Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions
Interaksi protein-ligan memainkan peranan penting dalam menyediakan produk farmaseutikal yang baharu. Kajian ini merupakan usaha untuk memahami struktur dan dinamik kompleks insulin-siklodekstrin sebagai formula insulin oral yang baharu. Pendokkan dan simulasi dinamik molekul telah dijalankan untuk...
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| Format: | Thesis |
| Language: | English |
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2016
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| Online Access: | http://eprints.usm.my/31627/1/ERMA_FATIHA_BINTI_MUHAMMAD_24.pdf |
| _version_ | 1825832575674875904 |
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| author | Muhammad, Erma Fatiha |
| author_facet | Muhammad, Erma Fatiha |
| author_sort | Muhammad, Erma Fatiha |
| collection | USM |
| description | Interaksi protein-ligan memainkan peranan penting dalam menyediakan produk farmaseutikal yang baharu. Kajian ini merupakan usaha untuk memahami struktur dan dinamik kompleks insulin-siklodekstrin sebagai formula insulin oral yang baharu. Pendokkan dan simulasi dinamik molekul telah dijalankan untuk mengkaji interaksi antara monomer insulin dan dimer insulin terhadap β-siklodekstrins (β-CDs). Kajian pendokkan molekul berganda telah dijalankan menggunakan program Autodock v4.2 untuk menentukan bilangan β-CD yang boleh terikat pada tapak ikatan insulin selain menentukan konformasi insulin-β-CD yang paling stabil. Pendokkan molekul dengan 100 struktur rawak menggunakan konformasi awal nisbah monomer insulin kepada β-CD dan dimer insulin-β-CD 1:1 telah dijalankan dan daripada struktur pendokkan terakhir, β-CD telah ditambah dan proses diulangi sehingga peningkatan tenaga didapati. Keputusan pendokkan molekul menunjukkan maksimum empat molekul β-CD boleh terikat kepada struktur insulin dan nisbah insulin kepada β-CD 1:3 menghasilkan tenaga bebas pengikatan terendah. Selain pembentukan ikatan hidrogen, keputusan pendokkan menunjukkan bahawa interaksi hidrofobik memainkan peranan penting dalam menentukan kestabilan kompleks insulin-β-CD.
Protein-ligand interactions play an essential role in the design of new pharmaceutical products. This study attempts to understand the theoretical basis on the structure and dynamics of insulin-cyclodextrin complex for new oral insulin formulation. Docking and molecular dynamics simulations were performed to explore the interactions between insulin monomer and insulin dimer with β-cyclodextrins (β-CDs). A multiple molecular docking study was performed using the Autodock v4.2 program to determine the number of β-CD that can adhere to the binding sites of insulin as well as to determine the most stable conformations of insulin to β-CDs. A 100 random structure docking using 1:1 insulin monomer-β-CD and insulin dimer-β-CD ratio were conducted and from the final docked structure, additional β-CDs were added and the process were repeated until the energy increase. Molecular docking results revealed that a maximum of four β-CDs can bind to an insulin structure with the 1:3 insulin-β-CD ratios having the lowest binding free energy. |
| first_indexed | 2024-03-06T14:54:54Z |
| format | Thesis |
| id | usm.eprints-31627 |
| institution | Universiti Sains Malaysia |
| language | English |
| last_indexed | 2024-03-06T14:54:54Z |
| publishDate | 2016 |
| record_format | dspace |
| spelling | usm.eprints-316272019-04-12T05:25:26Z http://eprints.usm.my/31627/ Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions Muhammad, Erma Fatiha QD1-999 Chemistry Interaksi protein-ligan memainkan peranan penting dalam menyediakan produk farmaseutikal yang baharu. Kajian ini merupakan usaha untuk memahami struktur dan dinamik kompleks insulin-siklodekstrin sebagai formula insulin oral yang baharu. Pendokkan dan simulasi dinamik molekul telah dijalankan untuk mengkaji interaksi antara monomer insulin dan dimer insulin terhadap β-siklodekstrins (β-CDs). Kajian pendokkan molekul berganda telah dijalankan menggunakan program Autodock v4.2 untuk menentukan bilangan β-CD yang boleh terikat pada tapak ikatan insulin selain menentukan konformasi insulin-β-CD yang paling stabil. Pendokkan molekul dengan 100 struktur rawak menggunakan konformasi awal nisbah monomer insulin kepada β-CD dan dimer insulin-β-CD 1:1 telah dijalankan dan daripada struktur pendokkan terakhir, β-CD telah ditambah dan proses diulangi sehingga peningkatan tenaga didapati. Keputusan pendokkan molekul menunjukkan maksimum empat molekul β-CD boleh terikat kepada struktur insulin dan nisbah insulin kepada β-CD 1:3 menghasilkan tenaga bebas pengikatan terendah. Selain pembentukan ikatan hidrogen, keputusan pendokkan menunjukkan bahawa interaksi hidrofobik memainkan peranan penting dalam menentukan kestabilan kompleks insulin-β-CD. Protein-ligand interactions play an essential role in the design of new pharmaceutical products. This study attempts to understand the theoretical basis on the structure and dynamics of insulin-cyclodextrin complex for new oral insulin formulation. Docking and molecular dynamics simulations were performed to explore the interactions between insulin monomer and insulin dimer with β-cyclodextrins (β-CDs). A multiple molecular docking study was performed using the Autodock v4.2 program to determine the number of β-CD that can adhere to the binding sites of insulin as well as to determine the most stable conformations of insulin to β-CDs. A 100 random structure docking using 1:1 insulin monomer-β-CD and insulin dimer-β-CD ratio were conducted and from the final docked structure, additional β-CDs were added and the process were repeated until the energy increase. Molecular docking results revealed that a maximum of four β-CDs can bind to an insulin structure with the 1:3 insulin-β-CD ratios having the lowest binding free energy. 2016-02 Thesis NonPeerReviewed application/pdf en http://eprints.usm.my/31627/1/ERMA_FATIHA_BINTI_MUHAMMAD_24.pdf Muhammad, Erma Fatiha (2016) Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions. Masters thesis, Universiti Sains Malaysia. |
| spellingShingle | QD1-999 Chemistry Muhammad, Erma Fatiha Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions |
| title | Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions |
| title_full | Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions |
| title_fullStr | Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions |
| title_full_unstemmed | Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions |
| title_short | Docking And Molecular Dynamics Simulation Studies Of Insulin-Β-Cyclodextrin Interactions |
| title_sort | docking and molecular dynamics simulation studies of insulin β cyclodextrin interactions |
| topic | QD1-999 Chemistry |
| url | http://eprints.usm.my/31627/1/ERMA_FATIHA_BINTI_MUHAMMAD_24.pdf |
| work_keys_str_mv | AT muhammadermafatiha dockingandmoleculardynamicssimulationstudiesofinsulinbcyclodextrininteractions |