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Kaur J, Farooqi H, Chandra K, Panda BP. Predicting the bioactive compounds of Lentinula edodes and elucidating its interaction with genes associated to obesity through network pharmacology and in-vitro cell-based assay. Heliyon 2024; 10:e27363. [PMID: 38495166 PMCID: PMC10940914 DOI: 10.1016/j.heliyon.2024.e27363] [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: 09/24/2023] [Revised: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Mushrooms are traditionally used for various medicinal purposes in traditional oriental medicine. The Japanese and Chinese are familiar with the medicinal macro fungus Lentinula edodes (Shiitake mushroom). This study aims to evaluate the role of chemical compounds from L. edodes using network pharmacology and in-vitro studies for management of Obesity. Bioactive compounds in extracts of L. edodes were identified by GC-MS analysis. Compounds were later screened for their drug-like property by Lipinski's rule. In addition, public databases (SEA, STP, Omim and DisGenet) were searched to identify genes associated with selected molecules and obesity, as well as genes that overlap obesity target genes with genes related to L. edodes. Additionally, analysis was performed using Enrichr KG to predict the disease targets of L. edodes. Finally, network was constructed between the overlapping genes and bioactive molecules using Rstudio. Further in-vitro studies were carried out using 3T3-L1 cell line. The genes related to the selected compounds and obesity were identified and overlapped. The disease targets of L. edodes was predicted by enrichment analysis and was found to be linked to obesity. Furthermore, the hub gene was found to be fatty acid amide hydrolase, and the key bioactive compound was hexadecanoic acid methyl ester. The in-vitro cell culture studies confirmed the inhibition of adipogenesis in mushroom extract-treated 3T3-L1 cells and the augmentation of adiponectin. The study suggests that the hub gene fatty acid amide hydrolase might alleviate obesity by inhibiting arachidonoyl ethanolamide signaling, which would enhance the action of fatty acid amide hydrolase and limit appetite in L. edodes extract.
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Affiliation(s)
- Jasmeet Kaur
- Microbial and Pharmaceutical Biotechnology Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Humaira Farooqi
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Kailash Chandra
- Department of Biochemistry, Hamdard Institute of Medical Sciences & Research (HIMSR), Jamia Hamdard, New Delhi 110062 India
| | - Bibhu Prasad Panda
- Microbial and Pharmaceutical Biotechnology Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
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Wang W, Yang C, Xia J, Li N, Xiong W. Luteolin is a potential inhibitor of COVID-19: An in silico analysis. Medicine (Baltimore) 2023; 102:e35029. [PMID: 37746970 PMCID: PMC10519465 DOI: 10.1097/md.0000000000035029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/14/2023] [Accepted: 08/09/2023] [Indexed: 09/26/2023] Open
Abstract
The severe respiratory syndrome 2019 novel coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread explosively, raising global health concerns. Luteolin shows antiviral properties, but its effect on SARS-CoV-2 and the associated mechanisms are not elucidated. We used network pharmacology, molecular docking and molecular dynamics to provide potential molecular support of luteolin (3,4,5,7-tetrahydroxyflavone) (LUT) against COVID-19. We employed network pharmacology, molecular docking, and molecular dynamics techniques to investigate how LUT affected COVID-19. Several databases were queried to determine potential target proteins related to LUT and COVID-19. Protein-protein interaction network was constructed, and core targets were filtered by degree value. Following that, functional enrichment was conducted. Molecular docking was utilized to ensure LUT was compatible with core target proteins. Finally, molecular dynamics was used to analyze the effects of the LUT on the optimal hub target. A total of 64 potential target genes for treating COVID-19 were identified, of which albumin, RAC-alpha serine/threonine-protein kinase, caspase-3, epidermal growth factor receptor, heat shock protein HSP 90-alpha, and mitogen-activated protein kinase 1 might be the most promising. In addition, molecular docking results showed that LUT could interact with SARS-CoV-2 major protease 3CL. LUT can bind to the active sites of 3CL protease and mitogen-activated protein kinase 1, showing an anti-SARS-CoV-2 potential.
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Affiliation(s)
- Wenxiang Wang
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, PR China
| | - Ce Yang
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, PR China
| | - Jing Xia
- Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Chongqing, PR China
| | - Ning Li
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, PR China
| | - Wei Xiong
- Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Chongqing, PR China
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Syukriya AJ, Bankeeree W, Prasongsuk S, Yanatatsaneejit P. In vitro antioxidant and anticancer activities of Smilax corbularia extract combined with Phellinus linteus extract against breast cancer cell lines. Biomed Rep 2023; 19:63. [PMID: 37614981 PMCID: PMC10442767 DOI: 10.3892/br.2023.1645] [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: 05/04/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023] Open
Abstract
Treatment with extracts from whole herbs has been reported to synergistically enhance the anticancer activities of therapeutic agents in recent studies. The present study evaluated the antioxidant and anticancer activities of Smilax corbularia Kunth (S. corbularia) and Phellinus linteus (P. linteus) crude extracts individually and in combination. S. corbularia was extracted using ethanol, whereas P. linteus was extracted using hot water. Both crude extracts underwent physiochemical characterization. Subsequently, the possible antioxidant activities of both crude extracts, individually and in combination, were evaluated using 2,2-Diphenyl-1-picrylhydrazyl and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) assays. Their effects on breast cancer cell cytotoxicity, proliferation and apoptosis were then assessed. The crude S. corbularia extract obtained was found to have a high level of total phenolic content, whilst the crude P. linteus extract had high levels of total polysaccharide content. The total phenolic content and total polysaccharide content results of the combinations depended on the respective ratios of the individual extracts. S. corbularia alone and combination 3 (which contained 75% S. corbularia: 25% P. linteus) demonstrated the greatest radical scavenging activity, followed by combination 1 (50% S. corbularia: 50% P. linteus), combination 2 (25% S. corbularia: 75% P. linteus) and P. linteus. The toxicity results of the extract samples on the cancer cells corresponded with their antioxidant activity. In particular, certain combinations demonstrated clearer inhibitory effects on cell proliferation against three types of breast cancer cells compared with those exerted by the two individual extracts. However, induction of apoptosis was limited, with the degree of apoptosis observed to be #x003C;5%. These findings suggested that treatment with combinations of these two extracts could confer enhanced antioxidant and antiproliferative effects on breast cancer cells. Therefore, the potential of these two extracts in combination as anticancer agents warrants further investigation.
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Affiliation(s)
| | - Wichanee Bankeeree
- Plant and Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sehanat Prasongsuk
- Plant and Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattamawadee Yanatatsaneejit
- Human Genetics Research Group and Plant Breeding Laboratory, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Oh KK. Network pharmacology-based analysis of signaling pathways of an anti-osteoporotic triterpenoid from Acyranthes bidentata Blume root. 3 Biotech 2022; 12:312. [PMID: 36276446 PMCID: PMC9537396 DOI: 10.1007/s13205-022-03362-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/12/2022] [Indexed: 11/01/2022] Open
Abstract
In Korea folk remedies, Acyranthes bidentata Blume is a functional food plant to treat bone diseases; especially, its roots have been used to alleviate osteoporosis (OP), but its key chemical compound(s) and mechanism of action against osteoporosis have not reported yet. This study suggests that Acyranthes bidentata Blume root (ABBR) has promising compound(s) against OP. We utilized network pharmacology to evaluate the therapeutic value. The chemical compounds from Acyranthes bidentata Blume root (ABBR) were identified by gas chromatography-mass spectrum (GC-MS); their physicochemical properties have been evaluated by SwissADME. Next, the target(s) related to a triterpenoid or OP-related targets were investigated by public databases. The signaling pathways from final targets were visualized, constructed, and analyzed by RPackage. Finally, we performed a molecular docking (MD) to explore key target(s) and compound(s) by employing AutoDockVina tools; the residues of amino acids interacted with ligands were identified by LigPlot + v.22. A total of 24 chemicals were accepted by the Lipinski's rules. We found a sole triterpenoid from ABBR via GC-MS, suggesting that might be a potent ligand to alleviate OP. Thereby, the 42 targets were associated with the triterpenoid; the 19 targets among them were connected to OP-targets (1426). The final 19 targets were related directly to 8 signaling pathways on STRING database. On Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and a key signaling pathway (PPAR signaling pathway), four key targets (PPARA, PPARD, FABP3, and FABP4) and a key compound (Methyl 3β-hydroxyolean-18-en-28-oate) were selected via MD. Collectively, the triterpenoid from ABBR might have potent anti-osteoporotic efficacy by activating PPARA, PPARD, FABP3, and FABP4 on PPAR signaling pathway. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03362-5.
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Affiliation(s)
- Ki Kwang Oh
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341 South Korea
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Analysis of Phellinus Igniarius Effects on Gastric Cancer Cells by Atomic Force Microscopy. Micron 2022; 164:103376. [DOI: 10.1016/j.micron.2022.103376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/02/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022]
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Guan Z, Liang Y, Wang X, Zhu Z, Yang A, Li S, Yu J, Niu B, Wang J. Unraveling the Mechanisms of Clinical Drugs-Induced Neural Tube Defects Based on Network Pharmacology and Molecular Docking Analysis. Neurochem Res 2022; 47:3709-3722. [PMID: 35960485 DOI: 10.1007/s11064-022-03717-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/23/2022] [Accepted: 07/31/2022] [Indexed: 11/30/2022]
Abstract
Chemotherapeutic agents such as methotrexate (MTX), raltitrexed (RTX), 5-fluorouracil (5-FU), hydroxyurea (HU), and retinoic acid (RA), and valproic acid (VPA), an antiepileptic drug, all can cause malformations in the developing central nervous system (CNS), such as neural tube defects (NTDs). However, the common pathogenic mechanisms remain unclear. This study aimed to explore the mechanisms of NTDs caused by MTX, RTX, 5-FU, HU, RA, and VPA (MRFHRV), based on network pharmacology and molecular biology experiments. The MRFHRV targets were integrated with disease targets, to find the potential molecules related to MRFHRV-induced NTDs. Protein-protein interaction analysis and molecular docking were performed to analyze these common targets. Utilizing the kyoto encyclopedia of genes and genomes (KEGG) signaling pathways, we analyzed and searched the possible causative pathogenic mechanisms by crucial targets and the signaling pathway. Results showed that MRFHRV induced NTDs through several key targets (including TP53, MAPK1, HSP90AA1, ESR1, GRB2, HDAC1, EGFR, PIK3CA, RXRA, and FYN) and multiple signaling pathways such as PI3K/Akt pathway, suggesting that abnormal proliferation and differentiation could be critical pathogenic contributors in NTDs induced by MRFHRV. These results were further validated by CCK8 assay in mouse embryonic stem cells and GFAP staining in embryonic brain tissue. This study indicated that chemotherapeutic and antiepileptic agents induced NTDs might through predicted targets TP53, MAPK1, GRB2, HDAC1, EGFR, PIK3CA, RXRA, and FYN and multiple signaling pathways. More caution was required for the clinical administration for women with childbearing potential and pregnant.
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Affiliation(s)
- Zhen Guan
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yingchao Liang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Xiuwei Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zhiqiang Zhu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Aiyun Yang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Shen Li
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Jialu Yu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Bo Niu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jianhua Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China.
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Mechanism of Action of Zhi Gan Cao Decoction for Atrial Fibrillation and Myocardial Fibrosis in a Mouse Model of Atrial Fibrillation: A Network Pharmacology-Based Study. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:4525873. [PMID: 35720023 PMCID: PMC9203184 DOI: 10.1155/2022/4525873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
Atrial fibrillation (AF), a commonly seen cardiac disease without optimal curative treatment option, is usually treated by traditional Chinese medicine in China. The Zhi-Gan-Cao decoction (ZGCD) is an alternative medicine for clinical use and has definitive effects. It remains to be defined regarding the specific components and related mechanisms of ZGCD for the treatment of AF. We determined the primary constituents and major targets of the herbs in ZGCD using the TCMSP, HERB, and BATMAN-TCM databases. The UniProt databank database amended and combined the prospective names to supply objective data and records. Every target connected to AF was generated using the GeneCards databank, Drugbank database, TTD, Disgenet database, and OMIM. After identifying possible common targets between ZGCD and AF, the interface network illustration “ZGCD component-AF-target” was created using Cytoscape. We obtained 175 constituents and 839 targets for seven herbal drug categories in the ZGCD and identified 1008 targets of AF. After merging and removing repetitions, 136 collective targets between the ZGCD and AF were removed using the Cytoscape system. These renowned targets were generated from 38 suitable components from among the 157 components. GO enhancement examination and KEGG enrichment analysis by Metascape identified the close connection between the critical target genes and 20 signaling pathways. Then, we injected isoproterenol subcutaneously into the mouse and gave gavage with roasted licorice soup. Two weeks later, mouse were processed and sampled for testing. The results of HE and Masson staining showed that ZGCD effectively alleviated the degree of myocardial fibrosis. As indicated by qRT-PCR and Western blotting, ZGCD significantly reduced COL1A1, COL1A2, COL3A1, and TGF-β1 in myocardial fibrotic tissue to reduce myocardial fibrosis and treat AF by interfering with the expression of COL1A1, COL1A2, COL3A1, and TGF-β1 in myocardial tissue. ZGCD may treat AF by lowering the degree of myocardial fibrosis.
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Oh KK, Adnan M, Cho DH. Uncovering a Hub Signaling Pathway of Antimicrobial-Antifungal-Anticancer Peptides’ Axis on Short Cationic Peptides via Network Pharmacology Study. Int J Mol Sci 2022; 23:ijms23042055. [PMID: 35216171 PMCID: PMC8875113 DOI: 10.3390/ijms23042055] [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: 01/12/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022] Open
Abstract
Short cationic peptides (SCPs) with therapeutic efficacy of antimicrobial peptides (AMPs), antifungal peptides (AFPs), and anticancer peptides (ACPs) are known as an enhancement of the host defense system. Here, we investigated the uppermost peptide(s), hub signaling pathway(s), and their associated target(s) through network pharmacology. Firstly, we selected SCPs with positive amino acid residues on N- and C- terminals under 500 Dalton via RStudio. Secondly, the overlapping targets between the bacteria-responsive targets (TTD and OMIM) and AMPs’ targets were visualized by VENNY 2.1. Thirdly, the overlapping targets between AFPs’ targets and fungal-responsive targets were exhibited by VENNY 2.1. Fourthly, the overlapping targets between cancer-related targets (TTD and OMIM) and fungal-responsive targets were displayed by VENNY 2.1. Finally, a molecular docking study (MDS) was carried out to discover the most potent peptides on a hub signaling pathway. A total of 1833 SCPs were identified, and AMPs’, AFPs’, and ACPs’ filtration suggested that 197 peptides (30 targets), 81 peptides (6 targets), and 59 peptides (4 targets) were connected, respectively. The AMPs―AFPs―ACPs’ axis indicated that 27 peptides (2 targets) were associated. Each hub signaling pathway for the enhancement of the host defense system was “Inactivation of Rap1 signaling pathway on AMPs”, “Activation of Notch signaling pathway on AMPs―AFPs’ axis”, and “Inactivation of HIF-1 signaling pathway on AMPs―AFPs―ACPs’ axis”. The most potent peptides were assessed via MDS; finally, HPIK on STAT3 and HVTK on NOS2 and on HIF-1 signaling pathway were the most stable complexes. Furthermore, the two peptides had better affinity scores than standard inhibitors (Stattic, 1400 W). Overall, the most potent SCPs for the human defense system were HPIK on STAT3 and HVTK on NOS2, which might inactivate the HIF-1 signaling pathway.
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Bian Z, Zhang W, Tang J, Fei Q, Hu M, Chen X, Su L, Fei C, Ji D, Mao C, Tong H, Yuan X, Lu T. Mechanisms Underlying the Action of Ziziphi Spinosae Semen in the Treatment of Insomnia: A Study Involving Network Pharmacology and Experimental Validation. Front Pharmacol 2022; 12:752211. [PMID: 35002696 PMCID: PMC8740267 DOI: 10.3389/fphar.2021.752211] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/25/2021] [Indexed: 01/13/2023] Open
Abstract
Purpose: This study aimed to investigate the potential mechanisms and related bioactive components of ZSS for the treatment of insomnia. Method: The insomnia model of rat induced by PCPA was established. After oral administration of ZSS extract, the general morphological observation, pentobarbital sodium-induced sleep test and histopathological evaluation were carried out. Network pharmacology, assisted by UHPLC-Q-Exactive-MS/MS analysis, was developed to identify the targets of ZSS in the treatment of insomnia, as well as the corresponding signaling pathways. In addition, we validated the identified targets and pathways by RT-qPCR and immunohistochemical analysis. Results: The pentobarbital sodium-induced sleep test, determination of 5-HT and GABA levles in hypothalamic tissues and HE staining showed that ZSS extract was an effective treatment for insomnia. Network pharmacology analysis identified a total of 19 candidate bioactive ingredients in ZSS extract, along with 433 potentially related targets. Next, we performed protein-protein interaction (PPI), MCODE clustering analysis, GO functional enrichment analysis, KEGG pathway enrichment analysis, and ingredient-target-pathway (I-T-P) sub-networks analysis. These methods allowed us to investigate the synergistic therapeutic effects of crucial pathways, including the serotonergic and GABAergic synapse pathways. Our analyses revealed that palmitic acid, coclaurine, jujuboside A, N-nornuciferine, caaverine, magnoflorine, jujuboside B, and betulinic acid, all played key roles in the regulation of these crucial pathways. Finally, we used the PCPA-induced insomnia in rats to validate the data generated by network pharmacology; these in vivo experiments clearly showed that pathways associated with the serotonergic and GABAergic system were activated in the rats model. Furthermore, ZSS treatment significantly suppressed high levels of HTR1A, GABRA1, and GABRG2 expression in the hypothalamus and reduced the expression levels of HTR2A. Conclusion: Based on the combination of comprehensive network pharmacology and in vivo experiments, we successfully identified the potential pharmacological mechanisms underlying the action of ZSS in the treatment of insomnia. The results provide a theoretical basis for further development and utilization of ZSS, and also provide support for the development of innovative drugs for the treatment of insomnia.
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Affiliation(s)
- Zhenhua Bian
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacy, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Wenming Zhang
- Department of Pharmacy, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Jingyue Tang
- Department of Pharmacy, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Qianqian Fei
- Department of Pharmacy, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Minmin Hu
- Department of Pharmacy, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Xiaowei Chen
- Department of Pharmacy, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Lianlin Su
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chenghao Fei
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - De Ji
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunqin Mao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huangjin Tong
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaohang Yuan
- Department of Pharmacy, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Tulin Lu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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Zhou M, Ren G, Zhang B, Ma F, Fan J, Qiu Z. Screening and identification of a novel antidiabetic peptide from collagen hydrolysates of Chinese giant salamander skin: Network pharmacology, inhibition kinetics and protection of IR-HepG2 cells. Food Funct 2022; 13:3329-3342. [DOI: 10.1039/d1fo03527d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, a novel peptide GPPGPA was screened from the collagen hydrolysates of Chinese giant salamander (Andrias davidianus) skin, and anti-diabetes mechanism was predicted by network pharmacology, and inhibitory...
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Material Basis and Mechanism of Chansu Injection for COVID-19 Treatment Based on Network Pharmacology and Molecular Docking Technology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:7697785. [PMID: 34671410 PMCID: PMC8523246 DOI: 10.1155/2021/7697785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 12/14/2022]
Abstract
Purpose The clinical efficacy of Chansu injection for COVID-19 treatment has been confirmed. Its mechanism of action remains unclear. We used network pharmacology and molecular docking technology to explore the potential material basis and mechanism of action of Chansu injection for COVID-19. Methods The main components of Chansu injection were determined using HPLC. The PharmMapper, SwissTargetPrediction, SEA, and TCMID databases were used to screen for the active ingredients and therapeutic targets of Chansu injection, while the OMIM and GeneCards Suite databases were used to search for COVID-19-related targets. The STRING database was used for protein-protein interaction (PPI) network construction and topological analysis, while DAVID was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the core targets. The main active compounds of Chansu injection were docked with 3CL protease, ACE2, RdRp, and spike protein. Results The three Chansu injection compounds were identified using HPLC. A total of 236 drug-related targets and 16,611 disease-related targets were identified, and 77 common targets were determined through mapping. The PPI mapping results revealed that 16 core targets were obtained through topological analysis and screening. Furthermore, GO and KEGG pathway enrichment analyses revealed that the PI3K and JAK-STAT signaling pathways are the major pathways. The molecular docking results suggest that the three Chansu injection components have high binding energies to the S protein. Conclusions The potential mechanism of Chansu injection for COVID-19 involves multiple targets and pathways, thereby providing a scientific basis for its clinical application and further research.
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Oh KK, Adnan M, Cho DH. Network Pharmacology-Based Study to Uncover Potential Pharmacological Mechanisms of Korean Thistle ( Cirsium japonicum var. maackii (Maxim.) Matsum.) Flower against Cancer. Molecules 2021; 26:5904. [PMID: 34641448 PMCID: PMC8513069 DOI: 10.3390/molecules26195904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
Cirsium japonicum var. maackii (Maxim.) Matsum. or Korean thistle flower is a herbal plant used to treat tumors in Korean folk remedies, but its essential bioactives and pharmacological mechanisms against cancer have remained unexplored. This study identified the main compounds(s) and mechanism(s) of the C. maackii flower against cancer via network pharmacology. The bioactives from the C. maackii flower were revealed by gas chromatography-mass spectrum (GC-MS), and SwissADME evaluated their physicochemical properties. Next, target(s) associated with the obtained bioactives or cancer-related targets were retrieved by public databases, and the Venn diagram selected the overlapping targets. The networks between overlapping targets and bioactives were visualized, constructed, and analyzed by RPackage. Finally, we implemented a molecular docking test (MDT) to explore key target(s) and compound(s) on AutoDockVina and LigPlot+. GC-MS detected a total of 34 bioactives and all were accepted by Lipinski's rules and therefore classified as drug-like compounds (DLCs). A total of 597 bioactive-related targets and 4245 cancer-related targets were identified from public databases. The final 51 overlapping targets were selected between the bioactive targets network and cancer-related targets. With Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, a total of 20 signaling pathways were manifested, and a hub signaling pathway (PI3K-Akt signaling pathway), a key target (Akt1), and a key compound (Urs-12-en-24-oic acid, 3-oxo, methyl ester) were selected among the 20 signaling pathways via MDT. Overall, Urs-12-en-24-oic acid, 3-oxo, methyl ester from the C. maackii flower has potent anti-cancer efficacy by inactivating Akt1 on the PI3K-Akt signaling pathway.
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Affiliation(s)
| | | | - Dong-Ha Cho
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (K.-K.O.); (M.A.)
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Oh KK, Adnan M, Cho DH. Network Pharmacology Study on Morus alba L. Leaves: Pivotal Functions of Bioactives on RAS Signaling Pathway and Its Associated Target Proteins against Gout. Int J Mol Sci 2021; 22:9372. [PMID: 34502281 PMCID: PMC8431517 DOI: 10.3390/ijms22179372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/27/2022] Open
Abstract
M. alba L. is a valuable nutraceutical plant rich in potential bioactive compounds with promising anti-gouty arthritis. Here, we have explored bioactives, signaling pathways, and key proteins underlying the anti-gout activity of M. alba L. leaves for the first-time utilizing network pharmacology. Bioactives in M. alba L. leaves were detected through GC-MS (Gas Chromatography-Mass Spectrum) analysis and filtered by Lipinski's rule. Target proteins connected to the filtered compounds and gout were selected from public databases. The overlapping target proteins between bioactives-interacted target proteins and gout-targeted proteins were identified using a Venn diagram. Bioactives-Proteins interactive networking for gout was analyzed to identify potential ligand-target and visualized the rich factor on the R package via the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway on STRING. Finally, a molecular docking test (MDT) between bioactives and target proteins was analyzed via AutoDock Vina. Gene Set Enrichment Analysis (GSEA) demonstrated that mechanisms of M. alba L. leaves against gout were connected to 17 signaling pathways on 26 compounds. AKT1 (AKT Serine/Threonine Kinase 1), γ-Tocopherol, and RAS signaling pathway were selected as a hub target, a key bioactive, and a hub signaling pathway, respectively. Furthermore, three main compounds (γ-Tocopherol, 4-Dehydroxy-N-(4,5-methylenedioxy-2-nitrobenzylidene) tyramine, and Lanosterol acetate) and three key target proteins-AKT1, PRKCA, and PLA2G2A associated with the RAS signaling pathway were noted for their highest affinity on MDT. The identified three key bioactives in M. alba L. leaves might contribute to recovering gouty condition by inactivating the RAS signaling pathway.
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Affiliation(s)
| | | | - Dong Ha Cho
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (K.K.O.); (M.A.)
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Sidhu H, Capalash N. Synergistic anti-cancer action of salicylic acid and cisplatin on HeLa cells elucidated by network pharmacology and in vitro analysis. Life Sci 2021; 282:119802. [PMID: 34237314 DOI: 10.1016/j.lfs.2021.119802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/13/2021] [Accepted: 06/30/2021] [Indexed: 01/20/2023]
Abstract
AIM To investigate the anti-cancer potential of salicylic acid and cisplatin combination in HeLa cells and the underlying mechanism. MAIN METHODS Drugs and disease targets were extracted from DrugBank, BATMAN-TCM, STITCH, PharmMapper and Comparative Toxigenomics Database. Cytoscape 3.8.2 was used to merge the protein-protein interaction networks and select core targets. GO and KEGG analysis was done using Metascape and WebGestalt. Effect of salicylic acid and cisplatin alone and in combination on cells viability was studied by MTT assay. The type of interaction between salicylic acid and cisplatin was determined by CompuSyn. Apoptosis was evaluated by molecular docking, Rhodamine-123, DAPI, AO/EtBr staining, flow cytometry, qRT-PCR and western blotting. Metastasis was studied using scratch assay and western blotting. UHRF1 transient silencing was performed by siRNA. KEY FINDINGS Out of 420, 1863 and 1362 respective targets of salicylic acid, cisplatin and cervical cancer, 18 core proteins were enriched in apoptosis and cell migration related pathways. IC50 value of cisplatin was reduced by 14 fold in combination with salicylic acid at IC20 (4 μM). There was loss of mitochondrial membrane potential and downregulation of UHRF1, pAkt, full length PARP and pro-caspase 3 expression. Transient silencing of UHRF1 also induced mitochondrial depolarization and apoptosis. The combination also exhibited anti-metastasis effect as it suppressed migration, upregulated PAX1 and downregulated MMP-2. SIGNIFICANCE Reduction in cisplatin concentration, enhanced anti-cancer effects and UHRF1 downregulation due to synergistic interaction between salicylic acid and cisplatin underscores the therapeutic importance of the combination to overcome chemo-resistance and side effects of cisplatin.
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Affiliation(s)
- Harsimran Sidhu
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh 160014, India.
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Network Pharmacology Study to Interpret Signaling Pathways of Ilex cornuta Leaves against Obesity. Processes (Basel) 2021. [DOI: 10.3390/pr9071106] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ilex cornuta Leaves (ICLs) are a representative and traditional prescription for controlling obesity. Nevertheless, the corresponding therapeutic compounds and related pharmacological mechanisms of such medication remain undocumented. The compounds from ICLs were identified by gas chromatography-mass spectrum (GC-MS), and SwissADME confirmed their physicochemical properties. Next, the target proteins related to compounds or obesity-associated proteins were retrieved from public databases. RPackage constructed the protein–protein interaction (PPI) network, a bubble chart, and signaling pathways–target proteins–compounds (STC) network. Lastly, a molecular docking test (MDT) was performed to evaluate the affinity between target proteins and ligands from ICLs. GC-MS detected a total of 51 compounds from ICLs. The public databases identified 219 target proteins associated with selective compounds, 3028 obesity-related target proteins, and 118 overlapping target proteins. Moreover, the STC network revealed 42 target proteins, 22 signaling pathways, and 39 compounds, which were viewed to be remedially significant. The NOD-like receptor (NLR) signaling pathway was considered a key signaling pathway from the bubble chart. In parallel, the MDT identified three target proteins (IL6, MAPK1, and CASP1) on the NLR signaling pathway and four compounds against obesity. Overall, four compounds from ICLs might show anti-obesity synergistic efficacy by inactivating the NLR signaling pathway.
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Oh KK, Adnan M, Cho DH. Network pharmacology approach to decipher signaling pathways associated with target proteins of NSAIDs against COVID-19. Sci Rep 2021; 11:9606. [PMID: 33953223 PMCID: PMC8100301 DOI: 10.1038/s41598-021-88313-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/12/2021] [Indexed: 02/08/2023] Open
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) showed promising clinical efficacy toward COVID-19 (Coronavirus disease 2019) patients as potent painkillers and anti-inflammatory agents. However, the prospective anti-COVID-19 mechanisms of NSAIDs are not evidently exposed. Therefore, we intended to decipher the most influential NSAIDs candidate(s) and its novel mechanism(s) against COVID-19 by network pharmacology. FDA (U.S. Food & Drug Administration) approved NSAIDs (19 active drugs and one prodrug) were used for this study. Target proteins related to selected NSAIDs and COVID-19 related target proteins were identified by the Similarity Ensemble Approach, Swiss Target Prediction, and PubChem databases, respectively. Venn diagram identified overlapping target proteins between NSAIDs and COVID-19 related target proteins. The interactive networking between NSAIDs and overlapping target proteins was analyzed by STRING. RStudio plotted the bubble chart of the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis of overlapping target proteins. Finally, the binding affinity of NSAIDs against target proteins was determined through molecular docking test (MDT). Geneset enrichment analysis exhibited 26 signaling pathways against COVID-19. Inhibition of proinflammatory stimuli of tissues and/or cells by inactivating the RAS signaling pathway was identified as the key anti-COVID-19 mechanism of NSAIDs. Besides, MAPK8, MAPK10, and BAD target proteins were explored as the associated target proteins of the RAS. Among twenty NSAIDs, 6MNA, Rofecoxib, and Indomethacin revealed promising binding affinity with the highest docking score against three identified target proteins, respectively. Overall, our proposed three NSAIDs (6MNA, Rofecoxib, and Indomethacin) might block the RAS by inactivating its associated target proteins, thus may alleviate excessive inflammation induced by SARS-CoV-2.
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Affiliation(s)
- Ki Kwang Oh
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Korea
| | - Md Adnan
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Korea
| | - Dong Ha Cho
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Korea.
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Oh KK, Adnan M, Cho DH. Network pharmacology of bioactives from Sorghum bicolor with targets related to diabetes mellitus. PLoS One 2020; 15:e0240873. [PMID: 33382706 PMCID: PMC7774932 DOI: 10.1371/journal.pone.0240873] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sorghum bicolor (SB) is rich in protective phytoconstituents with health benefits and regarded as a promising source of natural anti-diabetic substance. However, its comprehensive bioactive compound(s) and mechanism(s) against type-2 diabetes mellitus (T2DM) have not been exposed. Hence, we implemented network pharmacology to identify its key compounds and mechanism(s) against T2DM. METHODS Compounds in SB were explored through GC-MS and screened by Lipinski's rule. Genes associated with the selected compounds or T2DM were extracted from public databases, and the overlapping genes between SB-compound related genes and T2DM target genes were identified using Venn diagram. Then, the networking between selected compounds and overlapping genes was constructed, visualized, and analyzed by RStudio. Finally, affinity between compounds and genes was evaluated via molecular docking. RESULTS GC-MS analysis of SB detected a total of 20 compounds which were accepted by the Lipinski's rule. A total number of 16 compounds-related genes and T2DM-related genes (4,763) were identified, and 81 overlapping genes between them were selected. Gene set enrichment analysis exhibited that the mechanisms of SB against T2DM were associated with 12 signaling pathways, and the key mechanism might be to control blood glucose level by activating PPAR signaling pathway. Furthermore, the highest affinities were noted between four main compounds and six genes (FABP3-Propyleneglyco monoleate, FABP4-25-Oxo-27-norcholesterol, NR1H3-Campesterol, PPARA-β-sitosterol, PPARD-β-sitosterol, and PPARG-β-sitosterol). CONCLUSION Our study overall suggests that the four key compounds detected in SB might ameliorate T2DM severity by activating the PPAR signaling pathway.
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Affiliation(s)
- Ki Kwang Oh
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Md. Adnan
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Dong Ha Cho
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
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