Keyword search (4,163 papers available)

"simulation" Keyword-tagged Publications:

Title Authors PubMed ID
1 Laboratory-scale simulation study on the bioremediation of marine oil pollution by phosphate-solubilizing bacteria Bacillus subtilis PSB-1 Du Z; Li Z; Chen X; Liu M; Feng L; Li Q; Chen Z; Chen Q; 41707285
ENCS
2 Assessment of risk for aromatic hydrocarbons resulting from subsea Blowouts: A case study in eastern Canada Yang Z; Chen Z; Xin Q; Lee K; 39571296
ENCS
3 In silico molecular targets, docking, dynamics simulation and physiologically based pharmacokinetics modeling of oritavancin Fatoki TH; Balogun TC; Ojewuyi AE; Omole AC; Olukayode OV; Adewumi AP; Umesi AJ; Ijeoma NP; Apooyin AE; Chinedu CP; Idowu IE; Isah MJ; 39439008
CHEMBIOCHEM
4 What can optimized cost distances based on genetic distances offer? A simulation study on the use and misuse of ResistanceGA Daniel A; Savary P; FoltĂȘte JC; Vuidel G; Faivre B; Garnier S; Khimoun A; 39417711
BIOLOGY
5 Numerical Simulation of the Effect of Particle and Substrate Preheating on Porosity Level and Residual Stress of As-sprayed Ti6Al4V Components Khamsepour P; Moreau C; Dolatabadi A; 38624932
ENCS
6 In Silico Study of the Early Stages of Aggregation of β-Sheet Forming Antimicrobial Peptide GL13K Hamidabad MN; Watson NA; Wright LN; Mansbach RA; 38572930
PHYSICS
7 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
8 Design Optimization of a Hybrid-Driven Soft Surgical Robot with Biomimetic Constraints Roshanfar M; Dargahi J; Hooshiar A; 38275456
ENCS
9 Proteomics-based vaccine targets annotation and design of subunit and mRNA-based vaccines for Monkeypox virus (MPXV) against the recent outbreak Jin Y; Fayyaz A; Liaqat A; Khan A; Alshammari A; Wang Y; Gu RX; Wei DQ; 37116237
CONCORDIA
10 Evaluating Emotional Outcomes of Medical Students in Pediatric Emergency Medicine Telesimulation Nomura O; Sunohara M; Watanabe I; Itoh T; 36670719
PSYCHOLOGY
11 Energy, economic, and environmental impacts of enhanced ventilation strategies on railway coaches to reduce Covid-19 contagion risks Barone G; Buonomano A; Forzano C; Giuzio GF; Palombo A; 35754761
ENCS
12 Teaching Culturally Safe Care in Simulated Cultural Communication Scenarios During the COVID-19 Pandemic: Virtual Visits with Indigenous Animators Maar M; McGregor L; Desjardins D; Delaney KZ; Bessette N; Reade M; 35392591
HKAP
13 A Proposed Multi-Criteria Optimization Approach to Enhance Clinical Outcomes Evaluation for Diabetes Care: A Commentary Wan TTH; Matthews S; Luh H; Zeng Y; Wang Z; Yang L; 35372638
ENCS
14 Insights from a dyslexia simulation font: Can we simulate reading struggles of individuals with dyslexia? Stark Z; Franzen L; Johnson AP; 34854169
PSYCHOLOGY
15 A Simulation Toolkit for Testing the Sensitivity and Accuracy of Corticometry Pipelines OmidYeganeh M; Khalili-Mahani N; Bermudez P; Ross A; Lepage C; Vincent RD; Jeon S; Lewis LB; Das S; Zijdenbos AP; Rioux P; Adalat R; Van Eede MC; Evans AC; 34381348
PERFORM
16 Mitigating COVID-19 infection disease transmission in indoor environment using physical barriers Ren C; Xi C; Wang J; Feng Z; Nasiri F; Cao SJ; Haghighat F; 34306996
ENCS
17 Numerical assessment of directional energy performance for 3D printed midsole structures Sultana A; Kwok TH; Hsu CC; Ng HD; 34198446
ENCS
18 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
19 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
20 Multimodal 3D ultrasound and CT in image-guided spinal surgery: public database and new registration algorithms Masoumi N; Belasso CJ; Ahmad MO; Benali H; Xiao Y; Rivaz H; 33683544
PERFORM
21 Using Models to (Re-)Design Synthetic Circuits. McCallum G, Potvin-Trottier L 33405217
BIOLOGY
22 Simulation and computer modeling of asphaltene in different solvents on oil-water interfaces using a molecular dynamic methodology. Yuan J, Elektorowicz M, Chen Z, Segun GA, Vakili M, Zhong L, Wang B, Zhu J, Wu Y 31542686
ENCS
23 Simulations and error analysis of the CNC milling of a face gear tooth with given tool paths. Yi H, Zhou Y, Tang J, Chen ZC 31297425
ENCS

 

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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