Stochastic conformational search on the Lewis X (Lex) trisaccharide and three Lex analogues

Biased stochastic conformational searches using the MMFF94 force field and the Born continuum solvation model were applied to the molecular modeling of the Lewis X (Le(x)) trisaccharide (beta-D-Gal-(1,4)-[alpha-L-Fuc-(1,3)]-beta-D-GlcNAc-OH) and three Le(x) analogues, in which each of the three sugar units was replaced by another sugar residue, i.e., N-acetyl-glucosamine by glucose, galactose by glucose, and fucose by rhamnose. The stochastic search accurately identified a lowest energy conformation of the Le(x) determinant that corresponds to the reported conformations of Le(x) deduced experimentally in the solid state by X-ray crystallography and in solution by NMR measurements. In this conformation stacking exists between the galactosyl and fucosyl residues. Five new local minima for the Lex trisaccharide were found within 3 kcal mol(-1) of the global minimum using the stochastic search and metric scaling. Modeling studies of the analogues showed that the stacking observed in the Lex trisaccharide was maintained when either galactosyl or N-acetylglucosamine were replaced by glucosyl residues. In contrast, substitution of the fucose residue by rhamnose led to two conformers in which stacking of the galactose and rhamnose residues was no longer maintained. These results indicate that the substitution of the non-reducing end galactosyl or N-acetyl-glucosaminyl residues by a glucose unit in the dimeric Lewis X (dimLe(x)) tumour associated antigen could help in the development of a vaccine that cross-reacts with dimLe(x) but no longer displays Le(x) associated three-dimensional epitopes also presented by non-cancerous cells. In contrast, an analogue in which the fucosyl residue is replaced by rhamnose does not constitute a good vaccine candidate, since our results indicate that this substitution will induce an important conformational change that is likely to abolish cross-reactivity with the natural dimLe(x) tumor associated antigen.