Screening Ingredients from Herbs against Pregnane X Receptor in the Study of Inductive Herb-Drug Interactions: Combining Pharmacophore and Docking-Based Rank Aggregation.
The issue of herb-drug interactions has been widely reported. Herbal ingredients can activate nuclear receptors and further induce the gene expression alteration of drug-metabolizing enzyme and/or transporter. Therefore, the herb-drug interaction will happen when the herbs and drugs are coadministered. This kind of interaction is called inductive herb-drug interactions. Pregnane X Receptor (PXR) and drug-metabolizing target genes are involved in most of inductive herb-drug interactions. To predict this kind of herb-drug interaction, the protocol could be simplified to only screen agonists of PXR from herbs because the relations of drugs with their metabolizing enzymes are well studied. Here, a combinational in silico strategy of pharmacophore modelling and docking-based rank aggregation (DRA) was employed to identify PXR's agonists. Firstly, 305 ingredients were screened out from 820 ingredients as candidate agonists of PXR with our pharmacophore model. Secondly, DRA was used to rerank the result of pharmacophore filtering. To validate our prediction, a curated herb-drug interaction database was built, which recorded 380 herb-drug interactions. Finally, among the top 10 herb ingredients from the ranking list, 6 ingredients were reported to involve in herb-drug interactions. The accuracy of our method is higher than other traditional methods. The strategy could be extended to studies on other inductive herb-drug interactions.
Department of Bioinformatics, Tongji University, Shanghai 200092, China.
Zhijie
Z
Cui
Department of Bioinformatics, Tongji University, Shanghai 200092, China.
Hong
H
Kang
Department of Bioinformatics, Tongji University, Shanghai 200092, China.
Kailin
K
Tang
Department of Bioinformatics, Tongji University, Shanghai 200092, China.
Qi
Q
Liu
Department of Bioinformatics, Tongji University, Shanghai 200092, China ; Shanghai Center for Bioinformation Technology, Shanghai, China.
Zhiwei
Z
Cao
Department of Bioinformatics, Tongji University, Shanghai 200092, China ; School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, Liaoning, China.
Ruixin
R
Zhu
D003198:Computer Simulation; D016208:Databases, Factual; D015870:Gene Expression; D041743:Herb-Drug Interactions / Q000235:genetics*; D006801:Humans; D008658:Inactivation, Metabolic / Q000235:genetics; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D010946:Plants, Medicinal / Q000737:chemistry*; D000077297:Pregnane X Receptor; D011987:Receptors, Steroid / Q000819:agonists / Q000737:chemistry* / Q000235:genetics
D000077297:Pregnane X Receptor; D011987:Receptors, Steroid