Quantification of binding affinities of essential sugars with a tryptophan analogue and the ubiquitous role of C–H⋯π interactions

Abstract

The role of noncovalent interactions in carbohydrate recognition by aromatic amino acids has long been reported. To develop a molecular understanding of noncovalent interactions in the recognition process, we have examined a series of binary complexes between 3-methylindole (3-MeIn) and sugars. In particular, the geometries and binding affinities of 3-MeIn with α/β-D-glucose, β-D-galactose, α-D-mannose and α/β-L-fucose are obtained using the MP2(full)/6-31G(d,p) and the M06/TZV2D//MP2/6-31G(d,p) level of theories. The conventional hydrogen bonding such as N–H⋯O and C–H⋯O as well as nonconventional O–H⋯π and C–H⋯π type of interactions is, in general, identified as responsible for the moderately strong interaction energies. Large variations in the position–orientations of 3-MeIn with respect to saccharide are noticed, within the same sugar family, as well as across different sugar series. Furthermore, complexes with large differences in their geometries are recognized as capable of exhibiting very similar interaction energies, underscoring the significance of exhaustive conformation sampling, as carried out in the present study. These observations are readily attributed to the differences in the efficiency of the type of interactions enlisted above. The highest and lowest interaction energies, upon inclusion of 50% BSSE correction, are found to be −16.02 and −6.22 kcal mol⁻¹, respectively, for α-D-glucose (1a) and α-L-fucose (5j). While more number of prominent conventional hydrogen bonding contacts remains as a characteristic feature of the strongly bound complexes, the lower end of the interaction energy spectrum is dominated by multiple C–H⋯π interactions. The complexes exhibiting as many as four C–H⋯π contacts are identified in the case of α/β-D-glucose, β-D-galactose, and α/β-L-fucose with an interaction energy hovering around −8 kcal mol⁻¹. The presence of effective C–H⋯π interactions is found to be dependent on the saccharide configuration as well as the area of the apolar patch constituted by the C–H groups. The study offers a comprehensive set of binary complexes, across different saccharides, which serves as an illustration of the significance and ubiquitous nature of C–H⋯π interactions in carbohydrate binding in saccharide–protein complexes.