The use of peptidic frameworks for the construction of molecular receptors and devices

Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine

The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N-H···O=C, type II by a strong O-H···N hydrogen bond, type III by weak N-H···O-H hydrogen bonds, and type IV by a C=O···H-C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O-H···N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm(-1), respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG undergoes facile photofragmentation through two photochemical pathways that are favored for different initial conformations of the reactant: (a) decarboxylation, leading to CO2 plus benzylamine (the dominant photofragmentation channel in PG cis-COOH conformers ICa and ICc) and (b) decarbonylation, with generation of CO plus benzonitrile, H2O and H2 (prevalent in the case of the trans-COOH conformer, IITa).

Synthesis of stable and potent delta/mu opioid peptides: analogues of H-Tyr-c[D-Cys-Gly-Phe-D-Cys]-OH by ring-closing metathesis

Ring-closing metathesis has emerged as a powerful tool in organic synthesis for generating cyclic structures via C-C double bond formation. Recently, it has been successfully used in peptide chemistry for obtaining cyclic molecules bridged through an olefin unit in place of the usual disulfide bond. Here, we describe this approach for obtaining cyclic olefin bridged analogues of H-Tyr-c[D-Cys-Gly-Phe-Cys]-OH. The synthesis of the new ligands was performed using the second generation Grubbs' catalyst. The resulting cis-8 (cDADAE) and trans-9 (tDADAE) were fully characterized and tested at delta, mu, and kappa opioid receptors. Also the linear precursor 13 (lDADAE) and the hydrogenated derivative 11 (rDADAE) also were tested. All the cyclic products containing a olefinic bond are slightly selective but highly active and potent for the delta and mu opioid receptors. Activity toward the kappa opioid receptors was absent or very low.

Supramolecular Structures from Lysine Peptides and Carbon Dioxide

The design, synthesis, and characterization of novel linear and cross-linked supramolecular polymers that are easily available from biologically friendly lysine peptides and carbon dioxide (CO2) are reported here. Polymeric structures 5, 6, and 19 readily form from peptides 2, 3, and 15, respectively, at ambient temperatures by simply bubbling CO2 through their solutions in apolar organic solvents (CHCl3, benzene) and even in the presence of 10% MeOH. The resulting gels can be easily isolated from solution, dried, and stored refrigerated for several months. At the same time, they may thermally release CO2 and convert back to the corresponding monomers. As a consequence, their structures and physical properties are switchable. They may also trap, store, and release foreign molecules. The typical entrapment procedure was demonstrated for tripeptide 3, CO2, and the commercially available dye coumarin 2.

The Conformers of Phenylglycine

The neutral form of the unnatural amino acid phenylglycine was vaporized by laser ablation, and the presence of two conformers was detected in a supersonic expansion by Fourier transform microwave spectroscopy. Both conformers were unequivocally identified by comparison of their experimental rotational and quadrupole coupling constants with those calculated ab initio. The most stable conformer is stabilized by intramolecular hydrogen bonds N-H...O=C, N-H...pi (with the closest C-C bond in the aromatic ring), and a cis-COOH interaction. The other conformer exhibits a O-H...N hydrogen bond between the hydrogen atom of the hydroxyl group and the lone pair at the nitrogen atom.

General but Discriminating Fluorescent Chemosensor for Aliphatic Amines

Aliphatic amines are sensitively and discriminatively detected through binding with demethylated naphthol AS-BI (7-bromo-3-hydroxy-2-naphth-o-hydroxyanilide, 2) and fluorescence of the resulting complex. Recognition of the amine by the chemosensor 2 occurs via proton transfer of the naphtholic proton to the amine and is facilitated by the presence of the phenol group. Amine basicity is the primary controller of detection. Poorly basic aromatic and conjugated amines such as pyridine and aniline are not detected. Hydrogen bonding within the complex allows further differentiation of aliphatic amines. Doubly primary, conformationally flexible diamines are the most sensitive to detection, followed by secondary amines.

Synthesis of cationic porphyrin modified amino acids

Derivatives of amino acids bearing a porphyrin moiety on a side chain were synthesized by coupling a porphyrin to a glutamic acid side chain; the utility of these compounds was demonstrated by their use in solid-phase synthesis of a peptide bearing a cationic porphyrin and by studying its DNA-binding properties.

Role of Secondary Structure in the Asymmetric Acylation Reaction Catalyzed by Peptides Based on Chiral Cα-Tetrasubstituted α-Amino Acids

In a recent series of papers, Miller and co-workers were able to show that His(pi-Me)-based, terminally protected peptides are potent catalysts of the asymmetric acyl transfer reaction, useful for the kinetic resolution of alcohols. In a structure-supporting solvent, one of the most active compounds, an Aib-containing tetrapeptide, is folded in a doubly intramolecularly H-bonded beta-hairpin motif incorporating a type-II' beta-turn conformation. In this work, we have expanded the study of the Miller tetrapeptide by examining a set of analogues and shorter sequences (dipeptide amides), characterized by chiral C(alpha)-tetrasubstituted alpha-amino acids of diverging bulkiness and optical configuration. Peptide synthesis in solution, conformational analysis by FT-IR absorption and (1)H NMR techniques, and screening of catalytic activity as well have been performed. Our results confirm the close relationship between the beta-hairpin 3D-structure and the catalytic activity of the peptides. A tetrapeptide analogue slightly more selective than the Miller compound has been found. However, the terminally protected, industrially more appealing, dipeptide amides are poorly effective.

Design, synthesis, and characterization of peptide nanostructures having ion channel activity

We report the synthesis and the functional studies of multiple crown alpha-helical peptides designed to form artificial ion channels. The approach combines the versatility of solid phase peptide synthesis, the conformational predictability of peptidic molecules, and the solution synthesis of crown ethers with engineerable ion-binding abilities. Several biophysical methods were employed to characterize the activity and the mode of action of these crown peptide nanostructures. The 21 residue peptides bearing six 21-EC-7 turned out to facilitate the translocation of ions in a similar fashion to natural ion channels.

New tools for the control of peptide conformation and supramolecular chemistry: Crown-carrier, Cα-methyl L-DOPA amino acids

The preferred conformation of five, terminally protected, model peptide series to the hexamer level, based on three novel crowned, C(alpha)-methyl L-DOPA amino acids combined with either L-Ala/Aib or Gly/Aib, were assessed in structure supporting solvents using FT-IR absorption, (1)H NMR, and CD techniques. The FT-IR absorption spectra strongly suggest that the contribution of the crowned C(alpha)-tetrasubstituted residue to intramolecular H-bonding is equivalent to that of Aib and is much more significant than that of either L-Ala or Gly. In addition, the (1)H NMR titrations and the CD patterns resemble those typically exhibited by (right-handed) 3(10)-helical structures.

What to synthesize? from Emil Fischer to peptidomics

The driving forces, incentives and strategic targets of peptide synthesis have undergone considerable evolution during the centenary following the pioneer work of Emil Fischer. In those days peptide synthesis was considered as a way of confirming the polypeptide theory of protein structure. The scientific community also expected (naively) that the synthesis would eventually lead to the creation of artificial living organisms. Only in the 1950s, when the first exact amino acid sequences were established did peptide chemistry obtain firmer ground and clearly defined targets. The total synthesis of peptide hormones and antibiotics became possible, providing valuable material for elucidating structure-functional relationships and the mechanisms of biological action. In the following years the number of peptides isolated from various biological sources grew with impressive speed and peptides became known as the most abundant, ubiquitous group of low molecular bioregulators. The design and synthesis of novel peptide based pharmaceuticals became an important area of peptide chemistry. At present we are facing the challenge of analysing the structures and bioactivities of total sets of peptides, i.e. peptidoms, present in concrete tissues or groups of cells. The results obtained along these lines at the IBCH RAS Institute of Bioorganic Chemistry are briefly considered in the review.