New redox active ligands involving a tetrathiafulvalene vinylogue backbone

Two synthetic approaches towards a new bisthiopicoline substituted vinylogous tetrathiafulvalene (TTFV) are described. As evidenced by electrochemistry and ¹H NMR studies, this redox active ligand shows excellent coordinating properties towards Zn²⁺ metal ion.     

Pyridone dipeptide backbone scan to elucidate structural properties of a flexible peptide segment

Whereas the C-terminal fragment of neuropeptide Y (NPY) has been structurally well-defined both in solution and as membrane-bound, detailed structural information regarding the proline-rich N-terminus is still missing. The systematic variation of each position by a conformationally constrained pyridone dipeptide building block within the amino terminal segment of NPY leads to a systematic receptor subtype selectivity of the neuropeptide. Thereby, the systematic dipeptide scan proved superior to the traditional L-Ala scan because it showed how to modify the N-terminus in order to obtain increasingly more Y1 or Y5 receptor selective ligands. NMR and CD spectroscopic analyses were used to characterize the stepwise rigidification of the N-terminus of NPY when up to three dipeptide building blocks were incorporated by solid-phase peptide synthesis. The pyridone dipeptide increases the hydrophobicity of the amino terminus of NPY, and this allows the tuning of the membrane affinity of NPY. The amphiphilic C-terminal helix of 3-fold-substituted NPY thus becomes visible by selective line broadening in the (1)H NMR. Accordingly, we could structurally characterize protein segments that are too flexible for other methods.     

Low-energy (3-24 eV) electron damage to the peptide backbone

We report the mass spectrometric measurement of anions desorbed by 3-24 eV electron impact on thin films of formamide-1-d (DCONH2) and on the self-assembled monolayer (SAM) of two different Lys amide molecules used as a molecular model of the peptide backbone. In the present SAM configuration, the amides are elevated from a gold substrate by hydrocarbon chains to remove the effects of the metal substrate. Electron irradiation produces H- and D- from the formamide-1-d film and H-, CH3-, O-, and OH- from the SAM Lys amides. Below 13 eV, the dependence of the anion yields on the incident electron energy exhibits structures indicative of the dissociative electron attachment process, which is responsible for molecular fragmentation via the initial formation of core-excited anions. Above 13 eV, anion desorption is dominated principally by non-resonant dipolar dissociation. Our results suggest that the sensitivity of the peptide backbone to secondary electrons produced by ionizing radiation depends on the chemical environment (i.e., the amino acids sequence).     

Disulfide bond creates a small connecting loop in aminoxy peptide backbone

Disulfide-bond formation between the side chains of cysteine-cysteine pairs is often critical to the folding behavior, stability, and functionality of proteins. In this paper, we report that sulfur atoms can be introduced into the amide groups of aminoxy peptides to form a novel type of disulfide bridge, which creates a connecting loop in the peptide backbone.     

Structural requirements for the biosynthesis of backbone cyclic peptide libraries

BACKGROUND: Combinatorial methods for the production of molecular libraries are an important source of ligand diversity for chemical biology. Synthetic methods focus on the production of small molecules that must traverse the cell membrane to elicit a response. Genetic methods enable intracellular ligand production, but products must typically be large molecules in order to withstand cellular catabolism. Here we describe an intein-based approach to biosynthesis of backbone cyclic peptide libraries that combines the strengths of synthetic and genetic methods. RESULTS: Through site-directed mutagenesis we show that the DnaE intein from Synechocystis sp. PCC6803 is very promiscuous with respect to peptide substrate composition, and can generate cyclic products ranging from four to nine amino acids. Libraries with five variable amino acids and either one or four fixed residues were prepared, yielding between 10(7) and 10(8) transformants. The majority of randomly selected clones from each library gave cyclic products. CONCLUSIONS: We have developed a versatile method for producing intracellular libraries of small, stable cyclic peptides. Genetic encoding enables facile manipulation of vast numbers of compounds, while low molecular weight ensures ready pharmacophore identification. The demonstrated flexibility of the method towards both peptide length and composition makes it a valuable addition to existing methods for generating ligand diversity.     

Two enzymes catalyze the maturation of a lasso peptide in Escherichia coli

Microcin J25 (MccJ25) is a gene-encoded lasso peptide secreted by Escherichia coli which exerts a potent antibacterial activity by blocking RNA polymerase. Here we demonstrate that McjB and McjC, encoded by genes in the MccJ25 gene cluster, catalyze the maturation of MccJ25. Requirement for both McjB and McjC was shown by gene inactivation and complementation assays. Furthermore, the conversion of the linear precursor McjA into mature MccJ25 was obtained in vitro in the presence of McjB and McjC, all proteins being produced by recombinant expression in E. coli. Analysis of the amino acid sequences revealed that McjB could possess proteolytic activity, whereas McjC would be the ATP/Mg(2+)-dependent enzyme responsible for the formation of the Gly1-Glu8 amide bond. Finally, we show that putative lasso peptides are widespread among Proteobacteria and Actinobacteria.     

Selective recognition of pyrophosphate in water using a backbone modified cyclic peptide receptor

A cyclic peptide based receptor, bearing two dipicolylamino arms complexed to zinc(II) ions, binds pyrophosphate ions with high affinity and selectivity in aqueous solution as determined using an indicator displacement assay.     

Synthesis and DNA-recognition behavior of a novel peptide ribonucleic acid with a serine backbone (oxa-PRNA)

(2S)-2-Fmoc-amino-3-(5′-deoxyuridinylamino)-3-oxopropyloxyacetic acid was synthesized from l-serine as a monomer for preparing the second-generation peptide ribonucleic acid with an oxa-peptide backbone (oxa-PRNA). The ether linkage was incorporated to improve the modest solubility in aqueous solution of the original PRNA with an iso-glutamine backbone, without harming the ability of the amino-uridine side chain to switch the anti/syn nucleobase orientation by adding borax. Indeed, CD spectral examinations revealed that the Fmoc-protected oxa-PRNA uridine monomer (Fmoc-oxa-PRNA(U)), synthesized in three steps, switched the nucleobase orientation from anti to syn in phosphate buffer upon addition of borax. Homo-12mers of oxa-PRNA(U) with and without Arg end caps were prepared in moderate yields by the Fmoc solid-phase synthesis. Both of the N- and C-terminus-capped oxa-PRNA(U) 12mers thus synthesized were shown to hybridize with the complementary DNA 12mer (d(A₁₂)) with stabilities comparable to that observed for the natural pair.     

Aromatic interactions in unusual backbone nitrogen-coordinated zinc peptide complexes: a crystallographic and spectroscopic study

A series of zinc complexes with dipeptide ligands of the type Dpg-Xaa was synthesized, where Dpg is dipicolylglycine and Xaa is phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp), 2-naphthylalanine (Nal), or glycine (Gly). It was shown that aromatic interactions promote the unusual coordination of an anionic peptide backbone nitrogen atom to zinc. This binding mode was, for the first time, characterized by X-ray structure analyses of the electrically neutral complexes [(Dpg-Phe)(-H)Zn], [(Dpg-Tyr)(-H)Zn], [(Dpg-Trp)(-H)Zn], and [(Dpg-Nal)(-H)Zn]. The pKa values for amide nitrogen deprotonation were determined by 1H NMR titrations {[(Dpg-Phe)Zn], 7.17; [(Dpg-Tyr)Zn], 6.85; [(Dpg-Trp)Zn], 6.85; [(Dpg-Nal)Zn], 6.64; [(Dpg-Gly)Zn], 8.54}. It was calculated that aromatic interactions contribute ca. -8 to -11 kJ/mol of stabilizing free enthalpy changes in the derivatives with aromatic amino acid side chains. These are the first quantitative data obtained for crystallographically characterized metal complexes. A comparison with the literature shows that it is difficult to distinguish between pi-cation attraction and pi-pi stacking. However, it is evident that modification of small peptides with synthetic pyridine ligands enhances their ability to stabilize secondary structures by noncovalent interactions. This is an important consideration for the design of biomimetic metallopeptides.     

Organocatalyzed tandem process involving asymmetric protonations as a stereo-defining step

Enantioselective protonation reactions of enolates, enols, enol ethers, or enol esters have been extensively studied. On the other hand, their applications in tandem or cascade sequence have not been fully explored and examples of such reactions employing organocatalysts are few. This account describes some of the most common synthetic strategies recently developed to address such challenge.     

An aryl to imidoyl palladium migration process involving intramolecular C-H activation

Biologically interesting fluoren-9-one and xanthen-9-one derivatives have been prepared by a novel aryl to imidoyl palladium migration, followed by intramolecular arylation. The fluoren-9-one synthesis appears to involve both a palladium migration mechanism and a C-H activation process proceeding through an unprecedented organopalladium(IV) hydride intermediate. The results from deuterium labeling experiments are consistent with the proposed dual mechanism.     

Removal of methylated arsenic using a nanostructured zirconia-based sorbent: process performance and adsorption chemistry

A readily prepared nanostructured zirconia-based sorbent was developed and demonstrated to be effective on adsorption of monomethylarsonic acid (MMA) from water with a capacity of 1.43 mmol MMA/g sorbent, which is much higher than that of sorbents reported. It was found that the MMA uptake is highly pH-dependent. Better adsorption is obtained at lower pH, and the optimal pH is from 2.5 to 3.5. Most of the MMA uptake occurs rapidly in the first 48 h, followed by a relatively slow process. The adsorption kinetics and isotherm can be well described by pseudo-first order rate model and Langmuir equation, respectively. The temperature does not great influence on the adsorption isotherm. The MMA adsorption is independent on background electrolyte concentration, which implies the MMA forms inner-sphere complexes on the sorbent. The presence of humic acid does not pose noticeable effect on the adsorption. The coexisting HCO(3)(-) or F(-) obviously hinders the adsorption of MMA; however, the existence of PO(4)(3-) slightly enhances the adsorption. FTIR and XPS analyses demonstrated that hydroxyl and sulfur-containing functional groups are involved in the uptake of MMA. Based on the adsorption experimental results and spectroscopic analysis, an anion exchange mechanism is proposed for the adsorption of MMA.     

Dynamics simulation on the flexibility and backbone motions of HP1 chromodomain bound to free and lysine 9‐methylated histone H3 tails

Histone methylation has emerged as a central epigenetic modification with both activating and repressive roles in eukaryotic chromatin. Drosophila HP1 (heterochromatin‐associated protein 1) is one of the chromodomain proteins that contain the essential aromatic residues as the recognition pocket for lysine methylated histone H3 tail. The aromatic cage indicates that the complex of chromodomain protein binding lysine methylated histone H3 tail can be seen as a typical host–guest system between protein and protein. About 10‐ns molecular dynamics simulations have been carried out in this study to examine how the presence of mono‐, trimethylated lysine 9 histone H3 tail (Me1K9, Me3K9 H3) influences the motions of HP1 protein receptor. The study shows that the conformation of HP1 protein free of H3 tail easily changes, whereas that of HP1 protein bound to methylated H3 tail does not. But the conformation of inserted Me1K9 H3 changes obviously as the Me1K recognition makes hydrogen‐bonded interactions associated with the aromatic cage even more unstable than those in free HP1 protein. The conformational change of Me1K9 H3 is correlated with the motions of HP1 protein. As the recognition factor going from Me1K to Me3K produces a more favorable interaction for aromatic ring, hydrogen‐bonded interactions associated with aromatic cage in Me3K9 H3‐HP1 complex were observed to be much more stable than those in Me1K9 H3‐HP1 complex and free HP1. Because of correlation, the flexibility of Me3K9 H3 decreases. The simulations indicate that both the MeK and the surrounding histone tail sequence are necessary features of recognition which significantly affect the flexibility and backbone motions of HP1 chromodomain. These findings confirm a regulatory mechanism of protein–protein interactions through a trimethylated post‐translational modification. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Uranium determination in process chemicals: on the way to sub-pg/g concentrations

The detection limit of ICP-MS is affected by the sensitivity, the height of the blank and its relative stability i.e. precision, the accuracy and additionally by a bias or systematical error. The improvement of a single factor will improve the efficiency of the whole analytical system. For the example of uranium determination in process chemicals such as concentrated HF and HNO₃ the improvement or deterioration of the factors given above is demonstrated. The applied methods are matrix removal by evaporation, highly efficient nebulization with a USN, isotope dilution and use of a double-focusing instrument (ICP-SFMS_LR). The increase or decrease of each factor is compared to conventional nebulization ICP-QMS. To take full advantage of each single method, they can be combined with each other. Possible drawbacks of a single method are compensated by another method. Detection limits for uranium in concentrated process chemicals in the sub-pg/g range can be achieved.     

Using halogen bonds to address the protein backbone: a systematic evaluation

Halogen bonds are specific embodiments of the sigma hole bonding paradigm. They represent directional interactions between the halogens chlorine, bromine, or iodine and an electron donor as binding partner. Using quantum chemical calculations at the MP2 level, we systematically explore how they can be used in molecular design to address the omnipresent carbonyls of the protein backbone. We characterize energetics and directionality and elucidate their spatial variability in sub-optimal geometries that are expected to occur in protein-ligand complexes featuring a multitude of concomitant interactions. By deriving simple rules, we aid medicinal chemists and chemical biologists in easily exploiting them for scaffold decoration and design. Our work shows that carbonyl-halogen bonds may be used to expand the patentable medicinal chemistry space, redefining halogens as key features. Furthermore, this data will be useful for implementing halogen bonds into pharmacophore models or scoring functions making the QM information available for automatic molecular recognition in virtual high throughput screening.     

An unusual conformational similarity of two peptide folds featuring sulfonamide and carboxamide on the backbone

Two folded peptides featuring carboxamide and sulfonamide at the core of the peptide fold have been shown to possess almost similar conformational features, despite the well-known fact that carboxamides and sulfonamides have strikingly different hydrogen-bonding and geometrical preferences.     

Protein–Nucleic acid interactions: Investigations on the peptide backbone interaction with polynucleotides

Model building, difference spectroscopy, and ¹H and ¹³C NMR experiments have been carried out to study the binding of poly(L -Ser) with the polyribonucleotides poly(A) and poly(U) at pH 7.1. Studies have also been carried out with base paired duplexes poly(A)?poly(U). Peak doubling of C^α and carbonyl resonances in the ¹³C NMR spectrum of poly(L -Ser) in presence of polyribonucleotides is observed. From the chemical shifts and the linewidth, it is concluded that the interaction occurs through hydrogen bonding between the nucleic acid bases and the peptide backbone. In case of poly(A) and poly(U) the hydrogen bonding scheme with peptide backbone is different from that in the base paired poly(A)?poly(U). The possible binding schemes of double stranded DNA and peptide backbone have been investigated using model building and potential energy calculations. The hydrogen bonding schemes discriminate between various base pairs and their sequence. It is concluded that protein backbone can play an important role in protein–nucleic acid recognition schemes.