Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

• Publication year

  2017

• Venue

  Evidence-Based Complementary and Alternative Medicine

• Publication date

  2017-06-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1155/2017/7198645PMID 28690664PMCID 5485337
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A network analysis of the Chinese medicine Lianhua-Qingwen formula to identify its main effective components.

  2016cited by this paper
• Herb-target interaction network analysis helps to disclose molecular mechanism of traditional Chinese medicine

  2016cited by this paper
• Discovery of Novel 15-Lipoxygenase Activators To Shift the Human Arachidonic Acid Metabolic Network toward Inflammation Resolution.

  2016cited by this paper
• Modeling the mitotic regulatory network identifies highly efficient anti-cancer drug combinations.

  2015cited by this paper
• Mechanism of Action of Thalassospiramides, A New Class of Calpain Inhibitors

  2015cited by this paper
• TCMSP: a database of systems pharmacology for drug discovery from herbal medicines

  2014cited by this paper
• Blockade of EphA4 signaling ameliorates hippocampal synaptic dysfunctions in mouse models of Alzheimer’s disease

  2014cited by this paper
• Identification of diverse natural products as falcipain-2 inhibitors through structure-based virtual screening.

  2014cited by this paper
• Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis

  2014cited by this paper
• Network pharmacology study on the mechanism of traditional Chinese medicine for upper respiratory tract infection.

  2014cited by this paper
• Computational Systems Biology

  2013cited by this paper
• Predicting the Drug Safety for Traditional Chinese Medicine through a Comparative Analysis of Withdrawn Drugs Using Pharmacological Network

  2013cited by this paper
• Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods, and Applications

  2013cited by this paper
• Platelet Aggregation Pathway Network-Based Approach for Evaluating Compounds Efficacy

  2013cited by this paper
• Network pharmacology-based prediction of the active ingredients and potential targets of Chinese herbal Radix Curcumae formula for application to cardiovascular disease.

  2013cited by this paper
• A Systems-Pharmacology Analysis of Herbal Medicines Used in Health Improvement Treatment: Predicting Potential New Drugs and Targets

  2013cited by this paper
• Understanding traditional Chinese medicine anti-inflammatory herbal formulae by simulating their regulatory functions in the human arachidonic acid metabolic network.

  2013cited by this paper
• Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines

  2013cited by this paper
• Understanding molecular mechanisms of traditional Chinese medicine for the treatment of influenza viruses infection by computational approaches.

  2013cited by this paper
• An optimized algorithm for detecting and annotating regional differential methylation

  2013cited by this paper
• Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines

  2012cited by this paper
• TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis

  2012cited by this paper
• Future perspectives of personalized medicine in traditional Chinese medicine: a systems biology approach.

  2012cited by this paper
• A network-based analysis of traditional Chinese medicine cold and hot patterns in rheumatoid arthritis.

  2012cited by this paper
• Traditional Chinese Medicine-Based Network Pharmacology Could Lead to New Multicompound Drug Discovery

  2012cited by this paper
• Dynamic modeling of human 5-lipoxygenase-inhibitor interactions helps to discover novel inhibitors.

  2012cited by this paper
• A co-module approach for elucidating drug-disease associations and revealing their molecular basis

  2012cited by this paper
• Boolean modeling in systems biology: an overview of methodology and applications

  2012cited by this paper
• Drug-likeness analysis of traditional Chinese medicines: prediction of drug-likeness using machine learning approaches.

  2012cited by this paper
• A Network-Based Multi-Target Computational Estimation Scheme for Anticoagulant Activities of Compounds

  2011cited by this paper
• Fast and effective identification of the bioactive compounds and their targets from medicinal plants via computational chemical biology approach

  2011cited by this paper
• High performance screening, structural and molecular dynamics analysis to identify H1 inhibitors from TCM Database@Taiwan.

  2011cited by this paper
• Discovery of dual target inhibitors against cyclooxygenases and leukotriene A4 hydrolyase.

  2011cited by this paper
• The fundamental theory of traditional Chinese medicine and the consideration in its research strategy

  2011cited by this paper
• Drug-target network and polypharmacology studies of a Traditional Chinese Medicine for type II diabetes mellitus

  2011cited by this paper
• Drug design for hemagglutinin: Screening and molecular dynamics from traditional Chinese medicine database

  2011cited by this paper
• TCM Database@Taiwan: The World's Largest Traditional Chinese Medicine Database for Drug Screening In Silico

  2011cited by this paper
• Network target for screening synergistic drug combinations with application to traditional Chinese medicine

  2011cited by this paper
• Molecular dynamics simulations and drug discovery

  2011cited by this paper
• Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae

  2010cited by this paper
• Molecular networks for the study of TCM Pharmacology

  2010cited by this paper
• HIT: linking herbal active ingredients to targets

  2010cited by this paper
• Network-Based Relating Pharmacological and Genomic Spaces for Drug Target Identification

  2010cited by this paper
• Network Systems Underlying Traditional Chinese Medicine Syndrome and Herb Formula

  2009cited by this paper
• Finding multiple target optimal intervention in disease-related molecular network

  2008cited by this paper
• Network pharmacology: the next paradigm in drug discovery.

  2008cited by this paper
• Chinese medicine and its modernization demands.

  2008cited by this paper
• Network-based global inference of human disease genes

  2008cited by this paper
• Discovery of multitarget inhibitors by combining molecular docking with common pharmacophore matching.

  2008cited by this paper
• Efficient algorithms for ordinary differential equation model identification of biological systems.

  2007cited by this paper
• Computational methods for Traditional Chinese Medicine: A survey

  2007cited by this paper
• Dynamic Simulations on the Arachidonic Acid Metabolic Network

  2007cited by this paper
• Peptide deformylase is a potential target for anti‐Helicobacter pylori drugs: Reverse docking, enzymatic assay, and X‐ray crystallography validation

  2006cited by this paper
• TarFisDock: a web server for identifying drug targets with docking approach

  2006cited by this paper
• Metabolomics in the context of systems biology: bridging traditional Chinese medicine and molecular pharmacology

  2005cited by this paper
• Therapeutic wisdom in traditional Chinese medicine: a perspective from modern science.

  2005cited by this paper
• Network-targeted combination therapy : a new concept in cancer treatment

  2004cited by this paper
• The rediscovery of ancient Chinese herbal formulas

  2004cited by this paper
• Systems biology in drug discovery

  2004cited by this paper
• The efficiency of multi-target drugs: the network approach might help drug design.

  2004cited by this paper
• Asian medicine. The new face of traditional Chinese medicine.

  2003cited by this paper
• Computational systems biology

  2002cited by this paper
• A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs

  2002cited by this paper
• Traditional Chinese Medicine Database and Application on the Web

  2001influential reference
• KEGG: Kyoto Encyclopedia of Genes and Genomes

  2000cited by this paper
• KEGG: Kyoto Encyclopedia of Genes and Genomes

  1999cited by this paper
• Chemical Similarity Searching

  1998cited by this paper
• Molecular docking towards drug discovery

  1996cited by this paper

• Integrating Modern Technologies and Intelligence Systems for Infectious Disease Preparedness: A Strategic Review

  2025cites this paper
• Computer-Aided Drug Design in Research on Chinese Materia Medica: Methods, Applications, Advantages, and Challenges

  2025cites this paper
• Uses of Molecular Docking Simulations in Elucidating Synergistic, Additive, and/or Multi-Target (SAM) Effects of Herbal Medicines

  2024cites this paper
• Exploring the Molecular Mechanisms of Huaier on Modulating Metabolic Reprogramming of Hepatocellular Carcinoma: A Study based on Network Pharmacology, Molecular Docking and Bioinformatics.

  2024cites this paper
• Antibacterial and Anti-Inflammatory Potential of Chinese Medicinal Herbs: Lonicerae flos, Lonicerae japonicae flos, Scutellaria baicalensis Georgi, and Forsythia suspensa

  2022cites this paper
• Integrating bioinformatics with pharmacological evaluation for illustrating the action mechanism of herbal formula Jiao'e mixture in suppressing lung carcinoma.

  2021cites this paper
• Epigenetic Studies of Chinese Herbal Medicine: Pleiotropic Role of DNA Methylation

  2021cites this paper
• Mechanism of Yinqin Oral Liquid in the Treatment of Chronic Pharyngitis Based on Network Pharmacology

  2021cites this paper
• DDDT_A_324139 4413..4421

  2021cites this paper
• Development Strategy of Integrative Pharmacy

  2021cites this paper
• Detailed studies on the anticancer action of rosmarinic acid in human Hep-G2 liver carcinoma cells: evaluating its effects on cellular apoptosis, caspase activation and suppression of cell migration and invasion.

  2020cites this paper
• Essential Oil Phytocomplex Activity, a Review with a Focus on Multivariate Analysis for a Network Pharmacology-Informed Phytogenomic Approach

  2020cites this paper
• A Novel Strategy for Decoding and Validating the Combination Principles of Huanglian Jiedu Decoction From Multi-Scale Perspective

  2020cites this paper
• Editorial: The Potential Effect and Mechanism of Chinese Traditional Medicine on Vascular Homeostasis and Remodeling

  2020cites this paper
• Comparative comprehension on the anti-rheumatic Chinese herbal medicine Siegesbeckiae Herba: Combined computational predictions and experimental investigations.

  2019cites this paper
• Associating 197 Chinese herbal medicine with drug targets and diseases using the similarity ensemble approach

  2019cites this paper
• Herbal medicine for insomnia in elderly with hypertension: A systematic review and meta-analysis

  2019cites this paper
• Prediction of VEGF-C as a Key Target of Pure Total Flavonoids From Citrus Against NAFLD in Mice via Network Pharmacology

  2019cites this paper
• Xiaoerfupi alleviates the symptoms of functional dyspepsia by regulating the HTR3A and c-FOS.

  2019cites this paper
• From quality markers to data mining and intelligence assessment: A smart quality-evaluation strategy for traditional Chinese medicine based on quality markers.

  2018cites this paper
• Extraction of Amana edulis Induces Liver Cancer Apoptosis

  2018cites this paper
• Demystifying traditional Chinese medicines: Lycium barbarum as a model therapeutic

  2018cites this paper
• Title Identification of WT 1 as determinant of heptatocellular carcinoma and its inhibition by Chinese herbal medicine

  2017cites this paper
• Identification of WT1 as determinant of heptatocellular carcinoma and its inhibition by Chinese herbal medicine Salvia chinensis Benth and its active ingredient protocatechualdehyde

  2017cites this paper
• Integration of phytochemicals and phytotherapy into cancer precision medicine

  2017cites this paper