Sequential peptide ligation by using a controlled cysteinyl prolyl ester (CPE) autoactivating unit

A peptide building block containing a cysteinyl prolyl ester (CPE) autoactivating unit was ligated with a cysteinyl peptide under native chemical ligation conditions. The CPE autoactivating function can be controlled by the protection of the thiol group, permitting the selective ligation of the peptide building block at either the C or N terminus.     

Enhancement in the rate of conversion of peptide Cys-Pro esters to peptide thioesters by structural modification

We previously reported that the peptide containing a Cys-Pro ester (CPE) moiety is spontaneously transformed into a peptide thioester via an N to S acyl shift followed by diketopiperazine formation. In an attempt to identify more reactive structures for the formation of a peptide thioester, we modified the CPE structure, in which the Pro residue in the CPE moiety was replaced with N-substituted glycine derivatives. These peptides were transformed into a peptide thioester more rapidly. Alternatively, the addition of an amino acid residue at the C-terminus of the CPE moiety also accelerated thioester formation.     

Peptide dithiodiethanol esters for in situ generation of thioesters for use in native ligation

A new approach is described for the general Fmoc-based solid-phase synthesis of C-terminal peptide (thio)esters. One hydroxy group of 2,2-dithiodiethanol (used in large excess) was anchored on trityl resin, and the remaining hydroxy group was loaded with the first amino acid. Standard chain elongation and TFA-based peptide release yielded peptide C-terminal dithiodiethanol esters in good purities. Under standard conditions of native chemical ligation (excess thiol, neutral pH), the dithiodiethanol function is presumably reduced and rearranged (or equilibrated) to the thioester via a 5-membered intermediate. The resulting thioesters are shown to undergo native chemical ligation with N-terminal cysteine peptides. Notably, hydrolysis of the reduced ester is a major competing reaction, especially in the presence of 6 M guanidinium chloride, which is often required for solubilization of large peptide fragments.     

Peptide thioester preparation based on an N-S acyl shift reaction mediated by a thiol ligation auxiliary

Formation of peptide thioesters, based on an N to S acyl shift mediated by an auxiliary, N-4,5-dimethoxy-2-mercaptobenzyl (Dmmb) group, under acidic conditions, is described. The protected peptide was assembled on a hydroxymethylphenylacetamidomethyl resin via an N-Dmmb-amino acid residue according to standard Fmoc solid-phase peptide synthesis following treatment with trifluoroacetic acid. The peptide α-thioester was released from the resin by reaction with 2-mercaptoethanesulfonic acid in the presence of N,N-diisopropylethylamine.     

Sequential native chemical ligation utilizing peptide thioacids derived from newly developed Fmoc-based synthetic method

The first facile Fmoc-based synthetic procedure for peptide thioacids was developed. Successful application of the resulting thioacids to sequential native chemical ligation (NCL) in the N to C direction was achieved. Conversion of the peptide thioacids to the corresponding thioesters with Ellman's reagent followed by NCL in the presence of tris(2-carboxyethyl)phosphine (TCEP) and thiophenol was accomplished in a one-pot manner.     

Chemoselective coupling of peptide fragments using the Staudinger ligation

Here we report the first Staudinger ligations which yield tetra- and pentapeptides starting from N-terminal α-azido peptides and C-terminal peptideo-(diphenylphosphine)phenyl esters. Mass spectrometric analysis of the reaction mixture provided a better insight into the mechanism of the Staudinger ligation and has been used to explain the observed intermediates and to optimize the ligation reaction. As a result, the optimized reaction enables the chemoselective coupling of peptides containing amino acids other than glycine at the ligation site.     

Chemical synthesis of transactivation domain (TAD) of tumor suppressor protein p53 by native chemical ligation of three peptide segments

Chemical composition of tumor suppressor protein p53 is altered via multiple post-translational modifications which modulate its cellular lifetime and interactions with other biomolecules. Here we report total chemical synthesis of a 61-residue form of transactivation domain (TAD) of p53 based on native chemical ligation of three peptide segments. The experiments to characterize its binding to nuclear co-activator binding domain (NCBD) of CREB-binding protein confirmed native-like induced folding upon binding to NCBD. Thus, the synthetic approach described herein can be useful for the preparation of various post-translationally modified analogues of TAD-p53 for further functional biochemical and biophysical studies.     

(E)-Selective Wittig reactions of Garner's aldehyde with nonstabilized ylides

In the Wittig olefination reactions of Garner's aldehyde with certain nonstabilized ylides, the (E)-alkenes could be produced as a major product by simply quenching the reactions with a large excess of MeOH at −78 °C. Even under the salt-free conditions, more than a 10:1 ratio of the (E)- to (Z)-alkene was resulted consistently from the ylides of a linear alkyl chain. Without addition of MeOH, usual selectivity for the (Z)-alkene was obtained in a ratio of 94:6.     

‘O-Acyl isopeptide method’: racemization-free segment condensation in solid phase peptide synthesis

We disclosed a novel ‘racemization-free segment condensation’ based on the ‘O-acyl isopeptide method’ in which an N-segment including C-terminal O-acyl isopeptide structure with urethane-protected Ser/Thr residue was employed for the segment condensation, suggesting that the use of this method contributes to the effective convergent synthesis of long peptides/proteins.     

4-Isocyanopermethylbutane-1,1,3-triol (IPB): a convertible isonitrile for multicomponent reactions

The synthesis and applications of 4-isocyanopermethylbutane-1,1,3-triol (IPB) as a new convertible isonitrile (isocyanide) for isocyanide-based multicomponent reactions (IMCRs) like Ugi, Ugi-Smiles, and Passerini reactions are described. The primary products obtained from these IMCRs can be converted into highly activated N-acylpyrroles, which upon treatment with nucleophiles can be transformed into carboxylic acids, esters, amides, alcohols, and olefins. In this sense the reagent can be seen as a neutral carbanion equivalent to formate (HO₂C⁻), and carboxylates or carboxamides etc. (RNu-CO⁻).     

Efficient preparation of (Z)-alkenyl derivatives from (Z)-vinyl (N,N-diisopropyl)carbamate via Ni-catalysed coupling reactions

A (Z)-vinyl (N,N-diisopropyl)carbamate treated with Grignard reagents, under Wenkert Nickel-catalysed conditions, gave access to several substituted (Z)-alkenyl derivatives. These Nickel-catalysed reactions, carried out with vinyl-, phenyl-, p-methoxyphenyl-, trimethylsilylmethylmagnesium bromide and benzylmagnesium chloride, led to the corresponding (Z)-alkenyl derivatives in good yields and high stereoselectivities.     

‘O-Acyl isopeptide method’ for the efficient synthesis of difficult sequence-containing peptides: use of ‘O-acyl isodipeptide unit’

A novel ‘O-acyl isodipeptide unit’, Boc-Thr(Fmoc-Val)-OH 5 has been successfully used for the efficient synthesis of a difficult sequence-containing pentapeptide based on the ‘O-acyl isopeptide method’, in which racemization-inducible esterification could be omitted, suggesting that the use of O-acyl isodipeptide units allows the application of this method to fully automated protocols for the synthesis of long peptides or proteins.     

Generation of 5,6-dimethylene-2(1H)-pyridinones from [3,4-b] sulfolene pyridinones and application in Diels-Alder reactions

2(1H)-Pyrazinones were converted into various [3,4-b] sulfolene pyridinones 19-21, serving as precursors for thermolytic conversion into the corresponding 5,6-dimethylene 2(1H)-pyridinone ortho-quinodimethanes. These were trapped in situ by reaction with various dienophiles. Tethering of precursor 19 with a dienophilic side chain attached to the 7-position of the [3,4-b] sulfolene pyridinone also enabled intramolecular cycloaddition when no rearrangement by 1,5-H-shift was viable.     

Utility of a chiral 1,3-dioxane template in stereoselective intramolecular Diels-Alder reactions

The ethylidene acetal of d-erythrose was used as a template for stereoselective IMDA reactions: high endo selectivity and yields in favor of the cis product were observed with 1,3,9-trienes, resulting from a boat transition state. For natural product synthesis, the reaction was successfully applied to a diene with terminal Z-olefin.     

Universal fluorescent tri-probe ligation equipped with capillary electrophoresis for targeting SMN1 and SMN2 genes in diagnosis of spinal muscular atrophy

This is the first ligase chain reaction used for diagnosis of spinal muscular atrophy (SMA). Universal fluorescent tri-probe ligation (UFTPL), a novel strategy used for distinguishing the multi-nucleotide alternations at single base, is developed to quantitatively analyze the SMN1/SMN2 genes in diagnosis of SMA. Ligase chain reaction was performed by adding three probes including universal fluorescent probe, connecting probe and recognizing probe to differentiate single nucleotide polymorphisms in UFTPL. Our approach was based on the two UFTPL products of survival motor neuron 1 (SMN1) and SMN2 genes (the difference of 9 mer) and analyzed by capillary electrophoresis (CE). We successfully determined various gene dosages of SMN1 and SMN2 genes in homologous or heterologous subjects. By using the UFTPL-CE method, the SMN1 and SMN2 genes were fully resolved with the resolution of 2.16 ± 0.37 (n = 3). The r values of SMN1 and SMN2 regression curves over a range of 1–4 copies were above 0.9944. Of the 48 DNA samples, the data of gene dosages were corresponding to that analyzed by conformation sensitive CE and denatured high-performance liquid chromatography (DHPLC). This technique was found to be a good methodology for quantification or determination of the relative genes having multi-nucleotide variants at single base.     

Synthesis of an O-acyl isopeptide by using native chemical ligation to efficiently construct a hydrophobic polypeptide

By using dimethylformamide to suppress the O-to-N acyl migration, we efficiently synthesized an O-acyl isopeptide by native chemical ligation of a peptide-thioester and a Cys-O-acyl isopeptide. The reaction mixture was then loaded onto an octadecylsilane reverse-phase HPLC column, and the isopeptide was purified by using a linear gradient of CH₃CN in 0.1% aqueous trifluoroacetic acid. The recovery rate of the O-acyl isopeptide was considerably higher than that of the corresponding native polypeptide. Synthesis of O-acyl isopeptides via native chemical ligation, with O-to-N acyl migration as the final step to give the native form, has potential as an efficient method of constructing hydrophobic polypeptides.     

Photophysical processes and photochemical reactions involved in poly(N-vinylcarbazole) and in copolymers with carbazole units

This paper is devoted to the analysis of the photochemical behaviour of copolymers with carbazole units exposed to long-wavelength radiation. These copolymers are constituted of two types of carbazolylethyl methacrylate units (CEM) with octyl methacrylate moieties (OMA). The exposure of copolymers and PVK to UV light results in dramatic modifications of the physical and photophysical properties of the polymer. These modifications can be correlated with modifications of the chemical structure of the matrix. The photoageing of copolymers and PVK has been analysed by fluorescence, ESR, UV-vis and infrared spectroscopies. The effects of crosslinking and chain scissions were determined by gel fraction measurements and size exclusion chromatography.     

Backbone extended pyrrolidine PNA (bepPNA): a chiral PNA for selective RNA recognition

Synthesis of cationic, chiral PNA analogues with an extra atom in the backbone (bepPNA) is reported. The (2S,4S) geometry of the pyrrolidine ring, and an additional carbon atom in the backbone of homopyrimidine-bepPNAs resulted in the optimization of the inter-nucleobase distance, such that selective binding to complementary RNA over DNA was observed in the triplex mode. It was evident from circular dichroism studies that oligomers with mixed aminoethylglycyl-bep (aeg-bep) repeating units, and also bepPNA with homogeneous backbone attained structures quite different from those of aegPNA₂:RNA/DNA complexes. The bepPNA, when incorporated in a duplex forming mixed purine-pyrimidine sequence, also showed a preference for binding complementary RNA over DNA.     

Fluorinated phosphorus compounds: Part 8. The reactions of bis(fluoroalkyl) phosphorochloridates with sulfur nucleophiles

The reactivity of bis(fluoroalkyl) phosphorochloridates to nucleophiles is summarised. Previous data and the results described here indicate that reactivities decrease in the order: amines>alcohols>thiols. The synthesis of CF₃CH₂OP(O)(SEt)₂ in 30% yield was accomplished by treating CF₃CH₂OP(O)Cl₂ with two molar equivalents of EtSH and Et₃N in ether. The chloridates (CF₃CH₂O)₂P(O)Cl and (C₂F₅CH₂O)₂P(O)Cl did not react with MeSH in ether at −78 °C or when heated with Pb(SMe)₂ in benzene. Ethanethiol and propanethiol reacted with fluorinated chloridates in the presence of triethylamine to give thiolates (R_FO)₂P(O)SR in 13-41% yield where R_F was CF₃CH₂, C₂F₅CH₂, C₃F₇CH₂ or (CF₃)₂CH and R was Et or n-Pr. Similarly, reaction of phosphorobromidates (R_FCH₂O)₂P(O)Br, made by brominating the corresponding bis(fluoroalkyl) H-phosphonates, with benzenethiol gave derivatives (R_FCH₂O)₂P(O)SPh in 43 and 46% yield where R_F was CF₃ and C₂F₅, respectively. Treatment of the chloridothiolate Cl(EtO)P(O)SMe, prepared in two steps from triethyl phosphite, with fluoroalcohols and triethylamine in ether gave species R_FO(EtO)P(O)SMe in 62-74% yield where R_F was CF₃CH₂, C₂F₅CH₂, C₃F₇CH₂ or (CF₃)₂CH. The reactions of bis(trifluoroethyl) phosphorochloridate with 2-mercaptoethanol, 3-mercaptopropanol and ethane-1,2-dithiol gave several unexpected products whose structures were tentatively assigned.     

2-(4-Sulfophenylsulfonyl)ethoxycarbonyl group: a new water-soluble N-protecting group and its application to solid phase peptide synthesis in water

Solid phase peptide synthesis is carried out in organic solvents, creating environmental problems after disposal. To avoid this problem, we aimed to perform solid phase peptide synthesis in water. A new water-soluble N-protecting group, 2-(4-sulfophenylsulfonyl)ethoxycarbonyl (Sps) group, was designed and Sps-amino acids were prepared. To evaluate the utility of this technique, Leu-enkephalin amide was prepared by solid phase synthesis using Sps-amino acids in water.