The Interaction of a New Schiff Base Ligand with Human Serum Albumin: Molecular Docking and Molecular Dynamics Simulation Studies |
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| Authors: | Iman Khosravi Mehdi Sahihi Hadi Amiri Rudbari Ghazal Borhan Zahra Chavoshpour-Natanzi |
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| Institution: | 1. Department of Chemistry, Qeshm Branch, Islamic Azad University, Qeshm, Iran;2. Department of Chemistry, University of Isfahan, Isfahan, Iran;3. Clinical Laboratory, Isfahan University of Medical Science, Isfahan, Iran |
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| Abstract: | The interaction of a new heterocyclic Schiff base bearing pyridine and pyrimidine cycles, with human serum albumin (HSA) using molecular docking and molecular dynamics simulation methods was examined. Molecular docking studies showed that the ligand was bonded to the IB domain of the protein. It was found that there was one hydrogen bond interaction between HSA and the ligand. The standard Gibbs free energy for binding of the ligand to HSA was calculated as ?9.63 kcal.mol?1. The results of the molecular dynamics simulation showed that the root mean square deviation (RMSD) of the non-liganded HSA and the HSA–ligand complex reached equilibration after 1000 ps. The study of the radius of gyration revealed that there was a conformational change when the HSA–ligand complex was formed. Finally, analyzing the RMS fluctuations (RMSF) suggested that the structure of the ligand binding site remained approximately rigid during the simulation. |
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| Keywords: | human serum albumin molecular docking molecular dynamics simulation schiff base ligand |
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