Single-coordinate-driving method for molecular docking: application to modeling of guest inclusion in cyclodextrin

A Substrate-Independent Approach for Cyclodextrin Functionalized Surfaces

6-Amino-6-deoxy-beta-cyclodextrin can be immobilized onto a range of solid surfaces via reaction with a predeposited pulsed plasma poly(glycidyl methacrylate) layer. X-ray photoelectron spectroscopy, infrared spectroscopy, and quartz crystal microbalance measurements have been employed to monitor guest-host interactions between N,N-dimethylformamide or cholic acid and surface-tethered 6-amino-6-deoxy-beta-cyclodextrin barrels.

Modeling protein recognition of carbohydrates

We have a limited understanding of the details of molecular recognition of carbohydrates by proteins, which is critical to a multitude of biological processes. Furthermore, carbohydrate-modifying proteins such as glycosyl hydrolases and phosphorylases are of growing importance as potential drug targets. Interactions between proteins and carbohydrates have complex thermodynamics, and in general the specific positioning of only a few hydroxyl groups determines their binding affinities. A thorough understanding of both carbohydrate and protein structures is thus essential to predict these interactions. An atomic-level view of carbohydrate recognition through structures of carbohydrate-active enzymes complexed with transition-state inhibitors reveals some of the distinctive molecular features unique to protein-carbohydrate complexes. However, the inherent flexibility of carbohydrates and their often water-mediated hydrogen bonding to proteins makes simulation of their complexes difficult. Nonetheless, recent developments such as the parameterization of specific force fields and docking scoring functions have greatly improved our ability to predict protein-carbohydrate interactions. We review protein-carbohydrate complexes having defined molecular requirements for specific carbohydrate recognition by proteins, providing an overview of the different computational techniques available to model them.

Investigation of the complexation of (+)-catechin by beta-cyclodextrin by a combination of NMR, microcalorimetry and molecular modeling techniques

(+)-Catechin is a polyphenolic compound of natural origin that presents anti-oxidant properties of interest for therapeutics or cosmetics uses. Preliminary studies on inclusion into cyclodextrin cavities yielded contradictory results both for the quantitative (affinity constant) and qualitative description of the interaction. By a combination of several experimental and theoretical methods, the present study resolved the previous ambiguities about the interaction between (+)-catechin and beta-cyclodextrin. Thermodynamic data measured by isothermal titration calorimetry demonstrate that the binding is enthalpy driven. Excellent agreement has been obtained for the measurement of the association constant by NMR and microcalorimetry. The several docking modes obtained by systematic docking studies have been compared to intermolecular contacts measured by NMR and the overall geometry of the complex can be proposed.