Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action (MOA) has not been identified. Systems pharmacology methods have been used to overcome these challenges. However, there is a limitation as those similar mechanisms of similar components cannot be identified. In this study, comparisons of physicochemical descriptors, molecular docking analysis and RNA-seq analysis were performed to compare the MOA of similar compounds and to confirm the changes observed when similar compounds were mixed and used. Various analyses have confirmed that compounds with similar structures share similar MOA. We propose an advanced method for in silico experiments in herbal medicine research based on the results. Our study has three novel findings. First, an advanced network pharmacology research method was suggested by partially presenting a solution to the difficulty in identifying multi-component mechanisms. Second, a new natural product analysis method was proposed using large-scale molecular docking analysis. Finally, various biological data and analysis methods were used, such as in silico system pharmacology, docking analysis and drug response RNA-seq. The results of this study are meaningful in that they suggest an analysis strategy that can improve existing systems pharmacology research analysis methods by showing that natural product–derived compounds with the same scaffold have the same mechanism.

Effective treatments for patients experiencing temperature-related symptoms are limited. The hot and cold effects of traditional herbal medicines have been utilized to treat and manage these symptoms, but their molecular mechanisms are not fully understood. Previous studies with arbitrarily selected herbs and ingredients may have produced biased results. Here, we aim to systematically elucidate the molecular mechanisms of the hot and cold properties of herbal medicines through an unbiased large-scale investigation of herbal ingredients, their target genes, and the transcriptome signatures induced by them. Using data regarding 243 herbs retrieved from two herbal medicine databases, we statistically identify (R)-Linalool, (-)-alpha-pinene, peruviol, (L)-alpha-terpineol, and cymol as five new hot-specific ingredients that share a common target, a norepinephrine transporter. However, no significant ingredients are cold-specific. We also statistically identify 14 hot- and 8 cold-specific new target genes. Pathway enrichment analysis of hot-specific target genes reveals the associated pathways including neurotransmitter reuptake, cold-induced thermogenesis, blood pressure regulation, adrenergic receptor signaling, and cation symporter activity. Cold-specific target genes are associated with the steroid pathway. Transcriptome analysis also shows that hot herbs are more strongly associated with coagulation and synaptic transmission than cold herbs. Our results, obtained from novel connections between herbal ingredients, target genes, and pathways, may contribute to the development of pharmacological treatment strategies for temperature-related pain using medicinal plants.

Muscle atrophy, characterized by progressive loss of skeletal muscle mass and strength, remains a significant therapeutic challenge. Jakyak-gamcho-tang (JGT) is a traditional herbal formulation that has demonstrated promising muscle-protective effects; however, the key bioactive constituents and the influence of different extraction methods have not yet been fully elucidated. This study compared the muscle-protective effects of the ethanol and water extracts of JGT (JGT-E and JGT-W, respectively), while also identifying the principal bioactive compounds that contribute to the enhanced efficacy of JGT-E. An integrative methodological approach was adopted, incorporating transcriptomic profiling, network pharmacology analysis, antioxidant activity assays, and in vitro validation using C2C12 myoblasts and myotubes. This comprehensive investigation enabled a detailed assessment of the biological activities of both JGT-E and JGT-W. Transcriptomic analysis revealed that JGT-E significantly modulates key pathways involved in oxidative phosphorylation, mitochondrial biogenesis, and signaling cascades related to PGC-1α, mTORC1, and ERRα, while simultaneously inhibiting TGF-β-mediated muscle atrophic signaling. Functional assays demonstrated that under oxidative stress conditions, JGT-E preserved mitochondrial content more effectively, reduced reactive oxygen species levels, and enhanced both myoblast viability and myotube integrity. Network pharmacology analysis identified isoliquiritigenin, catechin, and glabridin as major bioactive compounds enriched in JGT-E, all of which play critical roles in mitigating oxidative stress and supporting mitochondrial function. These findings were further substantiated by antioxidant assays that confirmed the contribution of these compounds to the observed muscle-protective effects of JGT-E. Overall, JGT-E exhibited superior efficacy in preventing muscle atrophy compared to JGT-W, likely due to its enriched profile of potent bioactive constituents. These results highlight the critical role of extraction methods in herbal medicine research and support the potential of JGT-E as a promising candidate for the treatment of muscle atrophy.

In cell-based regenerative medicine, induced pluripotent stem cells (iPSCs) generated from reprogrammed adult somatic cells have emerged as a useful cell source due to the lack of ethical concerns and the low risk of immune rejection. To address the risk of teratoma formation, which is a safety issue in iPSC-based cell therapy, it is essential to selectively remove undifferentiated iPSCs remaining in the iPSC-derived differentiated cell product prior to in vivo transplantation. In this study, we explored whether an ethanol extract of coptidis rhizoma (ECR) exhibited anti-teratoma activity and identified the active components involved in the selective elimination of undifferentiated iPSCs. Transcriptome analysis of iPSCs confirmed that cell death-related pathways were significantly altered by ECR treatment. Our results demonstrate that ECR effectively induced apoptotic cell death and DNA damage in iPSCs, and that reactive oxygen species generation, mitochondrial damage, caspase activation, and p53 activation were involved in ECR-mediated iPSC death. However, in iPSC-derived differentiated cells (iPSC-Diff), reduced cell viability and the DNA damage response were not observed after ECR treatment. We co-cultured iPSCs and iPSC-Diff and found that ECR treatment selectively removed iPSCs, whereas iPSC-Diff remained intact. Prior to in ovo implantation, ECR treatment of a mixed cell culture of iPSCs and iPSC-Diff significantly suppressed iPSC-derived teratoma formation. Among the main components of the ECR, berberine and coptisine showed selective cytotoxicity to iPSCs but not to iPSC-Diff. Together, these results indicate the usefulness of ECRs in preparing safe and effective iPSC-based therapeutic cell products with no risk of teratoma formation.

Bongkyun Park, Kon Young Ji, Su-Jin Baek, Yu Ri Kim, Mudan Cai, Hyejin Shin, Yu Jin Kim, and So Min Lee. J Environ Health Sci. 2025;51:410-20. https://doi.org/10.5668/JEHS.2025.51.6.410