title: Molecular network and chemical fragment-based characteristics of medicinal herbs with cold and hot properties from Chinese medicine.
abstract: BACKGROUND
  Chinese herbal medicines (HMs) is one of the great herbal systems of the world, which play an important role in current health care system in many countries. In the view of tradition Chinese medicine (TCM) theory, Yin-yang and five-elements theory is the central theory, which is used to explain how the world and body work. Under the guidance of such philosophy, TCM considers that HMs have different properties, which are the important factors for prescribing herbal formulae; such prescriptions are based on TCM pattern classification in clinical practice. The cold and hot property are commonly defined for HM property identification; however, the biological activities that are related to the HM property remain a mystery because of a lack of appropriate methods. A bioinformatics approach was applied to identify the distinguishing biological activities of HMs that have these cold and hot properties.
  
  
  METHODS
  Twenty HMs with typical cold and hot properties (10 cold and 10 hot) were selected based on TCM clinical application records and Chinese pharmacopeia. The active target proteins of each HM were searched in the PubChem database and were analyzed in Ingenuity Pathway Analysis (IPA) platform to find out the HM property-related biological activities. In addition, the main compounds of the HMs were fragmented using a fragment-based approach and were analyzed for the purpose of deciphering the properties.
  
  
  RESULTS
  The main biological networks of HMs with cold and hot properties include cell cycle, cellular growth, proliferation and development, cancer, cytokine signaling, and intracellular and second messenger signaling; 11 specific pathways are presented to be perturbed only by HMs with the hot property, and the 27 specific target protein molecules include PRKACA, PRKCA, PRKCB, PRKCD, PRKCE, PRKCG, PRKD1, TLR4, TLR7, TLR8, TLR9, HTR4, HTR6, HTR7, HTR2A, HTR1B, HTR2B, GNAO1, GNAI1, TNF, IL8, ROCK2, AKT1, MAPK1, RPS6KA1, RPS6KA3 and JAK2, which are involved in the biological network. One specific pathway is detected to be involved in the biological network of HMs with the cold property, the specific molecules are RAN and KPNB1. Cold propertied HMs show intensive toxicity in the heart, liver and kidney compared with hot HMs, which is likely to be correlated with the specific chemical fragments constructions in the HMs with the cold property, such as long chain alkenes, Benzo heterocycle and azotic heterocycle according to the chemical fragment analysis for the HMs.
  
  
  CONCLUSIONS
  Inflammation and immunity regulation are more related to HMs with the hot property, and cold propertied HMs possess the tendency to impact cell growth, proliferation and development. Integrative bioinformatics analysis and chemical structure analysis are a promising methods for identifying the biological activity of HM properties.
authors.affiliation: Institute of Basic Research In Clinical Medicine, China Academy of Traditional Chinese Medicine, Beijing 100700, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Liang
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Maolin
authors.initials: M
authors.lastname: Wang
authors.forename: Xuyan
authors.initials: X
authors.lastname: Niu
authors.forename: Junping
authors.initials: J
authors.lastname: Zhan
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: He
authors.forename: Changyuan
authors.initials: C
authors.lastname: Yu
authors.forename: Miao
authors.initials: M
authors.lastname: Jiang
authors.forename: Aiping
authors.initials: A
authors.lastname: Lu
mesh_terms: D019295:Computational Biology; D004365:Drugs, Chinese Herbal; D008516:Medicine, Chinese Traditional; D010946:Plants, Medicinal; D011506:Proteins; D015398:Signal Transduction
chemical_list: D004365:Drugs, Chinese Herbal; D011506:Proteins
keywords: Bioinformatics; Herbal medicine; Ingenuity Pathway Analysis; Property; Tradition Chinese medicine