Jeremy R . Greenwood , Tyler Day , Robert Abel , Ramy S . Farid
نویسندگان
چکیده
7 ABSTRACT: Although many popular docking programs 8 include a facility to account for covalent ligands, large-scale 9 systematic docking validation studies of covalent inhibitors have 10 been sparse. In this paper, we present the development and 11 validation of a novel approach for docking and scoring covalent 12 inhibitors, which consists of conventional noncovalent docking, 13 heuristic formation of the covalent attachment point, and 14 structural refinement of the protein−ligand complex. This 15 approach combines the strengths of the docking program 16 Glide and the protein structure modeling program Prime and 17 does not require any parameter fitting for the study of additional 18 covalent reaction types. We first test this method by predicting 19 the native binding geometry of 38 covalently bound complexes. 20 The average RMSD of the predicted poses is 1.52 Å, and 76% of 21 test set inhibitors have an RMSD of less than 2.0 Å. In addition, the apparent affinity score constructed herein is tested on a 22 virtual screening study and the characterization of the SAR properties of two different series of congeneric compounds with 23 satisfactory success.
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