In Silico Insight the Prediction of Chlorogenic Acid in Coffee through Cyclooxygenase-2 (COX2) Interaction

Bare, Yohanes; Sari, Dewi Ratih Tirto; Rachmad, Yoga Tribakti; Krisnamurti, Gabriella Candrakirana; Elizabeth, Agustina; Maulidi, Andri

doi:10.24252/bio.v7i2.9847

Cited by 14 publications

(15 citation statements)

References 16 publications

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“…Inflammation that occurs in the body is correlated with inflammatory mediators such as COX-2. COX-2 has the function of initiating and maintaining physiological conditions during inflammation [11]. Compare to affinity character between chlorogenic acid and COX-2 in this research indicated that interaction was blocking at COX2 in different active site location compare to other ligands.…”

Section: Interactionmentioning

confidence: 57%

Molecular Docking Chlorogenic Acid and Isomer Compound as Cyclooxygenase-2 (COX-2) Inhibitor in Atherosclerosis

Nurarifa

Rachmawati

Utari³

2020

JSMARTech

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Atherosclerosis was an inflammatory disease caused by oxidized LDL. Chloroghenic acid (CGA) was a polyphenol compound and its isomers such as Caffeoylquinic acid (CQA) and Feruloylquinic acid (FQA) can increase the activity of antioxidant activity and can significantly reduce total cholesterol in the blood. Cyclooxygenase (COX) was an enzyme that correlates with the inflammatory process. COX was divided into two isoforms, COX-1 and COX-2. Prostanoid synthesis via the action of cyclooxygenase-2 (COX-2) was a component of the inflammatory response. All prepared compound of Chlorogenic acid (CGA) and its isomer, Caffeoylquinic acid (CQA) and Feruloylquinic acid (FQA) was used for molecular docking by using HEX 8.0.0. Visualization process was done by using Discovery Studio Client 4.1 software. The results showed docking between COX-2 with CGA compounds and its isomers also drug Ibuprofen shows energy binding COX-2 -CGA of -320 kcal / mol, COX-2 -CQA of -298 kcal / mol, COX-2 -FQA of -282 kcal / mol, and COX-2 -Ibuprofen of -230 kcal / mol. The docking results showed the CGA compound and its isomers have smaller energy bindings than the drug Ibuprofen. This showed that the CGA compound and its isomers were better to reduce COX-2 activity than the Ibuprofen drug so that it has the potential as an anti-inflammatory which can be used to prevent the formation of atherosclerosis.

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Section: Interactionmentioning

confidence: 57%

Molecular Docking Chlorogenic Acid and Isomer Compound as Cyclooxygenase-2 (COX-2) Inhibitor in Atherosclerosis

Nurarifa

Rachmawati

Utari³

2020

JSMARTech

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“…It is also known that silico molecular docking phytocompounds such as eriodyctiol, epicatechin, scutellarin, and ginkgolide A can bind to VEGF with tremendous energy as standard drugs for the 4T1 mammary carcinoma cell line [29,30]. We determined that the binding of eugenol and quercetin to VEGF resulted from the interaction of conventional hydrogen bonds and Pi-cation, Pi-sigma, and Pi-alkyl interactions, which significantly contributed to the stability of the bond structure [31][32][33][34]. Moreover, the binding interaction also supported the hydrogen's donor and acceptor abilities and thus may predict the antioxidant activity of quercetin and eugenol [16,35].…”

Section: Discussionmentioning

confidence: 98%

In silico molecular docking and in vitro analysis of ethanolic extract Ocimum sanctum Linn.: Inhibitory and apoptotic effects against non-small cell lung cancer

et al. 2021

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Background and Aim: Lung cancer, especially non-small cell lung cancer (NSCLC), has been identified as the leading cause of cancer deaths worldwide. The mortality rate from lung cancer has been estimated to be 18.4%. Until now, conventional treatments have not yielded optimal results, thus necessitating an investigation into the use of traditional herbal plants as potential candidates for its treatment. This study aimed to determine the inhibitory and apoptotic activity of the ethanolic extract from Ocimum sanctum Linn. (EEOS) by in silico molecular docking and through in vitro studies using NSCLC cells (A549 cell line). Materials and Methods: Dried simplicia of Ocimum sanctum was converted into EEOS using the maceration method. Spectrophotometry was then employed to analyze the EEOS compound. The known main active compounds were further analyzed for inhibitory and apoptotic effects on gene signaling using in silico molecular docking involving the downloading of active compounds from PubChem and target proteins from the Protein Data Bank; the active compounds and proteins were then prepared using the Discovery Studio software v. 19.0.0 and the PyRX 0.8 program, interacted with the HEX 8.0.0 program, and visualized with the Discovery Studio Visualizer v. 19.0. Finally, an in vitro analysis was performed using an antiproliferative-cytotoxic test (3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide assay in the NSCLC A549 cell line). Results: The analysis revealed that the active compounds in the ethanolic extract were dominated by quercetin (flavonoids) (47.23% b/b) and eugenol (phenolic) (12.14% b/b). These active compounds interacted with the active sites (residual amino acids) of the αvβ3 integrin, α5β1 integrin, caspase-3, caspase-9, and vascular endothelial growth factor. Hydrogen bonds and Pi-cation and Pi-alkyl interactions were involved in the relationships between the active compounds and the active sites and thus may reveal an antioxidant property of the extract. Furthermore, in vitro analysis showed the inhibitory and antiproliferative effects of the EEOS against non-small cell cancer (A549). Conclusion: Taken together, our data showed the ability of EEOS as an inhibitor and apoptotic agent for lung cancer; however, further research is needed to determine the exact mechanism of EEOS as an herbal medication.

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“…Docking of the receptor and small molecular ligand was performed using AutoDock Vina 1.1.2 [ 29 ]. The 2D complex and interactions of the docked ligand and receptor were analyzed using Discovery Studio Visualizer Version Client [ 30 ]. Affinity scores were used to evaluate the binding potential between the top four core targets and CUR.…”

Section: Methodsmentioning

confidence: 99%

Mechanistic insights into the renoprotective role of curcumin in cisplatin-induced acute kidney injury: network pharmacology analysis and experimental validation

et al. 2021

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Cisplatin-induced acute kidney injury (CP-AKI) is a severe complication in patients receiving CP chemotherapy. However, effective therapies for CP-AKI are currently lacking. Curcumin (CUR), a natural polyphenol, is extracted from the rhizome of turmeric and has been reported to have nephroprotective activity. However, the role of CUR in CP-AKI remains unclear. This study aimed to explore the mechanism of CUR in CP-AKI by combining a network pharmacology approach with experimental validations. The analysis revealed 176 potential targets of CUR based on the HERB database and 1,286 related targets of CP-AKI from the GeneCards, DrugBank, and OMIM databases. Further, 106 common targets of CUR against CP-AKI were obtained, and these common targets constructed a protein-protein interaction (PPI) network. In addition, the core targets were screened from the PPI network using Cytoscape. Molecular docking revealed that CUR displayed the best binding to AKT1. Gene Ontology (GO) analysis indicated that the primary biological processes of CUR against CP-AKI included cellular response to chemical stress and apoptotic regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested that the PI3K-Akt signaling pathway was most significantly enriched in CUR against CP-AKI. Western blotting and flow cytometry showed that CUR inhibited apoptosis induced by CP by activating the Akt signaling pathway in human kidney tubular epithelial cells (HK-2). Altogether, our findings demonstrated that CUR alleviated apoptosis by activating the Akt signaling pathway in CP-AKI in vitro . These data provide a scientific basis for future investigations into the clinical application of CUR against CP-AKI.

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In Silico Insight the Prediction of Chlorogenic Acid in Coffee through Cyclooxygenase-2 (COX2) Interaction

Cited by 14 publications

References 16 publications

Molecular Docking Chlorogenic Acid and Isomer Compound as Cyclooxygenase-2 (COX-2) Inhibitor in Atherosclerosis

Molecular Docking Chlorogenic Acid and Isomer Compound as Cyclooxygenase-2 (COX-2) Inhibitor in Atherosclerosis

In silico molecular docking and in vitro analysis of ethanolic extract Ocimum sanctum Linn.: Inhibitory and apoptotic effects against non-small cell lung cancer

Mechanistic insights into the renoprotective role of curcumin in cisplatin-induced acute kidney injury: network pharmacology analysis and experimental validation

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