Synthesis of peptidomimetics: An evaluation of the p-nitrophenyl carbamate of ethylenediamine

Summary The application of p-nitrophenyl carbamate of Boc-ethylenediamine for the solid-phase synthesis of peptidomimetrics was examined. The per step yield of coupling was estimated using mass spectrometry, based on the repeated coupling of the same monomer in the synthesis of alkylurea oligomers. Introduction of the urea moiety at the terminus of the chain adjacent to the resin was accomplished by the use of the BHA resin in the assembly of the chain and liquid HF in the cleavage step. In addition, an alkylurea oligomer was treated with bis(p-nitrophenyl) carbonate followed by ammonolysis in order to obtain a urea moiety at the terminus distant from the resin. Aside from the expected oligomer, a product was obtained in which the terminal alkylurea had undergone cyclization. Finally, four peptidomimetics, analogues of 1–4 enkephalin fragment, containing up to four alkylurea units instead of glycine residues, were synthesized. Two of these peptidomimetics were examined for opioid activity and turned out to be active in the guinea pig ileum assay.     

p-Nitrophenoxycarbonyl derivatives of Boc-protected diaminoalkanes in the synthesis of enkephalin peptidomimetics.

The synthesis of p-nitrophenoxycarbonyl derivatives of 1-Boc-1,2-diaminoethane, 1-Boc-1,3-diaminopropane and 1-Boc-1,4-diaminobutane is described. These derivatives were used to synthesize five peptidomimetics, analogues of enkephalin, containing alkylurea units inside the peptide chain and at the C-terminal. All syntheses were carried out in solid phase on MBHA resin. Peptidomimetics with alkylurea units inserted into the peptide chain were synthesized using the standard method employing the Boc-strategy, with TFA deprotection and HF cleavage. The analogue containing a C-terminal alkylurea unit was synthesized using the Boc-strategy, with HCl/dioxane deprotection and TFA cleavage. All of the analogues were examined for opioid activity in GPI and MVD assays. The activity of the analogue containing a C-terminal alkylurea unit was comparable to that of [Leu5]-enkephalin, while the other analogues were less active.     

A Dde resin based strategy for inverse solid-phase synthesis of amino terminated peptides, peptide mimetics and protected peptide intermediates.

This report describes a Dde resin based attachment strategy for inverse solid-phase peptide synthesis (ISPPS). This attachment strategy can be used for the synthesis of amino terminated peptides with side chains and the carboxyl terminus either protected or deprotected. Amino acid t-butyl esters were attached through their free amino group to the Dde resin. The t-butyl carboxyl protecting group was removed by 50% TFA, and inverse peptide synthesis cycles performed using an HATU/TMP based coupling method. Protected peptides were cleaved from the resin with dilute hydrazine. Side chain protecting groups could then be removed by treatment with TFMSA/TFA. The potential of this approach was demonstrated by the synthesis of several short protected and unprotected peptides in good yield and with low epimerization. Its potential for peptide mimetic synthesis was demonstrated by the synthesis of two peptide trifluoromethylketones.     

Binding of alkylurea inhibitors to epoxide hydrolase implicates active site tyrosines in substrate activation

The structures of two alkylurea inhibitors complexed with murine soluble epoxide hydrolase have been determined by x-ray crystallographic methods. The alkyl substituents of each inhibitor make extensive hydrophobic contacts in the soluble epoxide hydrolase active site, and each urea carbonyl oxygen accepts hydrogen bonds from the phenolic hydroxyl groups of Tyr(381) and Tyr(465). These hydrogen bond interactions suggest that Tyr(381) and/or Tyr(465) are general acid catalysts that facilitate epoxide ring opening in the first step of the hydrolysis reaction; Tyr(465) is highly conserved among all epoxide hydrolases, and Tyr(381) is conserved among the soluble epoxide hydrolases. In one enzyme-inhibitor complex, the urea carbonyl oxygen additionally interacts with Gln(382). If a comparable interaction occurs in catalysis, then Gln(382) may provide electrostatic stabilization of partial negative charge on the epoxide oxygen. The carboxylate side chain of Asp(333) accepts a hydrogen bond from one of the urea NH groups in each enzyme-inhibitor complex. Because Asp(333) is the catalytic nucleophile, its interaction with the partial positive charge on the urea NH group mimics its approach toward the partial positive charge on the electrophilic carbon of an epoxide substrate. Accordingly, alkylurea inhibitors mimic features encountered in the reaction coordinate of epoxide ring opening, and a structure-based mechanism is proposed for leukotoxin epoxide hydrolysis.     

A convenient method for europium‐labeling of a recombinant chimeric relaxin family peptide R3/I5 for receptor‐binding assays

Relaxin family peptides have important biological functions, and so far, four G‐protein‐coupled receptors have been identified as their receptors (RXFP1–4). A chimeric relaxin family peptide R3/I5, containing the B‐chain of relaxin‐3 and the A‐chain of INSL5, is a selective agonist for both RXFP3 and RXFP4. In a previous study, europium‐labeled R3/I5, as a nonradioactive and low‐background receptor‐binding tracer, was prepared through a chemical synthesis approach. In the present study, we established a convenient alternative approach for preparing the europium‐labeled R3/I5 tracer based on a recombinant R3/I5 designed to carry a solubilizing tag at the A‐chain N‐terminus and a pyroglutamate residue at the B‐chain N‐terminus. Because of the presence of a single primary amine moiety, the recombinant R3/I5 peptide was site‐specifically mono‐labeled at the A‐chain N‐terminus by a diethylenetriaminepentaacetic acid/europium moiety through a convenient one‐step procedure. The diethylenetriaminepentaacetic acid/Eu³⁺‐labeled R3/I5 bound both receptors RXFP3 and RXFP4 with high binding affinities and low nonspecific binding. Thus, we have presented a valuable nonradioactive tracer for future interaction studies on RXFP3 and RXFP4 with various natural or designed ligands. The present approach could also be adapted for preparing and labeling of other chimeric relaxin family peptides. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Interactions of myoglobin with urea and some alkylureas. I. Solvation in urea and alkylurea solutions

The interactions of myoglobin with urea, methyl-, N,N'-dimethyl- and ethylurea in aqueous solutions were studied by density measurements. From the densities at constant chemical potential and constant molality, the partial specific volumes of myoglobin in these solutions as well as the extent of preferential binding of urea and alkylurea to myoglobin were determined. It has been found that water and not the denaturant is preferentially bound in urea solutions and alkylurea solutions up to 4 M so that the Gibbs free energy of myoglobin, i.e., its chemical potential in a denaturant solution, is larger than in water. This behavior of myoglobin is different from that of other globular proteins for which preferential binding of urea has been found. It appears that preferential hydration of myoglobin is due to its high content of ionic groups.     

The precursor strategy: terminus methoxyoxalamido modifiers for single and multiple functionalization of oligodeoxyribonucleotides

Synthesis of new terminus modifiers, bearing, along with a phosphoramidite moiety, one, two or four methoxyoxalamido (MOX) precursor groups, is described. These modifiers are introduced onto the 5′-end of a synthetic oligodeoxyribonucleotide as the last step of an automated synthesis to form the MOX precursor oligonucleotide. The MOX groups are then post-synthetically derivatized with an appropriate primary amine to construct a 5′-modified oligonucleotide. The efficiency and simplicity of the novel modifying strategy were demonstrated in the synthesis of a number of 5′-functionalized oligonucleotides.     

Solid support-dependent alkylation of tryptophan residues in SPPS using a 2-methoxybenzyl alcohol-based linker

Summary Several side reactions can be encountered in the synthesis of Trp-containing peptides, due to molecular species originating from side chain-protecting groups or from the linker during acidolytic cleavage of the peptide from the resin. The linker can be the source of both alkylation in solution of the indole moiety of the tryptophan side chain and permanent readdition of the cleaved peptide to the resin. We report that both these reactions occur at a high level during the synthesis of Trp-containing peptides on a PEG-PS resin containing a 2-methoxybenzyl alcohol-based linker, in spite of the presence of suitable scavengers in the TFA-based cleavage mixture. Both side reactions are efficiently prevented by the use of a protected analogue of tryptophan, namely N^im-Boc-Trp, previously reported for the synthesis of peptides containing tryptophan and arginine residues.     

Solid phase synthesis of an amphiphilic peptide modified for immobilisation at the C-terminus

The solid phase peptide synthesis (SPPS) of the amphiphilic peptide Ac-(Leu-Ala-Arg-Leu)(3)-linker, which is modified at the C-terminus with 1,8-diamino-3,6-dioxaoctane as linker moiety, has been investigated. Two different approaches that allow for the synthesis of C-terminally modified, side-chain protected peptides were examined. The solid phase peptide synthesis using aliphatic safety-catch resin followed by activation and aminolysis with the mono-Boc protected linker was compared with the synthesis on 1,8-diamino-3,6-dioxaoctane loaded 2-chlorotrityl resin.     

Thermodynamics of denaturation of α-chymotrypsinogen A in aqueous urea and alkylurea solutions

The effects of pH, urea, and alkylureas on the thermal stability ofα-chymotrypsinogen A (α-ctg A) have been investigated by differential scanning calorimetry (DSC) and UV spectroscopy. Heat capacity changes and enthalpies of transition ofα-ctg A in the presence of urea and alkylureas were measured at the transition temperature. Using these data, the corresponding Gibbs free energies, enthalpies, and entropies of denaturation at 25°C were calculated. Comparison of these values shows that at 25°C denaturation with urea is characterized by a significantly smaller enthalpy and entropy of denaturation. At all denaturant concentrations the enthalpy term slightly dominates the entropy term in the Gibbs free energy function. The most obvious effect of alkylureas was lowering of the temperature of transition, which was increasing with alkylurea concentration and the size of alkyl chain. Destabilization of the folded protein in the presence of alkylureas appears to be primarily the result of the weakening of hydrophobic interactions due to diminished solvent ordering around the protein molecules. At pH lower than 2.0,α-ctg A still exists in a very stable form, probably the acid-denatured form (A-form).     

Solid-phase peptide synthesis in highly loaded conditions

The use of very highly substituted resins has been avoided for peptide synthesis due to the aggravation of chain-chain interactions within beads. To better evaluate this problem, a combined solvation-peptide synthesis approach was herein developed taking as models, several peptide-resins and with peptide contents values increasing up to near 85%. Influence of peptide sequence and loading to solvation characteristics of these compounds was observed. Moreover, chain-chain distance and chain concentration within the bead were also calculated in different loaded conditions. Of note, a severe shrinking of beads occurred during the α-amine deprotonation step only when in heavily loaded resins, thus suggesting the need for the modification of the solvent system at this step. Finally, the yields of different syntheses in low and heavily loaded conditions were comparable, thus indicating the feasibility of applying this latter “prohibitive” chemical synthesis protocol. We thought these results might be basically credited to the possibility, without the need of increasing molar excess of reactants, of carrying out the coupling reaction in higher concentration of reactants - near three to seven folds - favored by the use of smaller amount of resin. Additionally, the alteration in the solvent system at the α-amine deprotonation step might be also improving the peptide synthesis when in heavily loaded experimental protocol.     

Large fragments of nef-protein and gp110 envelope glycoprotein from HIV-1. Synthesis, CD analysis and immunoreactivity

Chemical synthesis of large peptide fragments (from 18 to 66 amino acid residues long) of the gp110 envelope glycoprotein and of nef-protein from HIV-1 was achieved by the solid phase method. Stepwise assembling of the peptide chains was carried out automatically on 4-(oxymethyl)-phenylacetamidomethyl resin using the N-alpha-butyloxycarbonyl amino acids with benzyl-based side chain protecting groups. Two elongation protocols were used depending on the peptide chain length: a standard cycle, mainly characterized by a single coupling step (Boc-amino acid symmetrical anhydride in dimethylformamide), and an optimized one for large peptides, based on a double coupling strategy (Boc-amino acid symmetrical anhydride first in dimethylformamide, then in dichloromethane). Final cleavage of the peptide from the solid support was carried out by anhydrous hydrogen fluoride and crude peptides were purified by C18 reverse phase medium pressure liquid chromatography after molecular filtration. Characterization of the purified peptides was done by analytical HPLC, amino acid content determination, and circular dichroism analysis both in polar (H2O) and in non-polar (TFE) environments. Immunoreactivity of anti-nef positive sera from HIV-1 infected patients by ELISA with the synthetic peptides was investigated. The results showed four major antigenic regions of nef-protein and mainly the immunodominance of the N- and C-termini of the molecule. Several of these peptides should prove to be useful for both diagnosis and vaccination purposes.     

The control of chondroitin sulphate biosynthesis and its influence on the structure of cartilage proteoglycans.

Chondroitin sulphate synthesis on proteoglycans was decreased in rat chondrosarcoma cell cultures in the presence of cycloheximide (0.1-1.0 muM) or p-nitrophenyl beta-D-xyloside (50 microM). In the presence of cycloheximide the proteoglycan monomer was of larger size, the chondroitin sulphate chains were increased in length, but a similar number of chains was attached to each proteoglycan and the size of the core protein was unaltered. In the presence of p-nitrophenyl beta-D-xyloside (50 microM), chondroitin sulphate synthesis was increased (by 60-80%), but the incorporation into proteoglycans was decreased (by 70%). The chondroitin sulphate chains were of shorter length than in control cultured and the number of chains attached to each proteoglycan was decreased. In cultures with cycloheximide or actinomycin D the synthesis of chondroitin sulphate was less inhibited on beta-xyloside than on endogenous proteoglycan. When the rate of chondroitin sulphate synthesis was decreased by lowering the temperature of cultures, the chains synthesized at 22 and 4 degrees C were much longer than at 37 degrees C, but in the presence of p-nitrophenyl beta-D-xyloside the chains were of the same length at all three temperatures. A model of chain elongation is thus proposed in which the rate of chain synthesis is determined by the concentration of xylosyl acceptor and the length of the chains is determined by the ratio of elongation activity to xylosyl-acceptor concentration.     

Effective chemoenzymatic synthesis of p-aminophenyl glycosides of sialyl N-acetyllactosaminide and analysis of their interactions with lectins

A convenient chemoenzymatic procedure for the synthesis of p-aminophenyl glycosides of sialyl N-acetyllactosaminide has been developed from p-nitrophenyl N-acetyl-beta-D-glucosaminide as starting material through three steps: synthesis of p-nitrophenyl N-acetyllactosaminide with beta-D-galactosidase, chemical reduction of the p-nitrophenyl group, and sialylation with sialyltransferase. The p-aminophenyl glycosides were then successfully biotin-labeled through the coupling with N-(+)-biotinyl-6-aminohexanoic acid to afford biotinylated oligosaccharides with an aminohexanosyl group and phenyl group as the spacers between the biotin and glycan. Furthermore, the biotin-labeled sugars were shown to be useful for immobilization and assay of the carbohydrate-lectin interactions by an optical biosensor based on surface plasmon resonance.     

A straightforward route to enantiopure 2-substituted-3,4-dehydro-β-proline via ring closing metathesis

The synthesis of unusual cyclic amino acids, that may be envisaged as proline analogs, is an area of great interest for their potential applications as scaffolds for the design of bioactive peptidomimetics or units for the creation of novel foldamers. We have carried out the preparation of cyclic dehydro-β-amino acids starting from allylic carbonates via a two-step allylic amination/ring closing metathesis (RCM) protocol. The introduction of the allylamino moiety has been carried out either without a catalyst, through an S_N2′ reaction, or in the presence of iridium complexes. The backbone of the allylamino intermediates contains two unsaturations, thus suggesting that RCM could be a valuable tool for the preparation of dihydropyrrole scaffolds. A similar reaction has been already reported in the literature for racemic aromatic-substituted substrates, but no examples of enantiopure derivatives bearing aliphatic chains have been reported. The reaction was optimized by testing different Grubbs’ catalysts and carbamate nitrogen protecting groups. Moreover, in view of a future application of these dehydro-β-amino acids as central core of peptidomimetics, the malonate chain was also used to protect nitrogen prior to RCM.     

Poly-lysine peptidomimetics having potent antimicrobial activity without hemolytic activity

Diversity of sequence and structure in naturally occurring antimicrobial peptides (AMPs) limits their intensive structure–activity relationship (SAR) study. In contrast, peptidomimetics have several advantages compared to naturally occurring peptide in terms of simple structure, convenient to analog synthesis, rapid elucidation of optimal physiochemical properties and low-cost synthesis. In search of short antimicrobial peptides using peptidomimetics, which provide facile access to identify the key factors involving in the destruction of pathogens through SAR study, a series of simple and short peptidomimetics consisting of multi-Lys residues and lipophilic moiety have been prepared and found to be active against several Gram-negative and Gram-positive bacteria containing methicillin-resistant Staphylococcus aureus (MRSA) without hemolytic activity. Based on the SAR studies, we found that hydrophobicity, +5 charges of multiple Lys residues, hydrocarbon tail lengths and cyclohexyl group were crucial for antimicrobial activity. Furthermore, membrane depolarization, dye leakage, inner membrane permeability and time-killing kinetics revealed that bacterial-killing mechanism of our peptidomimetics is different from the membrane-targeting AMPs (e. g. melittin and SMAP-29) and implied our peptidomimetics might kill bacteria via the intracellular-targeting mechanism as done by buforin-2.     

Synthetic fragments and analogues of elastin. I. The synthesis

The synthesis of some repetitive sequences of elastin and their simplified analogues, all comprising the structural unit Gly-X-Gly (X = Val, Leu, Ala), is described. In particular, the following peptides and polypeptides were synthesized and characterized: Boc-Gly-Val-Gly-Gly-Leu-OMe, Boc-Gly-Leu-Gly-Gly-Val-OMe, Boc-(Gly-Val-Gly-Gly-Leu)2-OMe, Boc-(Gly-Val-Gly-Gly-Leu)3-OMe, Boc-Gly-Val-Gly-Gly-OEt, Boc-Leu-Gly-Gly-Leu-OMe, Boc-Val-Gly-Gly-Val-OMe, poly(Ala-Gly-Gly), poly(Val-Gly-Gly), and poly(Leu-Gly-Gly). In every case, the synthesis was accomplished by classical procedures in solution, by using the p-nitrophenyl ester method for the polycondensation step, and the mixed anhydride or the azide methods for the coupling steps.     

Synthesis and serological characterization of L-glycero-alpha-D-manno-heptopyranose-containing di- and tri-saccharides of the non-reducing terminus of the Escherichia coli K-12 LPS core oligosaccharide

Synthesis of the title trisaccharide was accomplished by sugar chain extension starting from the non-reducing terminus: coupling of Glcp NAc with LD-Hepp, then adding Glcp-OAll. An alternative route started from the reducing end: coupling of LD-Hepp with Glcp-OAll, then addition of Glcp NAc. In the synthesis of the title disaccharide a modification of the first approach was employed. The allyl glycosides were coupled with cysteamine, activated with thiophosgene and conjugated to bovine serum albumin (BSA). The neoglycoconjugates obtained were used in immunochemical studies of monoclonal and polyclonal antibodies directed against Escherichia coli K-12 lipopolysaccharide.     

Solid-phase synthesis of peptides containing phosphoserine using phosphate tert.-butyl protecting group

In this paper, we report the solid-phase synthesis of peptides containing O-phosphonoserine using BOP as coupling reagent. Commercially available Fmoc amino-acids linked to p-alkoxybenzyl resin were used in the first step and Alloc amino acids in the following. Alloc group was removed by catalytic hydrostannolytic cleavage. Acid-labile side-chain protecting groups (including phosphate residue) were used. Thus, both removal of side-chain protecting groups and cleavage of the phosphopeptide from the resin were achieved in one step by treatment with TFA. Alloc serine was phosphorylated by the phosphoramidite method. This strategy enables the preparation of peptides with selectively phosphorylated residue and overcomes problems due to repetitive treatments with TFA and final cleavage with HF.