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My Final Year Project focused on structural bioinformatics, especially the study of protein and ligand binding using computational modelling. In this project I used molecular docking and molecular dynamics method to study the interaction between human serum albumin and leflunomide.
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Human Serum Albumin is the most prevalent protein in blood plasma that serves as the primary transport protein of the human circulatory system. Leflunomide, a drug used to treat rheumatoid arthritis that has been tested in several preclinical investigations as a potential cancer treatment. The aim of this research was to study the ligand-protein binding interaction between leflunomide (LEF) and human serum albumin (HSA) by using a computational modelling approach. The HSA structure was obtained from the Protein Data Bank (PDB) with the PDB ID of 1BM0 and had been further refined using MODELLER. The best model was then selected and validated through PROCHECK. The ligand structure of LEF was retrieved from PubChem in 3D format. Molecular docking was then performed targeted on two known binding sites of HSA, Site I and Site II. The results suggested a binding preference of LEF into Site I of HSA, with -6.33 kJ/mol binding energy. The protein-ligand complex was further employed in a complex molecular dynamics simulation with a duration of 10 ns. The result of the simulation indicated that the protein-ligand complex has a stable conformation with good binding energy. Hydrogen bonds and hydrophobic interactions are suggested to be the main intermolecular forces that stabilise the HSA-LEF complex.
Keywords: Human serum albumin, leflunomide, molecular docking, molecular dynamics simulation
To see my thesis you can contact me at [email protected]