computational methods utilized in systems pharmacology for studying herbal medicine. We also highlight recent studies that identify modes of action or novel indications of herbal medicine by harnessing drug-induced transcriptome data. [

Literature review on the interdisciplinary biomarkers of multi-target and multi-time herbal medicine therapy to modulate peripheral systems in cognitive impairment

“…Therefore, it is an excellent tool for analyzing the mechanisms of HM with multi-component and multi-target properties ( Liu Y. et al, 2015 ). Studies that have utilized transcriptome signatures, induced by the treatment of HM, have contributed to the better understanding of the various biological processes that affect AD and corroborate the implications of many previously described indications ( Lee M. et al, 2022 ). Recently, novel molecular mechanisms, such as wound healing through focal adhesion kinase regulation by Bupleuri Radix and anticancer effects through the regulation of the Aurora B pathway by Paeoniae Radix, were proposed, based on their transcriptome signatures ( Baek et al, 2022 ; Park et al, 2022 ).…”

“…Recently, novel molecular mechanisms, such as wound healing through focal adhesion kinase regulation by Bupleuri Radix and anticancer effects through the regulation of the Aurora B pathway by Paeoniae Radix, were proposed, based on their transcriptome signatures ( Baek et al, 2022 ; Park et al, 2022 ). Furthermore, gene signature data may contribute to the development of new indications for HM ( Lee M. et al, 2022 ). Pharmacological approach using transcriptome-based systems aim to identify drugs that show an inverse correlation with an altered disease gene signature by decreasing the expression of up-regulated genes and increasing the expression of down-regulated genes in disease models ( Chen et al, 2020 ).…”

“…In the current situation where transcriptome data is scarce, HMs effective in MCI can be explored through a network pharmacological approach, which analyses drug effects at the level of gene-drug interactions, rather than at the level of gene expression changes ( Lee M. et al, 2022 ). In a recent study, target genes important in MCI were selected from previous literature and databases through data mining, and then herbs with potential applicability in MCI were selected by analyzing the target-component-herb network ( Chang et al, 2022 ).…”

Icariin alleviates the apoptosis of chondrocytes in osteoarthritis through regulating SIRT‐1‐Nrf2‐HO‐1 signaling

“…Nowadays, Chinese herbal medicines have been gradually valued by researchers due to their safety and high efficiency. Also, they show unexpected effects in the treatment of many diseases, including cancer, diabetes and OA (Lee et al., 2022). Among them, icariin is a prenylated flavonol glycoside, which can be separated from Epimedium grandiflorum (He et al., 2020).…”

Exploring the Molecular Mechanism of Tong Xie Yao Fang in Treating Ulcerative Colitis Using Network Pharmacology and Molecular Docking

“…In treating diseases, herbs contain many ingredients and target multiple targets, making it difficult to identify their pharmacodynamic ingredients and molecular mechanisms. With the advancement of network technology, the combination of network pharmacology, molecular docking, and bioinformation provides a powerful method for uncovering the complex molecular mechanisms of TCM [ 14 ]. They increase the likelihood of discovering the best drug candidates and significantly cut down on the initial time and expense of conducting experiments to determine drug-target interactions [ 15 – 17 ].…”