Platelet Aggregation Pathway Network-Based Approach for Evaluating Compounds Efficacy

Gu, Jiangyong; Li, Qian; Chen, Lirong; Li, Youyong; Hou, Tingjun; Yuan, Gu; Xu, Xiaojie

doi:10.1155/2013/425707

Cited by 18 publications

(28 citation statements)

References 27 publications

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“…The edge values of the pathway network were reset according to the Michaelis-Menten equation, which used the binding constant and drug concentration to determine the degree of inhibition of the target protein in the pathway. The dose-response curve was sigmoid and the predicted effects of compounds were in good agreement with experimental results [5,[48][49][50]. Moreover, This approach can be used for predictions of drug combination and drug repositioning [5,89].…”

Section: Network Modeling and Pathway Analysissupporting

confidence: 74%

Computational methods and applications for quantitative systems pharmacology

Xie

2019

Quant. Biol.

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Background: Quantitative systems pharmacology (QSP) is an emerging discipline that integrates diverse data to quantitatively explore the interactions between drugs and multi-scale systems including small compounds, nucleic acids, proteins, pathways, cells, organs and disease processes. Results: Various computational methods such as ADME/T evaluation, molecular modeling, logical modeling, network modeling, pathway analysis, multi-scale systems pharmacology platforms and virtual patient for QSP have been developed. We reviewed the major progresses and broad applications in medical guidance, drug discovery and exploration of pharmacodynamic material basis and mechanism of traditional Chinese medicine. Conclusion: QSP has significant achievements in recent years and is a promising approach for quantitative evaluation of drug efficacy and systematic exploration of mechanisms of action of drugs.Author summary: Quantitative systems pharmacology (QSP) is an emerging discipline that integrates diverse data to quantitatively explore the interactions between drugs and multi-scale systems including small compounds, nucleic acids, proteins, pathways, cells, organs and disease processes. This review is an attempt to introduce the computational methods for QSP, including ADME/T (absorption, distribution, metabolism, excretion and toxicity) evaluation, molecular modeling, logical modeling, network modeling, pathway analysis, multi-scale systems pharmacology platforms and virtual patient as well as their applications in medical guidance, drug discovery and explorations of pharmacodynamics material basis and mechanism of traditional Chinese medicine.

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Section: Network Modeling and Pathway Analysissupporting

confidence: 74%

Computational methods and applications for quantitative systems pharmacology

Xie

2019

Quant. Biol.

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“…Many studies have been reported to elucidate the molecular mechanism of TCM formulae in systematic view23456789. Compound-target networks were constructed and analyzed in these studies, and the effectiveness of TCM formulae was evaluated at compound level.…”

Section: Discussionmentioning

confidence: 99%

“…Systematic docking and drug-target network analysis is widely applied in these studies23456789, however, the therapeutic effectiveness of TCM formulae is still ascribed to a few number of interactions between individual compounds and key target proteins. As TCMs are prescribed as herbs, compounds from one herb should be considered as a whole and mode of action at herb-level should be noticed.…”

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confidence: 99%

Herb-target interaction network analysis helps to disclose molecular mechanism of traditional Chinese medicine

Hao

Ruan

Ouyang

et al. 2016

Sci Rep

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Though many studies have been performed to elucidate molecular mechanism of traditional Chinese medicines (TCMs) by identifying protein-compound interactions, no systematic analysis at herb level was reported. TCMs are prescribed by herbs and all compounds from a certain herb should be considered as a whole, thus studies at herb level may provide comprehensive understanding of TCMs. Here, we proposed a computational strategy to study molecular mechanism of TCM at herb level and used it to analyze a TCM anti-HIV formula. Herb-target network analysis was carried out between 17 HIV-related proteins and SH formula as well as three control groups based on systematic docking. Inhibitory herbs were identified and active compounds enrichment was found to contribute to the therapeutic effectiveness of herbs. Our study demonstrates that computational analysis of TCMs at herb level can catch the rationale of TCM formulation and serve as guidance for novel TCM formula design.

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“…The center of binding site was located in the center of the original ligand. The molecular docking was conducted according to the protocol described previously [58]. …”

Section: Methodsmentioning

confidence: 99%

A Drug-Target Network-Based Approach to Evaluate the Efficacy of Medicinal Plants for Type II Diabetes Mellitus

Chen

Yuan

et al. 2013

Evidence-Based Complementary and Alternative Medicine

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The use of plants as natural medicines in the treatment of type II diabetes mellitus (T2DM) has long been of special interest. In this work, we developed a docking score-weighted prediction model based on drug-target network to evaluate the efficacy of medicinal plants for T2DM. High throughput virtual screening from chemical library of natural products was adopted to calculate the binding affinity between natural products contained in medicinal plants and 33 T2DM-related proteins. The drug-target network was constructed according to the strength of the binding affinity if the molecular docking score satisfied the threshold. By linking the medicinal plant with T2DM through drug-target network, the model can predict the efficacy of natural products and medicinal plant for T2DM. Eighteen thousand nine hundred ninety-nine natural products and 1669 medicinal plants were predicted to be potentially bioactive.

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Platelet Aggregation Pathway Network-Based Approach for Evaluating Compounds Efficacy

Cited by 18 publications

References 27 publications

Computational methods and applications for quantitative systems pharmacology

Computational methods and applications for quantitative systems pharmacology

Herb-target interaction network analysis helps to disclose molecular mechanism of traditional Chinese medicine

A Drug-Target Network-Based Approach to Evaluate the Efficacy of Medicinal Plants for Type II Diabetes Mellitus

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