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Jain NK, Tailang M, Chandrasekaran B, Khazaleh N, Thangavel N, Makeen HA, Albratty M, Najmi A, Alhazmi HA, Zoghebi K, Alagusundaram M, Jain HK. Integrating network pharmacology with molecular docking to rationalize the ethnomedicinal use of Alchornea laxiflora (Benth.) Pax & K. Hoffm. for efficient treatment of depression. Front Pharmacol 2024; 15:1290398. [PMID: 38505421 PMCID: PMC10949534 DOI: 10.3389/fphar.2024.1290398] [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: 09/08/2023] [Accepted: 02/12/2024] [Indexed: 03/21/2024] Open
Abstract
Background: Alchornea laxiflora (Benth.) Pax & K. Hoffm. (A. laxiflora) has been indicated in traditional medicine to treat depression. However, scientific rationalization is still lacking. Hence, this study aimed to investigate the antidepressant potential of A. laxiflora using network pharmacology and molecular docking analysis. Materials and methods: The active compounds and potential targets of A. laxiflora and depression-related targets were retrieved from public databases, such as PubMed, PubChem, DisGeNET, GeneCards, OMIM, SwissTargetprediction, BindingDB, STRING, and DAVID. Essential bioactive compounds, potential targets, and signaling pathways were predicted using in silico analysis, including BA-TAR, PPI, BA-TAR-PATH network construction, and GO and KEGG pathway enrichment analysis. Later on, with molecular docking analysis, the interaction of essential bioactive compounds of A. laxiflora and predicted core targets of depression were verified. Results: The network pharmacology approach identified 15 active compounds, a total of 219 compound-related targets, and 14,574 depression-related targets with 200 intersecting targets between them. SRC, EGFR, PIK3R1, AKT1, and MAPK1 were the core targets, whereas 3-acetyloleanolic acid and 3-acetylursolic acid were the most active compounds of A. laxiflora with anti-depressant potential. GO functional enrichment analysis revealed 129 GO terms, including 82 biological processes, 14 cellular components, and 34 molecular function terms. KEGG pathway enrichment analysis yielded significantly enriched 108 signaling pathways. Out of them, PI3K-Akt and MAPK signaling pathways might have a key role in treating depression. Molecular docking analysis results exhibited that core targets of depression, such as SRC, EGFR, PIK3R1, AKT1, and MAPK1, bind stably with the analyzed bioactive compounds of A. laxiflora. Conclusion: The present study elucidates the bioactive compounds, potential targets, and pertinent mechanism of action of A. laxiflora in treating depression. A. laxiflora might exert an antidepressant effect by regulating PI3K-Akt and MAPK signaling pathways. However, further investigations are required to validate.
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Affiliation(s)
- Nem Kumar Jain
- School of Pharmacy, ITM University, Gwalior, Madhya Pradesh, India
- School of Studies in Pharmaceutical Sciences, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Mukul Tailang
- School of Studies in Pharmaceutical Sciences, Jiwaji University, Gwalior, Madhya Pradesh, India
| | | | | | - Neelaveni Thangavel
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Hafiz A. Makeen
- Pharmacy Practice Research Unit, Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Hassan Ahmad Alhazmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - M. Alagusundaram
- School of Pharmacy, ITM University, Gwalior, Madhya Pradesh, India
| | - Hemant Kumar Jain
- Department of General Medicine, Government Medical College, Datia, Madhya Pradesh, India
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Wan Z, Rasheed M, Li Y, Li Q, Wang P, Li J, Chen Z, Du J, Deng Y. miR-218-5p and miR-320a-5p as Biomarkers for Brain Disorders: Focus on the Major Depressive Disorder and Parkinson's Disease. Mol Neurobiol 2023; 60:5642-5654. [PMID: 37329382 DOI: 10.1007/s12035-023-03391-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
Depression is one of the early and most persistent non-motor symptoms of Parkinson's disease (PD), which remains ignored, resulting in the underdiagnosis of PD. Unfortunately, scarce studies and the non-availability of diagnostic strategies cause countless complications, highlighting the need for appropriate diagnostic biomarkers. Recently, brain-enriched miRNAs regulating vital neurological functions have been proposed as potent biomarkers for therapeutic strategies. Therefore, the present study is aimed to identify the brain-enriched miR-218-5p and miR-320-5p in the serum of the Chinese depressed PD patients (n = 51) than healthy controls (n = 51) to identify their potency as biomarkers. For this purpose, depressive PD patients were recruited based on HAMA and HAMD scores and miR-218-5p and miR-320-5p and IL-6, and S100B levels were analyzed using real-time PCR (qRT-PCR) and ELISA assay, respectively. In silico analysis was performed to identify key biological pathways and hub genes involved in the psychopathology of depression in PD. Here, we found significantly downregulated miR-218-5p and miR-320-5p following higher levels of IL-6 and S100B in depressed PD patients than in control (p < 0.05). The correlation analysis revealed that both miRNAs were negatively correlated with HAMA and HAMD, and IL-6 scores, along with a positive correlation with PD duration and LEDD medication. ROC analysis showed AUC above 75% in both miRNAs in depressed PD patients, and in silico analysis revealed that both miRNA's targets regulate key neurological pathways such as axon guidance, dopaminergic synapse, and circadian rhythm. Additional analysis revealed PIK3R1, ATRX, BM1, PCDHA10, XRCC5, PPP1CB, MLLT3, CBL, PCDHA4, PLCG1, YWHAZ, CDH2, AGO3, PCDHA3, and PCDHA11 as hub-genes in PPI network. In summary, our findings show that miR-218-5p and miR-320-5p can be utilized as future biomarkers for depression in PD patients, which may aid in the early diagnosis and treatment of Parkinson's disease.
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Affiliation(s)
- Zhirong Wan
- Department of Neurology, Aerospace Central Hospital, Beijing, 100049, People's Republic of China
| | - Madiha Rasheed
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Yumeng Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Qin Li
- Department of Neurology, Aerospace Central Hospital, Beijing, 100049, People's Republic of China
| | - Peifu Wang
- Department of Neurology, Aerospace Central Hospital, Beijing, 100049, People's Republic of China
| | - Jilai Li
- Department of Neurology, Aerospace Central Hospital, Beijing, 100049, People's Republic of China
| | - Zixuan Chen
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Jichen Du
- Department of Neurology, Aerospace Central Hospital, Beijing, 100049, People's Republic of China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.
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Andalib KMS, Ahmed A, Habib A. Omics data analysis reveals common molecular basis of small cell lung cancer and COVID-19. J Biomol Struct Dyn 2023:1-16. [PMID: 37708006 DOI: 10.1080/07391102.2023.2257803] [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: 05/26/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
The impact of COVID-19 infection on individuals with small cell lung cancer (SCLC) poses a serious threat. Unfortunately, the molecular basis of this severe comorbidity has yet to be elucidated. The present study addresses this gap utilizing publicly available omics data of COVID-19 and SCLC to explore the key molecules and associated pathways involved in the convergence of these diseases. Findings revealed 402 genes, that exhibited differential expression patterns in SCLC patients and also play a pivotal role in COVID-19 pathogenesis. Subsequent functional enrichment analyses identified relevant ontologies and pathways that are significantly associated with these genes, revealing important insights into their potential biological, molecular and cellular functions. The protein-protein interaction network, constructed under four combinatorial topological assessments, highlighted SMAD3, CAV1, PIK3R1, and FN1 as the primary components to this comorbidity. Our results suggest that these components significantly regulate this cross-talk triggering the PI3K-AKT and TGF-β signaling pathways. Lastly, this study made a multi-step computational attempt and identified corylifol A and ginkgetin from natural sources that can potentially inhibit these components. Therefore, the outcomes of this study offer novel perspectives on the common molecular mechanisms underlying SCLC and COVID-19 and present future opportunities for drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K M Salim Andalib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Asif Ahmed
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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Zhang J, Zhou N, Wang Y, Liu T, Cao Y, Feng W, Zheng X. Protective effects of Descurainia sophia seeds extract and its fractions on pulmonary edema by untargeted urine and serum metabolomics strategy. Front Pharmacol 2023; 14:1080962. [PMID: 36865914 PMCID: PMC9971919 DOI: 10.3389/fphar.2023.1080962] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
Background: Descurainia sophia seeds (DS) is a herbal medicine in traditional Chinese medicine (TCM) for treating lung diseases. We aimed to evaluate the therapeutic effect of DS and five of its fractions upon pulmonary edema (PE) through metabolomics analysis (MA) of urine and serum samples of rats. Methods: A PE model was established by intrathoracic injection of carrageenan. Rats were pretreated with DS extract or its five fractions (polysaccharides (DS-Pol); oligosaccharides (DS-Oli); flavonoid glycosides (DS-FG); flavonoid aglycone (DS-FA); fat oil fraction (DS-FO)) for seven consecutive days. Forty-eight hours after carrageenan injection, lung tissues were subjected to histopathology. MA of urine and serum was done by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry, respectively. Principal component analysis and orthogonal partial least squares-discriminant analysis were operated for the MA of rats and potential biomarkers related to treatment. Heatmaps and metabolic networks were constructed to explore how DS and its five fractions act against PE. Results: DS and its five fractions could all attenuate pathologic lung injury to different degrees, and DS-Oli, DS-FG, and DS-FO had a more potent effect compared with DS-Pol and DS-FA. DS-Oli, DS-FG, DS-FA, and DS-FO could regulate the metabolic profiles of PE rats, but DS-Pol was less potent. According to MA, the five fractions could improve PE to some degree due to their anti-inflammatory, immunoregulatory, and renoprotective activities by mediating the metabolism of taurine, tryptophan, and arachidonic acid. However, DS-Oli, DS-FG, and DS-FO had more important roles in edema-fluid reabsorption, and reduction of vascular leakage through regulating the metabolism of phenylalanine, sphingolipid and bile acid. Finally, heatmaps and hierarchical clustering analysis indicated DS-Oli, DS-FG, and DS-FO to be more efficacious than DS-Pol or DS-FA against PE. The five fractions of DS had a synergistic effect on PE from different aspects, thereby constituting the entire efficacy of DS. DS-Oli, DS-FG, or DS-FO could be used as an alternative to DS. Conclusion: MA combined with use of DS and its fractions provided novel insights into the mechanism of action of TCM.
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Affiliation(s)
- Jinying Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Ning Zhou
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China,The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Yongxiang Wang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Tong Liu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yumin Cao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Weisheng Feng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China,The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China,Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan, Education Ministry of P.R, Zhengzhou, China,*Correspondence: Weisheng Feng, ; Xiaoke Zheng,
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China,The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China,Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan, Education Ministry of P.R, Zhengzhou, China,*Correspondence: Weisheng Feng, ; Xiaoke Zheng,
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Li SJ, Wang YQ, Zhuang G, Jiang X, Shui D, Wang XY. Overall metabolic network analysis of urine in hyperlipidemic rats treated with Bidens bipinnata L. Biomed Chromatogr 2023; 37:e5509. [PMID: 36097410 DOI: 10.1002/bmc.5509] [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: 04/14/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 12/15/2022]
Abstract
Hyperlipidemia has been highlighted as one of the most prominent and global chronic conditions nowadays. Bidens bipinnata L. (BBL), a folk medicine in contemporary China, has efficacy in the treatment of hyperlipidemia (HLP) in China. Although some physiological and pathological function parameters of hyperlipidemia have been investigated, little information about the changes in small metabolites in biofluids has been reported. In the present study, global metabolic profiling with high-performance liquid chromatography-linear ion trap/Orbitrap high-resolution mass spectrometry (HPLC-LTQ/Orbitrap MS) combined with a pattern recognition method was performed to discover the underlying lipid-regulating mechanisms of BBL on hyperlipidemic rats induced by high-fat diet (HFD). The total of four metabolites, up- or down-regulated (p < 0.05 or 0.01), were identified and contributed to the progression of hyperlipidemia. These promising identified biomarkers underpin the metabolic pathway, including glyoxylate and dicarboxylate metabolism, the TCA cycle, sphingolipid metabolism and purine metabolism. They are disturbed in hyperlipidemic rats, and are identified using pathway analysis with MetPA. The altered metabolite indices could be regulated closer to normal levels after BBL intervention. The results demonstrated that urinary metabolomics is a powerful tool in the clinical diagnosis and treatment of hyperlipidemia to provide information on changes in metabolite pathways.
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Affiliation(s)
- Shu-Jiao Li
- Center of Scientific Research, and Henan Key Laboratory of Traditional Chinese Medicine for Effective Substances and Quality Control, Nanyang Medical College, Nanyang, China
| | - Yu-Qing Wang
- Center of Scientific Research, and Henan Key Laboratory of Traditional Chinese Medicine for Effective Substances and Quality Control, Nanyang Medical College, Nanyang, China
| | - Guo Zhuang
- Center of Scientific Research, and Henan Key Laboratory of Traditional Chinese Medicine for Effective Substances and Quality Control, Nanyang Medical College, Nanyang, China
| | - Xu Jiang
- Center of Scientific Research, and Henan Key Laboratory of Traditional Chinese Medicine for Effective Substances and Quality Control, Nanyang Medical College, Nanyang, China
| | - Dong Shui
- Center of Scientific Research, and Henan Key Laboratory of Traditional Chinese Medicine for Effective Substances and Quality Control, Nanyang Medical College, Nanyang, China
| | - Xiao-Yu Wang
- Center of Scientific Research, and Henan Key Laboratory of Traditional Chinese Medicine for Effective Substances and Quality Control, Nanyang Medical College, Nanyang, China
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Liu S, Feng Y, Huang Y, Jiang X, Tang C, Tang F, Zeng C, Liu L. A GM1 gangliosidosis mutant mouse model exhibits activated microglia and disturbed autophagy. Exp Biol Med (Maywood) 2021; 246:1330-1341. [PMID: 33583210 PMCID: PMC8371306 DOI: 10.1177/1535370221993052] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/13/2021] [Indexed: 11/15/2022] Open
Abstract
GM1 gangliosidosis is a rare lysosomal storage disease caused by a deficiency of β-galactosidase due to mutations in the GLB1 gene. We established a C57BL/6 mouse model with Glb1G455R mutation using CRISPR/Cas9 genome editing. The β-galactosidase enzyme activity of Glb1G455R mice measured by fluorometric assay was negligible throughout the whole body. Mutant mice displayed no marked phenotype at eight weeks. After 16 weeks, GM1 ganglioside accumulation in the brain of mutant mice was observed by immunohistochemical staining. Meanwhile, a declining performance in behavioral tests was observed among mutant mice from 16 to 32 weeks. As the disease progressed, the neurological symptoms of mutant mice worsened, and they then succumbed to the disease by 47 weeks of age. We also observed microglia activation and proliferation in the cerebral cortex of mutant mice at 16 and 32 weeks. In these activated microglia, the level of autophagy regulator LC3 was up-regulated but the mRNA level of LC3 was normal. In conclusion, we developed a novel murine model that mimicked the chronic phenotype of human GM1. This Glb1G455R murine model is a practical in vivo model for studying the pathogenesis of GM1 gangliosidosis and exploring potential therapies.
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Affiliation(s)
- Sichi Liu
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yuyu Feng
- Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yonglan Huang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Xiaoling Jiang
- Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Chengfang Tang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Fang Tang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Chunhua Zeng
- Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
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