title: Herbalog: A tool for target-based identification of herbal drug efficacy through molecular docking.
abstract: BACKGROUND
  Traditionally, molecular docking is primarily employed to screen pure compounds; the top-ranking chemicals are subsequently selected for experimental validation. Unlike synthetic chemicals, most natural products are commercially unavailable. The isolation and purification of each natural product is extremely time-consuming, which has restricted the screening of lead compounds from natural products.
  
  
  OBJECTIVE
  We developed a protocol, Herbalog, to facilitate the identification of bioactive phytochemicals through molecular docking.
  
  
  METHODS
  We wrote a script using Python and Autodock Vina for docking; ligand displacement and adipolysis assays were used to determine the anti-fatty acid binding protein (FABP) 4 activity of bioactive extracts. An ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry system was applied for identifying major peaks of bioactive extracts.
  
  
  RESULTS
  Herbalog, a natural product database, contains 5,112 phytochemicals from 197 common herbs and a script that counts the number of hits from docking in each herb and calculates the hit rate of herbs. Herbalog prioritizes herbs according to their hit rates, and top-ranking herb candidates contain a large repertoire of hits. We used Herbalog as a screening tool and identified labdane diterpenoids from Andrographis paniculata as leading candidates of FABP4 inhibitors.
  
  
  CONCLUSIONS
  Herbalog facilitates the discovery of herbs that possess the highest number of inhibitors or activators against target proteins, which reduces the sample preparation time for preliminary validation.
authors.affiliation: School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
authors.forename: Jian-Shu
authors.initials: JS
authors.lastname: Hu
authors.affiliation: Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay Road, Hong Kong SAR, China.
authors.forename: Huang-Quan
authors.initials: HQ
authors.lastname: Lin
authors.affiliation: School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
authors.forename: Tsz-Ming
authors.initials: TM
authors.lastname: Ip
authors.affiliation: School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China. Electronic address: chicheongwan@cuhk.edu.hk.
authors.forename: David Chi-Cheong
authors.initials: DC
authors.lastname: Wan
mesh_terms: D035685:Andrographis / Q000737:chemistry*; D002853:Chromatography, Liquid; D016208:Databases, Factual; D004224:Diterpenes / Q000494:pharmacology*; D055808:Drug Discovery / Q000379:methods*; D004365:Drugs, Chinese Herbal / Q000494:pharmacology; D050556:Fatty Acid-Binding Proteins / Q000037:antagonists & inhibitors*; D029001:Herbal Medicine / Q000379:methods*; D006801:Humans; D013058:Mass Spectrometry; D062105:Molecular Docking Simulation / Q000379:methods*; D010936:Plant Extracts / Q000494:pharmacology*; D010946:Plants, Medicinal / Q000737:chemistry
chemical_list: D004224:Diterpenes; D004365:Drugs, Chinese Herbal; C493410:FABP4 protein, human; D050556:Fatty Acid-Binding Proteins; D010936:Plant Extracts
keywords: Andrographis paniculata; FABP4 inhibitor; Herbalog; Molecular docking; Natural product; Virtual screening