Potential synergism and inhibitors to multiple target enzymes of Xuefu Zhuyu Decoction in cardiac disease therapeutics: a computational approach.
ABSTRACT In order to study the drug-like features of Xuefu Zhuyu Decoction (XFZYD), a Traditional Chinese Medicinal recipe, three different computational methods were introduced to characterize the molecules in XFZYD, including chemical space distribution, docking protocol, and ADME prediction. Chemical space compared between the compound sets from XFZYD and drug/drug-like shows XFZYD may have desired interaction with broader protein targets. And the docking results show that the XFZYD is a broad-spectrum recipe inhibiting many important target enzymes. Together with the predictions of ADME properties, clue of potential synergism of XFZYD was obtained.
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ABSTRACT: In silico prediction of the new drug-target interactions from existing databases is of important value for the drug discovery process. Currently, the amount of protein targets that have been identified experimentally is still very small compared with the entire human proteins. In order to predict protein-ligand interactions in an accurate manner, we have developed a support vector machine (SVM) model based on the chemical-protein interactions from STITCH. New features from ligand chemical space and interaction networks have been selected and encoded as the feature vectors for SVM analysis. Both the 5-fold cross validation and independent test show high predictive accuracy that outperforms the state-of-the-art method based on ligand similarity. Moreover, 91 distinct pairs of features have been selected to rebuild a simplifier model, which still maintains the same performance as that based on all 332 features. Then, this refined model is used to search for the potential D-amino acid oxidase inhibitors from STITCH database and the predicted results are finally validated by our wet experiments. Out of 10 candidates obtained, seven D-amino acid oxidase inhibitors have been verified, in which four are newly found in the present study, and one may have a new application in therapy of psychiatric disorders other than being an antineoplastic agent. Clearly, our model is capable of predicting potential new drugs or targets on a large scale with high efficiency.Current pharmaceutical design 01/2014; · 4.41 Impact Factor
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ABSTRACT: The traditional Chinese medicine (TCM), which has thousands of years of clinical application among China and other Asian countries, is the pioneer of the "multicomponent-multitarget" and network pharmacology. Although there is no doubt of the efficacy, it is difficult to elucidate convincing underlying mechanism of TCM due to its complex composition and unclear pharmacology. The use of ligand-protein networks has been gaining significant value in the history of drug discovery while its application in TCM is still in its early stage. This paper firstly surveys TCM databases for virtual screening that have been greatly expanded in size and data diversity in recent years. On that basis, different screening methods and strategies for identifying active ingredients and targets of TCM are outlined based on the amount of network information available, both on sides of ligand bioactivity and the protein structures. Furthermore, applications of successful in silico target identification attempts are discussed in detail along with experiments in exploring the ligand-protein networks of TCM. Finally, it will be concluded that the prospective application of ligand-protein networks can be used not only to predict protein targets of a small molecule, but also to explore the mode of action of TCM.Evidence-based Complementary and Alternative Medicine 01/2013; 2013:806072. · 2.18 Impact Factor
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ABSTRACT: Stroke is an important cause of mortality and morbidity worldwide but effective therapeutic strategy for the prevention of brain injury in patients with cerebral ischemia is lacking. Although tissue plasminogen activator has been used to treat stroke patients, this therapeutic strategy is confronted with ill side effects and is limited to patients within 3 h of a stroke. Due to the complexity of the events and the disappointing results from single agent trials, the combination of thrombolytic therapy and effective neural protection therapy may be an alternative strategy for patients with cerebral ischemia. Chinese medicine (CM) is the most widely practiced form of herbalism worldwide, as it is a sophisticated system of medical theory and practice that is specifically different from Western medicine. Most traditional therapeutic formulations consist of a combination of several drugs. The combination of multiple drugs is thought to maximize therapeutic efficacy by facilitating synergistic actions and preventing possible adverse effects while at the same time marking at multiple targets. CM has been labeled in ancient medicine systems as a treatment for various diseases associated with stroke. This review summarizes various CMs, bioactive compounds and their effects on cerebral ischemia.Chinese Journal of Integrative Medicine 07/2014; · 1.40 Impact Factor