Structure of the lipopeptide antibiotic tsushimycin.

The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding.

Crystal structures of cephaibols.

The crystal structures of the peptaibol antibiotics cephaibol A, cephaibol B and cephaibol C have been determined at ca. 0.9 A resolution. All three adopt a helical conformation with a sharp bend (of about 55 degrees) at the central hydroxyproline. All isovalines were found to possess the D configuration, superposition of all four models (there are two independent molecules in the cephaibol B structure) shows that the N-terminal helix is rigid and the C-terminus is flexible. There are differences in the hydrogen bonding patterns for the three structures that crystallize in different space groups despite relatively similar unit cell dimensions, but only in the case of cephaibol C does the packing emulate the formation of a membrane channel believed to be important for their biological function.

Structure of the alpha-amylase inhibitor tendamistat at 0.93 A.

The crystal structure of the proteinaceous alpha-amylase inhibitor tendamistat has been determined at 100 K to a resolution of 0.93 A. The final R factor for all reflections with F > 4sigma(F) is 9.26%. The mean coordinate error for fully occupied protein atoms as derived from full-matrix inversion is 0.018 A. An extended network of multiple discrete conformations has been identified on the side of tendamistat that binds to the target molecule. Most notably, residue Tyr15, which interacts with the glycine-rich loop characteristic of mammalian amylases, and a cluster of amino-acid side chains surrounding it are found in two well defined conformations. The flexibility observed in this crystal structure together with information about residues fixed by lattice contacts in the crystal but found to be mobile in a previous NMR study supports a model in which most of the residues involved in binding are not fixed in the free form of the inhibitor, suggesting an induced-fit type of binding.

Ustilipids, acylated beta-D-mannopyranosyl D-erythritols from Ustilago maydis and Geotrichum candidum.

Ustilago species produce an extracellular oil that shows activity in various pharmaceutical assays. We isolated several complexes of this heterogeneous glycolipid from cultures of Ustilago maydis DSM 11494 and Geotrichum candidum ST 002515, and determined the chemical structures of these new compounds, termed ustilipids, on the basis of NMR experiments, mass spectra, and fatty acid analyses. They all possess a 4-O-beta-D-mannopyranosyl D-erythritol basic framework, the configuration of which was confirmed, after initial solvolysis, by a single-crystal X-ray structure analysis. All the investigated ustilipids and related compounds are similarly constructed: the three hydroxy groups of the erythritol side chain are free in all cases, whereas the hydroxy groups of the mannose residue are for the most part acylated. Medium-chain fatty acids have for the first time been detected as components of glycolipids produced by Ustilaginales. While the 2-hydroxy group of the mannose residue is esterified with a C2-C8 carboxylate side chain, the 3-hydroxy group is in all cases esterified by a longer, C12-C20 fatty acid residue. The oxygen functionalities at the 4 and 6 positions are either acetylated or present as free hydroxy groups. Ustilipids antagonize dopamine D3 receptors in micromolar quantities; other members of this class of compounds have been found to possess an inhibitory action on the neurotensin receptor. The hemolytic activity of ustilipids is low.

Coniosetin, a novel tetramic acid antibiotic from Coniochaeta ellipsoidea DSM 13856.

The coprophilic ascomycete Coniochaeta ellipsoidea DSM 13856 forms the new antibiotic coniosetin (1) in surface cultures grown on a medium containing malt extract and oatmeal. The structure of the compound C25H35NO4, MW 413, was determined by 2D-NMR and mass spectrometric studies. Coniosetin belongs to the class of tetramic acids; it consists of a substituted aliphatic bicyclic ring system linked to a tetramic acid subunit through a carbonyl center. The absolute configuration was determined by measuring its circular dichroism spectrum and comparing the data with those of equisetin. Coniosetin has a pronounced antibacterial and antifungal action, inhibiting even multi drug-resistant strains of Staphylococcus aureus at a concentration of 0.3 microg/ml, though it is inactive against Gram-negative bacteria.

Cyclipostins, novel hormone-sensitive lipase inhibitors from Streptomyces sp. DSM 13381. II. Isolation, structure elucidation and biological properties.

Hormone-sensitive lipase (HSL) is a key enzyme of lipid metabolism and its control is therefore a target in the treatment of diabetes mellitus. Cultures of the Streptomyces species DSM 13381 have been shown to potently inhibit HSL. Ten inhibitors of HSL, termed cyclipostins, have been isolated from the mycelium of this microorganism and a further nine related compounds detected. Their structures were characterized by 2-D NMR experiments and by mass spectrometry and were found to comprise neutral cyclic enol phosphate esters with an additional y-lactone ring. On account of their ester-bound fatty alcohol side chain, the cyclipostins have physicochemical properties similar to those of triglycerides. The outstanding characteristic of the cyclipostins is their strong anti-HSL activity, with IC50 values in the nanomolar range.

Structures of glycopeptide antibiotics with peptides that model bacterial cell-wall precursors.

The vancomycin-related antibiotics balhimycin and degluco-balhimycin have been crystallized in complexes with di-, tri- and pentapeptides that emulate bacterial cell-wall precursors, and four structures determined at atomic resolution (<1 A). In addition to the features expected from previous structural and spectroscopic studies, two new motifs were observed that may prove important in the design of antibiotics modified to overcome bacterial resistance. A changed binding mode was found in two dipeptide complexes, and a new type of face-to-face oligomerization (in addition to the well-established back-to-back dimerization) was seen when the model peptide reaches a critical fraction of the size of the cell-wall precursor pentapeptide. The extensive interactions involving both antibiotic and peptide molecules in this interface should appreciably enhance the kinetic and thermodynamic stability of the complexes. In the pentapeptide complex, the relative positions of the peptides are close to those required for d-Ala elimination, so this structure may provide a realistic model for the prevention of the enzyme-catalyzed cell-wall crosslinking by antibiotic binding.