Pyrrolidide formation as a side reaction during activation of carboxylic acids by phosphonium salt coupling reagents

Pyrrolidide derivatives are observed as unwanted by-products from slow reactions of activated carboxylates with nucleophilic amines, as mediated by phosphonium salt coupling reagents (PyAOP, PyBOP, PyBroP). This side reaction is attributed to the presence of small amounts (e.g., 0.5%, w/w) of pyrrolidine as a contaminant to commercial phosphonium salts, and does not occur when the reagents are crystallized before their use in coupling reactions.     

Evaluation of acid‐labile S‐protecting groups to prevent Cys racemization in Fmoc solid‐phase peptide synthesis

Phosphonium and uronium salt‐based reagents enable efficient and effective coupling reactions and are indispensable in peptide chemistry, especially in machine‐assisted SPPS. However, after the activating and coupling steps with these reagents in the presence of tertiary amines, Fmoc derivatives of Cys are known to be considerably racemized during their incorporation. To avoid this side reaction, a coupling method mediated by phosphonium/uronium reagents with a weaker base, such as 2,4,6‐trimethylpyridine, than the ordinarily used DIEA or that by carbodiimide has been recommended. However, these methods are appreciably inferior to the standard protocol applied for SPPS, that is, a 1 min preactivation procedure of coupling with phosphonium or uronium reagents/DIEA in DMF, in terms of coupling efficiency, and also the former method cannot reduce racemization of Cys(Trt) to an acceptable level (<1.0%) even when the preactivation procedure is omitted. Here, the 4,4′‐dimethoxydiphenylmethyl and 4‐methoxybenzyloxymethyl groups were demonstrated to be acid‐labile S‐protecting groups that can suppress racemization of Cys to an acceptable level (<1.0%) when the respective Fmoc derivatives are incorporated via the standard SPPS protocol of phosphonium or uronium reagents with the aid of DIEA in DMF. Furthermore, these protecting groups significantly reduced the rate of racemization compared to the Trt group even in the case of microwave‐assisted SPPS performed at a high temperature. © 2013 The Authors. European Peptide Society published by John Wiley & Sons, Ltd.     

Rapid esterification of nucleosides to solid-phase supports for oligonucleotide synthesis using uronium and phosphonium coupling reagents

Nucleosides can be esterified to solid-phase supports using uronium or phosphonium coupling reagents and a coupling additive, such as 1-hydroxybenzotriazole (HOBT), 7-aza-1-hydroxybenzotriazole (HOAT), N-methylimidazole (NMI), or 4-(dimethylamino)pyridine (DMAP). However, DMAP was far superior to other additives and high nucleoside loadings (up to 60 micromol/g) and rapid coupling reactions (< or = 10 min) were possible. Hydroxyl-derivatized CPG was attached to nucleosides with 3'-succinyl or 3'-hydroquinone-O, O'-diacetic acid (HQDA or Q-Linker) carboxyl groups through a primary ester linkage. Alternatively, supports derivatized with succinic acid or the Q-Linker were attached directly to the 3'-OH group of nucleosides through a secondary ester linkage. Uronium reagents (HATU or HBTU) gave the best results with the HQDA linker arm, while the bromophosphonium (BrOP or PyBrOP) reagents were best with the succinyl linker arm. In all cases, the coupling reactions were much faster than previous methods using carbodiimide coupling reagents. The ease and speed of the reaction make this support derivatization procedure suitable for automated in situ couplings on DNA synthesizers.     

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.     

Assessment of new 6-Cl-HOBt based coupling reagents for peptide synthesis. Part 1: Coupling efficiency study

The efficiency of a series of well-known coupling reagents (TBTU, HATU, and PyBOP) and of new in situ activating reagents (TCTU, HCTU, and DMTMM) was compared by synthesizing the 65–74 fragment of the Acyl Carrier Protein (H-Val-Gln-Ala-Ala-Ile-Asp-Tyr-Ile-Asn-Gly-NH₂₎, containing `a difficult sequence', as a test peptide, in a multiple peptide synthesizer. The longer sequence rMOG(35–55) was also synthesized. It was clear that the aminium salts are more efficient than the phosphonium salt (PyBOP) and that the new 6Cl-HOBt based reagents (HCTU and particularly TCTU) are very efficient, while DMTMM appeared to be not suitable for SPPS.     

Solid-phase synthesis and characterization of N-methyl-rich peptides.

A library of peptides required for a project investigating the factors relevant for blood-brain barrier transport was synthesized on solid phase. As a result of the high N-methylamino acid content in the peptides, their syntheses were challenging and form the basis of the work presented here. The coupling of protected N-methylamino acids with N-methylamino acids generally occurs in low yield. (7-azabenzotriazol-1-yloxy)-tris(pyrrolidino)phosphonium hexafluorophosphate (PyAOP) or PyBOP/1-hydroxy-7-azabenzotriazole (HOAt), are the most promising coupling reagents for these couplings. When a peptide contains an acetylated N-methylamino acid at the N-terminal position, loss of Ac-N-methylamino acid occurs during trifluoroacetic acid (TFA) cleavage of the peptide from the resin. Other side reactions resulting from acidic cleavage are described here, including fragmentation between consecutive N-methylamino acids and formation of diketopiperazines (DKPs). The time of cleavage is shown to greatly influence synthetic results. Finally, high-performance liquid chromatography (HPLC) profiles of N-methyl-rich peptides show multiple peaks because of slow conversion between conformers.     

Assessment of new 6-Cl-HOBt based coupling reagents for peptide synthesis. Part 1: Coupling efficiency study

Summary The efficiency of a series of well-known coupling reagents (TBTU, HATU, and PyBOP) and of newin situ activating reagents (TCTU, HCTU, and DMTMM) was compared by synthesizing the 65–74 fragment of the Acyl Carrier Protein (H-Val-Gln-Ala-Ala-Ile-Asp-Tyr-Ile-Asn-Gly-NH₂), containing ‘a difficult sequence’, as a test peptide, in a multiple peptide synthesizer. The longer sequence rMOG(35–55) was also synthesized. It was clear that the aminium salts are more efficient than the phosphonium salt (PyBOP) and that the new 6Cl-HOBt based reagents (HCTU and particularly TCTU) are very efficient, while DMTMM appeared to be not suitable for SPPS.     

Comparison of the efficiency of various coupling systems in the acylation of model secondary amines with thymin-1-ylacetic acid.

Peptide nucleic acids (PNAs) make a promising group of DNA analogues. The backbone of typical PNA oligomers is composed of N-(2-aminoethyl)glycine units, linked by the peptide bonds. The backbone secondary amine groups are acylated with carboxyalkyl derivatives of nucleobases. One of the PNA synthesis step causing some problems is the acylation of the monomer backbone with the nucleobase derivatives. The aim of the study was to compare the efficiency of various coupling systems in the acylation. Simple model compounds (piperidine and proline) were used, as well as equimolar amounts of the coupling reagents. Selected systems based on carbodiimides, aminium or phosphonium salts, mixed anhydride, and active esters were tested.     

A study of the efficiency and the problem of sulfonation of several condensing reagents and their mechanisms for the chemical synthesis of deoxyoligoribonucleotides.

The efficiencies and problems of sulfonation of several condensing reagents for deoxyoligoribonucleotide synthesis have been studied. While 2,4,6-triisopropylbenzenesulfonyl chloride (TPSC1) gave very low yield and slow rate of coupling, the new 1:3 mixture of TPSC1 and tetrazole afforded excellent yield and extremely fast rate of reaction with the lowest rate of sulfonation. The difference and advantages of this mixture over triisopropylbenzenesulfonyl tetrazole (TPSTe) and mesitylenesulfonyl tetrazole (MSTe) are discussed. Mechanisms for the coupling reactions with these condensing reagents to account for the difference in their rates and yields of coupling are discussed.     

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.     

Analytical studies of ''mixed sequence'' oligodeoxyribonucleotides synthesized by competitive coupling of either methyl- or beta-cyanoethyl-N,N-diisopropylamino phosphoramidite reagents, including 2''-deoxyinosine.

High-performance liquid chromatography (HPLC) and 1H/31P nuclear magnetic resonance (NMR) spectroscopy were used to measure the molar ratio of oligodeoxyribonucleotide products in mixtures obtained with automated DNA synthesizers that employed competitive coupling of either standard methyl- or newer beta-cyanoethyl-N,N-diisopropylamino phosphoramidite reagents, which include deoxyinosine. Mixtures of these reagents when used as freshly prepared solutions afforded ratios of products that indicated negligibly small differences among the rates of the various competitive coupling reactions. However, studies of reagent stability in solution revealed that both types of the N-isobutyryl deoxyguanosine reagent decompose faster than their corresponding dA, dC, and dT phosphoramidites, which led to significantly lower proportions of dG-containing sequences. This problem was attenuated for the beta-cyanoethyl reagents due to their slower rate of decomposition.     

BOP reagent for the coupling of pGlu and Boc-His(Tos) in solid phase peptide synthesis

The model peptide TRH was successfully synthesized using benzotriazol-1-yl-oxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP reagent). The coupling reactions were carried out in N,N-dimethylformamide or N-methylpyrrolidone. These solvents allowed the incorporation of the N-terminal pyroglutamic acid residue into the peptide chain, without using the derivative bearing the N-benzyloxycarbonyl group, which acts as a solubility promoter. A comparative racemization study showed that Boc-His(Tos) can be coupled by means of BOP reagent with less racemization than with DCC when the amount of diisopropylethylamine (DIEA) is kept minimal (same ratio of equivalents as for Boc-His(Tos), i.e. 3 equiv.). However, with the use of a larger amount of DIEA in the coupling mixture (9 equiv.), approximately 3% of epimer was found in the crude product. Our study showed that even under low DIEA conditions, the rate of coupling of the residues with BOP remained comparable to that observed with DCC.     

Design of phosphonium ionic liquids for lipase-catalyzed transesterification

Ionic liquids are now recognized as solvents for use in lipase-catalyzed reactions; however, there still remains a serious drawback in that the rate of reaction in an ionic liquid is slower than that in a conventional organic solvent. To overcome this problem, attempts have been made to evolve phosphonium ionic liquids appropriate for lipase-catalyzed reaction; several types of phosphonium salts have been prepared and their capability evaluated for use as solvent for the lipase-catalyzed reaction. Very rapid lipase PS-catalyzed transesterification of secondary alcohols was obtained when 2-methoxyethyl(tri-n-butyl)phosphonium bis(trifluoromethanesulfonyl)imide ([MEBu₃P][NTf₂]) was used as solvent, affording the first example of a reaction rate superior to that in diisopropyl ether.     

Synthesis of a biotinylated, iodinatable, and photoactivatable probe for angiotensin receptors

We propose here a biotinyl-aminohexanoyl-[Ala1, Phe(4N3)8]angiotensin II analog as a radioiodinatable and photoactivatable probe for covalent labeling, detection and isolation of angiotensin receptors. A combination of solid phase and minimum-protection segment-coupling strategy using hexafluorophosphate of (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium (BOP) as a coupling reagent is proposed for the synthesis of this probe. Optimized yields were obtained by HPLC monitoring of all reactions. A complete n.m.r. study suggests an extended conformation of this molecule, allowing a simultaneous recognition of receptor and avidin. The probe binds with high affinity (Kd = 2 nM) to angiotensin II receptors from rat liver membranes.     

Studies on sensitivity to racemization of activated residues in couplings of N-benzyloxycarbonyldipeptides.

A series of 24 peptides Z-Gly-Xaa(R)-OH where Xaa = 15 different residues and R = H, NH2, tBu, Bzl, Trt, Mtr, and StBu were coupled with valine benzyl ester in dimethylformamide or dichloromethane at +5 degrees. The accompanying racemization was determined by analysis of the epimeric products by normal phase high-performance liquid chromatography (HPLC) for Xaa(R) = Met, Cys(StBu) and Lys(Z) and by reversed-phase HPLC after removal of benzyl-based protecting groups for Xaa(R) = Ser(tBu), Thr(tBu) and Arg(Mtr). The coupling methods examined included mixed anhydride (MxAn) at -5 degrees, and N,N'-dicyclohexylcarbodiimide (DCC), benzotriazol-1-yl-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and O-benzotriazol-1-yl-N,N,N',N'-tetramethyluroniumhexafluorophosp hate (HBTU) in the presence of 1-hydroxybenzotriazole (HOBt). Very few couplings gave stereochemically pure products. The order of sensitivity to racemization of residues depended on the method of coupling and the solvent. It varied most when comparing MxAn to HOBt-assisted reactions; it varied moderately when comparing HOBt-assisted reactions. There was less variation in comparing BOP and HBTU reactions that are initiated by the same mechanism. Leu, Nle, Phe, Asn, Lys(Z) and Asp(OBzl) are identified as the residues least sensitive to racemization. DCC-HOBt generally led to less epimerization than the other methods.     

A Review: Synthesis of Aryl C-Glycosides Via the Heck Coupling Reaction

In this article, we focus on the synthesis of aryl C-glycosides via Heck coupling. It is organized based on the type of structures used in the assembly of the C-glycosides (also called C-nucleosides) with the following subsections: pyrimidine C-nucleosides, purine C-nucleosides, and monocyclic, bicyclic, and tetracyclic C-nucleosides. The reagents and conditions used for conducting the Heck coupling reactions are discussed. The subsequent conversion of the Heck products to the corresponding target molecules and the application of the target molecules are also described.     

A review: synthesis of aryl C-glycosides via the heck coupling reaction

In this article, we focus on the synthesis of aryl C-glycosides via Heck coupling. It is organized based on the type of structures used in the assembly of the C-glycosides (also called C-nucleosides) with the following subsections: pyrimidine C-nucleosides, purine C-nucleosides, and monocyclic, bicyclic, and tetracyclic C-nucleosides. The reagents and conditions used for conducting the Heck coupling reactions are discussed. The subsequent conversion of the Heck products to the corresponding target molecules and the application of the target molecules are also described.     

Tantalum pentachloride as a coupling agent for stereohindered amide bond formation

We have previously reported that tantalum carboxylates show high reactivity toward primary amines to give primary amides. We report herein that tantalum pentachloride, in contrast with the behavior of standard coupling reagents, mediates the couplings of secondary amines and the couplings of very hindered carboxylates. Such coupling reactions are particularly difficult to achieve, when using chiral carboxylates (including N-protected amino acids), without a significant degree of accompanying racemization. Racemization levels with the present systems are found to be very low in comparison with those obtained using a standard amide/peptide coupling system (DCC/HOBt).     

Efficient solid phase peptide synthesis. Use of methanesulfonic acid alpha-amino deprotecting procedure and new coupling reagent, 2-(benzotriazol-1-yl)oxy-1,3-dimethylimidazolidinium hexafluorophosphate (BOI).

An efficient method for solid phase peptide synthesis was developed, which consists of N alpha-selective deprotection by dilute methanesulfonic acid, in situ neutralization and rapid coupling reaction using benzotriazol-1-yloxytris(dimethylamino)phosphonium hexafluorophosphate (BOP) or 2-(benzotriazol-1-yl)oxy-1,3- dimethylimidazolidinium hexafluorophosphate (BOI) reagent. Selective removal of the N alpha-Boc group by dilute methanesulfonic acid was of more advantage than removal by TFA in terms of stability of semipermanent protecting groups and suppression of undesired side reactions. The use of in situ neutralization and rapid coupling method reduced intramolecular aminolytic cyclization by shortening exposure of the deprotected nucleophilic amino group. A successful synthesis of porcine brain natriuretic peptide (pBNP) has been achieved using this efficient solid phase peptide synthesis scheme.     

Different strategies for the chemical synthesis of lignans

This paper summarises the results of three projects. The first is concerned with developing general routes for the synthesis of lignans. In particular, two routes involving tandem conjugate addition reactions and Diels Alder reactions respectively that have been used to synthesise podophyllotoxin derivatives are described. The second project is concerned with the asymmetric synthesis of lignans and involves the application of these reactions, with the introduction of a menthyloxy group as a chiral auxiliary, to achieve the asymmetric synthesis of podophyllotoxin derivatives. The third project is concerned with the attempted biomimetic syntheses of podophyllotoxin derivatives using oxidative coupling reactions. Attention is focussed primarily on the use of hypervalent iodine reagents, which yield stegane and isostegane derivatives rather than podophyllotoxin derivatives. Other examples of biaryl coupling leading to stegane and isostegane derivatives are included, and other examples of lignan synthesis involving hypervalent iodine reagents are also described. Abbreviations: DDQ – 2,3-dichloro-5,6-dicyano-1,4-benzoquinone; DMAD – dimethyl acetylenedicarboxylate (dimethyl butynedioate); PIDA – phenyliodonium diacetate, iodobenzene diacetate; PIFA – phenyliodonium bis(trifluoroacetate), [bis(trifluoroacetoxy) iodobenzene]; Ra-Ni – Raney nickel; TBAF – tetrabutylammonium fluoride; TBDMS –t-butyldimethylsilyl; TFA – trifluoroacetic acid; TFAA – trifluoroacetic anhydride; TFE – 2,2,2-trifluoroethanol; TTFA – thallium(III) trifluoroacetate.