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In-Silico Study of Aptamer-Safranal Binding Using Molecular Docking and Dynamics Simulation
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Z Mohammadi   , M Jafari * , M Kashaninejad |
| Gorgan University of Agricultural Sciences and Natural Resources , smjafari@gau.ac.ir |
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Abstract: (33 Views) |
Background and Objective: In this work, the binding interactions between ssDNA and ssRNA aptamers and safranal, a bioactive substance produced from saffron, were examined using molecular docking and dynamics simulations. The main objective was to find appropriate aptamers that could bind safranal effectively, with an emphasis on dynamic stability and binding affinity.
Materials and Methods: ssRNA and ssDNA aptamers with PDB IDs of 6V9B and 8D2B and 6J2W, 7QB3, and 2L5K, respectively, were subjected to molecular docking using AutoDock Tools 1.5.7. Following molecular docking, two candidate aptamers were subjected to 200 ns of molecular dynamics simulation using GROMACS 2020.1, which was employed to evaluate the stability of aptamer-ligand complexes.
Findings: According to molecular docking results, the ΔG values for aptamers 6J2W, 7QB3, and 2L5K were determined to be -4.85, -4.39, and -4.53 kcal/mol, respectively, while the values for aptamers 6V9B and 8D2B were -5.27 and -5.31 kcal/mol. Among the ssRNA aptamers, 8D2B performed the best. The lowest ΔG value of the ssDNA aptamer 6J2W also led to its selection. The ssDNA aptamer exhibited higher stability in the molecular dynamics simulation, while the ssRNA aptamer showed notable fluctuations in RMSD after 40 ns and reached instability in interaction with safranal. The ssRNA-safranal interaction exhibited higher fluctuations , according to the RMSF results, than the reference ssRNA.
Conclusion: The ssDNA aptamer (6J2W) is proposed as a potential option to develop aptamer-based sensors; nevertheless, further experimental validation is required to confirm its effectiveness. The quality and purity of saffron can be monitored with the use of this study. |
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| Keywords: Safranal, Aptamer, Molecular Docking, Molecular Dynamics Simulation, Biosensor |
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Full-Text [PDF 1037 kb]
(6 Downloads)
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Article type: Research |
Subject:
Food Science
Received: 2024/10/6 | Accepted: 2024/12/3
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