ArticleBriefings in bioinformatics2023
Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Ephedrae Herba-Associated Adverse Events: A Disproportionality Analysis Integrated with Network Pharmacology.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Global Trends and Research Hotspots in Natural Products for Hyperuricemia: A Bibliometric Analysis (2004-2026).Pharmaceuticals (Basel, Switzerland) · 2026Review
- Multi-Bioinformatics Approach Reveals COX5B-Mediated Modulation of Oxidative Phosphorylation and ROS Levels by Water and Ethanol Extracts of Schisandrae Fructus in SW1783 Cells.Antioxidants (Basel, Switzerland) · 2026Article
- Review
- Visceral Leishmaniasis: Integrated In Silico Screening of Djiboutian Medicinal Plant Phytoconstituents TargetingPharmaceuticals (Basel, Switzerland) · 2026Article
- Integrated analysis of isorhamnetin-associated targets in chronic pancreatitis and pancreatic cancer: immune-infiltration associations and antitumor effects in pancreatic cancer cells.Frontiers in immunology · 2026Article
- Mining personalized core traditional Chinese medicine prescriptions for rheumatoid arthritis and elucidating their mechanisms via frequent closed Itemset compression and multilevel network pharmacology.Frontiers in molecular biosciences · 2026Article
- Multi-level association rule mining and network pharmacology to identify the polypharmacological effects of herbal materials and compounds in traditional medicine.Briefings in bioinformatics · 2025Article
- Ganoapplanilactone C fromAntioxidants (Basel, Switzerland) · 2025Article
- Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory.Briefings in bioinformatics · 2025Article
- Green Catalysis: The Role of Medicinal Plants as Food Waste Decomposition Enhancers/Accelerators.Life (Basel, Switzerland) · 2025Review
- Discovery and Prediction Study of the Dominant Pharmacological Action Organ ofInternational journal of molecular sciences · 2024Article
- Effect ofInternational journal of molecular sciences · 2024Article
- Phytochemical constituents analysis inCommunicative & integrative biology · 2024Article
- In Silico and In Vivo Evaluation of the Maqui Berry (Metabolites · 2023Article
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5 authors.
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Abstract
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.
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