Simulation of carbohydrate-protein interactions: Computer-aided design of a second generation GM1 mimic

The oligosaccharide of ganglioside GM1 [Gal beta1-3GalNAc
beta1-4(NeuAc alpha2-3)Gal beta1-4Glc beta1-1Cer] is the cellular target
of two bacterial enterotoxins: the cholera toxin (CT) and the
heat-labile toxin of E.coli (LT). We recently reported that the
pseudosaccharide 2[Gal beta1-3GalNAc beta1-4(NeuAc alpha2-3)DCCHD] is
a high-affinity ligand for CT, and thus a functional mimic of GM1
(Bernardi, A., Checchia, A., Brocca, P., Sonnino, S. and Zuccotto, F.,
J. Am. Chem. Soc., 121 (1999) 2032-2036). In this paper we describe the
design of a second-generation mimic, formally obtained from 2 by
inverting the configuration of a single stereocenter, thus transforming
a N-acetyl galactosamine into a N-acetyl glucosamine. The design process
involved modeling of the free ligand and its LT complex, followed by
qualitative and quantitative comparison with the corresponding
structures of 2. The protocol employed relied on both conformational
search and molecular dynamics methodologies to account for the
flexibility of both the ligand and the protein receptor. The
conformational search of the LT:inhibitor complex showed that, compared
to 2, the new compound can insert one more hydroxy group within the
protein binding site. Molecular dynamics simulations showed that, in
turn, this may trigger a series of rearrangements and reorientations of
side chains and crystallographic water molecules in the toxin, leading
to new H-bond contacts which may result in enhanced affinity of the new
inhibitor. FEP calculations were performed by mutating the structure of
2 in solution and in the protein complex, and the prediction was made
that the second-generation mimic should be a stronger binder than its
parent compound.