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Wang P, Yu Y, Liu J, Li B, Zhang Y, Li D, Xu W, Liu Q, Wang Z. IMCC: A Novel Quantitative Approach Revealing Variation of Global Modular Map and Local Inter-Module Coordination Among Differential Drug's Targeted Cerebral Ischemic Networks. Front Pharmacol 2021; 12:637253. [PMID: 33935725 PMCID: PMC8087074 DOI: 10.3389/fphar.2021.637253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/23/2021] [Indexed: 02/01/2023] Open
Abstract
Stroke is a common disease characterized by multiple genetic dysfunctions. In this complex disease, detecting the strength of inter-module coordination (genetic community interaction) and subsequent modular rewiring is essential to characterize the reactive biosystematic variation (biosystematic perturbation) brought by multiple-target drugs, whose effects are achieved by hitting on a series of targets (target profile) jointly. Here, a quantitative approach for inter-module coordination and its transition, named as IMCC, was developed. Applying IMCC to mouse cerebral ischemia–related gene microarray, we investigated a holistic view of modular map and its rewiring from ischemic stroke to drugs (baicalin, BA; ursodeoxycholic acid, UA; and jasminoidin, JA) perturbation states and locally identified the cooperative pathological module pair and its dissection. Our result suggested the global modular map in cerebral ischemia exhibited a characteristic “core–periphery” architecture, and this architecture was rewired by the effective drugs heterogeneously: BA and UA converged modules into an intensively connected integrity, whereas JA diverged partial modules and widened the remaining inter-module paths. Locally, the PMP dissociation brought by drugs contributed to the reversion of the pathological condition: the focus of the cellular function shift from survival after nervous system injury into development and repair, including neurotrophin regulation, hormone releasing, and chemokine signaling activation. The core targets and mechanisms were validated by in vivo experiments. Overall, our result highlights the holistic inter-module coordination rearrangement rather than a target or a single module that brings phenotype alteration. This strategy may lead to systematically explore detailed variation of inter-module pharmacological action mode of multiple-target drugs, which is the principal problem of module pharmacology for network-based drug discovery.
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Affiliation(s)
- Pengqian Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bing Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Dongfeng Li
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wenjuan Xu
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Qiong Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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Guan S, Liu Q, Gu H, Zhang YY, Wei PL, Qi YF, Liu J, Wang Z. Pluripotent anti-inflammatory immunomodulatory effects of papaverine against cerebral ischemic-reperfusion injury. J Pharmacol Sci 2020; 144:69-75. [DOI: 10.1016/j.jphs.2020.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 03/23/2020] [Accepted: 04/02/2020] [Indexed: 12/11/2022] Open
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Wei P, Wang P, Li B, Gu H, Liu J, Wang Z. Divergence and Convergence of Cerebral Ischemia Pathways Profile Deciphers Differential Pure Additive and Synergistic Mechanisms. Front Pharmacol 2020; 11:80. [PMID: 32161541 PMCID: PMC7053362 DOI: 10.3389/fphar.2020.00080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
Aim The variable mechanisms on additive and synergistic effects of jasminoidin (JA)-Baicalin (BA) combination and JA-ursodeoxycholic acid (UA) combination in treating cerebral ischemia are not completely understood. In this study, we explored the differential pure mechanisms of additive and synergistic effects based on pathway analysis that excluded ineffective interference. Methods The MCAO mice were divided into eight groups: sham, vehicle, BA, JA, UA, Concha Margaritifera (CM), BA-JA combination (BJ), and JA-UA combination (JU). The additive and synergistic effects of combination groups were identified by cerebral infarct volume calculation. The differentially expressed genes based on a microarray chip containing 16,463 oligoclones were uploaded to GeneGo MetaCore software for pathway analyses and function catalogue. The comparison of specific pathways and functions crosstalk between different groups were analyzed to reveal the underlying additive and synergistic pharmacological variations. Results Additive BJ and synergistic JU were more effective than monotherapies of BA, JA, and UA, while CM was ineffective. Compared with monotherapies, 43 pathways and six functions were found uniquely in BJ group, with 33 pathways and three functions in JU group. We found six overlapping pathways and six overlapping functions between BJ and JU groups, which mainly involved central nervous system development. Thirty-seven specific pathways and 10 functions were activated by additive BJ, which were mainly related to cell adhesion and G-protein signaling; and 27 specific pathways and three functions of synergistic JU were associated with regulation of metabolism, DNA damage, and translation. The overlapping and distinct pathways and functions may contribute to different additive and synergistic effects. Conclusion The divergence pathways of pure additive effect of BJ were mainly related to cell adhesion and G-protein signaling, while the pure synergistic mechanism of JU depended on metabolism, translation and DNA damage. Such a systematic analysis of pathways may provide an important paradigm to reveal the pharmacological mechanisms underlying drug combinations.
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Affiliation(s)
- Penglu Wei
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Pengqian Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bing Li
- Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hao Gu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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Wang PQ, Liu Q, Xu WJ, Yu YN, Zhang YY, Li B, Liu J, Wang Z. Pure mechanistic analysis of additive neuroprotective effects between baicalin and jasminoidin in ischemic stroke mice. Acta Pharmacol Sin 2018; 39:961-974. [PMID: 29345255 PMCID: PMC6256271 DOI: 10.1038/aps.2017.145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/18/2017] [Indexed: 02/06/2023] Open
Abstract
Both baicalin (BA) and jasminoidin (JA) are active ingredients in Chinese herb medicine Scutellaria baicalensis and Fructus gardeniae, respectively. They have been shown to exert additive neuroprotective action in ischemic stroke models. In this study we used transcriptome analysis to explore the pure therapeutic mechanisms of BA, JA and their combination (BJ) contributing to phenotype variation and reversal of pathological processes. Mice with middle cerebral artery obstruction were treated with BA, JA, their combination (BJ), or concha margaritifera (CM). Cerebral infarct volume was examined to determine the effect of these compounds on phenotype. Using the hippocampus microarray and ingenuity pathway analysis (IPA) software, we exacted the differentially expressed genes, networks, pathways, and functions in positive-phenotype groups (BA, JA and BJ) by comparing with the negative-phenotype group (CM). In the BA, JA, and BJ groups, a total of 7, 4, and 11 specific target molecules, 1, 1, and 4 networks, 51, 59, and 18 canonical pathways and 70, 53, and 64 biological functions, respectively, were identified. Pure therapeutic mechanisms of BA and JA were mainly overlapped in specific target molecules, functions and pathways, which were related to the nervous system, inflammation and immune response. The specific mechanisms of BA and JA were associated with apoptosis and cancer-related signaling and endocrine and hormone regulation, respectively. In the BJ group, novel target profiles distinct from mono-therapies were revealed, including 11 specific target molecules, 10 functions, and 10 pathways, the majority of which were related to a virus-mediated immune response. The pure additive effects between BA and JA were based on enhanced action in virus-mediated immune response. This pure mechanistic analysis may provide a clearer outline of the target profiles of multi-target compounds and combination therapies.
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MESH Headings
- Animals
- Apoptosis/drug effects
- Apoptosis/genetics
- Disease Models, Animal
- Drug Synergism
- Drug Therapy, Combination
- Flavonoids/pharmacology
- Gene Expression Profiling/methods
- Gene Expression Regulation
- Gene Regulatory Networks/drug effects
- Hippocampus/drug effects
- Hippocampus/immunology
- Hippocampus/metabolism
- Hippocampus/pathology
- Immunity, Innate/drug effects
- Immunity, Innate/genetics
- Infarction, Middle Cerebral Artery/drug therapy
- Infarction, Middle Cerebral Artery/genetics
- Infarction, Middle Cerebral Artery/metabolism
- Infarction, Middle Cerebral Artery/pathology
- Iridoids/pharmacology
- Male
- Mice
- Neuroprotective Agents/pharmacology
- Oligonucleotide Array Sequence Analysis
- Phenotype
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Signal Transduction/drug effects
- Signal Transduction/genetics
- Systems Biology/methods
- Transcriptome/drug effects
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Affiliation(s)
- Peng-qian Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiong Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wen-juan Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ya-nan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ying-ying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Bing Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
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Li B, Liu J, Yu Y, Wang P, Zhang Y, Ni X, Liu Q, Zhang X, Wang Z, Wang Y. Network-Wide Screen Identifies Variation of Novel Precise On-Module Targets Using Conformational Modudaoism. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017; 7:16-25. [PMID: 28925077 PMCID: PMC5784734 DOI: 10.1002/psp4.12253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/30/2017] [Accepted: 09/13/2017] [Indexed: 01/30/2023]
Abstract
Modular targeting is promising in drug research at the network level, but it is challenging to quantificationally identify the precise on-modules. Based on a proposed Modudaoism (MD), we defined conserved MD (MDc) and varied MD (MDv) to quantitatively evaluate the conformational and energy variations of modules, and thereby identify the conserved and discrepant allosteric modules (AMs). Compared to the Zsummary , MDc/MDv got an optimized result of module preserved ratio and modular structure. In the mice anti-ischemic networks, 3, 5, and 1 conserved AMs as well as 4, 1, and 3 on-modules of baicalin (BA), jasminoidin (JA), and ursodeoxycholic acid (UA) were identified by MDc and MDv, 5 unique AMs and their characteristic actions were revealed. Besides, co-immunoprecipitation (Co-IP) experiments validated the representative modular structure. MDc/MDv method can quantitatively define the conformational variations of modules and screen the precise on-modules network-wide, which may provide a promising strategy for drug discovery.
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Affiliation(s)
- Bing Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,ShanXi Buchang Pharmaceutical Co., Ltd., Heze, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Pengqian Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xumin Ni
- Department of Mathematics, School of Science, Beijing Jiaotong University, Beijing, China
| | - Qiong Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoxu Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongyan Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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Liu Q, Liu J, Wang P, Zhang Y, Li B, Yu Y, Dang H, Li H, Zhang X, Wang Z. Poly-dimensional network comparative analysis reveals the pure pharmacological mechanism of baicalin in the targeted network of mouse cerebral ischemia. Brain Res 2017; 1666:70-79. [PMID: 28465229 DOI: 10.1016/j.brainres.2017.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 12/12/2022]
Abstract
AIM This study aimed to investigate the pure pharmacological mechanisms of baicalin/baicalein (BA) in the targeted network of mouse cerebral ischemia using a poly-dimensional network comparative analysis. METHODS Eighty mice with induced focal cerebral ischemia were randomly divided into four groups: BA, Concha Margaritifera (CM), vehicle and sham group. A poly-dimensional comparative analysis of the expression levels of 374 stroke-related genes in each of the four groups was performed using MetaCore. RESULTS BA significantly reduced the ischemic infarct volume (P<0.05), whereas CM was ineffective. Two processes and 10 network nodes were shared between "BA vs CM" and vehicle, but there were no overlapping pathways. Two pathways, three processes and 12 network nodes overlapped in "BA vs CM" and BA. The pure pharmacological mechanism of BA resulted in targeting of pathways related to development, G-protein signaling, apoptosis, signal transduction and immunity. The biological processes affected by BA were primarily found to correlate with apoptotic, anti-apoptotic and neurophysiological processes. Three network nodes changed from up-regulation to down-regulation, while mitogen-activated protein kinase kinase 6 (MAP2K6, also known as MEK6) changed from down-regulation to up-regulation in "BA vs CM" and vehicle. The changed nodes were all related to cell death and development. CONCLUSION The pure pharmacological mechanism of BA is related to immunity, apoptosis, development, cytoskeletal remodeling, transduction and neurophysiology, as ascertained using a poly-dimensional network comparative analysis.
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Affiliation(s)
- Qiong Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Pengqian Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Yingying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Bing Li
- Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Yanan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Haixia Dang
- China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Haixia Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Xiaoxu Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing 100700, China.
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Fangjiomics: revealing adaptive omics pharmacological mechanisms of the myriad combination therapies to achieve personalized medicine. Acta Pharmacol Sin 2015; 36:651-3. [PMID: 26036241 DOI: 10.1038/aps.2015.33] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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