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Metabolomics-Based Pharmacodynamic Analysis of Zhuang Yao Shuang Lu Tong Nao Granules in a Rat Model of Ischemic Cerebral Infarction. Anal Cell Pathol (Amst) 2022; 2022:8776079. [PMID: 35846873 PMCID: PMC9277214 DOI: 10.1155/2022/8776079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/30/2022] [Accepted: 06/04/2022] [Indexed: 12/04/2022] Open
Abstract
This study used a metabolomic approach to reveal changes in the levels of metabolic biomarkers and related metabolic pathways before and after Zhuang Yao Shuang Lu Tong Nao granule (YHT) treatment in rats with cerebral ischemia. The neurological deficit scores were significantly higher in the MCAO_R group than in the NC group, indicating that the mice had significantly impaired motor functions. The YHT group had significantly lower scores than the MCAO_R group, suggesting that YHT significantly improved motor function in rats. TTC staining of the brain tissue revealed that YHT significantly reduced the area of cerebral infarction in the treated rats. The MCAO_R group was better separated from the NC rent, sham, and YHT groups via metabolomic PCA. Moreover, there were significant differences in the differential metabolites between the MACO_R and YHT groups. Eighteen common differential metabolites were detected between the MACO_R and NC groups, MACO_R and sham groups, and MACO_R and YHT groups, indicating that YHT significantly increased the levels of various metabolites in the serum of cerebral ischemic stroke (CIS) rats. Moreover, a total of 23 metabolic pathways were obtained. We identified 11 metabolic pathways with the most significant effects in the bubble plots. In conclusion, from a systems biology perspective, this metabolomics-based study showed that YHT could be used to treat ischemic stroke by modulating changes in endogenous metabolites.
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Li B, Wang Y, Gu H, Yu Y, Wang P, Liu J, Zhang Y, Chen Y, Niu Q, Wang B, Liu Q, Guan S, Li Y, Zhang H, Wang Z. Modular Screening Reveals Driver Induced Additive Mechanisms of Baicalin and Jasminoidin on Cerebral Ischemia Therapy. Front Cardiovasc Med 2022; 9:813983. [PMID: 35265682 PMCID: PMC8899124 DOI: 10.3389/fcvm.2022.813983] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Combination therapy with increased efficacy and reduced toxicity plays a crucial role in treating complex diseases, such as stroke, but it remains an insurmountable barrier to elucidate the mechanisms of synergistic effects. Here, we present a Driver-induced Modular Screening (DiMS) strategy integrated synergistic module and driver gene identification to elucidate the additive mechanisms of Baicalin (BA) and Jasminoidin (JA) on cerebral ischemia (CI) therapy. Based on anti-ischemia genomic networks BA, JA, and their combination (BJ), we obtained 4, 3, and 9 On-modules of BA, JA, and BJ by modular similarity analysis. Compared with the monotherapy groups, four additive modules (Add-module, BJ_Mod-4, 7, 9, and 13), 15 driver genes of BJ were identified by modular similarity and network control methods, and seven driver proteins (PAQR8, RhoA, EMC10, GGA2, VIPR1, FAM120A, and SEMA3F) were validated by animal experiments. The functional analysis found neuroprotective roles of the Add-modules and driver genes, such as the Neurotrophin signaling pathway and FoxO signaling pathway, which may reflect the additive mechanisms of BJ. Moreover, such a DiMS paradigm provides a new angle to explore the synergistic mechanisms of combination therapy and screen multi-targeted drugs for complex diseases.
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Affiliation(s)
- Bing Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Wang
- College of Nursing, Chengde Medical University, Chengde, China
| | - Hao Gu
- 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
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yinying Chen
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qikai Niu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bo Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qiong Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shuang Guan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanda Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Huamin Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Huamin Zhang
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- Zhong Wang
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Zhang YY, Zhao ZD, Kong PY, Gao L, Yu YN, Liu J, Wang PQ, Li B, Zhang XX, Yang LQ, Wang Z. A comparative pharmacogenomic analysis of three classic TCM prescriptions for coronary heart disease based on molecular network modeling. Acta Pharmacol Sin 2020; 41:735-744. [PMID: 32051552 PMCID: PMC7471444 DOI: 10.1038/s41401-019-0352-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/17/2019] [Indexed: 12/15/2022] Open
Abstract
Traditional Chinese medicine (TCM) has evolved over several thousands of years, which has been shown to be efficacious in the treatment of ischemic heart disease. Three classical TCM prescriptions, namely Xuefu Zhuyu Decoction, Zhishi Xiebai Guizhi Decoction, and Gualou Xiebai Banxia Decoction, have been extensively used in the treatment of coronary heart disease (CHD). Based on molecular network modeling, we performed a comparative pharmacogenomic analysis to systematically determine the drug-targeting spectrum of the three prescriptions at molecular level. Wide-area target molecules of CHD were covered, which was a common feature of the three decoctions, demonstrating their therapeutic functions. Meanwhile, collective signaling involved metabolic/pro-metabolic pathways, driving and transferring pathways, neuropsychiatric pathways, and exocrine or endocrine pathways. These organized pharmacological disturbance was mainly focused on almost all stages of CHD intervention, such as anti-atherosclerosis, lipid metabolism, inflammation, vascular wall function, foam cells formation, platelets aggregation, thrombosis, arrhythmia, and ischemia-reperfusion injury. In addition, heterogeneity analysis of the global pharmacological molecular spectrum revealed that signaling crosstalk, cascade convergence, and key targets were tendentious among the three decoctions. After all, it is unadvisable to rank the findings on targeting advantages of the three decoctions. Comparative pharmacological evidence may provide an appropriate decoction scheme for individualized intervention of CHD.
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Affiliation(s)
- Ying-Ying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zi-de Zhao
- Eye Hospital, China Academy of Chinese Medical Sciences, Beijing, 100040, China
| | - Peng-Yun Kong
- Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Lin Gao
- Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Ya-Nan Yu
- Institute of Basic Research in Clinical 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
| | - Peng-Qian Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Bing Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiao-Xu Zhang
- Eye Hospital, China Academy of Chinese Medical Sciences, Beijing, 100040, China
| | - Li-Qiang Yang
- Guangxi University of Chinese Medicine, Nanning, 530200, China.
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Effect of Huangqin Tang on Colonic Gene Expression in Rats with Ulcerative Colitis. Int J Genomics 2020; 2020:4238757. [PMID: 32300604 PMCID: PMC7140145 DOI: 10.1155/2020/4238757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/24/2019] [Accepted: 01/13/2020] [Indexed: 01/02/2023] Open
Abstract
In this study, we explored the pharmacological mechanisms of Huangqin Tang (HQT; a traditional Chinese medicine formula) in ulcerative colitis (UC) and provided evidence for potential roles HQT plays by gene expression profiling. The UC rat model was made via a compound method (trinitrobenzene sulfonic acid plus ethanol). After a ten-day treatment, microarray analysis was performed from the colon segment of the rats. Biological functions and specific signaling pathways were enriched based on differentially expressed genes (DEG), and corresponding gene networks were constructed via Ingenuity Pathway Analysis (IPA). Through the network, we screened the potential “candidate targets,” such as ITGB1, FN1, CASP3, and ITGA5 and FABP1, ABCB1, FABP2, and SLC51B. These potential candidate targets were functionally related to immune responses, inflammation, and metabolism. Moreover, HQT significantly decreased serum levels of proinflammatory factors nitrogen monoxide (NO), proinflammatory cytokines interleukin- (IL-) 17, and prostaglandin E2 (PGE2). The degree of HE staining of colonic tissue was severe in the model group but reduced significantly in the HQT group. HQT exhibited protective effects against colon damage by inhibiting the inflammatory response.
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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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Zhang Y, Li H, Guo H, Li B, Zhao Z, Wang P, Wu H, Liu J, Chen Y, Zhang X, Wu P, Wang Z, Wang J. Genome Analysis Reveals a Synergistic Mechanism of Ursodeoxycholic Acid and Jasminoidin in Mice Brain Repair After Ischemia/Reperfusion: Crosstalk Among Muti-Pathways. Front Pharmacol 2019; 10:1383. [PMID: 31920636 PMCID: PMC6920098 DOI: 10.3389/fphar.2019.01383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 10/30/2019] [Indexed: 01/19/2023] Open
Abstract
Studies have shown that combination drug therapy which corresponding treatment involves multiple genes and targets is more effective against cerebral ischemia. To identify the synergistic mechanism of ursodeoxycholic acid and jasminoidin based on differential pathway network, which protect against brain ischemia-reperfusion injury. Totally 115 mice with focal cerebral ischemia-reperfusion injury were allocated into five groups: sham, vehicle, ursodeoxycholic acid (UA), jasminoidin (JA), and JA and UA combination group (JU). The differentially expressed genes identified by microarray which consisted of 11,644 complementary DNAs were loaded to the GeneGo MetaCore™ software to analyze the enriched pathways and processes among different groups. Of the top 10 pathways and process networks, 5, 6, and 3 overlapping pathways as well as 5, 3, and 4 overlapping process networks were observed between UA and JA, UA and JU, and JA and JU, respectively. Of these, three pathways and three process networks overlapped across the three groups. Interestingly, four representative pathways and six process networks were only noted in the JU group. Gene Ontology process analysis showed 2 processes were shared by all three treatment groups in the top 10 processes. The UA and JA combination resulted in synergistic effects through affecting multi-signal transduction pathways, different locations in the same pathway, and the new signaling pathway emerged in drug combination group, those together may enhance the treatment of cerebral ischemia-reperfusion injury through promoting neural cell apoptosis, decreasing calcium levels, inhibiting inflammation, and protecting neurons.
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Affiliation(s)
- Yingying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China.,Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haixia Li
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Huan Guo
- Guang'anmen Hospital, 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
| | - Zide Zhao
- Eye Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Pengqian Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hongli Wu
- 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
| | - Yinying Chen
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoxu Zhang
- Eye Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ping Wu
- Guang'anmen Hospital, 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
| | - Jie Wang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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Sheng Z, Sun Y, Yin Z, Tang K, Cao Z. Advances in computational approaches in identifying synergistic drug combinations. Brief Bioinform 2019; 19:1172-1182. [PMID: 28475767 DOI: 10.1093/bib/bbx047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Indexed: 12/21/2022] Open
Abstract
Accumulated empirical clinical experience, supported by animal or cell line models, has initiated efforts of predicting synergistic combinatorial drugs with more-than-additive effect compared with the sum of the individual agents. Aiming to construct better computational models, this review started from the latest updated data resources of combinatorial drugs, then summarized the reported mechanism of the known synergistic combinations from aspects of drug molecular and pharmacological patterns, target network properties and compound functional annotation. Based on above, we focused on the main in silico strategies recently published, covering methods of molecular modeling, mathematical simulation, optimization of combinatorial targets and pattern-based statistical/learning model. Future thoughts are also discussed related to the role of natural compounds, drug combination with immunotherapy and management of adverse effects. Overall, with particular emphasis on mechanism of action of drug synergy, this review may serve as a rapid reference to design improved models for combinational drugs.
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Affiliation(s)
- Zhen Sheng
- School of Life Sciences and Technology, Tongji University
| | - Yi Sun
- School of Life Sciences and Technology, Tongji University
| | - Zuojing Yin
- School of Life Sciences and Technology, Tongji University
| | - Kailin Tang
- Advanced Institute of Translational Medicine, Tongji University
| | - Zhiwei Cao
- School of Life Sciences and Technology, Tongji University
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Wei PL, Gu H, Liu J, Wang Z. Development of Fangjiomics for Systems Elucidation of Synergistic Mechanism Underlying Combination Therapy. Comput Struct Biotechnol J 2018; 16:565-572. [PMID: 30546857 PMCID: PMC6279955 DOI: 10.1016/j.csbj.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 02/08/2023] Open
Abstract
The rapid development of omics technology provides an opportunity for fulfilling the understanding of the synergistic mechanism of combination therapy. However, a systems theory to analyze synergy remains an ongoing challenge. Fangjiomics is a novel systems science based on a holistic theory integrated with reductionism which has been utilized to systematically elucidate the synergistic mechanisms underlying combination therapy using multi-target-, pathway- or network-based quantitative methods. Besides, our ability to understand the polyhierarchical structure in synergy is driven based on multi-level omics data fusion in Fangjiomics. According to the basic principle of “Jun-Chen-Zuo-Shi”, further global integration across various omics platforms and phenotype-driven quantitative multi-scale modeling would accelerate development in Fangjiomics-based dissection of synergy in multi-drug combination therapies. Fangjiomics is a novel systems science based on a holistic theory integrated with reductionism. We developed the pathway-based analysis of synergistic mechanisms in Fangjiomics. The theory of network-based synergistic targets is proposed in Fangjiomics. The hierarchical relationship of synergy in multilevel omics is dissected in Fangjiomics. The principle of “Jun-Chen-Zuo-Shi” is proposed to accelerate the development in Fangjiomics-based dissection of synergy.
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Affiliation(s)
- Peng-Lu Wei
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hao Gu
- Institute of Basic Research in Clinical 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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Xu W, Zhang Y, Yu Y, Li B, Liu J, Wang P, Wu H, Liu Q, Wei Z, Xiao H, Wang Z. Dose-dependent target diversion of Danhong injection on the Glu-GLT-1/Gly-GlyRα dynamic balance module of cerebral ischemia. Pharmacol Res 2018; 135:80-88. [PMID: 30031913 DOI: 10.1016/j.phrs.2018.07.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Function-oriented modular structure analysis is a great challenge in module-based pharmacological studies. A strategy to uncover target-target interaction (TTI) and dynamic balance regularity (DBR) was established to discover the structural factors influencing modular functions and explore the mechanism of Danhong injection (DHI) in treating cerebral ischemia. The dose-related metabolic features of DHI intervention were investigated using metabolomics and modular pharmacology. The findings indicated that Glu/Gly was a biomarker and Glu-GLT-1/Gly-GlyRα was the core unit regulated by DHI. Gly and Glu displayed opposite patterns and functional roles, representing intra-modular balance. GlyRα was identified as the upstream target and GLT-1 as the downstream target by inhibiting or activating GlyRα, indicating that DHI has two dose-dependent regulatory modes. GlyRα was the major target at low doses, while GLT-1 was activated as the dominant target as doses accumulated. Our study reveals that target-target interaction and dynamic balance regularity are the key factors influencing modular functions, which is a promising breakthrough for module-based pharmacological studies.
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Affiliation(s)
- Wenjuan Xu
- School of Life Sciences, Research Center for Chinese Medical Analysis and Transformation, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yingying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China; Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yanan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, 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
| | - Pengqian Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hongli Wu
- Institute of Basic Research in Clinical Medicine, 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
| | - Ziyi Wei
- School of Life Sciences, Research Center for Chinese Medical Analysis and Transformation, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Hongbin Xiao
- School of Life Sciences, Research Center for Chinese Medical Analysis and Transformation, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Zhang GX, Zhang YY, Zhang XX, Wang PQ, Liu J, Liu Q, Wang Z. Different network pharmacology mechanisms of Danshen-based Fangjis in the treatment of stable angina. Acta Pharmacol Sin 2018; 39:952-960. [PMID: 29417948 PMCID: PMC6256275 DOI: 10.1038/aps.2017.191] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 11/26/2017] [Indexed: 01/30/2023] Open
Abstract
Danshen (Salvia miltiorrhiza) preparations such as Danhong injection, Danshen injection, Salvianolate injection, compound Danshen injection and Sodium Tanshinone IIA Sulfonate (STS) injection are widely used in China to treat stable angina (angina pectoris) caused by coronary heart disease. In this study we compared the network pharmacological mechanisms of the 5 Danshen preparations. Following a literature search performed in PubMed, EMBASE, Cochrane Library, China National Knowledge Infrastructure (CNKI) database, China Biology Medicine (CBM) database, China Conference Paper Database, Wanfang Database, VIP Database and Conference Proceedings Citation Index (through January 2015), 444 randomized controlled trial publications detailing the use of the 5 Danshen-based injections for treating stable angina were identified, and their combined data were analyzed using a network meta-analysis. All of the 5 Danshen-based preparations were effective in treating stable angina with clinical improvement rates of 72.4%-91.6% and electrocardiogram (ECG) improvement rates of 54.5%-71.6%. According to both clinical improvement and ECG improvement, the 5 Danshen-based preparations were ranked as follows: Danhong injection > Salvianolate injection > STS injection > compound Danshen injection > Danshen injection. There were no significant differences among the safety profiles of the 5 Danshen preparations. The meta-analysis results were further examined using a network pharmacology approach and functional enrichment analysis, which revealed that Danshen and Danhong injections affected 4 and 15 signaling pathways, respectively, and that the 4 signaling pathways affected by Danshen were a subset of those influenced by Danhong. Therefore, Danhong injection affected some unique signaling pathways that might regulate lipoprotein metabolism, oxidation, and inflammation, and protect vascular endothelia, reflecting the multi-component and multi-target characteristics of this traditional formula and its strengths in treating complex diseases.
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Affiliation(s)
- Guo-xia Zhang
- Luohu District Traditional Chinese Medicine Hospital, Shenzhen 518000, China
| | - Ying-ying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiao-xu Zhang
- Eye Hospital, China Academy of Chinese Medical Sciences, Beijing 100040, China
| | - Peng-qian Wang
- Institute of Chinese Materia Medica, 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
| | - Qiong 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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11
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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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12
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Zhang Y, Zhao Z, Yu Y, Liu J, Wang P, Li B, Zhang X, Chen Y, Wang Z. Mining the Synergistic Core Allosteric Modules Variation and Sequencing Pharmacological Module Drivers in a Preclinical Model of Ischemia. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2018; 7:269-280. [PMID: 29464871 PMCID: PMC5915616 DOI: 10.1002/psp4.12281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/20/2017] [Accepted: 01/12/2018] [Indexed: 12/02/2022]
Abstract
Identifying the variation of core modules and hubs seems to be critical for characterizing variable pharmacological mechanisms based on topological alteration of disease networks. We first identified a total of eight core modules by using an approach of multiple modular characteristic fusing (MMCF) from different targeted networks in ischemic mice. Interestingly, the value of module disturbance intensity (MDI) increased in drug combination group. Second, we redefined a weak allosteric module and a strong allosteric module. Then, we identified 15 pharmacological module drivers (PMDs) by leave‐one‐out screening with a cutoff of two folds, which were at least, in part, validated by expression and variation of topological contribution. Finally, we revealed the fusional and emergent variation of PMD in core modules contributing to multidimensional synergistic mechanism in ischemic mice and rats. Our findings provide a new set of drivers that might promote the pharmacological modular flexibility and offer a potential avenue for disease treatment.
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Affiliation(s)
- Yingying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Haiyuncang, Beijing, China.,Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,Shanxi Buchang Pharmaceutical Co. Ltd, Gaoxin Road, Xi'an, China
| | - Zide Zhao
- Eye Hospital, 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
| | - Pengqian Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,Institute of Chinese Materia Medica, 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
| | - Xiaoxu Zhang
- Eye Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yinying Chen
- Guang 'anmen Hospital, China Academy of Chinese Medical Sciences, Beixiange, Beijing, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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13
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Yu Y, Zhang X, Li B, Zhang Y, Liu J, Li H, Chen Y, Wang P, Kang R, Wu H, Wang Z. Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms. Exp Biol Med (Maywood) 2016; 241:2063-2074. [PMID: 27480252 DOI: 10.1177/1535370216662361] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Module-based network analysis of diverse pharmacological mechanisms is critical to systematically understand combination therapies and disease outcomes. We first constructed drug-target ischemic networks in baicalin, jasminoidin, ursodeoxycholic acid, and their combinations baicalin and jasminoidin as well as jasminoidin and ursodeoxycholic acid groups and identified modules using the entropy-based clustering algorithm. The modules 11, 7, 4, 8 and 3 were identified as baicalin, jasminoidin, ursodeoxycholic acid, baicalin and jasminoidin and jasminoidin and ursodeoxycholic acid-emerged responsive modules, while 12, 8, 15, 17 and 9 were identified as disappeared responsive modules based on variation of topological similarity, respectively. No overlapping differential biological processes were enriched between baicalin and jasminoidin and jasminoidin and ursodeoxycholic acid pure emerged responsive modules, but two were enriched by their co-disappeared responsive modules including nucleotide-excision repair and epithelial structure maintenance. We found an additive effect of baicalin and jasminoidin in a divergent pattern and a synergistic effect of jasminoidin and ursodeoxycholic acid in a convergent pattern on "central hit strategy" of regulating inflammation against cerebral ischemia. The proposed module-based approach may provide us a holistic view to understand multiple pharmacological mechanisms associated with differential phenotypes from the standpoint of modular pharmacology.
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Affiliation(s)
- Yanan Yu
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
| | - Xiaoxu Zhang
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
| | - Bing Li
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
| | - Yingying Zhang
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
| | - Jun Liu
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
| | - Haixia Li
- 2 Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Yinying Chen
- 2 Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Pengqian Wang
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
| | - Ruixia Kang
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
| | - Hongli Wu
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
| | - Zhong Wang
- 1 Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing 100700, China
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14
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Zhao Z, Zhang Y, Gai F, Wang Y. Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis. Mol Med Rep 2016; 14:2213-21. [PMID: 27430657 DOI: 10.3892/mmr.2016.5478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 05/27/2016] [Indexed: 11/06/2022] Open
Abstract
Despite ongoing research into diabetes and its complications, the underlying molecular associations remain to be elucidated. The systematic identification of molecular interactions in associated diseases may be approached using a network analysis strategy. The biomarker-target interrelated molecules associated with diabetes and its complications were identified via the Comparative Toxicogenomics Database (CTD); the Search Tool for Recurring Instances of Neighboring Genes was utilized for network construction. Functional enrichment analysis was performed with Database for Annotation, Visualization and Integrated Discovery software to investigate connections between diabetes and its complications. A total of 142 (including 122 biomarkers, 10 therapeutic targets and 10 overlapping molecules) biomarker-target interrelated molecules associated with diabetes and its complications were identified via the CTD database, and analysis of the network yielded 1,087 biological processes and fifteen Kyoto Encyclopedia of Genes and Genomes pathways with significant P‑values. Various critical aspects of the networks were examined in the present study: a) Intermolecular horizontal and vertical combinations in biomarkers and therapeutic targets associated with diabetes and its complicationb) network topology properties associated with molecular pathological responsec) contribution of key molecules to integrated regulation; and d) crosstalk between multiple pathways. Based on a multi-dimensional analysis, it was concluded that the integrated molecular pathological development of diabetes and its complications does not proceed randomly, which suggests a requirement for integrated, multi-target intervention.
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Affiliation(s)
- Zide Zhao
- Department of Neuro‑Ophthalmology, Eye Hospital, China Academy of Chinese Medical Sciences, Beijing 100040, P.R. China
| | - Yingying Zhang
- Laboratory of Pharmacology, Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, P.R. China
| | - Fengchun Gai
- Department of Infection Control, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin 130021, P.R. China
| | - Ying Wang
- Department of Neuro‑Ophthalmology, Eye Hospital, China Academy of Chinese Medical Sciences, Beijing 100040, P.R. China
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15
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Ilexonin A Promotes Neuronal Proliferation and Regeneration via Activation of the Canonical Wnt Signaling Pathway after Cerebral Ischemia Reperfusion in Rats. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2016; 2016:9753189. [PMID: 27057202 PMCID: PMC4739464 DOI: 10.1155/2016/9753189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/28/2015] [Indexed: 01/08/2023]
Abstract
Aims. Ilexonin A (IA), a component of the Chinese medicine Ilex pubescens, has been shown to be neuroprotective during ischemic injury. However, the specific mechanism underlying this neuroprotective effect remains unclear. Methods. In this study, we employed a combination of immunofluorescence staining, western blotting, RT-PCR, and behavioral tests, to investigate the molecular mechanisms involved in IA regulation of neuronal proliferation and regeneration after cerebral ischemia and reperfusion in rodents. Results. Increases in β-catenin protein and LEF1 mRNA and decreases in GSK3β protein and Axin mRNA observed in IA-treated compared to control rodents implicated the canonical Wnt pathway as a key signaling mechanism activated by IA treatment. Furthermore, rodents in the IA treatment group showed less neurologic impairment and a corresponding increase in the number of Brdu/nestin and Brdu/NeuN double positive neurons in the parenchymal ischemia tissue following middle cerebral artery occlusion compared to matched controls. Conclusion. Altogether, our data indicate that IA can significantly diminish neurological deficits associated with cerebral ischemia reperfusion in rats as a result of increased neuronal survival via modulation of the canonical Wnt pathway.
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16
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Dang H, Li K, Yu Y, Zhang Y, Liu J, Wang P, Li B, Wang H, Li H, Wang Z, Wang Y. Variation of pathways and network profiles reveals the differential pharmacological mechanisms of each effective component to treat middle cerebral artery ischemia-reperfusion mice. Exp Biol Med (Maywood) 2015; 241:79-89. [PMID: 26168995 DOI: 10.1177/1535370215594584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 05/12/2015] [Indexed: 12/25/2022] Open
Abstract
Using a system pharmacology strategy, this study evaluated the unique pharmacological characteristics of three different neuroprotective compounds for the treatment of cerebral ischemia-reperfusion. A microarray including 374 brain ischemia-related genes was used to identify the differentially expressed genes among five treatment groups: baicalin, jasminoidin, ursodeoxycholic acid, sham, and vehicle, and MetaCore analysis software was applied to identify the significantly altered pathways, processes and interaction network parameters. At pathway level, 46, 25, and 31 pathways were activated in the baicalin, jasminoidin, and ursodeoxycholic acid groups, respectively. Thirteen pathways mainly related with apoptosis and development were commonly altered in the three groups. Additionally, baicalin also targeted pathways related with development, neurophysiologic process and cytoskeleton remodeling, while jasminoidin targeted pathways related with cell cycle and ursodeoxycholic acid targeted those related with apoptosis and development. At process level, three processes were commonly regulated by the three groups in the top 10 processes. Further interaction network analysis revealed that baicalin, jasminoidin, and ursodeoxycholic acid displayed unique features either on network topological parameters or network structure. Additional overlapping analysis demonstrated that compared with ursodeoxycholic acid, the pharmacological mechanism of baicalin was more similar with that of jasminoidin in treating brain ischemia. The data presented in this study may contribute toward the understanding of the common and differential pharmacological mechanisms of these three compounds.
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Affiliation(s)
- HaiXia Dang
- China Academy of Chinese Medical Sciences, Beijing 100700, China Shanxi Buchang Pharmaceutical Co., Ltd, Shaanxi 710075
| | - KangNing Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - YaNan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - YingYing Zhang
- Institute of Basic Research in Clinical 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
| | - PengQian Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Bing Li
- Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - HaiNan Wang
- China Food and Drug Administration, Beijing 100053, China
| | - Haixia Li
- 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
| | - YongYan Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
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17
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Liu J, Wang Z. Diverse array-designed modes of combination therapies in Fangjiomics. Acta Pharmacol Sin 2015; 36:680-8. [PMID: 25864646 PMCID: PMC4594182 DOI: 10.1038/aps.2014.125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 10/30/2014] [Indexed: 12/11/2022] Open
Abstract
In line with the complexity of disease networks, diverse combination therapies have been demonstrated potential in the treatment of different patients with complex diseases in a personal combination profile. However, the identification of rational, compatible and effective drug combinations remains an ongoing challenge. Based on a holistic theory integrated with reductionism, Fangjiomics systematically develops multiple modes of array-designed combination therapies. We define diverse "magic shotgun" vertical, horizontal, focusing, siege and dynamic arrays according to different spatiotemporal distributions of hits on targets, pathways and networks. Through these multiple adaptive modes for treating complex diseases, Fangjiomics may help to identify rational drug combinations with synergistic or additive efficacy but reduced adverse side effects that reverse complex diseases by reconstructing or rewiring multiple targets, pathways and networks. Such a novel paradigm for combination therapies may allow us to achieve more precise treatments by developing phenotype-driven quantitative multi-scale modeling for rational drug combinations.
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Affiliation(s)
- 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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18
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Wang PQ, Li B, Liu J, Zhang YY, Yu YN, Zhang XX, Yuan Y, Guo ZL, Wu HL, Li HX, Dang HX, Guo SS, Wang Z. Phenotype-dependent alteration of pathways and networks reveals a pure synergistic mechanism for compounds treating mouse cerebral ischemia. Acta Pharmacol Sin 2015; 36:734-47. [PMID: 25960134 DOI: 10.1038/aps.2014.168] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 12/08/2014] [Indexed: 12/25/2022] Open
Abstract
AIM Our previous studies have showed that ursodeoxycholic acid (UA) and jasminoidin (JA) effectively reduce cerebral infarct volume in mice. In this study we explored the pure synergistic mechanism of these compounds in treatment of mouse cerebral ischemia, which was defined as synergistic actions specific for phenotype variations after excluding interference from ineffective compounds. METHODS Mice with focal cerebral ischemia were treated with UA, JA or a combination JA and UA (JU). Concha margaritifera (CM) was taken as ineffective compound. Cerebral infarct volume of the mice was determined, and the hippocampi were taken for microarray analysis. Particular signaling pathways and biological functions were enriched based on differentially expressed genes, and corresponding networks were constructed through Ingenuity Pathway Analysis. RESULTS In phenotype analysis, UA, JA, and JU significantly reduced the ischemic infarct volume with JU being superior to UA or JA alone, while CM was ineffective. As a result, 4 pathways enriched in CM were excluded. Core pathways in the phenotype-positive groups (UA or JA) were involved in neuronal homeostasis and neuropathology. JU-contributing pathways included all UA-contributing and the majority (71.7%) of JA-contributing pathways, and 10 new core pathways whose effects included inflammatory immunity, apoptosis and nervous system development. The functions of JU group included all functions of JA group, the majority (93.1%) of UA-contributing functions, and 3 new core functions, which focused on physiological system development and function. CONCLUSION The pure synergism between UA and JA underlies 10 new core pathways and 3 new core functions, which are involved in inflammation, immune responses, apoptosis and nervous system development.
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