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Shen Q, Ge L, Lu W, Wu H, Zhang L, Xu J, Tang O, Muhammad I, Zheng J, Wu Y, Wang SW, Zeng XX, Xue J, Cheng K. Transplanting network pharmacology technology into food science research: A comprehensive review on uncovering food-sourced functional factors and their health benefits. Compr Rev Food Sci Food Saf 2024; 23:e13429. [PMID: 39217524 DOI: 10.1111/1541-4337.13429] [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: 01/29/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024]
Abstract
Network pharmacology is an emerging interdisciplinary research method. The application of network pharmacology to reveal the nutritional effects and mechanisms of active ingredients in food is of great significance in promoting the development of functional food, facilitating personalized nutrition, and exploring the mechanisms of food health effects. This article systematically reviews the application of network pharmacology in the field of food science using a literature review method. The application progress of network pharmacology in food science is discussed, and the mechanisms of functional factors in food on the basis of network pharmacology are explored. Additionally, the limitations and challenges of network pharmacology are discussed, and future directions and application prospects are proposed. Network pharmacology serves as an important tool to reveal the mechanisms of action and health benefits of functional factors in food. It helps to conduct in-depth research on the biological activities of individual ingredients, composite foods, and compounds in food, and assessment of the potential health effects of food components. Moreover, it can help to control and enhance their functionality through relevant information during the production and processing of samples to guarantee food safety. The application of network pharmacology in exploring the mechanisms of functional factors in food is further analyzed and summarized. Combining machine learning, artificial intelligence, clinical experiments, and in vitro validation, the achievement transformation of functional factor in food driven by network pharmacology is of great significance for the future development of network pharmacology research.
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Affiliation(s)
- Qing Shen
- Laboratory of Food Nutrition and Clinical Research, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
- Panvascular Diseases Research Center, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Lijun Ge
- Laboratory of Food Nutrition and Clinical Research, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Weibo Lu
- Laboratory of Food Nutrition and Clinical Research, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Huixiang Wu
- Laboratory of Food Nutrition and Clinical Research, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Li Zhang
- Quzhou Hospital of Traditional Chinese Medicine, Quzhou, Zhejiang, China
| | - Jun Xu
- Ningbo Hospital of Traditional Chinese Medicine, Affiliated Hospital of Zhejiang Chinese Medical University, Ningbo, Zhejiang, China
| | - Oushan Tang
- Shaoxing Second Hospital, Shaoxing, Zhejiang, China
| | - Imran Muhammad
- Laboratory of Food Nutrition and Clinical Research, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Jing Zheng
- Panvascular Diseases Research Center, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Yeshun Wu
- Panvascular Diseases Research Center, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Si-Wei Wang
- Panvascular Diseases Research Center, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Xi-Xi Zeng
- Panvascular Diseases Research Center, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Jing Xue
- Laboratory of Food Nutrition and Clinical Research, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Keyun Cheng
- Panvascular Diseases Research Center, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
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Sun Y, Li Q, Huang Y, Yang Z, Li G, Sun X, Gu X, Qiao Y, Wu Q, Xie T, Sui X. Natural products for enhancing the sensitivity or decreasing the adverse effects of anticancer drugs through regulating the redox balance. Chin Med 2024; 19:110. [PMID: 39164783 PMCID: PMC11334420 DOI: 10.1186/s13020-024-00982-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 08/11/2024] [Indexed: 08/22/2024] Open
Abstract
Redox imbalance is reported to play a pivotal role in tumorigenesis, cancer development, and drug resistance. Severe oxidative damage is a general consequence of cancer cell responses to treatment and may cause cancer cell death or severe adverse effects. To maintain their longevity, cancer cells can rescue redox balance and enter a state of resistance to anticancer drugs. Therefore, targeting redox signalling pathways has emerged as an attractive and prospective strategy for enhancing the efficacy of anticancer drugs and decreasing their adverse effects. Over the past few decades, natural products (NPs) have become an invaluable source for developing new anticancer drugs due to their high efficacy and low toxicity. Increasing evidence has demonstrated that many NPs exhibit remarkable antitumour effects, whether used alone or as adjuvants, and are emerging as effective approaches to enhance sensitivity and decrease the adverse effects of conventional cancer therapies by regulating redox balance. Among them are several novel anticancer drugs based on NPs that have entered clinical trials. In this review, we summarize the synergistic anticancer effects and related redox mechanisms of the combination of NPs with conventional anticancer drugs. We believe that NPs targeting redox regulation will represent promising novel candidates and provide prospects for cancer treatment in the future.
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Affiliation(s)
- Yitian Sun
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Qinyi Li
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Yufei Huang
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Zijing Yang
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Guohua Li
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Xiaoyu Sun
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Xiaoqing Gu
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Yunhao Qiao
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Qibiao Wu
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China.
| | - Tian Xie
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China.
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
| | - Xinbing Sui
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China.
- College of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
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Wang Y, Sui Y, Yao J, Jiang H, Tian Q, Tang Y, Ou Y, Tang J, Tan N. Herb-CMap: a multimodal fusion framework for deciphering the mechanisms of action in traditional Chinese medicine using Suhuang antitussive capsule as a case study. Brief Bioinform 2024; 25:bbae362. [PMID: 39073832 DOI: 10.1093/bib/bbae362] [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: 03/05/2024] [Revised: 06/21/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
Herbal medicines, particularly traditional Chinese medicines (TCMs), are a rich source of natural products with significant therapeutic potential. However, understanding their mechanisms of action is challenging due to the complexity of their multi-ingredient compositions. We introduced Herb-CMap, a multimodal fusion framework leveraging protein-protein interactions and herb-perturbed gene expression signatures. Utilizing a network-based heat diffusion algorithm, Herb-CMap creates a connectivity map linking herb perturbations to their therapeutic targets, thereby facilitating the prioritization of active ingredients. As a case study, we applied Herb-CMap to Suhuang antitussive capsule (Suhuang), a TCM formula used for treating cough variant asthma (CVA). Using in vivo rat models, our analysis established the transcriptomic signatures of Suhuang and identified its key compounds, such as quercetin and luteolin, and their target genes, including IL17A, PIK3CB, PIK3CD, AKT1, and TNF. These drug-target interactions inhibit the IL-17 signaling pathway and deactivate PI3K, AKT, and NF-κB, effectively reducing lung inflammation and alleviating CVA. The study demonstrates the efficacy of Herb-CMap in elucidating the molecular mechanisms of herbal medicines, offering valuable insights for advancing drug discovery in TCM.
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Affiliation(s)
- Yinyin Wang
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yihang Sui
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211198, PR China
| | - Jiaqi Yao
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211198, PR China
| | - Hong Jiang
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211198, PR China
| | - Qimeng Tian
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130 Meilong Road, Shanghai 200237, China
| | - Yongyu Ou
- Beijing Haiyan Pharmaceutical Co., Ltd., Yangtze River Pharmaceutical Group, No. 16 Shengmingyuan Road, Beijing 102206, PR China
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki FI-00290, Finland
| | - Ninghua Tan
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211198, PR China
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Hou D, Lin H, Feng Y, Zhou K, Li X, Yang Y, Wang S, Yang X, Wang J, Zhao H, Zhang X, Fan J, Lu S, Wang D, Zhu L, Ju D, Chen YZ, Zeng X. CMAUP database update 2024: extended functional and association information of useful plants for biomedical research. Nucleic Acids Res 2024; 52:D1508-D1518. [PMID: 37897343 PMCID: PMC10767869 DOI: 10.1093/nar/gkad921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/23/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023] Open
Abstract
Knowledge of the collective activities of individual plants together with the derived clinical effects and targeted disease associations is useful for plant-based biomedical research. To provide the information in complement to the established databases, we introduced a major update of CMAUP database, previously featured in NAR. This update includes (i) human transcriptomic changes overlapping with 1152 targets of 5765 individual plants, covering 74 diseases from 20 027 patient samples; (ii) clinical information for 185 individual plants in 691 clinical trials; (iii) drug development information for 4694 drug-producing plants with metabolites developed into approved or clinical trial drugs; (iv) plant and human disease associations (428 737 associations by target, 220 935 reversion of transcriptomic changes, 764 and 154121 associations by clinical trials of individual plants and plant ingredients); (v) the location of individual plants in the phylogenetic tree for navigating taxonomic neighbors, (vi) DNA barcodes of 3949 plants, (vii) predicted human oral bioavailability of plant ingredients by the established SwissADME and HobPre algorithm, (viii) 21-107% increase of CMAUP data over the previous version to cover 60 222 chemical ingredients, 7865 plants, 758 targets, 1399 diseases, 238 KEGG human pathways, 3013 gene ontologies and 1203 disease ontologies. CMAUP update version is freely accessible at https://bidd.group/CMAUP/index.html.
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Affiliation(s)
- Dongyue Hou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hanbo Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuhan Feng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Kaicheng Zhou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xingxiu Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuan Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Shuaiqi Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xue Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiayu Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hui Zhao
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xuyao Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiajun Fan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - SongLin Lu
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Dan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Lyuhan Zhu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yu Zong Chen
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
- Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xian Zeng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
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Ye T, Su H, Zheng G, Meng H, Wang W, Guo Y. Multiomics Reveals the Key Microorganisms and Metabolites in the Resistance to Root Rot Disease of Paris polyphylla. Genes (Basel) 2023; 15:21. [PMID: 38254911 PMCID: PMC10815090 DOI: 10.3390/genes15010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Root rot of Paris polyphylla has received widespread attention due to its threat to yield and leads to serious economic losses. However, the relationship among the rhizosphere microbial community, metabolites and root rot disease remained largely unexplored. Herein, we used integrated 16S rRNA, ITS, RNA sequencing and UPLC-MS/MS to systematically investigate the differences between healthy and diseased P. polyphylla. We found that root rot reduced the microbial diversity in the diseased P. polyphylla compared with the healthy control. The relative abundance of the bacterial phylum Actinobacteria increased in the diseased rhizome of P. polyphylla. For the fungal community, root rot disease contributed to an increased relative abundance of Ascomycota and decreased Glomeromycota at the phylum level. The transcriptomic results showed that the differently expressed genes were significantly enriched in the "Biosynthesis of various alkaloids", "flavonoid biosynthesis" and "isoflavonoid biosynthesis" and "Phenylpropanoid biosynthesis" was dramatically enriched in healthy P. polyphylla compared with that in diseased P. polyphylla. Likewise, the metabolomic results showed that the biosynthesis of secondary metabolites and metabolic pathways was found to be significantly enriched by differential metabolites. Taken together, the study of combining metabolomics with microbiomes can help us enhance our understanding of the mechanisms of plant resistance to root rot disease, thereby discovering specific metabolites and microorganisms that can resist pathogen infection in P. polyphylla.
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Affiliation(s)
- Ting Ye
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen 361006, China; (T.Y.); (H.M.); (W.W.)
| | - Hailan Su
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Germplasm Resources Center, Fuzhou 350000, China;
| | - Guohua Zheng
- Plant Introduction & Quarantine Base and Plant Product Key Laboratory of Xiamen City, Xiamen Overseas Chinese Subtropical Plant Introduction Garden, Xiamen 361002, China;
| | - Hongyan Meng
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen 361006, China; (T.Y.); (H.M.); (W.W.)
| | - Wenhua Wang
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen 361006, China; (T.Y.); (H.M.); (W.W.)
| | - Ying Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen 361006, China; (T.Y.); (H.M.); (W.W.)
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Chen J, Wang Y, Di P, Wu Y, Qiu S, Lv Z, Qiao Y, Li Y, Tan J, Chen W, Yu M, Wei P, Xiao Y, Chen W. Phenotyping of Salvia miltiorrhiza Roots Reveals Associations between Root Traits and Bioactive Components. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0098. [PMID: 37791248 PMCID: PMC10545446 DOI: 10.34133/plantphenomics.0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/05/2023] [Indexed: 10/05/2023]
Abstract
Plant phenomics aims to perform high-throughput, rapid, and accurate measurement of plant traits, facilitating the identification of desirable traits and optimal genotypes for crop breeding. Salvia miltiorrhiza (Danshen) roots possess remarkable therapeutic effect on cardiovascular diseases, with huge market demands. Although great advances have been made in metabolic studies of the bioactive metabolites, investigation for S. miltiorrhiza roots on other physiological aspects is poor. Here, we developed a framework that utilizes image feature extraction software for in-depth phenotyping of S. miltiorrhiza roots. By employing multiple software programs, S. miltiorrhiza roots were described from 3 aspects: agronomic traits, anatomy traits, and root system architecture. Through K-means clustering based on the diameter ranges of each root branch, all roots were categorized into 3 groups, with primary root-associated key traits. As a proof of concept, we examined the phenotypic components in a series of randomly collected S. miltiorrhiza roots, demonstrating that the total surface of root was the best parameter for the biomass prediction with high linear regression correlation (R2 = 0.8312), which was sufficient for subsequently estimating the production of bioactive metabolites without content determination. This study provides an important approach for further grading of medicinal materials and breeding practices.
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Affiliation(s)
- Junfeng Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica,
Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yun Wang
- School of Medicine,
Shanghai University, Shanghai 200444, China
| | - Peng Di
- State Local Joint Engineering Research Center of Ginseng Breeding and Application,
Jilin Agricultural University, Changchun 130118, China
| | - Yulong Wu
- School of Computer Science,
Sichuan Normal University, Chengdu 610066, China
| | - Shi Qiu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica,
Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zongyou Lv
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica,
Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuqi Qiao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica,
Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yajing Li
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica,
Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jingfu Tan
- Shangyao Huayu (Linyi) Traditional Chinese Resources Co., Ltd., Linyi 276000, China
| | - Weixu Chen
- Shangyao Huayu (Linyi) Traditional Chinese Resources Co., Ltd., Linyi 276000, China
| | - Ma Yu
- School of Life Science and Engineering,
Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Ping Wei
- Sichuan Academy of Traditional Chinese Medicine, Chengdu 610041, China
| | - Ying Xiao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica,
Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wansheng Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica,
Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacy, Changzheng Hospital,
Second Military Medical University, Shanghai 200003, China
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7
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Yang S, Zhu G. Phytotherapy of abnormality of fear memory: A narrative review of mechanisms. Fitoterapia 2023; 169:105618. [PMID: 37482307 DOI: 10.1016/j.fitote.2023.105618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023]
Abstract
It is generally believed that in post-traumatic stress disorder (PTSD), the high expression of fear memory is mainly determined by amygdala hyperactivity and hippocampus hypoactivity. In this review, we firstly updated the mechanisms of fear memory, and then searched the experimental evidence of phytotherapy for fear memory in the past five years. Based on the summary of those experimental studies, we further discussed the future research strategies of plant medicines, including the study of the mechanism of specific brain regions, the optimal time for the prevention and treatment of fear memory-related diseases such as PTSD, and the development of new drugs with active components of plant medicines. Accordingly, plant medicines play a clear role in improving fear memory abnormalities and have the drug development potential in the treatment of fear-related disorders.
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Affiliation(s)
- Shaojie Yang
- The Second Affiliation Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230061, China; Key Laboratory of Xin'an Medicine, The Ministry of Education and Key Laboratory of Molecular Biology (Brain diseases), Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Guoqi Zhu
- Key Laboratory of Xin'an Medicine, The Ministry of Education and Key Laboratory of Molecular Biology (Brain diseases), Anhui University of Chinese Medicine, Hefei, Anhui 230012, China.
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8
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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9
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Song Q, Bi L, Jiao J, Shang J, Li Q, Shabuerjiang L, Bai M, Liu X. Zhachong Shisanwei Pill resists ischemic stroke by lysosome pathway based on proteomics and bioinformatics. JOURNAL OF ETHNOPHARMACOLOGY 2023; 301:115766. [PMID: 36183948 DOI: 10.1016/j.jep.2022.115766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/05/2022] [Accepted: 09/25/2022] [Indexed: 05/05/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Zhachong Shisanwei Pill (ZSP) is a commonly used Mongolian medicine in treating cerebrovascular diseases and plays a role in the clinical treatment of ischemic stroke (IS). AIM OF THE STUDY Based on determining the protective effect of ZSP on cerebral ischemia, they adopted the proteomics method to explore the mechanism of ZSP against IS. MATERIALS AND METHODS Rats with middle cerebral artery occlusion (MCAO) model were prepared by wire embolization method, and divided into sham group, model group, ZSP high-dose group, medium-dose group, low-dose group and positive drug group. We collected the brain tissue of rats for 12 h after modeling. Neurological deficit score and cerebral infarction volume ratio evaluated pharmacodynamics, and we selected the optimal dose for subsequent experiments. Proteomics was used to screen out possible ZSP anti-IS mediated pathways and differentially expression proteins. Network pharmacology was used to verify the correlation between diseases and drugs. Hematoxylin-eosin (HE) staining and transmission electron microscope (TEM) were used to explore further the pharmacodynamic effect of ZSP against IS and its possible mechanism. RESULTS The cerebral infarction rate and neurological function score in rats showed that the medium-dose ZSP group had the best efficacy. Proteomics results showed that the anti-IS action of ZSP was mainly through lysosome pathway. LAMP2, AP3M1, and SCARB2 were the differentially changed proteins in this pathway. Network pharmacology verified this. HE staining and TEM results showed that ZSP could improve the pathological state of neurons in MCAO rats and reduce the number of lysosomes in MCAO rats. Western blot (WB) results showed that compared with the model group, the protein expression levels of LAMP2 and AP3M1 in the ZSP group were significantly down-regulated, and the protein expression levels of SCARB2 were significantly up-regulated. CONCLUSION This study confirms that ZSP regulates the lysosomal pathway, which may protect IS by down-regulating LAMP2 and AP3M1 and up-regulating SCARB2.
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Affiliation(s)
- Qi Song
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 100029, Beijing, China.
| | - Lei Bi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 100029, Beijing, China.
| | - Jiakang Jiao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 100029, Beijing, China.
| | - Jinfeng Shang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 100029, Beijing, China.
| | - Qiannan Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 100029, Beijing, China.
| | - Lizha Shabuerjiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 100029, Beijing, China.
| | - Meirong Bai
- Key Laboratory of Mongolian Medicine Research and Development Engineering, Ministry of Education, Inner Mongolia Minzu University, 028000, Tongliao, China.
| | - Xin Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 100029, Beijing, China.
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10
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Light and Potassium Improve the Quality of Dendrobium officinale through Optimizing Transcriptomic and Metabolomic Alteration. Molecules 2022; 27:molecules27154866. [PMID: 35956813 PMCID: PMC9369990 DOI: 10.3390/molecules27154866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 12/18/2022] Open
Abstract
Background: Dendrobium officinale is a perennial epiphytic herb in Orchidaceae. Cultivated products are the main alternative for clinical application due to the shortage of wild resources. However, the phenotype and quality of D. officinale have changed post-artificial cultivation, and environmental cues such as light, temperature, water, and nutrition supply are the major influencing factors. This study aims to unveil the mechanisms beneath the cultivation-induced variation by analyzing the changes of the metabolome and transcriptome of D. officinale seedlings treated with red- blue LED light and potassium fertilizer. Results: After light- and K-treatment, the D. officinale pseudobulbs turned purple and the anthocyanin content increased significantly. Through wide-target metabolome analysis, compared with pseudobulbs in the control group (P), the proportion of flavonoids in differentially-accumulated metabolites (DAMs) was 22.4% and 33.5% post light- and K-treatment, respectively. The gene modules coupled to flavonoids were obtained through the coexpression analysis of the light- and K-treated D. officinale transcriptome by WGCNA. The KEGG enrichment results of the key modules showed that the DEGs of the D. officinale pseudobulb were enriched in phenylpropane biosynthesis, flavonoid biosynthesis, and jasmonic acid (JA) synthesis post-light- and K-treatment. In addition, anthocyanin accumulation was the main contribution to the purple color of pseudobulbs, and the plant hormone JA induced the accumulation of anthocyanins in D. officinale. Conclusions: These results suggested that light and potassium affected the accumulation of active compounds in D. officinale, and the gene-flavone network analysis emphasizes the key functional genes and regulatory factors for quality improvement in the cultivation of this medicinal plant.
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11
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Ma X, Tang K, Tang Z, Dong A, Xiao H, Meng Y, Wang P. An organ-specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein-coding genes, microRNAs, and regulatory networks. THE PLANT GENOME 2022; 15:e20210. [PMID: 35475547 DOI: 10.1002/tpg2.20210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
As one of the important species belonging to the Bletilla genus of Orchidaceae, Bletilla striata (Thunb.) Rchb. f., possesses both ornamental and medicinal values. Its dried tubers are used as a traditional Chinese medicine, and several secondary metabolites have been indicated to be the active ingredients. However, the molecular mechanisms related to the regulation of secondary metabolism have not been characterized in B. striata. In this study, integrated analysis of RNA sequencing (RNA-seq), small RNA sequencing (sRNA-seq), and degradome sequencing (degradome-seq) data from three organs (leaf, root, and tuber) of B. striata provided us with a comprehensive view of the microRNA (miRNA)-mediated regulatory network. Firstly, based on the RNA-seq data, the organ-specific expression patterns of the protein-coding genes, especially for those related to secondary metabolism, were investigated. Secondly, 342 conserved miRNA candidates were identified from B. striata. These miRNAs were assigned to 88 families, some of which were selected for expression pattern analysis. Additionally, 31 hairpin-structured precursors encoding 23 novel miRNAs were uncovered from the transcriptome assembly. Thirdly, based on the degradome signatures, 1,142 validated miRNA-target pairs (involving 167 conserved miRNAs and six novel miRNAs and 51 target genes) were included in the regulatory network. Organ-specific expression level comparison between the miRNAs and their targets revealed some interesting miRNA-target pairs. Fourthly, some valuable subnetworks were extracted for further functional studies. Additionally, some regulatory pathways were indicated to be monocot specific. Summarily, our results lay a solid basis for in-depth studies on the regulatory mechanisms underlying the production of the medicinal ingredients in B. striata.
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Affiliation(s)
- Xiaoxia Ma
- College of Pharmaceutical Science, Zhejiang Univ. of Technology, Hangzhou, 310014, China
- School of Pharmacy, Hangzhou Normal Univ., Hangzhou, 311121, China
| | - Kehua Tang
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou Univ., Zhangjiajie, 427000, China
| | - Zhonghai Tang
- College of Food Science and Technology, Hunan Agricultural Univ., Changsha, 410128, China
| | - Aiwen Dong
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, Jishou Univ., Zhangjiajie, 427000, China
| | - Hang Xiao
- Dep. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, USA
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal Univ., Hangzhou, 311121, China
| | - Pu Wang
- College of Pharmaceutical Science, Zhejiang Univ. of Technology, Hangzhou, 310014, China
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12
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Ghai D, Kaur A, Kahlon PS, Pawar SV, Sembi JK. A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:837563. [PMID: 35574139 PMCID: PMC9100589 DOI: 10.3389/fpls.2022.837563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Orchids have a huge reservoir of secondary metabolites making these plants of immense therapeutic importance. Their potential as curatives has been realized since times immemorial and are extensively studied for their medicinal properties. Secondary metabolism is under stringent genetic control in plants and several molecular factors are involved in regulating the production of the metabolites. However, due to the complex molecular networks, a complete understanding of the specific molecular cues is lacking. High-throughput omics technologies have the potential to fill up this lacuna. The present study deals with comparative analysis of high-throughput transcript data involving gene identification, functional annotation, and differential expression in more than 30 orchid transcriptome data sets, with a focus to elucidate the role of various factors in alkaloid and flavonoid biosynthesis. Comprehensive analysis of the mevalonate (MVA) pathway, methyl-d-erythritol 4-phosphate (MEP) pathway, and phenylpropanoid pathway provide specific insights to the potential gene targets for drug discovery. It is envisaged that a positive stimulation of these pathways through regulation of pivotal genes and alteration of specific gene expression, could facilitate the production of secondary metabolites and enable efficient tapping of the therapeutic potential of orchids. This further would lay the foundation for developing strategies for genetic and epigenetic improvement of these plants for development of therapeutic products.
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Affiliation(s)
- Devina Ghai
- Department of Botany, Panjab University, Chandigarh, India
| | - Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, India
| | - Parvinderdeep S. Kahlon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Sandip V. Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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13
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Serra A, Saarimäki LA, Pavel A, del Giudice G, Fratello M, Cattelani L, Federico A, Laurino O, Marwah VS, Fortino V, Scala G, Sofia Kinaret PA, Greco D. Nextcast: A software suite to analyse and model toxicogenomics data. Comput Struct Biotechnol J 2022; 20:1413-1426. [PMID: 35386103 PMCID: PMC8956870 DOI: 10.1016/j.csbj.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 11/28/2022] Open
Abstract
The recent advancements in toxicogenomics have led to the availability of large omics data sets, representing the starting point for studying the exposure mechanism of action and identifying candidate biomarkers for toxicity prediction. The current lack of standard methods in data generation and analysis hampers the full exploitation of toxicogenomics-based evidence in regulatory risk assessment. Moreover, the pipelines for the preprocessing and downstream analyses of toxicogenomic data sets can be quite challenging to implement. During the years, we have developed a number of software packages to address specific questions related to multiple steps of toxicogenomics data analysis and modelling. In this review we present the Nextcast software collection and discuss how its individual tools can be combined into efficient pipelines to answer specific biological questions. Nextcast components are of great support to the scientific community for analysing and interpreting large data sets for the toxicity evaluation of compounds in an unbiased, straightforward, and reliable manner. The Nextcast software suite is available at: ( https://github.com/fhaive/nextcast).
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Laura Aliisa Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Giusy del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Luca Cattelani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | | | - Veer Singh Marwah
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Giovanni Scala
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Pia Anneli Sofia Kinaret
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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14
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Wang A, Zhao W, Yan K, Huang P, Zhang H, Zhang Z, Zhang D, Ma X. Mechanisms and Efficacy of Traditional Chinese Medicine in Heart Failure. Front Pharmacol 2022; 13:810587. [PMID: 35281941 PMCID: PMC8908244 DOI: 10.3389/fphar.2022.810587] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/24/2022] [Indexed: 12/11/2022] Open
Abstract
Heart failure (HF) is one of the main public health problems at present. Although some breakthroughs have been made in the treatment of HF, the mortality rate remains very high. However, we should also pay attention to improving the quality of life of patients with HF. Traditional Chinese medicine (TCM) has a long history of being used to treat HF. To demonstrate the clinical effects and mechanisms of TCM, we searched published clinical trial studies and basic studies. The search results showed that adjuvant therapy with TCM might benefit patients with HF, and its mechanism may be related to microvascular circulation, myocardial energy metabolism, oxidative stress, and inflammation.
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Affiliation(s)
- Anzhu Wang
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China.,Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Zhao
- Yidu Central Hospital of Weifang, Weifang, China
| | - Kaituo Yan
- Yidu Central Hospital of Weifang, Weifang, China
| | - Pingping Huang
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China.,Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hongwei Zhang
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China.,Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhibo Zhang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Xiyuan Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Dawu Zhang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,National Clinical Research Center for Chinese Medicine Cardiology, Beijing, China
| | - Xiaochang Ma
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,National Clinical Research Center for Chinese Medicine Cardiology, Beijing, China
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15
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Vivek-Ananth RP, Sahoo AK, Srivastava A, Samal A. Virtual screening of phytochemicals from Indian medicinal plants against the endonuclease domain of SFTS virus L polymerase. RSC Adv 2022; 12:6234-6247. [PMID: 35424542 PMCID: PMC8982020 DOI: 10.1039/d1ra06702h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/16/2022] [Indexed: 12/25/2022] Open
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) causes a highly infectious disease with reported mortality in the range 2.8% to 47%. The replication and transcription of the SFTSV genome is performed by L polymerase, which has both an RNA dependent RNA polymerase domain and an N-terminal endonuclease (endoN) domain. Due to its crucial role in the cap-snatching mechanism required for initiation of viral RNA transcription, the endoN domain is an ideal antiviral drug target. In this virtual screening study for the identification of potential inhibitors of the endoN domain of SFTSV L polymerase, we have used molecular docking and molecular dynamics (MD) simulation to explore the natural product space of 14 011 phytochemicals from Indian medicinal plants. After generating a heterogeneous ensemble of endoN domain structures reflecting conformational diversity of the corresponding active site using MD simulations, ensemble docking of the phytochemicals was performed against the endoN domain structures. Apart from the ligand binding energy from docking, our virtual screening workflow imposes additional filters such as drug-likeness, non-covalent interactions with key active site residues, toxicity and chemical similarity with other hits, to identify top 5 potential phytochemical inhibitors of endoN domain of SFTSV L polymerase. Further, the stability of the protein–ligand docked complexes for the top 5 potential inhibitors was analyzed using MD simulations. The potential phytochemical inhibitors, predicted in this study using contemporary computational methods, are expected to serve as lead molecules in future experimental studies towards development of antiviral drugs against SFTSV. Virtual screening of a large phytochemical library from Indian medicinal plants to identify potential endonuclease inhibitors against emerging virus SFTSV.![]()
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Affiliation(s)
- R P Vivek-Ananth
- The Institute of Mathematical Sciences (IMSc) Chennai 600113 India .,Homi Bhabha National Institute (HBNI) Mumbai 400094 India
| | - Ajaya Kumar Sahoo
- The Institute of Mathematical Sciences (IMSc) Chennai 600113 India .,Homi Bhabha National Institute (HBNI) Mumbai 400094 India
| | - Ashutosh Srivastava
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar Gandhinagar 382355 India
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc) Chennai 600113 India .,Homi Bhabha National Institute (HBNI) Mumbai 400094 India
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16
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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17
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Wang C, Zhang Y, Ding H, Song M, Yin J, Yu H, Li Z, Han L, Zhang Z. Authentication of Zingiber Species Based on Analysis of Metabolite Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:705446. [PMID: 34880881 PMCID: PMC8647842 DOI: 10.3389/fpls.2021.705446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/11/2021] [Indexed: 05/10/2023]
Abstract
Zingiber corallinum and Zingiber montanum, which belong to the Zingiberaceae family, are traditional Chinese folk medicinal herbs in Guizhou and Yunnan Province of China. They share great similarities in morphology, chemical constituent, and DNA barcoding sequence. The taxonomy of the two Zingiber species is controversial and discrimination of traditional Chinese medicines directly affects the pharmacological and clinical effects. In the present study, we performed a systemic analysis of "super-barcode" and untargeted metabolomics between Z. corallinum and Z. montanum using chloroplast (cp) genome sequencing and gas chromatography-mass spectrometry (GC-MS) analysis. Comparison and phylogenetic analysis of cp genomes of the two Zingiber species showed that the cp genome could not guarantee the accuracy of identification. An untargeted metabolomics strategy combining GC-MS with chemometric methods was proposed to distinguish the Zingiber samples of known variety. A total of 51 volatile compounds extracted from Z. corallinum and Z. montanum were identified, and nine compounds were selected as candidate metabolic markers to reveal the significant difference between Z. corallinum and Z. montanum. The performance of the untargeted metabolomic approach was verified with unknown Zingiber samples. Although the cp genomes could not be used to identify Zingiber species in this study, it will still provide a valuable genomics resource for population studies in the Zingiberaceae family, and the GC-MS based metabolic fingerprint is more promising for species identification and safe application of Z. corallinum and Z. montanum.
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Affiliation(s)
- Chenxi Wang
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yue Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| | - Hui Ding
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Meifang Song
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| | - Jiaxin Yin
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Heshui Yu
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zheng Li
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lifeng Han
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhonglian Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
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18
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Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism. Mol Genet Genomics 2021; 296:1177-1202. [PMID: 34557965 DOI: 10.1007/s00438-021-01821-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/12/2021] [Indexed: 01/23/2023]
Abstract
Medicinal plants of the North-Western Himalayan region are known for their unprecedented biodiversity and valuable secondary metabolites that are unique to this dynamic geo-climatic region. From ancient times these medicinal herbs have been used traditionally for their therapeutic potentials. But from the last 2 decades increasing pharmaceutical demand, illegal and unorganized trade of these medicinal plants have accelerated the rate of over-exploitation in a non-scientific manner. In addition, climate change and anthropogenic activities also affected their natural habitat and driving most of these endemic plant species to critically endangered that foresee peril of mass extinction from this eco-region. Hence there is an urgent need for developing alternative sustainable approaches and policies to utilize this natural bioresource ensuring simultaneous conservation. Hither, arise the advent of sequencing-based transcriptomic studies significantly contributes to better understand the background of important metabolic pathways and related genes/enzymes of high-value medicinal herbs, in the absence of genomic information. The use of comparative transcriptomics in conjunction with biochemical techniques in North-Western Himalayan medicinal plants has resulted in significant advances in the identification of the molecular players involved in the production of secondary metabolic pathways over the last decade. This information could be used to further engineer metabolic pathways and breeding programs, ultimately leading to the development of in vitro systems dedicated to the production of pharmaceutically important secondary metabolites at the industrial level. Collectively, successful adoption of these approaches can certainly ensure the sustainable utilization of Himalayan bioresource by reducing the pressure on the wild population of these critically endangered medicinal herbs. This review provides novel insight as a transcriptome-based bioresource repository for the understanding of important secondary metabolic pathways genes/enzymes and metabolism of endangered high-value North-Western Himalayan medicinal herbs, so that researchers across the globe can effectively utilize this information for devising effective strategies for the production of pharmaceutically important compounds and their scale-up for sustainable usage and take a step forward in omics-based conservation genetics.
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Hussain N, Chanda R, Abir RA, Mou MA, Hasan MK, Ashraf MA. MPDB 2.0: a large scale and integrated medicinal plant database of Bangladesh. BMC Res Notes 2021; 14:301. [PMID: 34362451 PMCID: PMC8344187 DOI: 10.1186/s13104-021-05721-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/29/2021] [Indexed: 12/04/2022] Open
Abstract
Objective MPDB 2.0 is built to be the continuation of MPDB 1.0, to serve as a more comprehensive data repertoire for Bangladeshi medicinal plants, and to provide a user-friendly interface for researchers, health practitioners, drug developers, and students who wish to study the various medicinal & nutritive plants scattered around Bangladesh and the underlying phytochemicals contributing to their efficacy in Bangladeshi folk medicine. Results MPDB 2.0 database (https://www.medicinalplantbd.com/) comprises a collection of more than five hundred Bangladeshi medicinal plants, alongside a record of their corresponding scientific, family, and local names together with their utilized parts, information regarding ailments, active compounds, and PubMed ID of related publications. While medicinal plants are not limited to the borders of any country, Bangladesh and its Southeast Asian neighbors do boast a huge collection of potent medicinal plants with considerable folk-medicinal history compared to most other countries in the world. Development of MPDB 2.0 has been highly focused upon human diseases, albeit many of the plants indexed here can serve in developing biofuel (e.g.: Jatropha curcas used in biofuel) or bioremediation technologies (e.g.: Amaranthus cruentus helps to reduce cadmium level in soil) or nutritive diets (Terminalia chebula can be used in nutritive diets) or cosmetics (Aloe vera used in cosmetics), etc.
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Affiliation(s)
- Nazmul Hussain
- Department of Biochemistry and Molecular Biology, Tejgaon College, National University of Bangladesh, Gazipur, 1704, Bangladesh
| | - Rony Chanda
- Department of Biochemistry and Molecular Biology, Tejgaon College, National University of Bangladesh, Gazipur, 1704, Bangladesh
| | | | | | - Md Kamrul Hasan
- Department of Biochemistry and Molecular Biology, Tejgaon College, National University of Bangladesh, Gazipur, 1704, Bangladesh.
| | - M Arif Ashraf
- Biology department, University of Massachusetts Amherst, Amherst, MA, USA.
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Crosstalk of Multi-Omics Platforms with Plants of Therapeutic Importance. Cells 2021; 10:cells10061296. [PMID: 34071113 PMCID: PMC8224614 DOI: 10.3390/cells10061296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/25/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
From time immemorial, humans have exploited plants as a source of food and medicines. The World Health Organization (WHO) has recorded 21,000 plants with medicinal value out of 300,000 species available worldwide. The promising modern "multi-omics" platforms and tools have been proven as functional platforms able to endow us with comprehensive knowledge of the proteome, genome, transcriptome, and metabolome of medicinal plant systems so as to reveal the novel connected genetic (gene) pathways, proteins, regulator sequences and secondary metabolite (molecule) biosynthetic pathways of various drug and protein molecules from a variety of plants with therapeutic significance. This review paper endeavors to abridge the contemporary advancements in research areas of multi-omics and the information involved in decoding its prospective relevance to the utilization of plants with medicinal value in the present global scenario. The crosstalk of medicinal plants with genomics, transcriptomics, proteomics, and metabolomics approaches will be discussed.
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