Abstract
In a recent cell-based assay, it has been demonstrated that the F-19848A compound inhibits the binding of hyaluronan to the CD44 receptor, which is a cell-surface glycoprotein and a receptor for hyaluronan, a major component of the tumor extracellular matrix. The interaction between CD44 and hyaluronan has been shown to promote breast cancer metastasis according to evidence. In this study, the PubChem database contains more than 112 million compounds. This data is inputted for virtual screening find out top hits by combining Lipinski’s rule and docking method. With 20 configurations obtained by docking method, the lowest binding affinity ΔEbind achieved in the best docking mode was chosen as a scoring function for picking out top ligands. For inhibition the CD44 target, the top-leads compounds with binding energy less than -9.0 kcal.mol-1 and F-19848A have selected. By docking method, the binding site and other quantities were determined such as the number of hydrogen bonds (HB), non-bond contacts (NBC) of top ligands with CD44 target. Besides, the results also showed that the non-bonded contacts dominate over hydrogen bonds in the interaction between top ligands with CD44 target.
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