A new reagent for the mediation of amide bond formation in peptide synthesis.

The potential application of 1-oxo-1-chlorophospholane (5) as a novel reagent for the in situ activation of Nα -protected amino acids for use in peptide bond forming reactions has been examined. Wherever possible, 32.4Mhz ³¹P nuclear magnetic resonance (n.m.r.) spectroscopy was employed to follow both the formation of the intermediate phospholanic-carboxylic mixed anhydride and the subsequent aminolysis reaction.     

Charge relocation in cationic diene complexes: formation of an iminium-substituted allyl complex and its deprotonation to an enamine

The reaction of [Mo(NCME)₂(CO)₂(η⁵-C₉H₇)][BF₄] (1) with 1-dimethylaminocyclohexa-1,3-diene affords the cationic η³-allyl complex [Mo(η³-C₆H₇NMe₂)(CO)₂- (η⁵-C₉H₇)][BF₄] (3), in which the positive charge is located at an exocyclic iminium centre. Addition of Li[N(SiMe₃)₂] to 3 results in deprotonation and the formation of an enamine species [Mo(η³-C₆H₆NMe₂)(CO)₂(η⁵-C₉H₇)] (8), which undergoes stereofacial attack upon treatment with electrophiles.     

Oligonucleotides with 2'-O-carboxymethyl group: synthesis and 2'-conjugation via amide bond formation on solid phase

An efficient method for synthesis of oligonucleotide 2'-conjugates via amide bond formation on solid phase is described. Protected oligonucleotides containing a 2'-O-carboxymethyl group were obtained by use of a novel uridine 3'phosphoramidite, where the carboxylic acid moiety was introduced as its allyl ester. This protecting group is stable to the conditions used in solid-phase oligonucleotide assembly, but easily removed by Pd(0) and morpholine treatment. 2'-O-Carboxymethylated oligonucleotides were then efficiently conjugated on a solid support under normal peptide coupling conditions to various amines or to the N-termini of small peptides to give products of high purity in good yield. The method is well suited in principle for the preparation of peptide-oligonucleotide conjugates containing an amide linkage between the 2'-position of an oligonucleotide and the N-terminus of a peptide.     

Light-activated hydrogel formation via the triggered folding and self-assembly of a designed peptide

Photopolymerization can be used to construct materials with precise temporal and spatial resolution. Applications such as tissue engineering, drug delivery, the fabrication of microfluidic devices and the preparation of high-density cell arrays employ hydrogel materials that are often prepared by this technique. Current photopolymerization strategies used to prepare hydrogels employ photoinitiators, many of which are cytotoxic and require large macromolecular precursors that need to be functionalized with moieties capable of undergoing radical cross-linking reactions. We have developed a simple light-activated hydrogelation system that employs a designed peptide whose ability to self-assemble into hydrogel material is dependent on its intramolecular folded conformational state. An iterative design strategy afforded MAX7CNB, a photocaged peptide that, when dissolved in aqueous medium, remains unfolded and unable to self-assemble; a 2 wt % solution of freely soluble unfolded peptide is stable to ambient light and has the viscosity of water. Irradiation of the solution (260 < lambda < 360 nm) releases the photocage and triggers peptide folding to produce amphiphilic beta-hairpins that self-assemble into viscoelastic hydrogel material. Circular dichroic (CD) spectroscopy supports this folding and self-assembly mechanism, and oscillatory rheology shows that the resulting hydrogel is mechanically rigid (G' = 1000 Pa). Laser scanning confocal microscopy imaging of NIH 3T3 fibroblasts seeded onto the gel indicates that the gel surface is noncytotoxic, conducive to cell adhesion, and allows cell migration. Lastly, thymidine incorporation assays show that cells seeded onto decaged hydrogel proliferate at a rate equivalent to cells seeded onto a tissue culture-treated polystyrene control surface.     

Kinetic evidence that cysteine reacts with dopaminoquinone via reversible adduct formation to yield 5-cysteinyl-dopamine: an important precursor of neuromelanin

The reaction of cysteine (cys) with dopaminoquinone (DQ) to form (mainly) 5-cysteinyl-dopamine (5-cys-DA) is of interest because it is known to play a role in the production of melanin in the mammalian brain. To gain insight into this important reaction, an in vitro detailed kinetic study was undertaken. It has been established that cys reacts with DQ via the initial reversible formation of an intermediate adduct or complex and that this adduct then decomposes to form 5-cys-DA. A little 2-cys-DA, is almost certainly formed at the same time but its presence could not be kinetically investigated. Clarification of the kinetic data was aided by following the reaction of DQ with a cys analogue, mercaptoacetic acid (maa). Maa was found to react in a similar fashion, but also forms, reversibly, a bis-complex. This bis-complex, 2,5-(maa)(2)-dopaminoquinone, is in equilibrium with the di-protonated compound but neither of these species reacts further over the timescale employed in these kinetic studies. Equilibrium constants and first-order rate constants have been extracted from the data and the cys complex is found to be weaker than its maa analogue by an order of magnitude (K(cys)=(1.09 +/- 0.02 x 10(-3); K(1,maa)=(7.45 +/- 0.11 x 10(-3)). (Note that the possibility that cys also forms a bis-complex at much higher cys concentrations cannot be excluded.) The rates of decomposition differ markedly-the cys complex has the value k(cys)= 1830 +/- 50 s(-1) whereas the rate constant for the decomposition of the maa complex is k(maa)= 69.3 +/- 0.02 s(-1) and we attribute this difference to the effect of the positive charge carried by the amino-group on cys. Finally, the constants obtained are used to compare the reactivity of thiol addition with ring cyclization (U. El-Ayaan, E. Herlinger, R. F. Jameson, and W. Linert, J. Chem. Soc., Dalton Trans., 1997, 2813-2818) and we show how this has important implications concerning the production of neuromelanin.     

Investigation of aromatic-backbone amide interactions in the model peptide acetyl-Phe-Gly-Gly-N-methyl amide using molecular dynamics simulations and protein database search.

Weakly polar interactions between the side-chain aromatic rings and hydrogens of backbone amides (Ar-HN) are found in unique conformational regions. To characterize these conformational regions and to elucidate factors that determine the conformation of the Ar-HN interactions, four 4-ns molecular dynamics simulations were performed using four different low-energy conformations obtained from simulated annealing and one extended conformation of the model tripeptide Ac-Phe-Gly-Gly-NH-CH(3) as starting structures. The Ar(i)-HN(i+1) interactions were 4 times more frequent than were Ar(i)-HN(i+2) interactions. Half of the conformations with Ar(i)-HN(i+2) interactions also contained an Ar(i)-HN(i+1) interaction. The solvent access surface area of the Phe side chain and of the amide groups of Phe1, Gly2, and Gly3 involved in Ar-HN interactions was significantly smaller than in residues not involved in such interactions. The number of hydrogen bonds between the solvent and Phe1, Gly2, and Gly3 amide groups was also lower in conformations with Ar-HN interactions. For each trajectory, structures that contained Ar(i)-HN(i), Ar(i)-HN(i+1), and Ar(i)-HN(i+2) interactions were clustered on the basis of similarity of selected torsion angles. Attraction energies between the aromatic ring and the backbone amide in representative conformations of the clusters ranged from -1.98 to -9.24 kJ mol(-1) when an Ar-HN interaction was present. The most representative conformations from the largest clusters matched well with the conformations from the Protein Data Bank of Phe-Gly-Gly protein fragments containing Ar-HN interactions.     

Enantioselective alkylation of lactams and lactones via lithium enolate formation using a chiral tetradentate lithium amide in the presence of lithium bromide

Enantioselective alkylation of lactams and lactones can be realized up to 98% ee by deprotonation with a chiral tetradentate lithium amide (4b) in the presence of lithium bromide, and subsequent alkylation with active alkylating agents in non-chelating solvents.     

Hydrogen-bonded benzylidenebenzohydrazide macrocycles and oligomers: testing the robust capacity of an amide chain in promoting the formation of vesicles

This Letter describes 2-(2-(dioctylamino)-2-oxoethyl-amino)-2-oxoethoxyl (DOAOE)-tuned self-assembly of vesicles from rigid macrocycles and foldamer-like oligomers. The molecules are prepared through the formation of reversible hydrazone bonds from aldehyde and benzo-hydrazide precursors, which are further facilitated by intramolecular N?H-O hydrogen bonding. SEM, AFM, and fluorescent encapsulation studies reveal that the molecules all self-assemble into vesicular structures in methanol, while similar molecules bearing the triethylene glycol or n-decyl chains do not. The results illustrate that DOAOE is robust in promoting the formation of vesicles for aromatic systems in polar solvents.     

Influence of an amide group in methyl octadecanoates on the monolayer stability

The influence of a hydrogen bond donor and acceptor in the hydrophobic part of an amphiphile on the monolayer stability at the air/water interface is investigated. For that purpose, the amide group is integrated into the alkyl chain. Eight methyl octadecanoates have been synthesized with the amide group in two orientations and in different positions of the alkyl chain, namely, CH3O2C(CH2)m NHCO(CH2)n CH3 (n + m = 14): 1 (m = 1), 3 (m = 2), 5 (m = 3), 7 (m = 14); and CH3O2C(CH2)m CONH(CH2)n CH3: 2 (m = 1), 4 (m = 2), 6 (m = 3), 8 (m = 14). The monolayers have been characterized by their pi/A isotherms, their temperature dependence and Brewster angle microscopy (BAM). Amphiphile 1 with the amide group close to the ester group (m = 1) behaves like an unsubstituted fatty acid ester, while 3, 5, and 7, with the amide group in an intermediate and terminal position, exhibit a two-phase region. The amphiphiles 2, 4, 6, and 8, with a reversed orientation of the amide group, all exhibit a two-phase region with higher plateau pressures and lower collapse pressures than those of 1, 3, 5, and 7. For 7 and 8, domains of the liquid condensed (LC) phase are visualized by BAM in the two-phase region. The liquid expanded (LE)/LC-phase transitions are all exothermic with enthalpies deltaH ranging from -31 to -12 kJ/mol. Comparison with other bipolar amphiphiles indicates that the LC phase is better stabilized by the hydroxy and dihydroxy groups than by the amide group. For model compounds of 1-4, optimized conformers in the LE and LC phases have been determined by density functional theory (DFT) calculations.     

Activation of the amide group by acylation Hydroxy- and aminoacyl incorporation in peptide systems

A new reaction, the hydroxy- and aminoacyl incorporation in aliphatic and alicyclic N-hydrox-(amino)acl amides is described in detail. The reaction affording linear or cyclic peptides and depsipeptides proceeds via formation of cyclols. Its course depends on the nucleophilicity of the HO- and NH₂-groups, the electrophilicity of the amide carbonyl and, with cyclic amides, on the size of the ring. The cyclols which sometimes can be isolated display a number of unique properties, in particular, a tendency to undergo transformation into acylamides or macrocycles. Hydroxy- and aminoacyl incorporation is significant in the synthesis of peptides and depsipeptides. For example, it has been utilized in the synthesis of the antibiotic serratomolide and its analogues. A discussion of the biochemical and biogenetic implications of the reaction is given.     

Quantum-mechanical study on the mechanism of peptide bond formation in the ribosome

Ribosomes transform the genetic information encoded within genes into proteins. In recent years, there has been much progress in the study of this complex molecular machine, but the mechanism of peptide bond formation and the origin of the catalytic power of this ancient enzymatic system are still an unsolved puzzle. A quantum-mechanical study of different possible mechanisms of peptide synthesis in the ribosome has been carried out using the M06-2X density functional. The uncatalyzed processes in solution have been treated with the SMD solvation model. Concerted and two-step mechanisms have been explored. Three main points suggested in this work deserve to be deeply analyzed. First, no zwitterionic intermediates are found when the process takes place in the ribosome. Second, the proton shuttle mechanism is suggested to be efficient only through the participation of the A2451 2'-OH and two crystallographic water molecules. Finally, the mechanisms in solution and in the ribosome are very different, and this difference may help us to understand the origin of the efficient catalytic role played by the ribosome.     

Promotion of microvasculature formation in alginate composite hydrogels by an immobilized peptide GYIGSRG

The ability to create artificial thick tissues is a major tissue engineering problem,requiring the formation of a suitable vascular supply.In this work we examined the ability of inducing angiogenesis in a bioactive hydrogel.GYIGSRG(NH 2-Gly-Tyr-IleGly-Ser-Arg-Gly-COOH,GG) has been conjugated to sodium alginate(ALG) to synthesize a biological active biomaterial ALG-GG.The product was characterized by 1 H NMR,FT-IR and elemental analysis.A series of CaCO 3 /ALG-GG composite hydrogels were prepared by crosslinking ALG-GG with D-glucono-lactone/calcium carbonate(GDL/CaCO 3) in different molar ratios.The mechanical strength and swelling ratio of the composite hydrogels were studied.The results revealed that both of them can be regulated under different preparation conditions.Then,CaCO 3 /ALG-GG composite hydrogel was implanted in vivo to study the ability to induce angiogenesis.The results demonstrated that ALG-GG composited hydrogel can induce angiogenesis significantly compared with non-modified ALG group,and it may be valuable in the development of thick tissue engineering scaffold.     

On the mechanism of formation of dimeric and reduced products from an α-halo amide with sodium methoxide

Treatment of 2-bromo-N,N-dimethyl-2,2-diphenylacetamide 1 with sodium methoxide in 2,2-dimethoxypropane furnishes mixtures of the reduced product 2 and the dimer 5. Crossing experiments have shown that 2 is not a precursor of 5, supporting thereby the S_RN1 mechanism for the formation of both 5 and 2.     

Pairwise coupling in an Arg-Phe-Met triplet stabilizes alpha-helical peptide via shared rotamer preferences

The hydrophobic Arg-Phe and Phe-Met side chain interactions stabilize the alpha-helix by -0.29 and -0.59 kcal/mol, respectively, when placed i, i + 4 in an alanine-based peptide. When both interactions are present simultaneously, however, they stabilize the helix by an additional -0.75 kcal/mol, nearly as much as the sum of its parts. We attribute this coupling to a shared rotamer preference, as the central Phe is t in both bonds. The energetic cost of restricting the Phe residue into a t conformation is only paid once in the triplet, rather than twice when the interactions are separate. Coupling is thus demonstrated to have large effects on protein stability.     

Boron-capped tris(glyoximato) cobalt clathrochelate as a precursor for the electrodeposition of nanoparticles catalyzing H2 evolution in water

Electrochemical investigation of a boron-capped tris(glyoximato)cobalt clathrochelate complex in the presence of acid reveals that the catalytic activity toward hydrogen evolution results from an electrodeposition of cobalt-containing nanoparticles on the electrode surface at a modest cathodic potential. The deposited particles act as remarkably active catalysts for H(2) production in water at pH 7.