Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations
Context Diabetes mellitus (DM) is a metabolic disorder disease that causes hyperglycemia conditions and associated with various chronic complications leading to mortality. Due to high toxicity of conventional diabetic drugs, the exploration of natural compounds as alternative diabetes treatments has...
Gespeichert in:
| Veröffentlicht in: | Journal of molecular modeling 2024-08, Vol.30 (8), p.260-260, Article 260 |
|---|---|
| Hauptverfasser: | , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 260 |
|---|---|
| container_issue | 8 |
| container_start_page | 260 |
| container_title | Journal of molecular modeling |
| container_volume | 30 |
| creator | Maksum, Iman Permana Rustaman, Rustaman Deawati, Yusi Rukayadi, Yaya Utami, Ayudiah Rizki Nafisa, Zahra Khira |
| description | Context
Diabetes mellitus (DM) is a metabolic disorder disease that causes hyperglycemia conditions and associated with various chronic complications leading to mortality. Due to high toxicity of conventional diabetic drugs, the exploration of natural compounds as alternative diabetes treatments has been widely carried out. Previous
in silico
studies have highlighted berberine, a natural compound, as a promising alternative in antidiabetic therapy, potentially acting through various pathways, including the inhibition of the FOXO1 transcription factor in the gluconeogenesis pathway. However, the specific mechanism by which berberine interacts with FOXO1 remains unclear, and research in this area is relatively limited. Therefore, this study aims to determine the stability of berberine structure with FOXO1 based on RMSD, RMSF, binding energy, and trajectory analysis to determine the potential of berberine to inhibit the gluconeogenesis pathway. This research was conducted by
in silico
method with molecular docking using AutoDock4.2 and molecular dynamics study using Amber20, then visualized by VMD.
Methods
Docking between ligand and FOXO1 receptor was carried out with Autodock4.2. For molecular dynamics simulations, the force fields of DNA.OL15, protein.ff14SB, gaff2, and tip3p were used. |
| doi_str_mv | 10.1007/s00894-024-06060-6 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_3153731909</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3077945340</sourcerecordid><originalsourceid>FETCH-LOGICAL-c289t-75ecf1387423f3238f526116a0e27570461c5fad0553599976b0fc6497ee496e3</originalsourceid><addsrcrecordid>eNqFkc2OFCEUhYnROJ1xXsCFIXHjpvQCBRRLM3HUZJJeqIk7QlPQzVhAC1WLfg8fWNoaf-JCA-Qm53733JCD0FMCLwmAfFUBBtV3QNsT7XTiAdqA6oeOA2UP0YYIAh1VPVygq1rvAIBQLjilj9EFG9RAFCUb9O3DvIwnnD2eDw6bNIcxmJ2bg8XR2YNJocZzd-dKuyE5bHM85iWNOCd8s_28JXguJlVbwnEOTfPGzrk0u5KX_QHHPDm7TKbgMdsvIe3bkvFP9ZRMDLbiGmITzhb1CXrkzVTd1X29RJ9u3ny8ftfdbt--v35921k6qLmT3FlP2CB7yjyjbPCcCkKEAUcll9ALYrk3I3DOuFJKih14K3olneuVcOwSvVh9jyV_XVyddQzVumkyyeWlakY4k4woUP9HQUqlqKC0oc__Qu_yUlL7yEr1nPXQKLpStuRai_P6WEI05aQJ6HPCek1Yt4T1j4S1aEPP7q2XXXTjr5GfeTaArUBtrbR35ffuf9h-B_ATsZM</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3077945340</pqid></control><display><type>article</type><title>Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations</title><source>MEDLINE</source><source>SpringerLink Journals - AutoHoldings</source><creator>Maksum, Iman Permana ; Rustaman, Rustaman ; Deawati, Yusi ; Rukayadi, Yaya ; Utami, Ayudiah Rizki ; Nafisa, Zahra Khira</creator><creatorcontrib>Maksum, Iman Permana ; Rustaman, Rustaman ; Deawati, Yusi ; Rukayadi, Yaya ; Utami, Ayudiah Rizki ; Nafisa, Zahra Khira</creatorcontrib><description>Context
Diabetes mellitus (DM) is a metabolic disorder disease that causes hyperglycemia conditions and associated with various chronic complications leading to mortality. Due to high toxicity of conventional diabetic drugs, the exploration of natural compounds as alternative diabetes treatments has been widely carried out. Previous
in silico
studies have highlighted berberine, a natural compound, as a promising alternative in antidiabetic therapy, potentially acting through various pathways, including the inhibition of the FOXO1 transcription factor in the gluconeogenesis pathway. However, the specific mechanism by which berberine interacts with FOXO1 remains unclear, and research in this area is relatively limited. Therefore, this study aims to determine the stability of berberine structure with FOXO1 based on RMSD, RMSF, binding energy, and trajectory analysis to determine the potential of berberine to inhibit the gluconeogenesis pathway. This research was conducted by
in silico
method with molecular docking using AutoDock4.2 and molecular dynamics study using Amber20, then visualized by VMD.
Methods
Docking between ligand and FOXO1 receptor was carried out with Autodock4.2. For molecular dynamics simulations, the force fields of DNA.OL15, protein.ff14SB, gaff2, and tip3p were used.</description><identifier>ISSN: 1610-2940</identifier><identifier>ISSN: 0948-5023</identifier><identifier>EISSN: 0948-5023</identifier><identifier>DOI: 10.1007/s00894-024-06060-6</identifier><identifier>PMID: 38981921</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Antidiabetics ; berberine ; Berberine - chemistry ; Berberine - pharmacology ; Binding Sites ; Characterization and Evaluation of Materials ; Chemistry ; Chemistry and Materials Science ; Computer Appl. in Life Sciences ; Computer Applications in Chemistry ; computer simulation ; Diabetes ; Diabetes mellitus ; Dynamic structural analysis ; energy ; Forkhead Box Protein O1 - chemistry ; Forkhead Box Protein O1 - metabolism ; gluconeogenesis ; Humans ; Hyperglycemia ; Hypoglycemic Agents - chemistry ; Hypoglycemic Agents - pharmacology ; Ligands ; Metabolic disorders ; Molecular docking ; Molecular Docking Simulation ; Molecular dynamics ; Molecular Dynamics Simulation ; Molecular Medicine ; Molecular structure ; mortality ; Original Paper ; Protein Binding ; Theoretical and Computational Chemistry ; therapeutics ; Toxic diseases ; toxicity ; Trajectory analysis ; Transcription factors</subject><ispartof>Journal of molecular modeling, 2024-08, Vol.30 (8), p.260-260, Article 260</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c289t-75ecf1387423f3238f526116a0e27570461c5fad0553599976b0fc6497ee496e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00894-024-06060-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00894-024-06060-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38981921$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Maksum, Iman Permana</creatorcontrib><creatorcontrib>Rustaman, Rustaman</creatorcontrib><creatorcontrib>Deawati, Yusi</creatorcontrib><creatorcontrib>Rukayadi, Yaya</creatorcontrib><creatorcontrib>Utami, Ayudiah Rizki</creatorcontrib><creatorcontrib>Nafisa, Zahra Khira</creatorcontrib><title>Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations</title><title>Journal of molecular modeling</title><addtitle>J Mol Model</addtitle><addtitle>J Mol Model</addtitle><description>Context
Diabetes mellitus (DM) is a metabolic disorder disease that causes hyperglycemia conditions and associated with various chronic complications leading to mortality. Due to high toxicity of conventional diabetic drugs, the exploration of natural compounds as alternative diabetes treatments has been widely carried out. Previous
in silico
studies have highlighted berberine, a natural compound, as a promising alternative in antidiabetic therapy, potentially acting through various pathways, including the inhibition of the FOXO1 transcription factor in the gluconeogenesis pathway. However, the specific mechanism by which berberine interacts with FOXO1 remains unclear, and research in this area is relatively limited. Therefore, this study aims to determine the stability of berberine structure with FOXO1 based on RMSD, RMSF, binding energy, and trajectory analysis to determine the potential of berberine to inhibit the gluconeogenesis pathway. This research was conducted by
in silico
method with molecular docking using AutoDock4.2 and molecular dynamics study using Amber20, then visualized by VMD.
Methods
Docking between ligand and FOXO1 receptor was carried out with Autodock4.2. For molecular dynamics simulations, the force fields of DNA.OL15, protein.ff14SB, gaff2, and tip3p were used.</description><subject>Antidiabetics</subject><subject>berberine</subject><subject>Berberine - chemistry</subject><subject>Berberine - pharmacology</subject><subject>Binding Sites</subject><subject>Characterization and Evaluation of Materials</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Computer Appl. in Life Sciences</subject><subject>Computer Applications in Chemistry</subject><subject>computer simulation</subject><subject>Diabetes</subject><subject>Diabetes mellitus</subject><subject>Dynamic structural analysis</subject><subject>energy</subject><subject>Forkhead Box Protein O1 - chemistry</subject><subject>Forkhead Box Protein O1 - metabolism</subject><subject>gluconeogenesis</subject><subject>Humans</subject><subject>Hyperglycemia</subject><subject>Hypoglycemic Agents - chemistry</subject><subject>Hypoglycemic Agents - pharmacology</subject><subject>Ligands</subject><subject>Metabolic disorders</subject><subject>Molecular docking</subject><subject>Molecular Docking Simulation</subject><subject>Molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecular Medicine</subject><subject>Molecular structure</subject><subject>mortality</subject><subject>Original Paper</subject><subject>Protein Binding</subject><subject>Theoretical and Computational Chemistry</subject><subject>therapeutics</subject><subject>Toxic diseases</subject><subject>toxicity</subject><subject>Trajectory analysis</subject><subject>Transcription factors</subject><issn>1610-2940</issn><issn>0948-5023</issn><issn>0948-5023</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc2OFCEUhYnROJ1xXsCFIXHjpvQCBRRLM3HUZJJeqIk7QlPQzVhAC1WLfg8fWNoaf-JCA-Qm53733JCD0FMCLwmAfFUBBtV3QNsT7XTiAdqA6oeOA2UP0YYIAh1VPVygq1rvAIBQLjilj9EFG9RAFCUb9O3DvIwnnD2eDw6bNIcxmJ2bg8XR2YNJocZzd-dKuyE5bHM85iWNOCd8s_28JXguJlVbwnEOTfPGzrk0u5KX_QHHPDm7TKbgMdsvIe3bkvFP9ZRMDLbiGmITzhb1CXrkzVTd1X29RJ9u3ny8ftfdbt--v35921k6qLmT3FlP2CB7yjyjbPCcCkKEAUcll9ALYrk3I3DOuFJKih14K3olneuVcOwSvVh9jyV_XVyddQzVumkyyeWlakY4k4woUP9HQUqlqKC0oc__Qu_yUlL7yEr1nPXQKLpStuRai_P6WEI05aQJ6HPCek1Yt4T1j4S1aEPP7q2XXXTjr5GfeTaArUBtrbR35ffuf9h-B_ATsZM</recordid><startdate>20240801</startdate><enddate>20240801</enddate><creator>Maksum, Iman Permana</creator><creator>Rustaman, Rustaman</creator><creator>Deawati, Yusi</creator><creator>Rukayadi, Yaya</creator><creator>Utami, Ayudiah Rizki</creator><creator>Nafisa, Zahra Khira</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope></search><sort><creationdate>20240801</creationdate><title>Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations</title><author>Maksum, Iman Permana ; Rustaman, Rustaman ; Deawati, Yusi ; Rukayadi, Yaya ; Utami, Ayudiah Rizki ; Nafisa, Zahra Khira</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c289t-75ecf1387423f3238f526116a0e27570461c5fad0553599976b0fc6497ee496e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Antidiabetics</topic><topic>berberine</topic><topic>Berberine - chemistry</topic><topic>Berberine - pharmacology</topic><topic>Binding Sites</topic><topic>Characterization and Evaluation of Materials</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Computer Appl. in Life Sciences</topic><topic>Computer Applications in Chemistry</topic><topic>computer simulation</topic><topic>Diabetes</topic><topic>Diabetes mellitus</topic><topic>Dynamic structural analysis</topic><topic>energy</topic><topic>Forkhead Box Protein O1 - chemistry</topic><topic>Forkhead Box Protein O1 - metabolism</topic><topic>gluconeogenesis</topic><topic>Humans</topic><topic>Hyperglycemia</topic><topic>Hypoglycemic Agents - chemistry</topic><topic>Hypoglycemic Agents - pharmacology</topic><topic>Ligands</topic><topic>Metabolic disorders</topic><topic>Molecular docking</topic><topic>Molecular Docking Simulation</topic><topic>Molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>Molecular Medicine</topic><topic>Molecular structure</topic><topic>mortality</topic><topic>Original Paper</topic><topic>Protein Binding</topic><topic>Theoretical and Computational Chemistry</topic><topic>therapeutics</topic><topic>Toxic diseases</topic><topic>toxicity</topic><topic>Trajectory analysis</topic><topic>Transcription factors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Maksum, Iman Permana</creatorcontrib><creatorcontrib>Rustaman, Rustaman</creatorcontrib><creatorcontrib>Deawati, Yusi</creatorcontrib><creatorcontrib>Rukayadi, Yaya</creatorcontrib><creatorcontrib>Utami, Ayudiah Rizki</creatorcontrib><creatorcontrib>Nafisa, Zahra Khira</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Journal of molecular modeling</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Maksum, Iman Permana</au><au>Rustaman, Rustaman</au><au>Deawati, Yusi</au><au>Rukayadi, Yaya</au><au>Utami, Ayudiah Rizki</au><au>Nafisa, Zahra Khira</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations</atitle><jtitle>Journal of molecular modeling</jtitle><stitle>J Mol Model</stitle><addtitle>J Mol Model</addtitle><date>2024-08-01</date><risdate>2024</risdate><volume>30</volume><issue>8</issue><spage>260</spage><epage>260</epage><pages>260-260</pages><artnum>260</artnum><issn>1610-2940</issn><issn>0948-5023</issn><eissn>0948-5023</eissn><abstract>Context
Diabetes mellitus (DM) is a metabolic disorder disease that causes hyperglycemia conditions and associated with various chronic complications leading to mortality. Due to high toxicity of conventional diabetic drugs, the exploration of natural compounds as alternative diabetes treatments has been widely carried out. Previous
in silico
studies have highlighted berberine, a natural compound, as a promising alternative in antidiabetic therapy, potentially acting through various pathways, including the inhibition of the FOXO1 transcription factor in the gluconeogenesis pathway. However, the specific mechanism by which berberine interacts with FOXO1 remains unclear, and research in this area is relatively limited. Therefore, this study aims to determine the stability of berberine structure with FOXO1 based on RMSD, RMSF, binding energy, and trajectory analysis to determine the potential of berberine to inhibit the gluconeogenesis pathway. This research was conducted by
in silico
method with molecular docking using AutoDock4.2 and molecular dynamics study using Amber20, then visualized by VMD.
Methods
Docking between ligand and FOXO1 receptor was carried out with Autodock4.2. For molecular dynamics simulations, the force fields of DNA.OL15, protein.ff14SB, gaff2, and tip3p were used.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>38981921</pmid><doi>10.1007/s00894-024-06060-6</doi><tpages>1</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1610-2940 |
| ispartof | Journal of molecular modeling, 2024-08, Vol.30 (8), p.260-260, Article 260 |
| issn | 1610-2940 0948-5023 0948-5023 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_3153731909 |
| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Antidiabetics berberine Berberine - chemistry Berberine - pharmacology Binding Sites Characterization and Evaluation of Materials Chemistry Chemistry and Materials Science Computer Appl. in Life Sciences Computer Applications in Chemistry computer simulation Diabetes Diabetes mellitus Dynamic structural analysis energy Forkhead Box Protein O1 - chemistry Forkhead Box Protein O1 - metabolism gluconeogenesis Humans Hyperglycemia Hypoglycemic Agents - chemistry Hypoglycemic Agents - pharmacology Ligands Metabolic disorders Molecular docking Molecular Docking Simulation Molecular dynamics Molecular Dynamics Simulation Molecular Medicine Molecular structure mortality Original Paper Protein Binding Theoretical and Computational Chemistry therapeutics Toxic diseases toxicity Trajectory analysis Transcription factors |
| title | Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-19T16%3A24%3A19IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Study%20of%20the%20antidiabetic%20mechanism%20of%20berberine%20compound%20on%20FOXO1%20transcription%20factor%20through%20molecular%20docking%20and%20molecular%20dynamics%20simulations&rft.jtitle=Journal%20of%20molecular%20modeling&rft.au=Maksum,%20Iman%20Permana&rft.date=2024-08-01&rft.volume=30&rft.issue=8&rft.spage=260&rft.epage=260&rft.pages=260-260&rft.artnum=260&rft.issn=1610-2940&rft.eissn=0948-5023&rft_id=info:doi/10.1007/s00894-024-06060-6&rft_dat=%3Cproquest_cross%3E3077945340%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=3077945340&rft_id=info:pmid/38981921&rfr_iscdi=true |