Kinetics and mechanism of the [Ru(III)(edta)(H2O)](-)-mediated oxidation of cysteine by H2O2

The kinetics and mechanism of the [Ru(III)(edta)(H(2)O)](-)-mediated oxidation of cysteine (RSH) by hydrogen peroxide (edta(4-) = ethylenediaminetetraacetate), were studied in detail as a function of both the hydrogen peroxide and cysteine concentrations at pH 5.1 and room temperature. The kinetic traces reveal clear evidence for a catalytic process in which hydrogen peroxide reacts directly with cysteine coordinated to the Ru(III)(edta) complex in the form of [Ru(III)(edta)SR](2-). A parallel process in which [Ru(III)(edta)(H(2)O)](-) first reacts with H(2)O(2) to produce [Ru(V)(edta)O](-) and subsequently oxidizes cysteine, is orders of magnitude slower than the [Ru(III)(edta)(H(2)O)](-)-mediated oxidation in which cysteine rapidly coordinates to [Ru(III)(edta)(H(2)O)](-) prior to the reaction with H(2)O(2). HPLC product analyses revealed the formation of cystine (RSSR) as major product along with cysteine sulfinic acid (RSO(2)H) in the reaction system, and established the catalytic role of [Ru(III)(edta)(H(2)O)](-). Simulations were performed to account for the rather complex kinetic traces in terms of the suggested reaction mechanism. The results of the simulations support the proposed reaction mechanism that involves the oxidation of coordinated cysteine to cysteine sulfenic acid (RSOH), which subsequently rapidly reacts with H(2)O(2) and RSH to form RSO(2)H and RSSR, respectively.     

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.     

Profiling the reactivity of cyclic C-nucleophiles towards electrophilic sulfur in cysteine sulfenic acid

Oxidation of a protein cysteine thiol to sulfenic acid, termed S-sulfenylation, is a reversible post-translational modification that plays a crucial role in regulating protein function and is correlated with disease states. The majority of reaction-based small molecule and immunochemical probes used for detecting sulfenic acids are based on the 5,5-dimethyl-1,3-cyclohexanedione (dimedone) scaffold, which is selective, but suffers from low reactivity. In addition, mechanistic details and features that diminish or enhance nucleophile reactivity remain largely unknown. A significant hurdle to resolving the aforementioned issues has been the chemically unstable nature of small-molecule sulfenic acid models. Herein, we report a facile mass spectrometry-based assay and repurposed dipeptide-based model to screen a library of cyclic C-nucleophiles for reactivity with sulfenic acid under aqueous conditions. Observed rate constants for ∼100 cyclic C-nucleophiles were obtained and, from this collection, we have identified novel compounds with more than 200-fold enhanced reactivity, as compared to dimedone. The increase in reactivity and retention of selectivity of these C-nucleophiles were validated in secondary assays, including a protein model for sulfenic acid. Together, this work represents a significant step toward developing new chemical reporters for detecting protein S-sulfenylation with superior kinetic resolution. The enhanced rates and varied composition of the C-nucleophiles should enable more comprehensive analyses of the sulfenome and serve as the foundation for reversible or irreversible nucleophilic covalent inhibitors that target oxidized cysteine residues in therapeutically important proteins.     

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.     

L-cysteine, a versatile source of sulfenic acids. Synthesis of enantiopure alliin analogues

[reaction: see text] l-Cysteine is a stimulating starting product for the generation of transient sulfenic acids, such as 4, 6, 9, and 15, which add to suitable acceptors, allowing formation of sulfoxides showing a biologically active residue. These sulfoxides are easily isolated in enantiomerically pure form. For instance, N-(tert-butoxycarbonyl)-l-cysteine methyl ester (1a) furnished in few steps sulfenic acid 9a, which was readily converted into (R,S(S))-(2-tert-butoxycarbonylamino-2-methoxycarbonyl-ethylsulfinyl)ethene (22), the methyl ester of Boc-protected nor-alliin. Moreover, the addition of 9a to 2-methyl-1-buten-3-yne has led to a sulfur epimeric and separable mixture of (R)-2-(2-tert-butoxycarbonylamino-2-methoxycarbonyl-ethylsulfinyl)-3-methyl-buta-1,3-dienes 10a and 11a, still possessing a "masked" sulfenic acid function, producible from their cysteine moieties once the dienes have been converted into the desired derivatives.     

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.     

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.     

The mechanism of radical-trapping antioxidant activity of plant-derived thiosulfinates

It has long been recognized that garlic and petiveria, two plants of the Allium genus--which also includes onions, leeks and shallots--possess great medicinal value. In recent times, the biological activities of extracts of these plants have been ascribed to the antioxidant properties of the thiosulfinate secondary metabolites allicin and S-benzyl phenylmethanethiosulfinate (BPT), respectively. Herein we describe our efforts to probe the mechanism of the radical-trapping antioxidant activity of these compounds, as well as S-propyl propanethiosulfinate (PPT), a saturated analog representative of the thiosulfinates that predominate in non-medicinal alliums. Our experimental results, which include thiosulfinate-inhibited autoxidations of the polyunsaturated fatty acid (ester) methyl linoleate, investigations of their decomposition kinetics, and radical clock experiments aimed at obtaining some quantitative insights into their reactions with peroxyl radicals, indicate that the radical-trapping activity of thiosulfinates is paralleled by their propensity to undergo Cope elimination to yield a sulfenic acid. Since sulfenic acids are transient species, we complement our experimental studies with the results of theoretical calculations aimed at understanding the radical-trapping behaviour of the sulfenic acids derived from allicin, BPT and PPT, and contrasting the predicted thermodynamics and kinetics of their reactions with those of the parent thiosulfinates. The calculations reveal that sulfenic acids have among the weakest O-H bonds known (ca. 70 kcal mol(-1)), and that their reactions with peroxyl radicals take place by a near diffusion-controlled proton-coupled electron transfer mechanism. As such, it is proposed that the abundance of a thiosulfinate in a given plant species, and the ease with which it undergoes Cope elimination to form a sulfenic acid, accounts for the differences in antioxidant activity, and perhaps medicinal value, of extracts of these plants. Interestingly, while the Cope elimination of 2-propenesulfenic acid from allicin is essentially irreversible, the analogous reaction of BPT is readily reversible. Thus, in the absence of chain-carrying peroxyl radicals (or other appropriately reactive trapping agent), BPT is reformed.     

Kinetic study on hydrolysis and oxidation of formamidine disulfide in acidic solutions

Hydrolysis and oxidation of formamidine disulfide in acidic medium were investigated using high-performance liquid chromatography(HPLC) and mass spectrometry(MS) at 25 °C.By controlling the slow reaction rate and choosing appropriate mobile phase,HPLC provides the unique advantages over other methods(UV-Vis,chemical separation) in species tracking and kinetic study.In addition to thiourea and formamidine sulfinic acid,two unreported products were also detected in the hydrolysis reaction.Mass spectrometry measurement indicates these two products to be formamidine sulfenic acid and thiocyanogen with mass weights of 92.28 and 116.36,respectively.In the oxidation of formamidine disulfide by hydrogen peroxide,besides thiourea,formamidine sulfenic acid,formamidine sulfinic acid,thiocyanogen and urea,formamidine sulfonic acid and sulfate could be detected.The oxidation reaction was found to be first order in both formamidine disulfide and hydrogen peroxide.The rate constants of hydrolysis and oxidation reactions were determined in the pH range of 1.5-3.0.It was found both rate constants are increased with the increasing of pH.Experimental curves of different species can be effectively simulated via a mechanism scheme for formamidine disulfide oxidation,including hydrolysis equilibrium of formamidine disulfide and irreversible hydrolysis of formamidine sulfenic acid.     

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.     

Theoretical study of the reduction mechanism of sulfoxides by thiols

Theoretical computations have been carried out to investigate the reaction mechanism of the sulfoxide reduction by thiols in solution. This reaction is a suitable model for enzymatic processes involving methionine sulfoxide reductases (Msrs). Recent investigations on the Msr mechanism have clearly shown that a sulfenic acid intermediate is formed on the catalytic cysteine of the active site concomitantly to the methionine product. In contrast, experimental studies for the reaction of a number of thiols and sulfoxides in solution did not observe sulfenic acid formation. Only, a disulfide was identified as the final product of the process. The present study has been carried out at the MP2/6-311+G(3d2f,2df,2p)//B3LYP/6-311G(d,p) level of theory. The solvent effect in DMSO has been incorporated using a discrete-continuum model. The calculations provide a basic mechanistic framework that allows discussion on the apparent discrepancy existing between experimental data in solution and in the enzymes. They show that, in the early steps of the process in solution, a sulfurane intermediate is formed the rate of which is limiting. Then, a proton transfer from a second thiol molecule to the sulfurane leads to the formation of either a sulfenic acid or a disulfide though the latter is much more stable than the former. If a sulfenic acid is formed in solution, it should react with a thiol molecule making its experimental detection difficult or even unfeasible.     

A simple and effective strategy for labeling cysteine sulfenic acid in proteins by utilization of β-ketoesters as cleavable probes

β-ketoesters are robust probes for labeling sulfenic acid (-SOH) proteins allowing quantitative cleavage of the tag for improved analysis of the labeled peptides by MS.     

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     

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.     

Mechanism of the diphenyldisulfone-catalyzed isomerization of alkenes. Origin of the chemoselectivity: experimental and quantum chemistry studies

Polysulfone- and diphenyldisulfone-catalyzed alkene isomerizations are much faster for 2-alkyl-1-alkenes than for linear, terminal alkenes. The mechanism of these reactions has been investigated experimentally for the isomerization of methylidenecyclopentane into 1-methylcyclopentene, and theoretically [CCSD(T)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations] for the reactions of propene and 2-methylpropene with a methanesulfonyl radical, MeSO2*. On heating, polysulfones and (PhSO2)2 equilibrate with sulfonyl radicals, RSO2*. The latter abstract allylic hydrogen atoms in one-step processes giving allylic radical/RSO2H pairs that recombine within the solvent cage producing the corresponding isomerized alkene and RSO2*. The sulfinic acid, RSO2H, can diffuse out from the solvent cage (H/D exchange with MeOD,D2O) and reduce an allyl radical. Calculations did not support other possible mechanisms such as hydrogen exchange between alkenes, electron transfer, or addition/elimination process. Kinetic deuterium isotopic effects measured for the (PhSO2)2-catalyzed isomerization of methylidenecyclopentane and deuterated analogues and calculated for the H abstraction from 2-methylpropene and deuterated analogues by CH3SO2* are consistent also with the one-step hydrogen transfer mechanism. The high chemoselectivity for this reaction is not governed by an exothermicity difference but by a difference in ionization energies of the alkenes. Calculations for CH3SO2* + propene and CH3SO2* + 2-methylpropene show a charge transfer of 0.34 and 0.38 electron, respectively, from the alkenes to the sulfonyl radical in the transition states of these hydrogen abstractions.     

Kinetics of acid degradation of proton pump inhibitors in the presence of a thiol

An in vitro investigation of the kinetics of the complex system of acid‐catalyzed conversions and subsequent reactions of proton pump inhibitors (PPIs; omeprazole, lansoprazole and pantoprazole) was carried out using differential pulse polarography at the static mercury drop electrode. Reactions were investigated in the presence of 2‐mercaptoethanol, in solutions buffered to pH values ranging from 2.0 to 5.0. The first‐order reaction network was proposed for all conversions. The rate of degradation of PPIs and subsequent reactions with 2‐mercaptoethanol were found to follow the following general order: lansoprazole > omeprazole > pantoprazole. The rate of conversion of PPIs into sulfenic acid was found to be directly dependent on the basicity of benzimidazole nitrogen of PPIs, which determines the electrophilic reactivity of the adjacent carbon (C2). The rate of conversion of the sulfenic acid of PPIs into the disulfide (the inhibition reaction) was found to be dependent on the electrophilicity of the sulfur atom of the sulfenic acid. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 498–506, 2009     

Reactions of β-Sulfinyl α,β-Unsaturated Ketones with Dienes

β-Sulfinyl α,β-unsaturated ketones (2a-f) reacted in a regioselective manner with dienes such as butadiene (3a) and 1,3-pentadiene (3b) to give 1,4-cyclohexadiene derivatives (4-8) with the concomitant elimination of sulfenic acid, while the ketones (2a-c) reacted with cyclopentadiene (3c) to yield the norbornenes (9).     

Infrared spectra of the sulfenic ester CH3SOCH3 and its photodissociation products in solid argon

UV light irradiation of dimethyl sulfoxide (DMSO) in low temperature solid argon matrix produces sulfenic ester, CH 3SOCH 3, a high energy structural isomer of DMSO. The sulfenic ester molecule further dissociates to the CH 2O-CH 3SH complex under 266 nm laser irradiation. The CH 2S-CH 3OH complex is also formed upon UV light irradiation. The infrared spectra of the aforementioned species are assigned on the basis of isotopic substitutions ( (13)C and deuterium) as well as density functional frequency calculations.     

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.     

Sulfenic acids in the carbohydrate field. An example of straightforward access to novel multivalent thiosaccharides

[reaction: see text] Both anomers of O-protected 1-thio-D-gluco- and -D-mannopyranoses were selected to provide the substrates for developing a smooth and general methodology that gives access to anomeric glycosulfoxides. The behavior of the corresponding beta-D-galactopyran derivatives was also investigated. 2-[1-[(2,3,4,6-Tetra-O-acetyl-beta-D-glucopyranosyl)sulfinyl](1-methyl)ethyl]malonic acid diethyl esters 4 were thermolyzed in refluxing dichloromethane for generating 2,3,4,6-tetra-O-acetyl-beta-D-glucopyranose-1-sulfenic acid (8), in the presence of 2-propynyl beta-d-glucopyranoside tetraacetate (32). The syn-addition of transient 8 onto the triple bond of 32 furnished 2-[(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl)sulfonyl]-2-propenyl beta-d-glucopyranoside tetraacetate (34), after m-CPBA oxidation of the corresponding sulfinyl epimeric mixture 33. This synthetic pathway appears particularly attractive since it represents an example of a mild and versatile approach to thiodisaccharides of foreseeably significant biological behavior. Various carbohydrate-derived sulfenic acids, different in glycosyl moiety and sulfenic function positioning, and various alkynylated carbohydrates can be adopted as combining units in the synthesis of alkene-linked multivalent thiosaccharides.