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Here a molecular docking and 3D-QSAR study is reported on a series of 2-(oxalic monoamido)benzoic acid (OBA) inhibitors and protein tyrosine phosphatase 1B (PTP1B). Firstly, a flexible docking method (FlexX) was used to place 12 OBA inhibitors into the active site of PTP1B. The predicted binding affinities of the molecules were found to be linearly relevant to their experimental activities (pK(i), non-cross-validated R-2=0.859). After that, 33 OBA inhibitors were fixed into the predicted binding conformation, and were studied using CoMFA method. The resulting CoMFA model (cross-validated q(2) = 0.650) could predict the activity of 6 molecules in the test set within a mean unsigned error of 0.177, and match the characters of our binding mode perfectly. The discovered binding mode could provide hints to further modification of inhibitors.
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