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Background  Traditional Chinese medicine (TCM) herbal formulae provide valuable therapeutic strategies. However, the active ingredients and mechanisms of action remain unclear for most of these formulae. Therefore, the identification of complex mechanisms is a major challenge in TCM research.    Methods  This study used a network pharmacology approach to clarify the anti-inflammatory and cough suppressing mechanisms of the Chinese medicinal preparation  Eriobotrya japonica – Fritillaria usuriensis  dropping pills (ChuanbeiPipa dropping pills, CBPP). The chemical constituents of CBPP were identified by high-quality ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS), and anti-inflammatory ingredients were selected and analyzed using the PharmMapper and Kyoto Encyclopedia of Genes and Genomes (KEGG) bioinformatics websites to predict the target proteins and related pathways, respectively. Then, an RNA-sequencing (RNA-Seq) analysis was carried out to investigate the different expression of genes in the lung tissue of rats with chronic bronchitis.    Results  Six main constituents affected 19 predicted pathways, including ursolic acid and oleanolic acid from  Eriobotrya japonica  (Thunb.) Lindl. (  Eri  ), peiminine from  Fritillaria usuriensis  Maxim. (  Fri  ), platycodigenin and polygalacic acid from  Platycodon grandiflorum  (Jacq.) A. DC. (  Pla  ) and guanosine from  Pinellia ternata  (Thunb.) Makino. (  Pin  ). Expression of 34 genes was significantly decreased after CBPP treatment, affecting four therapeutic functions: immunoregulation, anti-inflammation, collagen formation and muscle contraction.    Conclusion  The active components acted on the mitogen activated protein kinase (MAPK) pathway, transforming growth factor (TGF)-beta pathway, focal adhesion, tight junctions and the action cytoskeleton to exert anti-inflammatory effects, resolve phlegm, and relieve cough. This novel approach of global chemomics-integrated systems biology represents an effective and accurate strategy for the study of TCM with multiple components and multiple target mechanisms.    Electronic supplementary material  The online version of this article (doi:10.1186/s12906-015-0983-y) contains supplementary material, which is available to authorized users.

bmc complementary and alternative medicine

An integrated global chemomics and system biology approach to analyze the mechanisms of the traditional Chinese medicinal preparation Eriobotrya japonica – Fritillaria usuriensis dropping pills for pulmonary diseases