Molecular Docking 6-shogaol and BCL11A for Beta Thalassemia Sekar Cahyo Nurani(a), Joko Setyono (b), Salman Fareza (a), Sarmoko(*a)
(a)Department of Pharmacy, Faculty of Health Sciences, Jenderal Soedirman University
(b) Department of Medicine, Faculty of Medicine, Jenderal Soedirman University
* Corresponding author: Jl. Dr. Soeparno, Karangwangkal, Purwokerto Utara, Central Java, Indonesia 53122. Email: sarmoko[at]unsoed.ac.id
Abstract
Beta thalassemia, a hereditary genetic disease, is characterized by low of beta-globin chain production. This study aims to predict the interaction between 6-shogaol and BCL11A (PDB ID 5VTB) protein by these steps: protein preparation, validation methods, and docking. The protein structure was prepared with removing the water molecules in AutoDockTools v.1.5.6. The validation step was performed by separating protein from native ligands in new PDB files. Further, the protein was docked with native ligands to obtain grid box coordinates on Vina, results in several conformations. The best conformation with low energy binding from the validation process was compared with the native ligand conformation in the PyMOL Molecular Graphics System and result in RSMD value 2.006 A. 6-shogaol was docked to protein using AutoDockTool with coordinates of the validation results. The lowest energy showed the best conformation of the compound in protein, which binding affinity was -5.9 kcal/mol. The best conformation was visualized 2D with Discovery Studio. 6-shogaol binds to BCL11A by hydrogen bond at the benzene\cdots hydroxyl group to 231 glutamic acid residue and 277 asparagine residue. We concluded that 6-shogaol have potential interaction with BCL11A. 6-Shogaol may inhibit BCL11A to increase HbF in beta- thalassemia.
