TCMSP: a database of systems pharmacology for drug discovery from herbal medicines

Abstract

BackgroundModern medicine often clashes with traditional medicine such as Chinese herbal medicine because of the little understanding of the underlying mechanisms of action of the herbs. In an effort to promote integration of both sides and to accelerate the drug discovery from herbal medicines, an efficient systems pharmacology platform that represents ideal information convergence of pharmacochemistry, ADME properties, drug-likeness, drug targets, associated diseases and interaction networks, are urgently needed.DescriptionThe traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) was built based on the framework of systems pharmacology for herbal medicines. It consists of all the 499 Chinese herbs registered in the Chinese pharmacopoeia with 29,384 ingredients, 3,311 targets and 837 associated diseases. Twelve important ADME-related properties like human oral bioavailability, half-life, drug-likeness, Caco-2 permeability, blood-brain barrier and Lipinski’s rule of five are provided for drug screening and evaluation. TCMSP also provides drug targets and diseases of each active compound, which can automatically establish the compound-target and target-disease networks that let users view and analyze the drug action mechanisms. It is designed to fuel the development of herbal medicines and to promote integration of modern medicine and traditional medicine for drug discovery and development.ConclusionsThe particular strengths of TCMSP are the composition of the large number of herbal entries, and the ability to identify drug-target networks and drug-disease networks, which will help revealing the mechanisms of action of Chinese herbs, uncovering the nature of TCM theory and developing new herb-oriented drugs. TCMSP is freely available at http://sm.nwsuaf.edu.cn/lsp/tcmsp.php.

Systems pharmacology exploration of botanic drug pairs reveals the mechanism for treating different diseases

“…In this section, based on our previous developed robust DTpre model and TCMSP database2723, the binding affinity of three Danshen pairs to their targets of interest incoronary heart disease, dysmenorrheal and nephrotic syndrome was investigated. Except for seven compounds (d-borneol, cedrol, shanzhiside methyl ester, uvaol, (−)-trans-Pinocarveol, dimethyl tetrasulfide, and dimethyllithospermate) that have no targets, total 85 candidate ingredients yielded 150 protein targets and 827 ingredient-target interactions were predicted for the Danshen, Yimucao, Xiangfu and Zelan (Table S3).…”

“…Previously, we built a TCMSP: Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (http://lsp.nwsuaf.edu.cn/tcmsp.php), which collected a total of 12144 chemical ingredients for all the 499 herbs registered in the Pharmacopoeia of the People’s Republic of China27. For Danshen-Yimucao, Danshen-Xiangfu and Danshe-Zelan, we have selected all available ingredients for each of four herbs, 204 for S. miltiorrhizae , 52 for H. leonuri , 104 for C. rotundus and 16 for E. Japonicum .…”

Systems pharmacology for traditional Chinese medicine with application to cardio-cerebrovascular diseases

“…10 Using this platform, a fundamental pharmacokinetics-pharmacodynamics theory for TCM can be constructed. The core of TCMSP is a series of integrated mathematical and computational models that are applied to efficiently explore the interactions among different elements (herbal compounds, drug targets, cells, tissues) and to reveal the functional mechanism of TCM theories.…”

Piper longum: A review of its phytochemicals and their network pharmacological evaluation

“…Relevant research articles from pubMed-NCBI (https://www.ncbi.nlm.nih.gov/pubmed/) were selected and manually scrutinized. Three databases UNPD (Universal Natural Products Database) (pkuxxj.pku.edu.cn/UNPD), TCMSP (Traditional Chinese Medicine Systems Pharmacology) (Ru et al, 2014) and PCIDB (PhytoChemical Interactions DB) (http://www.genome.jp/db/pcidb) were screened for the potentially active phytochemical present in P. longum. Chemical information of these phytochemicals was compiled from PubChem database (Bolton et al, 2008) and ChEMBL (Gaulton et al, 2011).…”