Conformation of Deoxy Oligosaccharides: Solution Conformation and Flexibility of the Antibiotic Kijanimicin Studied by NMR Spectroscopy and MMC Calculations

Abstract

AbstractThe solution conformation of the macrolide antibiotic kijanimicin (1) was deduced by a combination of NMR spectroscopy and potential energy calculations of the carbohydrate parts using the HSEA force field. The study was based on temperature dependent NMR spectroscopic shift data, 1D nuclear Overhauser enhancements (NOE) of selected protons and 2D rotating frame NOE of the complete antibiotic. NOEs in the oligosaccharide part of the antibiotic indicated some unusual short distances between the α‐linked digitoxose residues A and B, as well as between not directly linked residues A and C. Calculation of preferred conformations revealed a global minimum with ΦA,B/ΨA,B ≈ 70°/50°, ΦB,C/ΨB,C ≈ 60°/30°, and ΦB,D/ΨB,D ≈ −60°/5° for the oligosaccharide moiety. MMC simulations of the conformational flexibility indicated a high rigidity of the carbohydrate. The range of the glycosidic angles covered during MMC simulations was 50°–70° for the α‐linkages of the oligosaccharide. The ß‐glycosidic linkages of residue D and E showed slightly more flexibility, covering a range of 120° – 270°. Minimum energy calculations of the oligosaccharide part revealed a second minimum with different orientation of sugar residues A‐B and an energy difference of 2 kcal/mol to the global minimum. This energy difference increased to 12 kcal/mol when the complete antibiotic was calculated and MMC simulations did not show any transitions between the two minima. The experimental NOE in the oligosaccharide moiety and the enhancements between carbohydrate and lactone part agree well with theoretical NOEs that were obtained by sampling the global minimum in MMC simulations. The conformation of the macrolide moiety was evaluated by comparing experimental NOEs with the crystal structure of the isolated aglycon. The conformation found in solution is slightly altered around the sites of attachment of the carbohydrate parts. Constancy of the proton chemical shifts over a temperature range of 70°C indicated the high degree of rigidity of the carbohydrate moiety and most of the macrolide structure. Flexibility was observed for the C‐13/C‐20 part of the lactone ring. The antibiotic has a fairly unpolar surface and adopts a well defined and quite rigid conformation. magnified image