Sequencing of β-Peptides by Mass Spectrometry

Seven ?-peptides containing up to 18 β2-, β3- and β2,3-amino acids have been subjected to ESI-tandem mass spectrometry (low-energy fragmentation, positive ions). From the fragment ions formed from the free β-peptides, as well as from the corresponding methyl esters (+14 U) and N-acetyl derivatives (+42 U), the known sequences of β-amino acids could be confirmed unambiguously with the program Sherpa. Thus, the commonly used MS-sequencing procedure for α-peptides can be adopted for β-peptides without modification. However, there are pronounced differences in the fragmentation patterns of the two types of peptides: the β-peptides disclose their relationship to Mannich bases in the mass-spectrometric experiment by the elimination of ammonia from the N-terminus (→ RCH=CH-CO-NH-R') and the occurence of retro-Mannich cleavage (cf. formation of HN=CHR + CH3CO-NH-R' from β-amino-acid residues)

Biological and Pharmacokinetic Studies with β-Peptides

Interactions and cleavage reactions of β-amino acids and β-oligopeptides (up to nine residues, carrying the side chains of Ala, Val, Leu, Ile, Phe, Ser, Lys, and Hop) with biological systems, such as the most potent peptidases (pronase, proteinase K, 20S proteasome), microorganisms (Pseudomonas aeruginosa and Pseudomonas putida), and mammalian blood (intravenous application to rats) have been investigated and compared with ?-peptides. The results are: i) the three peptidases do not cleave β-peptides at all (within 24 h), and they are not inhibited by a β-peptide; ii) except for certain 3-aminobutanoic-acid (β-HAla) derivatives, neither free, nor N-acetyl-β-amino acids, nor β-peptides (offered as sole N and C source) lead to growth of the two bacteria tested; iii) two water-soluble β-heptapeptides (with Lys side chains) were shown to have elimination half-lives t1/2(β) of 3 and 10 h at 100- and 30-ng/ml levels, respectively, in the rodent blood – much larger than those of α-peptides. Thus, the preliminary results described here confirm the much greater stability of β-peptides, as compared to α-peptides, towards metabolization processes, but they also suggest that there may be interactions (by hitherto unknown mechanisms) between the worlds of α- and β-peptides

From the Biopolymer PHB to Biological Investigations of Unnatural β- and γ-Peptides

An overview is given of the past and present activities of our group in the field of chemical biology. Thus, the polymer of 3-hydroxybutanoic acid (PHS), which is omnipresent in living organisms, triggered our search for a better analytical method for detecting PHB and our syntheses of oligomers of 3-hydroxyalkanoic acids (OHSs). Also, the regulation of DNA replication by poly(β-malic acid) (PMA) in certain eukaryotes inspired synthetic work on the corresponding cyclic and open-chain oligomers. With these oligomers we not only tested the mechanisms of depolymerases, but were able to study the properties and activities of well-characterized compounds (also with isotope and fluorescence labeling). The role of PHS as component of ion transport systems through phospholipid bilayers was unambiguously established, and models for the channel structure were proposed. Replacement of amino acids by 3-hydroxybutanoic acid residues in peptides and replacement of the chain-bound oxygens in OHB by NH paved our way into the world of β- and γ-peptides, the synthesis and physiological and pharmacological properties of which are being investigated. β-Peptides are stable to peptidases, have a long lifetime in mammalian serum and are rather resistant to environmental microbial degradation. The peptides consisting of homologated (β) or doubly homologated (γ) amino acids form stable secondary structures in solution (helices, turns, sheets) which can be used as scaffolds for peptide mimics, such as a β-tetrapeptide with affinity to a somatostatin receptor or a β-nonapeptide that inhibits intestinal lipid-transport protein (SR-BI) in Caco-2 cells. Certain β-peptides have antibacterial, antiproliferative and haemolytic properties. The lessons from studies of β- and γ-peptides teach us about the central role of natural α-peptidic proteins

Excursions of Synthetic Organic Chemists to the World of Oligomers and Polymers

The activities of a group devoted to organic synthesis in the field of polymer and oligomer chemistry have led to new types of dendritic cross-linking compounds for the polymerization of styrene to give high-quality materials. In addition the synthesis of uniform ('monodisperse'), high-molecular weight oligomers of 3-hydroxybutanoic acid provided samples for investigations to prove the hypothesis that polyhydroxybutyrates are natural ion-channel components in living organisms. Oligomers of ?-amino acids were prepared and have been shown to form all the secondary structures known from natural peptides and proteins (composed of ?-amino acids), i.e. helices, pleated sheets, turns, hair pins and stacks with properties differing fundamentally from those of the natural analogs

Systems parasitology: effects of Fasciola hepatica on the neurochemical profile in the rat brain

We characterize the integrated response of a rat host to the liver fluke Fasciola hepatica using a combination of (1)H nuclear magnetic resonance spectroscopic profiles (liver, kidney, intestine, brain, spleen, plasma, urine, feces) and multiplex cytokine markers of systemic inflammation. Multivariate mathematical models were built to describe the main features of the infection at the systems level. In addition to the expected modulation of hepatic choline and energy metabolism, we found significant perturbations of the nucleotide balance in the brain, together with increased plasma IL-13, suggesting a shift toward modulation of immune reactions to minimize inflammatory damage, which may favor the co-existence of the parasite in the host. Subsequent analysis of brain extracts from other trematode infection models (i.e. Schistosoma mansoni, and Echinostoma caproni) did not elicit a change in neural nucleotide levels, indicating that the neural effects of F. hepatica infection are specific. We propose that the topographically extended response to invasion of the host as characterized by the modulated global metabolic phenotype is stratified across several bio-organizational levels and reflects the direct manipulation of host-nucleotide balanc

A Scheme for the Evaluation of Electron Delocalization and Conjugation Efficiency in Linearly π-Conjugated Systems

In this study, we present a scheme for the evaluation of electron delocalization and conjugation efficiency in lineraly pi-conjugated systems. The scheme, based on the natural bond orbital theory, allows monitoring the evolution of electron delocalization along an extended conjugation path as well as its response to chemical modification. The scheme presented is evaluated and illustrated by means of a computational investigation of;pi-conjugation in all-trans polyacetylene [PA; H(-CH=CH)(n)-H], polydiacetylene [PDA, H(-CC-CH CH)(n)-H], and polytriacetylene [PTA, H(-CC-CH=CH-C C)(n)-H] with up to 180 carbon atoms, all related by the number of ethynyl units incorporated in the chain. We are able to show that for short oligomers the incorporation of ethynyl spacers into the PA chain increases the pi-delocalization energy, but, on the other hand, reduces the efficiency with which pi-electron delocalization is promoted along the backbone. This explains the generally shorter effective conjugation lengths observed for the properties of the polyeneynes (PDA and PTA) relative to the polyenes (PA). It will also be shown that the reduced conjugation efficiency, within the NBO-based model presented in this work, can be related to the orbital interaction pattern along the pi-conjugated chain. We will show that the orbital interaction energy pattern is characteristic for the type and the length of the backbone and may therefore serve as a descriptor for linearly pi-conjugated chains