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Chowdhury MR, Reddy RVS, Nampoothiri NK, Erva RR, Vijaykumar SD. Exploring bioactive natural products for treating neurodegenerative diseases: a computational network medicine approach targeting the estrogen signaling pathway in amyotrophic lateral sclerosis and Parkinson's disease. Metab Brain Dis 2025; 40:169. [PMID: 40184012 DOI: 10.1007/s11011-025-01585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 03/17/2025] [Indexed: 04/05/2025]
Abstract
Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) share overlapping molecular mechanisms, including estrogen signaling dysregulation, oxidative stress, and neuroinflammation. Standard treatments often lead to adverse effects due to unintended cross-talk with the estrogen signaling pathway. Identifying key regulatory genes and bioactive plant-derived compounds that modulate estrogen signaling without interfering with standard therapies offers a promising neuroprotective strategy. A network medicine and systems biology approach was used, beginning with the screening of 29 medicinal plants for ALS and 49 for PD, identifying 12 shared plants with neuroprotective potential. Bioactive compounds were screened for gene, protein, and pathway interactions, leading to target prediction (846 ALS-related and 690 PD-related targets) and disease association mining, which identified 93 overlapping genes (OGs). Protein-protein interaction (PPI) network analysis and MCODE clustering revealed ESR1, EGFR, and SRC as key hub-bottleneck (HB) genes, further validated via differential gene expression analysis. Gene ontology (GO) and pathway enrichment analyses revealed significant enrichment in estrogen signaling confirming the involvement of HB genes in neurodegenerative disease progression. Differential expression analysis confirmed ESR1 upregulation in ALS but downregulation in PD, suggesting a converse disease-specific regulatory pattern. Gene regulatory network (GRN) analysis identified hsa-miR-145-5p (ALS) and hsa-miR-181a-5p (PD) as key regulators, while FOXC1, GATA2, and TP53 emerged as crucial transcription factors (TFs) influencing disease progression. Molecular docking and MD simulations validated strong and stable interactions of Eupalitin (CYP19A1, -9.0 kcal/mol), Hesperetin (ESR1, -8.1 kcal/mol), and Sumatrol (PIK3CA, -8.9 kcal/mol). These phytochemicals, derived from Rosmarinus officinalis, Artemisia scoparia, Ocimum tenuiflorum, and Indigofera tinctoria, maintained stable hydrogen bonding and hydrophobic interactions for over 30% of a 25 ns simulation, supporting their therapeutic potential. The identification of ESR1, EGFR, and SRC as key targets, alongside estrogen signaling involvement, highlights the need for targeted nutraceutical interventions. These findings pave the way for safer, plant-based therapies that mitigate neurodegeneration while preserving estrogen signaling integrity, offering a promising adjuvant strategy alongside existing treatments.
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Affiliation(s)
- Mayank Roy Chowdhury
- Department of Biotechnology, National Institute of Technology, Tadepalligudem, Andhra Pradesh, 534101, India
| | - Ramireddy Venkata Sai Reddy
- Department of Biotechnology, National Institute of Technology, Tadepalligudem, Andhra Pradesh, 534101, India
| | - Navaneeth K Nampoothiri
- Department of Biotechnology, National Institute of Technology, Tadepalligudem, Andhra Pradesh, 534101, India
| | - Rajeswara Reddy Erva
- Department of Biotechnology, National Institute of Technology, Tadepalligudem, Andhra Pradesh, 534101, India
| | - Sudarshana Deepa Vijaykumar
- Department of Biotechnology, National Institute of Technology, Tadepalligudem, Andhra Pradesh, 534101, India.
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Liu X, Ding Y, Jiang C, Ma X, Xin Y, Li Y, Zhang S, Shao B. Astragaloside IV ameliorates radiation-induced nerve cell damage by activating the BDNF/TrkB signaling pathway. Phytother Res 2023; 37:4102-4116. [PMID: 37226643 DOI: 10.1002/ptr.7872] [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: 10/10/2022] [Revised: 04/23/2023] [Accepted: 05/03/2023] [Indexed: 05/26/2023]
Abstract
Radiation can induce nerve cell damage. Synapse connectivity and functionality are thought to be the essential foundation of all cognitive functions. Therefore, treating and preventing damage to synaptic structure and function is an urgent challenge. Astragaloside IV (AS-IV) is a glycoside extracted from Astragalus membranaceus (Fisch.). Bunge is a widely used traditional Chinese medicine in China with various pharmacological properties, including protective effects on the central nervous system (CNS). In this study, the effect of AS-IV on synapse damage and BDNF/TrkB signaling pathway in radiated C57BL/6 mice with X-rays was investigated. PC12 cells and primary cortical neurons were exposed to UVA in vitro. Open field test and rotarod test were used to observe the effects of AS-IV on the motor and explore the abilities of radiated mice. The pathological changes in the brain were observed by hematoxylin and eosin and Nissl staining. Immunofluorescence analysis was used to detect the synapse damage. The expressions of the BDNF/TrkB pathway and neuroprotection-related molecules were detected by Western blotting and Quantitative-RTPCR, respectively. The results showed that AS-IV could improve the motor and explore abilities of radiated mice, reduce pathological damage to the cortex, enhance neuroprotection functions, and activate BDNF/TrkB pathway. In conclusion, AS-IV could relieve radiation-induced synapse damage, at least partly through the BDNF/TrkB pathway.
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Affiliation(s)
- Xin Liu
- Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yanping Ding
- School of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Chenxin Jiang
- Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Ma
- Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuanyuan Xin
- Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yingdong Li
- School of Traditional Chinese and Western Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Shengxiang Zhang
- Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Baoping Shao
- Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, China
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Lin L, Chen W, Yao C, Wu L, Yan Q, Cai X, Zhu S, Lao Y, Zhang G, Lan X, Chen Y. Exploring the target and molecular mechanism of Astragalus membranaceus in the treatment of vascular cognitive impairment based on network pharmacology and molecular docking. Medicine (Baltimore) 2023; 102:e33063. [PMID: 36961195 PMCID: PMC10036060 DOI: 10.1097/md.0000000000033063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/01/2023] [Indexed: 03/25/2023] Open
Abstract
Astragalus membranaceus (AM) is a traditional Chinese herbal medicine extensively utilized in vascular cognitive impairment (VCI) treatment. However, due to the complex components of AM, its exact molecular mechanism remains unclear. Therefore, this study investigated the target and molecular mechanism of AM to treat VCI based on network pharmacology and molecular docking. Firstly, the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, STITCH, and SwissTargetPrediction were utilized to gather the primary active ingredients of AM. The potential therapeutic targets of VCI were collected through GeneCards, OMIM, and DisGeNET databases. Secondly, the protein-protein interaction network was built using the STRING database. The enrichment analysis of gene ontology and the Kyoto Encyclopedia of Genes and Genome pathways was carried out in the R language. Finally, The network topology calculation of Cytoscape software was combined with module analysis to predict the binding properties of its active ingredients and targets. Twenty effective compounds and 733 targets were screened from AM, among which 158 targets were seen as possible targets of AM to treat VCI. MAPK3 and MMP9 were the critical targets of AM intervention in VCI. The crucial pathways include PI3K/Akt, MAPK, Rap1, and Ras signaling pathways. Besides, calycosin and quercetin might be the potential active compounds of AM for VCI treatment. AM intervenes in VCI through a multi-ingredient, multi-target, and multi-pathway coordination mechanism. These findings provide a foundation for a deeper understanding of the molecular mechanisms by which AM is effective in treating VCI.
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Affiliation(s)
- Long Lin
- Guangxi University of Chinese Medicine, Nanning, China
- Nanfang College·Guangzhou, Guangzhou, China
| | - Wei Chen
- Guangxi University of Chinese Medicine, Nanning, China
| | - Chun Yao
- Guangxi University of Chinese Medicine, Nanning, China
| | - Lin Wu
- Guangxi University of Chinese Medicine, Nanning, China
| | - Qian Yan
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | | | - Sijing Zhu
- University of Hong Kong, Hong Kong, China
| | - Yilin Lao
- Guangxi University of Chinese Medicine, Nanning, China
| | - Guangfa Zhang
- Guangxi University of Chinese Medicine, Nanning, China
| | - Xuelin Lan
- Guangxi University of Chinese Medicine, Nanning, China
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Katiyar D, Singhal S, Bansal P, Nagarajan K, Grover P. Nutraceuticals and phytotherapeutics for holistic management of amyotrophic lateral sclerosis. 3 Biotech 2023; 13:62. [PMID: 36714551 PMCID: PMC9880136 DOI: 10.1007/s13205-023-03475-5] [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: 10/18/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Amyotrophic lateral sclerosis" (ALS) is a progressive neuronal disorder that affects sensory neurons in the brain and spinal cord, causing loss of muscle control. Moreover, additional neuronal subgroups as well as glial cells such as microglia, astrocytes, and oligodendrocytes are also thought to play a role in the aetiology. The disease affects upper motor neurons and lowers motor neurons and leads to that either lead to muscle weakness and wasting in the arms, legs, trunk and periventricular area. Oxidative stress, excitotoxicity, programmed cell death, altered neurofilament activity, anomalies in neurotransmission, abnormal protein processing and deterioration, increased inflammation, and mitochondrial dysfunction may all play a role in the progression of ALS. There are presently hardly FDA-approved drugs used to treat ALS, and they are only beneficial in slowing the progression of the disease and enhancing functions in certain individuals with ALS, not really in curing or preventing the illness. These days, researchers focus on understanding the pathogenesis of the disease by targeting several mechanisms aiming to develop successful treatments for ALS. This review discusses the epidemiology, risk factors, diagnosis, clinical features, pathophysiology, and disease management. The compilation focuses on alternative methods for the management of symptoms of ALS with nutraceuticals and phytotherapeutics.
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Affiliation(s)
- Deepti Katiyar
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, Uttar Pradesh 201206 India
| | - Shipra Singhal
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, Uttar Pradesh 201206 India
| | - Priya Bansal
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, Uttar Pradesh 201206 India
| | - K. Nagarajan
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, Uttar Pradesh 201206 India
| | - Parul Grover
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, Uttar Pradesh 201206 India
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Li J, Yu H, Yang C, Ma T, Dai Y. Therapeutic Potential and Molecular Mechanisms of Echinacoside in Neurodegenerative Diseases. Front Pharmacol 2022; 13:841110. [PMID: 35185590 PMCID: PMC8855092 DOI: 10.3389/fphar.2022.841110] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Echinacoside (ECH) is a natural phenylethanoid glycoside (PhG) in Cistanche tubulosa. A large number of studies have shown that ECH has very promising potential in the inhibition of neurodegenerative disease progression. Experimental studies strongly suggest that ECH exhibits a variety of beneficial effects associated with in neuronal function, including protecting mitochondrial function, anti-oxidative stress, anti-inflammatory, anti-endoplasmic reticulum stress (ERS), regulating autophagy and so on. The aim of this paper is to provide an extensive and actual summarization of ECH and its neuroprotective efficacy in prevention and treatment of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and so on, based on published data from both in vivo and in vitro studies. There is a growing evidence that ECH may serve as an efficacious and safe substance in the future to counteract neurodegenerative disease.
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Affiliation(s)
- Jin Li
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hongni Yu
- Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Chuan Yang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tao Ma
- Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yuan Dai
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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