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Huang L, Ma B, Zhang C, Shi J, Shen R, Zhang E, Lian C, Wang C, Liu J. Unveiling poly(rC)-binding protein 2 as the target protein for curcusone C against prostate cancer: mechanism validation through click chemistry-activity based proteomics profiling approach. BMC Cancer 2023; 23:957. [PMID: 37814239 PMCID: PMC10563230 DOI: 10.1186/s12885-023-11467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/01/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND Prostate cancer is a disease that seriously troubles men. However, there are some inevitable limitations in interventional therapy for prostate cancer patients at present, most of which are caused by low selectivity and high toxic side effects due to unclear drug targets. In this study, we identified the target protein of Curcusone C with anti-prostate cancer potential activity and verified its target and mechanism of action. METHODS Click chemistry-activity based proteomics profiling (CC-ABPP) method was used to find target protein of Curcusone C against prostate cancer. Competitive CC-ABPP, drug affinity responsive target stability (DARTS) and surface plasmon resonance (SPR) methods were used to verifying the target protein. Moreover, potential mechanism was validated by western blot in vitro and by hematoxylin-eosin (HE) staining, detection of apoptosis in tumor tissue (TUNEL), and immunohistochemical (IHC) in vivo. RESULTS We found that poly(rC)-binding protein 2 (PCBP2) was the target protein of Curcusone C. In addition, Curcusone C might disrupt the Bax/Bcl-2 balance in PC-3 cells by inhibiting the expression of the target protein PCBP2, thereby inducing mitochondrial damage and activation of the mitochondrial apoptosis pathway, and ultimately inducing apoptosis of prostate cancer cells. CONCLUSIONS Curcusone C is a potential compound with anti-prostate cancer activity, and this effect occurs by targeting the PCBP2 protein, which in turn may affect the TGF/Smad signaling pathway and Bax/Bcl-2 balance. Our results laid a material and theoretical foundation for Curcusone C, to be widely used in anti-prostate cancer.
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Affiliation(s)
- Lan Huang
- School of medicine, Huaqiao University, Quanzhou, 362021, China
| | - Buqing Ma
- School of medicine, Huaqiao University, Quanzhou, 362021, China
| | - Chong Zhang
- School of medicine, Huaqiao University, Quanzhou, 362021, China
| | - Jiaqi Shi
- School of medicine, Huaqiao University, Quanzhou, 362021, China
| | - Rui Shen
- School of medicine, Huaqiao University, Quanzhou, 362021, China
| | - Erci Zhang
- School of medicine, Huaqiao University, Quanzhou, 362021, China
| | - Chenlei Lian
- School of medicine, Huaqiao University, Quanzhou, 362021, China
| | - Cuifang Wang
- Quanzhou Normal University, Quanzhou, 362000, China.
| | - Jieqing Liu
- School of medicine, Huaqiao University, Quanzhou, 362021, China.
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Meng WS, Sun J, Lu Y, Cao TT, Chi MY, Gong ZP, Li YT, Zheng L, Liu T, Huang Y. Biancaea decapetala (Roth) O.Deg. extract exerts an anti-inflammatory effect by regulating the TNF/Akt/NF-κB pathway. Phytomedicine 2023; 119:154983. [PMID: 37586161 DOI: 10.1016/j.phymed.2023.154983] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/13/2023] [Accepted: 07/15/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Biancaea decapetala (Roth) O.Deg. (Fabaceae) is used to treat colds, fever, and rheumatic pain caused by inflammation. However, the mechanism underlying its anti-inflammatory properties remains unclear. PURPOSE This study aimed to evaluate the anti-inflammatory activity of Biancaea decapetala extract (BDE) in vitro and in vivo and explore the possible underlying mechanism and potential targets. METHODS The release of nitric oxide (NO) and inflammatory cytokines in LPS-stimulated RAW264.7 cells and rats were measured using Griess reagent and enzyme-linked immunosorbent assay (ELISA). Hematoxylin and eosin (H&E) staining was employed to examine the pathology of animal tissues. Transcriptome analysis was performed to screen the pathways related to BDE-mediated inhibition of inflammation, and the expression of related proteins was measured using real-time quantitative polymerase chain reaction (RT-qPCR), western blotting, ELISA, and immunofluorescence methods. Surface Plasmon Resonance (SPR) and the Drug Affinity Reaction Target Stability (DARTS) method were used to verify whether BDE binds to TNF-α target protein, while a L929 cell model and NF-κB gene reporter systematic method were used to investigate the inhibitory effect of BDE on the activity of TNF-α protein. RESULTS BDE inhibited the expression of TNF-α, IL-1β, IL-6, and NO in RAW264.7 cells and rats, and improved the pathological changes in lung tissue. RNA-seq showed that BDE may regulate the TNF/Akt/NF-κB pathway to inhibit inflammation onset. BDE significantly downregulated the mRNA expression of TNF-α, IL-6, IL-1β, and that of relevant proteins, including TNF-α, p-p65, p-Akt, p-IκBα. Furthermore, BDE inhibited the nuclear translocation of NF-κB (p65) and the activation of the Akt pathway by SC79. The L929 cell model, luciferase reporter gene analysis, DARTS, and SPR experiments showed that BDE may bind to TNF-α and inhibit the TNF-α-NF-κB pathway. CONCLUSION BDE may target TNF-α to inhibit the TNF/Akt/NF-κB pathway, thereby attenuating inflammation. These findings reveal the anti-inflammatory effects and mechanisms of BDE and provide a theoretical basis for the further development and utilization of BDE.
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Affiliation(s)
- Wen-Sha Meng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China; School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550004, PR China
| | - Jia Sun
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China
| | - Yuan Lu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China
| | - Tao-Tao Cao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China; School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550004, PR China
| | - Ming-Yan Chi
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China
| | - Zi-Peng Gong
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China
| | - Yue-Ting Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China
| | - Lin Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China.
| | - Ting Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China.
| | - Yong Huang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Beijing Road 9, Guiyang 550004, PR China.
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Mijit A, Wang X, Li Y, Xu H, Chen Y, Xue W. Mapping synthetic binding proteins epitopes on diverse protein targets by protein structure prediction and protein-protein docking. Comput Biol Med 2023; 163:107183. [PMID: 37352638 DOI: 10.1016/j.compbiomed.2023.107183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023]
Abstract
Synthetic binding proteins (SBPs) are a class of artificial proteins engineered from privileged protein scaffolds, which can form highly specific molecular recognition interfaces with a variety of targets. Due to the characteristics of small size, high stability, and good tissue permeability, SBPs have important applications in biomedical research, disease diagnosis and treatment. However, knowledge of SBPs epitopes on the structures of target proteins is still limited, which hinder the development of novel SBPs. In this study, based on the currently available information of SBPs and their targets, 96 pairs of interacting proteins referring to 96 representative SBPs and 80 different targets, were systemically investigated using the state-of-the-art computational modeling techniques including AlphaFold2 protein structure prediction and Rosetta protein-protein docking. As a result, 71 out of the 96 pairs were successfully docked, of which 18, 33, and 20 pairs were defined as models with high, medium, and acceptable quality, respectively. In addition, the interface information was analyzed to decipher the interaction types driven SBPs and targets recognition. Overall, this work not only provides important structural information for understanding the mechanism of action of other SBPs with same protein scaffold, but also for aiding the rational protein engineering and to design of novel SBPs with biomedical applications.
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Affiliation(s)
- Arzu Mijit
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaona Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Yanlin Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Hangwei Xu
- School of Medicine, Hangzhou City University, Hangzhou, 310000, China
| | - Yingjun Chen
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
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Wu L, Wang G, Zhou L, Mo M, Shi Y, Li B, Yin L, Zhao Q, Yang Y, Wu C, Xu Z, Zhu W. Molecular dynamics study on the behavior and binding mechanism of target protein Transgelin-2 with its agonist TSG12 for anti-asthma drug discovery. Comput Biol Med 2023; 153:106515. [PMID: 36610217 DOI: 10.1016/j.compbiomed.2022.106515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/19/2022] [Accepted: 12/31/2022] [Indexed: 01/02/2023]
Abstract
Transgelin-2 (TG2) is a novel promising therapeutic target for the treatment of asthma as it plays an important role in relaxing airway smooth muscles and reducing pulmonary resistance in asthma. The compound TSG12 is the only reported TG2 agonist with in vivo anti-asthma activity. However, the dynamic behavior and ligand binding sites of TG2 and its binding mechanism with TSG12 remain unclear. In this study, we performed 12.6 μs molecular dynamics (MD) simulations for apo-TG2 and TG2-TSG12 complex, respectively. The results suggested that the apo-TG2 has 4 most populated conformations, and that its binding of the agonist could expand the conformation distribution space of the protein. The simulations revealed 3 potential binding sites in 3 most populated conformations, one of which is induced by the agonist binding. Free energy decomposition uncovered 8 important residues with contributions stronger than -1 kcal/mol. Computational alanine scanning for the important residues by 100 ns conventional MD simulation for each mutated TG2-TSG12 complexes demonstrated that E27, R49 and F52 are essential residues for the agonist binding. These results should be helpful to understand the dynamic behavior of TG2 and its binding mechanism with the agonist TSG12, which could provide some structural insights into the novel mechanism for anti-asthma drug development.
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Affiliation(s)
- Leyun Wu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangpu Wang
- Institute for Quantum Information & State Key Laboratory of High Performance Computing, College of Computer Science and Technology, National University of Defense Technology, Changsha, 410073, China
| | - Liping Zhou
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengxia Mo
- Institute for Quantum Information & State Key Laboratory of High Performance Computing, College of Computer Science and Technology, National University of Defense Technology, Changsha, 410073, China
| | - Yulong Shi
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Li
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leimiao Yin
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Qiang Zhao
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yongqing Yang
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Chengkun Wu
- Institute for Quantum Information & State Key Laboratory of High Performance Computing, College of Computer Science and Technology, National University of Defense Technology, Changsha, 410073, China.
| | - Zhijian Xu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Weiliang Zhu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Endo K, Sawa T, Kitamura H, Umezawa K, Makabe H, Tanaka S. Procyanidin B2 3,3″-di-O-gallate suppresses IFN-γ production in murine CD4 + T cells through the regulation of glutamine influx via direct interaction with ASCT2. Int Immunopharmacol 2023; 115:109617. [PMID: 36566519 DOI: 10.1016/j.intimp.2022.109617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/10/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Excessive activation of CD4+ T cells increases cytokine production substantially and induces immune-mediated diseases. Procyanidins are polyphenols with anti-inflammatory properties. Procyanidin B2 (PCB2) gallate [specifically, PCB2 3,3''-di-O-gallate (PCB2DG)] inhibits cytokine production through the suppression of glycolysis via mammalian target of rapamycin (mTOR) in T cells. Several amino acids play critical roles in T cell activation, especially glutamine, which is important in mTOR signaling and interferon-γ (IFN-γ) production in CD4+ T cells. However, the mechanisms underlying the effects of PCB2DG, including its interaction partners, have yet to be clarified. In the present study, the mechanisms underlying the inhibitory effect of PCB2DG on IFN-γ through glutamine metabolism regulation were investigated. We found that PCB2DG treatment reduced intracellular glutamine levels in CD4+ T cells, whereas the addition of glutamine abrogated the inhibitory effects of PCB2DG on IFN-γ production. The PCB2DG-induced reduction in intracellular glutamine accumulation led to the upregulated expression of activating transcription factor 4, which was induced by the cytoprotective signaling pathway in the amino acid response. In addition, the mRNA and protein expression levels of alanine serine cysteine transporter 2 (ASCT2), a major glutamine transporter in CD4+ T cells, were not altered by PCB2DG treatment. Further analysis using a target identification strategy revealed that PCB2DG binds to ASCT2, suggesting that PCB2DG interacts directly with this major glutamine transporter to inhibit glutamine influx. Overall, this study indicates that ASCT2 is a novel target protein of a dietary polyphenol and provides new insights into the mechanism underlying the immunomodulatory effects of polyphenols.
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Affiliation(s)
- Katsunori Endo
- Graduate School of Medicine, Science and Technology, Department of Science and Technology Agriculture, Division of Food Science and Biotechnology, Shinshu University, Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Toko Sawa
- Graduate School of Science and Technology, Department of Agriculture, Division of Food Science and Biotechnology, Shinshu University, Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Hidemitsu Kitamura
- Division of Functional Immunology, Section of Disease Control, Institute for Genetic Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-Ku, Sapporo 090-0815, Japan
| | - Koji Umezawa
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge, Division of Innovative Biomolecular Science, Shinshu University, 8304 Minami-minowa Kami-ina, Nagano 399-4598, Japan
| | - Hidefumi Makabe
- Graduate School of Medicine, Science and Technology, Department of Science and Technology Agriculture, Division of Food Science and Biotechnology, Shinshu University, Minami-minowa, Kami-ina, Nagano 399-4598, Japan; Graduate School of Science and Technology, Department of Agriculture, Division of Food Science and Biotechnology, Shinshu University, Minami-minowa, Kami-ina, Nagano 399-4598, Japan; Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge, Division of Innovative Biomolecular Science, Shinshu University, 8304 Minami-minowa Kami-ina, Nagano 399-4598, Japan
| | - Sachi Tanaka
- Graduate School of Medicine, Science and Technology, Department of Science and Technology Agriculture, Division of Food Science and Biotechnology, Shinshu University, Minami-minowa, Kami-ina, Nagano 399-4598, Japan; Graduate School of Science and Technology, Department of Agriculture, Division of Food Science and Biotechnology, Shinshu University, Minami-minowa, Kami-ina, Nagano 399-4598, Japan.
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Li R, Zhou Y, Zhang X, Yang L, Liu J, Wightman SM, Lv L, Liu Z, Wang CY, Zhao C. Identification of marine natural product Pretrichodermamide B as a STAT3 inhibitor for efficient anticancer therapy. Mar Life Sci Technol 2023; 5:94-101. [PMID: 37073329 PMCID: PMC10077262 DOI: 10.1007/s42995-022-00162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/22/2022] [Indexed: 05/03/2023]
Abstract
The Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) regulates the expression of various critical mediators of cancer and is considered as one of the central communication nodes in cell growth and survival. Marine natural products (MNP) represent great resources for discovery of bioactive lead compounds, especially anti-cancer agents. Through the medium-throughput screening of our in-house MNP library, Pretrichodermamide B, an epidithiodiketopiperazine, was identified as a JAK/STAT3 signaling inhibitor. Further studies identified that Pretrichodermamide B directly binds to STAT3, preventing phosphorylation and thus inhibiting JAK/STAT3 signaling. Moreover, it suppressed cancer cell growth, in vitro, at low micromolar concentrations and demonstrated efficacy in vivo by decreasing tumor growth in a xenograft mouse model. In addition, it was shown that Pretrichodermamide B was able to induce cell cycle arrest and promote cell apoptosis. This study demonstrated that Pretrichodermamide B is a novel STAT3 inhibitor, which should be considered for further exploration as a promising anti-cancer therapy. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00162-x.
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Affiliation(s)
- Rui Li
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yue Zhou
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Xinxin Zhang
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Lujia Yang
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Jieyu Liu
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Samantha M. Wightman
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 USA
| | - Ling Lv
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Zhiqing Liu
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Chang-Yun Wang
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Chenyang Zhao
- School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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Cai X, Jiang X, Zhao M, Su K, Tang M, Hong F, Ye N, Zhang R, Li N, Wang L, Xue L, Zhu Z, Chen L, Yang J, Wu W, Ye H. Identification of the target protein and molecular mechanism of honokiol in anti-inflammatory action. Phytomedicine 2023; 109:154617. [PMID: 36610140 DOI: 10.1016/j.phymed.2022.154617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/09/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Searching the targets of natural products is very important for drug discovery and elucidating the mechanism of drug action and disease. Honokiol (HK), as the major active component of Magnolia officinalis Rehder & E.H.Wilson, has been widely used in medicine and cosmetics. Among its bioactivities, its anti-inflammatory activity is particularly impressive. However, the target protein of HK in anti-inflammatory action and its regulatory mechanism are unclear. PURPOSE Here, we identified the target protein and molecular mechanism of the anti- inflammatory action of HK. METHODS First, an LPS-induced septic shock model and DSS-induced ulcerative colitis model were used to assess the anti-inflammatory efficacy of HK. Second, the drug affinity responsive target stability, proteomics analysis, thermal shift assays and cellular thermal shift assays were used to identify and validate the target of HK. Finally, western blot, ELISA, LDH immunofluorescence staining, shRNA and LC/MS for L-leucine analysis were performed to determine the mechanism of the anti-inflammatory action of HK. RESULTS This study revealed that HK significantly alleviated LPS-induced septic shock and DSS-induced ulcerative colitis in vivo, suggesting that HK has significant anti-inflammatory activity. HK treatment dramatically reduced IL-1β release and caspase-1 activation at different time points, showing that HK could inhibit both NLRP3 inflammasome priming and activation processes in cells. HK also suppressed adaptor apoptosis speck-like protein oligomerization. Mechanistically, SLC3A2 was identified as a direct target of HK in THP-1 cells. HK downregulated SLC3A2 expression by promoting its degradation via proteasome-mediated proteolysis. Further study demonstrated that HK triggered SLC3A2 to suppress NLRP3 inflammasome activation by significantly reducing the content of L-leucine transported into cells and lysosomes to block the mTORC1 pathway. CONCLUSIONS Our work identified HK as a promising anti-inflammatory drug candidate through the SLC3A2/L-leucine/mTORC1/NLRP3 pathways.
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Affiliation(s)
- Xiaoying Cai
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xueqin Jiang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Min Zhao
- Laboratory of Metabolomics and Drug-induced Liver Injury, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Kaiyue Su
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Minghai Tang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Feng Hong
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Neng Ye
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ruijia Zhang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Na Li
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lun Wang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Linlin Xue
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zejiang Zhu
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianhong Yang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenshuang Wu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Haoyu Ye
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Meena AK, Ilavarasan R, Perumal A, Singh R, Ojha V, Srikanth N, Dhiman KS. Evaluation for substitution of stem bark with small branches of Cassia fistula Linn for traditional medicinal uses: A comparative chemical profiling studies by HPLC, LC-MS, GC-MS. Heliyon 2022; 8:e10251. [PMID: 36033318 DOI: 10.1016/j.heliyon.2022.e10251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 05/06/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
Background The Aim of the present research article is to proposing a conservative approach for the Cassia fistula by using of small branches instead of stem bark because of plant has many important chemical constituents which show different medicinal activity so consumption of plant is high. We studied here Comparative preliminary phytochemical screening test of the ethanol extract and aqueous extract of the stem bark and small branches of Cassia fistula obtained by cold maceration process. Physicochemical analysis of Cassia fistula was done to ascertain the quality of the raw material used in the study. Successive soxhlet extraction method used for the successive extraction of stem bark and small branches with different solvents for comparative chemical profile study by HPLC, LCMS, and GCMS. Molecular Docking Interaction of Abundant Medicinal Phytochemicals in the Liquid Chromatography−Mass Spectrometry (LC−MS) Analysis Data of C. fistula with the L. donovani Drug Target Proteins and Pancreatic lipase colipase target protein. Result The pH of the small branches was found slightly higher as compared to stem bark and the percentage of other parameters like total ash content, acid insoluble ash, loss on drying at 105 °C, water soluble extractive and alcohol soluble extractive values were found fewer in the small branches as compare to stem bark of the plant. It was observed that the number of peaks in stem bark and small branches of the plant sample were almost similar and the retention time of each peak in stem bark was coincide with the retention of small branches of the sample. Therefore, similarity was observed in stem bark and small branches of the Cassia fistula plant in HPLC, LC-MS and GC-MS. The results obtained from HPLC analysis shows that stem bark contains 0.0084% and small branches having 0.0257% of rhein in Cassia fistula. Compounds 3, 9 and 12 are present in Stem bark as well as small branches of C. fistula and Compounds 22, 32 and 37 are present in small branches only. All the compounds have very good binding energy (Kcal/mol) with the respective target proteins. Conclusion The small branches have more active chemical constituents than stem bark against particular target proteins.
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Yang C, Xie L, Ma Y, Cai X, Yue G, Qin G, Zhang M, Gong G, Chang X, Qiu X, Luo L, Chen H. Study on the fungicidal mechanism of glabridin against Fusarium graminearum. Pestic Biochem Physiol 2021; 179:104963. [PMID: 34802513 DOI: 10.1016/j.pestbp.2021.104963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/07/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Glabridin is a natural plant-derived compound that has been widely used in medicine and cosmetic applications. However, the fungicidal mechanism of glabridin against phytopathogens remains unclear. In this study, we determined the biological activity and physiological effects of glabridin against F. graminearum. Then the differentially expressed proteins of F. graminearum were screened. The EC50 values of glabridin in inhibiting the mycelial growth and conidial germination of F. graminearum were 110.70 mg/L and 40.47 mg/L respectively. Glabridin-induced cell membrane damage was indicated by morphological observations, DiBAC4(3) and PI staining, and measurements of relative conductivity, ergosterol content and respiratory rates. These assays revealed that the integrity of the membrane was destroyed, the content of ergosterol decreased, and the respiratory rate was inhibited. A proteomics analysis showed that 186 proteins were up-regulated and 195 proteins were down-regulated. Mechanically sensitive ion channel proteins related to transmembrane transport and ergosterol biosynthesis ERG4/ERG24, related to ergosterol synthesis were blocked. It is speculated that glabridin acts on ergosterol synthesis-related proteins to destroy the integrity of the cell membrane, resulting in abnormal transmembrane transport and an increased membrane potential. Finally, the morphology of mycelia was seriously deformed, growth and development were inhibited. As a result death was even induced.
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Affiliation(s)
- Chunping Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Linjun Xie
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Yuqing Ma
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Xuewei Cai
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Guizhou Yue
- College of Science, Sichuan Agricultural University, Chengdu, China.
| | - Guangwei Qin
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Guoshu Gong
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Xiaoli Chang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Xiaoyan Qiu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Liya Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
| | - Huabao Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
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Huang L, Wang D, Zhang C. Drug Affinity Responsive Target Stability (DARTS ) Assay to Detect Interaction Between a Purified Protein and a Small Molecule. Methods Mol Biol 2021; 2213:175-82. [PMID: 33270202 DOI: 10.1007/978-1-0716-0954-5_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drug affinity responsive target stability (DARTS) assay is used to detect the interaction between a ligand and a protein based on the observation that some ligands can protect the target protein from degradation by proteases when mixed in a solution. To set up the assay, a ligand is first mixed with a purified candidate target protein or a total cell lysate that contains a candidate target protein. Then, different amounts of protease are added to the mixture to allow the enzyme to digest the protein in the mixture. After protease digestion, the candidate target protein is detected by assays such as western blot, silver staining, or Coomassie blue staining. In theory, the candidate protein should be protected by the ligand from protease digestion, which is reflected by higher abundance of the candidate protein in mixtures containing the ligand compared with the control treatment. There are a few significant advantages of DARTS: (a) the ligand does not need to be modified so the native ligand could be used; (b) the candidate target protein could be either purified protein or protein that is present in the total cell lysate; and (c) the assay can be used together with proteomics analysis to identify an unknown target protein. The assay is especially valuable to test the interaction between the ligand and membrane proteins that are often challenging to purify. In this chapter, we use Endosidin2 (ES2) and its target protein Arabidopsis thaliana EXO70A1 (AtEXO70A1) as an example to show the step-by-step procedure of the DARTS assay.
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Abstract
Target identification presents one of the biggest challenges to chemical genomic approaches. In recent years, several methods have been applied for target identification and validation in plant cells. Here, we describe a label-free method based on the thermodynamic stabilization of a protein by interaction with a small-molecule ligand. With increasing temperature, proteins undergo thermal denaturation resulting in irreversible aggregation and precipitation. The binding of a small molecule to its target can enhance protein stability resulting in an increased temperature of aggregation (Tagg). This distinct increase in the temperature of aggregation known as a thermal shift can identify a compound-target protein interaction in high-throughput assays or, validate a predicted interaction.
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Affiliation(s)
- Cecilia Rodriguez-Furlan
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Glenn R Hicks
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.,Uppsala Bio Center, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Zheng L, Zhang L, Huang J, Nandakumar KS, Liu S, Cheng K. Potential treatment methods targeting 2019-nCoV infection. Eur J Med Chem 2020; 205:112687. [PMID: 32771797 PMCID: PMC7385720 DOI: 10.1016/j.ejmech.2020.112687] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/18/2020] [Accepted: 07/19/2020] [Indexed: 01/08/2023]
Abstract
The novel coronavirus, 2019-nCoV, has quickly spread across the world and pose serious threat to public health because it can infect people very easily. The major clinical symptoms of 2019-nCoV infection include fever, dry cough, myalgia, fatigue, and diarrhea. The 2019-nCoV belongs to the betacoronavirus family, and gene sequencing results demonstrate that it is a single-stranded RNA virus, closely related to Severe Acute Respiratory Syndrome CoV (SARS-CoV) and Middle East Respiratory Syndrome CoV (MERS-CoV). It has been observed that the virus invades human body mainly through binding to angiotensin-converting enzyme 2 (ACE2) receptors similar to SARS-CoV and the main protease (Mpro) acts as a critical protease for digesting the polyprotein into functional polypeptides during the replication and transcription process of 2019-nCoV. In this review, we summarized the real-time information of 2019-nCoV treatment methods and mainly focused on the chemical drugs including lopinavir/ritonavir, chloroquine, hydroxychloroquine, arbidol, remdesivir, favipiravir and other potential innovative active molecules. Their potential targets, activity, clinical status and side effects are described. In addition, Traditional Chinese Medicine (TCM), Convalescent plasma therapy (CPT) and biological reagents available, as well as the promising vaccine candidates against 2019-nCoV are also discussed.
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Affiliation(s)
- Lu Zheng
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lina Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiamin Huang
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kutty Selva Nandakumar
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Southern Medical University, Guangzhou 510515, China.
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
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Wang Y, Jiang X, Feng F, Liu W, Sun H. Degradation of proteins by PROTACs and other strategies. Acta Pharm Sin B 2020; 10:207-238. [PMID: 32082969 PMCID: PMC7016280 DOI: 10.1016/j.apsb.2019.08.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Blocking the biological functions of scaffold proteins and aggregated proteins is a challenging goal. PROTAC proteolysis-targeting chimaera (PROTAC) technology may be the solution, considering its ability to selectively degrade target proteins. Recent progress in the PROTAC strategy include identification of the structure of the first ternary eutectic complex, extra-terminal domain-4-PROTAC-Von-Hippel-Lindau (BRD4-PROTAC-VHL), and PROTAC ARV-110 has entered clinical trials for the treatment of prostate cancer in 2019. These discoveries strongly proved the value of the PROTAC strategy. In this perspective, we summarized recent meaningful research of PROTAC, including the types of degradation proteins, preliminary biological data in vitro and in vivo, and new E3 ubiquitin ligases. Importantly, the molecular design, optimization strategy and clinical application of candidate molecules are highlighted in detail. Future perspectives for development of advanced PROTAC in medical fields have also been discussed systematically.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xueyang Jiang
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Feng
- Jiangsu Food and Pharmaceutical Science College, Huaian 223003, China
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
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Wu X, Han X, Li L, Fan S, Zhuang P, Yang Z, Zhang Y. iTRAQ-based quantitative proteomics and target-fishing strategies reveal molecular signatures on vasodilation of Compound Danshen Dripping Pills. Chem Biol Interact 2019; 316:108923. [PMID: 31838051 DOI: 10.1016/j.cbi.2019.108923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/26/2019] [Accepted: 12/10/2019] [Indexed: 10/25/2022]
Abstract
Angina pectoris can be used as an early warning for coronary artery disease. Vasodilation is an important mechanism of angina pectoris. Traditional Chinese medicine - Compound Danshen Dripping Pill (CDDP) is widely used to improve the symptoms of cardiovascular diseases (CVDs). To investigate the influence of vasodilation effect and underlying mechanisms of CDDP, we determined the vasodilation effect of thoracic aorta ring on rat induced by norepinephrine (NE). Then targets-fishing method was used to predict the potential mechanism of CDDP on vasodilation, based on the structures of the main components. Then, iTRAQ-based quantitative proteomics analysis was used for verification of the candidate target proteins and pathways to illustrate the underlying mechanisms. Furthermore, the differentially expressed proteins in the enriched pathways were validated by western blotting. In this study, we found that CDDP could significantly inhibit NE induced aortic contraction tension, and the mechanism may be related to platelet activation, cGMP - PKG signaling pathway and vascular smooth muscle contraction. The method provides a new way to uncover the vasodilation mechanism of CDDP, as well as other multi-component herbal medicines.
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Affiliation(s)
- Xin Wu
- Chinese Materia Medica College, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China; Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Xiujiang Han
- Department of Cardiology, Tianjin Hospital of ITCWM Nankai Hospital, Tianjin, 300100, China
| | - Lili Li
- Chinese Materia Medica College, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Simiao Fan
- Chinese Materia Medica College, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Pengwei Zhuang
- Chinese Materia Medica College, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Zhen Yang
- Chinese Materia Medica College, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China; Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Yanjun Zhang
- Chinese Materia Medica College, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
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Zheng Y, Peng H, Ghosh S, Lan C, Li J. Inverse similarity and reliable negative samples for drug side-effect prediction. BMC Bioinformatics 2019; 19:554. [PMID: 30717666 PMCID: PMC7402513 DOI: 10.1186/s12859-018-2563-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 12/07/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND In silico prediction of potential drug side-effects is of crucial importance for drug development, since wet experimental identification of drug side-effects is expensive and time-consuming. Existing computational methods mainly focus on leveraging validated drug side-effect relations for the prediction. The performance is severely impeded by the lack of reliable negative training data. Thus, a method to select reliable negative samples becomes vital in the performance improvement. METHODS Most of the existing computational prediction methods are essentially based on the assumption that similar drugs are inclined to share the same side-effects, which has given rise to remarkable performance. It is also rational to assume an inverse proposition that dissimilar drugs are less likely to share the same side-effects. Based on this inverse similarity hypothesis, we proposed a novel method to select highly-reliable negative samples for side-effect prediction. The first step of our method is to build a drug similarity integration framework to measure the similarity between drugs from different perspectives. This step integrates drug chemical structures, drug target proteins, drug substituents, and drug therapeutic information as features into a unified framework. Then, a similarity score between each candidate negative drug and validated positive drugs is calculated using the similarity integration framework. Those candidate negative drugs with lower similarity scores are preferentially selected as negative samples. Finally, both the validated positive drugs and the selected highly-reliable negative samples are used for predictions. RESULTS The performance of the proposed method was evaluated on simulative side-effect prediction of 917 DrugBank drugs, comparing with four machine-learning algorithms. Extensive experiments show that the drug similarity integration framework has superior capability in capturing drug features, achieving much better performance than those based on a single type of drug property. Besides, the four machine-learning algorithms achieved significant improvement in macro-averaging F1-score (e.g., SVM from 0.655 to 0.898), macro-averaging precision (e.g., RBF from 0.592 to 0.828) and macro-averaging recall (e.g., KNN from 0.651 to 0.772) complimentarily attributed to the highly-reliable negative samples selected by the proposed method. CONCLUSIONS The results suggest that the inverse similarity hypothesis and the integration of different drug properties are valuable for side-effect prediction. The selection of highly-reliable negative samples can also make significant contributions to the performance improvement.
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Affiliation(s)
- Yi Zheng
- Advanced Analytics Institute, FEIT, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Hui Peng
- Advanced Analytics Institute, FEIT, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Shameek Ghosh
- Advanced Analytics Institute, FEIT, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Chaowang Lan
- Advanced Analytics Institute, FEIT, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Jinyan Li
- Advanced Analytics Institute, FEIT, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia.
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Zhao X, Chen L, Lu J. A similarity-based method for prediction of drug side effects with heterogeneous information. Math Biosci 2018; 306:136-144. [PMID: 30296417 DOI: 10.1016/j.mbs.2018.09.010] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/22/2018] [Accepted: 09/25/2018] [Indexed: 12/25/2022]
Abstract
Drugs can produce intended therapeutic effects to treat different diseases. However, they may also cause side effects at the same time. For an approved drug, it is best to detect all side effects it can produce. Otherwise, it may bring great risks for pharmaceuticals companies as well as be harmful to human body. It is urgent to design quick and reliable identification methods to detect the side effects for a given drug. In this study, a binary classification model was proposed to predict drug side effects. Different from most previous methods, our model termed the pair of drug and side effect as a sample and convert the original problem to a binary classification problem. Based on the similarity idea, each pair was represented by five features, each of which was derived from a type of drug property. The strong machine learning algorithm, random forest, was adopted as the prediction engine. The ten-fold cross-validation on five datasets with different negative samples indicated that the proposed model yielded a good performance of Matthews correlation coefficient around 0.550 and AUC around 0.8492. In addition, we also analyzed the contribution of each drug property for construction of the model. The results indicated that drug similarity in fingerprint was most related to the prediction of drug side effects and all drug properties gave less or more contributions.
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Affiliation(s)
- Xian Zhao
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China; Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai 200241, People's Republic of China.
| | - Jing Lu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, People's Republic of China
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Ma J, Xia Q, Fu PP, Lin G. Pyrrole-protein adducts - A biomarker of pyrrolizidine alkaloid-induced hepatotoxicity. J Food Drug Anal 2018; 26:965-972. [PMID: 29976414 PMCID: PMC9303027 DOI: 10.1016/j.jfda.2018.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 12/11/2022] Open
Abstract
Pyrrolizidine alkaloids (PAs) are phytotoxins identified in over 6000 plant species worldwide. Approximately 600 toxic PAs and PA N-oxides have been identified in about 3% flowering plants. PAs can cause toxicities in different organs particularly in the liver. The metabolic activation of PAs is catalyzed by hepatic cytochrome P450 and generates reactive pyrrolic metabolites that bind to cellular proteins to form pyrrole-protein adducts leading to PA-induced hepatotoxicity. The mechanisms that pyrrole-protein adducts induce toxicities have not been fully characterized. Methods for qualitative and quantitative detection of pyrrole-protein adducts have been developed and applied for the clinical diagnosis of PA exposure and PA-induced liver injury. This mini-review addresses the mechanisms of PA-induced hepatotoxicity mediated by pyrrole-protein adducts, the analytical methods for the detection of pyrrole-protein adducts, and the development of pyrrole-protein adducts as the mechanism-based biomarker of PA exposure and PA-induced hepatotoxicity.
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Affiliation(s)
- Jiang Ma
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Joint Research Laboratory for Promoting Globalization of Traditional Chinese Medicines Between the Chinese University of Hong Kong and Shanghai Institute of Materia Medica, China Academy of Sciences, China
| | - Qingsu Xia
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Peter P Fu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
| | - Ge Lin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Joint Research Laboratory for Promoting Globalization of Traditional Chinese Medicines Between the Chinese University of Hong Kong and Shanghai Institute of Materia Medica, China Academy of Sciences, China.
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Murahashi M, Simizu S, Morioka M, Umezawa K. Identification of poly(rC) binding protein 2 (PCBP2) as a target protein of immunosuppressive agent 15-deoxyspergualin. Biochem Biophys Res Commun 2016; 476:445-449. [PMID: 27261432 DOI: 10.1016/j.bbrc.2016.05.142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 05/27/2016] [Indexed: 11/18/2022]
Abstract
15-Deoxyspergualin (DSG) is an immunosuppressive agent being clinically used. Unlike tacrolimus and cyclosporine A, it does not inhibit the calcineurin pathway, and its mechanism of action and target molecule have not been elucidated. Therefore, we previously prepared biotinylated derivative of DSG (BDSG) to fish up the target protein. In the present research, we identified poly(rC) binding protein 2 (PCBP2) as a DSG-binding protein using this probe. DSG was confirmed to bind to PCBP2 by pull-down assay. Intracellular localization of PCBP2 was changed from the nucleus to the cytoplasm by DSG treatment. DSG inhibited the cell growth, and over-expression of PCBP2 reduced the anti-proliferative activity of DSG. PCBP2 is known to regulate various proteins including STAT1/2. Thus, we found PCBP2 as the first target protein of DSG that can explain the immunosuppressive activity.
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Affiliation(s)
- Masataka Murahashi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Masahiko Morioka
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kazuo Umezawa
- Department of Molecular Target Medicine, Aichi Medical University School of Medicine, 1-1 Yazako-Karimata, Nagakute 480-1195, Japan.
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