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The Effect of Deoxyfluorination on Intermolecular Interactions in the Crystal Structures of 1,6-Anhydro-2,3-epimino-hexopyranoses.

ABSTRACT: The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-F_ax and C4-F_eq epimines presented here.

SUBMITTER: Jakubec M

PROVIDER: S-EPMC8746508 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Conformational itinerary of Pseudomonas aeruginosa 1,6-anhydro-N-acetylmuramic acid kinase during its catalytic cycle.

Project description:Anhydro-sugar kinases are unique from other sugar kinases in that they must cleave the 1,6-anhydro ring of their sugar substrate to phosphorylate it using ATP. Here we show that the peptidoglycan recycling enzyme 1,6-anhydro-N-acetylmuramic acid kinase (AnmK) from Pseudomonas aeruginosa undergoes large conformational changes during its catalytic cycle, with its two domains rotating apart by up to 32° around two hinge regions to expose an active site cleft into which the substrates 1,6-anhydroMurNAc and ATP can bind. X-ray structures of the open state bound to a nonhydrolyzable ATP analog (AMPPCP) and 1,6-anhydroMurNAc provide detailed insight into a ternary complex that forms preceding an operative Michaelis complex. Structural analysis of the hinge regions demonstrates a role for nucleotide binding and possible cross-talk between the bound ligands to modulate the opening and closing of AnmK. Although AnmK was found to exhibit similar binding affinities for ATP, ADP, and AMPPCP according to fluorescence spectroscopy, small angle x-ray scattering analyses revealed that AnmK adopts an open conformation in solution in the absence of ligand and that it remains in this open state after binding AMPPCP, as we had observed for our crystal structure of this complex. In contrast, the enzyme favored a closed conformation when bound to ADP in solution, consistent with a previous crystal structure of this complex. Together, our findings show that the open conformation of AnmK facilitates binding of both the sugar and nucleotide substrates and that large structural rearrangements must occur upon closure of the enzyme to correctly align the substrates and residues of the enzyme for catalysis.

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Crystal structures of two 2,3-diaryl-2,3-di-hydro-4H-1,3-benzo-thia-zin-4-ones.

Project description:The syntheses and crystal structures of 2,3-bis-[3-(tri-fluoro-meth-yl)phen-yl]-2,3-di-hydro-4H-1,3-benzo-thia-zin-4-one (di-m-CF3; C22H13F6NOS) (1) and 2,3-bis-(4-methyl-phen-yl)-2,3-di-hydro-4H-1,3-benzo-thia-zin-4-one (di-p-CH3; C22H19NOS) (2) are reported. Each structure is racemic: the asymmetric unit of 2 consists of two mol-ecules. In both 1 and 2, the six-membered 1,3-thia-zine ring is close to an envelope conformation with the chiral C atom forming the flap. In 1, the 2-aryl group is pseudo-equatorial, while in 2 it is pseudo-axial. In 1, the pendant aryl rings form a V shape with an inter-centroid distance of 3.938?(3)?Å and an acute dihedral angle of 48.3?(2)° between them. Both CF3 groups are disordered over two orientations in 0.687?(19):0.313?(19) and 0.667?(16):0.33?(16) ratios. In each of the independent mol-ecules of 2, the aryl rings are almost orthogonal to each other [dihedral angles = 85.50?(12) and 86.07?(11)°]. In both structures, the chiral C atom and the O atoms participate in C-H?O-type hydrogen bonding between symmetry-related mol-ecules of 1 or the independent enanti-omers in 2, forming chains along the c-axis direction in 1 and the b-axis direction in 2. Additionally, in 1, ?-? contacts of both face-to-face and edge-to-face type, as well as ?-H?O and ?-H?F inter-actions are observed. In 2, a racemic mixture of mol-ecules forms layers in the ac plane linked by weak ?-? and C-H?? inter-actions.

| S-EPMC5947804 | biostudies-other

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