DOLINA – Docking Based on a Local Induced-Fit Algorithm: Application toward Small-Molecule Binding to Nuclear Receptors

Docking algorithms allowing for ligand and – to various extent – also protein flexibility are nowadays replacing techniques based on rigid protocols. The algorithm implemented in the Dolina software relies on pharmacophore matching for generating potential ligand poses and treats associated local induced-fit changes by combinatorial rearrangement of side-chains lining the binding site. In Dolina, ligand flexibility is not treated internally, instead a pool of low-energy conformers identified in a conformational search is screened for extended binding-pose candidates. Grouping rearranged residues in sterically independent families and side-chain conformer clustering are employed to achieve efficient use of the computational resources along with a good accuracy of the generated poses. Dolina was applied toward docking of small-molecule ligands to three different nuclear receptor ligand binding domains for which in total 18 high-resolution crystal structures were used as reference. The selected nuclear receptors feature a deeply buried ligand-binding site where local induced-fit is to be expected, particularly for receptor antagonists. For each receptor, a crystal structure with a cocrystallized small steroid ligand (template) was chosen as a target system, to which several synthetic ligands of different sizes were docked. Poses within an <i>RMSD</i> of 2.0 Å from the crystal reference pose were generated in 91% of the cases. In 28%, the pose with the lowest <i>RMSD</i> to the reference pose was ranked as the top one, and in 76% it was ranked among the top five poses. Detailed descriptions of the docking algorithm and observed results are included. Dolina is available free of charge for academic institutions

Stabilization of Branched Oligosaccharides: Lewis^x Benefits from a Nonconventional C–H···O Hydrogen Bond

Although animal lectins usually show a high degree of specificity for glycan structures, their single-site binding affinities are typically weak, a drawback which is often compensated in biological systems by an oligovalent presentation of carbohydrate epitopes. For the design of monovalent glycomimetics, structural information regarding solution and bound conformation of the carbohydrate lead represents a valuable starting point. In this paper, we focus on the conformation of the trisaccharide Le^x (Gal­[Fucα(1–3)]­β(1–4)­Glc<i>N</i>Ac). Mainly because of the unfavorable tumbling regime, the elucidation of the solution conformation of Le^x by NMR has only been partially successful so far. Le^x was therefore attached to a ¹³C,¹⁵N-labeled protein. ¹³C,¹⁵N-filtered NOESY NMR techniques at ultrahigh field allowed increasing the maximal NOE enhancement, resulting in a high number of distance restraints per glycosidic bond and, consequently, a well-defined structure. In addition to the known contributors to the conformational restriction of the Le^x structure (exoanomeric effect, steric compression induced by the <i>N</i>HAc group adjacent to the linking position of l-fucose, and the hydrophobic interaction of l-fucose with the β-face of d-galactose), a nonconventional C–H···O hydrogen bond between H–C(5) of l-fucose and O(5) of d-galactose was identified. According to quantum mechanical calculations, this C–H···O hydrogen bond is the most prominent factor in stabilization, contributing 40% of the total stabilization energy. We therefore propose that the nonconventional hydrogen bond contributing to a reduction of the conformational flexibility of the Le^x core represents a novel element of the glycocode. Its relevance to the stabilization of related branched oligosaccharides is currently being studied