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Huynh DTN, Nguyen HT, Hsieh CM. Taiwan Chingguan Yihau may improve post-COVID-19 respiratory complications through PI3K/AKT, HIF-1, and TNF signaling pathways revealed by network pharmacology analysis. Mol Divers 2025; 29:2305-2321. [PMID: 39382736 DOI: 10.1007/s11030-024-10993-8] [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: 06/08/2024] [Accepted: 09/14/2024] [Indexed: 10/10/2024]
Abstract
The emergence of new SARS-CoV-2 variants with a higher contagious capability and faster transmissible speed has imposed an incessant menace on global health and the economy. The SARS-CoV-2 infection might reoccur and last much longer than expected. Thence, there is a high possibility that COVID-19 can cause long-term health problems. This condition needs to be investigated thoroughly, especially the post-COVID-19 complications. Respiratory tract disorders are common and typical complications after recovery. Until now, there has been a lack of data on specialized therapeutic medicine for post-COVID-19 complications. The clinical efficacy of NRICM101 has been demonstrated in hospitalized COVID-19 patients. This herbal medicine may also be a promising therapy for post-COVID-19 complications, thanks to its phytochemical constituents. The potential pharmacological mechanisms of NRICM101 in treating post-COVID-19 respiratory complications were investigated using network pharmacology combined with molecular docking, and the results revealed that NRICM101 may exert a beneficial effect through the three primary pathways: PI3K/AKT, HIF-1, and TNF signaling pathways. Flavonoids (especially quercetin) have a predominant role and synergize with other active compounds to produce therapeutic effectiveness. Most of the main active compounds exist in three chief herbal ingredients, including Liquorice root (Glycyrrhiza glabra), Scutellaria root (Scutellaria baicalensis), and Mulberry leaf (Morus alba). To our knowledge, this is the first study of the NRICM101 effect on post-COVID-19 respiratory complications. Our findings may provide a better understanding of the potential mechanisms of NRICM101 in treating SARS-CoV-2 infection and regulating the immunoinflammatory response to improve post-COVID-19 respiratory complications.
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Affiliation(s)
- Dung Tam Nguyen Huynh
- College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan
- Can Tho University of Medicine and Pharmacy, Can Tho City, 94117, Vietnam
| | - Hien Thi Nguyen
- Department of Nutrition and Food Safety, Faculty of Public Health, Can Tho University of Medicine and Pharmacy, Can Tho City, 94117, Vietnam
| | - Chien-Ming Hsieh
- College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan.
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Wang G, Chen J, Kong X, Wang K. Mechanistic insights into the anticancer effects of Pinellia ternata (Thunb.) Ten. ex Breitenb. and Ligusticum chuanxiong Hort. ex S. H. Qiu & al. on papillary thyroid carcinoma: A network pharmacology approach. Medicine (Baltimore) 2025; 104:e41841. [PMID: 40128073 PMCID: PMC11936596 DOI: 10.1097/md.0000000000041841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 02/23/2025] [Indexed: 03/26/2025] Open
Abstract
This study aims to elucidate the mechanisms of action of Pinellia ternata (Thunb.) Ten. ex Breitenb. and Ligusticum chuanxiong Hort. ex S. H. Qiu & al. (PAL) in treating papillary thyroid carcinoma (PTC) using bioinformatics and network analysis. Compounds in PAL were identified from the HERB database. Potential herbal targets were predicted using the SwissADME and SwissTargetPrediction platforms. Differential expression genes related to PTC were extracted from the GEO database and protein-protein interaction networks were constructed using the String database and Cytoscape software. Additionally, gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were conducted, and core compound-target interactions were validated through molecular docking. Effective components identified included 32 from Pinellia ternata (Thunb.) Ten. ex Breitenb. and 105 from Ligusticum chuanxiong Hort. ex S. H. Qiu & al., comprising 825 targets. A total of 2155 differential expression genes related to PTC were selected using GEO2R software, with 71 therapeutic targets identified. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses suggest that PAL may exert effects through cancer-related pathways and signal transduction processes. Molecular docking indicated high binding affinity between several compounds and their targets. Specific active components in PAL may act through various mechanisms on PTC, offering scientific bases for further drug development and treatment strategies.
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Affiliation(s)
- Gang Wang
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Jing Chen
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Xiangding Kong
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Kuanyu Wang
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
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Luo X, Chen L, Xu J, Li J. Naoxintong Is Involved in the Coagulation Regulation of Warfarin Through the MAPK Pathway. Pharmgenomics Pers Med 2025; 18:35-46. [PMID: 39906888 PMCID: PMC11792639 DOI: 10.2147/pgpm.s489820] [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: 08/02/2024] [Accepted: 01/21/2025] [Indexed: 02/06/2025] Open
Abstract
Objective To explore the effect of Naoxintong (NXT) on warfarin anticoagulation therapy and its potential mechanism. Methods TCSMP, SwissTargetprediction, SuperPred, SEA, and Batmanic-TCM were used to search for active ingredients and targets of NXT and warfarin; the DisGENT database was used to find disease targets of coagulation disorders. Cytoscape software was applied to construct the "drug-target"network; the protein interaction network (PPI) was used to study the protein-protein interaction. GO and KEGG were used for functional analysis. The effect of NXT on warfarin anticoagulation was then tested in rats by analyzing coagulation factors in blood before and after drug administration. The expression of MAPK in the liver tissue was determined by Western blot. Results The top five components of NXT affecting warfarin anticoagulation degree value were MOL000098, MOL000422, MOL000006, MOL000358, and MOL000449. TP53, AKT1, SRC, TNF, HSP90AA1, STAT3, JUN, IL6, EGFR, and ESR1 were the core targets of NXT, while MAPK9, MAP3K5, MAPK8, and MAPK1 in the MAPK family were important targets of NXT in the coagulation process. In vivo testing indicated that NXT may be able to participate in the regulation of the warfarin coagulation process through multiple targets and multiple pathways, which may be related to MAPK. Conclusion Our data suggests that NXT is involved in the coagulation regulation of warfarin through the MAPK pathway.
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Affiliation(s)
- Xiao Luo
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330000, People’s Republic of China
- Department of Cardiovascular Medicine, Jiujiang City Key Laboratory of Cell Therapy, Jiujiang No. 1 People’s Hospital, Jiujiang, Jiangxi, 332000, People’s Republic of China
| | - Ling Chen
- Department of Cardiovascular Medicine, Jiujiang City Key Laboratory of Cell Therapy, Jiujiang No. 1 People’s Hospital, Jiujiang, Jiangxi, 332000, People’s Republic of China
| | - Jingsong Xu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330000, People’s Republic of China
| | - Juxiang Li
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330000, People’s Republic of China
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Sun Y, Lei C, Qiao R, Li C. Recent advances in carrier-free natural small molecule self-assembly for drug delivery. Biomater Sci 2024; 12:6237-6252. [PMID: 39513256 DOI: 10.1039/d4bm01153h] [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: 11/15/2024]
Abstract
Natural small-molecule drugs have been used for thousands of years for the prevention and treatment of human diseases. Most of the natural products available on the market have been modified into various polymer materials for improving the solubility, stability, and targeted delivery of drugs. However, these nanomedicines formed based on polymer carriers would produce severe problems such as systemic toxicity and kidney metabolic stress. In contrast, the carrier-free nanomedicines formed by their self-assembly in water have inherent advantages such as low toxicity, good biocompatibility, and biodegradability. This review summarizes the assembly process and application of natural small-molecule products, which are mainly driven by multiple non-covalent interactions, and includes single-molecule assembly, bimolecular assembly, drug-modified assembly, and organogels. Meanwhile, the molecular mechanism involved in different self-assembly processes is also discussed. Self-assembly simulation and structural modification of natural small-molecule products or traditional Chinese medicine molecules using molecular dynamics simulation and computer-assisted methods are proposed, which will lead to the discovery of more carrier-free nanomedicine drug delivery systems. Overall, this review provides an important understanding and strategy to study single-molecule and multi-molecule carrier-free nanomedicines.
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Affiliation(s)
- Yehua Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
| | - Changyang Lei
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
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Ye J, Yao J, Xu S, Xiao G, Jia Y, Xie N, Yan J, Ying X, Zhang H. Elucidating the substance basis and pharmacological mechanism of Fufang Qiling granules in modulating xanthine oxidase for intervention in hyperuricemia. JOURNAL OF ETHNOPHARMACOLOGY 2024; 333:118410. [PMID: 38848973 DOI: 10.1016/j.jep.2024.118410] [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: 02/02/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Fufang Qiling granules (FQG), derived from the traditional Qiling Decoction with a longstanding clinical history, is utilized for the treatment of hyperuricemia (HUA). FQG is formulated with a combination of seven Chinese herbs based on the principles of traditional Chinese medicine (TCM) theories. Clinical evidence indicates that FQG exhibits favorable therapeutic effects in reducing uric acid (UA) levels and attenuating renal damage. AIM OF THIS STUDY To elucidate the potential active components and pharmacological mechanism of FQG in the treatment of HUA, and to provide an experimental basis for the development of efficient and low-toxicity TCM for HUA treatment. MATERIALS AND METHODS A HUA rat model induced by potassium oxonate and adenine was established to initially evaluate the hypouricemic effects of FQG. Chemical analyses were conducted using an ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Network pharmacology was used to investigate the active components and mechanism of FQG in the treatment of HUA. Potential Xanthine oxidase (XOD) inhibitors were screened from FQG based on ultrafiltration liquid chromatography and mass spectrometry (UF-LC-MS). Molecular docking, surface plasmon resonance (SPR) and circular dichroism (CD) spectroscopy were applied to validate the interactions between the active components and XOD. RESULTS In comparison to the model group, treatment with FQG significantly decreased serum UA, serum creatinine (CREA), serum blood urea nitrogen (BUN), and liver XOD activity. Additionally, the FQG administration notably ameliorated HUA-induced renal injury in rats. Through the pharmacodynamics of the HUA rat models and network pharmacology, it was found that XOD was a key pathway enzyme in UA metabolism. 18 XOD inhibitors were screened from FQG by UF-LC-MS, and 11 compounds with strong affinity were verified by SPR, molecular docking and CD spectroscopy. CONCLUSION In summary, flavonoids, organic acids and saponins may be the active components in FQG that alleviate HUA. The primary mechanism of FQG involves inhibiting XOD enzyme activity in the plasma to reduce UA production, alleviating renal tubular epithelial cell necrosis, tubulointerstitial injury, fibrosis, and urate deposition, ultimately exerting a therapeutic effect on HUA.
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Affiliation(s)
- Jiamin Ye
- College of Pharmaceutical Science, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, China
| | - Jiangyu Yao
- College of Pharmaceutical Science, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, China
| | - Shaojing Xu
- Research Institute of Chiatai Qingchunbao Pharmaceutical Co., Ltd., Hangzhou, 310030, China
| | - Guyu Xiao
- College of Pharmaceutical Science, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, China
| | - Yuwei Jia
- College of Pharmaceutical Science, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, China
| | - Ningjun Xie
- Research Institute of Chiatai Qingchunbao Pharmaceutical Co., Ltd., Hangzhou, 310030, China
| | - Jizhong Yan
- College of Pharmaceutical Science, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, China
| | - Xuhui Ying
- Research Institute of Chiatai Qingchunbao Pharmaceutical Co., Ltd., Hangzhou, 310030, China.
| | - Hui Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, China.
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Gong H, Xia Y, Jing G, Yuan M, Zhou H, Wu D, Zuo J, Lei C, Aidebaike D, Wu X, Song X. Berberine alleviates neuroinflammation by downregulating NFκB/LCN2 pathway in sepsis-associated encephalopathy: network pharmacology, bioinformatics, and experimental validation. Int Immunopharmacol 2024; 133:112036. [PMID: 38640713 DOI: 10.1016/j.intimp.2024.112036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/12/2024] [Accepted: 04/05/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND Sepsis refers to a systemic inflammatory response caused by infection, involving multiple organs. Sepsis-associated encephalopathy (SAE), as one of the most common complications in patients with severe sepsis, refers to the diffuse brain dysfunction caused by sepsis without central nervous system infection. However, there is no clear diagnostic criteria and lack of specific diagnostic markers. METHODS The main active ingredients of coptidis rhizoma(CR) were identified from TCMSP and SwissADME databases. SwissTargetPrediction and PharmMapper databases were used to obtain targets of CR. OMIM, DisGeNET and Genecards databases were used to explore targets of SAE. Limma differential analysis was used to identify the differential expressed genes(DEGs) in GSE167610 and GSE198861 datasets. WGCNA was used to identify feature module. GO and KEGG enrichment analysis were performed using Metascape, DAVID and STRING databases. The PPI network was constructed by STRING database and analyzed by Cytoscape software. AutoDock and PyMOL software were used for molecular docking and visualization. Cecal ligation and puncture(CLP) was used to construct a mouse model of SAE, and the core targets were verified in vivo experiments. RESULTS 277 common targets were identified by taking the intersection of 4730 targets related to SAE and 509 targets of 9 main active ingredients of CR. 52 common DEGs were mined from GSE167610 and GSE198861 datasets. Among the 25,864 DEGs in GSE198861, LCN2 showed the most significant difference (logFC = 6.9). GO and KEGG enrichment analysis showed that these 52 DEGs were closely related to "inflammatory response" and "innate immunity". A network containing 38 genes was obtained by PPI analysis, among which LCN2 ranked the first in Degree value. Molecular docking results showed that berberine had a well binding affinity with LCN2. Animal experiments results showed that berberine could inhibit the high expression of LCN2,S100A9 and TGM2 induced by CLP in the hippocampus of mice, as well as the high expression of inflammatory factors (TNFα, IL-6 and IL-1β). In addition, berberine might reduce inflammation and neuronal cell death by partially inhibiting NFκB/LCN2 pathway in the hippocampus of CLP models, thereby alleviating SAE. CONCLUSION Overall, Berberine may exert anti-inflammatory effects through multi-ingredients, multi-targets and multi-pathways to partially rescue neuronal death and alleviate SAE.
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Affiliation(s)
- Hailong Gong
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China
| | - Yun Xia
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China
| | - Guoqing Jing
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China
| | - Min Yuan
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China
| | - Huimin Zhou
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China
| | - Die Wu
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China
| | - Jing Zuo
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China
| | - Chuntian Lei
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China
| | - Delida Aidebaike
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China
| | - Xiaojing Wu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China.
| | - Xuemin Song
- Research Centre of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province 430071, China.
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Li W, Jiao R, Luo S, Liu Z, Song J, Chen Z. Mechanism of action of Coptidis Rhizome in treating periodontitis based on network pharmacology and in vitro validation. BMC Oral Health 2024; 24:530. [PMID: 38704553 PMCID: PMC11069132 DOI: 10.1186/s12903-024-04311-9] [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: 03/01/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
OBJECTIVE Explore the therapeutic mechanism of Coptidis Rhizome (CR) in periodontitis using network pharmacology, and validate it through molecular docking and in vitro experiments. METHODS Screened potential active components and target genes of CR from TCMSP and Swiss databases. Identified periodontitis-related target genes using GeneCards. Found common target genes using Venny. Conducted GO and KEGG pathway analysis. Performed molecular docking and in vitro experiments using Berberine, the main active component of CR, on lymphocytes from healthy and periodontitis patients. Assessed effects on inflammatory factors using CCK-8, flow cytometry, and ELISA. RESULTS Fourteen active components and 291 targets of CR were identified. 30 intersecting target genes with periodontitis were found. GO and KEGG analysis revealed oxidative stress response and IL-17 signaling pathway as key mechanisms. Molecular docking showed strong binding of Berberine with ALOX5, AKT1, NOS2, and TNF. In vitro experiments have demonstrated the ability of berberine to inhibit the expression of Th17 + and other immune related cells in LPS stimulated lymphocytes, and reduce the secretion of IL-6, IL-8, and IL-17. CONCLUSION CR treats periodontitis through a multi-component, multi-target, and multi-pathway approach. Berberine, its key component, acts through the IL-17 signaling pathway to exert anti-inflammatory effects.
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Affiliation(s)
- Wei Li
- Guiyang Hospital of Stomatology, Guiyang, Guizhou, 550005, China
| | - Ruofeng Jiao
- Guiyang Hospital of Stomatology, Guiyang, Guizhou, 550005, China
- Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Shiyi Luo
- Guiyang Hospital of Stomatology, Guiyang, Guizhou, 550005, China
- Medical College of Guizhou University, Guiyang, Guizhou, 550025, China
| | - Zefei Liu
- Guiyang Hospital of Stomatology, Guiyang, Guizhou, 550005, China
- Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Jukun Song
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Guizhou Medical University, Guiyang, 550001, China.
| | - Zhu Chen
- Guiyang Hospital of Stomatology, Guiyang, Guizhou, 550005, China.
- Zunyi Medical University, Zunyi, Guizhou, 563000, China.
- Medical College of Guizhou University, Guiyang, Guizhou, 550025, China.
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Li H, Sun M, Lei F, Liu J, Chen X, Li Y, Wang Y, Lu J, Yu D, Gao Y, Xu J, Chen H, Li M, Yi Z, He X, Chen L. Methyl rosmarinate is an allosteric inhibitor of SARS-CoV-2 3 CL protease as a potential candidate against SARS-cov-2 infection. Antiviral Res 2024; 224:105841. [PMID: 38408645 DOI: 10.1016/j.antiviral.2024.105841] [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: 11/10/2023] [Revised: 02/09/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been ongoing for more than three years and urgently needs to be addressed. Traditional Chinese medicine (TCM) prescriptions have played an important role in the clinical treatment of patients with COVID-19 in China. However, it is difficult to uncover the potential molecular mechanisms of the active ingredients in these TCM prescriptions. In this paper, we developed a new approach by integrating the experimental assay, virtual screening, and the experimental verification, exploring the rapid discovery of active ingredients from TCM prescriptions. To achieve this goal, 4 TCM prescriptions in clinical use for different indications were selected to find the antiviral active ingredients in TCMs. The 3-chymotrypsin-like protease (3CLpro), an important target for fighting COVID-19, was utilized to determine the inhibitory activity of the TCM prescriptions and single herb. It was found that 10 single herbs had better inhibitory activity than other herbs by using a fluorescence resonance energy transfer (FRET) - based enzymatic assay of SARS-CoV-2 3CLpro. The ingredients contained in 10 herbs were thus virtually screened and the predicted active ingredients were experimentally validated. Thus, such a research strategy firstly removed many single herbs with no inhibitory activity against SARS-CoV-2 3CLpro at the very beginning by FRET-based assay, making our subsequent virtual screening more effective. Finally, 4 active components were found to have stronger inhibitory effects on SARS-CoV-2 3CLpro, and their inhibitory mechanism was subsequently investigated. Among of them, methyl rosmarinate as an allosteric inhibitor of SARS-CoV-2 3CLpro was confirmed and its ability to inhibit viral replication was demonstrated by the SARS-CoV-2 replicon system. To validate the binding mode via docking, the mutation experiment, circular dichroism (CD), enzymatic inhibition and surface plasmon resonance (SPR) assay were performed, demonstrating that methyl rosmarinate bound to the allosteric site of SARS-CoV-2 3CLpro. In conclusion, this paper provides the new ideas for the rapid discovery of active ingredients in TCM prescriptions based on a specific target, and methyl rosmarinate has the potential to be developed as an antiviral therapeutic candidate against SARS-CoV-2 infection.
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Affiliation(s)
- Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Meng Sun
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Fuzhi Lei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China; Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; DP Technology, Beijing, China
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yueqiu Gao
- Department of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Infectious Diseases of Integrated Traditional Chinese and Western Medicine, China
| | - Jianrong Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Man Li
- Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Longhua Hospital Shanghai University of Traditional Chinese Medicine, 725 South Wanping Road, Shanghai, 200032, China.
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Cha M, Lee S, Yoon S, Lee SY, Gupta H, Ganesan R, Sharma SP, Won S, Jeong J, Kim DJ, Oh K, Suk K. New insight of chemical constituents in Persea americana fruit against obesity via integrated pharmacology. Clin Transl Sci 2024; 17:e13778. [PMID: 38515346 PMCID: PMC10958180 DOI: 10.1111/cts.13778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Persea americana fruit (PAF) is a favorable nutraceutical resource that comprises diverse unsaturated fatty acids (UFAs). UFAs are significant dietary supplementation, as they relieve metabolic disorders, including obesity (OB). In another aspect, this study was focused on the anti-OB efficacy of the non-fatty acids (NFAs) in PAF through network pharmacology (NP). Natural product activity & species source (NPASS), SwissADME, similarity ensemble approach (SEA), Swiss target prediction (STP), DisGeNET, and online Mendelian inheritance in man (OMIM) were utilized to gather significant molecules and its targets. The crucial targets were adopted to construct certain networks: protein-protein interaction (PPI), PAF-signaling pathways-targets-compounds (PSTC) networks, a bubble chart, molecular docking assay (MDA), and density function theory (DFT). Finally, the toxicities of the key compounds were validated by ADMETlab 2.0 platform. All 41 compounds in PAF conformed to Lipinski's rule, and the key 31 targets were identified between OB and PAF. On the bubble chart, PPAR signaling pathway had the highest rich factor, suggesting that the pathway might be an agonism for anti-OB. Conversely, estrogen signaling pathway had the lowest rich factor, indicating that the mechanism might be antagonism against OB. Likewise, the PSTC network represented that AKT1 had the greatest degree value. The MDA results showed that AKT1-gamma-tocopherol, PPARA-fucosterol, PPARD-stigmasterol, (PPARG)-fucosterol, (NR1H3)-campesterol, and ILK-alpha-tocopherol formed the most stable conformers. The DFT represented that the five molecules might be promising agents via multicomponent targeting. Overall, this study suggests that the NFAs in PAF might play important roles against OB.
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Affiliation(s)
- Min‐Gi Cha
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Su‐Been Lee
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Sang‐Jun Yoon
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Sang Youn Lee
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Haripriya Gupta
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Satya Priya Sharma
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Sung‐Min Won
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Jin‐Ju Jeong
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Dong Joon Kim
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Ki‐Kwang Oh
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
| | - Ki‐Tae Suk
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym UniversityChuncheonKorea
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Saima, Latha S, Sharma R, Kumar A. Role of Network Pharmacology in Prediction of Mechanism of Neuroprotective Compounds. Methods Mol Biol 2024; 2761:159-179. [PMID: 38427237 DOI: 10.1007/978-1-0716-3662-6_13] [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] [Indexed: 03/02/2024]
Abstract
Network pharmacology is an emerging pioneering approach in the drug discovery process, which is used to predict the therapeutic mechanism of compounds using various bioinformatic tools and databases. Emerging studies have indicated the use of network pharmacological approaches in various research fields, particularly in the identification of possible mechanisms of herbal compounds/ayurvedic formulations in the management of various diseases. These techniques could also play an important role in the prediction of the possible mechanisms of neuroprotective compounds. The first part of the chapter includes an introduction on neuroprotective compounds based on literature. Further, network pharmacological approaches are briefly discussed. The use of network pharmacology in the prediction of the neuroprotective mechanism of compounds is discussed in detail with suitable examples. Finally, the chapter concludes with the current challenges and future prospectives.
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Affiliation(s)
- Saima
- Department of Pharmacology, Delhi Pharmaceutical Science and Research University (DPSRU), New Delhi, India
| | - S Latha
- Department of Pharmacology, Delhi Pharmaceutical Science and Research University (DPSRU), New Delhi, India
| | - Ruchika Sharma
- Centre for Precision Medicine and Pharmacy, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
| | - Anoop Kumar
- Department of Pharmacology, Delhi Pharmaceutical Science and Research University (DPSRU), New Delhi, India
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Choi NR, Kwon MJ, Choi WG, Kim SC, Park JW, Nam JH, Kim BJ. The traditional herbal medicines mixture, Banhasasim-tang, relieves the symptoms of irritable bowel syndrome via modulation of TRPA1, NaV1.5 and NaV1.7 channels. JOURNAL OF ETHNOPHARMACOLOGY 2023; 312:116499. [PMID: 37059250 DOI: 10.1016/j.jep.2023.116499] [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: 03/05/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The cause of irritable bowel syndrome (IBS), a functional gastrointestinal (GI) disorder, remains unclear. Banhasasim-tang (BHSST), a traditional herbal medicines mixture, mainly used to treat GI-related diseases, may have a potential in IBS treatment. IBS is characterized by abdominal pain as the main clinical symptom, which seriously affects the quality of life. AIM OF THE STUDY We conducted a study to evaluate the effectiveness of BHSST and its mechanisms of action in treating IBS. MATERIALS AND METHODS We evaluated the efficacy of BHSST in a zymosan-induced diarrhea-predominant animal model of IBS. Electrophysiological methods were used to confirm modulation of transient receptor potential (TRP) and voltage-gated Na+ (NaV) ion channels, which are associated mechanisms of action. RESULTS Oral administration of BHSST decreased colon length, increased stool scores, and increased colon weight. Weight loss was also minimized without affecting food intake. In mice administered with BHSST, the mucosal thickness was suppressed, making it similar to that of normal mice, and the degree of tumor necrosis factor-α was severely reduced. These effects were similar to those of the anti-inflammatory drug-sulfasalazine-and antidepressant-amitriptyline. Moreover, pain-related behaviors were substantially reduced. Additionally, BHSST inhibited TRPA1, NaV1.5, and NaV1.7 ion channels associated with IBS-mediated visceral hypersensitivity. CONCLUSIONS In summary, the findings suggest that BHSST has potential beneficial effects on IBS and diarrhea through the modulation of ion channels.
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Affiliation(s)
- Na Ri Choi
- Department of Longevity and Biofunctional Medicine, Pusan National University School of Korean Medicine, Yangsan, 50612, Republic of Korea.
| | - Min Ji Kwon
- Department of Longevity and Biofunctional Medicine, Pusan National University School of Korean Medicine, Yangsan, 50612, Republic of Korea.
| | - Woo-Gyun Choi
- Department of Longevity and Biofunctional Medicine, Pusan National University School of Korean Medicine, Yangsan, 50612, Republic of Korea.
| | - Sang Chan Kim
- College of Oriental Medicine Daegu Haany University, Gyeongsan, 38610, Republic of Korea
| | - Jae-Woo Park
- Department of Clinical Korean Medicine, Graduate School of Kyung Hee University, Seoul, 02447, Republic of Korea; Department of Gastroenterology, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea.
| | - Joo Hyun Nam
- Department of Physiology, Dongguk University College of Medicine, Kyungju, 38066, Republic of Korea; Channelopathy Research Center (CRC), Dongguk University College of Medicine, Goyang, 10326, Republic of Korea.
| | - Byung Joo Kim
- Department of Longevity and Biofunctional Medicine, Pusan National University School of Korean Medicine, Yangsan, 50612, Republic of Korea.
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Khan SA, Lee TKW. Identifying potential pharmacological targets and molecular pathways of Meliae cortex for COVID-19 therapy. Front Immunol 2023; 14:1128164. [PMID: 36817449 PMCID: PMC9932519 DOI: 10.3389/fimmu.2023.1128164] [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: 12/20/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease-19 (COVID-19), caused by SARS-CoV-2, has contributed to a significant increase in mortality. Proinflammatory cytokine-mediated cytokine release syndrome (CRS) contributes significantly to COVID-19. Meliae cortex has been reported for its several ethnomedical applications in the Chinese Pharmacopoeia. In combination with other traditional Chinese medicines (TCM), the Meliae cortex suppresses coronavirus. Due to its phytoconstituents and anti-inflammatory capabilities, we postulated that the Meliae cortex could be a potential therapeutic for treating COVID-19. The active phytonutrients, molecular targets, and pathways of the Meliae cortex have not been explored yet for COVID-19 therapy. We performed network pharmacology analysis to determine the active phytoconstituents, molecular targets, and pathways of the Meliae cortex for COVID-19 treatment. 15 active phytonutrients of the Meliae cortex and 451 their potential gene targets were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) and SwissTargetPrediction website tool, respectively. 1745 COVID-19-related gene targets were recovered from the GeneCards. 104 intersection gene targets were determined by performing VENNY analysis. Using the DAVID tool, gene ontology (GO) and KEGG pathway enrichment analysis were performed on the intersection gene targets. Using the Cytoscape software, the PPI and MCODE analyses were carried out on the intersection gene targets, which resulted in 41 potential anti-COVID-19 core targets. Molecular docking was performed with AutoDock Vina. The 10 anti-COVID-19 core targets (AKT1, TNF, HSP90AA1, IL-6, mTOR, EGFR, CASP3, HIF1A, MAPK3, and MAPK1), three molecular pathways (the PI3K-Akt signaling pathway, the HIF-1 signaling pathway, and the pathways in cancer) and three active phytonutrients (4,8-dimethoxy-1-vinyl-beta-carboline, Trichilinin D, and Nimbolin B) were identified as molecular targets, molecular pathways, and key active phytonutrients of the Meliae cortex, respectively that significantly contribute to alleviating COVID-19. Molecular docking analysis further corroborated that three Meliae cortex's key active phytonutrients may ameliorate COVID-19 disease by modulating identified targets. Hence, this research offers a solid theoretic foundation for the future development of anti-COVID-19 therapeutics based on the phytonutrients of the Meliae cortex.
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Affiliation(s)
- Shakeel Ahmad Khan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China,*Correspondence: Shakeel Ahmad Khan, ; Terence Kin Wah Lee,
| | - Terence Kin Wah Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China,Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China,State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China,*Correspondence: Shakeel Ahmad Khan, ; Terence Kin Wah Lee,
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Nguyen HT, Do VM, Phan TT, Nguyen Huynh DT. The Potential of Ameliorating COVID-19 and Sequelae From Andrographis paniculata via Bioinformatics. Bioinform Biol Insights 2023; 17:11779322221149622. [PMID: 36654765 PMCID: PMC9841859 DOI: 10.1177/11779322221149622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/18/2022] [Indexed: 01/13/2023] Open
Abstract
The current coronavirus disease 2019 (COVID-19) outbreak is alarmingly escalating and raises challenges in finding efficient compounds for treatment. Repurposing phytochemicals in herbs is an ideal and economical approach for screening potential herbal components against COVID-19. Andrographis paniculata, also known as Chuan Xin Lian, has traditionally been used as an anti-inflammatory and antibacterial herb for centuries and has recently been classified as a promising herbal remedy for adjuvant therapy in treating respiratory diseases. This study aimed to screen Chuan Xin Lian's bioactive components and elicit the potential pharmacological mechanisms and plausible pathways for treating COVID-19 using network pharmacology combined with molecular docking. The results found terpenoid (andrographolide) and flavonoid (luteolin, quercetin, kaempferol, and wogonin) derivatives had remarkable potential against COVID-19 and sequelae owing to their high degrees in the component-target-pathway network and strong binding capacities in docking scores. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the PI3K-AKT signaling pathway might be the most vital molecular pathway in the pathophysiology of COVID-19 and long-term sequelae whereby therapeutic strategies can intervene.
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Affiliation(s)
- Hien Thi Nguyen
- Faculty of Public Health, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Van Mai Do
- Faculty of Traditional Medicine, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Thanh Thuy Phan
- Faculty of Pharmacy, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Dung Tam Nguyen Huynh
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei,Dung Tam Nguyen Huynh, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei.
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