Synthesis of Peptide Cysteine Dimedone Using Fmoc-Cys(Dmd)-OH: Glutathione Cysteine Dimedone as a Probe in Investigating the Sulfenic Acid Mediated Oxidation of Glutathione

Dimedone is the most widely used chemical probe for detection of cysteine sulfenic acid in peptides and proteins. The reaction of dimedone with cysteine sulfenic acid results in the formation of unique cysteine dimedone motif containing thioether bridge. Based on the structure of cysteine dimedone residue in polypeptide, a new building block of Fmoc-Cys(Dmd)-OH was developed for solid phase synthesis of peptide cysteine dimedone. Mass spectrometric sequencing of synthetic peptides have confirmed successful incorporation of cysteine dimedone in peptide chain using HBTU/HOBt as a coupling agent. The new method permits synthesis of peptides containing both cysteine thiol and cysteine dimedone in the same sequence which was difficult to achieve by conventional methods. The synthetic peptide of glutathione cysteine dimedone was used as a standard in probing the air-mediated oxidation of thiol to disulfide form of glutathione. The co-elution of standard peptide and reaction mixture of oxidation of glutathione in presence of dimedone using RP-HPLC have confirmed the formation of glutathione cysteine sulfenic as an intermediate in the air-mediated oxidation of glutathione. The synthetic peptides of cysteine dimedone may find application in the field of redox proteomics and generation of antibodies against modified cysteine residue.     

Proteomic analysis of peptides tagged with dimedone and related probes

Owing to its labile nature, a new role for cysteine sulfenic acid (–SOH) modification has emerged. This oxidative modification modulates protein function by acting as a redox switch during cellular signaling. The identification of proteins that undergo this modification represents a methodological challenge, and its resolution remains a matter of current interest. The development of strategies to chemically modify cysteinyl‐containing peptides for liquid chromatography–tandem mass spectrometry (LC‐MS/MS) analysis has increased significantly within the past decade. The method of choice to selectively label sulfenic acid is based on the use of dimedone or its derivatives. For these chemical probes to be effective on a proteome‐wide level, their reactivity toward –SOH must be high to ensure reaction completion. In addition, the presence of an adduct should not interfere with electrospray ionization, the efficiency of induced dissociation in MS/MS experiments or with the identification of Cys‐modified peptides by automated database searching algorithms. Herein, we employ a targeted proteomics approach to study the electrospray ionization and fragmentation effects of different –SOH specific probes and compared them to commonly used alkylating agents. We then extend our study to a whole proteome extract using shotgun proteomic approaches. These experiments enable us to demonstrate that dimedone adducts do not interfere with electrospray by suppressing the ionization nor impede product ion assignment by automated search engines, which detect a + 138 Da increase from unmodified peptides. Collectively, these results suggest that dimedone can be a powerful tool to identify sulfenic acid modifications by high‐throughput shotgun proteomics of a whole proteome. Copyright © 2014 John Wiley & Sons, Ltd.     

Spectroscopic and computational studies of nitrile hydratase: insights into geometric and electronic structure and the mechanism of amide synthesis

Nitrile hydratases (NHases) are mononuclear nonheme enzymes that catalyze the hydration of nitriles to amides. NHase is unusual in that it utilizes a low-spin (LS) Fe^III center and a unique ligand set comprised of two deprotonated backbone amides, cysteine-based sulfenic acid (RSO(H)) and sulfinic acid (RSO₂^–), and an unmodified cysteine trans to an exogenous ligand site. Electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD) and low-temperature absorption (LT-Abs) spectroscopies are used to determine the geometric and electronic structures of butyrate-bound (NHaseBA) and active (NHaseAq) NHase. These data calibrate DFT models, which are then extended to explore the mechanism of nitrile hydration by NHase. In particular, the nitrile is activated by coordination to the LS Fe^III and the sulfenate group is found to be deprotonated and a significantly better nucleophile than water that can attack the coordinated nitrile to form a cyclic species. Attack at the sulfenate S atom of the cyclic species is favorable and leads to a lower kinetic barrier than attack by water on coordinated, uncyclized nitrile, while attack at the C of the cyclic species is unfavorable. The roles of the unique ligand set and low-spin nature of the NHase active site in function are also explored. It is found that the oxidized thiolate ligands are crucial to maintaining the LS state, which is important in the binding and activation of nitrile susbtrates. The dominant role of the backbone amidate ligands appears to be as a chelate in keeping the sulfenate properly oriented for nucleophilic attack on the coordinated substrate.     

Reactive sulfur species: kinetics and mechanisms of the oxidation of cysteine by hypohalous acid to give cysteine sulfenic acid

Cysteine sulfenic acid has been generated in alkaline aqueous solution by oxidation of cysteine with hypohalous acid (HOX, X = Cl or Br). The kinetics and mechanisms of the oxidation reaction and the subsequent reactions of cysteine sulfenic acid have been studied by stopped-flow spectrophotometry between pH 10 and 14. Two reaction pathways were observed: (1) below pH 12, the condensation of two sulfenic acids to give cysteine thiosulfinate ester followed by the nucleophilic attack of cysteinate on cysteine thiosulfinate ester and (2) above pH 10, a pH-dependent fast equilibrium protonation of cysteine sulfenate that is followed by rate-limiting comproportionation of cysteine sulfenic acid with cysteinate to give cystine. The observation of the first reaction suggests that the condensation of cysteine sulfenic acid to give cysteine thiosulfinate ester can be competitive with the reaction of cysteine sulfenic acid with cysteine.     

Synthesis of two closely spaced cysteine barbiturates containing peptides by copper-catalyzed oxidation of contryphan disulfide

In this report, we are documenting the synthesis of peptide barbiturate through copper-catalyzed oxidation of peptide disulfide. Single disulfide-containing contryphans are used as models to access possibility of anchoring of barbituric acid (BRB) onto the peptide disulfide. Current method permits anchoring of two molecules of BRB onto the polypeptide and yield of peptide barbiturates varies from 59 to 84%. Formation of cysteine sulfenic acid (Cys-SOH) during oxidation of disulfide was confirmed using chemical probe of Cys-SOH dimedone. Mass spectrometric studies have confirmed the presence of cysteine barbiturate in anchored peptides. Based on the nature of reactive oxygen species involved in oxidation of peptide disulfide, possible mechanisms were proposed for anchoring of BRB onto the peptide disulfide through Cys-SOH. This is the first report on anchoring of two molecules of BRB onto the closely spaced cysteine residues of single polypeptide.     

Halomethyl-Triazoles for Rapid,Site-Selective Protein Modification

Post-translational modifications (PTMs) are used by organisms to control protein structure and function after protein translation, but their study is complicated and their roles are not often well understood as PTMs are difficult to introduce onto proteins selectively. Designing reagents that are both good mimics of PTMs, but also only modify select amino acid residues in proteins is challenging. Frequently, both a chemical warhead and linker are used, creating a product that is a misrepresentation of the natural modification. We have previously shown that biotin-chloromethyl-triazole is an effective reagent for cysteine modification to give S-Lys derivatives where the triazole is a good mimic of natural lysine acylation. Here, we demonstrate both how the reactivity of the alkylating reagents can be increased and how the range of triazole PTM mimics can be expanded. These new iodomethyl-triazole reagents are able to modify a cysteine residue on a histone protein with excellent selectivity in 30 min to give PTM mimics of acylated lysine side-chains. Studies on the more complicated, folded protein SCP-2L showed promising reactivity, but also suggested the halomethyl-triazoles are potent alkylators of methionine residues.     

Thermal rearrangement of 1,3-thiazolidine sulfoxides: Thiolsulfinate and thioaldehyde intermediates

Stereospecific ring opening of the sulfoxides cis- 13 and trans- 14 in refluxing toluene gave the corre sponding sulfenic acids 9 , 10 intermediates respectively. The sulfenic acid 9 dimerized to the thiolsulfinate 17 by dual function of the sulfenic acid as S-nucleophile/S-electrophile with loss of water while the sulfenic acid 10 was unchanged. The stereospecific recyclization of 10 to the parent sulfoxide 14 increases the higher pi-electron density of the double. The thermolysis of the thiolsulfinate 17 gave the transient sulfenic acid 9 , which dimerized again to repeat the process and unisolable thioaldehyde 21 . The thioaldehyde 21 was con verted to either pyrrole 15 by the action of a sulfinic acid 20 catalyst formed inevitably by hydrolysis of 17 under the reaction conditions, or thiazole 18 under neutral conditions. In these rearrangements, the amide carbonyl group facilitated the elimination of a neighboring hydrogen.     

Kinetic control in the formation of meso-dithia[3.3]-paracyclophane S,S′-dioxide

meso-(R,S)-Dithia[3.3]-paracyclophane S,S′-dioxide is formed with complete stereoselection by the thermolysis of 3,3′-[1,4-phenylene-bis(methylenesulfinyl)]-dipropanoate—that generates in situ two transient sulfenic acid functions—in the presence of p-diethynylbenzene. By employing an improved procedure that we have recently optimized, the title compound has been prepared in a 70% yield as a single diastereoisomer. A density functional B3LYP/6-311+G(d,p) study demonstrates that the final syn-addition cyclization step takes place under kinetic control, through a five-membered transition state that defines the stereochemistry of the resulting cyclophane.     

Characterization by tandem mass spectrometry of stable cysteine sulfenic acid in a cysteine switch peptide of matrix metalloproteinases

Cysteine sulfenic acid (Cys-SOH) is an elusive intermediate in reactive oxygen species-induced oxidation reactions of many proteins such as peroxiredoxins and tyrosine phosphatases. Cys-SOH is proposed to play a vital role in catalytic and signaling functions. The formation of cysteine sulfinic acid (Cys-SO(2)H) and cysteine sulfonic acid (Cys-SO(3)H) has been implicated in the activation of matrix metalloproteinase-7 (MMP-7) and oxidation of thiol to cysteine sulfinic acid has been associated with the autolytic cleavage of MMP-7. We have examined the formation of cysteine sulfenic acid in a synthetic peptide PRCGVPDVA, which is a cysteine switch domain of MMP-7 and other matrix metalloproteases. We have prepared the cysteine sulfenic acid containing peptide, PRC(SOH)GVPDVA, by reaction with hydroxyl radicals generated by the Fenton reaction (Fe(+2)/H(2)O(2)). We characterized this modified peptide by tandem mass spectrometry and accurate mass measurement experiments. In addition, we used 7-chloro-4-nitrobenzo-2-oxa-1,3-diazol (NBD-Cl) reagent to form an adduct with PRC(SOH)GVPDVA to provide additional evidence for the viability of PRC(SOH)GVPDVA in solution. We also characterized an intramolecular cysteine sulfinamide cross-link product PRC[S(O)N]GVPDVA based on tandem mass spectrometry and accurate mass measurement experiments. These results contribute to the understanding of a proteolytic cleavage mechanism that is traditionally associated with MMP activation.     

A chemical model for redox regulation of protein tyrosine phosphatase 1B (PTP1B) activity

Growing evidence indicates that endogenously produced hydrogen peroxide acts as a cellular signaling molecule that (among other things) can regulate the activity of some protein phosphatases. Recent X-ray crystallographic studies revealed an unexpected chemical transformation underlying the redox regulation of protein tyrosine phosphatase 1B, in which oxidative inactivation of the enzyme yields an intrastrand protein cross-link between the catalytic cysteine residue and its neighboring amide nitrogen. This work describes a small organic molecule that serves as an effective model for the redox-sensing assembly of functional groups at the active site of PTP1B. Findings obtained using this model system suggest that the oxidative transformation of PTP1B to its "crosslinked" inactive form can proceed directly via oxidation of the active-site cysteine to a sulfenic acid (RSOH). The remarkably facile nature of this protein cross-link-forming reaction, along with the widespread cellular occurrence of protein sulfenic acids generated via oxidation of cysteine residues, suggests that the type of oxidative protein cross-link formation first seen in the context of PTP1B represents a potentially general mechanism for redox "switching" of protein function. Thus, the chemistry characterized here could have broad relevance to both redox-regulated signal transduction and the toxic effects of oxidative stress.     

Redox regulation of protein tyrosine phosphatase 1B (PTP1B): a biomimetic study on the unexpected formation of a sulfenyl amide intermediate

The effect of steric and electronic environments around the sulfur and nitrogen atoms and the role of nonbonded S...O/N interactions on the cyclization reactions of amide substituted benzene sulfenic acids are described. The reaction profiles and the role of different substituents on the cyclization are investigated in detail by theoretical calculations. It is shown that the synthetic thiols having ortho-amide substituents may serve as good models for the enforced proximity of the amide and cysteine thiol groups at the active site of protein tyrosine phosphatase 1B (PTP1B). However, some of the sulfenic acids derived from such models do not effectively mimic the cyclization of protein sulfenic acids. This is mainly due to the requirement of very high energy for breaking the S-O bond to form a planar five-membered ring of isothiazolidinone. It is shown that the sulfenic acid having two substituents-an amide moiety and a heterocyclic group-in the ortho-positions undergoes a rapid cyclization reaction to produce the corresponding sulfenyl amide species. These studies reveal that the introduction of a substituent at the 6-position of the benzene ring enhances the cyclization process not only by facilitating a closer approach of the -OH group and the backbone -NH moiety but also by increasing the electrophilicity of the sulfur atom in the sulfenic acid.     

Investigations on the Synthesis,Reactivity, and Properties of Perfluoro-α-Benzo-Fused BOPHY Fluorophores

The synthesis and reactivity of 3,8-dibromo-dodecafluoro-benzo-fused BOPHY 2 are reported, via S_NAr with O-, N- S- and C-nucleophiles, and in Pd(0)-catalyzed cross-coupling reactions (Suzuki and Stille). The resulting perfluoro-BOPHY derivatives were investigated for their reactivity in the presence of various nucleophiles. BOPHY 3 displays reversible color change and fluorescence quenching in the presence of bases (Et₃N, DBU), whereas BOPHY 7 reacts preferentially at the α-pyrrolic positions, and BOPHY 8 undergoes regioselective fluorine substitution in the presence of thiols. The structural and electronic features of the fluorinated BOPHYs were studied by TD-DFT computations. In addition, their spectroscopic and cellular properties were investigated; BOPHY 10 shows the most red-shifted absorption/emission (λ_max 659/699 nm) and 7 the highest fluorescence (Φ_f=0.95), while all compounds studied showed low cytotoxicity toward human HEp2 cells and were efficiently internalized.     

Cyclic sulfenamide: versatile template for the synthesis of 1,4-benzothiazepines

Two efficient syntheses of 1,4-benzothiazepines, substituted in the positions 2 and 5, have been achieved either by a ring expansion reaction of cyclic sulfenamides with methylpropiolate or tosylacetylene catalyzed by pyridine, via a postulated allenolate intermediate; or by an α-sulfenylation reaction promoted by diethylamine and a subsequent acid catalyzed condensation reaction.     

Detection of S-palmitoylated Proteins in Mouse Heart Tissue Based on Different Precipitation Methods

The acyl-biotinyl exchange (ABE) is widely used for detection of S-palmitoylated proteins by replacing palmitic acid with biotin, which is a common method for detecting S-palmitoylated proteins. In this study, the effects of acetone precipitation and methanol-chloroform precipitation on the detection of S-palmitoylation proteins in acyl-biotin exchange method were compared, and the S-palmitoylated proteins in mouse cardiac tissue were analyzed. First, N-ethylmaleimide (NEM) was used to block free sulfhydryls within protein molecules. Then, biotinylation reagent (HPDP-Biotin) was used to label the newly produced cysteine thiols that were resulted from treatment by hydroxylamine (HA) in mouse heart tissue. During the ABE reaction, excess unreacted NEM, HA and HPDP-Biotin were removed by precipitation of the proteins. Then, the S-palmitoylated proteins from heart tissue were labeled with ABE reaction based on different precipitation methods, and the S-palmitoylated proteins labeled with biotin were enriched by streptavidin agarose beads. The enriched proteins were analyzed by mass spectrometry, and 50 S-palmitoylated proteins were identified. Specifically, 23 S-palmitoylated proteins were identified in acetone precipitation assay group, and 37 S-palmitoylated proteins in the methanol-chloroform precipitation assay group were identified. 10 palmitoylated proteins were identified in both groups. The results showed that the combination of different precipitation methods could be helpful for the identification of palmitoylated proteins.     

Chromatographic methods for determination of S-substituted cysteine derivatives—A comparative study

A novel HPLC method for determination of a wide variety of S-substituted cysteine derivatives in Allium species has been developed and validated. This method allows simultaneous separation and quantification of S-alk(en)ylcysteine S-oxides, γ-glutamyl-S-alk(en)ylcysteines and γ-glutamyl-S-alk(en)ylcysteine S-oxides in a single run. The procedure is based on extraction of these amino acids and dipeptides by methanol, their derivatization by dansyl chloride and subsequent separation by reversed phase HPLC. The main advantages of the new method are simplicity, excellent stability of derivatives, high sensitivity, specificity and the ability to simultaneously analyze the whole range of S-substituted cysteine derivatives. This method was critically compared with other chromatographic procedures used for quantification of S-substituted cysteine derivatives, namely with two other HPLC methods (derivatization by o-phthaldialdehyde/tert-butylthiol and fluorenylmethyl chloroformate), and with determination by gas chromatography or capillary electrophoresis. Major advantages and drawbacks of these analytical procedures are discussed. Employing these various chromatographic methods, the content and relative proportions of individual S-substituted cysteine derivatives were determined in four most frequently consumed alliaceous vegetables (garlic, onion, shallot, and leek).     

Kinetics of omeprazole degradation in the presence of 2-mercaptoethanol

The reactions of omeprazole, a potent proton pump inhibitor, were investigated in the presence of 2-mercapotoethanol. Reactions were monitored in solutions buffered to pH values ranging from 2.0 to 5.0 using differential pulse polarography at the static mercury drop electrode. First-order reaction network was proposed for all conversions. It is demonstrated that acid degradation predominates at pH values ∼2–3, whereas the reaction of sulfenic acid with the more nucleophilic thiol becomes prominent at pH values around 4–5. The acidic medium is necessary for the formation of sulfenic acid, the key intermediate believed to be the active inhibitor, but acid also converts this sulfenic acid into other degradation products that are unreactive toward thiol. The present work suggests that acid inhibition may occur at pH values higher than those previously thought. Thus, “highly acidic medium is required to achieve both accumulation and activation of omeprazole in the parietal cell, but less acidic medium is necessary for the reaction of sulfenic acid intermediate with the sulfhydryl groups of cysteine residues of H⁺/K⁺-ATPase proton pump in vivo.” © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 352–358, 2008     

Reusable silica-bonded S-sulfonic acid catalyst for three-component synthesis of 2-amino-5-oxo-5,6,7,8-tetrahydro-4H-chromenes and 2-amino-4H-pyrans in aqueous ethanol

Silica-bonded S-sulfonic acid (SBSSA)-catalyzed, facile, one-pot, three-component coupling of 5,5-dimethyl-1,3-cyclohexanedione (dimedone) or 5,5-dimethyl-1,3-cyclohexanedione, aromatic aldehydes, and malononitrile at reflux temperature is described for preparation of 2-amino-5-oxo-5,6,7,8-tetrahydro-4H-chromene derivatives. 2-Amino-3-cyano-6-methyl-4-phenyl-4H-pyran-5-ethylcarboxylate derivatives can also be prepared in good yield under the same experimental conditions by use of ethyl acetoacetate, aldehydes, and malononitrile. The catalyst, silica-bonded S-sulfonic acid, was reused and recycled without any loss of activity or product yield.     

Voltammetric study on interaction of cysteine with type I-collagen in the aqueous medium

Interaction of cysteine with type I-collagen from bovine achilles tendon in the aqueous solutions has been examined using square wave voltammetry (SWV) and cyclic voltammetry (CV) techniques. In the absence of cysteine, type I-collagen gives a reversible peak at ?0.114 V in Britton-Robinson (B-R) buffer (pH 4.0). The electrochemical parameters (I _p/f, E _p/f, E _p/pH, I _p/pH, I _p/v, I _p/v^1/2) of type I-collagen have been also studied. In addition, it has been determined that there is a linear relationship between current and concentration of type I-collagen. On the other hand, cysteine exhibits a reversible peak at ?0.383 V due to the reduction of mercurous cysteine thiolate. By using a hanging mercury drop electrode in aqueous solutions, SWV and CV voltammograms obtained for type I-collagen in the presence of cysteine indicate that there is an interaction between type I-collagen and cysteine. In the presence of cysteine, peak current of type I-collagen decreases and a new peak is observed at ?0.121 V for cysteine which is bonded to type I-collagen.     

Desymmetric hydrogenation of a meso-cyclic acid anhydride toward biotin synthesis

Catalytic reactivity in the hydrogenation of a cyclic anhydride to a biotin synthetic intermediate has been investigated on the basis of Lyons’ original method using Wilkinson Ru complex, revealing the high performance of DPPF and XANTPHOS diphosphines possessing wide bite angles. The results have shown a new trail for design of the corresponding asymmetric catalysts, and the potential utility of (S,S)-Et-FerroTANE and (S,S)-(R,R)-Ph-TRAP has been demonstrated.     

Reactive sulfur species: kinetics and mechanisms of the reaction of cysteine thiosulfinate ester with cysteine to give cysteine sulfenic acid

The kinetics and mechanisms of the reaction of cysteine with cysteine thiosulfinate ester in aqueous solution have been studied by stopped-flow spectrophotometry between pH 6 and 14. Two reaction pathways were observed for pH > 12: (1) an essentially pH-independent nucleophilic attack of cysteinate on cysteine thiosulfinate ester, and (2) a pH-dependent fast equilibrium protonation of cysteine sulfenate that is followed by rate-limiting comproportionation of cysteine sulfenic acid with cysteinate to give cystine. For 6 < pH < 12, the rate-determining reaction between cysteinate and cysteine thiosulfinate ester becomes pH-dependent due to the protonation of their amine groups. Hydrolysis of cysteine thiosulfinate ester does not play a role in the aforementioned mechanisms because the rate-determining nucleophilic attack by hydroxide is relatively slow.