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Li XL, Zhang JQ, Shen XJ, Zhang Y, Guo DA. Overview and limitations of database in global traditional medicines: A narrative review. Acta Pharmacol Sin 2024:10.1038/s41401-024-01353-1. [PMID: 39095509 DOI: 10.1038/s41401-024-01353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
The study of traditional medicine has garnered significant interest, resulting in various research areas including chemical composition analysis, pharmacological research, clinical application, and quality control. The abundance of available data has made databases increasingly essential for researchers to manage the vast amount of information and explore new drugs. In this article we provide a comprehensive overview and summary of 182 databases that are relevant to traditional medicine research, including 73 databases for chemical component analysis, 70 for pharmacology research, and 39 for clinical application and quality control from published literature (2000-2023). The review categorizes the databases by functionality, offering detailed information on websites and capacities to facilitate easier access. Moreover, this article outlines the primary function of each database, supplemented by case studies to aid in database selection. A practical test was conducted on 68 frequently used databases using keywords and functionalities, resulting in the identification of highlighted databases. This review serves as a reference for traditional medicine researchers to choose appropriate databases and also provides insights and considerations for the function and content design of future databases.
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Affiliation(s)
- Xiao-Lan Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Qing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xuan-Jing Shen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Suleman M, Sayaf AM, Khan A, Khan SA, Albekairi NA, Alshammari A, Agouni A, Yassine HM, Crovella S. Molecular screening of phytocompounds targeting the interface between influenza A NS1 and TRIM25 to enhance host immune responses. J Infect Public Health 2024; 17:102448. [PMID: 38815532 DOI: 10.1016/j.jiph.2024.05.005] [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: 01/26/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Influenza A virus causes severe respiratory illnesses, especially in developing nations where most child deaths under 5 occur due to lower respiratory tract infections. The RIG-I protein acts as a sensor for viral dsRNA, triggering interferon production through K63-linked poly-ubiquitin chains synthesized by TRIM25. However, the influenza A virus's NS1 protein hinders this process by binding to TRIM25, disrupting its association with RIG-I and preventing downstream interferon signalling, contributing to the virus's evasion of the immune response. METHODS In our study we used structural-based drug designing, molecular simulation, and binding free energy approaches to identify the potent phytocompounds from various natural product databases (>100,000 compounds) able to inhibit the binding of NS1 with the TRIM25. RESULTS The molecular screening identified EA-8411902 and EA-19951545 from East African Natural Products Database, NA-390261 and NA-71 from North African Natural Products Database, SA-65230 and SA- 4477104 from South African Natural Compounds Database, NEA- 361 and NEA- 4524784 from North-East African Natural Products Database, TCM-4444713 and TCM-6056 from Traditional Chinese Medicines Database as top hits. The molecular docking and binding free energies results revealed that these compounds have high affinity with the specific active site residues (Leu95, Ser99, and Tyr89) involved in the interaction with TRIM25. Additionally, analysis of structural dynamics, binding free energy, and dissociation constants demonstrates a notably stronger binding affinity of these compounds with the NS1 protein. Moreover, all selected compounds exhibit exceptional ADMET properties, including high water solubility, gastrointestinal absorption, and an absence of hepatotoxicity, while adhering to Lipinski's rule. CONCLUSION Our molecular simulation findings highlight that the identified compounds demonstrate high affinity for specific active site residues involved in the NS1-TRIM25 interaction, exhibit exceptional ADMET properties, and adhere to drug-likeness criteria, thus presenting promising candidates for further development as antiviral agents against influenza A virus infections.
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Affiliation(s)
- Muhammad Suleman
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar; Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Abrar Mohammad Sayaf
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia.
| | - Abbas Khan
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Salman Ali Khan
- Tunneling Group, Biotechnology Centre, Doctoral School, Silesian University of Technology, Akademicka 2, 44-100 Gliwice, Poland.
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia.
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia.
| | - Abdelali Agouni
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar; College of Health Sciences-QU Health, Qatar University, 2713 Doha, Qatar.
| | - Sergio Crovella
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar.
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3
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Wang Y, Liu M, Jafari M, Tang J. A critical assessment of Traditional Chinese Medicine databases as a source for drug discovery. Front Pharmacol 2024; 15:1303693. [PMID: 38738181 PMCID: PMC11082401 DOI: 10.3389/fphar.2024.1303693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 04/15/2024] [Indexed: 05/14/2024] Open
Abstract
Traditional Chinese Medicine (TCM) has been used for thousands of years to treat human diseases. Recently, many databases have been devoted to studying TCM pharmacology. Most of these databases include information about the active ingredients of TCM herbs and their disease indications. These databases enable researchers to interrogate the mechanisms of action of TCM systematically. However, there is a need for comparative studies of these databases, as they are derived from various resources with different data processing methods. In this review, we provide a comprehensive analysis of the existing TCM databases. We found that the information complements each other by comparing herbs, ingredients, and herb-ingredient pairs in these databases. Therefore, data harmonization is vital to use all the available information fully. Moreover, different TCM databases may contain various annotation types for herbs or ingredients, notably for the chemical structure of ingredients, making it challenging to integrate data from them. We also highlight the latest TCM databases on symptoms or gene expressions, suggesting that using multi-omics data and advanced bioinformatics approaches may provide new insights for drug discovery in TCM. In summary, such a comparative study would help improve the understanding of data complexity that may ultimately motivate more efficient and more standardized strategies towards the digitalization of TCM.
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Affiliation(s)
- Yinyin Wang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Minxia Liu
- Faculty of Life Science, Anhui Medical University, Hefei, China
| | - Mohieddin Jafari
- Department Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Department Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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4
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Das AP, Agarwal SM. Recent advances in the area of plant-based anti-cancer drug discovery using computational approaches. Mol Divers 2024; 28:901-925. [PMID: 36670282 PMCID: PMC9859751 DOI: 10.1007/s11030-022-10590-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/18/2022] [Indexed: 01/22/2023]
Abstract
Phytocompounds are a well-established source of drug discovery due to their unique chemical and functional diversities. In the area of cancer therapeutics, several phytocompounds have been used till date to design and develop new drugs. One of the desired interests of pharmaceutical companies and researchers globally is that new anti-cancer leads are discovered, for which phytocompounds can be considered a valuable source. Simultaneously, in recent years, the growth of computational approaches like virtual screening (VS), molecular dynamics (MD), pharmacophore modelling, Quantitative structure-activity relationship (QSAR), Absorption Distribution Metabolism Excretion and Toxicity (ADMET), network biology, and machine learning (ML) has gained importance due to their efficiency, reduced time-consuming nature, and cost-effectiveness. Therefore, the present review amalgamates the information on plant-based molecules identified for cancer lead discovery from in silico approaches. The mandate of this review is to discuss studies published in the last 5-6 years that aim to identify the phytomolecules as leads against cancer with the help of traditional computational approaches as well as newer techniques like network pharmacology and ML. This review also lists the databases and webservers available in the public domain for phytocompounds related information that can be harnessed for drug discovery. It is expected that the present review would be useful to pharmacologists, medicinal chemists, molecular biologists, and other researchers involved in the development of natural products (NPs) into clinically effective lead molecules.
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Affiliation(s)
- Agneesh Pratim Das
- Bioinformatics Division, ICMR-National Institute of Cancer Prevention and Research, I-7, Sector-39, Noida, Uttar Pradesh, 201301, India
| | - Subhash Mohan Agarwal
- Bioinformatics Division, ICMR-National Institute of Cancer Prevention and Research, I-7, Sector-39, Noida, Uttar Pradesh, 201301, India.
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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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Wang J, Li J, Hu M. Mechanism analysis of Buyang Huanwu decoction in treating atherosclerosis based on network pharmacology and in vitro experiments. Chem Biol Drug Des 2024; 103:e14447. [PMID: 38230788 DOI: 10.1111/cbdd.14447] [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: 09/28/2023] [Revised: 12/04/2023] [Accepted: 12/27/2023] [Indexed: 01/18/2024]
Abstract
Atherosclerosis (AS) is one of the main risk factors of ischemic cardiovascular and cerebrovascular diseases. Buyang Huanwu decoction (BYHWT) is a classic Chinese medicine prescription that is used for treating AS. However, the underlying pharmacological mechanism remains unclear. This study aims to clarify the molecular mechanism of BYHWT in treatment of AS through network pharmacology and in vitro experiments. Molecular structure information and targets of core components of BYHWT were obtained from PubChem and UniProtKB databases. Genes involved in AS were obtained from DisGeNet, GeneCards and OMIM databases. The core targets of BYHWT in AS treatment were identified by protein-protein interaction (PPI) network analysis with STRING platform, and analyzed by gene ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomics (KEGG) pathway enrichment analysis. Molecular docking was used to verify the binding affinity between the core targets and the bioactive ingredients. HUVEC viability, inflammatory response and mRNA expression levels of core target genes were evaluated by cell counting kit 8 assay, enzyme-linked immunosorbent assay (ELISA) and qRT-PCR. A total of 60 candidate compounds and 325 predicted target genes were screened. PPI network analysis suggested that TP53, SRC, STAT3, and AKT1 may be the core targets. BYHWT in AS treatment was associated with 46 signaling pathways. GA120, baicalein, and 3,9-di-o-methylnissolin had good binding affinity with core target proteins. Baicalein treatment could significantly promoted the viability and repress the inflammatory response of HUVEC cells stimulated by ox-LDL. In addition, Baicalein can regulate the expression of core targets including AKT1, MAPK1, PIK3CA, JUN, TP53, SRC, EGFR, and ESR1. In conclusion, BYHWT and its main bioactive component baicalein, inhibit inflammatory response and modulate multiple downstream genes of endothelial cells, and show good potential to block the progression of AS and cardiovascular/cerebrovascular diseases.
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Affiliation(s)
- Jing Wang
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiajun Li
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Hu
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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7
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Fan M, Jin C, Li D, Deng Y, Yao L, Chen Y, Ma YL, Wang T. Multi-level advances in databases related to systems pharmacology in traditional Chinese medicine: a 60-year review. Front Pharmacol 2023; 14:1289901. [PMID: 38035021 PMCID: PMC10682728 DOI: 10.3389/fphar.2023.1289901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023] Open
Abstract
The therapeutic effects of traditional Chinese medicine (TCM) involve intricate interactions among multiple components and targets. Currently, computational approaches play a pivotal role in simulating various pharmacological processes of TCM. The application of network analysis in TCM research has provided an effective means to explain the pharmacological mechanisms underlying the actions of herbs or formulas through the lens of biological network analysis. Along with the advances of network analysis, computational science has coalesced around the core chain of TCM research: formula-herb-component-target-phenotype-ZHENG, facilitating the accumulation and organization of the extensive TCM-related data and the establishment of relevant databases. Nonetheless, recent years have witnessed a tendency toward homogeneity in the development and application of these databases. Advancements in computational technologies, including deep learning and foundation model, have propelled the exploration and modeling of intricate systems into a new phase, potentially heralding a new era. This review aims to delves into the progress made in databases related to six key entities: formula, herb, component, target, phenotype, and ZHENG. Systematically discussions on the commonalities and disparities among various database types were presented. In addition, the review raised the issue of research bottleneck in TCM computational pharmacology and envisions the forthcoming directions of computational research within the realm of TCM.
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Affiliation(s)
- Mengyue Fan
- Innovation Research Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ching Jin
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, United States
| | - Daping Li
- Innovation Research Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yingshan Deng
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lin Yao
- Innovation Research Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yongjun Chen
- Innovation Research Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yu-Ling Ma
- Oxford Chinese Medicine Research Centre, University of Oxford, Oxford, United Kingdom
| | - Taiyi Wang
- Innovation Research Institute of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
- Oxford Chinese Medicine Research Centre, University of Oxford, Oxford, United Kingdom
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8
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Li L, Yang L, Yang L, He C, He Y, Chen L, Dong Q, Zhang H, Chen S, Li P. Network pharmacology: a bright guiding light on the way to explore the personalized precise medication of traditional Chinese medicine. Chin Med 2023; 18:146. [PMID: 37941061 PMCID: PMC10631104 DOI: 10.1186/s13020-023-00853-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/22/2023] [Indexed: 11/10/2023] Open
Abstract
Network pharmacology can ascertain the therapeutic mechanism of drugs for treating diseases at the level of biological targets and pathways. The effective mechanism study of traditional Chinese medicine (TCM) characterized by multi-component, multi-targeted, and integrative efficacy, perfectly corresponds to the application of network pharmacology. Currently, network pharmacology has been widely utilized to clarify the mechanism of the physiological activity of TCM. In this review, we comprehensively summarize the application of network pharmacology in TCM to reveal its potential of verifying the phenotype and underlying causes of diseases, realizing the personalized and accurate application of TCM. We searched the literature using "TCM network pharmacology" and "network pharmacology" as keywords from Web of Science, PubMed, Google Scholar, as well as Chinese National Knowledge Infrastructure in the last decade. The origins, development, and application of network pharmacology are closely correlated with the study of TCM which has been applied in China for thousands of years. Network pharmacology and TCM have the same core idea and promote each other. A well-defined research strategy for network pharmacology has been utilized in several aspects of TCM research, including the elucidation of the biological basis of diseases and syndromes, the prediction of TCM targets, the screening of TCM active compounds, and the decipherment of mechanisms of TCM in treating diseases. However, several factors limit its application, such as the selection of databases and algorithms, the unstable quality of the research results, and the lack of standardization. This review aims to provide references and ideas for the research of TCM and to encourage the personalized and precise use of Chinese medicine.
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Affiliation(s)
- Ling Li
- School of Comprehensive Health Management, Xihua University, Chengdu, Sichuan, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
| | - Lele Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
- Zhuhai UM Science and Technology Research Institute, Zhuhai, Guangdong, China
| | - Liuqing Yang
- School of Food and Bioengineering, Xihua University, Chengdu, Sichuan, China
| | - Chunrong He
- School of Food and Bioengineering, Xihua University, Chengdu, Sichuan, China
| | - Yuxin He
- School of Food and Bioengineering, Xihua University, Chengdu, Sichuan, China
| | - Liping Chen
- School of Comprehensive Health Management, Xihua University, Chengdu, Sichuan, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qin Dong
- School of Food and Bioengineering, Xihua University, Chengdu, Sichuan, China
| | - Huaiying Zhang
- School of Comprehensive Health Management, Xihua University, Chengdu, Sichuan, China
| | - Shiyun Chen
- School of Food and Bioengineering, Xihua University, Chengdu, Sichuan, China
| | - Peng Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
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Gómez-García A, Jiménez DAA, Zamora WJ, Barazorda-Ccahuana HL, Chávez-Fumagalli MÁ, Valli M, Andricopulo AD, Bolzani VDS, Olmedo DA, Solís PN, Núñez MJ, Rodríguez Pérez JR, Valencia Sánchez HA, Cortés Hernández HF, Medina-Franco JL. Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB. Pharmaceuticals (Basel) 2023; 16:1388. [PMID: 37895859 PMCID: PMC10609821 DOI: 10.3390/ph16101388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries.
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Affiliation(s)
- Alejandro Gómez-García
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
| | - Daniel A. Acuña Jiménez
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
| | - William J. Zamora
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
- Laboratory of Computational Toxicology and Artificial Intelligence (LaToxCIA), Biological Testing Laboratory (LEBi), University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT), Pavas, San José 1174-1200, Costa Rica
| | - Haruna L. Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Miguel Á. Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Adriano D. Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Vanderlan da S. Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Av. Prof. Francisco Degni, 55, Araraquara 14800-900, SP, Brazil;
| | - Dionisio A. Olmedo
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Pablo N. Solís
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Marvin J. Núñez
- Natural Product Research Laboratory, School of Chemistry and Pharmacy, University of El Salvador, Final Ave. Mártires Estudiantes del 30 de Julio, San Salvador 01101, El Salvador;
| | - Johny R. Rodríguez Pérez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
- GIEPRONAL Research Group, School of Basic Sciences, Technology and Engineering, Universidad Nacional Abierta y a Distancia, Dosquebradas 661001, Colombia
| | - Hoover A. Valencia Sánchez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - Héctor F. Cortés Hernández
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
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10
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Liu X, Liu J, Fu B, Chen R, Jiang J, Chen H, Li R, Xing L, Yuan L, Chen X, Zhang J, Li H, Guo S, Guo F, Guo J, Liu Y, Qi Y, Yu B, Xu F, Li D, Liu Z. DCABM-TCM: A Database of Constituents Absorbed into the Blood and Metabolites of Traditional Chinese Medicine. J Chem Inf Model 2023; 63:4948-4959. [PMID: 37486750 PMCID: PMC10428213 DOI: 10.1021/acs.jcim.3c00365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Indexed: 07/25/2023]
Abstract
Traditional Chinese medicine (TCM) not only maintains the health of Asian people but also provides a great resource of active natural products for modern drug development. Herein, we developed a Database of Constituents Absorbed into the Blood and Metabolites of TCM (DCABM-TCM), the first database systematically collecting blood constituents of TCM prescriptions and herbs, including prototypes and metabolites experimentally detected in the blood, together with the corresponding detailed detection conditions through manual literature mining. The DCABM-TCM has collected 1816 blood constituents with chemical structures of 192 prescriptions and 194 herbs and integrated their related annotations, including physicochemical, absorption, distribution, metabolism, excretion, and toxicity properties, and associated targets, pathways, and diseases. Furthermore, the DCABM-TCM supported two blood constituent-based analysis functions, the network pharmacology analysis for TCM molecular mechanism elucidation, and the target/pathway/disease-based screening of candidate blood constituents, herbs, or prescriptions for TCM-based drug discovery. The DCABM-TCM is freely accessible at http://bionet.ncpsb.org.cn/dcabm-tcm/. The DCABM-TCM will contribute to the elucidation of effective constituents and molecular mechanism of TCMs and the discovery of TCM-derived drug-like compounds that are both bioactive and bioavailable.
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Affiliation(s)
- Xinyue Liu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
| | - Jinying Liu
- College
of Traditional Chinese Medicine, Chengde
Medical University, Chengde 067000, China
| | - Bangze Fu
- School
of Biomedicine, Beijing City University, Beijing 100094, China
| | - Ruzhen Chen
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
| | - Jianzhou Jiang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
- School
of Life Sciences, Hebei University, Baoding 071002, China
| | - He Chen
- School
of Life Sciences, Hebei University, Baoding 071002, China
| | - Runa Li
- School
of Biomedicine, Beijing City University, Beijing 100094, China
| | - Lin Xing
- School
of Biomedicine, Beijing City University, Beijing 100094, China
| | - Liying Yuan
- School
of Life Sciences, Hebei University, Baoding 071002, China
| | - Xuetai Chen
- School
of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jing Zhang
- School
of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Honglei Li
- Beijing
Cloudna Technology Company, Limited, Beijing 100029, China
| | - Shuzhen Guo
- School
of Traditional Chinese Medicine, Beijing
University of Chinese Medicine, Beijing 100029, China
| | - Feifei Guo
- Institute
of Chinese Materia Medica, China Academy
of Chinese Medical Sciences, Beijing 100700, China
| | - Jiachen Guo
- School
of Life Sciences, Hebei University, Baoding 071002, China
| | - Yuan Liu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
| | - Yaning Qi
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
| | - Biyue Yu
- School
of Life Sciences, Hebei University, Baoding 071002, China
| | - Feng Xu
- School
of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Dong Li
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
| | - Zhongyang Liu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
- School
of Life Sciences, Hebei University, Baoding 071002, China
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11
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Cai Y, Liu S, Zeng F, Rao Z, Yan C, Xing Q, Chen Y. Exploring the protective effect of Sangggua Drink against type 2 diabetes mellitus in db/db mice using a network pharmacological approach and experimental validation. Heliyon 2023; 9:e18026. [PMID: 37483759 PMCID: PMC10362244 DOI: 10.1016/j.heliyon.2023.e18026] [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: 02/16/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023] Open
Abstract
Sanggua Drink (SGD) is an experienced formula for clinical treatment of type 2 diabetes mellitus (T2DM). Network pharmacology and experiments were combined to explore the potential mechanism of action of SGD on T2DM. The material basis and action mechanism of SGD were investigated to reveal the active components of SGD, potential target prediction was conducted from TargetNet, PharmMapper; Cytoscape was used to construct PPI network and component-target-pathway (C-T-P) network diagram to interpret biological processes and enrich action pathways. 54 compounds and 41 key target proteins were screened, and a total of 98 signaling pathways were obtained. In vivo experiments, the levels of p-AMPK (P < 0.01), p-ACC and p-AKT were significantly increased in the mice with SGD intervention compared to the db/db mice, while level of FOXO1 were decreased. The results suggested that SGD might improve insulin resistance and glucose metabolism in T2DM mice by activating the AMPK/Akt signaling pathway.
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Affiliation(s)
- Yu Cai
- Hubei Provincial Research Center for TCM Health Food Engineering, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Simin Liu
- Hubei Provincial Research Center for TCM Health Food Engineering, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Fei Zeng
- Hubei Provincial Research Center for TCM Health Food Engineering, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Zhiwei Rao
- Central Hospital of Xianning, The First Affiliate Hospital of Hubei University of Science, China
| | - Chunchao Yan
- Hubei Provincial Research Center for TCM Health Food Engineering, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Qichang Xing
- Hubei Provincial Research Center for TCM Health Food Engineering, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Yunzhong Chen
- Hubei Provincial Research Center for TCM Health Food Engineering, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
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12
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Zhang YQ, Li X, Shi Y, Chen T, Xu Z, Wang P, Yu M, Chen W, Li B, Jing Z, Jiang H, Fu L, Gao W, Jiang Y, Du X, Gong Z, Zhu W, Yang H, Xu HY. ETCM v2.0: An update with comprehensive resource and rich annotations for traditional chinese medicine. Acta Pharm Sin B 2023. [DOI: 10.1016/j.apsb.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
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13
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Fathifar Z, Kalankesh LR, Ostadrahimi A, Ferdousi R. New approaches in developing medicinal herbs databases. Database (Oxford) 2023; 2023:6980759. [PMID: 36625159 PMCID: PMC9830469 DOI: 10.1093/database/baac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/12/2022] [Accepted: 12/17/2022] [Indexed: 01/11/2023]
Abstract
Medicinal herbs databases have become a crucial part of organizing new scientific literature generated in medicinal herbs field, as well as new drug discoveries in the information era. The aim of this review was to track the current status of medicinal herbs databases. Search for finding medicinal herbs databases was carried out via Google and PubMed. PubMed was searched for papers introducing medicinal herbs databases by the recruited search strategy. Papers with an active database on the web were included in the review. Google was also searched for medicinal herbs databases. Both retrieved papers and databases were reviewed by the authors. In this review, the current status of 25 medicinal herbs databases was reviewed, and the important characteristics of databases were mentioned. The reviewed databases had a great variety in terms of characteristics and functions. Finally, some recommendations for the efficient development of medicinal herbs databases were suggested. Although contemporary medicinal herbs databases represent much useful information, adding some features to these databases could assist them to have better functionality. This work may not cover all the necessary information, but we hope that our review can provide readers with fundamental concepts, perspectives and suggestions for constructing more useful databases.
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Affiliation(s)
- Zahra Fathifar
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Daneshgah St., Tabriz 5165665811, Iran
| | - Leila R Kalankesh
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Daneshgah St., Tabriz 5165665811, Iran
| | - Alireza Ostadrahimi
- Nutrition Research Center, Department of Clinical Nutrition, School of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz /Ave. Golghast Atakar Neyshabouri, Tabriz 5166614711, Iran
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14
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Wang YX, Yang Z, Wang WX, Huang YX, Zhang Q, Li JJ, Tang YP, Yue SJ. Methodology of network pharmacology for research on Chinese herbal medicine against COVID-19: A review. JOURNAL OF INTEGRATIVE MEDICINE 2022; 20:477-487. [PMID: 36182651 PMCID: PMC9508683 DOI: 10.1016/j.joim.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 08/15/2022] [Indexed: 12/09/2022]
Abstract
Traditional Chinese medicine, as a complementary and alternative medicine, has been practiced for thousands of years in China and possesses remarkable clinical efficacy. Thus, systematic analysis and examination of the mechanistic links between Chinese herbal medicine (CHM) and the complex human body can benefit contemporary understandings by carrying out qualitative and quantitative analysis. With increasing attention, the approach of network pharmacology has begun to unveil the mystery of CHM by constructing the heterogeneous network relationship of "herb-compound-target-pathway," which corresponds to the holistic mechanisms of CHM. By integrating computational techniques into network pharmacology, the efficiency and accuracy of active compound screening and target fishing have been improved at an unprecedented pace. This review dissects the core innovations to the network pharmacology approach that were developed in the years since 2015 and highlights how this tool has been applied to understanding the coronavirus disease 2019 and refining the clinical use of CHM to combat it.
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Affiliation(s)
- Yi-xuan Wang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China,Department of Scientific Research, Shaanxi Provincial People’s Hospital, Xi’an 710068, Shaanxi Province, China
| | - Zhen Yang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Wen-xiao Wang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Yu-xi Huang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Qiao Zhang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Jia-jia Li
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Yu-ping Tang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China
| | - Shi-jun Yue
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an 712046, Shaanxi Province, China,Corresponding author
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15
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Chen G, Liu C, Zhang M, Wang X, Xu Y. Niloticin binds to MD-2 to promote anti-inflammatory pathway activation in macrophage cells. Int J Immunopathol Pharmacol 2022; 36:3946320221133017. [PMID: 36314579 PMCID: PMC9629566 DOI: 10.1177/03946320221133017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES Niloticin is an active compound isolated from Cortex phellodendri with uncharacterized anti-inflammatory activity. We assessed the drug potential of niloticin and examined its ability to target myeloid differentiation protein 2 (MD-2) to ascertain the mechanism for its anti-inflammatory activity. METHODS The Traditional Chinese Medicine Systems Pharmacology Database was used to evaluate niloticin. Bio-layer interferometry and molecular docking technologies were used to explore how niloticin targets MD-2, which mediates a series of toll-like receptor 4 (TLR4)-dependent inflammatory responses. The cytokines involved in the lipopolysaccharide (LPS)-TLR4/MD-2-NF-κB pathway were evaluated using ELISA, RT-qPCR, and western blotting. RESULTS Niloticin could bind to MD-2 and had no evident effects on cell viability. Niloticin treatment significantly decreased the levels of NO, IL-6, TNF-α, and IL-1β induced by LPS (p < 0.01). IL-1β, IL-6, iNOS, TNF-α, and COX-2 mRNA expression levels were decreased by niloticin (all p < 0.01). Compared with that in the control group, the increase in TLR4, p65, MyD88, p-p65, and iNOS expression levels induced by LPS were suppressed by niloticin (all p < 0.01). CONCLUSION Our results suggest that niloticin has therapeutic potential and binds to MD-2. Niloticin binding to MD-2 antagonized the effects of LPS binding to the TLR4/MD-2 complex, resulting in the inhibition of the LPS-TLR4/MD-2-NF-κB signaling pathway.
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Affiliation(s)
- Guirong Chen
- Hospital of the Joint Logistics Support Force of the Chinese People’s Liberation Army, Dalian, China,Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Chang Liu
- Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Mingbo Zhang
- Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Xiaobo Wang
- Hospital of the Joint Logistics Support Force of the Chinese People’s Liberation Army, Dalian, China,Xiaobo Wang, Hospital of the Joint Logistics Support Force of the Chinese People’s Liberation Army, Dalian, China.
| | - Yubin Xu
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China,Yubin Xu, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China.
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16
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Progress and Impact of Latin American Natural Product Databases. Biomolecules 2022; 12:biom12091202. [PMID: 36139041 PMCID: PMC9496143 DOI: 10.3390/biom12091202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Natural products (NPs) are a rich source of structurally novel molecules, and the chemical space they encompass is far from being fully explored. Over history, NPs have represented a significant source of bioactive molecules and have served as a source of inspiration for developing many drugs on the market. On the other hand, computer-aided drug design (CADD) has contributed to drug discovery research, mitigating costs and time. In this sense, compound databases represent a fundamental element of CADD. This work reviews the progress toward developing compound databases of natural origin, and it surveys computational methods, emphasizing chemoinformatic approaches to profile natural product databases. Furthermore, it reviews the present state of the art in developing Latin American NP databases and their practical applications to the drug discovery area.
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17
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Hao DC, Song Y, Xiao P, Zhong Y, Wu P, Xu L. The genus Chrysanthemum: Phylogeny, biodiversity, phytometabolites, and chemodiversity. FRONTIERS IN PLANT SCIENCE 2022; 13:973197. [PMID: 36035721 PMCID: PMC9403765 DOI: 10.3389/fpls.2022.973197] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/18/2022] [Indexed: 05/31/2023]
Abstract
The ecologically and economically important genus Chrysanthemum contains around 40 species and many hybrids and cultivars. The dried capitulum of Chrysanthemum morifolium (CM) Ramat. Tzvel, i.e., Flos Chrysanthemi, is frequently used in traditional Chinese medicine (TCM) and folk medicine for at least 2,200 years. It has also been a popular tea beverage for about 2,000 years since Han Dynasty in China. However, the origin of different cultivars of CM and the phylogenetic relationship between Chrysanthemum and related Asteraceae genera are still elusive, and there is a lack of comprehensive review about the association between biodiversity and chemodiversity of Chrysanthemum. This article aims to provide a synthetic summary of the phylogeny, biodiversity, phytometabolites and chemodiversity of Chrysanthemum and related taxonomic groups, focusing on CM and its wild relatives. Based on extensive literature review and in light of the medicinal value of chrysanthemum, we give some suggestions for its relationship with some genera/species and future applications. Mining chemodiversity from biodiversity of Chrysanthemum containing subtribe Artemisiinae, as well as mining therapeutic efficacy and other utilities from chemodiversity/biodiversity, is closely related with sustainable conservation and utilization of Artemisiinae resources. There were eight main cultivars of Flos Chrysanthemi, i.e., Hangju, Boju, Gongju, Chuju, Huaiju, Jiju, Chuanju and Qiju, which differ in geographical origins and processing methods. Different CM cultivars originated from various hybridizations between multiple wild species. They mainly contained volatile oils, triterpenes, flavonoids, phenolic acids, polysaccharides, amino acids and other phytometabolites, which have the activities of antimicrobial, anti-viral, antioxidant, anti-aging, anticancer, anti-inflammatory, and closely related taxonomic groups could also be useful as food, medicine and tea. Despite some progresses, the genetic/chemical relationships among varieties, species and relevant genera have yet to be clarified; therefore, the roles of pharmacophylogeny and omics technology are highlighted.
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Affiliation(s)
- Da-Cheng Hao
- School of Environment and Chemical Engineering, Biotechnology Institute, Dalian Jiaotong University, Dalian, China
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Yanjun Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
| | - Yi Zhong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peiling Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lijia Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
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18
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DRDB: A Machine Learning Platform to Predict Chemical-Protein Interactions towards Diabetic Retinopathy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1718353. [PMID: 35910835 PMCID: PMC9329024 DOI: 10.1155/2022/1718353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022]
Abstract
Diabetic retinopathy (DR), a diabetic microangiopathy caused by diabetes, affects approximately 93 million people, worldwide. However, the drugs used to treat DR have limited efficacy and the variety of side effects. This is possibly because the complicated pathogenesis of DR is associated with multiple proteins. In this work, we attempted to identify potential drugs against DR-associated proteins and predict potential targets for drugs using in silico prediction of chemical-protein interactions (CPI) based on multitarget quantitative structure-activity relationship (mt-QSAR) method. Therefore, we developed 128 binary classifiers to predict the CPI for 15 DR targets using random forest (RF), k-nearest neighbours (KNN), support vector machine (SVM), and neural network (NN) algorithms with MACCS, extended connectivity fingerprints (ECFP6) fingerprints, and protein descriptors. In order to facilitate discovery of the novel drugs and target identification using the 128 binary classifiers, a free web server (DRDB) was developed. Compound Danshen Dripping Pills (CDDP), composed of Salvia miltiorrhiza, Panax notoginseng, and borneol, is commonly used in the treatment of cardiovascular diseases. To explore the applicability of DRDB, the potential CPIs of CDDP in treatment of DR were investigated based on DRDB. In vitro experimental validation demonstrated that cryptotanshinone and protocatechuic acid, two key components of CDDP, are capable of targeting ICAM-1 which is one of the key target of DR. We hope that this work can facilitate development of more effective clinical strategies for the treatment of DR.
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Chen GY, Liu XY, Luo J, Yu XB, Liu Y, Tao QW. Integrating Network Pharmacology and Experimental Validation to Explore the Key Mechanism of Gubitong Recipe in the Treatment of Osteoarthritis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7858925. [PMID: 35720033 PMCID: PMC9200584 DOI: 10.1155/2022/7858925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/25/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023]
Abstract
Background Gubitong Recipe (GBT) is a prescription based on the Traditional Chinese Medicine (TCM) theory of tonifying the kidney yang and strengthening the bone. A previous multicentral randomized clinical trial has shown that GBT can effectively relieve joint pain and improve quality of life with a high safety in treating osteoarthritis (OA). This study is aimed at elucidating the active compounds, potential targets, and mechanisms of GBT for treating OA. Method The network pharmacology method was used to predict the key active compounds, targets, and mechanisms of GBT in treating OA. An OA rat model was established with Hulth surgery, and the pathological changes of articular cartilage were observed to evaluate the effects of GBT. Chondrocytes were stimulated with LPS to establish in vitro models, and key targets and mechanisms predicted by network pharmacology were verified via qRT-PCR, ELISA, western blot, and immunofluorescence. The Contribution Index Model and molecular docking were used to determine the key active compounds of GBT and the major nodes affecting predicted pathways. Result A total of 500 compounds were acquired from related databases, where 87 active compounds and their 254 corresponding targets were identified. 2979 OA-related genes were collected from three databases, 150 of which were GBT-regulating OA genes. The compound-target network weight analysis and PPI results showed that IL-6 and PGE2 are key targets of GBT in treating OA. KEGG results showed that PI3K/AKT, Toll-like receptor, NFκB, TNF, and HIF-1 are the key signaling pathways. An in vivo experiment showed that GBT could effectively suppress cartilage degradation of OA rats. In vitro experiments demonstrated that GBT can inhibit the key targets of KEGG-related pathways. Molecular-docking results suggested that luteolin, licochalcone A, and β-carotene were key targets of GBT, and the mechanisms may be associated with the NFκB signaling pathway. Blockage experiments showed that the NFκB pathway is the key pathway of GBT in treating OA. Conclusion This study verified that GBT can effectively protect articular cartilage through multitarget and multipathway, and its inhibitory effect on the NFκB pathway is the most key mechanism in treating OA.
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Affiliation(s)
- Guang-yao Chen
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiao-yu Liu
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jing Luo
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing 100029, China
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xin-bo Yu
- Beijing University of Chinese Medicine, Beijing 100029, China
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yi Liu
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Qing-wen Tao
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing 100029, China
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
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Luo L, Yang J, Wang C, Wu J, Li Y, Zhang X, Li H, Zhang H, Zhou Y, Lu A, Chen S. Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1123-1145. [PMID: 34705221 PMCID: PMC8548270 DOI: 10.1007/s11427-020-1959-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
As coronavirus disease 2019 (COVID-19) threatens human health globally, infectious disorders have become one of the most challenging problem for the medical community. Natural products (NP) have been a prolific source of antimicrobial agents with widely divergent structures and a range vast biological activities. A dataset comprising 618 articles, including 646 NP-based compounds from 672 species of natural sources with biological activities against 21 infectious pathogens from five categories, was assembled through manual selection of published articles. These data were used to identify 268 NP-based compounds classified into ten groups, which were used for network pharmacology analysis to capture the most promising lead-compounds such as agelasine D, dicumarol, dihydroartemisinin and pyridomycin. The distribution of maximum Tanimoto scores indicated that compounds which inhibited parasites exhibited low diversity, whereas the chemistries inhibiting bacteria, fungi, and viruses showed more structural diversity. A total of 331 species of medicinal plants with compounds exhibiting antimicrobial activities were selected to classify the family sources. The family Asteraceae possesses various compounds against C. neoformans, the family Anacardiaceae has compounds against Salmonella typhi, the family Cucurbitacea against the human immunodeficiency virus (HIV), and the family Ancistrocladaceae against Plasmodium. This review summarizes currently available data on NP-based antimicrobials against refractory infections to provide information for further discovery of drugs and synthetic strategies for anti-infectious agents.
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Affiliation(s)
- Lu Luo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Cheng Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100006, China
| | - Jie Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yafang Li
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xu Zhang
- weMED Health, Houston, 77054, USA
| | - Hui Li
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Zhang
- Akupunktur Akademiet, Aabyhoej, Aarhus, 8230, Denmark
| | - Yumei Zhou
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 518033, China
| | - Aiping Lu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Chu H, Moon S, Park J, Bak S, Ko Y, Youn BY. The Use of Artificial Intelligence in Complementary and Alternative Medicine: A Systematic Scoping Review. Front Pharmacol 2022; 13:826044. [PMID: 35431917 PMCID: PMC9011141 DOI: 10.3389/fphar.2022.826044] [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: 11/30/2021] [Accepted: 03/01/2022] [Indexed: 01/04/2023] Open
Abstract
Background: The development of artificial intelligence (AI) in the medical field has been growing rapidly. As AI models have been introduced in complementary and alternative medicine (CAM), a systematized review must be performed to understand its current status. Objective: To categorize and seek the current usage of AI in CAM. Method: A systematic scoping review was conducted based on the method proposed by the Joanna Briggs Institute. The three databases, PubMed, Embase, and Cochrane Library, were used to find studies regarding AI and CAM. Only English studies from 2000 were included. Studies without mentioning either AI techniques or CAM modalities were excluded along with the non-peer-reviewed studies. A broad-range search strategy was applied to locate all relevant studies. Results: A total of 32 studies were identified, and three main categories were revealed: 1) acupuncture treatment, 2) tongue and lip diagnoses, and 3) herbal medicine. Other CAM modalities were music therapy, meditation, pulse diagnosis, and TCM syndromes. The majority of the studies utilized AI models to predict certain patterns and find reliable computerized models to assist physicians. Conclusion: Although the results from this review have shown the potential use of AI models in CAM, future research ought to focus on verifying and validating the models by performing a large-scale clinical trial to better promote AI in CAM in the era of digital health.
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Affiliation(s)
- Hongmin Chu
- Daecheong Public Health Subcenter, Incheon, South Korea
| | - Seunghwan Moon
- Department of Global Public Health and Korean Medicine Management, Graduate School, Kyung Hee University, Seoul, South Korea
| | - Jeongsu Park
- Department of College of Korean Medicine, Wonkwang University, Iksan, South Korea
| | - Seongjun Bak
- Department of College of Korean Medicine, Wonkwang University, Iksan, South Korea
| | - Youme Ko
- National Institute for Korean Medicine Development (NIKOM), Seoul, South Korea
| | - Bo-Young Youn
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
- *Correspondence: Bo-Young Youn,
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Duan X, Zhang W, Li J, Xu H, Hu J, Zhao L, Ma Y. Comparative metabolomics analysis revealed biomarkers and distinct flavonoid biosynthesis regulation in Chrysanthemum mongolicum and C. rhombifolium. PHYTOCHEMICAL ANALYSIS : PCA 2022; 33:373-385. [PMID: 34750870 DOI: 10.1002/pca.3095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 09/15/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Chrysanthemums are traditional flowers that originated in China and have high ornamental, economic and medicinal value. They are widely used as herbal remedies and consumed as food or beverages in folk medicine. However, little is known about their metabolic composition. OBJECTIVES The aims of this work were to determine the metabolic composition of and natural variation among different species of Chrysanthemum and to explore new potential resources for drug discovery and sustainable utilisation of wild Chrysanthemum. METHODS The metabolomes of Chrysanthemum mongolicum (Ling) Tzvel. and Chrysanthemum rhombifolium H. Ohashi & Yonek. were compared using a widely targeted metabolomics approach based on liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS In total, 477 metabolites were identified, of which 72 showed significant differences in expression between C. mongolicum and C. rhombifolium, mainly in flavonoids, organic acids and nucleotides. The flavone and flavonol biosynthesis pathway showed significant enrichment among the differentially expressed metabolites. The contents of genkwanin, trigonelline, diosmin, narcissoside, 3,4-dihydroxyphenylacetic acid, linarin, N',N'-p-coumarin, C-hexosyl-tricetin O-pentoside, chrysoeriol, acacetin and kaempferol-3-O-gentiobioside were significantly different between the two species and represent potential biomarkers. CONCLUSION The types of flavonoid-related metabolites in the flavonoid biosynthesis pathway differed between C. mongolicum and C. rhombifolium. The mechanisms underlying the unique adaptations of these two species to their environments may involve variations in the composition and abundance of flavonoids, organic acids, and nucleotides. These methods are promising to identify functional compounds in Chrysanthemum species and can provide potential resources for drug discovery and the sustainable utilisation of Chrysanthemum plants.
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Affiliation(s)
- Xiaxia Duan
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Wenjie Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Jingjing Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Hongyuan Xu
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Jing Hu
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Liang Zhao
- College of Life Sciences, Yangling, China
| | - Yueping Ma
- College of Life and Health Sciences, Northeastern University, Shenyang, China
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Wang B, Ding Y, Zhao P, Li W, Li M, Zhu J, Ye S. Systems pharmacology-based drug discovery and active mechanism of natural products for coronavirus pneumonia (COVID-19): An example using flavonoids. Comput Biol Med 2022; 143:105241. [PMID: 35114443 PMCID: PMC8789666 DOI: 10.1016/j.compbiomed.2022.105241] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Recently, the value of natural products has been extensively considered because these resources can potentially be applied to prevent and treat coronavirus pneumonia 2019 (COVID-19). However, the discovery of nature drugs is problematic because of their complex composition and active mechanisms. METHODS This comprehensive study was performed on flavonoids, which are compounds with anti-inflammatory and antiviral effects, to show drug discovery and active mechanism from natural products in the treatment of COVID-19 via a systems pharmacological model. First, a chemical library of 255 potential flavonoids was constructed. Second, the pharmacodynamic basis and mechanism of action between flavonoids and COVID-19 were explored by constructing a compound-target and target-disease network, targets protein-protein interaction (PPI), MCODE analysis, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. RESULTS In total, 105 active flavonoid components were identified, of which 6 were major candidate compounds (quercetin, epigallocatechin-3-gallate (EGCG), luteolin, fisetin, wogonin, and licochalcone A). 152 associated targets were yielded based on network construction, and 7 family proteins (PTGS, GSK3β, ABC, NOS, EGFR, and IL) were included as central hub targets. Moreover, 528 GO items and 178 KEGG pathways were selected through enrichment of target functions. Lastly, molecular docking demonstrated good stability of the combination of selected flavonoids with 3CL Pro and ACEⅡ. CONCLUSION Natural flavonoids could enable resistance against COVID-19 by regulating inflammatory, antiviral, and immune responses, and repairing tissue injury. This study has scientific significance for the selective utilization of natural products, medicinal value enhancement of flavonoids, and drug screening for the treatment of COVID-19 induced by SARS-COV-2.
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Affiliation(s)
- Bin Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China
| | - Yan Ding
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China.
| | - Penghui Zhao
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China
| | - Wei Li
- Korean Medicine (KM) Application Center, Korea Institute of Oriental Medicine, Daegu, 41062, South Korea
| | - Ming Li
- College of Basic Medical Science, Dalian Medical University, Dalian, Liaoning, 116044, China
| | - Jingbo Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China; Institute of Chemistry and Applications of Plant Resources, Dalian Polytechnic University, Dalian, Liaoning, 116034, China
| | - Shuhong Ye
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, 116034, China.
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LTM-TCM: A Comprehensive Database for the Linking of Traditional Chinese Medicine with Modern Medicine at Molecular and Phenotypic Levels. Pharmacol Res 2022; 178:106185. [DOI: 10.1016/j.phrs.2022.106185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 02/07/2023]
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Wu N, Yuan T, Yin Z, Yuan X, Sun J, Wu Z, Zhang Q, Redshaw C, Yang S, Dai X. Network Pharmacology and Molecular Docking Study of the Chinese Miao Medicine Sidaxue in the Treatment of Rheumatoid Arthritis. Drug Des Devel Ther 2022; 16:435-466. [PMID: 35221674 PMCID: PMC8865873 DOI: 10.2147/dddt.s330947] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/24/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose This study aimed to investigate the molecular mechanisms of Compound Sidaxue (SX), a prescription of Chinese Miao medicine, in treating rheumatoid arthritis (RA) using network pharmacology and in vivo experimental approaches. Methods Network pharmacology was adopted to detect the active components of four Traditional Chinese herbal medicine (TCM) of SX, and the key targets and signaling pathways in the treatment of RA were predicted, and the key components and targets were screened for molecular docking. The predicted targets and pathways were validated in bovine type II collagen and incomplete Freund’s adjuvant emulsifier-induced rat RA model. Results In this study, we identified 33 active components from SX, predicted to act on 44 RA-associated targets by network pharmacology. PPI network demonstrated that TNF-α, VEGF-A, IL-2, IL-6, AKT, PI3K, STAT1 may serve as the key targets of SX for the treatment of RA. The main functional pathways involving these key targets include PI3K-AKT signaling pathway, TNF signaling pathway, NF-κB signaling pathway. Molecular docking analysis found that the active components β-amyrin, cajanin, eleutheroside A have high affinity for TNF-α, VEGFA, IL-2, AKT, and PI3K, etc. SX can improve joint swelling in Collagen-induced arthritis (CIA) rats, reduce inflammatory cell infiltration and angiogenesis in joint synovial tissue, and down-regulate IL-2, IL-6, TNF-α, VEGF, PI3K, AKT, p-AKT, NF-κBp65, the expression of p-NF-κBp65, STAT1, and PTGS2 are used to control the exacerbation of inflammation and alleviate the proliferation of synovial pannus, and at the same time play the role of cartilage protection to achieve the effect of treating RA. Conclusion Through a network pharmacology approach and animal study, we predicted and validated the active compounds of SX and their potential targets for RA treatment. The results suggest that SX can markedly alleviate CIA rat by modulating the VEGF/PI3K/AKT signaling pathway, TNF-α signaling pathway, IL/NF-κB signaling pathway.
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Affiliation(s)
- Ning Wu
- Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Taohua Yuan
- Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - ZhiXin Yin
- Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Xiaotian Yuan
- Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Jianfei Sun
- Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Zunqiu Wu
- Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Qilong Zhang
- Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
| | - Carl Redshaw
- Department of Chemistry, University of Hull, Hull, Yorkshire, HU6 7RX, UK
| | - Shenggang Yang
- Guizhou Medical University, Guiyang, Guizhou, People’s Republic of China
- Correspondence: Shenggang Yang, Guizhou Medical University, Guiyang, Guizhou, 550025, People’s Republic of China, Tel/Fax +86 13158000576, Email
| | - Xiaotian Dai
- Department of Mathematics and Statistics, University of Calgary, Calgary, AB, Canada
- Xiaotian Dai, Department of Mathematics and Statistics, University of Calgary, Calgary, AB, T2N 1N4, Canada, Tel/Fax +1 435 754 4980, Email
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Study on the Mechanism of Compound Kidney-Invigorating Granule for Osteoporosis based on Network Pharmacology and Experimental Verification. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6453501. [PMID: 35027934 PMCID: PMC8752261 DOI: 10.1155/2022/6453501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/24/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022]
Abstract
Background This study used a combination of network pharmacology and experimental confirmation to clarify the mechanism of the compound kidney-invigorating granule (CKG) in treating osteoporosis (OP). Methods The main bioactive compounds and corresponding targets of CKG were collected and screened via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Yet another Traditional Chinese Medicine (YaTCM), and UniProt databases. Disease targets of OP were summarized in GeneCards and the Comparative Toxicogenomics Database (CTD). Targets of CKG for OP were obtained by Venn diagram. The protein-protein interaction (PPI) network was constructed by the STRING database and then screened for hub genes through Cytoscape 3.7.2 software. The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were analyzed and visualized by R software. Then, CB-Dock was used for molecular docking verification. Finally, we confirmed the antiosteoporosis effect of CKG through animal and cell experiments. Results A total of 250 putative targets were obtained from 65 bioactive compounds in CKG. Among them, 140 targets were related to OP. Topological analysis of the PPI network yielded 23 hub genes. Enrichment analysis showed the targets of CKG in treating OP might concentrate on the MAPK signaling pathway, the TNF signaling pathway, the PI3K-Akt signaling pathway, etc. The results of molecular docking showed the bioactive components in CKG had good binding ability with the key targets. The experimental results showed that CKG-medicated serum had a promoting effect on proliferating hBMSCs, increasing the expression of AKT, PI3K, ERK1, and IkB in cells and decreasing the expression of IKK in cells. Conclusion CKG has a complex of multicomponent, multitarget, and multipathway. This study lays the theoretical foundation for further in vitro and in vivo experimental studies and further expands the clinical applications of CKG.
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Cai C, Xu L, Fang J, Dai Z, Wu Q, Liu X, Wang Q, Fang J, Liu AL, Du GH. In Silico Prediction and Bioactivity Evaluation of Chemical Ingredients Against Influenza A Virus From Isatis tinctoria L. Front Pharmacol 2021; 12:755396. [PMID: 34950027 PMCID: PMC8689007 DOI: 10.3389/fphar.2021.755396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/09/2021] [Indexed: 01/11/2023] Open
Abstract
Influenza A virus (IAV) is one of the major causes of seasonal endemic diseases and unpredictable periodic pandemics. Due to the high mutation rate and drug resistance, it poses a persistent threat and challenge to public health. Isatis tinctoria L. (Banlangen, BLG), a traditional herbal medicine widely used in Asian countries, has been reported to possess strong efficacy on respiratory viruses, including IAV. However, its effective anti-IAV components and the mechanism of actions (MOAs) are not yet fully elucidated. In this study, we first summarized the chemical components and corresponding contents in BLG according to current available chemical analysis literature. We then presented a network-based in silico framework for identifying potential drug candidates against IAV from BLG. A total of 269 components in BLG were initially screened by drug-likeness and ADME (absorption, distribution, metabolism, and excretion) evaluation. Thereafter, network predictive models were built via the integration of compound–target networks and influenza virus–host proteins. We highlighted 23 compounds that possessed high potential as anti-influenza virus agents. Through experimental evaluation, six compounds, namely, eupatorin, dinatin, linarin, tryptanthrin, indirubin, and acacetin, exhibited good inhibitory activity against wild-type H1N1 and H3N2. Particularly, they also exerted significant effects on drug-resistant strains. Finally, we explored the anti-IAV MOAs of BLG and showcased the potential biological pathways by systems pharmacology analysis. In conclusion, this work provides important information on BLG regarding its use in the development of anti-IAV drugs, and the network-based prediction framework proposed here also offers a powerfulful strategy for the in silico identification of novel drug candidates from complex components of herbal medicine.
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Affiliation(s)
- Chuipu Cai
- Division of Data Intelligence, Department of Computer Science, Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, College of Engineering, Shantou University, Shantou, China.,Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lvjie Xu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junfeng Fang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhao Dai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qihui Wu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoyi Liu
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiansong Fang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ai-Lin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guan-Hua Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Chen Q, Springer L, Gohlke BO, Goede A, Dunkel M, Abel R, Gallo K, Preissner S, Eckert A, Seshadri L, Preissner R. SuperTCM: A biocultural database combining biological pathways and historical linguistic data of Chinese Materia Medica for drug development. Biomed Pharmacother 2021; 144:112315. [PMID: 34656056 DOI: 10.1016/j.biopha.2021.112315] [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: 08/20/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 01/09/2023] Open
Abstract
AIM OF THE STUDY Botanicals used in Traditional Chinese Medicine (TCM) are a rich source for drug discovery and provide models for multi-component drug development. To facilitate the studies of the actions of TCM drugs and expand their applications, a comprehensive database is urgently required. METHODS One online resource connects all the relevant data from multiple scientific sources and languages. Drug information from published TCM databases and the official Chinese Pharmacopoeia as well as specialized meta-websites such as Kew's Medicinal Plant Names Service was integrated on a higher level. RESULTS Our database, SuperTCM, covers the aspects of TCM derived from medicinal plants, encompassing pharmacological recipes up to chemical compounds. It provides the information for 6516 TCM drugs (or "herbs") with 5372 botanical species, 55,772 active ingredients against 543 targets in 254 KEGG pathways associated with 8634 diseases. SuperTCM is freely available at http://tcm.charite.de/supertcm.
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Affiliation(s)
- Qiaofeng Chen
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany; China Scholarship Council (CSC), Beijing 100044, China
| | - Lena Springer
- King's College London, University College London, UK; Sichuan University, Key Institute for Chinese Folk Culture, China
| | - Björn Oliver Gohlke
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany; Science-IT, Germany
| | - Andrean Goede
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany
| | - Mathias Dunkel
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany; Science-IT, Germany
| | - Renata Abel
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany
| | - Kathleen Gallo
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany
| | - Saskia Preissner
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany
| | - Andreas Eckert
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany; Science-IT, Germany
| | | | - Robert Preissner
- Structural Bioinformatics Group, Institute for Physiology, 10115 Berlin, Germany; Science-IT, Germany.
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Wang T, Liang L, Zhao C, Sun J, Wang H, Wang W, Lin J, Hu Y. Elucidating direct kinase targets of compound Danshen dropping pills employing archived data and prediction models. Sci Rep 2021; 11:9541. [PMID: 33953309 PMCID: PMC8100098 DOI: 10.1038/s41598-021-89035-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/19/2021] [Indexed: 12/17/2022] Open
Abstract
Research on direct targets of traditional Chinese medicine (TCM) is the key to study the mechanism and material basis of it, but there is still no effective methods at present. We took Compound Danshen dropping pills (CDDP) as a study case to establish a strategy to identify significant direct targets of TCM. As a result, thirty potential active kinase targets of CDDP were identified. Nine of them had potential dose-dependent effects. In addition, the direct inhibitory effect of CDDP on three kinases, AURKB, MET and PIM1 were observed both on biochemical level and cellular level, which could not only shed light on the mechanisms of action involved in CDDP, but also suggesting the potency of drug repositioning of CDDP. Our results indicated that the research strategy including both in silico models and experimental validation that we built, were relatively efficient and reliable for direct targets identification for TCM prescription, which will help elucidating the mechanisms of TCM and promoting the modernization of TCM.
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Affiliation(s)
- Tongxing Wang
- GeneNet Pharmaceuticals Co. Ltd., No. 1, Tingjiang West Road, Beichen District, Tianjin, 300410, China
| | - Lu Liang
- College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Jinnan District, Tianjin, 300353, China
| | - Chunlai Zhao
- GeneNet Pharmaceuticals Co. Ltd., No. 1, Tingjiang West Road, Beichen District, Tianjin, 300410, China
| | - Jia Sun
- GeneNet Pharmaceuticals Co. Ltd., No. 1, Tingjiang West Road, Beichen District, Tianjin, 300410, China
| | - Hairong Wang
- GeneNet Pharmaceuticals Co. Ltd., No. 1, Tingjiang West Road, Beichen District, Tianjin, 300410, China
| | - Wenjia Wang
- GeneNet Pharmaceuticals Co. Ltd., No. 1, Tingjiang West Road, Beichen District, Tianjin, 300410, China
| | - Jianping Lin
- College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Jinnan District, Tianjin, 300353, China
| | - Yunhui Hu
- GeneNet Pharmaceuticals Co. Ltd., No. 1, Tingjiang West Road, Beichen District, Tianjin, 300410, China.
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Ye M, Luo G, Ye D, She M, Sun N, Lu YJ, Zheng J. Network pharmacology, molecular docking integrated surface plasmon resonance technology reveals the mechanism of Toujie Quwen Granules against coronavirus disease 2019 pneumonia. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 85:153401. [PMID: 33191068 PMCID: PMC7837196 DOI: 10.1016/j.phymed.2020.153401] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/03/2020] [Accepted: 10/25/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND The Coronavirus disease 2019 pneumonia broke out in 2019 (COVID-19) and spread rapidly, which causes serious harm to the health of people and a huge economic burden around the world. PURPOSE In this study, the network pharmacology, molecular docking and surface plasmon resonance technology (SPR) were used to explore the potential compounds and interaction mechanism in the Toujie Quwen Granules (TQG) for the treatment of coronavirus pneumonia 2019. STUDY DESIGN The chemical constituents and compound targets of Lonicerae Japonicae Flos, Pseudostellariae Radix, Artemisia Annua L, Peucedani Radix, Forsythiae Fructus, Scutellariae Radix, Hedysarum Multijugum Maxim, Isatidis Folium, Radix Bupleuri, Fritiliariae Irrhosae Bulbus, Cicadae Periostracum, Poria Cocos Wolf, Pseudobulbus Cremastrae Seu Pleiones, Mume Fructus, Figwort Root and Fritillariae Thunbrgii Bulbus in TQG were searched. The target name was translated to gene name using the UniProt database and then the Chinese medicine-compound-target network was constructed. Protein-protein interaction network (PPI), Gene ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the core targets were performed in the Metascape to predict its mechanism. The top 34 compounds in the Chinese medicine-compound-target network were docked with SARS-CoV-2 3CL enzyme and SARS--CoV--2 RNA-dependent RNA polymerase (RdRp) and then the 13 compounds with lowest affinity score were docked with angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 Spike protein and interleukin 6 to explore its interaction mechanism. Lastly, SPR experiments were done using the quercetin, astragaloside IV, rutin and isoquercitrin, which were screened from the Chinese medicine-compound-target network and molecular docking. RESULTS The Chinese medicine-compound-target network includes 16 medicinal materials, 111 compounds and 298 targets, in which the degree of PTGS2, TNF and IL-6 is higher compared with other targets and which are the disease target exactly. The result of GO function enrichment analysis included the response to the molecule of bacterial origin, positive regulation of cell death, apoptotic signaling pathway, cytokine-mediated signaling pathway, cytokine receptor binding and so on. KEGG pathway analysis enrichment revealed two pathways: signaling pathway- IL-17 and signaling pathway- TNF. The result of molecular docking showed that the affinity score of compounds including quercetin, isoquercitrin, astragaloside IV and rutin is higher than other compounds. In addition, the SPR experiments revealed that the quercetin and isoquercitrin were combined with SARS-CoV-2 Spike protein rather than Angiotensin-converting enzyme 2, while astragaloside IV and rutin were combined with ACE2 rather than SARS-CoV-2 Spike protein. CONCLUSION TQG may have therapeutic effects on COVID-19 by regulating viral infection, immune and inflammation related targets and pathways, in the way of multi-component, multi-target and multi-pathway.
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Affiliation(s)
- Miaobo Ye
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiwen Luo
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Dexiao Ye
- Golden Health (Guangdong) Biotechnology Co, Foshan 528225, China
| | - Mengting She
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Ning Sun
- The State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yu-Jing Lu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Jie Zheng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
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Towards the routine use of in silico screenings for drug discovery using metabolic modelling. Biochem Soc Trans 2021; 48:955-969. [PMID: 32369553 PMCID: PMC7329353 DOI: 10.1042/bst20190867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
Currently, the development of new effective drugs for cancer therapy is not only hindered by development costs, drug efficacy, and drug safety but also by the rapid occurrence of drug resistance in cancer. Hence, new tools are needed to study the underlying mechanisms in cancer. Here, we discuss the current use of metabolic modelling approaches to identify cancer-specific metabolism and find possible new drug targets and drugs for repurposing. Furthermore, we list valuable resources that are needed for the reconstruction of cancer-specific models by integrating various available datasets with genome-scale metabolic reconstructions using model-building algorithms. We also discuss how new drug targets can be determined by using gene essentiality analysis, an in silico method to predict essential genes in a given condition such as cancer and how synthetic lethality studies could greatly benefit cancer patients by suggesting drug combinations with reduced side effects.
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Fang S, Dong L, Liu L, Guo J, Zhao L, Zhang J, Bu D, Liu X, Huo P, Cao W, Dong Q, Wu J, Zeng X, Wu Y, Zhao Y. HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. Nucleic Acids Res 2021; 49:D1197-D1206. [PMID: 33264402 PMCID: PMC7779036 DOI: 10.1093/nar/gkaa1063] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/17/2020] [Accepted: 10/28/2020] [Indexed: 02/05/2023] Open
Abstract
Pharmacotranscriptomics has become a powerful approach for evaluating the therapeutic efficacy of drugs and discovering new drug targets. Recently, studies of traditional Chinese medicine (TCM) have increasingly turned to high-throughput transcriptomic screens for molecular effects of herbs/ingredients. And numerous studies have examined gene targets for herbs/ingredients, and link herbs/ingredients to various modern diseases. However, there is currently no systematic database organizing these data for TCM. Therefore, we built HERB, a high-throughput experiment- and reference-guided database of TCM, with its Chinese name as BenCaoZuJian. We re-analyzed 6164 gene expression profiles from 1037 high-throughput experiments evaluating TCM herbs/ingredients, and generated connections between TCM herbs/ingredients and 2837 modern drugs by mapping the comprehensive pharmacotranscriptomics dataset in HERB to CMap, the largest such dataset for modern drugs. Moreover, we manually curated 1241 gene targets and 494 modern diseases for 473 herbs/ingredients from 1966 references published recently, and cross-referenced this novel information to databases containing such data for drugs. Together with database mining and statistical inference, we linked 12 933 targets and 28 212 diseases to 7263 herbs and 49 258 ingredients and provided six pairwise relationships among them in HERB. In summary, HERB will intensively support the modernization of TCM and guide rational modern drug discovery efforts. And it is accessible through http://herb.ac.cn/.
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Affiliation(s)
- ShuangSang Fang
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - Lei Dong
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - Liu Liu
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - JinCheng Guo
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - LianHe Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - JiaYuan Zhang
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - DeChao Bu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - XinKui Liu
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - PeiPei Huo
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - WanChen Cao
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - QiongYe Dong
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - JiaRui Wu
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - Xiaoxi Zeng
- West China Biomedical Big Data Center, Division of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Zhao
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China.,Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
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Pan B, Wang Y, Wu C, Jia J, Huang C, Fang S, Liu L. A Mechanism of Action Study on Danggui Sini Decoction to Discover Its Therapeutic Effect on Gastric Cancer. Front Pharmacol 2021; 11:592903. [PMID: 33505310 PMCID: PMC7830678 DOI: 10.3389/fphar.2020.592903] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/25/2020] [Indexed: 01/05/2023] Open
Abstract
Danggui Sini Decoction (DSD), a classic Chinese herb medicine (CHM) formula, has been used to treat various diseases in China for centuries. However, it remains challenging to reveal its mechanism of action through conventional pharmacological methods. Here, we first explored the mechanism of action of DSD with the assistance of network pharmacology and bioinformatic analysis tools, and found a potential therapeutic effect of DSD on cancer. Indeed, our in vivo experiment demonstrated that oral administration of DSD could significantly inhibit the growth of xenografted gastric cancer (GC) on mice. The subsequent enrichment analyses for 123 candidate core targets evacuated from the drug/disease-target protein-protein interaction network showed that DSD could affect the key biological processes involving the survival and growth of GC cells, such as apoptosis and cell cycle, and the disturbance of these biological processes is likely attributed to the simultaneous inhibition of multiple signaling pathways, including PI3K/Akt, MAPK, and p53 pathways. Notably, these in silico results were further validated by a series of cellular functional and molecular biological assays in vitro. Moreover, molecular docking analysis suggested an important role of MCM2 in delivering the pharmacological activity of DSD against GC. Together, these results indicate that our network pharmacology and bioinformatics-guided approach is feasible and useful in exploring not only the mechanism of action, but also the "new use" of the old CHM formula.
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Affiliation(s)
- Boyu Pan
- Department of Gastrointestinal Cancer Biology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yun Wang
- Department of Integrated Traditional and Western Medicine, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Chunnuan Wu
- Department of Pharmacy, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Junrong Jia
- Public Laboratory, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Chen Huang
- Department of Gastrointestinal Cancer Biology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Senbiao Fang
- School of Information Science and Engineering, Central South University, Changsha, China
| | - Liren Liu
- Department of Gastrointestinal Cancer Biology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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Bailly C. Atractylenolides, essential components of Atractylodes-based traditional herbal medicines: Antioxidant, anti-inflammatory and anticancer properties. Eur J Pharmacol 2020; 891:173735. [PMID: 33220271 DOI: 10.1016/j.ejphar.2020.173735] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 12/20/2022]
Abstract
The rhizome of the plant Atractylodes macrocephala Koidz is the major constituent of the Traditional Chinese Medicine Baizhu, frequently used to treat gastro-intestinal diseases. Many traditional medicine prescriptions based on Baizhu and the similar preparation Cangzhu are used in China, Korea and Japan as Qi-booster. These preparations contain atractylenolides, a small group of sesquiterpenoids endowed with antioxidant and anti-inflammatory properties. Atractylenolides I, II and III also display significant anticancer properties, reviewed here. The capacity of AT-I/II/IIII to inhibit cell proliferation and to induce cancer cell death have been analyzed, together with their effects of angiogenesis, metastasis, cell differentiation and stemness. The immune-modulatory properties of ATs are discussed. AT-I has been tested clinically for the treatment of cancer-induced cachexia with encouraging results. ATs, alone or combined with cytotoxic drugs, could be useful to treat cancers or to reduce side effects of radio and chemotherapy. Several signaling pathways have been implicated in their multi-targeted mechanisms of action, in particular those involving the central regulators TLR4, NFκB and Nrf2. A drug-induced reduction of inflammatory cytokines production (TNFα, IL-6) also characterizes these molecules which are generally weakly cytotoxic and well tolerated in vivo. Inhibition of Janus kinases (notably JAK2 and JAK3 targeted by AT-I and AT-III, respectively) has been postulated. Information about their metabolism and toxicity are limited but the long-established traditional use of the Atractylodes and the diversity of anticancer effects reported with AT-I and AT-III should encourage further studies with these molecules and structurally related natural products.
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35
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Gao Y, Wang KX, Wang P, Li X, Chen JJ, Zhou BY, Tian JS, Guan DG, Qin XM, Lu AP. A Novel Network Pharmacology Strategy to Decode Mechanism of Lang Chuang Wan in Treating Systemic Lupus Erythematosus. Front Pharmacol 2020; 11:512877. [PMID: 33117150 PMCID: PMC7562735 DOI: 10.3389/fphar.2020.512877] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 09/11/2020] [Indexed: 01/26/2023] Open
Abstract
Complex disease is a cascade process which is associated with functional abnormalities in multiple proteins and protein-protein interaction (PPI) networks. One drug one target has not been able to perfectly intervene complex diseases. Increasing evidences show that Chinese herb formula usually treats complex diseases in the form of multi-components and multi-targets. The key step to elucidate the underlying mechanism of formula in traditional Chinese medicine (TCM) is to optimize and capture the important components in the formula. At present, there are several formula optimization models based on network pharmacology has been proposed. Most of these models focus on the 2D/3D similarity of chemical structure of drug components and ignore the functional optimization space based on relationship between pathogenetic genes and drug targets. How to select the key group of effective components (KGEC) from the formula of TCM based on the optimal space which link pathogenic genes and drug targets is a bottleneck problem in network pharmacology. To address this issue, we designed a novel network pharmacological model, which takes Lang Chuang Wan (LCW) treatment of systemic lupus erythematosus (SLE) as the case. We used the weighted gene regulatory network and active components targets network to construct disease-targets-components network, after filtering through the network attribute degree, the optimization space and effective proteins were obtained. And then the KGEC was selected by using contribution index (CI) model based on knapsack algorithm. The results show that the enriched pathways of effective proteins we selected can cover 96% of the pathogenetic genes enriched pathways. After reverse analysis of effective proteins and optimization with CI index model, KGEC with 82 components were obtained, and 105 enriched pathways of KGEC targets were consistent with enriched pathways of pathogenic genes (80.15%). Finally, the key components in KGEC of LCW were evaluated by in vitro experiments. These results indicate that the proposed model with good accuracy in screening the KGEC in the formula of TCM, which provides reference for the optimization and mechanism analysis of the formula in TCM.
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Affiliation(s)
- Yao Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, Hong Kong
| | - Ke-xin Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, Hong Kong
| | - Peng Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Xiao Li
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Jing-jing Chen
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, Hong Kong
- Zhijiang College, Zhejiang University of Technology, Shaoxing, China
| | - Bo-ya Zhou
- Department of Ultrasound, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Jun-sheng Tian
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Dao-gang Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Xue-mei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Ai-ping Lu
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, Hong Kong
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36
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Sorokina M, Steinbeck C. Review on natural products databases: where to find data in 2020. J Cheminform 2020; 12:20. [PMID: 33431011 PMCID: PMC7118820 DOI: 10.1186/s13321-020-00424-9] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/22/2020] [Indexed: 02/06/2023] Open
Abstract
Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.
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Affiliation(s)
- Maria Sorokina
- University Friedrich-Schiller, Lessing Strasse 8, 07743 Jena, Germany
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37
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Newman DJ. Modern traditional Chinese medicine: Identifying, defining and usage of TCM components. PHARMACOLOGICAL ADVANCES IN NATURAL PRODUCT DRUG DISCOVERY 2020; 87:113-158. [DOI: 10.1016/bs.apha.2019.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Chen Z, Wang X, Li Y, Wang Y, Tang K, Wu D, Zhao W, Ma Y, Liu P, Cao Z. Comparative Network Pharmacology Analysis of Classical TCM Prescriptions for Chronic Liver Disease. Front Pharmacol 2019; 10:1353. [PMID: 31824313 PMCID: PMC6884058 DOI: 10.3389/fphar.2019.01353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 10/25/2019] [Indexed: 12/15/2022] Open
Abstract
Chronic liver disease (CLD) has become a major global health problem while herb prescriptions are clinically observed with significant efficacy. Three classical Traditional Chinese Medicine (TCM) formulae, Yinchenhao Decoction (YCHT), Huangqi Decoction (HQT), and Yiguanjian (YGJ) have been widely applied in China to treat CLD, but no systematic study has yet been published to investigate their common and different mechanism of action (MOA). Partial limitation may own to deficiency of effective bioinformatics methods. Here, a computational framework of comparative network pharmacology is firstly proposed and then applied to herbal recipes for CLD disease. The analysis showed that, the three formulae modulate CLD mainly through functional modules of immune response, inflammation, energy metabolism, oxidative stress, and others. On top of that, each formula can target additional unique modules. Typically, YGJ ingredients can uniquely target the ATP synthesis and neurotransmitter release cycle. Interestingly, different formulae may regulate the same functional module in different modes. For instance, YCHT and YGJ can activate oxidative stress-related genes of SOD family while HQT are found to inhibit SOD1 gene. Overall, our framework of comparative network pharmacology proposed in our work may not only explain the MOA of different formulae treating CLD, but also provide hints to further investigate the biological basis of CLD subtypes.
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Affiliation(s)
- Zikun Chen
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaoning Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanyuan Li
- Department of Pharmacology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yahang Wang
- Department of Pharmacology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Kailin Tang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Dingfeng Wu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenyan Zhao
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yueming Ma
- Department of Pharmacology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ping Liu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Key Laboratory of Liver and Kidney Diseases of Ministry of Education of China, Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhiwei Cao
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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Abstract
Abstract
Natural product (NP)-derived drugs can be extracts, biological macromolecules, or purified small molecule substances. Small molecule drugs can be originally purified from NPs, can represent semisynthetic molecules, natural fragments containing small molecules, or are fully synthetic molecules that mimic natural compounds. New semisynthetic NP-like drugs are entering the pharmaceutical market almost every year and reveal growing interests in the application of fragment-based approaches for NPs. Thus, several NP databases were constructed to be implemented in the fragment-based drug design (FBDD) workflows. FBDD has been established previously as an approach for hit identification and lead generation. Several biophysical and computational methods are used for fragment screening to identify potential hits. Once the fragments within the binding pocket of the protein are identified, they can be grown, linked, or merged to design more active compounds. This work discusses applications of NPs and NP scaffolds to FBDD. Moreover, it briefly reviews NP databases containing fragments and reports on case studies where the approach has been successfully applied for the design of antimalarial and anticancer drug candidates.
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40
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Yu E, Xu Y, Shi Y, Yu Q, Liu J, Xu L. Discovery of novel natural compound inhibitors targeting estrogen receptor α by an integrated virtual screening strategy. J Mol Model 2019; 25:278. [PMID: 31463793 DOI: 10.1007/s00894-019-4156-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022]
Abstract
Estrogen receptor (ER) is a nuclear hormone receptor and plays an important role in mediating the cellular effects of estrogen. ER can be classified into two receptors: estrogen receptor alpha (ERα) and beta (ERβ), and the former is expressed in 50~80% of breast tumors and has been extensively investigated in breast cancer for decades. Excessive exposure to estrogen can obviously stimulate the growth of breast cancers primarily mediated by ERα, and thus anti-estrogen therapies by small molecules are of concern to clinicians and pharmaceutical industry in the treatment of ERα-positive breast cancers. Although a series of estrogen receptor modulators have been developed, these drugs can lead to resistance and side effects. Therefore, the development of small molecule inhibitors with high target specificity has been intensified. In this pursuit, an integrated computer-aided virtual screening technique, including molecular docking and pharmacophore model screening, was used to screen traditional Chinese medicine (TCM) databases. The compounds with high docking scores and fit values were subjected to ADME (adsorption, distribution, metabolism, excretion) and toxicity prediction, and ten hits were identified as potential inhibitors targeting ERα. Molecular docking was used to investigate the binding modes between ERα and three most potent hits, and molecular dynamic simulations were chosen to explore the stability of these complexes. The rank of the predicted binding free energies evaluated by MM/GBSA is consistent with the docking score. These novel scaffolds discovered in the present study can be used as critical starting point in the drug discovery process for treating ERα-positive breast cancer. Graphical abstract .
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Affiliation(s)
- Enguang Yu
- Department of Chinese Surgery, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Yueping Xu
- Department of Nursing, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Yanbo Shi
- Central Laboratory of Molecular Medicine Research Center, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Qiuyan Yu
- Department of Breast Surgery, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Jie Liu
- Department of Traditional Chinese Medicine Oncology, Jiaxing University Affiliated Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, 314000, Zhejiang, People's Republic of China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, Jiangsu, China.
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Luo M, Ni K, Jin Y, Yu Z, Deng L. Toward the Identification of Extra-Oral TAS2R Agonists as Drug Agents for Muscle Relaxation Therapies via Bioinformatics-Aided Screening of Bitter Compounds in Traditional Chinese Medicine. Front Physiol 2019; 10:861. [PMID: 31379593 PMCID: PMC6647893 DOI: 10.3389/fphys.2019.00861] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/20/2019] [Indexed: 12/29/2022] Open
Abstract
Significant advances have been made in the past decade in mapping the distributions and the physiological functions of extra-oral bitter taste receptors (TAS2Rs) in non-gustatory tissues. In particular, it has been found that TAS2Rs are expressed in various muscle tissues and activation of TAS2Rs can lead to muscle cell relaxation, which suggests that TAS2Rs may be important new targets in muscle relaxation therapy for various muscle-related diseases. So far, however, there is a lack of potent extra-oral TAS2R agonists that can be used as novel drug agents in muscle relaxation therapies. Interestingly, traditional Chinese medicine (TCM) often characterizes a drug’s property in terms of five distinct flavors (bitter, sweet, sour, salty, and pungent) according to its taste and function, and commonly regards “bitterness” as an intrinsic property of “good medicine.” In addition, many bitter flavored TCM are known in practice to cause muscle relaxation after long term use, and in lab experiments the compounds identified from some bitter flavored TCM do activate TAS2Rs and thus relax muscle cells. Therefore, it is highly possible to discover very useful extra-oral TAS2R agonists for muscle relaxation therapies among the abundant bitter compounds used in bitter flavored TCM. With this perspective, we reviewed in literature the distribution of TAS2Rs in different muscle systems with a focus on the map of bitter flavored TCM which can regulate muscle contractility and related functional chemical components. We also reviewed the recently established databases of TCM chemical components and the bioinformatics software which can be used for high-throughput screening and data mining of the chemical components associated with bitter flavored TCM. All together, we aim to present a knowledge-based approach and technological platform for identification or discovery of extra-oral TAS2R agonists that can be used as novel drug agents for muscle relaxation therapies through screening and evaluation of chemical compounds used in bitter flavored TCM.
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Affiliation(s)
- Mingzhi Luo
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
| | - Kai Ni
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
| | - Yang Jin
- Bioengineering College, Chongqing University, Chongqing, China
| | - Zifan Yu
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
| | - Linhong Deng
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
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Liu MZ, Zhou DC, Liu Q, Xie FL, Xiang DX, Tang GY, Luo SL. Osteogenesis activity of isocoumarin a through the activation of the PI3K-Akt/Erk cascade-activated BMP/RUNX2 signaling pathway. Eur J Pharmacol 2019; 858:172480. [PMID: 31228453 DOI: 10.1016/j.ejphar.2019.172480] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 11/18/2022]
Abstract
Bone formation refers to a series of complex events related to the activities of osteoblasts. In this study, we evaluated the osteogenesis activity of a natural compound named isocoumarin A that was isolated from the rhizomes of Polygonum amplexicaule on the non-transformed preosteoblastic cell line MC3T3-E1 for an in vitro study, and the results revealed that it increased the proliferation and promoted the mineralization of the extracellular matrix of MC3T3-E1 cells after treatment for 3 d in a dose-dependent manner. The cell metabolic activity peaked at 169% at 10 μM, and the activity of alkaline phosphatase (ALP) tripled to 15.94 U/mg compared with the control group. The protein levels of morphogenetic protein 2 (BMP-2), runt-related transcription factor 2 (RUNX2), ALP, and the mRNA levels of ALP, type I collagen (COL-1), and osteocalcin (OCN) were also upregulated after isocoumarin A administration. The mechanism investigation revealed that these effects were associated with the activation of the p-Akt/p-Erk1/2-activated BMP/RUNX2 signaling pathway. Subsequently, the in vivo investigation on the zebrafish embryos model demonstrated that isocoumarin A (0.30 mM) increased the number of vertebrae (5.38 ± 2.07 pcs) and the vertebral area (433.25 ± 111.77 μm2) in the development process of zebrafish embryos after a 7-day postfertilization (dpf) culture compared with the control group (2.50 ± 1.16 pcs and 209.75 ± 86.40 μm2). Together, these results indicated that isocoumarin A could be viewed as a promising candidate in early drug discovery and development to promote the healing of fractures and postmenopausal osteoporosis.
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Affiliation(s)
- Min-Zhen Liu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, PR China; Institute of Clinical Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, PR China
| | - Dong-Chu Zhou
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, PR China; Institute of Clinical Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, PR China
| | - Qiang Liu
- Department of Pharmacy, Yiyang Central Hospital, Yiyang, 41300, PR China
| | - Fu-Li Xie
- School of Medical Science, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine, Huaihua, 418000, PR China
| | - Da-Xiong Xiang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, PR China; Institute of Clinical Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, PR China
| | - Gen-Yun Tang
- School of Medical Science, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine, Huaihua, 418000, PR China
| | - Shi-Lin Luo
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, PR China; Institute of Clinical Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, PR China.
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Chen Y, de Bruyn Kops C, Kirchmair J. Resources for Chemical, Biological, and Structural Data on Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:37-71. [PMID: 31621010 DOI: 10.1007/978-3-030-14632-0_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural products from plants, marine life, animals, fungi, bacteria, and other organisms remain the most productive source of inspiration for small-molecule drug discovery. Today, a wealth of information on natural products that is particularly valuable to applications in cheminformatics is at our disposal. In this contribution, we provide a timely overview of relevant resources for measured chemical, biological, and structural data on natural products. In particular, we comment on the accessibility, scope, chemical space, and limitations of the individual data sources. The bottleneck of natural products remains the limited availability of material for testing. In this context, we analyze the number of natural products readily obtainable from commercial and other sources.
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Affiliation(s)
- Ya Chen
- Faculty of Mathematics, Informatics, and Natural Sciences, Department of Computer Science, Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
| | | | - Johannes Kirchmair
- Faculty of Mathematics, Informatics, and Natural Sciences, Department of Computer Science, Center for Bioinformatics, Universität Hamburg, Hamburg, Germany. .,Computational Biology Unit (CBU), University of Bergen, Bergen, Norway.
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