Metal complexes of a biconcave porphyrin with D4-structure--versatile chiral shift agents

Representative metal complexes of a biconcave D4-symmetric porphyrin were synthesised by metalion insertion into the porphyrin ligand 1. The NMR spectra suggested D4-symmetry for the ZnII and dioxo-RuVI complexes of 1 and C4-symmetry for the unsymmetrically ligated RuII and RhIII complexes. Metal complexes of 1 proved to be versatile chiral 1H NMR shift agents for a broad spectrum of organic amines, alcohols, carboxylic acids, esters, nitriles and nonpolar fullerene derivatives. A practical analysis of chiral substrates with 1 covers enantiomeric excesses beyond 99%. An X-ray structure of (1:1)-cocrystals of an achiral, biconcave CoII porphyrinate and C60 provided the first detailed insights into the structure of such a biconcave metallo-porphyrinate. It also showed remarkable packing of the carbon sphere against the main concave units of the porphyrin and gave clues about the relevant interactions between biconcave porphyrins and fullerenes.     

Simple test system for single molecule recognition force microscopy

We have established an easy-to-use test system for detecting receptor-ligand interactions on the single molecule level using atomic force microscopy (AFM). For this, avidin-biotin, probably the best characterized receptor-ligand pair, was chosen. AFM sensors were prepared containing tethered biotin molecules at sufficiently low surface concentrations appropriate for single molecule studies. A biotin tether, consisting of a 6 nm poly(ethylene glycol) (PEG) chain and a functional succinimide group at the other end, was newly synthesized and covalently coupled to amine-functionalized AFM tips. In particular, PEG₈₀₀ diamine was glutarylated, the mono-adduct NH₂-PEG-COOH was isolated by ion exchange chromatography and reacted with biotin succinimidylester to give biotin-PEG-COOH which was then activated as N-hydroxysuccinimide (NHS) ester to give the biotin-PEG-NHS conjugate which was coupled to the aminofunctionalized AFM tip. The motional freedom provided by PEG allows for free rotation of the biotin molecule on the AFM sensor and for specific binding to avidin which had been adsorbed to mica surfaces via electrostatic interactions. Specific avidin-biotin recognition events were discriminated from nonspecific tip-mica adhesion by their typical unbinding force (∼40 pN at 1.4 nN/s loading rate), unbinding length (<13 nm), the characteristic nonlinear force-distance relation of the PEG linker, and by specific block with excess of free d-biotin. The convenience of the test system allowed to evaluate, and compare, different methods and conditions of tip aminofunctionalization with respect to specific binding and nonspecific adhesion. It is concluded that this system is well suited as calibration or start-up kit for single molecule recognition force microscopy.     

Artifacts in the Determination of Trace Metal Binding Forms in Anoxic Sediments by Sequential Extraction

Abstract

The binding forms of Co, Cd, Cu, Pb, and Zn in an anoxic, sulfide-bearing sediment were investigated by performing both thermodynamic equilibrium calculations and sequential extractions. Care was taken to maintain oxygen-free conditions during the whole experiment. The calculations suggested that trace metals were bound to sulfidic minerals. Sequential extraction results, however, showed increased importance of exchangeable and reducible fractions in the order Cu < Cd < Pb < Zn < Co. Thermodynamic equilibrium calculations of the chemical reactions during extraction showed that Cd, Co, Pb, and Zn sulfides are to a significant extent soluble in the acetate-exchangeable (step 1 + 2) and oxalate-reducible (step 3) fractions. Neglecting the dissolution of sulfide minerals would lead to a misinterpretation of the experimental results.     

Efficient Entropy-Driven Inhibition of Dipeptidyl Peptidase III by Hydroxyethylene Transition-State Peptidomimetics

Dipeptidyl peptidase III (DPP3) is a ubiquitously expressed Zn-dependent protease, which plays an important role in regulating endogenous peptide hormones, such as enkephalins or angiotensins. In previous biophysical studies, it could be shown that substrate binding is driven by a large entropic contribution due to the release of water molecules from the closing binding cleft. Here, the design, synthesis and biophysical characterization of peptidomimetic inhibitors is reported, using for the first time an hydroxyethylene transition-state mimetic for a metalloprotease. Efficient routes for the synthesis of both stereoisomers of the pseudopeptide core were developed, which allowed the synthesis of peptidomimetic inhibitors mimicking the VVYPW-motif of tynorphin. The best inhibitors inhibit DPP3 in the low μM range. Biophysical characterization by means of ITC measurement and X-ray crystallography confirm the unusual entropy-driven mode of binding. Stability assays demonstrated the desired stability of these inhibitors, which efficiently inhibited DPP3 in mouse brain homogenate.     

Crystal structures of functional building blocks derived from bis(benzo[b]thiophen‐2‐yl)methane

The syntheses of three bis(benzo[b]thiophen‐2‐yl)methane derivatives, namely bis(benzo[b]thiophen‐2‐yl)methanone, C₁₇H₁₀OS₂, (I), 1,1‐bis(benzo[b]thiophen‐2‐yl)‐3‐(trimethylsilyl)prop‐2‐yn‐1‐ol, C₂₂H₂₀OS₂Si, (II), and 1,1‐bis(benzo[b]thiophen‐2‐yl)prop‐2‐yn‐1‐ol, C₁₉H₁₂OS₂, (III), are described and their crystal structures discussed comparatively. The conformation of ketone (I) and the respective analogues are rather similar for most of the compounds compared. This is true for the interplanar angles, the C_aryl—C_bridge—C_aryl angles and the dihedral angles. The best resemblance is found for a bioisotere of (I), viz. 2,2′‐dinaphthyl ketone, (VII). By way of interest, the crystal packings also reveal similarities between (I) and (VII). In (I), the edge‐to‐face interactions seen between two napthyl residues in (VII) are substituted by S…π contacts between the benzo[b]thiophen‐2‐yl units in (I). In the structures of the bis(benzo[b]thiophen‐2‐yl)methanols, i.e. (II) and (III), the interplanar angles are also quite similar compared with analogues and related active pharmaceutical ingredients (APIs) containing the dithiophen‐2‐ylmethane scaffold, though the dihedral angles show a larger variability and produce unsymmetrical molecules.     

REACTIVITY AND STEREOSELECTIVITY IN THE DIELS-ALDER REACTIONS BETWEEN CYCLOPENTADIENE AND SOME α, β-UNSATURATED THIOESTERS

Abstract

Some new norbornene thioester derivatives of endo configuration are sinthesized. Proofs are provided that thioester group has more preference for endo configuration than the ester group.     

Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.