Keyword search (4,163 papers available)

"MD simulations" Keyword-tagged Publications:

Title Authors PubMed ID
1 Insights into dietary phytochemicals targeting Parkinson's disease key genes and pathways: A network pharmacology approach Sasikumar DSN; Thiruselvam P; Sundararajan V; Ravindran R; Gunasekaran S; Madathil D; Kaliamurthi S; Peslherbe GH; Selvaraj G; Sudhakaran SL; 38460310
CHEMBIOCHEM
2 Structure-Based Virtual Screening Reveals Ibrutinib and Zanubrutinib as Potential Repurposed Drugs against COVID-19 Kaliamurthi S; Selvaraj G; Selvaraj C; Singh SK; Wei DQ; Peslherbe GH; 34209188
CHEMBIOCHEM
3 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2 Nguyen K; Chakraborty S; Mansbach RA; Korber B; Gnanakaran S; 34067878
PHYSICS

 

Title:Insights into dietary phytochemicals targeting Parkinson's disease key genes and pathways: A network pharmacology approach
Authors:Sasikumar DSNThiruselvam PSundararajan VRavindran RGunasekaran SMadathil DKaliamurthi SPeslherbe GHSelvaraj GSudhakaran SL
Link:https://pubmed.ncbi.nlm.nih.gov/38460310/
DOI:10.1016/j.compbiomed.2024.108195
Publication:Computers in biology and medicine
Keywords:BaicaleinCREBBPDopaminergic neuronsEP300ERK2MAPK1MD simulationsNetwork pharmacologyParkinson's diseaseRasagiline
PMID:38460310 Category: Date Added:2024-03-10
Dept Affiliation: CHEMBIOCHEM
1 Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India.
2 Department of Biotechnology, Indian Institute of Technology (Madras), Chennai, TN, 600036, India.
3 Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College, Chennai, TN, 600106, India.
4 Jindal Institute of Behavioral Sciences, O.P Jindal Global University, Sonipat, Haryana, 131001, India.
5 Centre for Research in Molecular Modeling (CERMM), Department of Chemistry and Biochemistry, Concordia University, Loyola Campus, Montreal, QC, H4B 1R6, Canada.
6 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. Electronic address: gurudeeban.selvaraj@concordia.ca.
7 Integrative Multiomics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India. Electronic address: ssajithalulu@vit.ac.in.

Description:

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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