Solid-phase synthesis of polymyxin B1 and analogues via a safety-catch approach.

As part of a program towards the development of novel antibiotics, a convenient method for solid-phase synthesis of the cyclic cationic peptide polymyxin B1 and analogues thereof is described. The methodology, based on cleavage-by-cyclization using Kenner's safety-catch linker, yields crude products with purities ranging from 37-67%. Antibacterial assays revealed that analogues 23-26, in which the (S)-6-methyloctanoic acid moiety is replaced with shorter acyl chains, exhibit distinct antimicrobial activity. The results suggest that the length of the acyl chain is rather critical for antimicrobial activity. On the other hand, substitution of the hydrophobic ring-segment D-Phe-6/Leu-7 in polymyxin B1 with dipeptide mimics (i.e. analogues 27-33) resulted in almost complete loss of antimicrobial activity.

Stereoselective transformations on D-glucose-derived eight-membered ring carbocycles.

[structure: see text]. The cyclooctenol derivative 1 can be transformed into the nine-membered ring lactone 3, as well as the amino-containing carbocycles 4 and 5. The corresponding ketone 2 gives access to the conformationally locked azasugar 6.

Construction of a full three-dimensional model of the transpeptidase domain of Streptococcus pneumoniae PBP2x starting from its Calpha-atom coordinates.

A new method is described for generating all-atom protein structures from Calpha-atom information. The method, which combines both local structural trace alignments and comparative side chain modeling with ab initio side chain modeling, makes use of both the virtual-bond and the dipole-path methods. Provided that 3D structures of structurally and functionally related proteins exist, the method presented here is highly suitable for generating all-atom coordinates of partly solved, low-resolution crystal structures. Particularly the active site region can be modeled accurately with this procedure, which enables investigation of the binding modes of different classes of ligands with molecular dynamics simulations. The method is applied to the trace of Streptococcus pneumoniae, in order to construct an all-atom structure of the transpeptidase domain. Since after generation of full coordinates of the transpeptidase domain the structure had been solved to 2.4 A resolution, new X-ray coordinates for the worst modeled loop (residues T370 to M386; 17 out of a total number of 351 residues constituting the transpeptidase domain) were incorporated, as kindly provided by Dr. Dideberg. The structure was relaxed with molecular dynamics simulations and simulated annealing methods. The RMS deviation between the 144 aligned Calpha-atoms and the corresponding ones in the originally solved 3.5 A resolution crystal structure was 0.98. The 351 Calpha-atoms of the whole transpeptidase domain of the final model showed an RMS deviation of 1.58. The Ramachandran plot showed that 79.3% of the residues are in the most favored regions, with only 1.0% occurring in disallowed regions. The model presented here can be used to investigate the three-dimensional influences of mutations around the active site of PBP2x.

Preparation of spacer-containing di-, tri-, and tetrasaccharide fragments of the circulating anodic antigen of Schistosoma mansoni for diagnostic purposes.

The chemical synthesis of beta-D-GlcpA-(1-->3)-beta-D-GalpNAc-(1-->O)CH2CH = CH2, beta-D-Galp-NAc-(1-->6)-[beta-D-GlcpA-(1-->3)]-beta-D-GalpNAc-(1-- >O)CH2CH = CH2, and beta-D-GlcpA-(1-->3)-beta-D-GalpNAc-(1-->6)-[beta-D-GlcpA-(1 -->3)] -beta-D-GalpNAc-(1-->O)CH2CH = CH2 is described. These oligosaccharides represent fragments of th circulating anodic antigen, secreted by the parasite Schistosoma mansoni in the circulatory system of the host. The applied synthesis strategy includes the preparation of a non-oxidised backbone oligosaccharide, with a levulinoyl group at O-6 of the beta-D-glucose residue. After the selective removal of the levulinoyl group, the obtained hydroxyl functions were converted into carboxyl groups, using pyridinium dichromate and acetic anhydride in dichloromethane, to afford the desired glucuronic-acid-containing oligosaccharides. Subsequently, the allyl glycosides have been elongated with cysteamine to give the corresponding amine-spacer-containing oligosaccharides.