COMU: A third generation of uronium‐type coupling reagents

COMU is a third generation of uronium‐type coupling reagent based on ethyl 2‐cyano‐2‐(hydroxyimino)acetate (Oxyma) as well as a morpholino carbon skeleton. The presence of the morpholino group has a marked influence on the solubility, stability and reactivity of the reagent. COMU performed extremely well in the presence of only 1 equiv. of base, thereby confirming the effect of the hydrogen bond acceptor in the reaction. The by‐products of COMU are water soluble and easily removed, making it an excellent choice of coupling reagent for solution‐phase peptide synthesis. Finally, COMU shows a less hazardous safety profile than benzotriazole‐based reagents, such as HATU and HBTU, which in addition exhibit unpredictable autocatalytic decompositions and therefore a higher risk of explosion. Furthermore, in contrast to benzotriazole‐based reagents, COMU is significantly less likely to cause allergic reaction. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Fast conventional Fmoc solid-phase peptide synthesis with HCTU.

1H-Benzotriazolium 1-[bis(dimethyl-amino)methylene]-5-chloro-hexafluorophosphate (1-),3-oxide (HCTU) is a nontoxic, nonirritating and noncorrosive coupling reagent. Seven biologically active peptides (GHRP-6, (65-74)ACP, oxytocin, G-LHRH, C-peptide, hAmylin(1-37), and beta-amyloid(1-42)) were synthesized with reaction times reduced to deprotection times of 3 min or less and coupling times of 5 min or less using HCTU as the coupling reagent. Expensive coupling reagents or special techniques were not used. Total peptide synthesis times were dramatically reduced by as much as 42.5 h (1.8 days) without reducing the crude peptide purities. It was shown that HCTU can be used as an affordable, efficient coupling reagent for fast Fmoc solid-phase peptide synthesis.     

The nature of functional groups in the active center of antitumor glutamin-(asparagin-)ase

The effect of two reagents on glutamin (asparagin) ase from Pseudomonas aurantiaca-548 has been studied. 2,3-butanedione which modified arginine residues was ineffective for the inactivation of the enzyme. The enzyme was completely inactivated in the presence of N-ethyl-5-phenylisoxazolium-3'-sulfonate (Woodward's reagent K). The effects of pH, reagent concentration, competitive inhibitors and their analogues on the rate or degree of enzyme inactivation were studied. The experimental results suggest that the carboxyl groups localized at the active site of glutamin (asparagin) ase are probably essential for the substrate binding.     

Easy parallel screening of reagent stability,quality control,and metrology in solid phase peptide synthesis (SPPS) and peptide couplings for microarrays

Evaluating the stability of coupling reagents, quality control (QC), and surface functionalization metrology are all critical to the production of high quality peptide microarrays. We describe a broadly applicable screening technique for evaluating the fidelity of solid phase peptide synthesis (SPPS), the stability of activation/coupling reagents, and a microarray surface metrology tool. This technique was used to assess the stability of the activation reagent 1‐{[1‐(Cyano‐2‐ethoxy‐2‐oxo‐ethylidenaminooxy)dimethylamino‐morpholinomethylene]}methaneaminiumHexafluorophosphate (COMU) (Sigma‐Aldrich, St. Louis, MO, USA) by SPPS of Leu‐Enkephalin (YGGFL) or the coupling of commercially synthesized YGGFL peptides to (3‐aminopropyl)triethyoxysilane‐modified glass surfaces. Coupling efficiency was quantitated by fluorescence signaling based on immunoreactivity of the YGGFL motif. It was concluded that COMU solutions should be prepared fresh and used within 5 h when stored at ~23 °C and not beyond 24 h if stored refrigerated, both in closed containers. Caveats to gauging COMU stability by absorption spectroscopy are discussed. Commercial YGGFL peptides needed independent QC, due to immunoreactivity variations for the same sequence synthesized by different vendors. This technique is useful in evaluating the stability of other activation/coupling reagents besides COMU and as a metrology tool for SPPS and peptide microarrays. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Search for optimal coupling reagent in multiple peptide synthesizer

Ten different coupling reagents and their combinations were tested in parallel in the synthesis of four model peptide sequences. Significant differences were found between uronium and phosphonium salt-based reagents and carbodiimide. Diisopropylcarbodiimide was identified as an optimal reagent based on the purity of the product, stability of the reagent, and convenience of handling on plate-based multiple parallel centrifugation synthesizer.     

Enantiomeric impurities in chiral catalysts,auxiliaries, and synthons used in enantioselective syntheses. Part 5

The enantiomeric excess of chiral starting materials is one of the important factors determining the enantiopurity of products in asymmetric synthesis. Fifty‐one commercially available chiral reagents used as building blocks, catalysts, and auxiliaries in various enantioselective syntheses were assayed for their enantiomeric purity. The test results were classified within five impurities level (ie, <0.01%, 0.01%‐0.1%, 0.1%‐1%, 1%‐10%, >10%). Previously from 1998 to 2013, several reports have been published on the enantiomeric composition of more than 300 chiral reagents. This series of papers is necessitated by the fact that new reagents are forthcoming and that the enantiomeric purity of the same reagent can vary from batch to batch and/or from supplier to supplier. This report presents chiral liquid chromatography (LC) and gas chromatography (GC) methods to separate enantiomers of chiral compounds and evaluate their enantiomeric purities. The accurate and efficient LC analysis was done using newly introduced superficially porous particle (SPP 2.7 μm) based chiral stationary phases (TeicoShell, VancoShell, LarihcShell‐P, and NicoShell).     

Identifying novel targets in renal cell carcinoma: Design and synthesis of affinity chromatography reagents

Two novel scaffolds, 4-pyridylanilinothiazoles (PAT) and 3-pyridylphenylsulfonyl benzamides (PPB), previously identified as selective cytotoxins for von Hippel–Lindau-deficient Renal Carcinoma cells, were used as templates to prepare affinity chromatography reagents to aid the identification of the molecular targets of these two classes. Structure–activity data and computational models were used to predict possible points of attachment for linker chains. In the PAT class, Click coupling of long chain azides with 2- and 3-pyridylanilinothiazoleacetylenes gave triazole-linked pyridylanilinothiazoles which did not retain the VHL-dependent selectivity of parent analogues. For the PPB class, Sonagashira coupling of 4-iodo-(3-pyridylphenylsulfonyl)benzamide with a propargyl hexaethylene glycol carbamate gave an acetylene which was reduced to the corresponding alkyl 3-pyridylphenylsulfonylbenzamide. This reagent retained the VHL-dependent selectivity of the parent analogues and was successfully utilized as an affinity reagent.     

Synthesis of "long", hydrophilic, protein-cross-linking reagents

Since most of the protein cross-linking reagents in use are strongly hydrophobic, their length cannot be increased beyond approximately 20 Å between the protein-reactive groups, before denaturation of most proteins becomes noticeable at already a very few cross-links per molecule. The synthesis of longer reagents, coupling to lysine or cysteine side chains, and containing strongly hydrophilic oligoproline chains, is described. As they bear an azodye, linking the oligoproline parts, the cross-links effected are amenable to a mild cleavage by reduction with dithionite. A trifunctional reagent was constructed by reacting trimesinic acid chloride with β-alanine ethyl ester; the carboxyl groups of this amino acid could then be activated for protein cross-linking by reactions leading to the hydrazide, and azides.To compare the new reagents with the compounds in use at present, they were tested out on hemoglobin. The amount of reagent molecules coupled to the protein, and the fractions bifunctionally attached, as well as interchain linking were determined. The “long” reagents reached a distinctly higher efficiency in interchain cross-linking in this system, while showing smaller denaturing effects upon the protein. Thus, more than 11 reagent residues could be coupled to the hemoglobin tetramers without changes in its spectrum indicating denaturation of the heme environment, while shorter and more hydrophobic reagents had permitted the attachment of not more than four to six crosslinks.     

The use of BrCN for assembling modified DNA duplexes and DNA-RNA hybrids; comparison with water-soluble carbodiimide.

Both cyanogen bromide (BrCN) and 1-ethyl-3-(3'-dimethylaminopropyl) carbodiimide may be used as coupling reagents for the template-directed assembly of DNA duplexes containing the sugar-phosphate backbone modification. Both reagents show similar ligation site structure-specific trend. Practical recommendations are given for selection of the condensing reagent depending on the properties of the duplex. Based on 31P NMR spectroscopy data, a scheme is suggested for BrCN activation of the nucleotide phosphomonoester group. Using both condensing reagents, we studied the condensation of oligonucleotides containing ribo-segments (from mononucleotide residue to full sequence) on the DNA template. Efficiency of the chemical ligation of RNA oligomers was shown to be much lower than that of DNA analogues. The coupling yield depends on the position of the RNA segment in the hybrid duplexes and on the position of the phosphate group in the nick.     

Fluorescent dye phosphoramidite labelling of oligonucleotides.

A series of fluorescein phosphoramidites (FAM) have been synthesized for use on automated DNA synthesizers. After coupling of the FAM reagents to the 5' hydroxyl of the oligonucleotide on the DNA synthesizer, the excess reagent is removed by washing the solid support. The dye, and its linkage to the oligonucleotide, are stable during the conditions of DNA synthesis and cleavage/deprotection conditions. Purification is attained with the OPC (Oligonucleotide Purification Cartridge), a polystyrene based affinity matrix, which selectively retains hydrophobic oligonucleotide conjugates. Analysis by MicroGel capillary electrophoresis effectively separates fluorescent dye labelled oligonucleotides from unlabelled products.     

Synthesis of symmetrically and asymmetrically branched pegylating reagents.

A solution-phase procedure using an orthogonal protection scheme was developed for the synthesis of a novel family of multi-pegylating reagents. The procedure was exemplified by the synthesis of bis- and tris-pegylating reagents prepared by stepwise insertion of the poly(ethylene glycol) units thereby enabling the preparation of both symmetrical and asymmetrical pegylating reagents. Asymmetrical pegylation and tris-pegylation of peptides and proteins introduces new variables for use in the optimization of pegylated peptides and proteins. These reagents are ideally suited for conjugation to peptides and proteins as they possess a required functional group and will be useful intermediates for the synthesis of a new generation of pegylated products. Tris-pegylation can also provide more effective protection from proteolysis by shielding the protein surface from approaching macromolecules. To illustrate this potential, conditions were developed for the successful coupling of the tris-pegylating reagent to a model pentapeptide.     

Reactivity of UNCAs with Grignard reagents

Summary The reactivity of Grignard reagents with UNCAs (Urethane N-protected Carboxyanhydrides of Amino acids) is described. We observed that, depending on the method of addition of the organometallic compounds, the reaction proceeded differently: (i) when the UNCA was added to the Grignard reagent, we obtained a mixture of five different products which were all identified; and (ii) when the organometallic reagent was added to the UNCA, we also obtained a mixture of the same products but in different proportions, with the major component corresponding to the urethane N-protectedN-acyl amino acid derivative.     

Multiple oligodeoxyribonucleotide syntheseson a reusable solid-phase CPG support via the hydroquinone-O,O'-diacetic acid (Q-Linker) linker arm

A strategy for oligodeoxyribonucleotide synthesis on a reusable CPG solid-phase support, derivatized with hydroxyl groups instead of amino groups, has been developed. Ester linkages, through a base labile hydroquinone- O, O '-diacetic acid ( Q-Linker ) linker arm, were used to couple the first nucleoside to the hydroxyl groups on the support. This coupling was rapidly accomplished (10 min) using O -benzotriazol-1-yl- N, N, N ', N '-tetramethyluronium hexafluorophosphate (HBTU) and 1-hydroxybenzotriazole as the activating reagents. Oligodeoxyribonucleotide synthesis was performed using existing procedures and reagents, except a more labile capping reagent, such as chloro-acetic anhydride, methoxyacetic anhydride or t-butylphenoxyacetic anhydride, was used instead of acetic anhydride. After each oligodeoxyribonucleotide synthesis, the product was cleaved from the support with ammonium hydroxide (3 min) and deprotected as usual. Residual linker arms or capping groups were removed by treatment with ammonium hydroxide/methylamine reagent and the regenerated support was capable of reuse. Up to six different oligodeoxyribonucleotide syntheses or up to 25 cycles of nucleoside derivatization and cleavage were consecutively performed on the reusable support. This method may provide a significant cost advantage over conventional single-use solid supports currently used for the manufacture of antisense oligodeoxyribonucleotides.     

The Evaluation and Choice of Laboratory Equipment and Reagents

Many new types of laboratory equipment are appearing on the market, as well as a large number of reagent sets or kits. The importance of adequate evaluation of the reliability of such new products cannot be overemphasized.Commercially prepared reagent sets or kits fall into two categories. In the one, a set of reagents is offered for use in performance of a particular conventional procedure; this type of prepared reagent should present no problem, provided that the reagents are stable. In the other category, a reagent kit or set is offered which has been designed to simplify the performance of a laboratory analysis, often by combining reagents and reducing the number of steps and the time required. Such a kit should be evaluated carefully in order to determine its efficiency and limitations. In general it is difficult to simplify greatly a laboratory procedure without sacrificing its accuracy.     

Synthesis of cyclopentapeptides and cycloheptapeptides by DEPBT and the influence of some factors on cyclization.

Three cyclic peptides - cyclo(GlyAlaTyrLeuAla), cyclo(GlyProTyrLeuAla) and cyclo(GlyTyrGlyGlyProPhePro) - isolated and identified from medicinal herbs were chosen as model cyclic peptides to study the influence of the linear precursors and coupling reagents on cyclization. The 17 linear precursors of these three cyclic peptides were synthesized and cyclized using 3-(diethoxyphosphoryloxy)-(1-3)-benzotriazin-4 (3H)-one (DEPBT) as the major coupling reagent. The present work shows that: (i) the effects of linear peptide precursors on the cyclization are complex but some guidelines for choosing suitable precursor for cyclization could be considered; and (ii) DEPBT results in a higher cyclization yield compared with other coupling reagents. In addition, it was confirmed that peptides containing alternating D and L residues favor cyclization.     

Oligomycin sensitivity of mitochondrial sulfhydryl groups

Dithionitrobenzoate has been used to titrate sulfhydryl groups of rat liver mitochondria in glutamate buffer, pH 7.4.Reaction with oligomycin and different SH reagents preceded the SH titration. Under these conditions it was found that 2-mercaptopropionylglycine and N-ethylmaleimide reacted in an oligomycin-sensitive manner, so that the control values (in the absence of SH reagent) were obtained.Similar concentrations of mersalyl and of N-(N-acetyl-4-sulfamoylphenyl) maleimide, in the presence of oligomycin, enhanced reactivity toward Nbs₂.The concentration range of oligomycin-sensitive SH groups was thus defined between approx. 5 and 9 nmol reagent/mg mitochondrial protein.In this way, a differentiation between SH groups, which are implicated in phosphate transport and those, which react in an oligomycin-sensitive manner, and which are probably connected with the coupling mechanism, was achieved.     

New 21- and 24-atom Aib-containing cyclopeptides.

The synthesis of two Aib-containing cyclic octapeptides, cyclo(Leu-Aib-Phe-Aib-Gly-Aib-Phe-Aib) (1) and cyclo(Gly-Aib-Aib-Val-Aib-Leu-Aib-Phe) (2), and a cyclic heptapeptide cyclo(Gly-Aib-Val-Aib-Leu-Aib-Phe) (3), is described. The linear precursors of 1-3 were prepared using solution-phase techniques, and the cyclisation was also accomplished in solution. Among the coupling reagents examined in the final macrolactamisation step, PyAOP, HATU and DEPC/DEPBT efficiently yielded cyclised products. However, the success of the cyclisation was found to be dependent on the coupling reagent used. The two octapeptides 1 and 2 were obtained in much better yields (up to 63%) than the cycloheptapeptide 3 (30-37%). In addition, crystal-state conformational analysis of 2 was performed by X-ray crystallography. Six intramolecular hydrogen bonds stabilise the structure characterised by two consecutive type II'/I beta-turns, two consecutive type II/III' beta-turns, one gamma-turn, and one inverse gamma-turn. Copyright (c) 2008 European Peptide Society and John Wiley & Sons, Ltd.     

Automated solid-phase peptide synthesis: use of 2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium tetrafluoroborate for coupling of tert-butyloxycarbonyl amino acids.

2-(1H-Benzotriazol-1-yl)-1,1,3,3-tetramethyluronium tetrafluoroborate (TBTU) has been adapted for use as a coupling reagent for tert-butyloxycarbonyl (Boc) amino acids in automated solid-phase peptide synthesis. When compared to the existing preformed symmetrical anhydride procedure employing dicyclohexyl-carbodiimide (DCC), the use of TBTU in the presence of 1-hydroxybenzotriazole (HOBt) provides a more efficient coupling procedure for Boc-amino acid derivatives. Overall cycle times using TBTU/HOBt coupling reagents (30 min) compare favorably to those of the DCC-mediated procedure (approx 65 min). Dimethylformamide can be used as the sole solvent for both activation and coupling reactions. Implementation of TBTU/HOBt coupling conditions does not require replumbing of any lines of the Applied Biosystems Model 430A instrument and necessitates changes to only three reagent bottle positions. The variable coupling efficiencies of Boc-asparagine following activation with TBTU/HOBt (as low as 89%) can be overcome by protection of the amide function of Boc-asparagine with the 9-xanthyl group. Examples of the synthesis and characterization of a number of peptides ranging in length from 13 to 29 residues are given.     

Photolytic cleavage of DNA by nitrobenzamido ligands linked to 9-aminoacridines gives DNA polymerase substrates in a wavelength-dependent reaction.

A series of reagents containing 3- or 4-nitrobenzamido ligands tethered to 9-aminoacridine via variable-length linkers have been prepared and their properties as photochemical DNA cleavers (photonucleases) examined. When irradiated with approximately 300-nm light, where the nitrobenzamido ligand can absorb, they cleave DNA in an oxygen-independent reaction presumably involving oxygen transfer from the nitro group to the deoxyribose units of the DNA backbone (Nielsen et al., 1988b). This reaction is pH independent and only slightly affected by the linker length, and the DNA fragments are not substrates for DNA polymerase. When approximately 420-nm light is used, were only the 9-aminoacridinyl ligands absorb, the DNA cleavage is also oxygen-independent but pH dependent, requires DNA saturation with the reagent (base pair:reagent less than or equal to 2), and is most efficient with the longer linkers. The cleavage is specific for guanine residues and results in 5'-phosphate termini and heterogeneous (more than four products) 3'-termini. One of the products is presumably 3'-hydroxy since DNA photocleaved with nitrobenzamido acridine reagents and 420-nm radiation are substrates for DNA polymerase in a nick translation assay as well as for the Klenow fragment. An electron-transfer mechanism is suggested.     

Heterogeneity of protein labeling with a fluorogenic reagent, 3-(2-furoyl)quinoline-2-carboxaldehyde

Fluorogenic reagents are used for protein labeling when high-sensitivity fluorescence detection is required. Similar to traditional labeling with activated fluorescent dyes, such as fluorescein isothiocyanate, a fluorogenic reaction is expected to change the physical-chemical properties of proteins. Knowledge of these changes may be essential for efficient separation and identification of labeled proteins. Here we studied the effect of labeling of myoglobin with a fluorogenic reagent on the acid-base properties of the protein. The fluorogenic reagent used was 3-(2-furoyl)quinoline-2-carboxaldehyde (FQ). In slab-gel isoelectric focusing, we found that the labeling reaction generated at least six species with pI values lower than that of non-labeled myoglobin. These species can be identified as products of progressive labeling of myoglobin with one to six FQ molecules. The same series of FQ-labeled species were observed when the reaction products were analyzed by capillary zone electrophoresis. The comparison of experimental and theoretical pI values allowed us to elucidate the labeling pattern--the number of FQ molecules corresponding to each labeled product detected by isoelectric focusing.