The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: Heat-labile enterotoxin, a multivalent test case

Molecular docking studies of carbohydrate derivatives in protein binding si tes are often challenging because of water-mediated interactions and the in herent flexibility of the many terminal hydroxyl groups. Using the recognit ion process between heat-labile enterotoxin from Escherichia coli and gangl ioside GM(1) as a paradigm, we developed a modeling protocol that includes incremental conformational flexibility of the ligand and predicted water in teractions. The strategy employs a modified version of the Monte Carlo dock ing program AUTODOCK and water affinity potentials calculated with GRID. Af ter 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 bin ding modes of four galactose derivatives: lactulose, melibionic acid, thiod igalactoside, and m-nitrophenyl-alpha-galactoside. Subsequent crystal struc ture determinations have demonstrated that our docking strategy can predict the correct binding modes of carbohydrate derivatives within 1.0 Angstrom from experiment. In addition, it is shown that repeating the docking simula tions in each of the seemingly identical binding sites of the multivalent t oxin increases the chance of finding the correct binding mode.