Conformers of cysteine and cysteine sulfenic acid and mechanisms of the reaction of cysteine sulfenic acid with 5,5-dimethyl-1,3-cyclohexanedione (dimedone)

Benchmark Ab Initio Determination of the Conformers, Proton Affinities, and Gas-Phase Basicities of Cysteine

A systematic conformational mapping combined with literature data leads to 85 stable neutral cysteine conformers. The implementation of the same mapping process for the protonated counterparts reveals 21 N-(amino-), 64 O-(carbonyl-), and 37 S-(thiol-)protonated cysteine conformers. Their relative energies and harmonic vibrational frequencies are given at the MP2/aug-cc-pVDZ level of theory. Further benchmark ab initio computations are performed for the 10 lowest-lying neutral and protonated amino acid conformers (for each type) such as CCSD(T)-F12a/cc-pVDZ-F12 geometry optimizations (and frequency computations for cysteine) as well as auxiliary correction computations of the basis set effects up to CCSD(T)-F12b/cc-pVQZ-F12, electron correlation effects up to CCSDT(Q), core correlation effects, second-order Douglass-Kroll relativistic effects, and zero-point energy contributions. Boltzmann-averaged 0 (298.15) K proton affinity and [298.15 K gas-phase basicity] values of cysteine are predicted to be 214.96 (216.39) [208.21], 201.83 (203.55) [194.16], and 193.31 (194.74) [186.40] kcal/mol for N-, O-, and S-protonation, respectively, also considering the previously described auxiliary corrections.

Organocatalyzed Heterocyclic Transformations In Green Media: A Review

Background:

Since the discovery of metal-free catalysts or organocatalysts about twenty years ago, a number of small molecules with different structures have been used to accelerate organic transformations. With the development of environmental awareness, to obtain highly efficient scaffolds, scientists have directed their studies towards synthetic methodologies that minimize or preferably eliminate the formation of waste, avoid toxic solvents and reagents and use renewable starting materials as far as possible.

Methods:

In this connection, the organocatalytic reactions providing efficiency and selectivity for most of the transformations have become an endless topic in organic chemistry since several advantages from both practical and environmental standpoints. Organocatalysts contributing to the transformation of reactants into products with the least possible waste production, have been serving the concept of green chemistry.

Results and Conclusion:

Organocatalysts have been classified based on their binding capacity to the substrate with covalent or noncovalent interactions involving hydrogen bonding and electrostatic interaction. Diverse types of small organic compounds including proline and its derivatives, phase-transfer catalysts, (thio)urease, phosphoric acids, sulfones, N-oxides, guanidines, cinchona derivatives, aminoindanol, and amino acids have been utilized as hydrogen bonding organocatalysts in different chemical transformations.

Unbiased Detection of Cysteine Sulfenic Acid by 473 nm Photodissociation Mass Spectrometry: Toward Facile In Vivo Oxidative Status of Plasma Proteins

Cysteine (Cys) is prone to diverse post-translational modifications in proteins, including oxidation into sulfenic acid (Cys-SOH) by reactive oxygen species generated under oxidative stress. Detection of low-concentration and metastable Cys-SOH within complex biological matrices is challenging due to the dynamic concentration range of proteins in the samples. Herein, visible laser-induced dissociation (LID) implemented in a mass spectrometer was used for streamlining the detection of Cys oxidized proteins owing to proper derivatization of Cys-SOH with a chromophore tag functionalized with a cyclohexanedione group. Once grafted, peptides undergo a high fragmentation yield under LID, leading concomitantly to informative backbone ions and to a chromophore reporter ion. Seventy-nine percent of the Cys-containing tryptic peptides derived from human serum albumin and serotransferrin tracked by parallel reaction monitoring (PRM) were detected as targets subjected to oxidation. These candidates as well as Cys-containing peptides predicted by in silico trypsin digestion of five other human plasma proteins were then tracked in real plasma samples to pinpoint the endogenous Cys-SOH subpopulation. Most of the targeted peptides were detected in all plasma samples by LID-PRM, with significant differences in their relative amounts. By eliminating the signal of interfering co-eluted compounds, LID-PRM surpasses conventional HCD (higher-energy collisional dissociation)-PRM in detecting grafted Cys-SOH-containing peptides and allows now to foresee clinical applications in large human cohorts.

Synchrotron X-radiolysis of l-cysteine at the sulfur K-edge: Sulfurous products, experimental surprises, and dioxygen as an oxidoreductant

In situ inventory of sulfurous products from the sulfur K-edge synchrotron X-radiolysis of l-cysteine in solid-phase and anaerobic (pH 5) and air-saturated (pH 5, 7, and 9) solutions without and with 40% glycerol is reported. Sequential K-edge X-ray Absorption Spectroscopic (XAS) spectra were acquired. l-cysteine degraded systematically in the X-ray beam. Radiolytic products were inventoried by fits using the XAS spectra of sulfur model compounds. Solid l-cysteine declined to 92% fraction after a single K-edge XAS scan. After six scans, 60% remained, accompanied by 14% cystine, 16% thioether, 5.4% elemental sulfur, and smaller fractions of more highly oxidized products. In air-saturated pH 5 solution, 73% of l-cysteine remained after ten scans, with 2% cystine and 19% elemental sulfur. Oxidation increased with 40% glycerol, yielding 67%, 5%, and 23% fractions, respectively, after ten scans. Higher pH solutions exhibited less radiolytic chemistry. All the reactivity followed first-order kinetics. The anaerobic experiment displayed two reaction phases, with sharp changes in kinetics and radiolytic chemistry. Unexpectedly, the radiolytic oxidation of l-cysteine was increased in anaerobic solution. After ten scans, only 60% of the l-cysteine remained, along with 17% cystine, 22% elemental sulfur, and traces of more highly oxidized products. A new aerobic reaction cycle is hypothesized, wherein dissolved dioxygen captures radiolytic H• or eaq -, enters HO2 •/O2 •-, reductively quenches cysteine thiyl radicals, and cycles back to O2. This cycle is suggested to suppress the radiolytic production of cystine in aerobic solution.

Protein Sulfenylation: A Novel Readout of Environmental Oxidant Stress

Oxidative stress is a commonly cited mechanism of toxicity of environmental agents. Ubiquitous environmental chemicals such as the diesel exhaust component 1,2-naphthoquinone (1,2-NQ) induce oxidative stress by redox cycling, which generates hydrogen peroxide (H2O2). Cysteinyl thiolate residues on regulatory proteins are subjected to oxidative modification by H2O2 in physiological contexts and are also toxicological targets of oxidant stress induced by environmental contaminants. We investigated whether exposure to environmentally relevant concentrations of 1,2-NQ can induce H2O2-dependent oxidation of cysteinyl thiols in regulatory proteins as a readout of oxidant stress in human airway epithelial cells. BEAS-2B cells were exposed to 0-1000 μM 1,2-NQ for 0-30 min, and levels of H2O2 were measured by ratiometric spectrofluorometry of HyPer. H2O2-dependent protein sulfenylation was measured using immunohistochemistry, immunoblotting, and isotopic mass spectrometry. Catalase overexpression was used to investigate the relationship between H2O2 generation and protein sulfenylation in cells exposed to 1,2-NQ. Multiple experimental approaches showed that exposure to 1,2-NQ at concentrations as low as 3 μM induces H2O2-dependent protein sulfenylation in BEAS-2B cells. Moreover, the time of onset and duration of 1,2-NQ-induced sulfenylation of the regulatory proteins GAPDH and PTP1B showed significant differences. Oxidative modification of regulatory cysteinyl thiols in human lung cells exposed to relevant concentrations of an ambient air contaminant represents a novel marker of oxidative environmental stress.

Biological chemistry and functionality of protein sulfenic acids and related thiol modifications

Selective modification of proteins at cysteine residues by reactive oxygen, nitrogen or sulfur species formed under physiological and pathological states is emerging as a critical regulator of protein activity impacting cellular function. This review focuses primarily on protein sulfenylation (-SOH), a metastable reversible modification connecting reduced cysteine thiols to many products of cysteine oxidation. An overview is first provided on the chemistry principles underlining synthesis, stability and reactivity of sulfenic acids in model compounds and proteins, followed by a brief description of analytical methods currently employed to characterize these oxidative species. The following chapters present a selection of redox-regulated proteins for which the -SOH formation was experimentally confirmed and linked to protein function. These chapters are organized based on the participation of these proteins in the regulation of signaling, metabolism and epigenetics. The last chapter discusses the therapeutic implications of altered redox microenvironment and protein oxidation in disease.

Mechanisms of reactions of sulfur hydride hydroxide: tautomerism, condensations, and C-sulfenylation and O-sulfenylation of 2,4-pentanedione

The conformations, equilibrium structures, hydrogen bonds, and non-covalent interactions involved in the mechanisms of tautomerization, condensations, and C-sulfenylation and O-sulfenylation of 2,4-pentanedione by sulfur hydride hydroxide (hydrogen thioperoxide, oxadisulfane, H-SOH) have been studied using BD(T), CCSD(T), and QCISD(T) with the cc-pVTZ basis set and using B3LYP, B3PW91, CAM-B3LYP, PBE1PBE, PBEh1PBE, LC-ωPBE, M06-2X, and ωB97XD with the 6-311+G(d,p) basis set. All levels of theory predict the sulfenyl (H-SOH) tautomer of hydrogen thioperoxide to be lower in energy than the sulfinyl (H2S═O) tautomer. Four reasonable mechanisms were considered for the tautomerization of the sulfenyl tautomer of hydrogen thioperoxide to the sulfinyl tautomer: a cyclic three-membered water-free transition state (TS, CCSD(T) activation energy barrier E(⧧) = 65.1 kcal/mol), a cyclic five-membered transition state with one water molecule (TSH2O, E(⧧) = 31.1 kcal/mol), a cyclic seven-membered transition state with two water molecules (TS2H2O, E(⧧) = 14.5 kcal/mol), and a cyclic nine-membered transition state with three water molecules (TS3H2O, E(⧧) = 5.6 kcal/mol). The mechanisms involve hydrogen-bonded reactant complexes and hydrogen-bonded product complexes. The CCSD(T)-predicted energy barriers for the condensation of hydrogen thioperoxide to form thiosulfinic acid through transition states with zero, one, and two waters are E(⧧) = 42.0, 18.3, and 0 kcal/mol, respectively. Mixed condensation reactions are predicted to afford organosulfur products and compounds containing sulfur-selenium bonds. Hydrogen thioperoxide is predicted to add to 2,4-pentanedione to form C-sulfenylated (sulfide, thioether) and O-sulfenylated (sulfenate ester) products. Similar mechanistic trends and reaction pathways are observed in the tautomerism, condensations, and C-sulfenylation and O-sulfenylation reactions of hydrogen thioperoxide. The water molecules set up proton relay networks (bridges) that reduce ring strain, generate favorable conformations for reactivity, lower energy barriers, and increase the numbers of stabilizing hydrogen bonds and nonbonding interactions.

Mechanism of the cysteine sulfenic acid O-sulfenylation of 1,3-cyclohexanedione

The density functionals B3LYP, B3PW91, M062X, and CAM-B3LYP with the 6-311+G(d,p) basis set predict the cysteine sulfenic acid O-sulfenylation of the s-cis-ketoenol tautomer of 1,3-cyclohexanedione proceeds through a cyclic 14-membered transition state structure containing three water molecules.