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Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes

Background: Herbal medicines traditionally target organs for treatment based on medicinal properties, and this theory is widely used for prescriptions. However, the scientific evidence explaining how herbs act on specific organs by biological methods has been still limited. This study used bioinform...

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Autores principales: Tran, Minh Nhat, Baek, Su-Jin, Jun, Hyeong Joon, Lee, Sanghun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10448535/
https://www.ncbi.nlm.nih.gov/pubmed/37637410
http://dx.doi.org/10.3389/fphar.2023.1187896
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author Tran, Minh Nhat
Baek, Su-Jin
Jun, Hyeong Joon
Lee, Sanghun
author_facet Tran, Minh Nhat
Baek, Su-Jin
Jun, Hyeong Joon
Lee, Sanghun
author_sort Tran, Minh Nhat
collection PubMed
description Background: Herbal medicines traditionally target organs for treatment based on medicinal properties, and this theory is widely used for prescriptions. However, the scientific evidence explaining how herbs act on specific organs by biological methods has been still limited. This study used bioinformatic tools to identify the target organ locations of Radix Achyranthis Bidentatae (RAB), a blood-activating herb that nourishes the liver and kidney, strengthens bones, and directs prescription to the lower body. Methods: RAB’s active compounds and targets were collected and predicted using databases such as TCMSP, HIT2.0, and BATMAN-TCM. Next, the RAB’s target list was analyzed based on two approaches to obtain target organ locations. DAVID and Gene ORGANizer enrichment-based approaches were used to enrich an entire gene list, and the BioGPS and HPA gene expression-based approaches were used to analyze the expression of core genes. Results: RAB’s targets were found to be involved in whole blood, blood components, and lymphatic organs across all four tools. Each tool indicated a particular aspect of RAB’s target organ locations: DAVID-enriched genes showed a predominance in blood, liver, and kidneys; Gene ORGANizer showed the effect on low body parts as well as bones and joints; BioGPS and HPA showed high gene expression in bone marrow, lymphoid tissue, and smooth muscle. Conclusion: Our bioinformatics-based target organ location prediction can serve as a modern interpretation tool for the target organ location theory of traditional medicine. Future studies should predict therapeutic target organ locations in complex prescriptions rather than single herbs and conduct experiments to verify predictions.
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spelling pubmed-104485352023-08-25 Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes Tran, Minh Nhat Baek, Su-Jin Jun, Hyeong Joon Lee, Sanghun Front Pharmacol Pharmacology Background: Herbal medicines traditionally target organs for treatment based on medicinal properties, and this theory is widely used for prescriptions. However, the scientific evidence explaining how herbs act on specific organs by biological methods has been still limited. This study used bioinformatic tools to identify the target organ locations of Radix Achyranthis Bidentatae (RAB), a blood-activating herb that nourishes the liver and kidney, strengthens bones, and directs prescription to the lower body. Methods: RAB’s active compounds and targets were collected and predicted using databases such as TCMSP, HIT2.0, and BATMAN-TCM. Next, the RAB’s target list was analyzed based on two approaches to obtain target organ locations. DAVID and Gene ORGANizer enrichment-based approaches were used to enrich an entire gene list, and the BioGPS and HPA gene expression-based approaches were used to analyze the expression of core genes. Results: RAB’s targets were found to be involved in whole blood, blood components, and lymphatic organs across all four tools. Each tool indicated a particular aspect of RAB’s target organ locations: DAVID-enriched genes showed a predominance in blood, liver, and kidneys; Gene ORGANizer showed the effect on low body parts as well as bones and joints; BioGPS and HPA showed high gene expression in bone marrow, lymphoid tissue, and smooth muscle. Conclusion: Our bioinformatics-based target organ location prediction can serve as a modern interpretation tool for the target organ location theory of traditional medicine. Future studies should predict therapeutic target organ locations in complex prescriptions rather than single herbs and conduct experiments to verify predictions. Frontiers Media S.A. 2023-08-10 /pmc/articles/PMC10448535/ /pubmed/37637410 http://dx.doi.org/10.3389/fphar.2023.1187896 Text en Copyright © 2023 Tran, Baek, Jun and Lee. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Pharmacology
Tran, Minh Nhat
Baek, Su-Jin
Jun, Hyeong Joon
Lee, Sanghun
Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes
title Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes
title_full Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes
title_fullStr Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes
title_full_unstemmed Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes
title_short Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes
title_sort identifying target organ location of radix achyranthis bidentatae: a bioinformatics approach on active compounds and genes
topic Pharmacology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10448535/
https://www.ncbi.nlm.nih.gov/pubmed/37637410
http://dx.doi.org/10.3389/fphar.2023.1187896
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