The Role of Waters in Docking Strategies with Incremental Flexibility for Carbohydrate Derivatives:  Heat-Labile Enterotoxin, a Multivalent Test Case

Abstract

Molecular docking studies of carbohydrate derivatives in protein binding sites are often challenging because of water-mediated interactions and the inherent flexibility of the many terminal hydroxyl groups. Using the recognition process between heat-labile enterotoxin from Escherichia coli and ganglioside GM1 as a paradigm, we developed a modeling protocol that includes incremental conformational flexibility of the ligand and predicted water interactions. The strategy employs a modified version of the Monte Carlo docking program AUTODOCK and water affinity potentials calculated with GRID. After calibration of the protocol on the basis of the known binding modes of galactose and lactose to the toxin, blind predictions were made for the binding modes of four galactose derivatives: lactulose, melibionic acid, thiodigalactoside, and m-nitrophenyl-alpha-galactoside. Subsequent crystal structure determinations have demonstrated that our docking strategy can predict the correct binding modes of carbohydrate derivatives within 1.0 A from experiment. In addition, it is shown that repeating the docking simulations in each of the seemingly identical binding sites of the multivalent toxin increases the chance of finding the correct binding mode.

Second-Generation Mimics of Ganglioside GM1 Oligosaccharide: A Three-Dimensional View of Their Interactions with Bacterial Enterotoxins by NMR and Computational Methods

“…As expected on the basis of Verlinde×s report, [24] Autodock performs remarkably well in the identification of the Galbinding site, which is recognized and reproduced correctly in all low-energy clusters. In all cases, the galactose ring of 2 ± 4 interacts strongly with the protein, in accordance with the NMR results, and is located in the area above the Trp-88 side chain, which is the known binding site for all the complexes formed by the two bacterial enterotoxins with Gal-containing ligands ( Figure SI1 ± SI3 in Supporting Information).…”

“…Such MacroModel calculations were in fact performed (see Supporting Information); however, to get a more comprehensive view of the possible binding modes, the initial docking studies of 2 ± 4 were performed by using Autodock. Autodock has recently been validated for use with LT complexes by Verlinde et al [24] who have worked out a viable protocol that is capable of predicting the correct binding mode of carbohydrate derivatives within 1 ä from experiment. Our calculations were performed by using essentially the same protocol, and retaining the two crystallographic water molecules at sites 2 and 3.…”

Binding Mode Prediction of Cytochrome P450 and Thymidine Kinase Protein−Ligand Complexes by Consideration of Water and Rescoring in Automated Docking

“…It was essential to modify the AutoGrid program (part of the AutoDock package) to enable docking in the presence of water. This program was changed so that it considered an oxygen atom bound to two hydrogen atoms as a potential hydrogen bond acceptor, as was done in an earlier AutoDock study 23 (the modified code for AutoGrid is available upon request). Docking Studies.…”

Structure-Based Approach for Binding Site Identification on AmpC β-Lactamase

“…Water molecules are observed to bind in some of these sites, and it is unclear whether they should be treated as displaceable or structurally integral components of the protein. 12,13 The challenge of finding the "hot spots" for ligand binding is common to most structure-based efforts. Several techniques have been introduced to address this problem.…”