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

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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 Escherichiacoli 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-α-galactoside. Subsequent crystal structure determinations have demonstrated that our docking strategy can predict the correct binding modes of carbohydrate derivatives within 1.0 Å 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.