Loading…
Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations
Abstract Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action (MOA) has not been identified. Systems pharmacology methods have been used to overcome these challenges. However, there is a limitation as thos...
Saved in:
| Published in: | Briefings in bioinformatics 2023-09, Vol.24 (6) |
|---|---|
| Main Authors: | , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c381t-45f597a02846f4a435be963b6e399b852409ce1d06e41901bfb27faffd6975e43 |
|---|---|
| cites | cdi_FETCH-LOGICAL-c381t-45f597a02846f4a435be963b6e399b852409ce1d06e41901bfb27faffd6975e43 |
| container_end_page | |
| container_issue | 6 |
| container_start_page | |
| container_title | Briefings in bioinformatics |
| container_volume | 24 |
| creator | Park, Musun Baek, Su-Jin Park, Sang-Min Yi, Jin-Mu Cha, Seongwon |
| description | Abstract
Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action (MOA) 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, molecular docking analysis and RNA-seq analysis were performed to compare the MOA of similar compounds and to confirm the changes observed when similar compounds were mixed and used. Various analyses have confirmed that compounds with similar structures share similar MOA. We propose an advanced method for in silico experiments in herbal medicine research based on the results. 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 multi-component 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. |
| doi_str_mv | 10.1093/bib/bbad344 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10555731</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/bib/bbad344</oup_id><sourcerecordid>2874260523</sourcerecordid><originalsourceid>FETCH-LOGICAL-c381t-45f597a02846f4a435be963b6e399b852409ce1d06e41901bfb27faffd6975e43</originalsourceid><addsrcrecordid>eNp9ksuKFTEQhhtRnIuufIGAIMJwnKSTdLpXMhy8wYAbXYckXZnO2J20uRydh_IdTXMOgi5cVah89ddf8DfNC4LfEDzQa-30tdZqpIw9as4JE2LHMGePt3cndpx19Ky5SOke4xaLnjxtzqgQQ99yct782odlVVFldwCUchkfULAoT4AWMJPyLi1bw6tcopqRqXQofkzoh8sTSm5xs4p1MBZTCUioJOfv0BjMt60qP6IclU8mujWHBdCoskI2ROSWNYbDBjlfhWZnApog6rplgdEZ5wHBzxWiW8DnajD49Kx5YtWc4PmpXjZf37_7sv-4u_384dP-5nZnaE_yjnHLB6Fw27POMsUo1zB0VHdAh0H3vGV4MEBG3AEjAyba6lZYZe3YDYIDo5fN26PuWnQ1Y6qBer1cqxcVH2RQTv79490k78JBEsw5F5RUhdcnhRi-F0hZLi4ZmGflIZQk216wtsO8pRV9-Q96H0r09T7ZDpxTLAjeBK-OlIkhpQj2jxuC5ZYDWXMgTzmo9KsjHcr6X_A3gHS4CQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2955307101</pqid></control><display><type>article</type><title>Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations</title><source>Open Access: PubMed Central</source><source>Business Source Ultimate</source><source>Oxford University Press Journals</source><creator>Park, Musun ; Baek, Su-Jin ; Park, Sang-Min ; Yi, Jin-Mu ; Cha, Seongwon</creator><creatorcontrib>Park, Musun ; Baek, Su-Jin ; Park, Sang-Min ; Yi, Jin-Mu ; Cha, Seongwon</creatorcontrib><description>Abstract
Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action (MOA) 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, molecular docking analysis and RNA-seq analysis were performed to compare the MOA of similar compounds and to confirm the changes observed when similar compounds were mixed and used. Various analyses have confirmed that compounds with similar structures share similar MOA. We propose an advanced method for in silico experiments in herbal medicine research based on the results. 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 multi-component 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.</description><identifier>ISSN: 1467-5463</identifier><identifier>EISSN: 1477-4054</identifier><identifier>DOI: 10.1093/bib/bbad344</identifier><identifier>PMID: 37798251</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Comparative studies ; Herbal medicine ; Molecular docking ; Natural products ; Pharmacology ; Review ; Transcriptomes</subject><ispartof>Briefings in bioinformatics, 2023-09, Vol.24 (6)</ispartof><rights>The Author(s) 2023. Published by Oxford University Press. 2023</rights><rights>The Author(s) 2023. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c381t-45f597a02846f4a435be963b6e399b852409ce1d06e41901bfb27faffd6975e43</citedby><cites>FETCH-LOGICAL-c381t-45f597a02846f4a435be963b6e399b852409ce1d06e41901bfb27faffd6975e43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10555731/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10555731/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,733,786,790,891,1591,27957,27958,53827,53829</link.rule.ids></links><search><creatorcontrib>Park, Musun</creatorcontrib><creatorcontrib>Baek, Su-Jin</creatorcontrib><creatorcontrib>Park, Sang-Min</creatorcontrib><creatorcontrib>Yi, Jin-Mu</creatorcontrib><creatorcontrib>Cha, Seongwon</creatorcontrib><title>Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations</title><title>Briefings in bioinformatics</title><description>Abstract
Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action (MOA) 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, molecular docking analysis and RNA-seq analysis were performed to compare the MOA of similar compounds and to confirm the changes observed when similar compounds were mixed and used. Various analyses have confirmed that compounds with similar structures share similar MOA. We propose an advanced method for in silico experiments in herbal medicine research based on the results. 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 multi-component 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.</description><subject>Comparative studies</subject><subject>Herbal medicine</subject><subject>Molecular docking</subject><subject>Natural products</subject><subject>Pharmacology</subject><subject>Review</subject><subject>Transcriptomes</subject><issn>1467-5463</issn><issn>1477-4054</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNp9ksuKFTEQhhtRnIuufIGAIMJwnKSTdLpXMhy8wYAbXYckXZnO2J20uRydh_IdTXMOgi5cVah89ddf8DfNC4LfEDzQa-30tdZqpIw9as4JE2LHMGePt3cndpx19Ky5SOke4xaLnjxtzqgQQ99yct782odlVVFldwCUchkfULAoT4AWMJPyLi1bw6tcopqRqXQofkzoh8sTSm5xs4p1MBZTCUioJOfv0BjMt60qP6IclU8mujWHBdCoskI2ROSWNYbDBjlfhWZnApog6rplgdEZ5wHBzxWiW8DnajD49Kx5YtWc4PmpXjZf37_7sv-4u_384dP-5nZnaE_yjnHLB6Fw27POMsUo1zB0VHdAh0H3vGV4MEBG3AEjAyba6lZYZe3YDYIDo5fN26PuWnQ1Y6qBer1cqxcVH2RQTv79490k78JBEsw5F5RUhdcnhRi-F0hZLi4ZmGflIZQk216wtsO8pRV9-Q96H0r09T7ZDpxTLAjeBK-OlIkhpQj2jxuC5ZYDWXMgTzmo9KsjHcr6X_A3gHS4CQ</recordid><startdate>20230922</startdate><enddate>20230922</enddate><creator>Park, Musun</creator><creator>Baek, Su-Jin</creator><creator>Park, Sang-Min</creator><creator>Yi, Jin-Mu</creator><creator>Cha, Seongwon</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>TOX</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SC</scope><scope>8FD</scope><scope>FR3</scope><scope>JQ2</scope><scope>K9.</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20230922</creationdate><title>Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations</title><author>Park, Musun ; Baek, Su-Jin ; Park, Sang-Min ; Yi, Jin-Mu ; Cha, Seongwon</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c381t-45f597a02846f4a435be963b6e399b852409ce1d06e41901bfb27faffd6975e43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Comparative studies</topic><topic>Herbal medicine</topic><topic>Molecular docking</topic><topic>Natural products</topic><topic>Pharmacology</topic><topic>Review</topic><topic>Transcriptomes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Park, Musun</creatorcontrib><creatorcontrib>Baek, Su-Jin</creatorcontrib><creatorcontrib>Park, Sang-Min</creatorcontrib><creatorcontrib>Yi, Jin-Mu</creatorcontrib><creatorcontrib>Cha, Seongwon</creatorcontrib><collection>Open Access: Oxford University Press Open Journals</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Briefings in bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Park, Musun</au><au>Baek, Su-Jin</au><au>Park, Sang-Min</au><au>Yi, Jin-Mu</au><au>Cha, Seongwon</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations</atitle><jtitle>Briefings in bioinformatics</jtitle><date>2023-09-22</date><risdate>2023</risdate><volume>24</volume><issue>6</issue><issn>1467-5463</issn><eissn>1477-4054</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>Abstract
Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action (MOA) 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, molecular docking analysis and RNA-seq analysis were performed to compare the MOA of similar compounds and to confirm the changes observed when similar compounds were mixed and used. Various analyses have confirmed that compounds with similar structures share similar MOA. We propose an advanced method for in silico experiments in herbal medicine research based on the results. 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 multi-component 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.</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>37798251</pmid><doi>10.1093/bib/bbad344</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1467-5463 |
| ispartof | Briefings in bioinformatics, 2023-09, Vol.24 (6) |
| issn | 1467-5463 1477-4054 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10555731 |
| source | Open Access: PubMed Central; Business Source Ultimate; Oxford University Press Journals |
| subjects | Comparative studies Herbal medicine Molecular docking Natural products Pharmacology Review Transcriptomes |
| title | Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-09-22T10%3A31%3A21IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparative%20study%20of%20the%20mechanism%20of%20natural%20compounds%20with%20similar%20structures%20using%20docking%20and%20transcriptome%20data%20for%20improving%20in%20silico%20herbal%20medicine%20experimentations&rft.jtitle=Briefings%20in%20bioinformatics&rft.au=Park,%20Musun&rft.date=2023-09-22&rft.volume=24&rft.issue=6&rft.issn=1467-5463&rft.eissn=1477-4054&rft_id=info:doi/10.1093/bib/bbad344&rft_dat=%3Cproquest_pubme%3E2874260523%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c381t-45f597a02846f4a435be963b6e399b852409ce1d06e41901bfb27faffd6975e43%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2955307101&rft_id=info:pmid/37798251&rft_oup_id=10.1093/bib/bbad344&rfr_iscdi=true |