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Yang K, Shan X, Songru Y, Fu M, Zhao P, Guo W, Xu M, Chen H, Lu R, Zhang C. Network pharmacology integrated with experimental validation to elucidate the mechanisms of action of the Guizhi-Gancao Decoction in the treatment of phenylephrine-induced cardiac hypertrophy. PHARMACEUTICAL BIOLOGY 2024; 62:456-471. [PMID: 38773737 PMCID: PMC11123502 DOI: 10.1080/13880209.2024.2354335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 04/28/2024] [Indexed: 05/24/2024]
Abstract
CONTEXT The mechanisms of Traditional Chinese Medicine (TCM) Guizhi-Gancao Decoction (GGD) remain unknown. OBJECTIVE This study explores the mechanisms of GGD against cardiac hypertrophy. MATERIALS AND METHODS Network pharmacology analysis was carried out to identify the potential targets of GGD. In vivo experiments, C57BL/6J mice were divided into Con, phenylephrine (PE, 10 mg/kg/d), 2-chloroadenosine (CADO, the stable analogue of adenosine, 2 mg/kg/d), GGD (5.4 g/kg/d) and GGD (5.4 g/kg/d) + CGS15943 (a nonselective adenosine receptor antagonist, 4 mg/kg/d). In vitro experiments, primary neonatal rat cardiomyocytes (NRCM) were divided into Con, PE (100 µM), CADO (5 µM), GGD (10-5 g/mL) and GGD (10-5 g/mL) + CGS15943 (5 µM). Ultrasound, H&E and Masson staining, hypertrophic genes expression and cell surface area were conducted to verify the GGD efficacy. Adenosine receptors (ADORs) expression were tested via real-time polymerase chain reaction (PCR), western blotting and immunofluorescence analysis. RESULTS Network pharmacology identified ADORs among those of the core targets of GGD. In vitro experiments demonstrated that GGD attenuated PE-induced increased surface area (with an EC50 of 5.484 × 10-6 g/mL). In vivo data shown that GGD attenuated PE-induced ventricular wall thickening. In vitro and in vivo data indicated that GGD alleviated PE-induced hypertrophic gene expression (e.g., ANP, BNP and MYH7/MYH6), A1AR over-expression and A2aAR down-expression. Moreover, CADO exerts effects similar to GGD, whereas CGS15943 eliminated most effects of GGD. DISCUSSION AND CONCLUSIONS Our findings suggest the mechanism by which GGD inhibits cardiac hypertrophy, highlighting regulation of ADORs as a potential therapeutic strategy for HF.
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Affiliation(s)
- Kaijing Yang
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoli Shan
- Public Laboratory Platform, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yang Songru
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mengwei Fu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Pei Zhao
- Public Laboratory Platform, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Guo
- Department of Pathology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ming Xu
- Department of Physiology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huihua Chen
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Lu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chen Zhang
- Department of Pathology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Zhou HM, Yang XY, Yue SJ, Wang WX, Zhang Q, Xu DQ, Li JJ, Tang YP. The identification of metabolites from gut microbiota in coronary heart disease via network pharmacology. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:145-155. [PMID: 38412071 DOI: 10.1080/21691401.2024.2319827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
Although the gut microbial metabolites exhibit potential effects on coronary heart disease (CHD), the underlying mechanism remains unclear. In this study, the active gut microbial metabolites acting on CHD and their potential mechanisms of action were explored through a network pharmacological approach. We collected a total of 208 metabolites from the gutMgene database and 726 overlapping targets from the similarity ensemble approach (SEA) and SwissTargetPrediction (STP) database, and ultimately identified 610 targets relevant to CHD. In conjunction with the gutMGene database, we identified 12 key targets. The targets of exogenous substances were removed, and 10 core targets involved in CHD were eventually retained. The microbiota-metabolites-targets-signalling pathways network analysis revealed that C-type lectin receptor signalling pathway, Lachnospiraceae, Escherichia, mitogen-activated protein kinase 1, prostaglandin-endoperoxidase synthase 2, phenylacetylglutamine and alcoholic acid are notable components of CHD and play important roles in the development of CHD. The results of molecular docking experiments demonstrated that AKT1-glycocholic acid and PTGS2-phenylacetylglutamine complexes may act on C-type lectin receptor signalling pathways. In this study, the key substances and potential mechanisms of gut microbial metabolites were analysed via network pharmacological methods, and a scientific basis and comprehensive idea were provided for the effects of gut microbial metabolites on CHD.
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Affiliation(s)
- Hao-Ming Zhou
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Xin-Yu Yang
- Department of Pharmacy, Beijing Key Laboratory of Bio-characteristic Profiling for Evaluation of Rational Drug Use, Beijing Shijitan Hospital, Capital Medical University, Beijing, 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), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Wen-Xiao Wang
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Hebei University of Chinese Medicine, Shijiazhuang, 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), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Ding-Qiao Xu
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, 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), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, 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), Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, China
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Zhang X, Wu D, Zhang L, Zhang H, Yang L, Wei L, Mei H, Luo L, Jiang Z, Huang C. Predicting the potential mechanism of radix chimonanthi pracecocis in treating osteoarthritis by network pharmacology analysis combined with experimental validation. JOURNAL OF ETHNOPHARMACOLOGY 2024; 331:118231. [PMID: 38718891 DOI: 10.1016/j.jep.2024.118231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Radix Chimonanthi Pracecocis (RCP), also known as Tiekuaizi, widely used by the Miao community in Guizhou, exhibits diverse biological activities and holds promise for the treatment of osteoarthritis (OA). However, there is a lack of contemporary pharmacological research in this area. AIMS OF THE STUDY This study aims to explore the potential of targets and mechanisms of RCP in the treatment of OA. MATERIALS AND METHODS The chemical components of RCP were identified using UPLC-MS/MS, and active components were determined based on the Lipinski rule. RCP and OA-related targets were retrieved from public databases such as TCMSP and GeneCards. Network pharmacology approaches were employed to identify key genes. The limma package (version 3.40.2) in R 4.3.2 was used to screen for differentially expressed genes (DEGs) between OA and healthy individuals in GSE82107. DEGs were analyzed using an independent sample t-test and receiver operating characteristic analysis in GraphPad Prism 9.5.1. Additionally, molecular docking (SYBYL2.1.1) was used to analyze the binding interactions between the active components and target proteins. Finally, we established a papain-induced osteoarthritis (OA) rat model and treated it with RCP aqueous extract by gavage. We validated relevant indicators using real-time fluorescence quantitative polymerase chain reaction, Western blot, immunohistochemistry, and enzyme-linked immunosorbent assays. RESULTS Seven active components and 53 targets were identified. The results of GO and KEGG enrichment analyses confirmed the significant role of RCP in the regulation of pyroptosis. Hypoxia-inducible factor-1α (HIF-1α) was identified as a key gene involved in the main biological functions. Molecular docking analysis revealed that Praecoxin, Isofraxidin, Esculin, and Naringenin can bind to the nucleotide-binding domain, leucine-rich repeat, and pyrin domain-containing protein 3 (NLRP3) (T-Score >5). Additionally, Praecoxin can bind to HIF-1α (T-Score >5). In vivo experiments demonstrated that RCP significantly affects the NLRP3 inflammasome, which is regulated by the HIF-1α pathway. RCP inhibited pyroptosis and reduced synovial inflammation. CONCLUSIONS This study confirmed the efficacy of RCP aqueous extract in the treatment of OA and identified seven active components (esculin, dihydrokaempferol, naringenin, praecoxin, carnosol, hydroxyvalerenic acid, isofraxidin) that may play an anti-pyroptosis role in the treatment of OA by downregulating the expression of HIF-1α and NLRP3 inflammasome.
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Affiliation(s)
- Xudong Zhang
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Dongwen Wu
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Lukai Zhang
- Hangzhou Xiaoshan District Chinese Medicine Hospital, Hangzhou, 311200, China
| | - Hongyan Zhang
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Liping Yang
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Li Wei
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Huimin Mei
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Liying Luo
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Zong Jiang
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Cong Huang
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China; Anshun Hospital of Traditional Chinese Medicine, Anshun, 561000, China.
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Zhaoyu L, Xiaomeng Y, Na L, Jiamin S, Guanhua D, Xiuying Y. Roles of natural products on myokine expression and secretion in skeletal muscle atrophy. Gen Comp Endocrinol 2024; 355:114550. [PMID: 38768928 DOI: 10.1016/j.ygcen.2024.114550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Skeletal muscles serve both in movement and as endocrine organs. Myokines secreted by skeletal muscles activate biological functions within muscles and throughout the body via autocrine, paracrine, and/or endocrine pathways. Skeletal muscle atrophy can influence myokine expression and secretion, while myokines can impact the structure and function of skeletal muscles. Regulating the expression and secretion of myokines through the pharmacological approach is a strategy for alleviating skeletal muscle atrophy. Natural products possess complex structures and chemical properties. Previous studies have demonstrated that various natural products exert beneficial effects on skeletal muscle atrophy. This article reviewed the regulatory effects of natural products on myokines and summarized the research progress on skeletal muscle atrophy associated with myokine regulation. The focus is on how small-molecule natural products affect the regulation of interleukin 6 (IL-6), irisin, myostatin, IGF-1, and FGF-21 expression. We contend that the development of small-molecule natural products targeting the regulation of myokines holds promise in combating skeletal muscle atrophy.
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Affiliation(s)
- Liu Zhaoyu
- Beijing Key Laboratory of Drug Target Identification and New Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Ye Xiaomeng
- Beijing Key Laboratory of Drug Target Identification and New Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li Na
- Beijing Key Laboratory of Drug Target Identification and New Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Shang Jiamin
- Beijing Key Laboratory of Drug Target Identification and New Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Du Guanhua
- Beijing Key Laboratory of Drug Target Identification and New Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
| | - Yang Xiuying
- Beijing Key Laboratory of Drug Target Identification and New Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China.
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Hu B, Wang C, Wu Y, Han C, Liu J, Chen R, Wang T. Revealing the mechanism of ethyl acetate extracts of Semen Impatientis against prostate cancer based on network pharmacology and transcriptomics. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118228. [PMID: 38643863 DOI: 10.1016/j.jep.2024.118228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/30/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Prostate cancer (PCa) is the most common malignancy of the male genitourinary system and currently lacks effective treatment. Semen Impatientis, the dried ripe seed of Impatiens balsamina L., is described by the Chinese Pharmacopoeia as a traditional Chinese medicine (TCM) and is used in clinical practice to treat tumors, abdominal masses, etc. In our previous study, the ethyl acetate extracts of Semen Impatientis (EAESI) was demonstrated to be the most effective extract against PCa among various extracts. However, the biological effects of EAESI against PCa in vivo and the specific antitumor mechanisms involved remain unknown. AIM OF THE STUDY In this study, we aimed to investigate the antitumor effect of EAESI on PCa in vitro and in vivo by performing network pharmacology analysis, transcriptomic analysis, and experiments to explore and verify the underlying mechanisms involved. MATERIALS AND METHODS The antitumor effect of EAESI on PCa in vitro and in vivo was investigated via CCK-8, EdU, flow cytometry, and wound healing assays and xenograft tumor models. Network pharmacology analysis and transcriptomic analysis were employed to explore the underlying mechanism of EAESI against PCa. Activating transcription factor 3 (ATF3) and androgen receptor (AR) were confirmed to be the targets of EAESI against PCa by RT‒qPCR, western blotting, and rescue assays. In addition, the interaction between ATF3 and AR was assessed by coimmunoprecipitation, immunofluorescence, and nuclear-cytoplasmic separation assays. RESULTS EAESI decreased cell viability, inhibited cell proliferation and migration, and induced apoptosis in AR+ and AR- PCa cells. Moreover, EAESI suppressed the growth of xenograft tumors in vivo. Network pharmacology analysis revealed that the hub targets of EAESI against PCa included AR, AKT1, TP53, and CCND1. Transcriptomic analysis indicated that activating transcription factor 3 (ATF3) was the most likely critical target of EAESI. EAESI downregulated AR expression and decreased the transcriptional activity of AR through ATF3 in AR+ PCa cells; and EAESI promoted the expression of ATF3 and exerted its antitumor effect via ATF3 in AR+ and AR- PCa cells. CONCLUSIONS EAESI exerts good antitumor effects on PCa both in vitro and in vivo, and ATF3 and AR are the critical targets through which EAESI exerts antitumor effects on AR+ and AR- PCa cells.
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Affiliation(s)
- Bintao Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chengwei Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yue Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chenglin Han
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ruibao Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Wu JW, Gao W, Shen LP, Chen YL, Du SQ, Du ZY, Zhao XD, Lu XJ. Leonurus japonicus Houtt. modulates neuronal apoptosis in intracerebral hemorrhage: Insights from network pharmacology and molecular docking. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118223. [PMID: 38642624 DOI: 10.1016/j.jep.2024.118223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Leonurus japonicus Houtt. (Labiatae), commonly known as Chinese motherwort, is a herbaceous flowering plant that is native to Asia. It is widely acknowledged in traditional medicine for its diuretic, hypoglycemic, antiepileptic properties and neuroprotection. Currently, Leonurus japonicus (Leo) is included in the Pharmacopoeia of the People's Republic of China. Traditional Chinese Medicine (TCM) recognizes Leo for its myriad pharmacological attributes, but its efficacy against ICH-induced neuronal apoptosis is unclear. AIMS OF THE STUDY This study aimed to identify the potential targets and regulatory mechanisms of Leo in alleviating neuronal apoptosis after ICH. MATERIALS AND METHODS The study employed network pharmacology, UPLC-Q-TOF-MS technique, molecular docking, pharmacodynamic studies, western blotting, and immunofluorescence techniques to explore its potential mechanisms. RESULTS Leo was found to assist hematoma absorption, thus improving the neurological outlook in an ICH mouse model. Importantly, molecular docking highlighted JAK as Leo's potential therapeutic target in ICH scenarios. Further experimental evidence demonstrated that Leo adjusts JAK1 and STAT1 phosphorylation, curbing Bax while augmenting Bcl-2 expression. CONCLUSION Leo showcases potential in mitigating neuronal apoptosis post-ICH, predominantly via the JAK/STAT mechanism.
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Affiliation(s)
- Jia-Wei Wu
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Wei Gao
- Department of Neurology, Wuxi Ninth People's Hospital Affiliated to Soochow University, Wuxi, Jiangsu Province, 214122, PR China
| | - Li-Ping Shen
- Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Yong-Lin Chen
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Shi-Qing Du
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Zhi-Yong Du
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Xu-Dong Zhao
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China.
| | - Xiao-Jie Lu
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China.
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Gertsch J, Chicca A. CNS Drug Discovery in Academia: Where Basic Research Meets Innovation. Chembiochem 2024:e202400397. [PMID: 38958639 DOI: 10.1002/cbic.202400397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/27/2024] [Indexed: 07/04/2024]
Abstract
The involvement of academic research in drug discovery is consistently growing. However, academic projects seldom advance to clinical trials. Here, we assess the landscape of drug discovery within the National Centre of Competence in Research (NCCR) TransCure launched by the Swiss National Science Foundation to foster basic research and early-stage drug discovery on membrane transporters. This included transporters in central nervous system (CNS) disorders, which represent a huge unmet medical need. While idea championship, sustainable funding, collaborations between disciplines at the interface of academia and industry are important for translational research, Popperian falsifiability, strong intellectual property and a motivated startup team are key elements for innovation. This is exemplified by the NCCR TransCure spin-off company Synendos Therapeutics, a clinical stage biotech company developing the first selective endocannabinoid reuptake inhibitors (SERIs) as novel treatment for neuropsychiatric disorders. We provide a perspective on the challenges related to entering an uncharted druggable space and bridging the often mentioned "valley of death". The high attrition rate of drug discovery projects in the CNS field within academia is often due to the lack of meaningful animal models that can provide pharmacological proof-of-concept for potentially disruptive technologies at the earliest stages, and the absence of solid intellectual property.
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Affiliation(s)
- Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Andrea Chicca
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
- Synendos Therapeutics, Barfüsserplatz, 3, 4051, Basel, Switzerland
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Singh M, Verma H, Gera N, Baddipadige R, Choudhary S, Bhandu P, Silakari O. Evaluation of Cordyceps militaris steroids as anti-inflammatory agents to combat the Covid-19 cytokine storm: a bioinformatics and structure-based drug designing approach. J Biomol Struct Dyn 2024; 42:5159-5177. [PMID: 37551029 DOI: 10.1080/07391102.2023.2245039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/08/2023] [Indexed: 08/09/2023]
Abstract
Since the SARS-CoV-2 epidemic, researchers have been working on figuring out ways to tackle multi-organ failure and hyperinflation, which are brought on by a cytokine storm. Angiotensin-converting enzyme 2 (ACE2), a SARS-CoV-2 spike glycoprotein's cellular receptor, is involved in complicated molecular processes that result in hyperinflammation. Cordyceps militaris is one of the traditional Chinese medicines that is used as an immune booster, and it has exhibited efficacy in lowering blood glucose levels, seminal emissions, and infertility. In the current study, we explored the potential of Cordyceps militaris steroids as key agents in managing the anger of cytokine storm in Covid-19 using network ethnopharmacological techniques and structure-based drug designing approaches. The steroids present in Cordyceps militaris were initially screened against the targets involved in inflammatory pathways. The results revealed that out of 16 steroids, 5 may be effective against 17 inflammatory pathways by targeting 11 pathological proteins. Among the five steroids, beta-sitosterol, Cholest-5-en-3β-ol, 3β, and 7α-Dihydroxycholest-5-ene were found to interact with thrombin (F2), an important protein reported to reduce the severity of inflammatory mediators and Cholest-4-en-3-one was found to target Glucocorticoid receptor (NR3C1). The top docked steroid displayed key interactions with both targets, which retained key interactions throughout the 100 ns simulation period. These compounds were also shown high binding free energy scores in water swap studies. Based on obtained results the current study suggests the use of Cordyceps militaris as an add-on therapy that may reduce the progression of inflammatory co-morbidities among patients infected with SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manmeet Singh
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Himanshu Verma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Narendra Gera
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Raju Baddipadige
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Shalki Choudhary
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Priyanka Bhandu
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
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Wang W, Li X, Wu H, Shi F, Zhang Z, Lv H. Explore the underlying oral efficacy of α-, β-, γ-Cyclodextrin against the ulcerative colitis using in vitro and in vivo studies assisted by network pharmacology. J Biomol Struct Dyn 2024; 42:4985-5000. [PMID: 37517028 DOI: 10.1080/07391102.2023.2239901] [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: 02/21/2023] [Accepted: 06/05/2023] [Indexed: 08/01/2023]
Abstract
The incidence of ulcerative colitis (UC) is rising worldwide. As a refractory and recurrent disease, UC could seriously affect the patients' quality of life. However, current clinical medical treatments for UC are accompanied by various side effects, especially for long-term applications. Here, the underlying efficacy of cyclodextrins (CDs) was studied. As common excipients, CDs endow proven safety for long-term applications. Results of predictive methods derived from network pharmacology prompted the potential anti-inflammatory effects of CDs by oral administration. RAW264.7 cell experiments verified that CDs could inhibit the excessive secretion of TNF-α (β-CD > α-CD ≈ γ-CD), IL-6, and NO (α-CD > β-CD ≈ γ-CD) as predicted. In mice with DSS-induced acute UC, oral administration of CDs could effectively mitigate the pathological damage of colon tissue and reduce the level of inflammatory mediators. Moreover, 16S rRNA sequencing displayed that gut microbes disturbed by DSS were significantly regulated by CDs. Conclusively, the study showed the therapeutic application prospects of CDs in UC treatment and indicated the feasibility and advantages of developing 'new' therapeutic activities of 'old' ingredients.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Weiqin Wang
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xuefeng Li
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hangyi Wu
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fanli Shi
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhenhai Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Huixia Lv
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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10
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Chai Y, Chen F, Li H, Sun X, Yang P, Xi Y. Mechanism of salidroside regulating autophagy based on network pharmacology and molecular docking. Anticancer Drugs 2024; 35:525-534. [PMID: 38502854 DOI: 10.1097/cad.0000000000001601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Salidroside is a natural product of phenols with a wide range of pharmacological functions, but whether it plays a role in regulating autophagy is unclear. We systematically investigated the regulatory effect and molecular mechanism of salidroside on autophagy through network pharmacology, which provided a theoretical basis for subsequent experimental research. First, the target genes of salidroside were obtained using the Chinese Medicine System Pharmacology Database and Analysis Platform, and the target genes were converted into standardized gene names using the Uniprot website. At the same time, autophagy-related genes were collected from GeneCards, and preliminary handling of data to obtain intersecting genes. Then, the String website was used to construct a protein-protein interaction network, and to perform the Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis. To observe the specific molecular mechanism by which salidroside regulates autophagy, we constructed a drug component-target genes-autophagy network. Finally, we performed molecular docking to verify the possible binding conformation between salidroside and the candidate target. By searching the database and analyzing the data, we found that 113 target genes in salidroside interact with autophagy. Salidroside regulate autophagy in relation to a number of important oncogenes and signaling pathways. Molecular docking confirmed that salidroside has high affinity with mTOR, SIRT1, and AKT1. Through network pharmacology combined with molecular docking-validated research methods, we revealed the underlying mechanism of salidroside regulation of autophagy. This study not only provides new systematic insights into the underlying mechanism of salidroside in autophagy, but also provides new ideas for network approaches for autophagy-related research.
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Affiliation(s)
- Yihong Chai
- The First Clinical Medical College of Lanzhou University
| | - Feng Chen
- The First Clinical Medical College of Lanzhou University
| | - Hongxing Li
- The First Clinical Medical College of Lanzhou University
- Department of Obstetrics and Gynaecology
| | - Xiaohong Sun
- The First Clinical Medical College of Lanzhou University
| | - Panpan Yang
- The First Clinical Medical College of Lanzhou University
- Department of Obstetrics and Gynaecology
| | - YaMing Xi
- The First Clinical Medical College of Lanzhou University
- Department of Hematology, First Hospital of Lanzhou University, Lanzhou, China
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11
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Zuo C, Cai L, Li Y, Ding C, Liu G, Zhang C, Wang H, Zhang Y, Ji M. The Molecular Mechanism of Radix Paeoniae Rubra.-Cortex Moutan. Herb Pair in the Treatment of Atherosclerosis: A Work Based on Network Pharmacology and In Vitro Experiments. Cardiovasc Toxicol 2024:10.1007/s12012-024-09881-2. [PMID: 38951468 DOI: 10.1007/s12012-024-09881-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024]
Abstract
Radix Paeoniae Rubra. (Chishao, RPR) and Cortex Moutan. (Mudanpi, CM) are a pair of traditional Chinese medicines that play an important role in the treatment of atherosclerosis (AS). The main objective of this study was to identify potential synergetic function and underlying mechanisms of RPR-CM in the treatment of AS. The main active ingredients, targets of RPR-CM and AS-related genes were obtained from public databases. A Venn diagram was utilized to screen the common targets of RPR-CM in treating AS. The protein-protein interaction network was established based on STRING database. Biological functions and pathways of potential targets were analyzed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Cytoscape was used to construct the drug-compound-target-signal pathway network. Molecular docking was performed to verify the binding ability of the bioactive ingredients and the target proteins. The endothelial inflammation model was constructed with human umbilical vein endothelial cells stimulated with ox-LDL, and the function of RPR-CM in treating AS was verified by CCK-8 assay, enzyme-linked immunosorbent assay, and qPCR. In this study, 12 active components and 401 potential target genes of RPR-CM were identified, among which quercetin, kaempferol and baicalein were considered to be the main active components. A total of 1903 AS-related genes were identified through public databases and four GEO datasets (GSE57691, GSE72633, GSE6088 and GSE199819). There are 113 common target genes of RPR-CM in treating AS. PPI network analysis identified 17 genes in cluster 1 as the core targets. Bioinformatics analysis showed that RPR-CM in AS treatment was associated with multiple downstream biological processes and signal pathways. PTGS2, JUN, CASP3, TNF, IL1B, IL6, FOS, STAT1 were identified as the core targets of RPR-CM, and molecular docking showed that the main bioactive components of RPR-CM had good binding ability with the core targets. RPR-CM extract significantly inhibited the levels of inflammatory factors TNF-α, IL-6, IL-1β, MCP-1, VCAM-1 and ICAM-1 in HUVECs, and inhibited endothelial inflammation. This study revealed the active ingredients of RPR-CM, and identified the key downstream targets and signaling pathways in the treatment of AS, providing theoretical basis for the application of RPR-CM in prevention and treatment of AS.
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Affiliation(s)
- Caojian Zuo
- Department of Cardiology, Lianshui People's Hospital, Kangda College of Nanjing Medical University, Lianshui County, No 6, Hongri East Avenue, Huai'an, 223400, Jiangsu, China.
- Department of Cardiology, Shanghai Deji Hospital, Qingdao University, Shanghai, 200331, China.
| | - Lidong Cai
- Department of Cardiology, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Ya Li
- Department of Cardiology, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Chencheng Ding
- Department of Cardiology, Shanghai Deji Hospital, Qingdao University, Shanghai, 200331, China
| | - Guiying Liu
- Department of Cardiology, Shanghai Deji Hospital, Qingdao University, Shanghai, 200331, China
| | - Changmei Zhang
- Department of Cardiology, Shanghai Deji Hospital, Qingdao University, Shanghai, 200331, China
| | - Hexiang Wang
- Department of Cardiology, Shanghai Deji Hospital, Qingdao University, Shanghai, 200331, China
| | - Yang Zhang
- Department of Cardiology, Shanghai Deji Hospital, Qingdao University, Shanghai, 200331, China
| | - Mingyue Ji
- Department of Cardiology, Lianshui People's Hospital, Kangda College of Nanjing Medical University, Lianshui County, No 6, Hongri East Avenue, Huai'an, 223400, Jiangsu, China
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12
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Li S, Zhu Z, Chen Z, Guo Z, Wang Y, Li X, Ma K. Network pharmacology-based investigation of the effects of Shenqi Fuzheng injection on glioma proliferation and migration via the SRC/PI3K/AKT signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118128. [PMID: 38561056 DOI: 10.1016/j.jep.2024.118128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/23/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In the clinic, Shenqi Fuzheng Injection (SFI) is used as an adjuvant for cancer chemotherapy. However, the molecular mechanism is unclear. AIM OF THE STUDY We screened potential targets of SFI action on gliomas by network pharmacology and performed experiments to validate possible molecular mechanisms against gliomas. MATERIALS AND METHODS We consulted relevant reports on the SFI and glioma incidence from PubMed and Web of Science and focused on the mechanism through which the SFI inhibits glioma. According to the literature, two primary SFI components-Codonopsis pilosula (Franch.) Nannf. and Astragalus membranaceus (Fisch.) Bunge-have been found. All plant names have been sourced from "The Plant List" (www.theplantlist.org). The cell lines U87, T98G and GL261 were used in this study. The inhibitory effects of SFI on glioma cells U87 and T98G were detected by CCK-8 assay, EdU, plate cloning assay, scratch assay, Transwell assay, immunofluorescence, flow cytometry and Western blot. A subcutaneous tumor model of C57BL/6 mice was constructed using GL261 cells, and the SFI was evaluated by HE staining and immunohistochemistry. The targets of glioma and the SFI were screened using network pharmacology. RESULTS A total of 110 targets were enriched, and a total of 26 major active components in the SFI were investigated. There were a total of 3,343 targets for gliomas, of which 79 targets were shared between the SFI and glioma tissues. SFI successfully prevented proliferation and caused cellular S-phase blockage in U87 and T98G cells, thus decreasing their growth. Furthermore, SFI suppressed cell migration by downregulating EMT marker expression. According to the results of the in vivo tests, the SFI dramatically decreased the development of tumors in a transplanted tumour model. Network pharmacological studies revealed that the SRC/PI3K/AKT signaling pathway may be the pathway through which SFI exerts its anti-glioma effects. CONCLUSIONS The findings revealed that the SRC/PI3K/AKT signaling pathway may be involved in the mechanism through which SFI inhibits the proliferation and migration of glioma cells.
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Affiliation(s)
- Shuang Li
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Pathophysiology, School of Medicine, Shihezi University, Shihezi, 832000, China.
| | - Zhenglin Zhu
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Pathophysiology, School of Medicine, Shihezi University, Shihezi, 832000, China.
| | - Zhijian Chen
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Pathophysiology, School of Medicine, Shihezi University, Shihezi, 832000, China.
| | - Zhenli Guo
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Physiology, Shihezi University Medical College, Shihezi, 832000, China.
| | - Yan Wang
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China.
| | - Xinzhi Li
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Pathophysiology, School of Medicine, Shihezi University, Shihezi, 832000, China.
| | - Ketao Ma
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Physiology, Shihezi University Medical College, Shihezi, 832000, China.
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13
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Gao J, Xiang X, Yan Q, Ding Y. CDCS-TCM: A framework based on complex network theory to analyze the causality and dynamic correlation of substances in the metabolic process of traditional Chinese medicine. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118100. [PMID: 38537843 DOI: 10.1016/j.jep.2024.118100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/08/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese medicine, with the feature of synergistic effects of multi-component, multi-pathway and multi-target, plays an important role in the treatment of cancer, cardiovascular and cerebrovascular diseases, etc. However, chemical components in traditional Chinese medicine are complex and most of the pharmacological mechanisms remain unclear, especially the relationships of chemical components change during the metabolic process. AIM OF STUDY Our aim is to provide a method based on complex network theory to analyze the causality and dynamic correlation of substances in the metabolic process of traditional Chinese medicine. MATERIALS AND METHODS We proposed a framework named CDCS-TCM to analyze the causality and dynamic correlation between substances in the metabolic process of traditional Chinese medicine. Our method mainly consists two parts. The first part is to discover the local and global causality by the causality network. The second part is to investigate the dynamic correlations and identify the essential substance by dynamic substance correlation network. RESULTS We developed a CDCS-TCM method to analyze the causality and dynamic correlation of substances. Using the XiangDan Injection for ischemic stroke as an example, we have identified the important substances in the metabolic process including substance pairs with strong causality and the dynamic changes of the core effector substance clusters. CONCLUSION The proposed framework will be useful for exploring the correlations of active ingredients in traditional Chinese medicine more effectively and will provide a new perspective for the elucidation of drug action mechanisms and the new drug discovery.
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Affiliation(s)
- Jiaxuan Gao
- School of Science, Jiangnan University, Wuxi, Jiangsu, PR China.
| | - Xiaoyang Xiang
- School of Science, Jiangnan University, Wuxi, Jiangsu, PR China.
| | - Qunfang Yan
- School of Science, Jiangnan University, Wuxi, Jiangsu, PR China.
| | - Yanrui Ding
- School of Science, Jiangnan University, Wuxi, Jiangsu, PR China.
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14
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Yu S, Lai Z, Xue H, Zhu J, Yue G, Wang J, Jin LH. Inonotus obliquus aqueous extract inhibits intestinal inflammation and insulin metabolism defects in Drosophila. Toxicol Mech Methods 2024:1-15. [PMID: 38872277 DOI: 10.1080/15376516.2024.2368795] [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: 03/25/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
In biomedical research, the fruit fly (Drosophila melanogaster) is among the most effective and flexible model organisms. Through the use of the Drosophila model, molecular mechanisms of human diseases can be investigated and candidate pharmaceuticals can be screened. White rot fungus Inonotus obliquus is a member of the family Hymenochaetaceae. Due to its multifaceted pharmacological effects, this fungus has been the subject of scientific investigation. Nevertheless, the precise mechanisms by which Inonotus obliquus treats diseases remain unclear. In this study, we prepared an aqueous extract derived from Inonotus obliquus and demonstrated that it effectively prevented the negative impacts of inflammatory agents on flies, including overproliferation and overdifferentiation of intestinal progenitor cells and decreased survival rate. Furthermore, elevated reactive oxygen species levels and cell death were alleviated by Inonotus obliquus aqueous extract, suggesting that this extract inhibited intestinal inflammation. Additionally, Inonotus obliquus aqueous extract had an impact on the insulin pathway, as it alleviated growth defects in flies that were fed a high-sugar diet and in chico mutants. In addition, we determined the composition of Inonotus obliquus aqueous extract and conducted a network pharmacology analysis in order to identify prospective key compounds and targets. In brief, Inonotus obliquus aqueous extract exhibited considerable potential as a therapeutic intervention for human diseases. Our research has established a foundational framework that supports the potential clinical implementation of Inonotus obliquus.
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Affiliation(s)
- Shichao Yu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhixian Lai
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Hongmei Xue
- Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Jiahua Zhu
- Department of Basic Medical, Shenyang Medical College, Shenyang, China
| | - Guanhua Yue
- Department of Basic Medical, Shenyang Medical College, Shenyang, China
| | - Jiewei Wang
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Li Hua Jin
- College of Life Science, Northeast Forestry University, Harbin, China
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15
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Lembo V, Bottegoni G. Systematic Investigation of Dual-Target-Directed Ligands. J Med Chem 2024; 67:10374-10385. [PMID: 38843874 PMCID: PMC11215722 DOI: 10.1021/acs.jmedchem.4c00838] [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: 04/08/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Multitarget-directed ligands (MTDLs) are compounds rationally designed to affect multiple targets, aiming for a better therapeutic profile. For over 20 years, MTDLs have garnered increasing attention, the idea being that their full potential would have been achieved, thanks to unprecedented target combinations and advanced medicinal chemistry strategies. This study presents a literature mining effort resulting in a data set of dual-target-directed ligands (DTDLs), the fundamental example of MTDLs. We used this data set to evaluate the rationale behind target selection and the chemical novelty of DTDLs targeting specific protein combinations. Our analysis focused on DTDL targets in terms of biological function, disease association, structure, and chemogenomic traits. We also compared DTDLs with single-target compounds. We found that well-known target pathology associations often guide DTDL design, leveraging existing chemical scaffolds and binding pocket similarities. These findings highlight the current state of the field and suggest substantial untapped potential for rational polypharmacology.
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Affiliation(s)
- Vittorio Lembo
- Department
of Biomolecular Sciences, Università
degli Studi di Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, Italy
- Computational
and Chemical Biology, Istituto Italiano
di Tecnologia, Via Morego
30, 16163 Genova, Italy
| | - Giovanni Bottegoni
- Department
of Biomolecular Sciences, Università
degli Studi di Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, Italy
- Institute
of Clinical Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
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16
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Del Giudice G, Serra A, Pavel A, Torres Maia M, Saarimäki LA, Fratello M, Federico A, Alenius H, Fadeel B, Greco D. A Network Toxicology Approach for Mechanistic Modelling of Nanomaterial Hazard and Adverse Outcomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400389. [PMID: 38923832 DOI: 10.1002/advs.202400389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Indexed: 06/28/2024]
Abstract
Hazard assessment is the first step in evaluating the potential adverse effects of chemicals. Traditionally, toxicological assessment has focused on the exposure, overlooking the impact of the exposed system on the observed toxicity. However, systems toxicology emphasizes how system properties significantly contribute to the observed response. Hence, systems theory states that interactions store more information than individual elements, leading to the adoption of network based models to represent complex systems in many fields of life sciences. Here, they develop a network-based approach to characterize toxicological responses in the context of a biological system, inferring biological system specific networks. They directly link molecular alterations to the adverse outcome pathway (AOP) framework, establishing direct connections between omics data and toxicologically relevant phenotypic events. They apply this framework to a dataset including 31 engineered nanomaterials with different physicochemical properties in two different in vitro and one in vivo models and demonstrate how the biological system is the driving force of the observed response. This work highlights the potential of network-based methods to significantly improve their understanding of toxicological mechanisms from a systems biology perspective and provides relevant considerations and future data-driven approaches for the hazard assessment of nanomaterials and other advanced materials.
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Affiliation(s)
- Giusy Del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00790, Finland
| | - Angela Serra
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00790, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, 33100, Finland
| | - Alisa Pavel
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Marcella Torres Maia
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Laura Aliisa Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00790, Finland
| | - Michele Fratello
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Antonio Federico
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00790, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, 33100, Finland
| | - Harri Alenius
- Human Microbiome Research Program (HUMI), University of Helsinki, Helsinki, 00014, Finland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Bengt Fadeel
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00790, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, 33100, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, 00790, Finland
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17
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Xue L, Wang L, Xu Y, Shen Y, Shi Z, Li X, Feng H, Xie X, Xie L, Wang G, Liang Y. The regulation of GSH/GPX4-mediated lipid accumulation confirms that schisandra polysaccharides should be valued equally as lignans. JOURNAL OF ETHNOPHARMACOLOGY 2024; 333:118483. [PMID: 38914150 DOI: 10.1016/j.jep.2024.118483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/12/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Acetaminophen (APAP) induced liver injury (AILI) is a common cause of clinical hepatic damage and even acute liver failure. Our previous research has shown that Schisandra chinensis lignan extract (SLE) can exert a hepatoprotective effect by regulating lipid metabolism. Although polysaccharides from Schisandra chinensis (S. chinensis), like lignans, are important components of S. chinensis, their pharmacological activity and target effects on AILI have not yet been explored. AIM OF THE STUDY This study aims to quantitatively reveal the role of SCP in the pharmacological activity of S. chinensis, and further explore the pharmacological components, potential action targets and mechanisms of S. chinensis in treating AILI. MATERIALS AND METHODS The therapeutic effect of SCP on AILI was systematically determined via comparing the efficacy of SCP and SLE on in vitro and in vivo models. Network pharmacology, molecular docking and multi-omics techniques were then used to screen and verify the action targets of S. chinensis against AILI. RESULTS SCP intervention could significantly improve AILI, and the therapeutic effect was comparable to that of SLE. Notably, the combination of SCP and SLE did not produce mutual antagonistic effects. Subsequently, we found that both SCP and SLE could significantly reverse the down-regulation of GPX4 caused by the APAP modeling, and then further improving lipid metabolism abnormalities. CONCLUSIONS Hepatoprotective effects of SCP and SLE is most correlated with their regulation of GSH/GPX4-mediated lipid accumulation. This is the first exploration of the hepatoprotective effect and potential mechanism of SCP in treating AILI, which is crucial for fully utilizing S. chinensis and developing promising AILI therapeutic agents.
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Affiliation(s)
- Lijuan Xue
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Leyi Wang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Yexin Xu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Yun Shen
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Zechang Shi
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Xiaorun Li
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Haoyang Feng
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Xinrui Xie
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Lin Xie
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Guangji Wang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
| | - Yan Liang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, PR China.
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Yang J, Zhuang Q, Tang K, Liu X. Exploring the action mechanism of Gegensan in the treatment of alcoholic liver disease based on network pharmacology and bioinformatics. Medicine (Baltimore) 2024; 103:e38315. [PMID: 38905402 PMCID: PMC11191986 DOI: 10.1097/md.0000000000038315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/30/2024] [Indexed: 06/23/2024] Open
Abstract
Gegensan (GGS) has been reported for the treatment of alcoholic liver disease (ALD), but its therapeutic mechanism is still unclear. This paper aims to determine the therapeutic mechanism and targets of action of GGS on alcoholic liver disease utilizing network pharmacology and bioinformatics. The active ingredients in GGS were screened in the literature and databases, and common targets of ALD were then obtained from public databases to construct the network diagram of traditional Chinese medicine-active ingredient targets. Based on the common targets, Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to find target enrichment pathways, and the core targets were screened out by combining differential analysis and protein-protein interaction network analysis. Molecular docking was performed to verify the binding effect between the core targets and the corresponding active ingredients. ALD and GGS have 84 common targets, corresponding to 91 active ingredients. After subsequent differential analysis and protein-protein interaction network analysis, 10 core targets were identified. Gene Ontology and KEGG enrichment analyses showed that the main BPs corresponding to the common targets included the response to lipopolysaccharide, inflammatory response, etc. The KEGG pathways involved in the regulation of the common targets included the lipid-atherosclerosis pathway and the alcoholic liver disease pathway, etc. Further molecular docking showed that the core targets CYP1A1, CYP1A2, CXCL8, ADH1C, MMP1, SERPINE1, COL1A1, APOB, MMP1, and their corresponding 4 active ingredients, Naringenin, Kaempferol, Quercetin, and Stigmasterol, have a greater docking potential. The above results suggest that GGS can regulate lipid metabolism and inflammatory response in the ALD process, and alleviate the lipid accumulation and oxidative stress caused by ethanol. This study analyzed the core targets and mechanisms of action of GGS on ALD, which provides certain theoretical support for the further development of GGS in the treatment of ALD, and provides a reference for the subsequent research on the treatment of ALD.
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Affiliation(s)
- Jiakai Yang
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong Province 250303, China
| | - Qianqian Zhuang
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong Province 250303, China
| | - Ke Tang
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong Province 250303, China
| | - Xinli Liu
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong Province 250303, China
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Zhang Y, Huang W, Tian Q, Bai G, Wu W, Yin H, Hu L, Chen X. Network pharmacology and biochemical experiments reveal the antiapoptotic mechanism of huperzine A for treating diabetic retinopathy. Br J Ophthalmol 2024; 108:989-998. [PMID: 37339867 DOI: 10.1136/bjo-2023-323639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND/AIMS Diabetic retinopathy is the most common eye disease that causes blindness in the working population. Neurodegeneration is the early sign of diabetic retinopathy, but no drug has been approved for delaying or reversing retinal neurodegeneration. Huperzine A, a natural alkaloid isolated from Huperzia serrata, displays neuroprotective and antiapoptotic effects in treating neurodegenerative disorders. Our study aims to investigate the effect of huperzine A in preventing retinal neurodegeneration of diabetic retinopathy and its possible mechanism. METHODS Diabetic retinopathy model was induced by streptozotocin. H&E staining, optical coherence tomography, immunofluorescence staining and angiogenic factors were used to determine the degree of retinal pathological injury. The possible molecular mechanism was unrevealed by network pharmacology analysis and further validated by biochemical experiments. RESULTS In our study, we demonstrated that huperzine A has a protective effect on the diabetes retina in a diabetic rat model. Based on the network pharmacology analysis and biochemical studies, huperzine A may treat diabetic retinopathy via key target HSP27 and apoptosis-related pathways. Huperzine A may modulate the phosphorylation of HSP27 and activate the antiapoptotic signalling pathway. CONCLUSION Our findings revealed that huperzine A might be a potential therapeutic drug to prevent diabetic retinopathy. It is the first-time combining network pharmacology analysis with biochemical studies to explore the mechanism of huperzine A in preventing diabetic retinopathy.
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Affiliation(s)
- Ying Zhang
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Lab of Ophthalmology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wunan Huang
- Lanzhou University First Affiliated Hospital, Lanzhou University, Lanzhou, Gansu, China
| | - Qing Tian
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Lab of Ophthalmology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Guannan Bai
- National Clinical Research Center for Child Health, Zhejiang University School of Medicine Children's Hospital, Hangzhou, Zhejiang, China
| | - Wei Wu
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Lab of Ophthalmology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Houfa Yin
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Lab of Ophthalmology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lidan Hu
- National Clinical Research Center for Child Health, Zhejiang University School of Medicine Children's Hospital, Hangzhou, Zhejiang, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Lab of Ophthalmology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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20
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Ranjan A, Bess A, Alvin C, Mukhopadhyay S. MDF-DTA: A Multi-Dimensional Fusion Approach for Drug-Target Binding Affinity Prediction. J Chem Inf Model 2024. [PMID: 38888163 DOI: 10.1021/acs.jcim.4c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Drug-target affinity (DTA) prediction is an important task in the early stages of drug discovery. Traditional biological approaches are time-consuming, effort-consuming, and resource-consuming due to the large size of genomic and chemical spaces. Computational approaches using machine learning have emerged to narrow down the drug candidate search space. However, most of these prediction models focus on single feature encoding of drugs and targets, ignoring the importance of integrating different dimensions of these features. We propose a deep learning-based approach called Multi-Dimensional Fusion for Drug Target Affinity Prediction (MDF-DTA) incorporating different dimensional features. Our model fuses 1D, 2D, and 3D representations obtained from different pretrained models for both drugs and targets. We evaluated MDF-DTA on two standard benchmark data sets: DAVIS and KIBA. Experimental results show that MDF-DTA outperforms many state-of-the-art techniques in the DTA task across both data sets. Through ablation studies and performance evaluation metrics, we evaluate the importance of individual representations and the impact of each representation on MDF-DTA.
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Affiliation(s)
- Amit Ranjan
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Adam Bess
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Chris Alvin
- Department of Computer Science, Furman University, Greenville, South Carolina 29613, United States
| | - Supratik Mukhopadhyay
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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21
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Lazzara F, Conti F, Sasmal PK, Alikunju S, Rossi S, Drago F, Platania CBM, Bucolo C. Anti-angiogenic and antioxidant effects of axitinib in human retinal endothelial cells: implications in diabetic retinopathy. Front Pharmacol 2024; 15:1415846. [PMID: 38953109 PMCID: PMC11215076 DOI: 10.3389/fphar.2024.1415846] [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: 04/11/2024] [Accepted: 05/17/2024] [Indexed: 07/03/2024] Open
Abstract
Diabetic retinopathy is a secondary microvascular complication of diabetes mellitus. This disease progresses from two stages, non-proliferative and proliferative diabetic retinopathy, the latter characterized by retinal abnormal angiogenesis. Pharmacological management of retinal angiogenesis employs expensive and invasive intravitreal injections of biologic drugs (anti-vascular endothelial growth factor agents). To search small molecules able to act as anti-angiogenic agents, we focused our study on axitinib, which is a tyrosine kinase inhibitor and represents the second line treatment for renal cell carcinoma. Axitinib is an inhibitor of vascular endothelial growth factor receptors, and among the others tyrosine kinase inhibitors (sunitinib and sorafenib) is the most selective towards vascular endothelial growth factor receptors 1 and 2. Besides the well-known anti-angiogenic and immune-modulatory functions, we hereby explored the polypharmacological profile of axitinib, through a bioinformatic/molecular modeling approach and in vitro models of diabetic retinopathy. We showed the anti-angiogenic activity of axitinib in two different in vitro models of diabetic retinopathy, by challenging retinal endothelial cells with high glucose concentration (fluctuating and non-fluctuating). We found that axitinib, along with inhibition of vascular endothelial growth factor receptors 1 (1.82 ± 0.10; 0.54 ± 0.13, phosphorylated protein levels in fluctuating high glucose vs . axitinib 1 µM, respectively) and vascular endothelial growth factor receptors 2 (2.38 ± 0.21; 0.98 ± 0.20, phosphorylated protein levels in fluctuating high glucose vs . axitinib 1 µM, respectively), was able to significantly reduce (p < 0.05) the expression of Nrf2 (1.43 ± 0.04; 0.85 ± 0.01, protein levels in fluctuating high glucose vs . axitinib 1 µM, respectively) in retinal endothelial cells exposed to high glucose, through predicted Keap1 interaction and activation of melanocortin receptor 1. Furthermore, axitinib treatment significantly (p < 0.05) decreased reactive oxygen species production (0.90 ± 0.10; 0.44 ± 0.06, fluorescence units in high glucose vs . axitinib 1 µM, respectively) and inhibited ERK pathway (1.64 ± 0.09; 0.73 ± 0.06, phosphorylated protein levels in fluctuating high glucose vs . axitinib 1 µM, respectively) in HRECs exposed to high glucose. The obtained results about the emerging polypharmacological profile support the hypothesis that axitinib could be a valid candidate to handle diabetic retinopathy, with ancillary mechanisms of action.
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Affiliation(s)
- Francesca Lazzara
- Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
| | - Federica Conti
- Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
| | | | | | - Settimio Rossi
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
- Center for Research in Ocular Pharmacology-CERFO, University of Catania, Catania, Italy
| | - Chiara Bianca Maria Platania
- Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
- Center for Research in Ocular Pharmacology-CERFO, University of Catania, Catania, Italy
| | - Claudio Bucolo
- Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
- Center for Research in Ocular Pharmacology-CERFO, University of Catania, Catania, Italy
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22
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Tan M, Wang J, Chen Z, Xie X. Exploring global research trends in Chinese medicine for atherosclerosis: a bibliometric study 2012-2023. Front Cardiovasc Med 2024; 11:1400130. [PMID: 38952541 PMCID: PMC11216286 DOI: 10.3389/fcvm.2024.1400130] [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: 03/13/2024] [Accepted: 05/15/2024] [Indexed: 07/03/2024] Open
Abstract
Background While Traditional Chinese Medicine (TCM) boasts an extensive historical lineage and abundant clinical expertise in addressing atherosclerosis, this field is yet to be penetrated adequately by bibliometric studies. This study is envisaged to evaluate the contemporary scenario of TCM in conjunction with atherosclerosis over the preceding decade while also identifying forthcoming research trends and emerging topics via the lens of bibliometric analysis. Methods Literature pertaining to TCM and atherosclerosis, circulated between January 1, 2012 and November 14, 2023, was garnered for the purpose of this research. The examination embraced annual publications, primary countries/regions, engaged institutions and authors, scholarly journals, references, and keywords, utilizing analytical tools like Bibliometrix, CiteSpace, ScimagoGraphica, and VOSviewer present in the R package. Result This field boasts a total of 1,623 scholarly articles, the majority of which have been contributed by China in this field, with significant contributions stemming from the China Academy of Traditional Chinese Medicine and the Beijing University of Traditional Chinese Medicine. Moreover, this field has received financial support from both the National Natural Science Foundation of China and the National Key Basic Research Development Program. Wang Yong tops the list in terms of publication count, while Xu Hao's articles take the lead for the total number of citations, positioning them at the core of the authors' collaborative network. The Journal of Ethnopharmacology leads with the most publications and boasts the greatest total number of citations. Principal research foci within the intersection of Chinese Medicine and Atherosclerosis encompass disease characteristics and pathogenic mechanisms, theoretical underpinnings and syndrome-specific treatments in Chinese medicine, potentialities of herbal interventions, and modulation exerted by Chinese medicines on gut microbiota. Conclusion This analysis offers a sweeping survey of the contemporary condition, principal foci, and progressive trends in worldwide research related to Traditional Chinese Medicine (TCM) and atherosclerosis. It further delves into an in-depth dissection of prominent countries, research institutions, and scholars that have made noteworthy strides in this discipline. Additionally, the report analyzes the most cited articles, research developments, and hotspots in the field, providing a reference for future research directions for clinical researchers and practitioners.
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Affiliation(s)
- Moye Tan
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Jiuyuan Wang
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Zhengxin Chen
- College of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuejiao Xie
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
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Pocasap P, Prawan A, Kongpetch S, Senggunprai L. Network pharmacology- and cell-based assessments identify the FAK/Src pathway as a molecular target for the antimetastatic effect of momordin Ic against cholangiocarcinoma. Heliyon 2024; 10:e32352. [PMID: 38961933 PMCID: PMC11219314 DOI: 10.1016/j.heliyon.2024.e32352] [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: 09/08/2023] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024] Open
Abstract
Previous studies have indicated the efficacy of momordin Ic (MIc), a plant-derived triterpenoid, against several types of cancers, implying its potential for further development. However, comprehensive insights into the molecular mechanisms and targets of MIc in cholangiocarcinoma (CCA) are lacking. This study aimed to investigate the actions of MIc against CCA at the molecular level. Network pharmacology analysis was first employed to predict the mechanisms and targets of MIc. The results unveiled the potential involvement of MIc in apoptosis and cell migration, pinpointing Src and FAK as key targets. Subsequently, cell-based assays, in accordance with FAK/Src-associated metastasis, were conducted, demonstrating the ability of MIc to attenuate the metastatic behaviours of KKU-452 cells. The in vitro results further indicated the capability of MIc to suppress the epithelial-mesenchymal transition (EMT) process, notably by downregulating EMT regulators, including N-cadherin, vimentin, ZEB2 and FOXC1/2 expression. Furthermore, MIc suppressed the activation of the FAK/Src signalling pathway, influencing critical downstream factors such as MMP-9, VEGF, ICAM-1, and c-Myc. Molecular docking simulations also suggested that MIc could interact with FAK and Src domains and restrain kinases from being activated by hindering ATP binding. In conclusion, this study employs a comprehensive approach encompassing network pharmacology analysis, in vitro assays, and molecular docking to unveil the mechanisms and targets of MIc in CCA. MIc mitigates metastatic behaviours and suppresses key pathways, offering a promising avenue for future therapeutic strategies against this aggressive cancer.
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Affiliation(s)
- Piman Pocasap
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Auemduan Prawan
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sarinya Kongpetch
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Laddawan Senggunprai
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, 40002, Thailand
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24
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Xie Y, Gong S, Wang L, Yang Z, Yang C, Li G, Zha H, Lv S, Xiao B, Chen X, Di Z, He Q, Wang J, Weng Q. Unraveling the treatment effects of huanglian jiedu decoction on drug-induced liver injury based on network pharmacology, molecular docking and experimental validation. BMC Complement Med Ther 2024; 24:219. [PMID: 38849824 PMCID: PMC11157734 DOI: 10.1186/s12906-024-04517-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
Huanglian Jiedu Decoction (HJD) is a well-known Traditional Chinese Medicine formula that has been used for liver protection in thousands of years. However, the therapeutic effects and mechanisms of HJD in treating drug-induced liver injury (DILI) remain unknown. In this study, a total of 26 genes related to both HJD and DILI were identified, which are corresponding to a total of 41 potential active compounds in HJD. KEGG analysis revealed that Tryptophan metabolism pathway is particularly important. The overlapped genes from KEGG and GO analysis indicated the significance of CYP1A1, CYP1A2, and CYP1B1. Experimental results confirmed that HJD has a protective effect on DILI through Tryptophan metabolism pathway. In addition, the active ingredients Corymbosin, and Moslosooflavone were found to have relative strong intensity in UPLC-Q-TOF-MS/MS analysis, showing interactions with CYP1A1, CYP1A2, and CYP1B1 through molecule docking. These findings could provide insights into the treatment effects of HJD on DILI.
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Affiliation(s)
- Yaochen Xie
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Shuchen Gong
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
- Taizhou Institute of Zhejiang University, Taizhou, 318000, China
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lingkun Wang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Zhaoxu Yang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Chen Yang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Guilin Li
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Huiyan Zha
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Shuying Lv
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Boneng Xiao
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoyu Chen
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Zhenning Di
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qiaojun He
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
- ZJU-Xinchang Joint Innovation Center (TianMu Laboratory), Gaochuang Hi-Tech Park, Xinchang, 312500, Zhejiang, China
- Department of Cardiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jincheng Wang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China.
- Taizhou Institute of Zhejiang University, Taizhou, 318000, China.
- Beijing Life Science Academy, Beijing, 102200, China.
| | - Qinjie Weng
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China.
- Taizhou Institute of Zhejiang University, Taizhou, 318000, China.
- ZJU-Xinchang Joint Innovation Center (TianMu Laboratory), Gaochuang Hi-Tech Park, Xinchang, 312500, Zhejiang, China.
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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Wang S, Lee HC, Lee S. Predicting herb-disease associations using network-based measures in human protein interactome. BMC Complement Med Ther 2024; 24:218. [PMID: 38845010 PMCID: PMC11157705 DOI: 10.1186/s12906-024-04503-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Natural herbs are frequently used to treat diseases or to relieve symptoms in many countries. Moreover, as their safety has been proven for a long time, they are considered as main sources of new drug development. However, in many cases, the herbs are still prescribed relying on ancient records and/or traditional practices without scientific evidences. More importantly, the medicinal efficacy of the herbs has to be evaluated in the perspective of MCMT (multi-compound multi-target) effects, but most efforts focus on identifying and analyzing a single compound experimentally. To overcome these hurdles, computational approaches which are based on the scientific evidences and are able to handle the MCMT effects are needed to predict the herb-disease associations. RESULTS In this study, we proposed a network-based in silico method to predict the herb-disease associations. To this end, we devised a new network-based measure, WACP (weighted average closest path length), which not only quantifies proximity between herb-related genes and disease-related genes but also considers compound compositions of each herb. As a result, we confirmed that our method successfully predicts the herb-disease associations in the human protein interactome (AUROC = 0.777). In addition, we observed that our method is superior than the other simple network-based proximity measures (e.g. average shortest and closest path length). Additionally, we analyzed the associations between Brassica oleracea var. italica and its known associated diseases more specifically as case studies. Finally, based on the prediction results of the WACP, we suggested novel herb-disease pairs which are expected to have potential relations and their literature evidences. CONCLUSIONS This method could be a promising solution to modernize the use of the natural herbs by providing the scientific evidences about the molecular associations between the herb-related genes targeted by multiple compounds and the disease-related genes in the human protein interactome.
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Affiliation(s)
- Seunghyun Wang
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Chang Lee
- Division of Environmental Science and Ecological Engineering, Korea University, 145 Anam-ro, Seungbuk-gu, Seoul, 02841, Republic of Korea
| | - Sunjae Lee
- School of Life Sciences, GIST, 123 Cheomdan-gwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea.
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Garaci E, Paci M, Matteucci C, Costantini C, Puccetti P, Romani L. Phenotypic drug discovery: a case for thymosin alpha-1. Front Med (Lausanne) 2024; 11:1388959. [PMID: 38903817 PMCID: PMC11187271 DOI: 10.3389/fmed.2024.1388959] [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: 02/20/2024] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
Phenotypic drug discovery (PDD) involves screening compounds for their effects on cells, tissues, or whole organisms without necessarily understanding the underlying molecular targets. PDD differs from target-based strategies as it does not require knowledge of a specific drug target or its role in the disease. This approach can lead to the discovery of drugs with unexpected therapeutic effects or applications and allows for the identification of drugs based on their functional effects, rather than through a predefined target-based approach. Ultimately, disease definitions are mostly symptom-based rather than mechanism-based, and the therapeutics should be likewise. In recent years, there has been a renewed interest in PDD due to its potential to address the complexity of human diseases, including the holistic picture of multiple metabolites engaging with multiple targets constituting the central hub of the metabolic host-microbe interactions. Although PDD presents challenges such as hit validation and target deconvolution, significant achievements have been reached in the era of big data. This article explores the experiences of researchers testing the effect of a thymic peptide hormone, thymosin alpha-1, in preclinical and clinical settings and discuss how its therapeutic utility in the precision medicine era can be accommodated within the PDD framework.
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Affiliation(s)
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Paolo Puccetti
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luigina Romani
- San Raffaele Sulmona, L’Aquila, Italy
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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27
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Franco LS, de Jesus BDSM, Pinheiro PDSM, Fraga CAM. Remapping the Chemical Space and the Pharmacological Space of Drugs: What Can We Expect from the Road Ahead? Pharmaceuticals (Basel) 2024; 17:742. [PMID: 38931408 PMCID: PMC11207054 DOI: 10.3390/ph17060742] [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: 03/31/2024] [Revised: 05/26/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
This work examines the current landscape of drug discovery and development, with a particular focus on the chemical and pharmacological spaces. It emphasizes the importance of understanding these spaces to anticipate future trends in drug discovery. The use of cheminformatics and data analysis enabled in silico exploration of these spaces, allowing a perspective of drugs, approved drugs after 2020, and clinical candidates, which were extracted from the newly released ChEMBL34 (March 2024). This perspective on chemical and pharmacological spaces enables the identification of trends and areas to be occupied, thereby creating opportunities for more effective and targeted drug discovery and development strategies in the future.
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Affiliation(s)
- Lucas Silva Franco
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil; (L.S.F.); (B.d.S.M.d.J.)
- Instituto Nacional de Ciência e Tecnologia de Fármacos e Medicamentos (INCT-INOFAR), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal (PPGFQM), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Bárbara da Silva Mascarenhas de Jesus
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil; (L.S.F.); (B.d.S.M.d.J.)
- Programa de Pós-Graduação em Farmacologia e Química Medicinal (PPGFQM), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil; (L.S.F.); (B.d.S.M.d.J.)
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil; (L.S.F.); (B.d.S.M.d.J.)
- Instituto Nacional de Ciência e Tecnologia de Fármacos e Medicamentos (INCT-INOFAR), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal (PPGFQM), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
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Alshehri FF, Alshehri ZS. Network pharmacology-based screening of active constituents of Avicennia marina and their clinical biochemistry related mechanism against breast cancer. J Biomol Struct Dyn 2024; 42:4506-4521. [PMID: 37306420 DOI: 10.1080/07391102.2023.2220801] [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: 12/08/2022] [Accepted: 05/29/2023] [Indexed: 06/13/2023]
Abstract
Breast cancer is the second major cause of cancer death in women globally. Avicennia marina is a medicinal plant that belongs to the family Acanthaceae and is known as grey or white mangrove. It has antioxidant, antiviral, anticancer, anti-inflammatory, and antibacterial activity in the treatment of various diseases including cancer. The goal of the study is to use a network pharmacology method to identify the potential phenomena of bioactive compounds of A. marina in the treatment of breast cancer and explore clinical biochemistry related aspects. A total of 74 active compounds of A. marina were retrieved from various databases as well as a literature review and collectively 429 targets of these compounds were identified by STITCH and Swiss Target Prediction databases. Breast cancer related 15606 potential targets were retrieved from the GeneCards database. A Venn diagram was drawn to find common key targets. To check the biological functions, the GO enrichment and KEGG pathways analysis of 171 key targets were performed through the DAVID database. To understand the interactions among key targets, Protein-protein interaction (PPI) studies were completed using the STRING database, and the Protein-Protein Interaction (PPI) network, as well as the compound-target-pathway network, was constructed using Cytoscape 3.9.0. Finally, molecular docking analysis of 5 hub genes named tumor protein 53 (TP53), catenin beta 1 (CTNNB1), interleukin 6 (IL6), tumor necrosis factor (TNF), and RAC-alpha serine/threonine protein kinases 1 (AKT1) with the active constituent of A. marina against breast cancer were performed. Additionally, a molecular docking study demonstrates that active drugs have a higher affinity for the target that may be used to decrease breast cancer. The molecular dynamic simulation analysis predicted the very stable behavior of docked complexes with no global structure deviations seen. The MMGBSA further supported strong intermolecular interactions with net energy values as; AKT1_Betulinic_acid (-20.97 kcal/mol), AKT1_Stigmasterol (-44.56 kcal/mol), TNF_Betulinic_acid (-28.68 kcal/mol) and TNF_Stigmastero (-29.47 kcal/mol).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faez Falah Alshehri
- College of Applied Medical Sciences, Shaqra University, Aldawadmi, Saudi Arabia
| | - Zafer Saad Alshehri
- College of Applied Medical Sciences, Shaqra University, Aldawadmi, Saudi Arabia
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Shi Y, Yan D, Nan C, Sun Z, Zhuo Y, Huo H, Jin Q, Yan H, Zhao Z. Salvianolic acid A inhibits ferroptosis and protects against intracerebral hemorrhage. Sci Rep 2024; 14:12427. [PMID: 38816543 PMCID: PMC11140002 DOI: 10.1038/s41598-024-63277-4] [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: 12/24/2023] [Accepted: 05/27/2024] [Indexed: 06/01/2024] Open
Abstract
Intracerebral hemorrhage (ICH) is a common cerebral vascular disease with high incidence, disability, and mortality. Ferroptosis is a regulated type of iron-dependent, non-apoptotic programmed cell death. There is increasing evidence that ferroptosis may lead to neuronal damage mediated by hemorrhagic stroke mediated neuronal damage. Salvianolic acid A (SAA) is a natural bioactive polyphenol compound extracted from salvia miltiorrhiza, which has anti-inflammatory, antioxidant, and antifibrosis activities. SAA is reported to be an iron chelator that inhibits lipid peroxidation and provides neuroprotective effects. However, whether SAA improves neuronal ferroptosis mediated by hemorrhagic stroke remains unclear. The study aims to evaluate the therapeutic effect of SAA on Ferroptosis mediated by Intracerebral hemorrhage and explore its potential mechanisms. We constructed in vivo and in vitro models of intracerebral hemorrhage in rats. Multiple methods were used to analyze the inhibitory effect of SAA on ferroptosis in both in vivo and in vitro models of intracerebral hemorrhage in rats. Then, network pharmacology is used to identify potential targets and mechanisms for SAA treatment of ICH. The SAA target ICH network combines SAA and ICH targets with protein-protein interactions (PPIs). Find the specific mechanism of SAA acting on ferroptosis through molecular docking and functional enrichment analysis. In rats, SAA (10 mg/kg in vivo and 50 μM in vitro, p < 0.05) alleviated dyskinesia and brain injury in the ICH model by inhibiting ferroptosis (p < 0.05). The molecular docking results and functional enrichment analyses suggested that AKT (V-akt murine thymoma viral oncogene homolog) could mediate the effect of SAA. NRF2 (Nuclear factor erythroid 2-related factor 2) was a potential target of SAA. Our further experiments showed that salvianolic acid A enhanced the Akt /GSK-3β/Nrf2 signaling pathway activation in vivo and in vitro. At the same time, SAA significantly expanded the expression of GPX4, XCT proteins, and the nuclear expression of Nrf2, while the AKT inhibitor SH-6 and the Nrf2 inhibitor ML385 could reduce them to some extent. Therefore, SAA effectively ameliorated ICH-mediated neuronal ferroptosis. Meanwhile, one of the critical mechanisms of SAA inhibiting ferroptosis was activating the Akt/GSK-3β/Nrf2 signaling pathway.
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Affiliation(s)
- Yunpeng Shi
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Dongdong Yan
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Chengrui Nan
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Zhimin Sun
- Department of Neurosurgery, Third Hospital of Shijiazhuang, Shijiazhuang, 050000, Hebei, China
| | - Yayu Zhuo
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Haoran Huo
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Qianxu Jin
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Hongshan Yan
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Zongmao Zhao
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China.
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China.
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Jangwan NS, Khan M, Das R, Altwaijry N, Sultan AM, Khan R, Saleem S, Singh MF. From petals to healing: consolidated network pharmacology and molecular docking investigations of the mechanisms underpinning Rhododendron arboreum flower's anti-NAFLD effects. Front Pharmacol 2024; 15:1366279. [PMID: 38863975 PMCID: PMC11165132 DOI: 10.3389/fphar.2024.1366279] [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: 01/06/2024] [Accepted: 04/25/2024] [Indexed: 06/13/2024] Open
Abstract
Rhododendron arboreum: Sm., also known as Burans is traditionally used as an anti-inflammatory, anti-diabetic, hepatoprotective, adaptogenic, and anti-oxidative agent. It has been used since ancient times in Indian traditional medicine for various liver disorders. However, the exact mechanism behind its activity against NAFLD is not known. The aim of the present study is to investigate the molecular mechanism of Rhododendron arboreum flower (RAF) in the treatment of NAFLD using network pharmacology and molecular docking methods. Bioactives were also predicted for their drug-likeness score, probable side effects and ADMET profile. Protein-protein interaction (PPI) data was obtained using the STRING platform. For the visualisation of GO analysis, a bioinformatics server was employed. Through molecular docking, the binding affinity between potential targets and active compounds were assessed. A total of five active compounds of RAF and 30 target proteins were selected. The targets with higher degrees were identified through the PPI network. GO analysis indicated that the NAFLD treatment with RAF primarily entails a response to the fatty acid biosynthetic process, lipid metabolic process, regulation of cell death, regulation of stress response, and cellular response to a chemical stimulus. Molecular docking and molecular dynamic simulation exhibited that rutin has best binding affinity among active compounds and selected targets as indicated by the binding energy, RMSD, and RMSF data. The findings comprehensively elucidated toxicity data, potential targets of bioactives and molecular mechanisms of RAF against NAFLD, providing a promising novel strategy for future research on NAFLD treatment.
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Affiliation(s)
- Nitish Singh Jangwan
- Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Mausin Khan
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Dehradun, Uttarakhand, India
| | - Richa Das
- Department of Biotechnology, Parul Institute of Applied Science, Parul University, Vadodara, Gujarat, India
| | - Najla Altwaijry
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ahlam Mansour Sultan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ruqaiyah Khan
- Department of Basic Health Sciences, Deanship of Preparatory Year for the Health Colleges, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health, College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Mamta F. Singh
- College of Pharmacy, COER University, Roorkee, Uttarakhand, India
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Lei H, Zhang H, Yu Y, Yu X, Guo M, Yuan Y. Exploring Potential Targets and Pathways of Toxicity Attenuation Through Serum Pharmacochemistry and Network Pharmacology in the Processing of Aconiti Lateralis Radix Praeparata. Biomed Chromatogr 2024:e5890. [PMID: 38800964 DOI: 10.1002/bmc.5890] [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: 01/13/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Abstract
Aconiti Lateralis Radix Praeparata (Fuzi, FZ) is a frequently utilized traditional Chinese medicine (TCM) in clinical settings. However, its toxic and side effects, particularly cardiac injury, are apparent, necessitating processing before use. To investigate the mechanism of toxicity induced by absorbed components and the mitigating effect of processed FZ, we established a comprehensive method combining serum pharmacochemistry and a network pharmacology approach. In total, 31 chemical components were identified in the plasma, with a general decrease in response intensity observed for these components in processed FZ. Subsequently, four components were selected for network pharmacology analysis. This analysis revealed 150 drug action targets and identified 1162 cardiac toxicity targets. Through intersection analysis, 41 key targets related to cardiac toxicity were identified, along with 9 significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The most critical targets identified were AKT1, MTOR, and PARP1. The key biological pathways implicated were adrenergic signaling in cardiomyocytes, proteoglycans in cancer, and the calcium signaling pathway. Significant differences were observed in histological staining and biochemical indicators in the cardiac tissue of rats treated with FZ, indicating that processing could indeed reduce its cardiotoxicity. Indeed, this article presents a valuable strategy for elucidating the toxification mechanism of toxic TCM.
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Affiliation(s)
- Huibo Lei
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongli Zhang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Yating Yu
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyan Yu
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meili Guo
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongfang Yuan
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Luo G, Gao M, Lin Q. Integration of bioinformatics analysis, molecular docking and animal experiments to study the therapeutic mechanisms of berberine against allergic rhinitis. Sci Rep 2024; 14:11999. [PMID: 38796469 PMCID: PMC11127925 DOI: 10.1038/s41598-024-60871-4] [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: 10/21/2023] [Accepted: 04/29/2024] [Indexed: 05/28/2024] Open
Abstract
Allergic rhinitis is a prevalent inflammatory condition that impacts individuals of all age groups. Despite reports indicating the potential of berberine in alleviating allergic rhinitis symptoms, the specific molecular mechanisms and therapeutic targets of berberine remain unclear. This research aims to explore the pharmacological mechanism of berberine in the treatment of allergic rhinitis through bioinformatic analyses and experimental validation. The research utilized public databases to identify potential targets of berberine. Furthermore, differentially expressed genes (DEGs) related to allergic rhinitis were pinpointed from the GSE52804 dataset. Through bioinformatics techniques, the primary targets were discovered and key KEGG and GO-BP pathways were established. To confirm the therapeutic mechanisms of berberine on allergic rhinitis, an OVA-induced allergic rhinitis model was developed using guinea pigs. We identified 32 key genes responsible for the effectiveness of berberine in treating allergic rhinitis. In addition, five central genes (Alb, Il6, Tlr4, Ptas2, and Il1b) were pinpointed. Further examination using KEGG and GO-BP pathways revealed that the main targets were primarily involved in pathways such as NF-kappa B, IL-17, TNF, and inflammatory response. Molecular docking analysis demonstrated that berberine exhibited strong affinity towards these five key targets. Furthermore, the expression levels of IL-6, TLR4, PTGS2, and IL-1β were significantly upregulated in the model group but downregulated following berberine treatment. This research has revealed the mechanism through which berberine combats allergic rhinitis and has identified its potential to regulate pathways linked to inflammation. These discoveries provide valuable insights for the development of novel medications for the treatment of allergic rhinitis.
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Affiliation(s)
- Gaoqing Luo
- Department of Otolaryngology, Fujian Provincial Governmental Hospital, Fuzhou, 350003, China.
| | - Ming Gao
- Department of Otolaryngology, People's Hospital of Changji Hui Autonomous Prefecture, Changji, 831100, China
| | - Qinghua Lin
- Department of Otolaryngology, Fujian Provincial Governmental Hospital, Fuzhou, 350003, China
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Mihaylova S, Tsvetkova A, Georgieva E, Vankova D. Bioactive Phyto-Compounds with Antimicrobial Effects and AI: Results of a Desk Research Study. Microorganisms 2024; 12:1055. [PMID: 38930437 PMCID: PMC11205534 DOI: 10.3390/microorganisms12061055] [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: 04/23/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Resistance of microorganisms to antibiotics represents a formidable global challenge, manifesting in intricate public health ramifications including escalated mortality rates and augmented healthcare costs. The current efforts to manage antimicrobial resistance (AMR) are limited mainly to the standard therapeutic approaches. The aim of this study is to present and analyze the role of artificial intelligence (AI) in the search for new phyto-compounds and novel interactions with antimicrobial effects. The ambition of the current research study is to support researchers by providing summarized information and ideas for future research in the battle with AMR. Inevitably, the AI role in healthcare is growing exponentially. The reviewed AI models reveal new data on essential oils (EOs) as potential therapeutic agents. In terms of antibacterial activity, EOs show activity against MDR bacteria, reduce resistance by sensitizing bacteria to the action of antibiotics, and improve therapeutic efficiency when combined with antibiotics. AI models can also serve for the detailed study of other therapeutic applications of EOs such as respiratory diseases, immune diseases, neurodegenerative diseases, and oncological diseases. The last 5 years have seen an increasing application of AI in the search for potential plant sources to control AMR. For the time being, the application of machine-learning (ML) models is greater in the studies of EOs. Future attention of research teams may also be directed toward a more efficient search for plant antimicrobial peptides (PAMPs). Of course, investments in this direction are a necessary preface, but the excitement of new possibilities should not override the role of human intelligence in directing research processes. In this report, tradition meets innovation to address the "silent pandemic" of AMR.
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Affiliation(s)
- Silviya Mihaylova
- Medical College, Medical University of Varna, 9002 Varna, Bulgaria; (A.T.); (E.G.)
| | - Antoaneta Tsvetkova
- Medical College, Medical University of Varna, 9002 Varna, Bulgaria; (A.T.); (E.G.)
| | - Emiliya Georgieva
- Medical College, Medical University of Varna, 9002 Varna, Bulgaria; (A.T.); (E.G.)
| | - Desislava Vankova
- Department of Social Medicine and Health Care Organisation, Faculty of Public Health, Medical University of Varna, 9002 Varna, Bulgaria;
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Shi H, Duan X, Dong J, Tao Y, Lei Y. RNA-seq combined network pharmacology reveals that Fu-Gan-Wan (FGW) inhibits liver fibrosis via NF-κB/CCL2/CCR2 and lipid peroxidation via Nrf2/HMOX1 signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 326:117963. [PMID: 38387680 DOI: 10.1016/j.jep.2024.117963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Liver fibrosis is a serious complication of liver disease characterized by excessive collagen deposition, without effective therapeutic agents in the clinic. Fu-Gan-Wan (FGW) is an empirical formula used for the clinical treatment of hepatitis and cirrhosis. It has been shown to reverse experimental liver fibrosis. However, its corresponding mechanisms remain unclear. AIM OF THE REVIEW This study aimed to elucidate the key pathways and target genes of FGW in attenuating liver fibrosis. MATERIALS AND METHODS The therapeutic effects of different doses of FGW on liver fibrosis were investigated using a 2 mL/kg 15% CCl4-induced mouse model. Then, RNA-seq combined with network pharmacology was used to analyze the key biological processes and signaling pathways underlying the anti-liver fibrosis exertion of FGW. These findings were validated in a TGF-β1-induced model of activation and proliferation of mouse hepatic stellate cell line JS-1. Finally, the key signaling pathways and molecular targets were validated using animal tissues, and the effect of FGW on tissue lipid peroxidation was additionally observed. RESULTS We found that 19.5 g/kg FGW significantly down-regulated CCl4-induced elevation of hepatic ALT and AST, decreased collagen deposition, and inhibited the expression of pro-fibrotic factors α-SMA, COL1α1, CTGF, TIMP-1, as well as pro-inflammatory factor TGF-β1. Additionally, FGW at doses of 62.5, 125, and 250 μg/mL dose-dependently blocked JS-1 proliferation, migration, and activation. Furthermore, RNA-seq identified the NF-κB signaling pathway as a key target molecular pathway for FGW against liver fibrosis, and network pharmacology combined with RNA-seq focused on 11 key genes. Significant changes were identified in CCL2 and HMOX1 by tissue RT-PCR, Western blot, and immunohistochemistry. We further demonstrated that FGW significantly attenuated CCl4-induced increases in p-p65, CCL2, CCR2, and HMOX1, while significantly elevating Nrf2. Finally, FGW significantly suppressed the accumulation of lipid peroxidation products MDA and 4-HNE and reconfigured the oxidation-reduction balance, including promoting the increase of antioxidants GPx, GSH, and SOD, and the decrease of peroxidation products ROS and GSSG. CONCLUSIONS This study demonstrated that FGW exhibits potential in mitigating CCl4-induced hepatic fibrosis, lipid peroxidation, and iron metabolism disorders in mice. This effect may be mediated through the NF-κB/CCL2/CCR2 and Nrf2/HMOX1 pathways.
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Affiliation(s)
- Hanlin Shi
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China; Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Xiaohong Duan
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China; Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Yanyan Tao
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Yang Lei
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China; Institutes of Integrative Medicine, Fudan University, Shanghai, China.
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Zheng H, Zeng J, Bi P, Xu W, Yang Y, Chen H, Jin D. Integrated network analysis and experimental verification of the mechanisms employed by Compound Jixuecao Decoction to improve endoplasmic reticulum stress and apoptosis in chronic renal failure. JOURNAL OF ETHNOPHARMACOLOGY 2024; 326:117959. [PMID: 38423413 DOI: 10.1016/j.jep.2024.117959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/09/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Compound Jixuecao Decoction (CJD) is a traditional Chinese herbal medicine prescribed in China to treat chronic renal failure (CRF). Previous studies have shown that CJD affects cell apoptosis and proliferation. However, the mechanism of its renal protective action has not been characterized. AIM OF THE STUDY To explore the mechanism(s) underlying the effect of CJD on endoplasmic reticulum stress (ERS) and apoptosis in the treatment of CRF using network pharmacology, molecular docking, molecular dynamics simulations, and in vivo studies. MATERIALS AND METHODS The compounds comprising CJD were extracted from the Traditional Chinese Medicine Systems Pharmacology Database. A Swiss target prediction database and similarity integration approach were employed to identify potential targets of these components. The GeneCards and DisGeNET databases were used to identify targets associated with CRF, apoptosis, and ERS. The STRING database was employed to analyze the protein-protein interactions (PPIs) associated with drug-disease crossover. A chemical composition-shared target network was established, and critical pathways were identified through gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The Protein Data Bank database was used to search key proteins, while molecular docking and dynamics simulations were performed between the top four CJD active ingredients and proteins involved in apoptosis and ERS in CRF. Subsequent in vivo studies using a 5/6 nephrectomy rat model of CRF were performed to verify the findings. RESULTS The 80 compounds identified in CJD yielded 875 target genes, of which 216 were potentially related to CRF. PPI network analysis revealed key targets via topology filtering. Enrichment analysis, molecular docking, and molecular dynamics simulation results suggested that CJD primarily targets mitofusin-2 (MFN2), B-cell lymphoma-2 (BCL2), BAX, protein kinase RNA-like ER kinase (PERK), and C/EBP homologous protein (CHOP) during CRF treatment. In vivo, CJD significantly increased the abundance of MFN2, BCL2, and significantly reduced the abundance of BAX, PERK, CHOP proteins in kidney tissues, indicating that CJD could improve apoptosis and ERS in CRF rats. CONCLUSIONS This study provides evidence that CJD effectively delays CFR through modulation of the MFN2 and PERK-eIF2α-ATF4-CHOP signaling pathways.
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Affiliation(s)
- Huihong Zheng
- Department of Nephrology, Hangzhou Hospital of Traditional Chinese Medicine, Affiliated to Zhejiang University of Traditional Chinese Medicine, Hangzhou, 310007, China
| | - Jiali Zeng
- Department of Nephrology, Hangzhou Hospital of Traditional Chinese Medicine, Affiliated to Zhejiang University of Traditional Chinese Medicine, Hangzhou, 310007, China
| | - Peng Bi
- Department of Nephrology, Hangzhou Hospital of Traditional Chinese Medicine, Affiliated to Zhejiang University of Traditional Chinese Medicine, Hangzhou, 310007, China
| | - Wanyue Xu
- Department of Nephrology, Hangzhou Hospital of Traditional Chinese Medicine, Affiliated to Zhejiang University of Traditional Chinese Medicine, Hangzhou, 310007, China
| | - Yazhen Yang
- Department of Nephrology, Hangzhou Hospital of Traditional Chinese Medicine, Affiliated to Zhejiang University of Traditional Chinese Medicine, Hangzhou, 310007, China
| | - Hongyu Chen
- Department of Nephrology, Hangzhou Hospital of Traditional Chinese Medicine, Affiliated to Zhejiang University of Traditional Chinese Medicine, Hangzhou, 310007, China.
| | - De Jin
- Department of Nephrology, Hangzhou Hospital of Traditional Chinese Medicine, Affiliated to Zhejiang University of Traditional Chinese Medicine, Hangzhou, 310007, China.
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Gao Y, Yang Z, Ji T, Zhou P, Geng L, Gao X. Anti-papillary thyroid carcinoma effects of dioscorea bulbifera L. through ferroptosis and the PI3K/AKT pathway based on network pharmacology and experimental validation. JOURNAL OF ETHNOPHARMACOLOGY 2024; 326:117912. [PMID: 38387682 DOI: 10.1016/j.jep.2024.117912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Papillary thyroid carcinoma (PTC) is the predominant form of thyroid cancer with a rising global incidence. Despite favorable prognoses, a significant recurrence rate persists. Dioscorea bulbifera L. (DBL), a traditional Chinese medicine, has been historically used for thyroid-related disorders. However, its therapeutic effects and mechanisms of action on PTC remain unclear. AIM OF THE STUDY To explore the potential therapeutic effects, principal active components, and molecular mechanisms of DBL in the treatment of PTC through network pharmacology and molecular docking, with experimental validation conducted to corroborate these findings. MATERIALS AND METHODS The Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) was utilized as a systematic tool for collecting and screening the phytochemical components of DBL, and for establishing associations between these components and molecular targets. Based on this, network data was visually processed using Cytoscape software (version 3.8.0). Concurrently, precise molecular docking studies of the principal active components of DBL and their corresponding targets were conducted using Autodock software. Additionally, PTC-related genes were selected through the GeneCards and GEO databases. We further employed the DAVID bioinformatics resources to conduct comprehensive Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses on the intersecting genes between DBL and PTC. These analyses aid in predicting the potential therapeutic actions of DBL on PTC and its mechanisms of action. To validate these findings, corresponding in vitro experimental studies were also conducted. RESULTS In this investigation, 14 bioactive compounds of DBL and 195 corresponding molecular targets were identified, with 127 common targets shared between DBL and PTC. Molecular docking revealed strong binding affinities between major bioactive compounds and target proteins. GO enrichment analysis unveiled key processes involved in DBL's action. KEGG analysis highlighted DBL's modulation of the PI3K/AKT signaling pathway. Experimental outcomes demonstrated DBL's potential in inhibiting PTC cell proliferation and migration, suppressing PI3K/AKT pathway activation, and promoting ferroptosis. CONCLUSION In conclusion, DBL offers a multifaceted therapeutic approach for PTC, targeting multiple molecular entities and influencing diverse biological pathways. Network pharmacology and molecular docking shed light on DBL's potential utility in PTC treatment, substantiated by experimental validation. This study contributes valuable insights into using DBL as a promising therapeutic agent for PTC management.
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Affiliation(s)
- Yuzhi Gao
- Department of Central Laboratory, Clinical College of Lianyungang, Bengbu Medical University, Lianyungang, 222002, Jiangsu, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Kangda College of Nanjing Medical University, Lianyungang 222002, Jiangsu, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Zhendong Yang
- Department of Ultrasonography, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Tuo Ji
- Department of Central Laboratory, Clinical College of Lianyungang, Bengbu Medical University, Lianyungang, 222002, Jiangsu, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Kangda College of Nanjing Medical University, Lianyungang 222002, Jiangsu, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Ping Zhou
- Endocrinology Department, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Lei Geng
- Department of Radiology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China
| | - Xuzhu Gao
- Department of Central Laboratory, Clinical College of Lianyungang, Bengbu Medical University, Lianyungang, 222002, Jiangsu, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Kangda College of Nanjing Medical University, Lianyungang 222002, Jiangsu, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222002, Jiangsu, China.
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Ye J, Yang R, Li L, Zhong S, Jiang R, Hu Z. Molecular mechanism of Danxiong Tongmai Granules in treatment of coronary heart disease. Aging (Albany NY) 2024; 16:8843-8865. [PMID: 38775721 PMCID: PMC11164497 DOI: 10.18632/aging.205845] [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: 06/26/2023] [Accepted: 02/21/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Danxiong Tongmai Granules (DXTMG) are widely utilized in treating coronary heart disease (CHD) in China. This study aims to explore the molecular mechanisms underlying the therapeutic effects of DXTMG on CHD by employing a network pharmacology approach, complemented with experimental validation. METHODS Traditional Chinese Medicine (TCM) compounds and targets were identified via searches in the BATMAN-TCM database, and the GeneCards database was used to obtain the main target genes involved in CHD. We combined disease targets with the drug targets to identify common targets. The "TCM-compound-target" network was plotted using Cytoscape 3.7.2 software and a protein-protein interaction (PPI) network was constructed using the STRING database from which core targets were obtained. Gene ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for common drug-disease targets using R Version 4.0.4 (64 bit) software. Molecular docking of core protein-small molecule ligand interaction was modeled using AutoDock software. A molecular dynamics simulation was conducted on the optimal protein-small molecule complex identified through molecular docking, using Amber18 software. The rat model for myocardial ischemia was established through pre-gavage administration of DXTMG, followed by dorsal hypodermic injection of isoprenaline. Myocardial tissues from the rats were analyzed using hematoxylin and eosin (HE) staining and Masson's trichrome staining. Relevant targets were validated by enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry. RESULTS 162 potential targets of DXTMG involved in CHD were identified. These included INS, ALB, IL-6 and TNF according to PPI network studies. GO enrichment analysis identified a total of 3365 GO pathways, including 3049 biological process pathways (BP) concerned with the heart and circulatory system; 109 cellular component (CC) pathways, including cation channels and membrane rafts and 207 molecular function (MF) pathways related to receptor ligands and activators. KEGG analysis revealed a total of 137 pathways (P < 0.05), including those related to AGE-RAGE signaling associated with diabetic complications, fluid shear stress and atherosclerosis. The results of molecular docking and molecular dynamics simulations demonstrated the robust binding affinity between the compounds and target proteins. Animal experiment findings indicated that, compared with the model group, the DXTMG group effectively ameliorated inflammation and fibrosis in rat myocardial tissues, reduced LDH, cTn-I, and MDA levels (P < 0.05, P < 0.01), elevated SOD and GSH-PX levels (P < 0.05), and reduced the percentage of positive area for IL-6 and TNF-α (P < 0.05). CONCLUSION This study preliminarily suggests that DXTMG can modulate oxidative stress, inflammation response, and cardiomyocyte regulation, thereby mitigating the onset and progression of CHD.
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Affiliation(s)
- Jiahao Ye
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Ruiping Yang
- Basic Medical Sciences College, Hubei University of Chinese Medicine, Wuhan, Hubei 430065, China
| | - Lin Li
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Senjie Zhong
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Ruixue Jiang
- Basic Medical Sciences College, Hubei University of Chinese Medicine, Wuhan, Hubei 430065, China
| | - Zhixi Hu
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
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Brown SD, Klimi E, Bakker WAM, Beqqali A, Baker AH. Non-coding RNAs to treat vascular smooth muscle cell dysfunction. Br J Pharmacol 2024. [PMID: 38773733 DOI: 10.1111/bph.16409] [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: 11/17/2023] [Revised: 02/19/2024] [Accepted: 03/14/2024] [Indexed: 05/24/2024] Open
Abstract
Vascular smooth muscle cell (vSMC) dysfunction is a critical contributor to cardiovascular diseases, including atherosclerosis, restenosis and vein graft failure. Recent advances have unveiled a fascinating range of non-coding RNAs (ncRNAs) that play a pivotal role in regulating vSMC function. This review aims to provide an in-depth analysis of the mechanisms underlying vSMC dysfunction and the therapeutic potential of various ncRNAs in mitigating this dysfunction, either preventing or reversing it. We explore the intricate interplay of microRNAs, long-non-coding RNAs and circular RNAs, shedding light on their roles in regulating key signalling pathways associated with vSMC dysfunction. We also discuss the prospects and challenges associated with developing ncRNA-based therapies for this prevalent type of cardiovascular pathology.
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Affiliation(s)
- Simon D Brown
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Eftychia Klimi
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Abdelaziz Beqqali
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew H Baker
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, The Netherlands
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Kim Y, Han Y, Hopper C, Lee J, Joo JI, Gong JR, Lee CK, Jang SH, Kang J, Kim T, Cho KH. A gray box framework that optimizes a white box logical model using a black box optimizer for simulating cellular responses to perturbations. CELL REPORTS METHODS 2024; 4:100773. [PMID: 38744288 PMCID: PMC11133856 DOI: 10.1016/j.crmeth.2024.100773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
Predicting cellular responses to perturbations requires interpretable insights into molecular regulatory dynamics to perform reliable cell fate control, despite the confounding non-linearity of the underlying interactions. There is a growing interest in developing machine learning-based perturbation response prediction models to handle the non-linearity of perturbation data, but their interpretation in terms of molecular regulatory dynamics remains a challenge. Alternatively, for meaningful biological interpretation, logical network models such as Boolean networks are widely used in systems biology to represent intracellular molecular regulation. However, determining the appropriate regulatory logic of large-scale networks remains an obstacle due to the high-dimensional and discontinuous search space. To tackle these challenges, we present a scalable derivative-free optimizer trained by meta-reinforcement learning for Boolean network models. The logical network model optimized by the trained optimizer successfully predicts anti-cancer drug responses of cancer cell lines, while simultaneously providing insight into their underlying molecular regulatory mechanisms.
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Affiliation(s)
- Yunseong Kim
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Younghyun Han
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Corbin Hopper
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jonghoon Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jae Il Joo
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jeong-Ryeol Gong
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Chun-Kyung Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Seong-Hoon Jang
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Junsoo Kang
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Taeyoung Kim
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Kwang-Hyun Cho
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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Abdel-Maksoud MA, Askar MA, Abdel-rahman IY, Gharib M, Aufy M. Integrating Network Pharmacology and Molecular Docking Approach to Elucidate the Mechanism of Commiphora wightii for the Treatment of Rheumatoid Arthritis. Bioinform Biol Insights 2024; 18:11779322241247634. [PMID: 38765022 PMCID: PMC11102677 DOI: 10.1177/11779322241247634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/28/2024] [Indexed: 05/21/2024] Open
Abstract
Background Rheumatoid arthritis (RA) is considered a notable prolonged inflammatory condition with no proper cure. Synovial inflammation and synovial pannus are crucial in the onset of RA. The "tumor-like" invading proliferation of new arteries is a keynote of RA. Commiphora wightii (C wightii) is a perennial, deciduous, and trifoliate plant used in several areas of southeast Asia to cure numerous ailments, including arthritis, diabetes, obesity, and asthma. Several in vitro investigations have indicated C wightii's therapeutic efficacy in the treatment of arthritis. However, the precise molecular action is yet unknown. Material and methods In this study, a network pharmacology approach was applied to uncover potential targets, active therapeutic ingredients and signaling pathways in C wightii for the treatment of arthritis. In the groundwork of this research, we examined the active constituent-compound-target-pathway network and evaluated that (Guggulsterol-V, Myrrhahnone B, and Campesterol) decisively donated to the development of arthritis by affecting tumor necrosis factor (TNF), PIK3CA, and MAPK3 genes. Later on, docking was employed to confirm the active components' efficiency against the potential targets. Results According to molecular-docking research, several potential targets of RA bind tightly with the corresponding key active ingredient of C wightii. With the aid of network pharmacology techniques, we conclude that the signaling pathways and biological processes involved in C wightii had an impact on the prevention of arthritis. The outcomes of molecular docking also serve as strong recommendations for future research. In the context of this study, network pharmacology combined with molecular docking analysis showed that C wightii acted on arthritis-related signaling pathways to exhibit a promising preventive impact on arthritis. Conclusion These results serve as the basis for grasping the mechanism of the antiarthritis activity of C wightii. However, further in vivo/in vitro study is needed to verify the reliability of these targets for the treatment of arthritis.
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Affiliation(s)
- Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mostafa A Askar
- Radiation Biology Department, National Centre for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Ibrahim Y Abdel-rahman
- Radiation Biology Department, National Centre for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Mustafa Gharib
- Radiation Biology Department, National Centre for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Mohammed Aufy
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
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Qu J, Lu S, Wang B, Wang S, Yang Z, Tang H, He J, Zhao Y, Wang X, Liu X, Rao B. Network pharmacology and molecular docking technology for exploring the effect and mechanism of high-dose vitamin c on ferroptosis of tumor cells: A review. Medicine (Baltimore) 2024; 103:e38189. [PMID: 38758839 PMCID: PMC11098213 DOI: 10.1097/md.0000000000038189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/18/2024] [Indexed: 05/19/2024] Open
Abstract
To investigate the mechanism by which high-dose vitamin C (HVC) promotes ferroptosis in tumor cells via network pharmacology, vitamin C-related and ferroptosis-related targets were obtained from the PharmMapper and GeneCards databases, respectively, and their common targets were compared using the Venn diagram. Common targets were imported into the STRING database for protein-protein interaction analysis, and core targets were defined. Core targets were enriched for Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways using the R language packages. A map of the core target-based interaction network and a map of the mechanism by which HVC regulates ferroptosis were constructed. A total of 238 vitamin C-related and 721 ferroptosis-related targets were identified, of which 21 targets were common to both. Furthermore, ALDOA, AHCY, LDHB, HSPA8, LGALS3, and GSTP1 were identified as core targets. GO enrichment analysis suggested that the main biological processes included the extrinsic apoptotic signaling pathway and pyruvate metabolic process. KEGG enrichment analysis suggested that HVC regulates ferroptosis mainly through the amino acid and carbohydrate metabolic pathways. The targets were validated by molecular docking. In conclusion, HVC may promote ferroptosis in tumor cells by regulating metabolic pathways, and there is a synergistic effect between HVC and type I ferroptosis inducers. Glycolysis-dependent tumors may be beneficial for HVC therapy. Our study provides a reference for further clinical studies on HVC antitumor therapy.
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Affiliation(s)
- Jinxiu Qu
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Shuai Lu
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Bing Wang
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Shiwan Wang
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Zhenpeng Yang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Huazhen Tang
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Jia He
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Yuan Zhao
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Xin Wang
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Xiaozhu Liu
- Department of Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Benqiang Rao
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Center of Metabolism and Nutrition of Cancer, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
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Hu H, Serra C, Zhang W, Scrivo A, Fernández-Carasa I, Consiglio A, Aytes A, Pujana MA, Llebaria A, Antolin AA. Identification of differential biological activity and synergy between the PARP inhibitor rucaparib and its major metabolite. Cell Chem Biol 2024; 31:973-988.e4. [PMID: 38335967 DOI: 10.1016/j.chembiol.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 08/16/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
The (poly)pharmacology of drug metabolites is seldom comprehensively characterized in drug discovery. However, some drug metabolites can reach high plasma concentrations and display in vivo activity. Here, we use computational and experimental methods to comprehensively characterize the kinase polypharmacology of M324, the major metabolite of the PARP1 inhibitor rucaparib. We demonstrate that M324 displays unique PLK2 inhibition at clinical concentrations. This kinase activity could have implications for the efficacy and safety of rucaparib and therefore warrants further clinical investigation. Importantly, we identify synergy between the drug and the metabolite in prostate cancer models and a complete reduction of α-synuclein accumulation in Parkinson's disease models. These activities could be harnessed in the clinic or open new drug discovery opportunities. The study reported here highlights the importance of characterizing the activity of drug metabolites to comprehensively understand drug response in the clinic and exploit our current drug arsenal in precision medicine.
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Affiliation(s)
- Huabin Hu
- Center for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Carme Serra
- Medicinal Chemistry and Synthesis (MCS) Laboratory, Institut de Química Avançada de Catalunya (IQAC-CSIC), 08034 Barcelona, Spain; Synthesis of High Added Value Molecules (SIMChem), Institut de Química Avançada de Catalunya (IQAC-CSIC), 08034 Barcelona, Spain
| | - Wenjie Zhang
- ProCURE, Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Catalonia, Spain
| | - Aurora Scrivo
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Irene Fernández-Carasa
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Antonella Consiglio
- Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain; Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alvaro Aytes
- ProCURE, Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Catalonia, Spain
| | - Miguel Angel Pujana
- ProCURE, Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Catalonia, Spain
| | - Amadeu Llebaria
- Medicinal Chemistry and Synthesis (MCS) Laboratory, Institut de Química Avançada de Catalunya (IQAC-CSIC), 08034 Barcelona, Spain; Synthesis of High Added Value Molecules (SIMChem), Institut de Química Avançada de Catalunya (IQAC-CSIC), 08034 Barcelona, Spain.
| | - Albert A Antolin
- Center for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK; ProCURE, Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Catalonia, Spain.
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Li Y, Lai J, Ran M, Yi T, Zhou L, Luo J, Liu X, Tang X, Huang M, Xie X, Li H, Yang Y, Zou W, Wu J. Alnustone promotes megakaryocyte differentiation and platelet production via the interleukin-17A/interleukin-17A receptor/Src/RAC1/MEK/ERK signaling pathway. Eur J Pharmacol 2024; 971:176548. [PMID: 38570080 DOI: 10.1016/j.ejphar.2024.176548] [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: 10/31/2023] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
OBJECTIVES Thrombocytopenia is a disease in which the number of platelets in the peripheral blood decreases. It can be caused by multiple genetic factors, and numerous challenges are associated with its treatment. In this study, the effects of alnustone on megakaryocytes and platelets were investigated, with the aim of developing a new therapeutic approach for thrombocytopenia. METHODS Random forest algorithm was used to establish a drug screening model, and alnustone was identified as a natural active compound that could promote megakaryocyte differentiation. The effect of alnustone on megakaryocyte activity was determined using cell counting kit-8. The effect of alnustone on megakaryocyte differentiation was determined using flow cytometry, Giemsa staining, and phalloidin staining. A mouse model of thrombocytopenia was established by exposing mice to X-rays at 4 Gy and was used to test the bioactivity of alnustone in vivo. The effect of alnustone on platelet production was determined using zebrafish. Network pharmacology was used to predict targets and signaling pathways. Western blotting and immunofluorescence staining determined the expression levels of proteins. RESULTS Alnustone promoted the differentiation and maturation of megakaryocytes in vitro and restored platelet production in thrombocytopenic mice and zebrafish. Network pharmacology and western blotting showed that alnustone promoted the expression of interleukin-17A and enhanced its interaction with its receptor, and thereby regulated downstream MEK/ERK signaling and promoted megakaryocyte differentiation. CONCLUSIONS Alnustone can promote megakaryocyte differentiation and platelet production via the interleukin-17A/interleukin-17A receptor/Src/RAC1/MEK/ERK signaling pathway and thus provides a new therapeutic strategy for the treatment of thrombocytopenia.
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Affiliation(s)
- Yueyue Li
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Jia Lai
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China; School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
| | - Mei Ran
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
| | - Taian Yi
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Ling Zhou
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
| | - Jiesi Luo
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
| | - Xiaoxi Liu
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
| | - Xiaoqin Tang
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
| | - Miao Huang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Xiang Xie
- School of Basic Medical Sciences, Public Center of Experimental Technology, Model Animal and Human Disease Research of Luzhou Key Laboratory, Southwest Medical University, Luzhou, China.
| | - Hong Li
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
| | - Yan Yang
- Education Ministry Key Laboratory of Medical Electrophysiology, Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou, 646000, China.
| | - Wenjun Zou
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Jianming Wu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China; School of Pharmacy, Southwest Medical University, Luzhou, 646000, China; Education Ministry Key Laboratory of Medical Electrophysiology, Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou, 646000, China.
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Lu DD, Yuan L, Wang ZZ, Zhao JJ, Du YH, Ning N, Chen GQ, Huang SC, Yang Y, Zhang Z, Nan Y. To explore the mechanism of Yigong San anti-gastric cancer and immune regulation. World J Gastrointest Oncol 2024; 16:1965-1994. [PMID: 38764819 PMCID: PMC11099436 DOI: 10.4251/wjgo.v16.i5.1965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 02/20/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND Yigong San (YGS) is a representative prescription for the treatment of digestive disorders, which has been used in clinic for more than 1000 years. However, the mechanism of its anti-gastric cancer and regulate immunity are still remains unclear. AIM To explore the mechanism of YGS anti-gastric cancer and immune regulation. METHODS Firstly, collect the active ingredients and targets of YGS, and the differentially expressed genes of gastric cancer. Secondly, constructed a protein-protein interaction network between the targets of drugs and diseases, and screened hub genes. Then the clinical relevance, mutation and repair, tumor microenvironment and drug sensitivity of the hub gene were analyzed. Finally, molecular docking was used to verify the binding ability of YGS active ingredient and hub genes. RESULTS Firstly, obtained 55 common targets of gastric cancer and YGS. The Kyoto Encyclopedia of Genes and Genomes screened the microtubule-associated protein kinase signaling axis as the key pathway and IL6, EGFR, MMP2, MMP9 and TGFB1 as the hub genes. The 5 hub genes were involved in gastric carcinogenesis, staging, typing and prognosis, and their mutations promote gastric cancer progression. Finally, molecular docking results confirmed that the components of YGS can effectively bind to therapeutic targets. CONCLUSION YGS has the effect of anti-gastric cancer and immune regulation.
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Affiliation(s)
- Dou-Dou Lu
- School of Clinical Medicine, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Ling Yuan
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Zhao-Zhao Wang
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Jian-Jun Zhao
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yu-Hua Du
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Na Ning
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Guo-Qing Chen
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Shi-Cong Huang
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yi Yang
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Zhe Zhang
- Department of Chinese Medical Gastrointestinal, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yi Nan
- Key Laboratory of Ningxia Minority Medicine Modernization Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
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Gnanamurthy P, Narasimhan MK, Sabarathinam S. GC-MS analysis of an ethanolic extract of Ocimum species: a network pharmacology analysis insight towards obesity. Future Sci OA 2024; 10:FSO940. [PMID: 38827792 PMCID: PMC11140659 DOI: 10.2144/fsoa-2023-0202] [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: 09/19/2023] [Accepted: 11/10/2023] [Indexed: 06/05/2024] Open
Abstract
Aim: In this study, we have selected two different Ocimum tenuiflorum plants, Ocimum tenuiflorum (Rama tulsi) (OTRT) and Ocimum tenuiflorum (Krishna tulsi) (OTKT). Materials & methods: In the present investigation, ethanol was used as a solvent to estimate the bioactive compounds present in it through gas chromatography-mass spectrometry (GC-MS). Results: Based on the GC-MS data benzenepropanoic acid, 3-methoxy-alpha,4-bis[(trimethylsilyl)oxy was found to be the potent compound in OTRT (MW: 428.74 g/mol) and methyl 3-(4-benzyloxy-3,5-dimethoxyphenyl)-2-methylpropanoate in OTKT (MW: 342.39 g/mol). To estimate its pharmacological application, an integrated Network Pharmacology approach is performed toward the disease target obesity. Conclusion: From the protein-protein interaction from the string database, SRC, BCL2, EGFR, MTOR, CDK1, ERBB2, MAPK1, FYN, AR and MAPK14 are the top-ranked targets.
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Affiliation(s)
- Priyadharshini Gnanamurthy
- Department of Genetic Engineering, School of Bioengineering, College of Engineering & Technology, SRM Institute of Science & Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Manoj K Narasimhan
- Department of Genetic Engineering, School of Bioengineering, College of Engineering & Technology, SRM Institute of Science & Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Sarvesh Sabarathinam
- Drug Testing Laboratory, Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science & Technology, SRM IST, Kattankulathur, Chennai, Tamil Nadu, 603203, India
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Li C, Yu J, Feng Y, Sun X, Sun M, Ni W, Shao J, Wang B. Rhein suppresses esophageal cancer development by regulating cell cycle through DNMT3B gene. Med Oncol 2024; 41:153. [PMID: 38743323 DOI: 10.1007/s12032-024-02359-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/15/2024] [Indexed: 05/16/2024]
Abstract
The mechanism by which DNMT3B facilitates esophageal cancer (ESCA) progression is currently unknown, despite its association with adverse prognoses in several cancer types. To investigate the potential therapeutic effects of the Chinese herbal medicine rhubarb on esophageal cancer (ESCA), we adopted an integrated bioinformatics approach. Gene Set Enrichment Analysis (GSEA) was first utilized to screen active anti-ESCA components in rhubarb. We then employed Weighted Gene Co-expression Network Analysis (WGCNA) to identify key molecular modules and targets related to the active components and ESCA pathogenesis. This system-level strategy integrating multi-omics data provides a powerful means to unravel the molecular mechanisms underlying the anticancer activities of natural products, like rhubarb. To investigate module gene functional enrichment, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. In addition, we evaluated the predictive impact of DNMT3B expression on ESCA patients utilizing the Kaplan-Meier method. Finally, we conducted experiments on cell proliferation and the cell cycle to explore the biological roles of DNMT3B. In this study, we identified Rhein as the main active ingredient of rhubarb that exhibited significant anti-ESCA activity. Rhein markedly suppressed ESCA cell proliferation. Utilizing Weighted Gene Co-expression Network Analysis (WGCNA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we determined that the blue module was associated with Rhein target genes and the cell cycle. Additionally, DNMT3B was identified as a Rhein target gene. Analysis of The Cancer Genome Atlas (TCGA) database revealed that higher DNMT3B levels were associated with poor prognosis in ESCA patients. Furthermore, Rhein partially reversed the overexpression of DNMT3B to inhibit ESCA cell proliferation. In vitro studies demonstrated that Rhein and DNMT3B inhibition disrupted the S phase of the cell cycle and affected the production of cell cycle-related proteins. In this study, we found that Rhein exerts its anti-proliferative effects in ESCA cells by targeting DNMT3B and regulating the cell cycle.
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Affiliation(s)
- Cheng Li
- Department of Pharmacy, The Third Affiliated Hospital of Qiqihar Medical University, 3 Tai Shun Street, Tiefeng District, Qiqihar City, Heilongjiang Province, China
| | - Jingjing Yu
- Department of Pharmacy, The Third Affiliated Hospital of Qiqihar Medical University, 3 Tai Shun Street, Tiefeng District, Qiqihar City, Heilongjiang Province, China
| | - Ying Feng
- Department of Pharmacy, The Third Affiliated Hospital of Qiqihar Medical University, 3 Tai Shun Street, Tiefeng District, Qiqihar City, Heilongjiang Province, China
| | - Xiaoxue Sun
- Department of Pharmacy, The Third Affiliated Hospital of Qiqihar Medical University, 3 Tai Shun Street, Tiefeng District, Qiqihar City, Heilongjiang Province, China
| | - Mingming Sun
- Department of Pharmacy, The Third Affiliated Hospital of Qiqihar Medical University, 3 Tai Shun Street, Tiefeng District, Qiqihar City, Heilongjiang Province, China
| | - Weihui Ni
- Department of Pharmacy, The Third Affiliated Hospital of Qiqihar Medical University, 3 Tai Shun Street, Tiefeng District, Qiqihar City, Heilongjiang Province, China
| | - Jun Shao
- Department of Pharmacy, The Third Affiliated Hospital of Qiqihar Medical University, 3 Tai Shun Street, Tiefeng District, Qiqihar City, Heilongjiang Province, China
| | - Baoxin Wang
- Department of Pharmacy, The Third Affiliated Hospital of Qiqihar Medical University, 3 Tai Shun Street, Tiefeng District, Qiqihar City, Heilongjiang Province, China.
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Yi M, Zhang Z, Luo Z, Luo A, Zeng H, Li P, Wang T, Yang J, Nie H. PolyphyllinVI alleviates the spared nerve injury-induced neuropathic pain based on P2X3 receptor-mediated the release of inflammatory mediators. JOURNAL OF ETHNOPHARMACOLOGY 2024; 325:117886. [PMID: 38355027 DOI: 10.1016/j.jep.2024.117886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/21/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE PolyphyllinVI (PPⅥ) is the main bioactive component of Chonglou which is a traditional Chinese herbal with various effects, including antitumor, anti-inflammatory, and analgesia. AIM OF THE STUDY This study aimed to investigate the properties and mechanisms of the analgesia of PPⅥ by using neuropathic pain (NPP) mice. MATERIALS AND METHODS The potential targets and mechanisms of PPⅥ in alleviating NPP were excavated based on the network pharmacology. Subsequently, the construction of a spared nerve injury (SNI) mice model was used to evaluate the effect of PPⅥ on NPP and the expression of the P2X3 receptor. We identified the signaling pathways of PPⅥ analgesia by RNA sequencing. RESULTS The results of network pharmacology showed that BCL2, CASP3, JUN, STAT3, and TNF were the key targets of the analgesic effect of PPⅥ. PPⅥ increased the MWT and TWL of SNI mice and decreased the level of P2X3 receptors in the dorsal root ganglion (DRG) and spinal cord (SC). Additionally, PPⅥ reduced the release of pro-inflammatory mediators (TNF-α, IL-1β, and IL-6) in the DRG, SC, and serum. Based on the KEGG enrichment of differentially expressed genes (DEGs) identified by RNA-Seq, PPVI may relieve NPP by regulating the AMPK/NF-κB signaling pathway. Western blotting results showed that the AMPK signaling pathway was activated, followed by inhibition of the NF-κB signaling pathway. CONCLUSION PPⅥ increased the MWT and TWL of SNI mice maybe by inhibiting the expression of the P2X3 receptor and the release of inflammatory mediators. The properties of the analgesia of PPⅥ may be based on the AMPK/NF-κB pathway.
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Affiliation(s)
- Mengqin Yi
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhenglang Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhenhui Luo
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Anqi Luo
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Hekun Zeng
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Peiyang Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Tingting Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Jingwen Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Hong Nie
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
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Ding X, Li S, Huang H, Shen J, Ding Y, Chen T, Ma L, Liu J, Lai Y, Chen B, Wang Y, Tan Q. Bioactive triterpenoid compounds of Poria cocos (Schw.) Wolf in the treatment of diabetic ulcers via regulating the PI3K-AKT signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 325:117812. [PMID: 38301984 DOI: 10.1016/j.jep.2024.117812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/13/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Diabetic ulcers represent a chronic condition characterized by prolonged hyperglycemia and delayed wound healing, accompanied by endocrine disorders, inflammatory responses, and microvascular damage in the epidermal tissue, demanding effective clinical treatment approaches. For thousands of years, ancient Chinese ethnopharmacological studies have documented the use of Poria cocos (Schw.) Wolf in treating diabetic ulcers. Recent research has substantiated the diverse pharmacological effects of Poria cocos (Schw.) Wolf, including its potential to alleviate hyperglycemia and exhibit anti-inflammatory, antioxidant, and immune regulatory properties, which could effectively mitigate diabetic ulcer symptoms. Furthermore, being a natural medicine, Poria cocos (Schw.) Wolf has demonstrated promising therapeutic effects and safety in the management of diabetic ulcers, holding significant clinical value. Despite its potential clinical efficacy and applications in diabetic ulcer treatment, the primary active components and underlying pharmacological mechanisms of Poria cocos (Schw.) Wolf remains unclear. Further investigations are imperative to establish a solid foundation for drug development in this domain. AIM OF THE STUDY AND MATERIALS AND METHODS In this study, we aimed to identify the active compounds and potential targets of Poria cocos (Schw.) Wolf using UHPLC-Q-TOF-MS and TCMSP databases. Additionally, we attempt to identify targets related to diabetic ulcers. Following enrichment analysis, a network of protein-protein interactions was constructed to identify hub genes based on the common elements between the two datasets. To gain insights into the binding activities of the hub genes and active ingredients, molecular docking analysis was employed. Furthermore, to further validate the therapeutic effect of Poria cocos (Schw.) Wolf, we exerted in vitro experiments using human umbilical vein vascular endothelial cells and human myeloid leukemia monocytes (THP-1). The active ingredient of Poria cocos (Schw.) Wolf was applied in these experiments. Our investigations included various assays, such as CCK-8, scratch test, immunofluorescence, western blotting, RT-PCR, and flow cytometry, to explore the potential of Poria cocos (Schw.) Wolf triterpenoid extract (PTE) in treating diabetic ulcers. RESULTS The findings here highlighted PTE as the primary active ingredient in Poria cocos (Schw.) Wolf. Utilizing network pharmacology, we identified 74 potential targets associated with diabetic ulcer treatment for Poria cocos (Schw.) Wolf, with five hub genes (JUN, MAPK1, STAT3, AKT1, and CTNNB1). Enrichment analysis revealed the involvement of multiple pathways in the therapeutic process, with the PI3K-AKT signaling pathway showing significant enrichment. Through molecular docking, we discovered that relevant targets within this pathway exhibited strong binding with the active components of Poria cocos (Schw.) Wolf. In vitro experiments unveiled that PTE (10 mg/L) facilitated the migration of human umbilical vein vascular endothelial cells (P < 0.05). PTE also increased the expression of CD31 and VEGF mRNA (P < 0.05) while activating the expressions of p-PI3K and p-AKT (P < 0.05). Moreover, PTE demonstrated its potential by reducing the expression of IL-1β, IL-6, TNF-α, and NF-κB mRNA in THP-1 (P < 0.05) and fostering M2 macrophage polarization. These results signify the potential therapeutic effects of PTE in treating diabetic ulcers, with its beneficial actions mediated through the PI3K-AKT signaling pathway. CONCLUSIONS PTE is the main active ingredient in Poria cocos (Schw.) Wolf that exerts therapeutic effects. Through PI3K-AKT signaling pathway activation and inflammatory response reduction, PTE promotes angiogenesis, thereby healing diabetic ulcers.
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Affiliation(s)
- Xiaofeng Ding
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China
| | - Shiyan Li
- Department of Burns and Plastic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, NO. 321, Zhongshan Road, Nanjing, Jiangsu, China
| | - Heyan Huang
- Department of Burns and Plastic Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing 210008, China
| | - Jiayun Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Youjun Ding
- Department of Burns and Plastic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, NO. 321, Zhongshan Road, Nanjing, Jiangsu, China
| | - Timson Chen
- Adolph Innovation Laboratory, Guangzhou Degu Personal Care Products Co., Ltd., Guangzhou, 510000, China
| | - Ling Ma
- Adolph Innovation Laboratory, Guangzhou Degu Personal Care Products Co., Ltd., Guangzhou, 510000, China
| | - Jinfang Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Yongxian Lai
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China
| | - Bin Chen
- Institute of Plant Resources and Chemistry, Nanjing Research Institute for Comprehensive Utilization of Wild Plants, Nanjing, 210042, China.
| | - Yiwei Wang
- Jiangsu Provincial Engineering Research Centre of TCM External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Qian Tan
- Department of Burns and Plastic Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing 210008, China.
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Du S, Chen X, Ren R, Li L, Zhang B, Wang Q, Meng Y, Qiu Z, Wang G, Zheng G, Hu J. Integration of network pharmacology, lipidomics, and transcriptomics analysis to reveal the mechanisms underlying the amelioration of AKT-induced nonalcoholic fatty liver disease by total flavonoids in vine tea. Food Funct 2024; 15:5158-5174. [PMID: 38630029 DOI: 10.1039/d4fo00586d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the main reason for chronic liver diseases and malignancies. Currently, there is a lack of approved drugs for the prevention or treatment of NAFLD. Vine tea (Ampelopsis grossedentata) has been used as a traditional Chinese beverage for centuries. Vine tea carries out several biological activities including the regulation of plasma lipids and blood glucose, hepato-protective function, and anti-tumor activity and contains the highest content of flavonoids. However, the underlying mechanisms of total flavonoids from vine tea (TF) in the attenuation of NAFLD remain unclear. Therefore, we investigated the interventions and mechanisms of TF in mice with NAFLD using an integrated analysis of network pharmacology, lipidomics, and transcriptomics. Staining and biochemical tests revealed a significant increase in AKT-overexpression-induced (abbreviated as AKT-induced) NAFLD in mice. Lipid accumulation in hepatic intracellular vacuoles was alleviated after TF treatment. In addition, TF reduced the hepatic and serum triglyceride levels in mice with AKT-induced NAFLD. Lipidomics results showed 32 differential lipids in the liver, mainly including triglycerides (TG), diglycerides (DG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE). Transcriptomic analysis revealed that 314 differentially expressed genes were commonly upregulated in the AKT group and downregulated in the TF group. The differential regulation of lipids by the genes Pparg, Scd1, Chpt1, Dgkz, and Pla2g12b was further revealed by network enrichment analysis and confirmed by RT-qPCR. Furthermore, we used immunohistochemistry (IHC) to detect changes in the protein levels of the key proteins PPARγ and SCD1. In summary, TF can improve hepatic steatosis by targeting the PPAR signaling pathway, thereby reducing de novo fatty acid synthesis and modulating the glycerophospholipid metabolism.
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Affiliation(s)
- Siyu Du
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Center of Traditional Chinese Medicine Modernization for Liver Diseases, Hubei University of Chinese Medicine, Wuhan, People's Republic of China
- Hubei Shizhen Laboratory, Wuhan, People's Republic of China
| | - Xin Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Hubei Shizhen Laboratory, Wuhan, People's Republic of China
| | - Rumeng Ren
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Center of Traditional Chinese Medicine Modernization for Liver Diseases, Hubei University of Chinese Medicine, Wuhan, People's Republic of China
| | - Li Li
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Center of Traditional Chinese Medicine Modernization for Liver Diseases, Hubei University of Chinese Medicine, Wuhan, People's Republic of China
| | - Baohui Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Hubei Shizhen Laboratory, Wuhan, People's Republic of China
| | - Qi Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Hubei Shizhen Laboratory, Wuhan, People's Republic of China
| | - Yan Meng
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Center of Traditional Chinese Medicine Modernization for Liver Diseases, Hubei University of Chinese Medicine, Wuhan, People's Republic of China
- Hubei Shizhen Laboratory, Wuhan, People's Republic of China
| | - Zhenpeng Qiu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Center of Traditional Chinese Medicine Modernization for Liver Diseases, Hubei University of Chinese Medicine, Wuhan, People's Republic of China
- Hubei Shizhen Laboratory, Wuhan, People's Republic of China
| | - Guihong Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
| | - Guohua Zheng
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Center of Traditional Chinese Medicine Modernization for Liver Diseases, Hubei University of Chinese Medicine, Wuhan, People's Republic of China
- Hubei Shizhen Laboratory, Wuhan, People's Republic of China
| | - Junjie Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, People's Republic of China.
- Center of Traditional Chinese Medicine Modernization for Liver Diseases, Hubei University of Chinese Medicine, Wuhan, People's Republic of China
- Hubei Shizhen Laboratory, Wuhan, People's Republic of China
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50
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Wang N, Sun G, Zhang Q, Gao Q, Wang B, Guo L, Cheng G, Hu Y, Huang J, Ren R, Wang C, Chen C. Broussonin E against acute respiratory distress syndrome: the potential roles of anti-inflammatory. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:3195-3209. [PMID: 37906275 DOI: 10.1007/s00210-023-02801-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023]
Abstract
We applied network pharmacology and molecular docking analyses to study the efficacy of Broussonin E (BRE) in acute respiratory distress syndrome (ARDS) treatment and to determine the core components, potential targets, and mechanism of action of BRE. The SwissTargetprediction and SEA databases were used to predict BRE targets, and the GeneCards and OMIM databases were used to predict ARDS-related genes. The drug targets and disease targets were mapped to obtain an intersecting drug target gene network, which was then uploaded into the String database for protein-protein interaction network analysis. The intersecting gene was also uploaded into the DAVID database for gene ontology enrichment analysis and Kyoto encyclopedia of genes and genomes pathway analysis. Molecular docking analysis was performed to verify the interaction of BRE with the key targets. Finally, to validate the experiment in vivo, we established an oleic acid-induced ARDS rat model and evaluated the protective effect of BRE on ARDS by histological evaluation and enzyme-linked immunosorbent assay. Overall, 79 targets of BRE and 3974 targets of ARDS were predicted, and 79 targets were obtained after intersection. Key genes such as HSP90AA1, JUN, ESR1, MTOR, and PIK3CA play important roles in the nucleus and cytoplasm by regulating the tumor necrosis factor, nuclear factor-κB, and PI3K-Akt signaling pathways. Molecular docking results showed that small molecules of BRE could freely bind to the active site of the target proteins. In vivo experiments showed that BRE could reduce ARDS-related histopathological changes, release of inflammatory factors, and infiltration of macrophages and oxidative stress reaction. BRE exerts its therapeutic effect on ARDS through target and multiple pathways. This study also predicted the potential mechanism of BRE on ARDS, which provides the theoretical basis for in-depth and comprehensive studies of BRE treatment on ARDS.
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Affiliation(s)
- Ning Wang
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China
| | - Guangcheng Sun
- Department of Cardiology, Anhui Chest Hospital, Hefei, Anhui, China
| | - Qiaoyun Zhang
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China
| | - Qian Gao
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China
- Department of Genetics, School of Life Science, Anhui Medical University, Hefei, Anhui, China
| | - Bingjie Wang
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China
| | - Lingling Guo
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China
| | - Gao Cheng
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China
| | - Yuexia Hu
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China
| | - Jian Huang
- Department of Thoracic Surgery, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, No.17, Lujiang Road, Luyang District, Hefei, 230001, Anhui, China.
| | - Ruguo Ren
- Department of Cardiovascular Hospital, Xi'an No.1 Hospital and The First Affiliated Hospital of Northwest University, Beilin District, No.30, South Street powder Lane, Xi'an, 710002, Shaanxi, China.
| | - Chunhui Wang
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China.
| | - Chen Chen
- Department of Anesthesiology, The First Affiliated Hospital of Anhui Medical University and Anhui Public Health Clinical Center, Xinzhan District, No.100, Huaihai Road, Hefei, 230011, Anhui, China.
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