FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4366998744> ?p ?o ?g. }

• W4366998744 abstract "Abstract Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action has not been identified. Systems pharmacology methods have been used to overcome these challenges. However, there is a limitation as those similar mechanisms of similar components cannot be identified. In this study, comparisons of physicochemical descriptors, large-scale molecular docking analysis, and RNA-seq analysis were performed to compare the mechanisms of action of similar compounds and to confirm the changes observed when similar compounds were mixed and used. We propose an advanced method for in silico experiments in herbal medicine research based on the results. First, physicochemical descriptors were calculated based on the chemical structures of oleanolic acid (OA), hederagenin (HG), and gallic acid (GA). Similarities were confirmed by calculating the Euclidean, cosine, and Tanimoto distances between the descriptors. Next, the mechanisms of action of OA, HG, and GA were compared and confirmed through in silico-based systems pharmacology analysis using the BATMAN-TCM platform. The proteins interacting with the three compounds were verified through large-scale molecular docking analysis using the druggable proteome. Finally, a drug response transcriptome study was performed using OA, HG, GA, and a combination of OA and HG (COH) with similar structures.A comparison of physicochemical descriptors confirmed that OA and HG were very close. In particular, the two compounds showed a concordance rate of > 99% at cosine and Tanimoto distances. The systems pharmacology analysis results confirmed that OA and HG shared more than 86% of their predicted target proteins and differed only in GA. Systems pharmacology analysis revealed that OA and HG share the mechanisms of cardiac muscle contraction, oxidative phosphorylation, and non-alcoholic fatty liver disease. In a molecular docking analysis of the 50 major druggable proteins, OA and HG shared 38 proteins, while GA shared a few with proteins derived from the other two compounds. In addition, OA and HG were confirmed to act on gonadotropin-releasing hormone (GnRH) secretion, type 2 diabetes mellitus, cholinergic synapses, and calcium signaling pathways, and docking analysis visualization confirmed that the two components interact at the same site. RNA-seq analysis also showed that the differentially expressed genes and pathways derived from OA and HG were similar, and it was confirmed that COH had similar results to OA and HG. Our study has three novel findings. First, an advanced network pharmacology research method was suggested by partially presenting a solution to the difficulty in identifying multicomponent mechanisms. Second, a new natural product analysis method was proposed using large-scale molecular docking analysis. Finally, various biological data and analysis methods were used, such as in silico system pharmacology, docking analysis, and drug response RNA-seq. The results of this study are meaningful in that they suggest an analysis strategy that can improve existing systems pharmacology research analysis methods by showing that natural product-derived compounds with the same scaffold have the same mechanism." @default.
• W4366998744 created "2023-04-27" @default.
• W4366998744 creator A5008610118 @default.
• W4366998744 creator A5016743635 @default.
• W4366998744 creator A5041860681 @default.
• W4366998744 creator A5078758711 @default.
• W4366998744 creator A5088539981 @default.
• W4366998744 date "2023-04-25" @default.
• W4366998744 modified "2023-09-24" @default.
• W4366998744 title "Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations" @default.
• W4366998744 cites W1981737096 @default.
• W4366998744 cites W2010457001 @default.
• W4366998744 cites W2018478612 @default.
• W4366998744 cites W2033377040 @default.
• W4366998744 cites W2045665834 @default.
• W4366998744 cites W2070050178 @default.
• W4366998744 cites W2071810654 @default.
• W4366998744 cites W2097233276 @default.
• W4366998744 cites W2114104545 @default.
• W4366998744 cites W2119412782 @default.
• W4366998744 cites W2124679671 @default.
• W4366998744 cites W2130410032 @default.
• W4366998744 cites W2134967712 @default.
• W4366998744 cites W2142844050 @default.
• W4366998744 cites W2146436588 @default.
• W4366998744 cites W2148016904 @default.
• W4366998744 cites W2158703410 @default.
• W4366998744 cites W2159675211 @default.
• W4366998744 cites W2160697532 @default.
• W4366998744 cites W2169678694 @default.
• W4366998744 cites W2177317049 @default.
• W4366998744 cites W2179438025 @default.
• W4366998744 cites W2268755124 @default.
• W4366998744 cites W2321752471 @default.
• W4366998744 cites W2562257444 @default.
• W4366998744 cites W2767571742 @default.
• W4366998744 cites W2791355014 @default.
• W4366998744 cites W2899140056 @default.
• W4366998744 cites W2971393852 @default.
• W4366998744 cites W3154487399 @default.
• W4366998744 cites W4210941951 @default.
• W4366998744 cites W4213444898 @default.
• W4366998744 cites W4224869291 @default.
• W4366998744 cites W4230274588 @default.
• W4366998744 cites W4294216483 @default.
• W4366998744 doi "https://doi.org/10.1101/2023.04.23.538005" @default.
• W4366998744 hasPublicationYear "2023" @default.
• W4366998744 type Work @default.
• W4366998744 citedByCount "1" @default.
• W4366998744 countsByYear W43669987442023 @default.
• W4366998744 crossrefType "posted-content" @default.
• W4366998744 hasAuthorship W4366998744A5008610118 @default.
• W4366998744 hasAuthorship W4366998744A5016743635 @default.
• W4366998744 hasAuthorship W4366998744A5041860681 @default.
• W4366998744 hasAuthorship W4366998744A5078758711 @default.
• W4366998744 hasAuthorship W4366998744A5088539981 @default.
• W4366998744 hasBestOaLocation W43669987441 @default.
• W4366998744 hasConcept C104317684 @default.
• W4366998744 hasConcept C159110408 @default.
• W4366998744 hasConcept C185592680 @default.
• W4366998744 hasConcept C2775905019 @default.
• W4366998744 hasConcept C41685203 @default.
• W4366998744 hasConcept C55493867 @default.
• W4366998744 hasConcept C70721500 @default.
• W4366998744 hasConcept C71924100 @default.
• W4366998744 hasConcept C86803240 @default.
• W4366998744 hasConceptScore W4366998744C104317684 @default.
• W4366998744 hasConceptScore W4366998744C159110408 @default.
• W4366998744 hasConceptScore W4366998744C185592680 @default.
• W4366998744 hasConceptScore W4366998744C2775905019 @default.
• W4366998744 hasConceptScore W4366998744C41685203 @default.
• W4366998744 hasConceptScore W4366998744C55493867 @default.
• W4366998744 hasConceptScore W4366998744C70721500 @default.
• W4366998744 hasConceptScore W4366998744C71924100 @default.
• W4366998744 hasConceptScore W4366998744C86803240 @default.
• W4366998744 hasLocation W43669987441 @default.
• W4366998744 hasOpenAccess W4366998744 @default.
• W4366998744 hasPrimaryLocation W43669987441 @default.
• W4366998744 hasRelatedWork W1974040436 @default.
• W4366998744 hasRelatedWork W2064956914 @default.
• W4366998744 hasRelatedWork W2123563726 @default.
• W4366998744 hasRelatedWork W2329711804 @default.
• W4366998744 hasRelatedWork W2461721650 @default.
• W4366998744 hasRelatedWork W2530096667 @default.
• W4366998744 hasRelatedWork W2895061860 @default.
• W4366998744 hasRelatedWork W2942512732 @default.
• W4366998744 hasRelatedWork W4200181702 @default.
• W4366998744 hasRelatedWork W4287332072 @default.
• W4366998744 isParatext "false" @default.
• W4366998744 isRetracted "false" @default.
• W4366998744 workType "article" @default.