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Identifying drug-target proteins based on network features

Science China(Life Sciences) 2009年第4期52卷 398-404页

作者： ZHU MingZhu1, GAO Lei1, LI Xia1,2 & LIU ZhiCheng1 1 School of Biomedical Engineering, Capital Medical University, Beijing 100069, China 2 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China 1. School of Biomedical Engineering Capital Medical University Beijing 100069 China 2. College of Bioinformatics Science and Technology Harbin Medical University Harbin 150081 China

Proteins rarely function in isolation inside and outside cells, but operate as part of a highly intercon- nected cellular network called the interaction network. Therefore, the analysis of the properties of drug-target proteins in the biological network is especially helpful for understanding the mechanism of drug action in terms of informatics. At present, no detailed characterization and description of the topological features of drug-target proteins have been available in the human protein-protein interac- tion network. In this work, by mapping the drug-targets in drugBank onto the interaction network of human proteins, five topological indices of drug-targets were analyzed and compared with those of the whole protein interactome set and the non-drug-target set. The experimental results showed that drug-target proteins have higher connectivity and quicker communication with each other in the PPI network. Based on these features, all proteins in the interaction network were ranked. The results showed that, of the top 100 proteins, 48 are covered by drugBank; of the remaining 52 proteins, 9 are drug-target proteins covered by the TTD, Matador and other databases, while others have been dem- onstrated to be drug-target proteins in the literature.

关键词： drug-target protein-protein interaction topological features

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Computational pharmacological studies on cardiovascular disease by Qishen Yiqi Diwan

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Science China Chemistry 2009年第11期52卷 1871-1878页

作者： GU JiangYong YUAN Gu ZHU YongHong XU XiaoJie Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and ApplicationsCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China Academy of Tasly Pharmaceutical Co. LTDTianjin 300410China

Computational pharmacological methods were used to study the distribution of 1729 compounds contained in a Chinese medicine,Qishen Yiqi Diwan,in chemical *** results show that most of these compounds have good drug-like *** docking was used to study the interactions between 1729 compounds of Qishen Yiqi Diwan and 26 drug targets related to cardiovascular disease and the distribution of 1729 compounds in drug-target *** results may shed light on the action mechanism and the search for the active compounds in Qishen Yiqi Diwan.

关键词： chemical space drug-target space molecular docking computational pharmacology

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Study on the multi-targets mechanism of YiQiFuMai powder injection on cardio-cerebral ischemic diseases based on network pharmacology

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中国药理学通报 2015年第B11期31卷 132-133页

Aim YiQiFuMai Powder Injection is a well-known traditional Chinese medicine formula that has been used extensively in clinical treatment of cardio-cerebral ischemic diseases in China. However, the mechanisms under-lying its clinical efficacy remain unknown. In this study, a network pharmacology approach was employed to identify the YiQiFuMai Powder Injection＇s potential pathways and targets against cardio-cerebral ischemia. The target-path- way interaction network clustered the signaling pathways based on high degree nodes of the drug-target network. The potential protein targets presented in the highly scored clustered pathways were the key network hubs and concentrated on one or limited functional signaling pathways amenable to experimental verification. Twelve main functional annota- tion clusters and main signaling pathways for YiQiFuMai Powder Injection were established by Biocarta analysis, in- eluding the NF-KB signaling pathway, the MAPKinase signaling pathway and the mTOR-signaling pathway and so on. YiQiFuMai Powder Injection is hypothesized to target multiple proteins with a high degree and betweenness of net- work. In addition, the most related pathways were also confirmed in tumor necrosis factor-alpha （TNF-oL） induced human vascular endothelial cell line EA. hy926 by Western blot. This study elucidates the systematic network and pathway analysis of multi-targets in YiQiFuMai Powder Injection. The results provide the possible mechanisms for its mode of action against cardio-cerebral ischemic diseases and may also reveal new clues for its potential application in the inflammatory diseases or tumors.

关键词： YiQiFuMai powder injection cardio-cerebral ischemic diseases network pharmacology target-pathwayinteraction network drug-target network NF-KB signaling pathway

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Systems psychopharmacology:A network approach to developing novel therapies

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World Journal of Psychiatry 2016年第1期6卷 66-83页

作者： Peter J Gebicke-Haerter Central Institute of Mental Health Medical Faculty MannheimHeidelberg University

The multifactorial origin of most chronic disorders of the brain, including schizophrenia, has been well accepted. Consequently, pharmacotherapy would require multitargeted strategies. This contrasts to the majority of drug therapies used until now, addressing more or less specifically only one target molecule. Nevertheless, quite some searches for multiple molecular targets specific for mental disorders have been undertaken. For example, genome-wide association studies have been conducted to discover new target genes of disease. Unfortunately, these attempts have not fulfilled the great hopes they have started with. Polypharmacology and network pharmacology approaches of drug treatment endeavor to abandon the one-drug one-target thinking. To this end, most approaches set out to investigate network topologies searching for modules, endowed with "important" nodes, such as "hubs" or "bottlenecks", encompassing features of disease networks, and being useful as tentative targets of drug therapies. This kind of research appears to be very promising. However, blocking or inhibiting "important" targets may easily result in destruction of network integrity. Therefore, it is suggested here to study functions of nodes with lower centrality for more subtle impact on network behavior. targeting multiple nodes with low impact on network integrity by drugs with multiple activities("dirty drugs") or by several drugs, simultaneously, avoids to disrupt network integrity and may reset deviant dynamics of disease. Natural products typically display multi target functions and therefore could help to identify useful biological targets. Hence, future efforts should consider to combine drug-target networks with target-disease networks using mathematical(graph theoretical) tools, which could help to develop new therapeutic strategies in long-term psychiatric disorders.

关键词： Polypharmacology drug-target networks Network topology Disease networks Genome-wide association studies Epigenetics Schizophrenia Herbal extracts

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