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 ha...
| Main Authors: | , , , , , |
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| Format: | Article |
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Springer Science and Business Media Deutschland GmbH
2024
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| Online Access: | http://psasir.upm.edu.my/id/eprint/113615/ |
| _version_ | 1848866275334291456 |
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| author | Maksum, Iman Permana Rustaman, Rustaman Deawati, Yusi Rukayadi, Yaya Utami, Ayudiah Rizki Nafisa, Zahra Khira |
| author_facet | Maksum, Iman Permana Rustaman, Rustaman Deawati, Yusi Rukayadi, Yaya Utami, Ayudiah Rizki Nafisa, Zahra Khira |
| author_sort | Maksum, Iman Permana |
| building | UPM Institutional Repository |
| collection | Online Access |
| 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. |
| first_indexed | 2025-11-15T14:18:01Z |
| format | Article |
| id | upm-113615 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T14:18:01Z |
| publishDate | 2024 |
| publisher | Springer Science and Business Media Deutschland GmbH |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1136152024-11-14T03:28:13Z http://psasir.upm.edu.my/id/eprint/113615/ Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations Maksum, Iman Permana Rustaman, Rustaman Deawati, Yusi Rukayadi, Yaya Utami, Ayudiah Rizki Nafisa, Zahra Khira 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. Springer Science and Business Media Deutschland GmbH 2024 Article PeerReviewed Maksum, Iman Permana and Rustaman, Rustaman and Deawati, Yusi and Rukayadi, Yaya and Utami, Ayudiah Rizki and Nafisa, Zahra Khira (2024) Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations. Journal of Molecular Modeling, 30 (8). art. no. 260. ISSN 1610-2940; eISSN: 0948-5023 https://link.springer.com/article/10.1007/s00894-024-06060-6?error=cookies_not_supported&code=b6e6fa34-81d9-4715-b19d-62a2ffbf64fc 10.1007/s00894-024-06060-6 |
| spellingShingle | Maksum, Iman Permana Rustaman, Rustaman Deawati, Yusi Rukayadi, Yaya Utami, Ayudiah Rizki Nafisa, Zahra Khira Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations |
| title | Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations |
| title_full | Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations |
| title_fullStr | Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations |
| title_full_unstemmed | Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations |
| title_short | Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations |
| title_sort | study of the antidiabetic mechanism of berberine compound on foxo1 transcription factor through molecular docking and molecular dynamics simulations |
| url | http://psasir.upm.edu.my/id/eprint/113615/ http://psasir.upm.edu.my/id/eprint/113615/ http://psasir.upm.edu.my/id/eprint/113615/ |