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Yue G, Gu H, Zhang K, Song Y, Hao Y. ACE inhibitors from Suaeda salsa: 3D-QSAR modeling, metabolomics, molecular docking and molecular dynamics simulations. In Silico Pharmacol 2024; 12:59. [PMID: 38912325 PMCID: PMC11192713 DOI: 10.1007/s40203-024-00233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/18/2024] [Indexed: 06/25/2024] Open
Abstract
Inhibition of ACE is considered as one of the main strategies to reduce hypertension. ACE inhibitors derived from Suaeda salsa (S. salsa) present a novel antihypertensive agent source. This study employed 3D-QSAR pharmacophore, metabolomics, docking-based screening, and molecular dynamics simulations to identify ACE inhibitors from S. salsa. A set of 53 known molecules was chemically diverse to construct a 3D-QSAR model for predictive purposes. S. salsa was characterized using UPLC-QqQ-MS/MS and UPLC-Q-TOF-LC-MS techniques, 211 and 586 kinds of bioactive metabolites were identified, respectively. A total of 680 compounds were collected for database construction and virtual screening. An ADMET assessment was conducted to evaluate drug-likeness and pharmacokinetics parameters. Moreover, molecular docking results show that six top hit compounds bind to ACE tightly. Specially, diosmin could interact with ACE by hydrogen bond, Pi-cation bond, and metal bond. Molecular dynamics (MD) simulation and MMPBSA calculations were subsequently employed to elucidate complex stability and the interaction between diosmin and ACE, indicating it a strong ACE inhibitory activity. In conclusion, this study suggests that S.salsa represents a potential source of antihypertensive agents. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00233-0.
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Affiliation(s)
- Guanhua Yue
- Department of Basic Medical, Shenyang Medical College, No.146, Huanghe Road, Shenyang, 110034 China
| | - Heze Gu
- Department of Basic Medical, Shenyang Medical College, No.146, Huanghe Road, Shenyang, 110034 China
| | - Kuocheng Zhang
- Department of Basic Medical, Shenyang Medical College, No.146, Huanghe Road, Shenyang, 110034 China
| | - YuanLong Song
- Department of Basic Medical, Shenyang Medical College, No.146, Huanghe Road, Shenyang, 110034 China
| | - Yangguang Hao
- Department of Basic Medical, Shenyang Medical College, No.146, Huanghe Road, Shenyang, 110034 China
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Zhao Z, Ma R, Ma Y, Zhao L, Wang L, Fang Y, Zhang Y, Wu X, Wang X. Discovery of Nine Dipeptidyl Peptidase-4 Inhibitors from Coptis chinensis Using Virtual Screening, Bioactivity Evaluation, and Binding Studies. Molecules 2024; 29:2304. [PMID: 38792165 PMCID: PMC11123979 DOI: 10.3390/molecules29102304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The objective of this study was to identify multiple alkaloids in Coptis chinensis that demonstrate inhibitory activity against DPP-4 and systematically evaluate their activity and binding characteristics. A combined strategy that included molecular docking, a DPP-4 inhibition assay, surface plasmon resonance (SPR), and a molecular dynamics simulation technique was employed. The results showed that nine alkaloids in Coptis chinensis directly inhibited DPP-4, with IC50 values of 3.44-53.73 μM. SPR-based binding studies revealed that these alkaloids display rapid binding and dissociation characteristics when interacting with DPP-4, with KD values ranging from 8.11 to 29.97 μM. A molecular dynamics analysis revealed that equilibrium was rapidly reached by nine DPP-4-ligand systems with minimal fluctuations, while binding free energy calculations showed that the ∆Gbind values for the nine test compounds ranged from -31.84 to -16.06 kcal/mol. The most important forces for the binding of these alkaloids with DPP-4 are electrostatic interactions and van der Waals forces. Various important amino acid residues, such as Arg125, His126, Phe357, Arg358, and Tyr547, were involved in the inhibition of DPP-4 by the compounds, revealing a mechanistic basis for the further optimization of these alkaloids as DPP-4 inhibitors. This study confirmed nine alkaloids as direct inhibitors of DPP-4 and characterized their binding features, thereby providing a basis for further research and development on novel DPP-4 inhibitors.
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Affiliation(s)
- Zixi Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Ruonan Ma
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Yuqing Ma
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Liqiang Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Lele Wang
- School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China; (L.W.); (Y.F.)
| | - Yuzhen Fang
- School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China; (L.W.); (Y.F.)
| | - Yuxin Zhang
- School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China; (L.W.); (Y.F.)
| | - Xia Wu
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
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Cao Y, Shi H, Lan Z, He K, Chen Q, Zhang C, Feng S, Shan L. Efficient separation of aristolochic acid I from Caulis aristolochiae manshuriensis (Guan-mu-tong) with copper mediated magnetic molecularly imprinted polymer. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4555-4562. [PMID: 37644819 DOI: 10.1039/d3ay00920c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Screening bioactive compounds from natural products is one of the most effective ways for new drug research and development. However, obtaining a single extract component on a large scale and with high purity from a complex matrix is still an arduous and challenging task. Herein, one metal mediated magnetic molecularly imprinted polymer (mMIP) was rationally designed and prepared for specifically capturing Aristolochic acid I (AAI). The preparation was done with copper(II) as binding pivot, (3-aminopropyl) triethoxysilane as functional monomer, and Fe3O4 as core, by a one-step sol-gel method. Under the optimized conditions, the apparent maximum binding amount of copper mediated mMIP (Cu-mMIP) reaches as high as 349.72 mg g-1, the highest among the reported AAI-MIPs. Moreover, the nanoparticles exhibit excellent specificity and selectivity, good reproducibility and stability, high superparamagnetism (60.32 emu g-1), and high imprinting efficiency (an imprinting factor of 7). By simulating an industrial-scale separation, 16.56 mg AAI (purity of 95.11%) is obtained after six cycles with 100 mg nanoparticles from 20 g Caulis aristolochiae manshuriensis (Guan-mu-tong). Notably, this takes only 3 hours and consumes 50 mL of methanol. The study provides a potent tool for the green, fast, and specific extraction of high-purity ingredients from natural plants in the manufacturing industry and conventional analysis in the lab.
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Affiliation(s)
- Yu Cao
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, China.
| | - Haizhu Shi
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, China.
| | - Zhuo Lan
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, China.
| | - Kunlin He
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, China.
| | - Qian Chen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, China.
| | - Chungu Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, China.
| | - Shun Feng
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, China.
| | - Lianhai Shan
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, China.
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Pang HQ, Zhou P, Meng XW, Yang H, Li Y, Xing XD, Wang HY, Yan FR, Li P, Gao W. An image-based fingerprint-efficacy screening strategy for uncovering active compounds with interactive effects in Yindan Xinnaotong soft capsule. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 96:153911. [PMID: 35026505 DOI: 10.1016/j.phymed.2021.153911] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/19/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Yindan Xinnaotong soft capsule (YDXNT) is a clinically effective herbal prescription used for the treatment of cardiovascular and cerebrovascular diseases. Since Chinese medicines (CMs) exert their effects via a "multiple-components and multiple-targets" mode, discovery of the active compounds with interactive effects may contribute to reveal their mechanisms of action. PURPOSE This study aimed to establish an image-based fingerprint-efficacy screening strategy to identify active compounds with interaction effects from CM prescription, using YDXNT to inhibit microglia-mediated neuroinflammation as an instance. METHODS A multi-component random content-oriented chemical library of YDXNT was constructed by uniform design, and their chemical fingerprint was profiled by liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) methods. Then the neuroinflammation activities of chemical library members of YDXNT were determined by image-based dual phenotypic quantification. Subsequently, fingerprint-efficacy correlation and random forest analysis were applied to predict the potentially active compounds with interactive effects. Finally, the interactive effects among the active compounds were confirmed by quantitative polymerase chain reaction (qPCR) and apoptosis analysis, and network pharmacology was applied to explore the possible mechanisms. RESULTS Image-based fingerprint-efficacy correlation analysis revealed that six tanshinones (TNs) and four flavonoids (FAs) were potential anti-neuroinflammatory compounds. The inter-family of TNs and FAs possessed obvious interactive effects (combination index ≤ 0.825). Moreover, the combination of scutellarein and tanshinone I (2:1, w/w) was discovered as the possible interactive combinatorial components, which, comparing with individual scutellarein or tanshinone I, shown more powerful effects on anti-inflammatory and anti-apoptotic effects in lipopolysaccharide (LPS)-induced BV2 cells. Network pharmacology showed that the active compounds might suppress microglia-mediated neuroinflammation via multiple targets in the T cell receptor, Jak-STAT, and Toll-like receptor signaling pathways. CONCLUSION The image-based fingerprint-efficacy strategy simplifies the screening process of efficacious component combinations in CMs for complex diseases, which also offers a promising approach to explore the integrative therapeutic mechanisms of CMs.
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Affiliation(s)
- Han-Qing Pang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China
| | - Ping Zhou
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China
| | - Xiao-Wei Meng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China
| | - Hua Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China
| | - Yi Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China
| | - Xu-Dong Xing
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China
| | - Hui-Ying Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China
| | - Fang-Rong Yan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China.
| | - Wen Gao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No.24, Tongjia Lane, Nanjing 210009, China.
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Chen Y, Wang X, Zhai H, Zhang Y, Huang J. Identification of Potential Human Ryanodine Receptor 1 Agonists and Molecular Mechanisms of Natural Small-Molecule Phenols as Anxiolytics. ACS OMEGA 2021; 6:29940-29954. [PMID: 34778666 PMCID: PMC8582060 DOI: 10.1021/acsomega.1c04468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Natural small-molecule phenols (NSMPs) possess certain ubiquitous bioactivities including the anxiolytic effect. Ryanodine receptor 1 (RyR1) may be one of the potentially critical pharmacological targets for studying the anxiolytic activity of NSMPs. However, detailed molecular mechanisms of NSMPs have not been fully clarified. This research was intended to identify potent hRyR1 agonists from NSMPs and investigate whether RyR1 plays a role in their anxiolytic effect. Homology modeling and molecular docking analysis were performed using Accelrys Discovery Studio 2.5. The most appropriate concentrations of NSMPs to activate RyR1 were measured using the MTT assay. Fluorescence analyses of the intracellular calcium levels and western blotting analysis were carried out to validate whether NSMPs could regulate the calcium flux to some extent by activating RyR1. The results demonstrated that xanthotoxol and 5-hydroxy-1,4-naphthalenedione can be screened as hit compounds for potential agonists of hRyR1 to exert the anxiolytic effect. In conclusion, NSMPs might be a kind of pharmacological signal carrier, acting on RyR1 as an agonist and resulting in calcium ion mobilization from intracellular calcium ion store.
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Affiliation(s)
- Yahong Chen
- School
of Chinese Materia Medica, Beijing University
of Chinese Medicine, Yangguang South Road, Fangshan District, Beijing 102488, China
| | - Xiaohong Wang
- School
of Chinese Materia Medica, Beijing University
of Chinese Medicine, Yangguang South Road, Fangshan District, Beijing 102488, China
| | - Haifeng Zhai
- National
Institute on Drug Dependence, Peking University, 38#, Xueyuan Road, Haidian District, Beijing 100191, China
| | - Yanling Zhang
- School
of Chinese Materia Medica, Beijing University
of Chinese Medicine, Yangguang South Road, Fangshan District, Beijing 102488, China
| | - Jianmei Huang
- School
of Chinese Materia Medica, Beijing University
of Chinese Medicine, Yangguang South Road, Fangshan District, Beijing 102488, China
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Li Y, Zhang Y, Wu X, Gao Y, Guo J, Tian Y, Lin Z, Wang X. Discovery of natural 15-LOX small molecule inhibitors from Chinese herbal medicine using virtual Screening, biological evaluation and molecular dynamics studies. Bioorg Chem 2021; 115:105197. [PMID: 34426159 DOI: 10.1016/j.bioorg.2021.105197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 11/19/2022]
Abstract
Chinese herbal medicines (CHM) are frequently used to treat different types of inflammatory diseases and 15-Lipoxygenase (15-LOX) is a critical target enzyme for treating various inflammatory diseases. In this study, natural 15-LOX inhibitors were identified in CHM using an approach of virtual screening combined with the biological assays. First, an in-house Chinese medicine database containing 360 compounds was screened using a virtual screening approach based on pharmacophore and molecular docking to uncover several novel potential 15-LOX inhibitors. Secondly, the inhibitory effect of virtual screening hits against the 15-LOX enzyme was validated in an in vitro enzyme inhibition assay. Then, a tumor necrosis factor-α (TNF-α) release assay was carried out to explore the anti-inflammatory response of the active compounds. Furthermore, molecular dynamics (MD) simulation and binding free energy calculation were applied to analyze the process of inhibitors binding and also compared the mode of binding of the inhibitors by using the Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) method. Finally, licochalcone B and eriodictyol were confirmed as inhibitors of the 15-LOX enzyme with IC50 values of 9.67 and 18.99 μM, respectively. In vitro cell-based assay showed that licochalcone B and eriodictyol inhibited the release of TNF-α factor in RAW264.7 cells stimulated by lipopolysaccharides (LPS) in a dose-dependent manner. Molecular dynamics and binding free energy analysis showed that the two 15-LOX-ligand systems immediately attained equilibrium with almost 1 Å fluctuation, the calculated binding free energies were found around -18.89 and -12.96 kcal/mol for licochalcone B and eriodictyol, respectively. Thr412, Arg415, Val420, Thr429, Ile602 and Trp606 were the main amino acid residues for the inhibition of 15-LOX enzyme activity. The current study confirms that licochalcone B and eriodictyol are 15-LOX inhibitors and can suppress the release of the TNF-α factor in RAW264.7 cells stimulated by LPS, thus providing a basis for the follow-up research and development for 15-LOX inhibitors.
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Affiliation(s)
- Yatong Li
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yuxin Zhang
- Key Laboratory of Ethnomedicine, School of Pharmacy, Ministry of Education, Minzu University of China, Haidian District, Beijing 100081, China
| | - Xia Wu
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yanbin Gao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Junfang Guo
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yulang Tian
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Ziyue Lin
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China.
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Yongzhong Lu, Zhao J, Cheng L. Virtual Screening of Antimicrobial Agents from Medicinal Plants. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021040154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Qu L, Zhang X, Wang J, Zhou H, Hou T, Wei L, Xu F, Liang X. Phenotypic assessment and ligand screening of ETA/ETB receptors with label-free dynamic mass redistribution assay. Naunyn Schmiedebergs Arch Pharmacol 2019; 393:937-950. [PMID: 31781785 DOI: 10.1007/s00210-019-01756-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/23/2019] [Indexed: 01/16/2023]
Abstract
Endothelin receptors, consisting of two subtypes, ETA and ETB, are expressed in various tissues and widely regulate cardiovascular systems. The two receptors show distinct biological characteristics and are involved in different downstream pathways. Hence, to evaluate the ETA and ETB receptors on the same platform is helpful to display their pharmacological features. In this study, we developed a label-free dynamic mass redistribution (DMR) assay to investigate the phenotypic features of the ETA and ETB receptors in native cell lines. Meanwhile, specific agonists and antagonists were investigated for their pharmacological parameters. Results indicated that the DMR response of endothelin 1 (ET-1, an endogenous ETA/ETB agonist) was cell line dependent on ETA receptors and this ligand generated a biphasic dose-response curve in SH-SY5Y as well as PC3 cell lines. ET-1 and IRL 1620 (an ETB agonist) showed different DMR responses in U251 cells. IC50 values of antagonists were consistent with the Ki values previously reported. Furthermore, a list of compounds was screened on the ETA and ETB receptor models established by the high-throughput DMR assays. This study demonstrated that the DMR assay had great potential in the phenotypic-based investigation and ligand screening of GPCRs.
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Affiliation(s)
- Lala Qu
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiuli Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215006, China.
- Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
| | - Jixia Wang
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Han Zhou
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tao Hou
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lai Wei
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Fangfang Xu
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinmiao Liang
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226019, China.
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Zhang X, Qiao L, Chen Y, Zhao B, Gu Y, Huo X, Zhang Y, Li G. In Silico Analysis of the Association Relationship between Neuroprotection and Flavors of Traditional Chinese Medicine Based on the mGluRs. Int J Mol Sci 2018; 19:ijms19010163. [PMID: 29320397 PMCID: PMC5796112 DOI: 10.3390/ijms19010163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 01/30/2023] Open
Abstract
The metabotropic glutamate receptors (mGluRs) are known as both synaptic receptors and taste receptors. This feature is highly similar to the Property and Flavor theory of Traditional Chinese medicine (TCM), which has the pharmacological effect and flavor. In this study, six ligand based pharmacophore (LBP) models, seven homology modeling models, and fourteen molecular docking models of mGluRs were built based on orthosteric and allosteric sites to screening potential compounds from Traditional Chinese Medicine Database (TCMD). Based on the Pharmacopoeia of the People's Republic of China, TCMs of compounds and their flavors were traced and listed. According to the tracing result, we found that the TCMs of the compounds which bound to orthosteric sites of mGluRs are highly correlated to a sweet flavor, while the allosteric site corresponds to a bitter flavor. Meanwhile, the pharmacological effects of TCMs with highly frequent flavors were further analyzed. We found that those TCMs play a neuroprotective role through the efficiencies of detumescence, promoting blood circulation, analgesic effect, and so on. This study provides a guide for developing new neuroprotective drugs from TCMs which target mGluRs. Moreover, it is the first study to present a novel approach to discuss the association relationship between flavor and the neuroprotective mechanism of TCM based on mGluRs.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Liansheng Qiao
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yankun Chen
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Bowen Zhao
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yu Gu
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Xiaoqian Huo
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yanling Zhang
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Gongyu Li
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
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Fan HT, Guo JF, Zhang YX, Gu YX, Ning ZQ, Qiao YJ, Wang X. The rational search for PDE10A inhibitors from Sophora flavescens roots using pharmacophore‑ and docking‑based virtual screening. Mol Med Rep 2017; 17:388-393. [PMID: 29115449 DOI: 10.3892/mmr.2017.7871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/31/2017] [Indexed: 11/06/2022] Open
Abstract
Phosphodiesterase 10A (PDE10A) has been confirmed to be an important target for the treatment of central nervous system (CNS) disorders. The purpose of the present study was to identify PDE10A inhibitors from herbs used in traditional Chinese medicine. Pharmacophore and molecular docking techniques were used to virtually screen the chemical molecule database of Sophora flavescens, a well‑known Chinese herb that has been used for improving mental health and regulating the CNS. The pharmacophore model generated recognized the common functional groups of known PDE10A inhibitors. In addition, molecular docking was used to calculate the binding affinity of ligand‑PDE10A interactions and to investigate the possible binding pattern. Virtual screening based on the pharmacophore model and molecular docking was performed to identify potential PDE10A inhibitors from S. flavescens. The results demonstrated that nine hits from S. flavescens were potential PDE10A inhibitors, and their biological activity was further validated using literature mining. A total of two compounds were reported to inhibit cyclic adenosine monophosphate phosphodiesterase, and one protected against glutamate‑induced oxidative stress in the CNS. The remaining six compounds require further bioactivity validation. The results of the present study demonstrated that this method was a time‑ and cost‑saving strategy for the identification of bioactive compounds from traditional Chinese medicine.
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Affiliation(s)
- Han-Tian Fan
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, P.R. China
| | - Jun-Fang Guo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, P.R. China
| | - Yu-Xin Zhang
- Key Laboratory of TCM‑Information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, P.R. China
| | - Yu-Xi Gu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, P.R. China
| | - Zhong-Qi Ning
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, P.R. China
| | - Yan-Jiang Qiao
- Key Laboratory of TCM‑Information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, P.R. China
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, P.R. China
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Wang X, Zhang Y, Yang Y, Wu X, Fan H, Qiao Y. Identification of berberine as a direct thrombin inhibitor from traditional Chinese medicine through structural, functional and binding studies. Sci Rep 2017; 7:44040. [PMID: 28276481 PMCID: PMC5343495 DOI: 10.1038/srep44040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/03/2017] [Indexed: 12/22/2022] Open
Abstract
Thrombin acts as a key enzyme in the blood coagulation cascade and represents a potential drug target for the treatment of several cardiovascular diseases. The aim of this study was to identify small-molecule direct thrombin inhibitors from herbs used in traditional Chinese medicine (TCM). A pharmacophore model and molecular docking were utilized to virtually screen a library of chemicals contained in compositions of traditional Chinese herbs, and these analyses were followed by in vitro bioassay validation and binding studies. Berberine (BBR) was first confirmed as a thrombin inhibitor using an enzymatic assay. The BBR IC50 value for thrombin inhibition was 2.92 μM. Direct binding studies using surface plasmon resonance demonstrated that BBR directly interacted with thrombin with a KD value of 16.39 μM. Competitive binding assay indicated that BBR could bind to the same argartroban/thrombin interaction site. A platelet aggregation assay demonstrated that BBR had the ability to inhibit thrombin-induced platelet aggregation in washed platelets samples. This study proved that BBR is a direct thrombin inhibitor that has activity in inhibiting thrombin-induced platelet aggregation. BBR may be a potential candidate for the development of safe and effective thrombin-inhibiting drugs.
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Affiliation(s)
- Xing Wang
- Beijing Key Lab of Traditional Chinese Medicine (TCM) Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, 10 Youanmen, Xitoutiao, Beijing 100069, China
| | - Yuxin Zhang
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, 6 Central Ring South Road, Wangjing, Beijing 100102, China
| | - Ying Yang
- Core Facilities Center, Capital Medical University, 10 Youanmen, Xitoutiao, Beijing 100069, China
| | - Xia Wu
- Beijing Key Lab of Traditional Chinese Medicine (TCM) Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, 10 Youanmen, Xitoutiao, Beijing 100069, China
| | - Hantian Fan
- Beijing Key Lab of Traditional Chinese Medicine (TCM) Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, 10 Youanmen, Xitoutiao, Beijing 100069, China
| | - Yanjiang Qiao
- Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, 6 Central Ring South Road, Wangjing, Beijing 100102, China
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12
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Su P, Guan H, Zhang Y, Wang X, Gao L, Zhao Y, Hu T, Zhou J, Ma B, Tu L, Tong Y, Huang L, Gao W. Probing the Single Key Amino Acid Responsible for the Novel Catalytic Function of ent-Kaurene Oxidase Supported by NADPH-Cytochrome P450 Reductases in Tripterygium wilfordii. FRONTIERS IN PLANT SCIENCE 2017; 8:1756. [PMID: 29081786 PMCID: PMC5645531 DOI: 10.3389/fpls.2017.01756] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/25/2017] [Indexed: 05/07/2023]
Abstract
Tripterygium wilfordii produces not only ent-kaurene, which is an intermediate of gibberellin (GA) biosynthesis in flowering plants, but also 16α-hydroxy-ent-kaurane, whose physiological role has not been characterized. The two compounds are biosynthesized from the universal diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate (GGPP) by diterpene synthases, which have been discovered and functionally characterized in T. wilfordii. Here, we described the functional characterization of four cytochrome P450 reductases (TwCPR) and one ent-kaurene oxidase (TwKO). Four TwCPRs were found to have relatively ubiquitous expression in T. wilfordii root, stem, leaf, and flower tissues. Co-expression of both a TwCPR and TwKO in yeast showed that TwCPR3 has a slightly better activity for providing the electrons required for these reactions, indicating that TwCPR3 is more suitable for use in the functional analysis of other cytochrome P450 monooxygenases. TwKO catalyzed the three-step oxidation of the C4α methyl of the tetracyclic diterpene intermediate ent-kaurene to form ent-kaurenoic acid as an early step in GA biosynthesis. Notably, TwKO could also convert 16α-hydroxy-ent-kaurane to 16α-hydroxy-ent-kaurenoic acid, indicating an important function of 16α-hydroxy-ent-kaurane in the anti-HIV principle tripterifordin biosynthetic pathway in planta. Homology modeling and molecular docking were used to investigate the unknown crucial active amino acid residue involved in the catalytic reaction of TwKO, and one key residue (Leu387) contributed to the formation of 16α-hydroxy-ent-kaurenoic acid, most likely by forming hydrogen bonds with the hydroxyl group (-OH) of 16α-hydroxy-ent-kaurane, which laid the basis for further investigation of the multifunctional nature of KO catalysis. Also, our findings paved the way for the complete biosynthesis of the anti-HIV principle tripterifordin.
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Affiliation(s)
- Ping Su
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Hongyu Guan
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Yifeng Zhang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Lab of TCM Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Linhui Gao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yujun Zhao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tianyuan Hu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jiawei Zhou
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Baowei Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuru Tong
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Luqi Huang, Wei Gao,
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Lab of TCM Collateral Disease Theory Research, School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- *Correspondence: Luqi Huang, Wei Gao,
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13
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Li M, Wen F, Zhao S, Wang P, Li S, Zhang Y, Zheng N, Wang J. Exploring the Molecular Basis for Binding of Inhibitors by Threonyl-tRNA Synthetase from Brucella abortus: A Virtual Screening Study. Int J Mol Sci 2016; 17:E1078. [PMID: 27447614 PMCID: PMC4964454 DOI: 10.3390/ijms17071078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/19/2016] [Accepted: 06/29/2016] [Indexed: 01/18/2023] Open
Abstract
Targeting threonyl-tRNA synthetase (ThrRS) of Brucella abortus is a promising approach to developing small-molecule drugs against bovine brucellosis. Using the BLASTp algorithm, we identified ThrRS from Escherichia coli (EThrRS, PDB ID 1QF6), which is 51% identical to ThrRS from Brucella abortus (BaThrRS) at the amino acid sequence level. EThrRS was used as the template to construct a BaThrRS homology model which was optimized using molecular dynamics simulations. To determine the residues important for substrate ATP binding, we identified the ATP-binding regions of BaThrRS, docked ATP to the protein, and identified the residues whose side chains surrounded bound ATP. We then used the binding site of ATP to virtually screen for BaThrRS inhibitors and got seven leads. We further characterized the BaThrRS-binding site of the compound with the highest predicted inhibitory activity. Our results should facilitate future experimental effects to find novel drugs for use against bovine brucellosis.
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Affiliation(s)
- Ming Li
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Fang Wen
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Shengguo Zhao
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Pengpeng Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Songli Li
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Yangdong Zhang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jiaqi Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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