Rapid action of mechanism investigation of Yixin Ningshen tablet in treating depression by combinatorial use of systems biology and bioinformatics tools
JOURNAL OF ETHNOPHARMACOLOGY
Authors: Wu, Ruoming; Wang, Huijun; Lv, Xing; Shen, Xiaoyan; Ye, Guan
Abstract
Ethnopharmacological relevance: Yixin Ningshen tablet is a CFDA-approved TCM formula for treating depression clinically. However, little is known about its active compounds and related potential target proteins, so far, no researches have been performed to investigate its mechanism of action for the treatment of depression. Aim of the study: Here we develop an original bioinformatics pipeline composed of text mining tools, database querying and systems biology combinatorial analysis, which is applied to rapidly explore the mechanism of action of Yixin Ningshen tablet in treating depression. Materials and methods: Text mining and database query were applied to identify active compounds in Yixin Ningshen tablet for the treatment of depression. Then SwissTargetPrediction was used to predict their potential target proteins. PubMed was retrieved to summarize known depression related systems biology results. Ingenuity Pathway Analysis (IPA) tools and STRING were applied to construct a compound-target protein-gene protein-differential protein-differential metabolite network with the integration of compound-target interaction and systems biology results, as well as enrich the target proteins related pathways. ChEMBL and CDOCKER were used to validate the compound-target interactions. Results: 62 active compounds and their 286 potential target proteins were identified in Yixin Ningshen tablet for the treatment of depression. The construction of compound-target protein-gene protein-differential protein-differential metabolite network shrinked the number of potential target proteins from 286 to 133. Pathway enrichment analysis of target proteins indicated that Neuroactive ligand-receptor interaction, Calcium signaling pathway, Serotonergic synapse, cAMP signaling pathway and Gap junction were the common primary pathways regulated by both Yixin Ningshen Tablet and anti-depressant drugs, and MAPK, Relaxin, AGE-RAGE, Estrogen, HIF-1, Jak-STAT signaling pathway, Endocrine resistance, Arachidonic acid metabolism and Regulation of actin cytoskeleton were the specifically main pathways regulated by Yixin Ningshen tablet for the treatment of depression. Further validations based on references and molecular docking results demonstrated that Yixin Ningshen tablet could primarily target MAPT, CHRM1 and DRD1, thus regulating serotonergic neurons, cholinergic transmission, norepinephrine and dopamine reuptake for the treatment of depression. Conclusions: This study displays the power of extensive mining of public data and bioinformatical repositories to provide answers for a specific pharmacological question. It furthermore demonstrates how the usage of such a combinatorial approach is advantageous for the biologist in terms of experimentation time and costs.
Levels of [H-3]pirenzepine binding in Brodmann's area 6 from subjects with schizophrenia is not associated with changes in the transcription factor SP1 or BACE1
SCHIZOPHRENIA RESEARCH
Authors: Dean, Brian; Soulby, Andrew; Evin, Genevieve M.; Scarr, Elizabeth
Abstract
Decreased muscarinic M1 receptor (CHRM1) mRNA has been reported in Brodmann's area (BA) 6 from subjects with schizophrenia. We have extended this study by measuring levels of CHRM1 ([H-3]pirenzepine binding), CHRM3 ([H-3]4-DAMP binding), the transcription factor SP1 and the CHRM1 downstream target beta-site APP-cleaving enzyme 1 (BACE1) in BA 6 from 19 subjects with schizophrenia and 19 control subjects. Radioligand binding was quantified using either in situ radioligand binding with autoradiography or, in cohorts of 10 control subjects and 10 subjects with schizophrenia, membrane enriched fraction (MEF) CNS ([H-3]pirenzepine binding only). Levels of SP1 and BACE1 were measured by Western blotting. [H-3]pirenzepine binding to tissue sections was in two layers, binding to tissue sections (Binding layer 1: p < 0.01; Binding layer 2: p<0.001) and MEF (p<0.05) were decreased in schizophrenia. Levels of [H-3]4-DAMP binding, SP1 and BACE1 were not altered in subjects with the disorder. This study shows a decrease in levels of CHRM1 in BA 6 from subjects with schizophrenia; as CHRM1 and BA 6 are important in maintaining normal cognitive function, these data support the hypothesis that decreased levels of cortical CHRM1 may contribute to the cognitive deficits associated with schizophrenia. Our findings on BACE1 suggest that the schizophrenia phenotype reported in BACE(-/-) mice is not simply due to lack of that protein in the cortex. (C) 2008 Elsevier B.V. All rights reserved.