Synthesis and structural analysis of vinylogous peptides

A Z- or E-ethenyl group has been inserted between the -carbon andthe carboxyl group of the proline residue by stereoselective Hornersynthesis. The resulting vinylogous amino acid has been coupled with aminocompounds by classical methods, and model amino acid derivatives anddipeptides containing a Z- or E-CH=CMe group have been investigated insolution by ¹H-NMR and IR spectroscopy, and in the solid stateby X-ray diffraction. The E-ethenyl group gives rise to an openconformation and the Z-conformer to a folded structure with anintramolecular hydrogen bond closing a nine-membered pseudocycle.     

Synthesis and structural analysis of vinylogous peptides

Summary A Z-orE-ethenyl group has been inserted between the α-carbon and the carboxyl group of the proline residue by stereoselective Horner synthesis. The resulting vinylogous amino acid has been coupled with amino compounds by classical methods, and model amino acid derivatives and dipeptides containing a Z-orE-CH=CMe group have been investigated in solution by¹H-NMR and IR spectroscopy, and in the solid state by X-ray diffraction. TheE-ethenyl group gives rise to an open conformation and the Z-conformer to a folded structure with an intramolecular hydrogen bond closing a ninemembered pseudocycle.     

Synthesis and nmr conformational studies of polyoxyethylene-bound, alpha-deuterated glutamate oligopeptides

The syntheses of three series of glutamate oligopeptides attached to a macromolecular solubilizing polyoxyethylene (POE) group Boc-[Glu(OMe)]_n-OPOE, Ac-[Glu(OMe)]_n-OPOE, pGlu-[Glu(OMe)]_n?1-OPOE (n ? 1–7) and their various analogs specifically deuterated at individual α-CH positions using the liquid-phase method of peptide synthesis are described. It was shown that stepwise synthesis using the symmetrical anhydride gave homo-oligopeptides that are analytically pure. Fragment condensation methods using DCC-HOBt yield POE-peptides with POE-HOBt impurities but the peptide synthesis may be carried stoichiometrically with smaller quantities of amino acid derivatives. 360 MHz ¹H-nmr conformational studies of these homo-oligopeptides in DMSO-d₆ are presented. The α-deuterated peptides are shown to allow unequivocal homoligopeptide backbone NH assignments.     

Synthesis and conformational analysis of an expanded cyclic ketoxime‐hexapeptide

In this work the synthesis of a linear hexapeptide with a hydroxylamine functionality at the N‐terminus and a ketone instead of the carboxylic acid at the C‐terminus is described. Cyclization by ketoxime formation yields the 19‐membered ring‐expanded cyclic hexapeptide cyclo[Goly‐Val‐Ala‐Pro‐Leu‐Kly] which adopts a main conformer with two intramolecular hydrogen bonds. The hydrolytic stability of a ketoxime lies between the inert amide and the labile imine. The substitution of an amide bond for an iminium bond transforms the irreversible macrocyclization into a reversible process, but macrocyclic imines are difficult to isolate because they are prone to hydrolysis. The enhanced chemical stability of the ketoxime justifies its application in ligation protocols. The detailed NMR analysis of a ketoxime linkage presented here identifies its local conformational preferences in a constrained peptide environment. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Vibrational spectroscopy and X-ray diffraction methods to establish the differences between hardwood and softwood

FT-IR spectrometry and X-ray diffraction were applied to probe the differences between pulp fibers from Eucalyptus wood (hardwood) and Norway spruce wood (softwood). Wood processing was found to induce certain structural alterations within its components depending on the type of wood and the applied procedure. These differences were established by using techniques such as; spectral comparison of wood samples with those of individual component fractions, derivative spectroscopy, bands deconvolution, etc. FT-IR spectroscopy was shown to be an important tool that provided details about the structural characteristics of hardwood and softwood samples. Using second-derivative spectra and deconvolution processes small differences between spectra became apparent that allowed correlations to be made related to wood composition. In addition a correlation was established between the integral absorptions for the various bands and lignin content as well as the lignin/carbohydrate content. Relations between various spectral characteristics and the degree of crystallinity and sample composition were established.     

Synthesis and conformational analysis of the repeating units of bacterial spore peptidoglycan

Deprotection of the fully blocked disacharide allyl O-(2-amino-4,6-O-benzylidene-3-O-[(R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranosyl-1',2-lactam)-(1-->4)-2-acetamido-3,6-di-O-benzyl-2-deoxy-beta-D-glucopyranoside by selective de-O-allylation and parallel removal of the benzylidene and O-benzyl groups is described. The resulting beta-muramyl lactam-(1-->4)-GlcNAc disaccharide is characterised as the per-O-acetylated derivative by 1H and 13C NMR spectroscopy and X-ray structure analysis. Conformational analysis about glycosidic bond of repeating units of bacterial spore cortex is based on experimental data and molecular modelling.     

Heterochiral Ala/(αMe)Aze sequential oligopeptides: Synthesis and conformational study

α‐Amino acid residues with a ?,ψ constrained conformation are known to significantly bias the peptide backbone 3D structure. An intriguing member of this class of compounds is (αMe)Aze, characterized by an N^α‐alkylated four‐membered ring and C^α‐methylation. We have already reported that (S)‐(αMe)Aze, when followed by (S)‐Ala in the homochiral dipeptide sequential motif ‐(S)‐(αMe)Aze‐(S)‐Ala‐, tends to generate the unprecedented γ‐bend ribbon conformation, as formation of a regular, fully intramolecularly H‐bonded γ‐helix is precluded, due to the occurrence of a tertiary amide bond every two residues. In this work, we have expanded this study to the preparation and 3D structural analysis of the heterochiral (S)‐Ala/(R)‐(αMe)Aze sequential peptides from dimer to hexamer. Our conformational results show that members of this series may fold in type‐II β‐turns or in γ‐turns depending on the experimental conditions.     

Synthesis and structural analysis of copper(II) cysteine complexes

This report describes the synthesis and structural analysis of stable copper(II) cysteine complexes. Pale pink copper(II) cysteine complexes were synthesized in mole ratios of 1:2, 1:4, and 1:6 of copper(II):cysteine in ethanol. Infrared spectroscopy and X-ray absorption spectroscopy confirmed that copper(II) binding occurred via the thiol ligand of cysteine. XANES analysis showed that the oxidation state of copper remained as copper(II) and the local atomic geometry was similar in all of the cysteine complexes. The EXAFS data indicate that the copper(II) cysteine complexes are forming ring type structures with sulfur ligands from the cysteines acting as bridging ligands. X-ray diffraction revealed that the copper(II) cysteine complexes formed monoclinic cells with maximum crystallinity found in the 1:4 copper(II):cysteine complex.     

Synthesis and conformational study in solution and in solid state of oligopeptides containing L-leucine and glycine

The synthesis and conformational studies of the oligopeptide N-tert.-butyloxycarbonyl-L-Leu-(L-Leu-Gly)n-OBzl (n = 1, 3, 5) and N-tert.-butyloxycarbonyl-(L-Leu-Gly)2-OBzl are described. The peptides were synthesized by stepwise and fragment condensation techniques using dicyclohexylcarbodiimide as the condensing agent in solution. The conformational study of the oligopeptides was carried out using CD, u.v. and i.r. spectra. The conformation in solution was examined in trifluoroethanol, hexafluoroisopropanol, hexafluoroacetone trihydrate, and methanol. CD spectra in trifluoroethanol exhibited a gradual variation with increasing peptide chain length. This can be interpreted as a formation of an ordered structure which is already present in the heptapeptide and, to a greater extent, in the undecapeptide. The results obtained from the CD profiles and i.r. spectra showed the presence of beta structure with antiparallel chains in the heptapeptide and undecapeptide. Finally, CD spectra revealed in trifluoroethanol-water solution the binding of Ca2+ to heptapeptide and undecapeptide together with a contemporaneous conformational change. This change is probably due to the formation of beta-turns. No change in the CD profiles was obtained by using Mg2+, K+, Na+, and Li+ ions instead of Ca2+.     

Single-crystal and powder X-ray diffraction and solid-state C NMR of p-nitrophenyl glycopyranosides, the derivatives of d-galactose, d-glucose, and d-mannose

The X-ray diffraction patterns, ¹³C CP MAS NMR spectra, and powder X-ray diffraction analyses were obtained for selected p-nitrophenyl glycosides: α- and β-d-galactopyranosides (1 and 2), α- and β-d-glucopyranosides (3 and 4), and α- and β-d-mannopyranosides (5 and 6). In X-ray diffraction analysis of 1 and 2, characteristic shortening and lengthening of selected bonds were observed in the molecules of 1 due to anomeric effect, and in the crystal lattice of 1 and 2, hydrogen bonds of complex network were detected. In the crystal asymmetric unit of 1 there were two independent molecules, whereas in 2 there was one molecule. For 1 and 3–6 the number of resonances in solid-state ¹³C NMR spectra exceeded the number of the carbon atoms in the molecules, while for 2 there were distinct singlet resonances in its solid-state NMR spectrum. Furthermore, the powder X-ray diffraction (PXRD) performed for 1–3 and 5 revealed that 1, 3, and 5 existed as single polymorphs proving that the doublets observed in appropriate solid-state NMR spectra were connected with two non-equivalent molecules in the crystal asymmetric unit. On the other hand 2 existed as a mixture of two polymorphs, one of them was almost in agreement with the calculated pattern obtained from XRD (the difference in volumes of the unit cells), and the subsequent unknown polymorph existed in small amounts and therefore it was not observed in solid-state NMR measurements.     

Synthesis, spectroscopic characterization, and crystal structures of two chlorodiorganotin(IV) 4-(2-methoxyphenyl)piperazine-1-carbodithioates

Two chlorodiorganotin(IV) complexes of 4-(2-methoxyphenyl)piperazine-1-carbodithioate (MPPDA) have been synthesized by 1:1 mole-ratio reactions of the parent acid (MPPDAH) with Me₂SnCl₂ or Et₂SnCl₂ in dry methanol. The products have been characterized by Raman and multinuclear NMR (¹H, ¹³C and ¹¹⁹Sn) spectroscopy, elemental analysis, and mass spectrometry. Single-crystal X-ray diffraction studies indicate that both complexes have distorted trigonal bipyramidal geometries around the central Sn atom.     

Effects of a synthetic antitumoral catechin and its tyrosinase-processed product on the structural properties of phosphatidylcholine membranes

Catechin flavonoids are the main components of green tea extracts which present broad potential physiological activities. Several of their biological activities seem to affect membrane-dependent cellular processes and it is known that some catechins interact with phospholipid membranes. In this study we examine the interactions of a 3-O-(3,4,5-trimethoxybenzoyl)-(−)-catechin (TMCG), and its quinone methide (QM) activated product with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes by means of differential scanning calorimetry, X-ray diffraction, Fourier-Transform infrared spectroscopy and molecular dynamics simulation. We report that there are extensive interactions between TMCG and DPPC involving the perturbation of the thermotropic gel to liquid crystalline phase transition of the phospholipid, the decrease of bilayer thickness and the promotion of interdigitated gel phase, together with an increase of the hydrogen bonding pattern of the interfacial region of the bilayer. In contrast, QM shows a weak interaction with the phospholipid bilayer. Molecular dynamics simulation indicates that TMCG locates in the interior of the bilayer, while QM is found interacting with the surface of the membrane. The observations are interpreted in terms of the mechanism of membrane prodrug activation and the underlying membrane perturbations of the biological actions of natural catechins.     

X-ray fibre diffraction study of conformational changes in hyaluronate induced in the presence of sodium,potassium and calcium cations

Hyaluronate purified from all cations by ion exchange chromatography was introduced to the cations sodium, potassium and calcium in a controlled way. The conformations formed in the presence of these ions were studied as a function of ionic strength, hydrogen ion activity, humidity and temperature using X-ray fibre diffraction. In sodium hyaluronate above pH 4.0 a contracted helix is found which approximates to a four-fold helix with an axial rise per disaccharide of 0.84 nm. There is no requirement for water molecules in the unit cell as the Na⁺ can be coordinate by the hyaluronate chains alone. On crystallizing hyaluronate below pH 4.0 an extended 2-fold helix with an axial rise per disaccharide of 0.98 nm is formed. In the presence of potassium above pH 4.0 a conformation similar, but not identical, to that of sodium was found where the helix backbone is again four-fold with an axial rise per disaccharide h=0.90 nm. To maintain the coordination of the potassium ion, four water molecule/disaccharide are required and on removal of these the conformation is destabilized going to a new helix where n = 4 and h = 0.97 nm. Below pH 4.0 the conformation is a contracted 4-fold helix with h = 0.82 nm. In this structure two antiparallel chains intertwine to form a double helix. The packing of the double helical units is stabilized by water molecules, the unit cell requiring 8 water molecules/disaccharide. Formation of the calcium hyaluronate complex above pH 3.5 yields a three-fold helix with h = 0.95 nm. The requirement for water in the unit cell to maintain full crystallinity is high, at 9 water molecules/disaccharide; however, on removal of this water, though the crystallinity is disrupted, the conformation remains constant. The acid form of calcium-hyaluronate yields an equivalent conformation to that of sodium under the same condition, i.e. a helix with n = 2, h = 0.98 nm. The presence of small quantities of calcium in what are otherwise potassium or sodium solutions of hyaluronate yield the 3-fold conformation for hyaluronate. Thus calcium has an important role to play in deciding the dominating conformation present in hyaluronate. The variety of conformations yielded by the different cations indicates a subtle interaction between hyaluronate and its environment, in which the balance between the cations will control to some degree the interactions between hyaluronate chains and thus affect the mechanical properties of the matrix which they form. The conformations of individual chains are all stabilized in varying degrees by intra-chain hydrogen bonds.     

Interactions of a bacterial biosurfactant trehalose lipid with phosphatidylserine membranes

Trehalose lipids are biosurfactants produced by rhodococci that, in addition to their well known potential industrial and environmental uses, are gaining interest in their use as therapeutic agents. The study of the interaction of biosurfactants with membranes is important in order to understand the molecular mechanism of their biological actions. In this work we look into the interactions of a bacterial trehalose lipid produced by Rhodococcus sp. with dimyristoylphosphatidylserine membranes by using differential scanning calorimetry, X-ray diffraction and infrared spectroscopy. Differential scanning calorimetry and X-ray diffraction show that trehalose lipid broadens and shifts the phospholipid gel to liquid-crystalline phase transition to lower temperatures, does not modify the macroscopic bilayer organization and presents good miscibility both in the gel and the liquid-crystalline phases. Infrared experiments show that trehalose lipid increases the fluidity of the phosphatidylserine acyl chains, changed the local environment of the polar head group, and decreased the hydration of the interfacial region of the bilayer. Trehalose lipid was also able to affect the thermotropic transition of dimyristoylphosphatidyserine in the presence of calcium. These results support the idea that trehalose lipid incorporates into the phosphatidylserine bilayers and produces structural perturbations which might affect the function of the membrane.     

Revisiting 23-iodospirostanes. New facts and full characterization

In addition to a previous report, the reaction of tigogenin acetate with ICl in refluxing CHCl₃ produced the hitherto unknown 23R-iodotigogenin acetate, bearing an axial iodine atom at C-23 and its already reported 23S-epimer. The same treatment of sarsasapogenin acetate led to a single diasteromer characterized as 23S-iodosarsasapogenin acetate. A full characterization of the obtained compound including ¹H, ¹³C NMR, MS and X-ray diffraction is provided.     

Modeling ganglioside headgroups by conformational analysis and molecular dynamics

The conformations and dynamics of gangliosides GM1, GM2, 6-GM2 and GM4 have been studied by computational means, and the results compared to NMR data. Unconstrained conformational searches were run using the AMBER* force field augmented by MNDO derived parameters for the Neu5Ac anomeric torsion, the GB/SA water solvation model, and the MC/EM alogorithm; extended (10–12[emsp4 ]ns) dynamic simulations in GB/SA water were performed with the MC/SD protocol, and the stored structures were minimized. The overall mobility of the Neu5Ac2,3Gal linkage and the position of its minimum energy conformation have been shown to depend mainly on the presence or the absence of a GalNAc residue at the adjacent position. The best quantitative agreement with the available NOE data was achieved after minimization of the structures stored during the MC/SD dynamic runs. The latter protocol appears to reproduce satisfactorily the available experimental data, and can be used with confidence to build three-dimensional models of ganglioside headgroups.     

Isolation and structural elucidation of two new labdane diterpenoids from the aerial part of Roylea cinerea

Two new labdane diterpenoids, cinereanoid A (1) and cinereanoid B (2), along with five known compounds, calyone (3), pilloin (4), 1-methylindole-3-carboxaldehyde (5), β-sitosterol (6) and stigmasterol (7) were isolated from the aerial parts of Roylea cinerea (Lamiaceae). The new structures were determined by using IR, MS, 1D, 2D NMR spectroscopy. The structure of both new compounds was further confirmed by single crystal X-ray crystallographic analysis. In this study we have also reported single crystal X-ray structure of compound 3 which unambiguously confirmed the relative stereochemistry of tertiary hydroxyl and methyl groups, as it was not established by earlier report. Compounds 4 and 5 were isolated for the first time from this plant. In view of very few reports about this species, this report has increased the phytochemical knowledge about R. cinerea.     

Crystallization and preliminary X-ray crystallographic analysis of ImmE7 protein of colicin E7

The ImmE7 protein, which can bind specifically to the DNase colicin E7 and neutralize its bactericidal activity, has been purified and crystallized in two different crystal forms by vapor diffusion method. The orthorhombic crystals belong to space group I222 or I2₁2₁2₁ and have unit cell dimensions a = 75.1 Å, b = 50.5 Å, and c = 45.4 Å. The second form is monoclinic space group P2₁ with ceil dimensions a = 29.3 Å, b = 102.7 Å, c = 53.0 Å and β = 91.5°. The orthorhombic crystals diffract to 1.8 Å resolution, and are suitable for high-resolution X-ray analysis. © 1995 Wiley-Liss, Inc.     

Synthesis and characterization of heteroscorpionate dioxo-tungsten(VI) complexes

Twelve new dioxo W(VI) complexes of a family of heteroscorpionate ligands of the type [(L)WO₂Y], where L = N₂X ligand and Y = Cl or OR, have been synthesized and characterized. With the more sterically bulky ligands we show that these complexes exist as isolable cis and trans isomers and compare the rate of such isomerization with their corresponding dioxo Mo(VI) analogs.     

Synthesis, conformational analysis, and spectroscopic characterization of peptides based on Daf, the first rigid transition-metal receptor, cyclic C(alpha,alpha)-disubstituted glycine

Three series of terminally protected model oligopeptides to the nonamer level, based on 9-amino-4,5-diazafluorene-9-carboxylic acid, the first rigid bipyridine-type C(alpha,alpha)-disubstituted glycine, and either Gly, L-Ala, or Aib residues were synthesized by solution methods and fully characterized. The molecular structures of two derivatives and one tripeptide were determined in the crystal state by x-ray diffraction. Moreover, the solution preferred conformations of these peptides were assessed by Fourier transform infrared absorption and (1)H-NMR techniques. A comparison with the known structural tendencies of the strictly related C(alpha,alpha)-disubstituted glycyl residues 1-aminocyclopentane-1-carboxylic acid and 9-aminofluorene-9-carboxylic acid is made, and the implications for the use of the 9-amino-4,5-diazafluorene-9-carboxylic acid residue in conformationally constrained analogs of bioactive peptides are briefly examined. A spectroscopic (uv absorption, fluorescence, CD) characterization of this novel heteroaromatic C(alpha,alpha)-disubstituted glycine is also reported. Finally, preliminary conformational data and membrane activity measurements are discussed for an analog of the lipopeptaibol antibiotic [L-Leu(11)-OMe] trichogin GA IV in which a 9-amino-4,5-diazafluorene-9-carboxylic acid residue was synthetically incorporated in position 1 (replacing the original Aib residue).