Expanded utility of the native chemical ligation reaction

The post-genomic era heralds a multitude of challenges for chemists and biologists alike, with the study of protein functions at the heart of much research. The elucidation of protein structure, localization, stability, post-translational modifications, and protein interactions will steadily unveil the role of each protein and its associated biological function in the cell. The push to develop new technologies has necessitated the integration of various disciplines in science. Consequently, the role of chemistry has never been so profound in the study of biological processes. By combining the strengths of recombinant DNA technology, protein splicing, organic chemistry, and the chemoselective chemistry of native chemical ligation, various strategies have been successfully developed and applied to chemoselectively label proteins, both in vitro and in live cells, with biotin, fluorescent, and other small molecule probes. The site-specific incorporation of molecular entities with unique chemical functionalities in proteins has many potential applications in chemical and biological studies of proteins. In this article, we highlight recent progress of these strategies in several areas related to proteomics and chemical biology, namely, in vitro and in vivo protein biotinylation, protein microarray technologies for large-scale protein analysis, and live-cell bioimaging.     

Theoretical insights into enantioselective catalysis: the mechanism of the Kharasch-Sosnovsky reaction

The mechanism of the Kharasch-Sosnovsky reaction has been investigated using B3 LYP/6-31G* calculations on a chiral reaction model [cyclohexene+tert-butyl perbenzoate-->cyclohex-2-enyl benzoate+tert-butyl alcohol, catalyzed by a chiral bisoxazoline-copper(I) complex]. Although two previous reaction mechanisms have been considered, the results are consistent with a new mechanistic pathway. This path involves ligand exchange between the catalyst-cyclohexene complex with tert-butyl perbenzoate to give a catalyst-perester complex, which undergoes an (either one- or two-step) oxidative addition reaction to yield a copper(III) complex. The limiting step of the Kharasch-Sosnovsky reaction consists of an intramolecular step involving the abstraction of an allylic hydrogen from cyclohexene [which is pi-bound to the copper(III) complex]. The resulting allyl-copper(III) complex (subsequent to the loss of tert-butanol) can undergo a haptotropic rearrangement by means of an eta1-allyl/eta3-allyl equilibrium, leading to scrambling between vinylic and allylic positions when an isotopically labeled substrate is used. The allyl-copper(III) ion undergoes a stereospecific reductive elimination involving the pi-bond migration to yield a reaction product-catalyst complex, which can regenerate the alkene-copper(I) complex by ligand exchange. The proposed reaction mechanism is consistent with all known experimental results (including enantioselectivity data).     

Insights into reaction mechanisms in heterogeneous catalysis revealed by in situ NMR spectroscopy

This tutorial review intends to show the possibilities of in situ solid state NMR spectroscopy in the elucidation of reaction mechanisms and the nature of the active sites in heterogeneous catalysis. After a brief overview of the more usual experimental devices used for in situ solid state NMR spectroscopy measurements, some examples of applications taken from the recent literature will be presented. It will be shown that in situ NMR spectroscopy allows: (i) the identification of stable intermediates and transient species using indirect methods, (ii) to prove shape selectivity in zeolites, (iii) the study of reaction kinetics, and (iv) the determination of the nature and the role played by the active sites in a catalytic reaction. The approaches and methodology used to get this information will be illustrated here summarizing the most relevant contributions on the investigation of the mechanisms of a series of reactions of industrial interest: aromatization of alkanes on bifunctional catalysts, carbonylation reaction of methanol with carbon monoxide, ethylbenzene disproportionation, and the Beckmann rearrangement reaction. Special attention is paid to the research carried out on the role played by carbenium ions and alkoxy as intermediate species in the transformation of hydrocarbon molecules on solid acid catalysts.     

An investigation into the origin of the dramatically reduced reactivity of peptide-prolyl-thioesters in native chemical ligation

The low reactivity of peptide-prolyl-thioesters in native chemical ligation is not due to steric effects at the β-carbon, but rather to the presence of a carbonyl moiety on the nitrogen atom of the proline.     

Oxo-ester mediated native chemical ligation: concept and applications

A direct oxo-ester peptide ligation method has been developed. Through the use of an activated C-terminal para nitrophenyl ester (1), it is possible to achieve direct cysteine ligations (1 + 2 --> 4). Peptide substrates incorporating bulky C-terminal amino acids (1) can be accommodated with high reaction efficiency.     

Insights into the reaction mechanism between propadienylidene and ethylene: a DFT study

The reaction mechanism between propadienylidene and ethylene has been systematically investigated employing the B3LYP/6-311++G** and MP2/cc-pVTZ levels of theory to better understand the reactivity of propadienylidene with unsaturated hydrocarbons. Geometry optimization, vibrational analysis, and energy property for the involved stationary points on the potential energy surface have been calculated. Two important initial reaction complexes characterized by three- and four-membered ring structures have been located firstly. After that, three different products possessing three-, four-, and five-membered ring characters have been obtained through three reaction pathways. In the first reaction pathway, a three-membered ring alkyne compound has been obtained. As for the second reaction pathway, it is a diffusion-controlled reaction, resulting in the formation of the four-membered ring conjugated diene compound. A five-membered conjugated diene compound has been obtained in the third reaction pathway, which is the most stable product in the available products thermodynamically. On the other hand, the second reaction pathway is the most favorable reaction to proceed kinetically.     

On-resin native chemical ligation for cyclic peptide synthesis

A novel cysteine derivative, N(alpha)-trityl-S-(9H-xanthen-9-yl)-l-cysteine [Trt-Cys(Xan)-OH] has been introduced for peptide synthesis, specifically for application to a new strategy for the preparation of cyclic peptides. The following steps were carried out to synthesize the cyclic model peptide cyclo(Cys-Thr-Abu-Gly-Gly-Ala-Arg-Pro-Asp-Phe): (i). side-chain anchoring of Fmoc-Asp-OAl via its free beta-carboxyl as a p-alkoxybenzyl ester to a solid support; (ii). stepwise chain elongation of the peptide by standard Fmoc/tBu solid-phase chemistry; (iii). removal of the N-terminal Fmoc group; (iv). coupling of Trt-Cys(Xan)-OH; (v). selective Pd(0)-promoted cleavage of the C-terminal allyl ester; (vi). coupling of the C-terminal residue, i.e., H-Phe-SBzl, preactivated as a thioester; (vii). selective removal of the N(alpha)-Trt and S-Xan protecting groups under very mild acid conditions; (viii). on-resin cyclization by native chemical ligation in an aqueous milieu; and (ix). final acidolytic cleavage of the cyclic peptide from the resin. The strategy was evaluated for three supports: poly[N,N-dimethacrylamide-co-poly(ethylene glycol)] (PEGA), cross-linked ethoxylate acrylate resin (CLEAR), and poly(ethylene glycol)-polystyrene (PEG-PS) graft resin supports. For PEGA and CLEAR, the desired cyclic product was obtained in 76-86% overall yield with initial purities of approximately 70%, whereas for PEG-PS (which does not swell nearly as well in water), results were inferior. Solid-phase native chemical ligation/cyclization methodology appears to have advantages of convenience and specificity, which make it promising for further generalization.     

Simplifying native chemical ligation with an N-acylsulfonamide linker

We report a simplified procedure for the chemical ligation of peptides by using the sulfamylbutyryl linker as a mildly activating group capable of participating in ligation. When the peptidyl N-methylsulfonamide is directly added with excess thiols to ligation reactions, the speed of reaction is comparable to native chemical ligation.     

Synthesis of a selenocysteine-containing peptide by native chemical ligation

[reaction in text] A new method for the synthesis of selenocysteine derivatives and selenocysteine-containing peptides is described. Fmoc-Se-p-methoxybenzylselenocysteine (1) was prepared and used for solid-phase synthesis of peptides with an N-terminal unprotected selenocysteine. Subsequent native chemical ligation with a peptide thioester provided a 17-mer that corresponds to the C-terminus of ribonucleotide reductase with selenocysteine in place of cysteine.     

Optimisation of chemical protein cleavage for erythropoietin semi-synthesis using native chemical ligation

Selective protein cleavage at methionine residues is a useful method for the production of bacterially derived protein fragments containing an N-terminal cysteine residue required for native chemical ligation. Here we describe an optimised procedure for cyanogen bromide-mediated protein cleavage, and ligation of the resulting fragments to afford biologically active proteins.     

A novel neoglycopeptide linkage compatible with native chemical ligation

The straightforward synthesis of a novel class of neoglycopeptide and its fusion with a larger peptide thioester using sequential chemoselective ligations is described.     

Synthesis of thiazolidine thioester peptides and acceleration of native chemical ligation

Thiazolidine thioester peptides were synthesized by reacting bis(2-sulfanylethyl)amido peptides with glyoxylic acid at pH 1. A significant increase in Native Chemical Ligation (NCL) rate was observed with thiazolidine thioesters compared to 3-mercaptopropionic acid-thioester analogues. The method is of particular interest for accelerating valine-cysteine peptide bond formation.     

Rapid chemical ligation of oligonucleotides by the Diels-Alder reaction

Extremely fast and efficient Diels-Alder chemical ligation of furan and maleimide oligonucleotides has been carried out in aqueous buffer. It was possible to ligate three oligonucleotides simultaneously in a controlled manner with the aid of a complementary splint. The templated reactions proceeded within 1 min at room temperature whereas non-templated reactions were slow and incomplete. Rapid and clean methods of DNA ligation such as the one demonstrated here have potential uses in biology and nanotechnology.     

Insights into the reaction mechanism of soluble epoxide hydrolase from theoretical active site mutants

Density functional theory calculations of active site mutants are used to gain insights into the reaction mechanism of the soluble epoxide hydrolases (sEHs). The quantum chemical model is based on the X-ray crystal structure of the human soluble epoxide hydrolase. The role of two conserved active site tyrosines is explored through in silico single and double mutations to phenylalanine. Full potential energy curves for hydrolysis of (1S,2S)-beta-methylstyrene oxide are presented. The results indicate that the two active site tyrosines act in concert to lower the activation barrier for the alkylation step. For the wild-type and three different tyrosine mutant models, the regioselectivity of epoxide opening is compared for the substrates (1S,2S)-beta-methylstyrene oxide and (S)-styrene oxide. An additional part of our study focuses on the importance of the catalytic histidine for the alkylation half-reaction. Different models are presented to explore the protonation state of the catalytic histidine in the alkylation step and to evaluate the possibility of an interaction between the nucleophilic aspartate and the catalytic histidine.     

A computational foray into the mechanism and catalysis of the adduct formation reaction of guanine with crotonaldehyde

Crotonaldehyde, a common environmental pollutant and product of endogenous lipid peroxidation, reacts with guanine to form DNA adducts with pronounced genotoxicity and mutagenicity. Here, we explore the molecular mechanism of this adduct formation using double-hybrid density functional theory methods. The reaction can be envisaged to occur in a two-step fashion via an aza-Michael addition leading to an intermediate ring-open adduct followed by a cyclization reaction giving the mutagenic ring-closed adduct. We find that (i) a 1,2-type addition is favored over a 1,4-type addition for the aza-Michael addition, and (ii) an initial tautomerization of the guanine moiety in the resulting ring-open adduct significantly reduces the barrier toward cyclization compared to the direct cyclization of the ring-open adduct in its keto-form. Overall, the aza-Michael addition is found to be rate-determining. We further find that participation of a catalytic water molecule significantly reduces the energy barriers of both the addition and cyclization reaction. © 2018 Wiley Periodicals, Inc.     

Convergent synthesis of peptide nucleic acids by native chemical ligation

[reaction: see text] A convergent strategy for synthesizing long contiguous PNA by a native chemical ligation-like technique of PNA segment couplings is presented. This approach required the synthesis of a new PNA-monomer featuring a 1-amino-2-thiol group. It is shown that the additional mercaptomethyl group leaves the hybridization properties of PNA ligation products unaffected. Furthermore, rapid and efficient fluorescence labeling of the ligation products is demonstrated.