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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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Annadurai Y, Easwaran M, Sundar S, Thangamani L, Meyyazhagan A, Malaisamy A, Natarajan J, Piramanayagam S. SPP1, a potential therapeutic target and biomarker for lung cancer: functional insights through computational studies. J Biomol Struct Dyn 2024; 42:1336-1351. [PMID: 37096999 DOI: 10.1080/07391102.2023.2199871] [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: 10/27/2022] [Accepted: 03/30/2023] [Indexed: 04/26/2023]
Abstract
NIH reported 128 different types of cancer of which lung cancer is the leading cause of mortality. Globally, it is estimated that on average one in every seventeen hospitalized patients was deceased. There are plenty of studies that have been reported on lung cancer draggability and therapeutics, but yet a protein that plays a central specific to cure the disease remains unclear. So, this study is designed to identify the possible therapeutic targets and biomarkers that can be used for the potential treatment of lung cancers. In order to identify differentially expressed genes, 39 microarray datasets of lung cancer patients were obtained from various demographic regions of the GEO database available at NCBI. After annotating statistically, 6229 up-regulated genes and 10324 down-regulated genes were found. Out of 17 up-regulated genes and significant genes, we selected SPP1 (osteopontin) through virtual screening studies. We found functional interactions with the other cancer-associated genes such as VEGF, FGA, JUN, EGFR, and TGFB1. For the virtual screening studies,198 biological compounds were retrieved from the ACNPD database and docked with SPP1 protein (PDBID: 3DSF). In the results, two highly potential compounds secoisolariciresinol diglucoside (-12.9 kcal/mol), and Hesperidin (-12.0 kcal/mol) showed the highest binding affinity. The stability of the complex was accessed by 100 ns simulation in an SPC water model. From the functional insights obtained through these computational studies, we report that SPP1 could be a potential biomarker and successive therapeutic protein target for lung cancer treatment.
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Affiliation(s)
- Yamuna Annadurai
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Murugesh Easwaran
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Shobana Sundar
- Department of Biotechnology, PSG College of Technology, Coimbatore, Tamil Nadu, India
| | - Lokesh Thangamani
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Arun Meyyazhagan
- Dipartimento di Medicina e Chirurgia, Università di Perugia, Perugia, Italy
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru, Karnataka, India
- Department of Translation Medicine and Surgery, Perugia University, Perugia, Italy
| | - Arunkumar Malaisamy
- Transcription Regulation Group, International centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Jeyakumar Natarajan
- Text Mining Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Shanmughavel Piramanayagam
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
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Fakhri S, Abdian S, Moradi SZ, Delgadillo BE, Fimognari C, Bishayee A. Marine Compounds, Mitochondria, and Malignancy: A Therapeutic Nexus. Mar Drugs 2022; 20:md20100625. [PMID: 36286449 PMCID: PMC9604966 DOI: 10.3390/md20100625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The marine environment is important yet generally underexplored. It contains new sources of functional constituents that can affect various pathways in food processing, storage, and fortification. Bioactive secondary metabolites produced by marine microorganisms may have significant potential applications for humans. Various components isolated from disparate marine microorganisms, including fungi, microalgae, bacteria, and myxomycetes, showed considerable biological effects, such as anticancer, antioxidant, antiviral, antibacterial, and neuroprotective activities. Growing studies are revealing that potential anticancer effects of marine agents could be achieved through the modulation of several organelles. Mitochondria are known organelles that influence growth, differentiation, and death of cells via influencing the biosynthetic, bioenergetic, and various signaling pathways related to oxidative stress and cellular metabolism. Consequently, mitochondria play an essential role in tumorigenesis and cancer treatments by adapting to alterations in environmental and cellular conditions. The growing interest in marine-derived anticancer agents, combined with the development and progression of novel technology in the extraction and cultures of marine life, led to revelations of new compounds with meaningful pharmacological applications. This is the first critical review on marine-derived anticancer agents that have the potential for targeting mitochondrial function during tumorigenesis. This study aims to provide promising strategies in cancer prevention and treatment.
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Affiliation(s)
- Sajad Fakhri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran
| | - Sadaf Abdian
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah 6714415153, Iran
| | - Seyed Zachariah Moradi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran
| | - Blake E. Delgadillo
- College of Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA
| | - Carmela Fimognari
- Department for Life Quality Studies, University of Bologna, 47921 Rimini, Italy
| | - Anupam Bishayee
- College of Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA
- Correspondence: or
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Song N, Cui K, Zhang K, Yang J, Liu J, Miao Z, Zhao F, Meng H, Chen L, Chen C, Li Y, Shao M, Zhang J, Wang H. The Role of m6A RNA Methylation in Cancer: Implication for Nature Products Anti-Cancer Research. Front Pharmacol 2022; 13:933332. [PMID: 35784761 PMCID: PMC9243580 DOI: 10.3389/fphar.2022.933332] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/27/2022] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is identified as the most common, abundant and reversible RNA epigenetic modification in messenger RNA (mRNA) and non-coding RNA, especially within eukaryotic messenger RNAs (mRNAs), which post-transcriptionally directs many important processes of RNA. It has also been demonstrated that m6A modification plays a pivotal role in the occurrence and development of tumors by regulating RNA splicing, localization, translation, stabilization and decay. Growing number of studies have indicated that natural products have outstanding anti-cancer effects of their unique advantages of high efficiency and minimal side effects. However, at present, there are very few research articles to study and explore the relationship between natural products and m6A RNA modification in tumorigenesis. m6A is dynamically deposited, removed, and recognized by m6A methyltransferases (METTL3/14, METTL16, WTAP, RBM15/15B, VIRMA, CBLL1, and ZC3H13, called as “writers”), demethylases (FTO and ALKBH5, called as “erasers”), and m6A-specific binding proteins (YTHDF1/2/3, YTHDC1/2, IGH2BP1/2/3, hnRNPs, eIF3, and FMR1, called as “readers”), respectively. In this review, we summarize the biological function of m6A modification, the role of m6A and the related signaling pathway in cancer, such as AKT, NF-kB, MAPK, ERK, Wnt/β-catenin, STAT, p53, Notch signaling pathway, and so on. Furthermore, we reviewed the current research on nature products in anti-tumor, and further to get a better understanding of the anti-tumor mechanism, thus provide an implication for nature products with anti-cancer research by regulating m6A modification in the future.
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Affiliation(s)
- Na Song
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Kai Cui
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Ke Zhang
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Jie Yang
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Jia Liu
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Zhuang Miao
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Feiyue Zhao
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Hongjing Meng
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Lu Chen
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Chong Chen
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Yushan Li
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Minglong Shao
- The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Jinghang Zhang
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- *Correspondence: Jinghang Zhang, ; Haijun Wang,
| | - Haijun Wang
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Jinghang Zhang, ; Haijun Wang,
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