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Article ; Online: You must be flexible enough to be trained, Mr. Dynamics simulator.

Danazumi, Ammar Usman / Umar, Haruna Isiyaku

2023

Abstract: This article highlights two major problems associated with molecular dynamics studies: poor parameterization of systems and misleading interpretation of data. To address these issues, we advocate for meticulous system parameterization and careful ... ...

Abstract	This article highlights two major problems associated with molecular dynamics studies: poor parameterization of systems and misleading interpretation of data. To address these issues, we advocate for meticulous system parameterization and careful interpretation of statistics within the framework of the study system, with a focus on high-quality and rigorous simulations. Our letter aims to encourage the adoption of the best practices in the field.
Language	English
Publishing date	2023-07-12
Publishing country	Netherlands
Document type	Letter
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10689-5
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Zs.A 4946: Show issues

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Article ; Online: Computer-aided analysis of quercetin mechanism of overcoming docetaxel resistance in docetaxel-resistant prostate cancer.

Omoboyede, Victor / Ibrahim, Ochapa / Umar, Haruna Isiyaku / Oke, Grace Ayomide / Onile, Olugbenga Samson / Chukwuemeka, Prosper Obed

Journal, genetic engineering & biotechnology

2023 Volume 21, Issue 1, Page(s) 47

Abstract: Background: Prostate cancer (PC) is a silent but potent killer among men. In 2018, PC accounted for more than 350, 000 death cases while more than 1.2 million cases were diagnosed. Docetaxel, a chemotherapeutic drug belonging to the taxane family of ... ...

Abstract	Background: Prostate cancer (PC) is a silent but potent killer among men. In 2018, PC accounted for more than 350, 000 death cases while more than 1.2 million cases were diagnosed. Docetaxel, a chemotherapeutic drug belonging to the taxane family of drugs, is one of the most potent drugs in combating advanced PC. However, PC cells often evolve resistance against the regimen. Hence, necessitating the search for complementary and alternative therapies. Quercetin, a ubiquitous phytocompound with numerous pharmacological properties, has been reported to reverse docetaxel resistance (DR) in docetaxel-resistant prostate cancer (DRPC). Therefore, this study aimed to explore the mechanism via which quercetin reverses DR in DRPC using an integrative functional network and exploratory cancer genomic data analyses. Results: The putative targets of quercetin were retrieved from relevant databases, while the differentially expressed genes (DEGs) in docetaxel-resistant prostate cancer (DRPC) were identified by analysing microarray data retrieved from the Gene Expression Omnibus (GEO) database. Subsequently, the protein-protein interaction (PPI) network of the overlapping genes between the DEGs and quercetin targets was retrieved from STRING, while the hub genes, which represent the key interacting genes of the network, were identified using the CytoHubba plug-in of Cytoscape. The hub genes were further subjected to a comprehensive analysis aimed at identifying their contribution to the immune microenvironment and overall survival (OS) of PC patients, while their alterations in PC patients were also revealed. The biological roles played by the hub genes in chemotherapeutic resistance include the positive regulation of developmental process, positive regulation of gene expression, negative regulation of cell death, and epithelial cell differentiation among others. Conclusion: Further analysis revealed epidermal growth factor receptor (EGFR) as the most pertinent target of quercetin in reversing DR in DRPC, while molecular docking simulation revealed an effective interaction between quercetin and EGFR. Ultimately, this study provides a scientific rationale for the further exploration of quercetin as a combinational therapy with docetaxel.
Language	English
Publishing date	2023-04-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2637420-1
ISSN	2090-5920 ; 1687-157X ; 2090-5920
ISSN (online)	2090-5920
ISSN	1687-157X ; 2090-5920
DOI	10.1186/s43141-023-00498-6
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Article ; Online: Repurposing the inhibitors of MMP-9 and SGLT-2 against ubiquitin specific protease 30 in Parkinson's disease: computational modelling studies.

Alshehri, Mohammed M / Danazumi, Ammar Usman / Alshammari, Mohammed Kanan / Bello, Ridwan Opeyemi / Alghazwni, Mohammed Khalid / Alshehri, Ahmed Mughram / Alshlali, Omaymah Mohammed / Umar, Haruna Isiyaku

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 3, Page(s) 1307–1318

Abstract: Ubiquitin specific protease 30 (USP30) has been attributed to mitochondrial dysfunction and impediment of mitophagy in Parkinson's disease (PD). This happens once ubiquitin that supposed to bind with deformed mitochondria at the insistence of Parkin, it' ... ...

Abstract	Ubiquitin specific protease 30 (USP30) has been attributed to mitochondrial dysfunction and impediment of mitophagy in Parkinson's disease (PD). This happens once ubiquitin that supposed to bind with deformed mitochondria at the insistence of Parkin, it's been recruited by USP30
MeSH term(s)	Humans ; Parkinson Disease/genetics ; Matrix Metalloproteinase 9 ; Molecular Docking Simulation ; Drug Repositioning ; Protein Kinases/metabolism ; Mitochondrial Proteins/chemistry ; Thiolester Hydrolases/chemistry ; Thiolester Hydrolases/genetics ; Thiolester Hydrolases/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Specific Proteases/metabolism
Chemical Substances	Matrix Metalloproteinase 9 (EC 3.4.24.35) ; Protein Kinases (EC 2.7.-) ; Mitochondrial Proteins ; Thiolester Hydrolases (EC 3.1.2.-) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Ubiquitin ; Ubiquitin-Specific Proteases (EC 3.4.19.12)
Language	English
Publishing date	2023-05-03
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2208223
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Article ; Online: An integrative computational approach for the identification of dual inhibitors of isocitrate dehydrogenase 1 and 2 from phytocompounds of

Bello, Ridwan Opeyemi / Okunlola, Salihaat Toyin / Kumar, Neeraj / Victor, Omoboyede / Jimoh, Tajudeen O / Abdulsalam, Zainab Naeem / Kehinde, Idayat Oyinkansola / Umar, Haruna Isiyaku

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–17

Abstract: Genetic alterations of the genes encoding the isocitrate dehydrogenase (IDH) enzymes have been identified in about 20% of acute myeloid leukemia (AML) cases as well as many other forms of cancers. Notable among these alterations are the neomorphic ... ...

Abstract	Genetic alterations of the genes encoding the isocitrate dehydrogenase (IDH) enzymes have been identified in about 20% of acute myeloid leukemia (AML) cases as well as many other forms of cancers. Notable among these alterations are the neomorphic IDH1_R132H and IDH2_R140Q mutations which lead to the production of an oncometabolite. Hence, their inhibition is widely considered a therapeutic strategy in the treatment of many cancers. While many inhibitors of the mutant enzymes have been developed, an inhibitor that is capable of co-inhibiting both enzymes are currently lacking while drug resistance has also limited the clinical usage of previously identified mono inhibitors. Consequently, this study employed molecular modeling approaches, such as molecular docking, molecular mechanics generalized Born Surface area (MM/GBSA), molecular dynamics (MD) simulation, and density functional theory (DFT) analysis to identify potential dual inhibitors of the previously mentioned mutant IDH1/2 from the phytocompounds of
Language	English
Publishing date	2023-08-09
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2245494
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Article ; Online: Fig (Ficus exasperata and Ficus asperifolia)-Supplemented diet improves sexual function, endothelial nitric oxide synthase and suppresses tumour necrosis factor-alpha genes in hypertensive rats.

Ajeigbe, Olufunke Florence / Oboh, Ganiyu / Ademosun, Ayokunle Olubode / Umar, Haruna Isiyaku

Andrologia

2021 Volume 54, Issue 1, Page(s) e14289

Abstract: We measured the effect of varieties of Fig leaves, Ficus exasperata Vahl. (FE) and Ficus asperifolia Miq (FA), commonly found in Sub-sahara Africa for managing hypertension on sexual performance in hypertensive rats, which is unknown. Hypertensive rats ... ...

Abstract	We measured the effect of varieties of Fig leaves, Ficus exasperata Vahl. (FE) and Ficus asperifolia Miq (FA), commonly found in Sub-sahara Africa for managing hypertension on sexual performance in hypertensive rats, which is unknown. Hypertensive rats experienced erectogenic damage after exposure to 40 mg kg
MeSH term(s)	Animals ; Blood Pressure ; Diet ; Ficus ; Hypertension ; NG-Nitroarginine Methyl Ester ; Nitric Oxide ; Nitric Oxide Synthase Type III/genetics ; Rats ; Tumor Necrosis Factor-alpha/genetics
Chemical Substances	Tumor Necrosis Factor-alpha ; Nitric Oxide (31C4KY9ESH) ; Nitric Oxide Synthase Type III (EC 1.14.13.39) ; NG-Nitroarginine Methyl Ester (V55S2QJN2X)
Language	English
Publishing date	2021-10-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	7280-1
ISSN	1439-0272 ; 0303-4569
ISSN (online)	1439-0272
ISSN	0303-4569
DOI	10.1111/and.14289
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Zs.A 665: Show issues

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Article ; Online: Chemical Composition Antioxidant and Anti-Inflammatory Activities of

Belahcene, Samia / Kebsa, Widad / Akingbade, Tomilola Victor / Umar, Haruna Isiyaku / Omoboyowa, Damilola Alex / Alshihri, Abdulaziz A / Abo Mansour, Adel / Alhasaniah, Abdulaziz Hassan / Oraig, Mohammed A / Bakkour, Youssef / Leghouchi, Essaid

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 4

Abstract: Compounds derived from natural sources continue to serve as chemical scaffolds for designing prophylactic/therapeutic options for human healthcare. In this study, we aimed to systematically unravel the chemical profile and antioxidant and anti- ... ...

Abstract	Compounds derived from natural sources continue to serve as chemical scaffolds for designing prophylactic/therapeutic options for human healthcare. In this study, we aimed to systematically unravel the chemical profile and antioxidant and anti-inflammatory activities of myrtle methanolic extract (MMEx) using in vitro, in vivo, and in silico approaches. High levels of TPC (415.85 ± 15.52 mg GAE/g) and TFC (285.80 ± 1.64 mg QE/g) were observed. Mass spectrophotometry (GC-MS) analysis revealed the presence of 1,8-cineole (33.80%), α-pinene (10.06%), linalool (4.83%), p-dimethylaminobenzophenone (4.21%), thunbergol (4%), terpineol (3.60%), cis-geranyl acetate (3.25%), and totarol (3.30%) as major compounds. MMEx induced pronounced dose-dependent inhibition in all assays, and the best antioxidant activity was found with H
MeSH term(s)	Humans ; Antioxidants/pharmacology ; Myrtus/chemistry ; Molecular Docking Simulation ; Hydrogen Peroxide ; Anti-Inflammatory Agents/pharmacology ; Plant Extracts/pharmacology ; Abietanes
Chemical Substances	Antioxidants ; totarol (67NH2854WW) ; Hydrogen Peroxide (BBX060AN9V) ; Anti-Inflammatory Agents ; Plant Extracts ; Abietanes
Language	English
Publishing date	2024-02-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules29040849
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Article ; Online: Computer-aided drug discovery of c-Abl kinase inhibitors from plant compounds against chronic myeloid leukemia.

Alshehri, Mohammed M / Kumar, Neeraj / Kuthi, Najwa Ahmad / Olaide, Zainab / Alshammari, Mohammed Kanan / Bello, Ridwan Opeyemi / Alghazwni, Mohammed Khalid / Alshehri, Ahmed Mughram / Alshlali, Omaymah Mohammed / Ashimiyu-Abdusalam, Zainab / Umar, Haruna Isiyaku

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–21

Abstract: Chronic myeloid leukemia (CML) is a hematological malignancy characterized by the neoplastic transformation of hematopoietic stem cells, driven by the Philadelphia (Ph) chromosome resulting from a translocation between chromosomes 9 and 22. This Ph ... ...

Abstract	Chronic myeloid leukemia (CML) is a hematological malignancy characterized by the neoplastic transformation of hematopoietic stem cells, driven by the Philadelphia (Ph) chromosome resulting from a translocation between chromosomes 9 and 22. This Ph chromosome harbors the breakpoint cluster region (BCR) and the Abelson (ABL) oncogene (BCR-ABL1) which have a constitutive tyrosine kinase activity. However, the tyrosine kinase activity of BCR-ABL1 have been identified as a key player in CML initiation and maintenance through c-Abl kinase. Despite advancements in tyrosine kinase inhibitors, challenges such as efficacy, safety concerns, and recurring drug resistance persist. This study aims to discover potential c-Abl kinase inhibitors from plant compounds with anti-leukemic properties, employing drug-likeness assessment, molecular docking, in silico pharmacokinetics (ADMET) screening, density function theory (DFT), and molecular dynamics simulations (MDS). Out of 58 screened compounds for drug-likeness, 44 were docked against c-Abl kinase. The top hit compound (isovitexin) and nilotinib (control drug) were subjected to rigorous analyses, including ADMET profiling, DFT evaluation, and MDS for 100 ns. Isovitexin demonstrated a notable binding affinity (-15.492 kcal/mol), closely comparable to nilotinib (-16.826 kcal/mol), showcasing a similar binding pose and superior structural stability and reactivity. While these findings suggest isovitexin as a potential c-Abl kinase inhibitor, further validation through urgent
Language	English
Publishing date	2024-03-22
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2329297
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Article ; Online: HPLC/ESI-MS Characterization of Phenolic Compounds from Cnicus benedictus L. Roots: A Study of Antioxidant, Antibacterial, Anti-Inflammatory, and Anti-Alzheimer's Activity.

Rezig, Khalid / Benkaci-Ali, Farid / Foucaunier, Marie-Laure / Laurent, Sophie / Umar, Haruna Isiyaku / Alex, Omoboyowa Damilola / Tata, Samira

Chemistry & biodiversity

2023 Volume 21, Issue 1, Page(s) e202300724

Abstract: The phenolic composition of Cnicus benedictus roots from four Algerian regions was investigated. Extractions were performed in both hydro-methanolic (30 : 70, v/v) and hydro-ethanolic (30 : 70, v/v) solvents. Their efficiency was determined in terms of ... ...

Abstract	The phenolic composition of Cnicus benedictus roots from four Algerian regions was investigated. Extractions were performed in both hydro-methanolic (30 : 70, v/v) and hydro-ethanolic (30 : 70, v/v) solvents. Their efficiency was determined in terms of the qualitative and quantitative composition in phenolic compounds by HPLC-LC/MS of the different extracts isolated from C. Benedictus roots. Cnicus benedictus roots extract have been characterized by high content of phenolic compounds, where the trans chalcone, 2,3-dihydro flavone, 3-hydroxy flavone and cinnamic acid constitute the major components, in addition to fourteen minor acidic compounds and flavonoids as rutin. The hydro-methanolic extract was the richest in phenolic compounds yield from C benedictus. On the other hand, hydro methanolic (30 : 70, v/v) and hydro ethanolic (30 : 70, v/v) extracts exhibited a high anti-inflammatory activity by in vitro 5-lipoxygenase inhibitory activity (IC
MeSH term(s)	Antioxidants/pharmacology ; Centaurea benedicta ; Chromatography, High Pressure Liquid ; Chalcones ; Phenols/pharmacology ; Phenols/analysis ; Flavonoids ; Anti-Bacterial Agents/pharmacology ; Flavones ; Methanol ; Anti-Inflammatory Agents/pharmacology ; Plant Extracts/pharmacology
Chemical Substances	Antioxidants ; Chalcones ; Phenols ; Flavonoids ; Anti-Bacterial Agents ; Flavones ; Methanol (Y4S76JWI15) ; Anti-Inflammatory Agents ; Plant Extracts
Language	English
Publishing date	2023-12-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2139001-0
ISSN	1612-1880 ; 1612-1872
ISSN (online)	1612-1880
ISSN	1612-1872
DOI	10.1002/cbdv.202300724
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Article ; Online: In silico studies of bioactive compounds from selected African plants with inhibitory activity against nitric oxide synthase and arginase implicated in asthma

Haruna Isiyaku Umar / Tolulope Peter Saliu / Sunday Solomon Josiah / Adeola Ajayi / Jamilu Bala Danjuma

Egyptian Journal of Medical Human Genetics, Vol 22, Iss 1, Pp 1-

2021 Volume 16

Abstract: Abstract Background It is a known fact that arginine is a common substrate for arginase and nitric oxide synthase (NOS). However, an imbalance between both enzymes could lead to a change in airway responses. Reports suggest that increased activities of ... ...

Abstract	Abstract Background It is a known fact that arginine is a common substrate for arginase and nitric oxide synthase (NOS). However, an imbalance between both enzymes could lead to a change in airway responses. Reports suggest that increased activities of both enzymes could lead to airway hyper-responsiveness. Thus, the requests for NOS inhibitors that can also inhibit arginase as the elevated activities of both enzymes have detrimental consequence on airways in asthma. Bioactive compounds from Azadirachta indica, Crinum glaucum, and Mangifera indica are documented for anti-inflammatory, immunomodulatory, anti-histaminic, smooth-muscle relaxants, and anti-allergic potentials. However, the mechanisms of action of these bioactive compounds in conferring the aforementioned protections are not well characterized. The objective of this present study is to assess in silico inhibitory potentials of these bioactive compounds against NOS and arginase via binding at their active sites. The crystal structures of NOS and arginase were retrieved from the protein database, while the bioactive compounds were retrieved from PubChem. Drug-likeness of the selected bioactive compounds was assessed using DruLiTo software. The successful compounds were docked with active sites of enzymes using AutoDock Vina docking software, and the docked complexes were analyzed using LigPlot and protein-ligand profiler web server. Results The findings of the study revealed that the bioactive compounds from A. indica, C. glaucum, and M. indica were able to interact with the active sites of NOS and arginase with the exception of gallic acid (from M. indica) and nimbandiol (from A. indica); these compounds showed differential binding energies (kcal/mol) and a number of them had higher binding energies than l-arginine when docked with NOS. Conclusion Conclusively, the in silico analysis proposes that these compounds could prove to be probable anti-asthmatic drugs.
Keywords	ADMET ; Arginase ; Asthma ; Azadirachta indica ; Crinum glaucum ; In silico ; Medicine (General) ; R5-920 ; Genetics ; QH426-470
Subject code	540
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
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Article ; Online: Quercetin and catechin assuage redox imbalance and neurochemical dysfunction in rotenone-induced neurotoxicity

Sunday Solomon Josiah / Haruna Isiyaku Umar / Ibrahim Olabayode Saliu / Afolabi Clement Akinmoladun

Phytomedicine Plus, Vol 1, Iss 4, Pp 100077- (2021)

A comparative in vivo experiment supported by in silico study

2021

Abstract: Background: Quercetin and catechin are structurally-related compounds that are capable of preventing or attenuating oxidative damage and mitochondrial dysfunction. Rotenone is a naturally occurring compound that has been used to model neurotoxicity ... ...

Abstract	Background: Quercetin and catechin are structurally-related compounds that are capable of preventing or attenuating oxidative damage and mitochondrial dysfunction. Rotenone is a naturally occurring compound that has been used to model neurotoxicity characterized by Parkinson disease-like symptoms. Purpose: This study investigated the comparative property of quercetin and catechin, to ameliorate oxidative damage and neurochemical dysfunction in hippocampal and cortical regions of brain of rats intoxicated with rotenone in vivo, supported by in silico study. Method: Male Wistar rats were subcutaneously administered rotenone for 10 days followed by post-treatment with catechin or quercetin (5, 10 and 20 mg/kg) for 3 days. Markers of oxidative stress and neurochemical dysfunction were biochemically estimated in the hippocampus and cortex of the brain of rats while in silico study was carried out to evaluate the molecular interaction of some neurochemical enzymes with the compounds. Result: Quercetin and catechin ameliorated the reduction in complex 1 and Na+K+ATPase activities while attenuating the elevated lactate dehydrogenase activity in the brain of rotenone-intoxicated rats. Disturbances in acetylcholine, dopamine and glutamate metabolism as well as the evoked oxidative stress in rotenone-intoxicated rats were mitigated by quercetin and catechin. The in silico study revealed the key molecular interaction between the flavonoids and targeted enzymes (tyrosine hydroxylase, monoamine oxidase, glutamine synthetase and Na+K+ATPase) to be by hydrogen bond and hydrophobic interaction. Conclusion: Catechin and quercetin significantly assuaged cortical and hippocampal redox stress and attenuated neurochemical dysfunction caused by rotenone toxicity. Furthermore, this study highlighted that the neuroprotective potentials of the flavonoids is a function of their structural patterns, and quercetin elicited superior activity over catechin due to its structural advantages.
Keywords	Catechin ; In silico ; Neurotoxicity ; Quercetin ; Rotenone ; Structure-function relationships ; Other systems of medicine ; RZ201-999
Subject code	572
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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