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Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation

In our study, molecular docking and molecular dynamics (MD) simulations were performed in order to explore the interactions between human insulin and β-cyclodextrin (β-CD). Molecular docking study was performed using the Autodock v4.2 program to determine the number of β-CD molecules that adhere to...

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Main Authors: Muhammad, Erma Fatiha, Adnan, Rohana, Mohammad Latif, Muhammad Alif, Abdul Rahman, Mohd Basyaruddin
Format: Article
Language:English
Published: Springer Netherlands 2016
Online Access:http://psasir.upm.edu.my/id/eprint/53117/1/Theoretical%20investigation%20on%20insulin%20dimer%20-%20b%20-%20cyclodextrin%20interactions%20using%20docking%20and%20molecular%20dynamics%20simulation.pdf
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spelling oai:psasir.upm.edu.my:53117 http://psasir.upm.edu.my/id/eprint/53117/ Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation Muhammad, Erma Fatiha Adnan, Rohana Mohammad Latif, Muhammad Alif Abdul Rahman, Mohd Basyaruddin In our study, molecular docking and molecular dynamics (MD) simulations were performed in order to explore the interactions between human insulin and β-cyclodextrin (β-CD). Molecular docking study was performed using the Autodock v4.2 program to determine the number of β-CD molecules that adhere to the binding sites of insulin. A random structure docking approach using an initial ratio of 1:1 insulin-β-CD was conducted and from these, additional β-CDs were added. Molecular docking results revealed that a maximum of four β-CDs are able to bind to the insulin structure with the 1:3 insulin-β-CD ratio producing the lowest binding free energy. The docked conformations showed that hydrophobic interactions played a crucial role in insulin-β-CD conformational stability in addition to the formation of hydrogen bonds. A 50 ns MD simulation was further conducted using an NPT ensemble to verify the results obtained by molecular docking. The analysis of the MD simulation results of the 1:3 insulin-β-CD formation system conclude that a good interaction exists between insulin and β-CDs and the RMSD value obtained was 4.00 ± 0.50 Å. The RMSF profiles of insulin in the 1:3 insulin-β-CD formation also show reduced amino acid residues flexibility as compared to the free insulin system. The theoretical results indicated the presence of significant interactions between insulin and β-CD which could provide interesting insights into an insulin formulation. Springer Netherlands 2016 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/53117/1/Theoretical%20investigation%20on%20insulin%20dimer%20-%20b%20-%20cyclodextrin%20interactions%20using%20docking%20and%20molecular%20dynamics%20simulation.pdf Muhammad, Erma Fatiha and Adnan, Rohana and Mohammad Latif, Muhammad Alif and Abdul Rahman, Mohd Basyaruddin (2016) Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation. Journal of Inclusion Phenomena and Macrocyclic Chemistry, 84 (1-2). pp. 1-10. ISSN 1388-3127 10.1007/s10847-015-0576-x
institution UPM IR
collection UPM IR
language English
description In our study, molecular docking and molecular dynamics (MD) simulations were performed in order to explore the interactions between human insulin and β-cyclodextrin (β-CD). Molecular docking study was performed using the Autodock v4.2 program to determine the number of β-CD molecules that adhere to the binding sites of insulin. A random structure docking approach using an initial ratio of 1:1 insulin-β-CD was conducted and from these, additional β-CDs were added. Molecular docking results revealed that a maximum of four β-CDs are able to bind to the insulin structure with the 1:3 insulin-β-CD ratio producing the lowest binding free energy. The docked conformations showed that hydrophobic interactions played a crucial role in insulin-β-CD conformational stability in addition to the formation of hydrogen bonds. A 50 ns MD simulation was further conducted using an NPT ensemble to verify the results obtained by molecular docking. The analysis of the MD simulation results of the 1:3 insulin-β-CD formation system conclude that a good interaction exists between insulin and β-CDs and the RMSD value obtained was 4.00 ± 0.50 Å. The RMSF profiles of insulin in the 1:3 insulin-β-CD formation also show reduced amino acid residues flexibility as compared to the free insulin system. The theoretical results indicated the presence of significant interactions between insulin and β-CD which could provide interesting insights into an insulin formulation.
format Article
author Muhammad, Erma Fatiha
Adnan, Rohana
Mohammad Latif, Muhammad Alif
Abdul Rahman, Mohd Basyaruddin
spellingShingle Muhammad, Erma Fatiha
Adnan, Rohana
Mohammad Latif, Muhammad Alif
Abdul Rahman, Mohd Basyaruddin
Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation
author_facet Muhammad, Erma Fatiha
Adnan, Rohana
Mohammad Latif, Muhammad Alif
Abdul Rahman, Mohd Basyaruddin
author_sort Muhammad, Erma Fatiha
title Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation
title_short Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation
title_full Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation
title_fullStr Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation
title_full_unstemmed Theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation
title_sort theoretical investigation on insulin dimer - b - cyclodextrin interactions using docking and molecular dynamics simulation
publisher Springer Netherlands
publishDate 2016
url http://psasir.upm.edu.my/id/eprint/53117/1/Theoretical%20investigation%20on%20insulin%20dimer%20-%20b%20-%20cyclodextrin%20interactions%20using%20docking%20and%20molecular%20dynamics%20simulation.pdf
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score 13.4562235

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