ChemBioChem

Guardian of the genome: Covalent modification of proteins with poly(ADP-ribose) (see picture), catalysed by the enzyme poly(ADP-ribose) polymerase-1 (PARP-1), is a rapid cellular response to DNA damage and contributes to genome stabilization in cells under genotoxic stress. Interestingly, the capacity of lymphocytes to produce poly(ADP-ribose) is correlated with the life span of mammalian species, thus suggesting a functional role for PARP-1 in longevity.

Biocatalysis in action: Ribozymes provide an opportunity to observe biocatalysis in a simplified situation, and thereby throw down a challenge to chemical biology to explain the mechanistic origins of this biocatalysis. A crystal structure of the hairpin ribozyme gives valuable insight into the catalytic process (The local geometry at the active site is shown). The new structure provides evidence for both conformational assistance and nucleobase catalysis, but none for the direct participation of metal ions in this system.

Oxidative cleavage of DNA and RNA by 1,10-phenanthroline–copper(I) complexes provides a method for studying their interaction with proteins and oligonucleotides. In addition to studying the reaction mechanism of the scission, it has been shown that the single-strand region of the open-complex bacterial promoters is five nucleotides long (see picture; RNAP=RNA polymerase) and that DNA-binding proteins can direct promoter-specific scission.

The selection of high-affinity peptides targeting carbohydrates has been developed by using phage display. The strategy may lead to the development of high-affinity D-peptides targeting cell-surface carbohydrates when mirror-image sugars are used as ligands in the selection process (schematically shown for sialic acid).

Clustered derivatives of quinic and shikimic acid attached to a lysinyl core (see schematic representation) appear as efficient mannose receptor ligands, as demonstrated by cytofluorimetric analysis using human dendritic cells. This has been further confirmed by competitive inhibition assays, confocal microscopy, and transfection experiments. Thus, simple, commercially available polyhydroxylated carbocycles can be considered as carbohydrate mimics and used in lectin-mediated targeting of drugs to cells.

Excellent selectivities were obtained when galactoside prodrugs of the novel methyl-seco-CBI analogue of the highly potent antibiotic CC-1065 (see picture) were prepared and tested for their biological activity. Liberation of the active drug through hydrolysis of the glycosidic bond could be achieved by addition of the enzyme β-D-galactosidase.

More-selective mutants: Insight into the basis of lipase enantiorecognition allowed alteration of the enantioselectivity. Through rational design and creation of lipase mutants, the enantioselectivity of the enzyme in the kinetic resolution of 1-chloro-2-octanol (see scheme) was doubled. The enantioselectivity was also annihilated by a single-point mutation.

Not generally harmful: The antimicrobial and hemolytic activity of amphiphilic β-homo (β-H) peptides with the general formula H-(β-HAla-β-HLys-β-HPhe)-OH (see schematic representation) were investigated to unravel their potential for applications in medicinal chemistry. Only moderate activities were found for some of the peptides tested, critically depending on the side-chain composition of the amphiphilic helix.

A highly sensitive fluorescence-based assay for screening DNA polymerase libraries (see schematic picture) revealed a surprising activity of the wild-type Klenow fragment of Escherichia coli DNA polymerase I: This enzyme, which has emerged during natural evolution as a polymerase “fit” for natural substrates, retains full activity in the sole presence of artificial nucleotides that are labeled with a fluorescent dye of the rhodamine type. This unusual finding opens up the horizon for generating DNA exclusively from rhodamine-labeled analogues—a necessary prerequisite to realizing the idea of “single-molecule sequencing”.

No anomer discrimination: Concanavalin A (Con A) binds branched 6^I-(α- and 6^I-(β-D-mannopyranosylthioureido)cyclomaltoheptaoses with the same efficiency (see picture), in contrast with the known lectin specificity for the α anomer in the O-mannopyranosyl series. In addition, the presence of the cyclodextrin core slightly improves the binding efficiency. Unexpectedly, the heptakis(6-mannopyranosylthioureido)-β-cyclodextrins are not recognized. Reverse (6^I→6)-linked thioureidomannosyl ligands are only weakly bound. These results underline the influence of the spatial organization of saccharide epitopes on the functional affinity of glycoclusters.

Despite the simple structure and widespread occurrence of benzoic acid, its biosynthesis has resisted complete elucidation. However, recent studies reveal that the conversion of cinnamoyl-CoA into benzoyl-CoA (see scheme; R=Ph) can proceed by a route that resembles fatty acid β-oxidation. Feeding studies and sequence analyses show that both pathways not only proceed with the same stereochemistry, but are also mechanistically related.