Salicyaldehyde-based fluorescent sensors with high sensitivity for amino acids

Structurally simple salicylaldehyde-based fluoreseent sensors for amino acids have been obtained by one-step or two-step synthesis.These sensors show significant fluorescence enhancement in the presence of many amino acids at concentrations as low as 10~5 mol/L.The reversible reaction of the aldehydes with amino acids to form imines in aqueous solution is proposed to account for the observed fluorescence enhancement.     

DNA hybridization chain reaction and DNA supersandwich self-assembly for ultrasensitive detection

The fabrication of sensitive sensors with high selectivity is highly desirable for the detection of some important biomarkers,such as nucleic acids,proteins,small molecules and ions.DNA hybridization chain reaction(HCR) and DNA supersandwich self-assembly(SSA) are two prevalent enzyme-free signal amplification strategies to improve sensitivity of the sensors.In this review,we firstly describe the characteristics about DNA HCR and DNA SSA,and then summarize the advances in the one-dimensional DNA nanostructures assisted by HCR and SSA.This review has been divided into three parts according to the two signal amplification methods and highlights recent progress in these two strategies to improve the detection sensitivity of proteins,nucleic acids,small molecules and ions.     

Carbon nanomaterials and metallic nanoparticles-incorporated electrochemical sensors for small metabolites: Detection methodologies and applications

Detection of small metabolite biomarkers at different concentrations could be powerfully used for disease diagnosis and progression. To enhance detection capabilities, nanomaterials possessing excellent optical and electrochemical properties have been integrated into a wide range of sensing or detection platforms. This review will highlight recent developments in creating electrochemical sensors alongside biosensors using carbon nanomaterials and metallic nanoparticles that target small metabolites. Moreover, electrochemical sensors having different detection strategies toward metabolites (such as amino acids, amino acid–derived neurotransmitters, vitamins, adenosine triphosphate, and purine derivatives) will be discussed. Finally, certain challenging issues and future aspects of nanomaterials-integrated electrochemical sensors for small metabolites will be discussed.     

Serine‐Selective Aerobic Cleavage of Peptides and a Protein Using a Water‐Soluble Copper–Organoradical Conjugate

The site‐specific cleavage of peptide bonds is an important chemical modification of biologically relevant macromolecules. The reaction is not only used for routine structural determination of peptides, but is also a potential artificial modulator of protein function. Realizing the substrate scope beyond the conventional chemical or enzymatic cleavage of peptide bonds is, however, a formidable challenge. Here we report a serine‐selective peptide‐cleavage protocol that proceeds at room temperature and near neutral pH value, through mild aerobic oxidation promoted by a water‐soluble copper–organoradical conjugate. The method is applicable to the site‐selective cleavage of polypeptides that possess various functional groups. Peptides comprising D ‐amino acids or sensitive disulfide pairs are competent substrates. The system is extendable to the site‐selective cleavage of a native protein, ubiquitin, which comprises more than 70 amino acid residues.     

Direct mono-N-methylation of solid-supported amino acids: a useful application of the Matteson rearrangement of alpha-aminoalkylboronic esters

[reaction: see text] A novel solid-phase method for the mono-N-methylation of resin-supported amino acids was developed on the basis of Matteson's 1,2-carbon-to-nitrogen migration of boron in alpha-aminoalkylboronic esters. Amino acids supported on either Wang resin or the highly acid-sensitive SASRIN resin can be methylated by reaction with pinacol chloromethylboronic ester, followed by rearrangement of the resulting aminomethylboronate and subsequent cleavage of the boronate group. This direct method requires only a simple and expedient oxidative resin wash to repair overalkylated sites.     

Chiral auxiliary based approach toward the synthesis of C-glycosylated amino acids

[reaction in text] In a chiral auxiliary based method C-glycosylated amino acids can be obtained by a 1,3-dipolar cycloaddition of a chiral glycine equivalent and C-1 allyl- or vinyl-derived carbohydrate building blocks as the key step. The products are formed regio- and diastereoselectively. Reductive cleavage of the N-O bond of the isoxazolidine and of the chiral auxiliary leads to C-glycosylated amino acids. The use of (-)-menthone to (+)-menthone as the auxiliary leads to the corresponding diastereomers.     

Efficient Fmoc-Protected Amino Ester Hydrolysis Using Green Calcium(II) Iodide as a Protective Agent

In order to modify amino acids, the C-terminus carboxylic acid usually needs to be protected, typically as a methyl ester. However, standard cleavage of methyl esters requires either highly basic or acidic conditions, which are not compatible with Fmoc or acid-labile protecting groups. This highlights the need for orthogonal conditions that permit selective deprotection of esters to create SPPS-ready amino acids. Herein, mild orthogonal ester hydrolysis conditions are systematically explored using calcium(II) iodide as a protective agent for the Fmoc protecting group and optimized for a broad scope of amino esters. Our optimized reaction improved on the already known trimethyltin hydroxide, as it produced better yields with greener, inexpensive chemicals and a less extensive energy expenditure.     

Further studies on the fragmentation of protonated ions of peptides containing aspartic acid, glutamic acid, cysteine sulfinic acid, and cysteine sulfonic acid

Here we examined the fragmentation, on a quadrupole ion-trap mass spectrometer, of the protonated ions of a group of peptides containing one arginine and two different acidic amino acids, one being aspartic acid (Asp) or glutamic acid (Glu) and the other being cysteine sulfinic acid [C(SO2H)] or cysteine sulfonic acid [C(SO3H)]. Our results showed that, upon collisional activation, the cleavage of the peptide bond C-terminal to C(SO2H) is much more facile than that of the peptide bond C-terminal to Asp, Glu, or C(SO3H). There is no significant difference, however, in susceptibility to cleavage of peptide bonds that are C-terminal to Asp, Glu, and C(SO3H). To understand these experimental observations, we carried out B3LYP/6-31G* density functional theory calculations for a model cleavage reaction of GXG --> b2 + Gly, in which X is Asp, Glu, C(SO2H), or C(SO3H). Our calculation results showed that the cleavage reaction is thermodynamically more favorable when X = C(SO2H) than when X = Asp or C(SO3H). We attributed the less facile cleavage of the amide bond after Glu to that the formation of a six-membered ring b ion for Glu-bearing peptides is kinetically not as favorable as the formation of a five-membered ring b ion for peptides containing the other three acidic amino acids. The results from this study may provide useful tools for peptide sequencing.     

Short peptides as biosensor transducers

This review deals with short peptides (up to 50 amino acids) as biomimetic active recognition elements in sensing systems. Peptide-based sensors have been developed in recent years according to different strategies. Synthetic peptides have been designed on the basis of known interactions between single or a few amino acids and targets, with attention being paid to the presence of peptide motifs known to allow intermolecular self-organization of the sensing peptides over the sensor surface. Sensitive and sophisticated sensors have been obtained in this way, but the use of designed peptides is limited by severe difficulties in their in silico design. Short peptides from random phage display have been selected in a random way from large, unfocussed, and often preexisting and commercially available phage display libraries, with no design elements. Such peptides often perform better than antibodies, but they are difficult to select when the target is a small molecule because of the need to immobilize it with considerable modifications of its structure. Artificial, miniaturized receptors have been obtained from the reduction of the known sequence of a natural receptor down to a synthesizable and yet stable one. Alternatively, binding sites have been created over a designed, stable peptide scaffold. Short peptides have also been used as active elements for the detection of their own natural receptors: pathogenic bacteria have been detected with antimicrobial and cell-penetrating peptides, but key challenges such as detection of bacteria in real samples, improved sensitivity, and improved selectivity have to be faced. Peptide substrates have been conjugated to fluorescent quantum dots to obtain disposable sensors for protease activity with high sensitivity. Ferrocene–peptide conjugates have been used for electrochemical sensing of protease activity.     

Sterically biased 3,3-sigmatropic rearrangement of azides: efficient preparation of nonracemic alpha-amino acids and heterocycles

[reaction: see text] Homochiral alpha-amino acids, heterocycles, and carbocycles are efficiently constructed via a short sequence of reactions starting from the chiral auxiliary p-menthane-3-carboxaldehyde. The key feature of the sequence is a highly selective tandem Mitsunobu/3,3-sigmatropic rearrangement of hydrazoic acid that procures enantiomerically enriched allylic azides. The sequence is either terminated by oxidative cleavage to provide amino acids or by ring-closing metathesis to provide heterocycles or carbocycles bearing nitrogen.     

An automated fluorescence protein sequencer using 7-methylthio-4-(2,1,3-benzoxadiazolyl) isothiocyanate (MTBD-NCS) as an Edman reagent

An automated fluorescence protein sequencer using 7-methylthio-5-(2,1,3-benzoxadiazolyl) isithiocyanate (MTBD-NCS), a fluorescent Edman reagent, is developed by the modification of a commercial protein sequencer. The generated MTBD-thiohydantoin amino acids fluoresced strongly, whereas the by-products such as MTBD-thiocarbamoyl amino acids and MTBD-carbamoly amino acids did not fluoresce. A few interfering peaks were observed in the chromatogram and amino acid sequence was easily determined. The coupling and cyclization/cleavage reaction conditions and extraction conditions of generated MTBD-thiazolinone amino acids were optimized using an autonalyzer. Finally, the sequence of a synthetic peptide (25 pmol), leucine-enkephalin-Thr-amide, was determined and up to six residues were successively analyzed.     

Enantioselective alpha-silyl amino acid synthesis by reverse-aza-Brook rearrangement

[reaction: see text] Asymmetric reverse-aza-Brook rearrangement of N-Boc-N-trialkylsilyl allylamine yields an enantiomerically enriched alpha-amino allylsilane. Oxidative cleavage of the alkene leads to a Boc-protected amino acid with the configuration of naturally occurring amino acids (L). Standard coupling protocols, including the use of trifluoroacetic acid for removal of the Boc group, yield a tripeptide with a central silane amino acid.     

Reactions of an aromatic σ,σ-biradical with amino acids and dipeptides in the gas phase

Gas-phase reactivity of a positively charged aromatic σ,σ-biradical (N-methyl-6,8-didehydroquinolinium) was examined toward six aliphatic amino acids and 15 dipeptides by using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) and laser-induced acoustic desorption (LIAD). While previous studies have revealed that H-atom and NH₂ abstractions dominate the reactions of related monoradicals with aliphatic amino acids and small peptides, several additional, unprecedented reaction pathways were observed for the reactions of the biradical. For amino acids, these are 2H-atom abstraction, H₂O abstraction, addition — CO₂, addition — HCOOH, and formation of a stable adduct. The biradical reacts with aliphatic dipeptides similarly as with aliphatic amino acids, but undergoes also one additional reaction pathway, addition/C-terminal amino acid elimination (addition — CO — NHCHR_C). These reactions are initiated by H-atom abstraction by the biradical from the amino acid or peptide, or nucleophilic addition of an NH₂ or a HO group of the amino acid or peptide at the radical site at C-6 in the biradical. Reactions of the unquenched C-8 radical site then yield the products not observed for related monoradicals. The biradical reacts with aromatic dipeptides with an aromatic ring in N-terminus (i.e., Tyr-Leu, Phe-Val, and Phe-Pro) similarly as with aliphatic dipeptides. However, for those aromatic dipeptides that contain an aromatic ring in the C-terminus (i.e., Leu-Tyr and Ala-Phe), one additional pathway, addition/N-terminal amino acid elimination (addition — CO — NHCHR_N), was observed. This reaction is likely initiated by radical addition of the biradical at the aromatic ring in the C-terminus. Related monoradicals add to aromatic amino acids and small peptides, which is followed by Cα-Cβ bond cleavage, resulting in side-chain abstraction by the radical. For biradicals, with one unquenched radical site after the initial addition, the reaction ultimately results in the loss of the N-terminal amino acid. Similar to monoradicals, the C-S bond in amino acids and dipeptides was found to be especially susceptible to biradical attack.     

Evaluation of gaseous hydrogen fluoride as a convenient reagent for parallel cleavage from the solid support

We have tested the limits of gaseous hydrogen fluoride as an agent for parallel detachment of organic molecules from the solid support. Peptides were chosen as relatively sensitive models for this reaction. Acid-catalyzed amide bond hydrolysis, side chain modification (tryptophan and other unnatural amino acids) by the protecting group residues as well as dehydration of serine and asparagine was followed. The technique of cleavage of side chain protection prior to the resin cleavage has given satisfactory results. Two-step deprotection and cleavage from benzhydrylamine resin by TFA and HF was compared to the deprotection and cleavage by TFA from Knorr resin.     

Solid-phase synthesis of peptide and glycopeptide thioesters through side-chain-anchoring strategies

An efficient new strategy for the synthesis of peptide and glycopeptide thioesters is described. The method relies on the side-chain immobilization of a variety of Fmoc-amino acids, protected at their C-termini, on solid supports. Once anchored, peptides were constructed using solid-phase peptide synthesis according to the Fmoc protocol. After unmasking the C-terminal carboxylate, either thiols or amino acid thioesters were coupled to afford, after cleavage, peptide and glycopeptide thioesters in high yields. Using this method a significant proportion of the proteinogenic amino acids could be incorporated as C-terminal amino acid residues, therefore providing access to a large number of potential targets that can serve as acyl donors in subsequent ligation reactions. The utility of this methodology was exemplified in the synthesis of a 28 amino acid glycopeptide thioester, which was further elaborated to an N-terminal fragment of the glycoprotein erythropoietin (EPO) by native chemical ligation.     

Efficient Ring Opening of Aziridines with Carboxylic Acids

An efficient ring cleavage of aziridines with acids has been studied in the absence of any catalyst. The hydrolysis of the products, amino esters, leads to the corresponding amino alcohols. The reaction has been extended to chiral cycloalkyl aziridines, leading to the formation of diastereomers. After separation, these diastereomers have been converted to optically pure amino alcohols in two steps.     

Functionalized ionic liquids as new supports for peptide coupling and traceless catalyzed carbon-carbon coupling reactions

A new strategy to obtain pure ionic liquid support with a high loading (3 mmol/g) of primary amino groups is reported. The compatibility of the imidazolium unit was demonstrated with DIC or DCC coupling reactions of protected amino acids and with classical cleavage of BOC or Fmoc protecting groups. In addition, this is the first report of a traceless ionic liquid support based on a silicon linker with a high loading (3 mmol/g) of aryl bromide reactive groups used in a palladium-catalyzed carbon-carbon coupling reaction.     

New stable backbone linker resins for solid-phase peptide synthesis

[reaction: see text] Two new 4-methoxybenzaldehyde backbone linker resins were developed for the solid-phase synthesis of peptides. The linkers are very stable during the cleavage of common protecting groups for amines (Fmoc, Boc) and carboxylic acids (Me, All, tBu) in peptide synthesis. Cleavage from the resin with refluxing TFA is sufficiently mild for peptides containing polar and nonpolar amino acids.     

Vinyl Ether/Tetrazine Pair for the Traceless Release of Alcohols in Cells

The cleavage of a protecting group from a protein or drug under bioorthogonal conditions enables accurate spatiotemporal control over protein or drug activity. Disclosed herein is that vinyl ethers serve as protecting groups for alcohol‐containing molecules and as reagents for bioorthogonal bond‐cleavage reactions. A vinyl ether moiety was installed in a range of molecules, including amino acids, a monosaccharide, a fluorophore, and an analogue of the cytotoxic drug duocarmycin. Tetrazine‐mediated decaging proceeded under biocompatible conditions with good yields and reasonable kinetics. Importantly, the nontoxic, vinyl ether duocarmycin double prodrug was successfully decaged in live cells to reinstate cytotoxicity. This bioorthogonal reaction presents broad applicability and may be suitable for in vivo applications.     

Traceless Approach for the Synthesis of 3,5-Disubstituted Thiohydantoins on Functionalized Ionic-Liquid Support

A traceless approach for the synthesis of 3,5-disubstituted thiohydantoins on a novel functionalized ionic-liquid support, 5, is described. Acylation of benzylamine functionalized ionic-liquid support with amino acids yielded ionic-liquid-supported amino acids, which reacted with isothiocyanates to afford ionic-liquid-supported thioureas. Following intramolecular cyclization cleavage from the ionic-liquid support by trifluoroacetic acid (TFA), the desired 3,5-disubstituted thiohydantoins were obtained in good yields and purities. The efficiency of this ionic-liquid-phase strategy facilitated isolation and analysis of intermediates and removal of excess reagents and by-products during the reaction process.