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Sasikumar DSN, Thiruselvam P, Sundararajan V, Ravindran R, Gunasekaran S, Madathil D, Kaliamurthi S, Peslherbe GH, Selvaraj G, Sudhakaran SL. Insights into dietary phytochemicals targeting Parkinson's disease key genes and pathways: A network pharmacology approach. Comput Biol Med 2024; 172:108195. [PMID: 38460310 DOI: 10.1016/j.compbiomed.2024.108195] [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: 09/03/2023] [Revised: 01/26/2024] [Accepted: 02/18/2024] [Indexed: 03/11/2024]
Abstract
Parkinson's disease (PD) is a complex neurological disease associated with the degeneration of dopaminergic neurons. Oxidative stress is a key player in instigating apoptosis in dopaminergic neurons. To improve the survival of neurons many dietary phytochemicals have gathered significant attention recently. Thus, the present study implements a comprehensive network pharmacology approach to unravel the mechanisms of action of dietary phytochemicals that benefit disease management. A literature search was performed to identify ligands (i.e., comprising dietary phytochemicals and Food and Drug Administration pre-approved PD drugs) in the PubMed database. Targets associated with selected ligands were extracted from the search tool for interactions of chemicals (STITCH) database. Then, the construction of a gene-gene interaction (GGI) network, analysis of hub-gene, functional and pathway enrichment, associated transcription factors, miRNAs, ligand-target interaction network, docking were performed using various bioinformatics tools together with molecular dynamics (MD) simulations. The database search resulted in 69 ligands and 144 unique targets. GGI and subsequent topological measures indicate histone acetyltransferase p300 (EP300), mitogen-activated protein kinase 1 (MAPK1) or extracellular signal-regulated kinase (ERK)2, and CREB-binding protein (CREBBP) as hub genes. Neurodegeneration, MAPK signaling, apoptosis, and zinc binding are key pathways and gene ontology terms. hsa-miR-5692a and SCNA gene-associated transcription factors interact with all the 3 hub genes. Ligand-target interaction (LTI) network analysis suggest rasagiline and baicalein as candidate ligands targeting MAPK1. Rasagiline and baicalein form stable complexes with the Y205, K330, and V173 residues of MAPK1. Computational molecular insights suggest that baicalein and rasagiline are promising preclinical candidates for PD management.
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Affiliation(s)
- Devi Soorya Narayana Sasikumar
- Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Premkumar Thiruselvam
- Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Vino Sundararajan
- Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Radhika Ravindran
- Department of Biotechnology, Indian Institute of Technology (Madras), Chennai, TN, 600036, India
| | - Shoba Gunasekaran
- Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College, Chennai, TN, 600106, India
| | - Deepa Madathil
- Jindal Institute of Behavioral Sciences, O.P Jindal Global University, Sonipat, Haryana, 131001, India
| | - Satyavani Kaliamurthi
- Centre for Research in Molecular Modeling (CERMM), Department of Chemistry and Biochemistry, Concordia University, Loyola Campus, Montreal, QC, H4B 1R6, Canada
| | - Gilles H Peslherbe
- Centre for Research in Molecular Modeling (CERMM), Department of Chemistry and Biochemistry, Concordia University, Loyola Campus, Montreal, QC, H4B 1R6, Canada
| | - Gurudeeban Selvaraj
- Centre for Research in Molecular Modeling (CERMM), Department of Chemistry and Biochemistry, Concordia University, Loyola Campus, Montreal, QC, H4B 1R6, Canada; Bioinformatics Unit, Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS) University, Chennai, TN, 600077, India.
| | - Sajitha Lulu Sudhakaran
- Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India.
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Detection of Herbal Combinations and Pharmacological Mechanisms of Clinical Prescriptions for Coronary Heart Disease Using Data Mining and Network Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:9234984. [PMID: 34725557 PMCID: PMC8557045 DOI: 10.1155/2021/9234984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022]
Abstract
Though widely used in the treatment of coronary heart disease (CHD), the mechanism of traditional Chinese medicine (TCM) is still unclear because of its complex prescription rules. This study prospectively collected 715 prescriptions of TCM for the treatment of CHD. The characteristics of TCM in prescriptions were described and analyzed, and the rules of prescriptions were analyzed by using association rules. Frequency statistics showed that the high-frequency herbs with a frequency of more than 60% were Gan-cao, Huang-qi, Dang-gui, Chuan-xiong, Yan-hu-suo, and San-qi. The high-frequency herb combinations were summarized by using association rules. By using the method of the “Top N groups” to excavate the empirical prescriptions, the basic prescriptions for treating CHD were summarized. We named the intersection herbs of the basic prescriptions and the high frequency herbs as the core herbal prescription. To explore the possible mechanisms underlying the anti-CHD effect of the core herbal prescription, the bioactive components of core herbal prescription and their targets were screened out by using network pharmacology. Molecular docking was performed between the bioactive components and core targets. A total of 28 potential active ingredients and 5 core targets were identified for the treatment of CHD with core herbal prescription. The enrichment analysis results indicated that the mechanism of action mainly involved neuroactive ligand-receptor interaction and calcium signaling pathway. The commonly used herbal pairs for CHD with qi deficiency and blood stasis syndrome were Huang-qi and Dang-gui. The mechanism of action of common herbal pairs was also studied by network pharmacology. This study summarized the prescription rule of TCM in the treatment of CHD and may provide a new idea for the treatment of CHD.
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Koszła O, Stępnicki P, Zięba A, Grudzińska A, Matosiuk D, Kaczor AA. Current Approaches and Tools Used in Drug Development against Parkinson's Disease. Biomolecules 2021; 11:897. [PMID: 34208760 PMCID: PMC8235487 DOI: 10.3390/biom11060897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease is a progressive neurodegenerative disorder characterized by the death of nerve cells in the substantia nigra of the brain. The treatment options for this disease are very limited as currently the treatment is mainly symptomatic, and the available drugs are not able to completely stop the progression of the disease but only to slow it down. There is still a need to search for new compounds with the most optimal pharmacological profile that would stop the rapidly progressing disease. An increasing understanding of Parkinson's pathogenesis and the discovery of new molecular targets pave the way to develop new therapeutic agents. The use and selection of appropriate cell and animal models that better reflect pathogenic changes in the brain is a key aspect of the research. In addition, computer-assisted drug design methods are a promising approach to developing effective compounds with potential therapeutic effects. In light of the above, in this review, we present current approaches for developing new drugs for Parkinson's disease.
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Affiliation(s)
- Oliwia Koszła
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20-093 Lublin, Poland; (O.K.); (P.S.); (A.Z.); (A.G.); (D.M.)
| | - Piotr Stępnicki
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20-093 Lublin, Poland; (O.K.); (P.S.); (A.Z.); (A.G.); (D.M.)
| | - Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20-093 Lublin, Poland; (O.K.); (P.S.); (A.Z.); (A.G.); (D.M.)
| | - Angelika Grudzińska
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20-093 Lublin, Poland; (O.K.); (P.S.); (A.Z.); (A.G.); (D.M.)
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20-093 Lublin, Poland; (O.K.); (P.S.); (A.Z.); (A.G.); (D.M.)
| | - Agnieszka A. Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20-093 Lublin, Poland; (O.K.); (P.S.); (A.Z.); (A.G.); (D.M.)
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland
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