Theoretical Analysis of the Detailed Mechanism of Native Chemical Ligation Reactions

The method of native chemical ligation between an unprotected peptide α‐thioester and an N‐terminal cysteine–peptide to give a native peptide in aqueous solution is one of the most effective peptide ligation methods. In this work, a systematic theoretical study was carried out to fully understand the detailed mechanism of ligation. It was found that for the conventional native chemical ligation reaction between a peptide thioalkyl ester and a cysteine in combination with an added aryl thiol as catalyst, both the thiol‐thioester exchange step and the transthioesterification step proceed by an anionic concerted S_N2 displacement mechanism, whereas the intramolecular rearrangement proceeds by an addition–elimination mechanism, and the rate‐limiting step is the thiol‐thioester exchange step. The theoretical method was then extended to study the detailed mechanism of the auxiliary‐mediated peptide ligation between a peptide thiophenyl ester and an N‐2‐mercaptobenzyl peptide in which both the thiol‐thioester exchange step and intramolecular acyl‐transfer step proceed by a concerted S_N2‐type displacement mechanism. The energy barrier of the thiol‐thioester exchange step depends on the side‐chain steric hindrance of the C‐terminal amino acid, whereas that of the acyl‐transfer step depends on the side‐chain steric hindrance of the N‐terminal amino acid.     

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.     

Imidazole‐Aided Native Chemical Ligation: Imidazole as a One‐Pot Desulfurization‐Amenable Non‐Thiol‐Type Alternative to 4‐Mercaptophenylacetic Acid

Various bioactive proteins have been synthesized by native chemical ligation (NCL) and its combination with subsequent desulfurization (e.g., conversion from Cys to Ala). In NCL, excess 4‐mercaptophenylacetic acid (MPAA) is generally added to facilitate the reaction. However, co‐elution of MPAA with the ligation product during preparative high‐performance liquid chromatography sometimes reduces its usefulness. In addition, contamination of MPAA disturbs subsequent desulfurization. Here, we report for the first time that imidazole can be adopted as an alternative to MPAA in NCL using a peptide‐alkylthioester. The efficiency of the imidazole‐aided NCL (Im‐NCL) is similar to that of traditional MPAA‐aided NCL. As model cases, we successfully synthesized adiponectin(19‐107) and [Ser(PO₃H₂)⁶⁵]‐ubiquitin using Im‐NCL with a one‐pot desulfurization.     

Design of thiol-containing amino acids for native chemical ligation at non-Cys sites

<正>Protein chemical synthesis usually relies on the use of native chemical ligation that couples peptide thioester with a Cys-peptide.A limitation of this method is the difficulty of finding an appropriate Cys ligation site in many synthetic targets.To overcome this problem,the ligation-desulfurization approach has been developed.This approach involves the use of a thiol-containing amino acid as the ligation partner.After the sequence assembly is completed,the thiol group is removed through a desulfurization reaction to generate the standard amino acids.Currently this strategy has been applied to the ligations at a number of amino acids including Ala,Phe,Val,Lys,Thr,Leu,Pro and Gln.The present article reviews the design and synthesis of these thiol-containing amino acids for native chemical ligation at non-Cys sites.     

N-to-C sequential ligation using peptidyl N,N-bis(2-mercaptoethyl)amide building blocks

A novel N- to C-terminus sequential chemical ligation approach has been developed for protein synthesis. Key to this strategy is the relative stability of the N,N-bis(2-mercaptoethyl)amide (BMEA) to the conventional conditions of native chemical ligation. We have also found a new thiol additive for the BMEA-mediated ligation reaction. The usefulness of this approach was demonstrated in the syntheses of a medium-sized peptide and ubiquitin.     

Sugar-assisted glycopeptide ligation

The chemical synthesis of glycopeptides and glycoproteins from readily available materials presents an attractive route to homogeneous products for structural and functional studies. Chemical synthesis of glycopeptides and glycoproteins based on native chemical ligation represents one of the useful methods for the synthesis of natural glycopeptide structures. Here we describe a method that allows for the synthesis of glycopeptides from cysteine-free peptides. This method utilizes a peptide thioester and a glycopeptide in which the sugar moiety is modified with a thiol handle at the C-2 position. Upon completion of the ligation reaction, the thiol handle can be reduced with H2/metal to the acetamide moiety, furnishing the unmodified glycopeptides. Together, this sequence of reactions displays an attractive potential in glycopeptides and glycoproteins synthesis.     

Synthesis of l‐ and d‐Ubiquitin by One‐Pot Ligation and Metal‐Free Desulfurization

Native chemical ligation combined with desulfurization has become a powerful strategy for the chemical synthesis of proteins. Here we describe the use of a new thiol additive, methyl thioglycolate, to accomplish one‐pot native chemical ligation and metal‐free desulfurization for chemical protein synthesis. This one‐pot strategy was used to prepare ubiquitin from two or three peptide segments. Circular dichroism spectroscopy and racemic protein X‐ray crystallography confirmed the correct folding of ubiquitin. Our results demonstrate that proteins synthesized chemically by streamlined 9‐fluorenylmethoxycarbonyl (Fmoc) solid‐phase peptide synthesis coupled with a one‐pot ligation–desulfurization strategy can supply useful molecules with sufficient purity for crystallographic studies.     

Monitoring the Thiol/Thiophenol Molecule-Modulated Plasmon-Mediated Silver Oxidation with Dark-Field Optical Microscopy

Surface plasmon can trigger or accelerate many photochemical reactions, especially useful in energy and environmental industries. Recently, molecular adsorption has proven effective in modulating plasmon-mediated photochemistry, however the realized chemical reactions are limited and the underlying mechanism is still unclear. Herein, by using in situ dark-field optical microscopy, the plasmon-mediated oxidative etching of silver nanoparticles (Ag NPs), a typical hot-hole-driven reaction, is monitored continuously and quantitatively. The presence of thiol or thiophenol molecules is found essential in the silver oxidation. In addition, the rate of silver oxidation is modulated by the choice of different thiol or thiophenol molecules. Compared with the molecules having electron donating groups, the ones having electron accepting groups accelerate the silver oxidation dramatically. The thiol/thiophenol modulation is attributed to the modulation of the charge separation between the Ag NPs and the adsorbed thiol or thiophenol molecules. This work demonstrates the great potential of molecular adsorption in modulating the plasmon-mediated photochemistry, which will pave a new way for developing highly efficient plasmonic photocatalysts.     

蔗糖酯的合成研究进展

综述了蔗糖酯的合成方法及工艺的研究进展,并对其反应机理进行了阐述.蔗糖酯的合成方法主要有四种:溶剂法、微乳化法、无溶剂法以及酶催化法.溶剂法采用DMF或DMSO为溶剂,但是这两种溶剂均有毒,限制了蔗糖酯在食品等行业的应用.微乳化法采用丙二醇或水代替溶剂法所使用的有毒溶剂,并加入乳化剂,使反应体系近似为均相体系.无溶剂法则是通过在反应体系中加入乳化剂或表面活性剂等使熔融相成均一相,反应平稳.但是一般无溶剂法反应温度较高,反应不易进行,产率低,且产品质量得不到保证.酶催化合成法是一种新的生物合成方法,采用生物酶代替传统的催化剂合成蔗糖酯,该法催化活性高、反应条件温和、选择性强、产物易分离等优点.文中还对蔗糖酯粗品的纯化工艺进行了介绍.     

A practical procedure for the synthesis of multifunctional aldehydes through the Fukuyama reduction and elucidation of the reaction site and mechanism

A highly efficient heterogeneous Pd/C catalyst D1 was found to effect the reduction of thiol esters 1 to the corresponding aldehydes 2 with such a low catalyst loading as 0.5-1.0 mol %. The chemical properties of the Pd/C catalysts together with the XRF analysis reveal that the reduction is most likely to proceed on the solid surface of the Pd/C catalyst rather than in the solution phase outside the pores. A reaction mechanism through oxidative addition of Pd to the thiol esters 1 was postulated by detection of the oxidative addition intermediate by React IR analysis. A practical purification of 2 was accomplished by conversion to water-soluble bisulfite adducts 7.     

Synthesis of a dicarba analogue of human β-defensin-1 using a combined ring closing metathesis--native chemical ligation strategy

We herein describe the first synthesis of the native antimicrobial protein HBD-1 making use of an orthogonal thiol protection strategy and a novel dicarba analogue thereof. The robust hydrocarbon linkage was installed by replacement of one disulfide bond using on-resin ring closing metathesis. The unprecedented 59-membered C-terminal cysteine macrocyclic fragment thus formed then engages in native chemical ligation allowing convergent access to this unique synthetic protein analogue.     

Ionic liquid 1-ethyl-3-methylimidazolium acetate: an attractive solvent for native chemical ligation of peptides

The ionic liquid 1-ethyl-3-methylimidazolium acetate ([C₂mim][OAc]) was successfully used as alternative solvent for native chemical ligation of peptide fragments to produce model peptide LYRAXCRANK (X = G, A, L, N, Q, K, and F). The commonly used buffer system including thiol additives such as thiophenol and benzyl mercaptan can be replaced by the nontoxic ionic liquid [C₂mim][OAc]. In addition to improving the solubility of the peptides in [C₂mim][OAc], yields and rates of the ligation reactions were found to be efficiently enhanced.     

Use of thiosulfonate for the protection of thiol groups in peptide ligation by the thioester method

Use of thiosulfonate for protecting thiol (-SH) groups in peptide ligation by the thioester method was examined. Thiosulfonate was introduced and was stable in the presence of silver ion, 4-dihydro-3-hydroxy-4-oxo-1,2,3-benzotriazine, and diisopropylethylamine. Based on these results, a strategy for using the thioester method and the native chemical ligation method in the synthesis of a single polypeptide is described.     

Photooxidative coupling of thiophenol derivatives to disulfides

Disulfide bonds play an important role in determining the structure and stability of proteins and nanoparticles. Despite extensive studies on the oxidation of thiols for the synthesis of disulfides, little is known about the photooxidation of thiols, which may be a clean, safe, and economical alternative to the use of harmful and expensive metal-containing oxidants and catalysts. In this paper, we report the photooxidative coupling of thiophenol derivatives to disulfides. Para-substituted thiophenol derivatives, p-SHC(6)H(4)X (X = NO(2), COOH, Cl, and OCH(3)), are irradiated, and disulfides, X(2)(C(6)H(4))(2)S(2), are identified as the major photoproducts using Raman, UV-vis, IR, and NMR spectroscopies. For p-nitrothiophenol (pNTP), 4,4'-dinitrodiphenyldisulfide (DNDPDS) is produced in 81% yield. The product yield changes with pH, being the highest at pH ≈ 5, suggesting that both neutral thiol and anionic thiolate forms of pNTP are required for the photoreaction to occur. Excitation at 455 nm, at which the thiolate form of pNTP absorbs strongly, leads to the largest yield of DNDPDS, whereas very little DNDPDS is formed by excitation of the thiol form of pNTP at 325 nm. Our observations suggest that the photooxidation occurs via collisions of the electronically excited thiolate form of pNTP with the surrounding neutral thiol forms of pNTP. The photooxidation reaction happens regardless of the electron-withdrawing or electron-donating properties of the substituents if the pH and excitation wavelengths are properly chosen. The versatility of light and generality of the photooxidative coupling reaction of thiophenol derivatives may open new possibilities for selective and site-specific photocontrol of disulfide bond formation in biology and nanomaterial science as well as in synthetic chemistry.     

Nanoscale organization of thiol and arylsulfonic acid on silica leads to a highly active and selective bifunctional, heterogeneous catalyst

Ordered mesoporous silicas functionalized with alkylsulfonic acid and thiol group pairs have been shown to catalyze the synthesis of bisphenols from the condensation of phenol and various ketones, with activity and selectivity highly dependent on the distance between the acid and thiol. Here, a new route to thiol/sulfonic acid paired catalysts is reported. A bis-silane precursor molecule containing both a disulfide and a sulfonate ester bond is grafted onto the surface of ordered mesoporous silica, SBA-15, followed by simultaneous disulfide reduction and sulfonate ester hydrolysis. The resulting catalyst, containing organized pairs of arylsulfonic acid and thiol groups, is significantly more active than the alkylsulfonic acid/thiol paired catalyst in the synthesis of bisphenol A and Z, and this increase in activity does not lead to a loss of regioselectivity. The paired catalyst has activity similar to that of a randomly bifunctionalized arylsulfonic acid/thiol catalyst in the bisphenol A reaction but exhibits greater activity and selectivity than the randomly bifunctionalized catalyst in the bisphenol Z reaction.     

Effect of copper salts on peptide bond formation using peptide thioesters

[reaction: see text] In the present paper, systematic studies revealed that Cu(I) salts in general and Cu(II) salts under certain circumstances promote effective reaction between peptide thiol esters and the N-terminal amino function of a second peptide segment to give the native amide bond for both solution- and solid-phase syntheses. Chiral integrity was retained. Reaction conditions were optimized and applied to the synthesis of a small protein, the identity of which was confirmed by NMR analysis.     

Pedal to the Metal: The Homogeneous Catalysis of the Native Chemical Ligation Reaction

The native chemical ligation reaction of peptide thioesters with cysteinyl peptides is a pivotal chemical process in the production of native or modified peptides and proteins, and well beyond in the preparation of various biomolecule analogs and materials. To benefit from this reaction at its fullest and to access all the possible applications, the experimentalist needs to know the factors affecting its rate and how to control it. This concept article presents the fundamental principles underlying the rate of the native chemical ligation and its homogeneous catalysis by nucleophiles. It has been prepared to serve as a quick guide in the search for an appropriate catalyst.     

Construction of a FRET-based ratiometric fluorescent thiol probe

We have rationally constructed a novel FRET-based ratiometric thiol probe suitable for ratiometric imaging in living cells based on the native chemical ligation reaction.     

Thiol–Ene “Click” Reaction Triggered by Neutral Ionic Liquid: The “Ambiphilic” Character of [hmim]Br in the Regioselective Nucleophilic Hydrothiolation

Thiol–ene “click” chemistry has emerged as a powerful strategy to construct carbon–heteroatom (C? S) bonds, which generally results in the formation of two regioisomers. To this end, the neutral ionic liquid [hmim]Br has been explored as a solvent cum catalyst for the synthesis of linear thioethers from activated and inactivated styrene derivatives or secondary benzyl alcohols and thiols without the requirement of using a metal complex, base, or free radical initiator. Furthermore, detailed mechanistic investigations using ¹H NMR spectroscopy and quadrupole time‐of‐flight electrospray ionization mass spectrometry (Q‐TOF ESI‐MS) revealed that the “ambiphilic” character of the ionic liquid promotes the nucleophilic addition of thiol to styrene through an anti‐Markovnikov pathway. The catalyst recyclability and the extension of the methodology for thiol–yne click chemistry are additional benefits. A competitive study among thiophenol, styrene, and phenyl acetylene revealed that the rate of reaction is in the order of thiol–yne>thiol–ene>dimerization of thiol in [hmim]Br.     

Transesterification of Soybean Oil Catalyzed by Calcium Hydroxide which Obtained from Hydrolysis Reaction of Calcium Carbide

Calcium carbide residue (CCR) was investigated in transesterification reaction of triglycerides to determine its viability as a solid catalyst for biodiesel synthesis. Literature survey showed that CCR has never been studied as a solid catalyst in the transesterification of triglyceride. The scope of the study includes the effects of CCR calcination temperature, calcination time, the alcohol/oil molar ratio, the catalyst amount (wt % of oil) and the reaction time. The relationship between chemical composition and catalytic activity of waste cement was also investigated. These CCR catalysts, thermally activated at 600 °C, can give rise to fatty acid methyl esters (FAME) purity higher than 99.5%, after 3 h of reaction, when oil/methanol molar ratio of 1/12 and 1 wt % of the catalyst were employed. Application of CCR as catalyst for biodiesel production in this study may not only provide a cost‐effective and environment friendly way of recycling CCR waste but also reduce hopefully the cost of biodiesel production.