Chemoselective ligation of sulfinic acids with aryl-nitroso compounds

Synthesis of Naphthalimide Azocarboxylates Showing Turn-On Fluorescence by Substitution Reaction with Sulfinates

The synthesis and characterization of sulfinate addition-responsive fluorescent molecules are described. We found that addition reaction of sulfinates to naphthalimide-substituted azocarboxylates afforded the corresponding sulfonyl hydrazides with high fluorescence quantum yields (up to 0.91 in THF and 0.54 in methanol), which exhibited a large Stokes shift (105 nm) in protic methanol solvent, while the unsubstituted hydrazide and the sulfonyl-position isomer showed no fluorescence in polar solvents.

Nitro-sulfinate Reductive Coupling to Access (Hetero)aryl Sulfonamides

A method to assemble (hetero)aryl sulfonamides via the reductive coupling of aryl sulfinates and nitroarenes is reported. Various reducing conditions with sodium bisulfite and with or without tin(II) chloride in DMSO were developed using an ultrasound bath to improve reaction homogeneity and mixing. A range of (hetero)aryl sulfonamides bearing a selection of functional groups were prepared, and the mechanism of the transformation was investigated. These investigations have led us to propose the formation of nitrosoarene intermediates, which were established via an independent molecular coupling strategy.

Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway

Multiple anticancer drugs have been proposed to cause cell death, in part, by increasing the steady-state levels of cellular reactive oxygen species (ROS). However, for most of these drugs, exactly how the resultant ROS function and are sensed is poorly understood. It remains unclear which proteins the ROS modify and their roles in drug sensitivity/resistance. To answer these questions, we examined 11 anticancer drugs with an integrated proteogenomic approach identifying not only many unique targets but also shared ones-including ribosomal components, suggesting common mechanisms by which drugs regulate translation. We focus on CHK1 that we find is a nuclear H2O2 sensor that launches a cellular program to dampen ROS. CHK1 phosphorylates the mitochondrial DNA-binding protein SSBP1 to prevent its mitochondrial localization, which in turn decreases nuclear H2O2. Our results reveal a druggable nucleus-to-mitochondria ROS-sensing pathway-required to resolve nuclear H2O2 accumulation and mediate resistance to platinum-based agents in ovarian cancers.

Identification of chemotherapy targets reveals a nucleus-to-mitochondria ROS sensing pathway

Multiple chemotherapies are proposed to cause cell death in part by increasing the steady-state levels of cellular reactive oxygen species (ROS). However, for most of these drugs exactly how the resultant ROS function and are sensed is poorly understood. In particular, it's unclear which proteins the ROS modify and their roles in chemotherapy sensitivity/resistance. To answer these questions, we examined 11 chemotherapies with an integrated proteogenomic approach identifying many unique targets for these drugs but also shared ones including ribosomal components, suggesting one mechanism by which chemotherapies regulate translation. We focus on CHK1 which we find is a nuclear H ₂ O ₂ sensor that promotes an anti-ROS cellular program. CHK1 acts by phosphorylating the mitochondrial-DNA binding protein SSBP1, preventing its mitochondrial localization, which in turn decreases nuclear H ₂ O ₂ . Our results reveal a druggable nucleus-to-mitochondria ROS sensing pathway required to resolve nuclear H ₂ O ₂ accumulation, which mediates resistance to platinum-based chemotherapies in ovarian cancers.

EDA mediated S-N bond coupling of nitroarenes and sodium sulfinate salts

Despite their long-known photochemical properties and their industrial value, the use of nitroarenes as a productive photochemical handle in organic synthesis has remained relatively unexplored. More specifically, the photochemical formation of nitrogen-sulfur bonds from nitroarenes remains to be demonstrated. Herein, we report the design and application of a sulfinate-nitroarene electron donor-acceptor (EDA) complex and its subsequent use in the first light mediated catalyst-free synthesis of N-hydroxy-sulfonamides. The presence of the EDA was assessed spectroscopically and studied via DFT and TD-DFT calculations. A total of 32 examples including both electron withdrawing and electron donating groups were synthesized under our oxygen- and water-tolerant conditions.

Novel AIE Probe for In Situ Imaging of Protein Sulfonation to Assess Cigarette Smoke-Induced Inflammatory Damage

Cysteine sulfonic acid, a product of protein oxidative damage, is an important sign by which the body and cells sense oxidative stress. Cigarette smoke (CS) can trigger inflammatory reactions in humans that lead to higher levels of oxidative stress and reactive oxygen species (ROS) in the body. Available evidence indicates a possible relationship between protein oxidative damage and cigarette smoke, which is poorly understood due to the limitations of analytical techniques. Herein, we developed a donor-acceptor structured aggregation-induced emission (AIE) fluorescence probe H-1, which exhibited excellent optical properties for the highly sensitive and specific detection of sulfonic acid biomacromolecules. The probe could be easily synthesized by click chemistry conjugating triazole heterocycles onto a triphenylamine fluorophore, followed by a cationization reaction. Due to low cytotoxity, the probe was successfully applied for in situ imaging of intracellular protein sulfonation, achieving visualization of protein sulfonation in cigarette smoke stimulation-induced inflammatory RAW264.7 cell models. Moreover, an immunofluorescence study of the aorta and lung revealed that significant blue fluorescence signals could be observed only in CS-stimulated vascular. It indicated that CS-stimulated vascular sulfonation injury can be monitored using H-1. This study will provide an efficient method for revealing CS-induced oxidative damage-relevant diseases.

Functional group divergence and the structural basis of acridine photocatalysis revealed by direct decarboxysulfonylation

The reactivity of the sulfonyl group varies dramatically from nucleophilic sulfinates through chemically robust sulfones to electrophilic sulfonyl halides-a feature that has been used extensively in medicinal chemistry, synthesis, and materials science, especially as bioisosteric replacements and structural analogs of carboxylic acids and other carbonyls. Despite the great synthetic potential of the carboxylic to sulfonyl functional group interconversions, a method that can convert carboxylic acids directly to sulfones, sulfinates and sulfonyl halides has remained out of reach. We report herein the development of a photocatalytic system that for the first time enables direct decarboxylative conversion of carboxylic acids to sulfones and sulfinates, as well as sulfonyl chlorides and fluorides in one step and in a multicomponent fashion. A mechanistic study prompted by the development of the new method revealed the key structural features of the acridine photocatalysts that facilitate the decarboxylative transformations and provided an informative and predictive multivariate linear regression model that quantitatively relates the structural features with the photocatalytic activity.

Oxidative Cysteine Modification of Thiol Isomerases in Thrombotic Disease: A Hypothesis

Significance: Oxidative stress is a characteristic of many systemic diseases associated with thrombosis. Thiol isomerases are a family of oxidoreductases important in protein folding and are exquisitely sensitive to the redox environment. They are essential for thrombus formation and represent a previously unrecognized layer of control of the thrombotic process. Yet, the mechanisms by which thiol isomerases function in thrombus formation are unknown. Recent Advances: The oxidoreductase activity of thiol isomerases in thrombus formation is controlled by the redox environment via oxidative changes to active site cysteines. Specific alterations can now be detected owing to advances in the chemical biology of oxidative cysteine modifications. Critical Issues: Understanding of the role of thiol isomerases in thrombus formation has focused largely on identifying single disulfide bond modifications in isolated proteins (e.g., α_IIbβ₃, tissue factor, vitronectin, or glycoprotein Ibα [GPIbα]). An alternative approach is to conceptualize thiol isomerases as effectors in redox signaling pathways that control thrombotic potential by modifying substrate networks. Future Directions: Cysteine-based chemical biology will be employed to study thiol-dependent dynamics mediated by the redox state of thiol isomerases at the systems level. This approach could identify thiol isomerase-dependent modifications of the disulfide landscape that are prothrombotic.

Photoinduced C(sp3)-H sulfination empowers the direct and chemoselective introduction of the sulfonyl group

Direct installation of the sulfinate group by the functionalization of unreactive aliphatic C-H bonds can provide access to most classes of organosulfur compounds, because of the central position of sulfinates as sulfonyl group linchpins. Despite the importance of the sulfonyl group in synthesis, medicine, and materials science, a direct C(sp³)-H sulfination reaction that can convert abundant aliphatic C-H bonds to sulfinates has remained elusive, due to the reactivity of sulfinates that are incompatible with typical oxidation-driven C-H functionalization approaches. We report herein a photoinduced C(sp³)-H sulfination reaction that is mediated by sodium metabisulfite and enables access to a variety of sulfinates. The reaction proceeds with high chemoselectivity and moderate to good regioselectivity, affording only monosulfination products and can be used for a solvent-controlled regiodivergent distal C(sp³)-H functionalization.

Cysteinyl radicals in chemical synthesis and in nature

Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.

Contemporary proteomic strategies for cysteine redoxome profiling

Protein cysteine residues are susceptible to oxidative modifications that can affect protein functions. Proteomic techniques that comprehensively profile the cysteine redoxome, the repertoire of oxidized cysteine residues, are pivotal towards a better understanding of the protein redox signaling. Recent technical advances in chemical tools and redox proteomic strategies have greatly improved selectivity, in vivo applicability, and quantification of the cysteine redoxome. Despite this substantial progress, still many challenges remain. Here, we provide an update on the recent advances in proteomic strategies for cysteine redoxome profiling, compare the advantages and disadvantages of current methods and discuss the outstanding challenges and future perspectives for plant redoxome research.

Roles of Ion Fluxes, Metabolism, and Redox Balance in Cancer Therapy

Recent Advances: The 2019 Nobel Prize awarded to the mechanisms for oxygen sensing and adaptation according to oxygen availability, highlighting the fundamental importance of gaseous molecules. Gaseous molecules, including reactive oxygen species (ROS), can interact with different cations generated during metabolic and redox dysregulation in cancer cells. Cross talk between calcium signaling and metabolic/redox pathways leads to network-based dyregulation in cancer. Significance: Recent discovery on using small molecules targeting the ion channels, redox signaling, and protein modification on metabolic enzymes can effectively inhibit cancer growth. Several FDA-approved drugs and clinical trials are ongoing to target the calcium channels, such as TRPV6 and TRPM8. Multiple small molecules from natural products target metablic and redox enzymes to exert an anticancer effect. Critical Issues: Small molecules targeting key ion channels, metabolic enzymes that control key aspects of metabolism, and redox proteins are promising, but their action mechanisms of the target are needed to be elucidated with advanced-omic technologies, which can give network-based and highly dimensioal data. In addition, small molecules that can directly modify the protein residues have emerged as a novel anticancer strategy. Future Directions: Advanced technology accelerates the detection of ions and metabolic and redox changes in clinical samples for diagnosis and informs the decision of cancer treatment. The improvement of ROS detection, ROS target identification, and computational-aid drug discovery also improves clincal outcome.Overall, network-based or holistic regulations of cancer via ion therapy and metabolic and redox intervention are promising as new anticancer strategies. Antioxid. Redox Signal. 34, 1108-1127.

Characterization of cellular oxidative stress response by stoichiometric redox proteomics

The thiol redox proteome refers to all proteins whose cysteine thiols are subjected to various redox-dependent posttranslational modifications (PTMs) including S-glutathionylation (SSG), S-nitrosylation (SNO), S-sulfenylation (SOH), and S-sulfhydration (SSH). These modifications can impact various aspects of protein function such as activity, binding, conformation, localization, and interactions with other molecules. To identify novel redox proteins in signaling and regulation, it is highly desirable to have robust redox proteomics methods that can provide global, site-specific, and stoichiometric quantification of redox PTMs. Mass spectrometry (MS)-based redox proteomics has emerged as the primary platform for broad characterization of thiol PTMs in cells and tissues. Herein, we review recent advances in MS-based redox proteomics approaches for quantitative profiling of redox PTMs at physiological or oxidative stress conditions and highlight some recent applications. Considering the relative maturity of available methods, emphasis will be on two types of modifications: 1) total oxidation (i.e., all reversible thiol modifications), the level of which represents the overall redox state, and 2) S-glutathionylation, a major form of reversible thiol oxidation. We also discuss the significance of stoichiometric measurements of thiol PTMs as well as future perspectives toward a better understanding of cellular redox regulatory networks in cells and tissues.

Are Reactive Sulfur Species the New Reactive Oxygen Species?

Significance: Oxidative stress in moderation positively affects homeostasis through signaling, while in excess it is associated with adverse health outcomes. Both activities are generally attributed to reactive oxygen species (ROS); hydrogen peroxide as the signal, and cysteines on regulatory proteins as the target. However, using antioxidants to affect signaling or benefit health has not consistently translated into expected outcomes, or when it does, the mechanism is often unclear. Recent Advances: Reactive sulfur species (RSS) were integral in the origin of life and throughout much of evolution. Sophisticated metabolic pathways that evolved to regulate RSS were easily "tweaked" to deal with ROS due to the remarkable similarities between the two. However, unlike ROS, RSS are stored, recycled, and chemically more versatile. Despite these observations, the relevance and regulatory functions of RSS in extant organisms are generally underappreciated. Critical Issues: A number of factors bias observations in favor of ROS over RSS. Research conducted in room air is hyperoxic to cells, and promotes ROS production and RSS oxidation. Metabolic rates of rodent models greatly exceed those of humans; does this favor ROS? Analytical methods designed to detect ROS also respond to RSS. Do these disguise the contributions of RSS? Future Directions: Resolving the ROS/RSS issue is vital to understand biology in general and human health in particular. Improvements in experimental design and analytical methods are crucial. Perhaps the most important is an appreciation of all the attributes of RSS and keeping an open mind.

Profiling of post-translational modifications by chemical and computational proteomics

Post-translational modifications (PTMs) diversify the molecular structures of proteins and play essential roles in regulating their functions. Abnormal PTM status has been linked to a variety of developmental disorders and human diseases, highlighting the importance of studying PTMs in understanding physiological processes and discovering novel nodes and links with therapeutic intervention potential. Classical biochemical methods are suitable for studying PTMs on individual proteins; however, global profiling of PTMs in proteomes remains a challenging task. In this feature article, we start with a brief review of the traditional affinity-based strategies and shift the emphasis to summarizing recent progress in the development and application of chemical and computational proteomic strategies to delineate the global landscapes of functional PTMs. Finally, we discuss current challenges in PTM detection and provide future perspectives on how the field can be further advanced.

Cysteine oxidation to the sulfinic acid induces oxoform-specific lanthanide binding and fluorescence in a designed peptide

Cysteine sulfinic acid (Cys-SO₂^-) is a protein post-translational modification that is formed reversibly under oxidative conditions. A short, encodable peptide was developed whose metal binding and terbium luminescence are dependent on cysteine (Cys) oxidation to the sulfinic acid. The protein design is based on the modification of a key metal-binding aspartate (Asp) in a canonical EF-Hand motif (DKDADGWISPAEAK) to Cys. In this design, Cys in the thiol oxidation state does not mimic the native Asp, and thus the peptide binds terbium(III) (Tb³⁺) poorly and exhibits weak terbium luminescence (fluorescence). In contrast, when Cys is oxidized to the Cys sulfinic acid oxoform, the Cys sulfinate effectively mimics Asp, resulting in a significant increase in terbium affinity and luminescence. Asp residues at positions 1, 3, and 5 of the EF-Hand motif were examined as potential sites for Cys oxidation-responsive metal binding. The peptide with Cys at residue 1 exhibited the highest Tb³⁺ affinity in both oxidation states. The peptide with Cys at residue 3 exhibited a 4.2-fold distinction in affinity between the oxidation states. Most significantly, the peptide with Cys at residue 5 had only modest Tb³⁺ affinity as the Cys thiol, but exhibited a 30-fold increase in Tb³⁺ affinity and an 18-fold increase in Tb³⁺ luminescence on Cys oxidation to the sulfinic acid. This peptide (Ac-DKDACGWISPAEAK-NH₂) exhibited selective Tb³⁺ binding via Cys-SO₂^- over the thiol, S-glutathionyl, S-nitrosyl, and sulfonic acid oxoforms, indicating substantially greater Lewis basicity of the sulfinate than the sulfonate. NMR spectroscopy and quantum homology modeling indicated that the designed peptide binds metal with an overall geometry similar to that of an EF-Hand motif, with the Cys sulfinate effectively replacing Asp as a metal-binding ligand. This peptide was applied to detect Cys oxidation to the sulfinic acid by fluorescence spectroscopy, suggesting its broader application in understanding Cys sulfinic acid biology.

Structural preferences of cysteine sulfinic acid: The sulfinate engages in multiple local interactions with the peptide backbone

Cysteine sulfinic acid (Cys-SO₂^-) is a non-enzymatic oxidative post-translational modification (PTM) that has been identified in hundreds of proteins. However, the effects of cysteine sulfination are in most cases poorly understood. Cys-SO₂^- is structurally distinctive, with long sulfur-carbon and sulfur-oxygen bonds, and with tetrahedral geometry around sulfur due to its lone pair. Cys-SO₂^- thus has a unique range of potential interactions with the protein backbone which could facilitate protein structural changes. Herein, the structural effects of cysteine oxidation to the sulfinic acid were investigated in model peptides and folded proteins using NMR spectroscopy, circular dichroism, bioinformatics, and computational studies. In the PDB, Cys-SO₂^- shows a greater preference for α-helix than Cys. In addition, Cys-SO₂^- is more commonly found in structures with φ > 0, including in multiple types of β-turn. Sulfinate oxygens engage in hydrogen bonds with adjacent (i or i + 1) amide hydrogens. Over half of sulfinates have at least one hydrogen bond with an adjacent amide, and several structures have hydrogen bonds with both adjacent amides. Alternately, sulfur or either oxygen can act as an electron donor for n→π* interactions with the backbone carbonyl of the same residue, as indicated by frequent S⋯CO or O⋯CO distances below the sums of their van der Waals radii in protein structures. In peptides, Cys-SO₂^- favored α-helical structure at the N-terminus, consistent with helix dipole effects and backbone hydrogen bonds with the sulfinate promoting α-helix. Cys-SO₂^- has only modestly greater polyproline II helix propensity than Cys-SH, likely due to competition from multiple side chain-backbone interactions. Cys-SO₂^- stabilizes the i+1 position of a β-turn relative to Cys-SH. Within proteins, the range of side chain-main chain interactions available to Cys-SO₂^- compared to Cys-SH provides a basis for potential changes in protein structure and function due to cysteine oxidation to the sulfinic acid.

Introduction to approaches and tools for the evaluation of protein cysteine oxidation

Oxidative modifications of cysteine thiols in cellular proteins are pivotal to the way signal-stimulated reactive oxygen species are sensed and elicit appropriate or sometimes pathological responses, but the dynamic and often transitory nature of these modifications offer a challenge to the investigator trying to identify such sites and the responses they elicit. A number of reagents and workflows have been developed to identify proteins undergoing oxidation and to query the timing, extent and location of such modifications, as described in this minireview. While no approach is perfect to capture all the redox information in a functioning cell, best practices described herein can enable considerable insights into the "redox world" of cells and organisms.

Activity-Based Sensing for Site-Specific Proteomic Analysis of Cysteine Oxidation

Oxidative post-translational modifications (OxiPTMs) of cysteine residues are the molecular foundation of thiol-based redox regulation that modulates physiological events such as cell proliferation, differentiation, and migration and, when dysregulated, can lead to biomolecule damage and cell death. Common OxiPTMs of cysteine thiols (-SH) include reversible modifications such as S-sulfenylation (-SOH), S-glutathionylation (-SSG), disulfide formation (-SSR), S-nitrosylation (-SNO), and S-sulfhydration (-SSH) as well as more biologically stable modifications like S-sulfinylation (-SO₂H) and S-sulfonylation (-SO₃H). In the past decade, our laboratory has developed first-in-class chemistry-based tools and proteomic methods to advance the field of thiol-based redox biology and oxidative stress. In this Account, we take the reader through the historical aspects of probe development and application in our laboratory, highlighting key advances in our understanding of sulfur chemistry, in the test tube and in living systems. Offering superior resolution, throughput, accuracy, and reproducibility, mass spectrometry (MS)-based proteomics coupled to chemoselective "activity-based" small-molecule probes is the most rigorous technique for global mapping of cysteine OxiPTMs. Herein, we describe the evolution of this field from indirect detection to state-of-the-art site-centric quantitative chemoproteomic approaches that enable mapping of physiological and pathological changes in cysteine oxidation. These methods enable protein and site-level identification, mechanistic studies, mapping fold-changes, and modification stoichiometry. In particular, this Account focuses on activity-based methods for profiling S-sulfenylation, S-sulfinylation, and S-sulfhydration with an eye toward new reactions and methodologies developed in our group as well as their applications that have shed new light on fundamental processes of redox biology. Among several classes of sulfenic acid probes, dimedone-based C-nucleophiles possess superior chemical selectivity and compatibility with tandem MS. Cell-permeable dimedone derivatives with a bioconjugation handle are capable of detecting of S-sulfenylation in living cells. In-depth screening of a C-nucleophile library has yielded several entities with significantly enhanced reactivity over dimedone while maintaining selectivity, and reversible linear C-nucleophiles that enable controlled target release. C-Nucleophiles have also been implemented in tag-switch methods to detect S-sulfhydration. Most recently, activity-based detection of protein S-sulfinylation with electrophilic nitrogen species (ENS), such as C-nitroso compounds and electron deficient diazines, offers significant advantages in simplicity-of-use and target specificity compared to label-free methods. When feasible, the rich information provided by site-centric quantitative proteomics should not be tainted by oxidation artifacts from cell lysis. Therefore, chemoselective probes that function in a native environment with low cytotoxicity, good cell-permeability, and competitive kinetics are desired in modern redox chemoproteomics approaches. As our understanding of sulfur chemistry and redox signaling evolves, newly discovered cysteine OxiPTMs in microorganisms, plants, cells, tissues, and disease models should innovatively promote mechanistic and therapeutic research.

Chemoproteomic profiling of protein-metabolite interactions

Small molecule metabolites play important roles in regulating protein functions, which are acted through either covalent non-enzymatic post-translational modifications or non-covalent binding interactions. Chemical proteomic strategies can help delineate global landscapes of cellular protein-metabolite interactions and provide molecular insights about their mechanisms of action. In this review, we summarized the recent progress in developments and applications of chemoproteomic strategies to profile protein-metabolite interactions.

Green Synthesis of Substituted Anilines and Quinazolines from Isatoic Anhydride-8-amide

Synthetic methods used to generate substituted anilines and quinazolines, both privileged pharmacological structures, are cumbersome, hazardous or, in some cases, unavailable. We developed a straightforward method for making isatoic anhydride-8-amide from isatin-7-carboxylic acid as a tool to easily produce a range of quinazoline and substituted aniline derivatives using adaptable pH-sensitive cyclization chemistry. The approaches are inexpensive, simple, fast, efficient at room temperature and scalable, enabling the synthesis of both established and new quinazolines and also highly substituted anilines including cyano derivatives.

Chemical Probes for Redox Signaling and Oxidative Stress

SIGNIFICANCE

Cellular reactive oxygen species (ROS) mediate redox signaling cascades that are critical to numerous physiological and pathological processes. Analytical methods to monitor cellular ROS levels and proteomic platforms to identify oxidative post-translational modifications (PTMs) of proteins are critical to understanding the triggers and consequences of redox signaling. Recent Advances: The prevalence and significance of redox signaling has recently been illuminated through the use of chemical probes that allow for sensitive detection of cellular ROS levels and proteomic dissection of oxidative PTMs directly in living cells.

CRITICAL ISSUES

In this review, we provide a comprehensive overview of chemical probes that are available for monitoring ROS and oxidative PTMs, and we highlight the advantages and limitations of these methods.

FUTURE DIRECTIONS

Despite significant advances in chemical probes, the low levels of cellular ROS and low stoichiometry of oxidative PTMs present challenges for accurately measuring the extent and dynamics of ROS generation and redox signaling. Further improvements in sensitivity and ability to spatially and temporally control readouts are essential to fully illuminate cellular redox signaling.

Chemical proteomics reveals new targets of cysteine sulfinic acid reductase

Cysteine sulfinic acid or S-sulfinylation is an oxidative post-translational modification (OxiPTM) that is known to be involved in redox-dependent regulation of protein function but has been historically difficult to analyze biochemically. To facilitate the detection of S-sulfinylated proteins, we demonstrate that a clickable, electrophilic diazene probe (DiaAlk) enables capture and site-centric proteomic analysis of this OxiPTM. Using this workflow, we revealed a striking difference between sulfenic acid modification (S-sulfenylation) and the S-sulfinylation dynamic response to oxidative stress, which is indicative of different roles for these OxiPTMs in redox regulation. We also identified >55 heretofore-unknown protein substrates of the cysteine sulfinic acid reductase sulfiredoxin, extending its function well beyond those of 2-cysteine peroxiredoxins (2-Cys PRDX1-4) and offering new insights into the role of this unique oxidoreductase as a central mediator of reactive oxygen species-associated diseases, particularly cancer. DiaAlk therefore provides a novel tool to profile S-sulfinylated proteins and study their regulatory mechanisms in cells.

Redox Signaling by Reactive Electrophiles and Oxidants

The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.

Water-promoted C-S bond formation reactions

Allylic sulfones, owning to their widespread distributions in biologically active molecules, received increasing attention in the past few years. However, the synthetic method under mild conditions is still a challenging task. In this paper, we report a sulfinic acids ligation with allylic alcohols via metal-free dehydrative cross-coupling. Both aliphatic and aromatic sulfinic acids react with various allylic alcohols to deliver the desired allylic sulfones in high yields with excellent selectivity. This carbon-sulfur bond formation reaction is highly efficient and practical since it works under metal-free, neutral, aqueous media and at room temperature in which the products even can be obtained by simple filtration without the need for organic extraction or column chromatography. Water is found to be essential for the success of this carbon-sulfur bond formation reaction. DFT calculations imply that water acts as promoter in this transformation via intermolecular hydrogen bonds.

Can dimedone be used to study selenoproteins? An investigation into the reactivity of dimedone toward oxidized forms of selenocysteine

Dimedone is a widely used reagent to assess the redox state of cysteine-containing proteins as it will alkylate sulfenic acid residues, but not sulfinic acid residues. While it has been reported that dimedone can label selenenic acid residues in selenoproteins, we investigated the stability, and reversibility of this label in a model peptide system. We also wondered whether dimedone could be used to detect seleninic acid residues. We used benzenesulfinic acid, benzeneseleninic acid, and model selenocysteine-containing peptides to investigate possible reactions with dimedone. These peptides were incubated with H₂ O₂ in the presence of dimedone and then the reactions were followed by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS). The native peptide, H-PTVTGCUG-OH (corresponding to the native amino acid sequence of the C-terminus of mammalian thioredoxin reductase), could not be alkylated by dimedone, but could be carboxymethylated with iodoacetic acid. However the "mutant peptide," H-PTVTGAUG-OH, could be labeled with dimedone at low concentrations of H₂ O₂ , but the reaction was reversible by addition of thiol. Due to the reversible nature of this alkylation, we conclude that dimedone is not a good reagent for detecting selenenic acids in selenoproteins. At high concentrations of H₂ O₂ , selenium was eliminated from the peptide and a dimeric form of dimedone could be detected using LCMS and ¹ H NMR. The dimeric dimedone product forms as a result of a seleno-Pummerer reaction with Sec-seleninic acid. Overall our results show that the reaction of dimedone with oxidized cysteine residues is quite different from the same reaction with oxidized selenocysteine residues.

Chemical methods for mapping cysteine oxidation

Methods to characterise oxidative modifications of cysteine help clarify their role in protein function in both healthy and diseased cells.

Profiling Protein S-Sulfination with Maleimide-Linked Probes

Cysteine residues are susceptible to oxidation to form S-sulfinyl (R-SO₂ H) and S-sulfonyl (R-SO₃ H) post-translational modifications. Here we present a simple bioconjugation strategy to label S-sulfinated proteins by using reporter-linked maleimides. After alkylation of free thiols with iodoacetamide, S-sulfinated cysteines react with maleimide to form a sulfone Michael adduct that remains stable under acidic conditions. Using this sequential alkylation strategy, we demonstrate differential S-sulfination across mouse tissue homogenates, as well as enhanced S-sulfination following pharmacological induction of endoplasmic reticulum stress, lipopolysaccharide stimulation, and inhibitors of the electron transport chain. Overall, this study reveals a broadened profile of maleimide reactivity across cysteine modifications, and outlines a simple method for profiling the physiological role of cysteine S-sulfination in disease.

Proteomic approaches to quantify cysteine reversible modifications in aging and neurodegenerative diseases

Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling, and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases.

Molecular Basis for Redox Activation of Epidermal Growth Factor Receptor Kinase

Epidermal growth factor receptor (EGFR) is a target of signal-derived H2O2, and oxidation of active-site cysteine 797 to sulfenic acid enhances kinase activity. Although a major class of covalent drugs targets C797, nothing is known about its catalytic importance or how S-sulfenylation leads to activation. Here, we report the first detailed functional analysis of C797. In contrast to prior assumptions, mutation of C797 diminishes catalytic efficiency in vitro and cells. The experimentally determined pKa and reactivity of C797 toward H2O2 correspondingly distinguish this residue from the bulk of the cysteinome. Molecular dynamics simulation of reduced versus oxidized EGFR, reinforced by experimental testing, indicates that sulfenylation of C797 allows new electrostatic interactions to be formed with the catalytic loop. Finally, we show that chronic oxidative stress yields an EGFR subpopulation that is refractory to the FDA-approved drug afatinib. Collectively, our data highlight the significance of redox biology to understanding kinase regulation and drug pharmacology.

Simultaneous Enrichment of Cysteine-containing Peptides and Phosphopeptides Using a Cysteine-specific Phosphonate Adaptable Tag (CysPAT) in Combination with titanium dioxide (TiO2) Chromatography

Cysteine is a rare and conserved amino acid involved in most cellular functions. The thiol group of cysteine can be subjected to diverse oxidative modifications that regulate many physio-pathological states. In the present work, a Cysteine-specific Phosphonate Adaptable Tag (CysPAT) was synthesized to selectively label cysteine-containing peptides (Cys peptides) followed by their enrichment with titanium dioxide (TiO₂) and subsequent mass spectrometric analysis. The CysPAT strategy was developed using a synthetic peptide, a standard protein and subsequently the strategy was applied to protein lysates from Hela cells, achieving high specificity and enrichment efficiency. In particular, for Cys proteome analysis, the method led to the identification of 7509 unique Cys peptides from 500 μg of HeLa cell lysate starting material. Furthermore, the method was developed to simultaneously enrich Cys peptides and phosphorylated peptides. This strategy was applied to SILAC labeled Hela cells subjected to 5 min epidermal growth factor (EGF) stimulation. In total, 10440 unique reversibly modified Cys peptides (3855 proteins) and 7339 unique phosphopeptides (2234 proteins) were simultaneously identified from 250 μg starting material. Significant regulation was observed in both phosphorylation and reversible Cys modification of proteins involved in EGFR signaling. Our data indicates that EGF stimulation can activate the well-known phosphorylation of EGFR and downstream signaling molecules, such as mitogen-activated protein kinases (MAPK1 and MAPK3), however, it also leads to substantial modulation of reversible cysteine modifications in numerous proteins. Several protein tyrosine phosphatases (PTPs) showed a reduction of the catalytic Cys site in the conserved putative phosphatase HC(X)5R motif indicating an activation and subsequent de-phosphorylation of proteins involved in the EGF signaling pathway. Overall, the CysPAT strategy is a straight forward, easy and promising method for studying redox proteomics and the simultaneous enrichment strategy offers an excellent solution for characterization of cross-talk between phosphorylation and redox induced reversible cysteine modifications.

Harnessing Redox Cross-Reactivity To Profile Distinct Cysteine Modifications

Cysteine S-nitrosation and S-sulfination are naturally occurring post-translational modifications (PTMs) on proteins induced by physiological signals and redox stress. Here we demonstrate that sulfinic acids and nitrosothiols react to form a stable thiosulfonate bond, and leverage this reactivity using sulfinate-linked probes to enrich and annotate hundreds of endogenous S-nitrosated proteins. In physiological buffers, sulfinic acids do not react with iodoacetamide or disulfides, enabling selective alkylation of free thiols and site-specific analysis of S-nitrosation. In parallel, S-nitrosothiol-linked probes enable enrichment and detection of endogenous S-sulfinated proteins, confirming that a single sulfinic acid can react with a nitrosothiol to form a thiosulfonate linkage. Using this approach, we find that hydrogen peroxide addition increases S-sulfination of human DJ-1 (PARK7) at Cys106, whereas Cys46 and Cys53 are fully oxidized to sulfonic acids. Comparative gel-based analysis of different mouse tissues reveals distinct profiles for both S-nitrosation and S-sulfination. Quantitative proteomic analysis demonstrates that both S-nitrosation and S-sulfination are widespread, yet exhibit enhanced occupancy on select proteins, including thioredoxin, peroxiredoxins, and other validated redox active proteins. Overall, we present a direct, bidirectional method to profile select redox cysteine modifications based on the unique nucleophilicity of sulfinic acids.

Chemical approaches to discovery and study of sources and targets of hydrogen peroxide redox signaling through NADPH oxidase proteins

Hydrogen peroxide (H2O2) is a prime member of the reactive oxygen species (ROS) family of molecules produced during normal cell function and in response to various stimuli, but if left unchecked, it can inflict oxidative damage on all types of biological macromolecules and lead to cell death. In this context, a major source of H2O2 for redox signaling purposes is the NADPH oxidase (Nox) family of enzymes, which were classically studied for their roles in phagocytic immune response but have now been found to exist in virtually all mammalian cell types in various isoforms with distinct tissue and subcellular localizations. Downstream of this tightly regulated ROS generation, site-specific, reversible covalent modification of proteins, particularly oxidation of cysteine thiols to sulfenic acids, represents a prominent posttranslational modification akin to phosphorylation as an emerging molecular mechanism for transforming an oxidant signal into a dynamic biological response. We review two complementary types of chemical tools that enable (a) specific detection of H2O2 generated at its sources and (b) mapping of sulfenic acid posttranslational modification targets that mediate its signaling functions, which can be used to study this important chemical signal in biological systems.

The Expanding Landscape of the Thiol Redox Proteome

Cysteine occupies a unique place in protein chemistry. The nucleophilic thiol group allows cysteine to undergo a broad range of redox modifications beyond classical thiol-disulfide redox equilibria, including S-sulfenylation (-SOH), S-sulfinylation (-SO(2)H), S-sulfonylation (-SO(3)H), S-nitrosylation (-SNO), S-sulfhydration (-SSH), S-glutathionylation (-SSG), and others. Emerging evidence suggests that these post-translational modifications (PTM) are important in cellular redox regulation and protection against oxidative damage. Identification of protein targets of thiol redox modifications is crucial to understanding their roles in biology and disease. However, analysis of these highly labile and dynamic modifications poses challenges. Recent advances in the design of probes for thiol redox forms, together with innovative mass spectrometry based chemoproteomics methods make it possible to perform global, site-specific, and quantitative analyses of thiol redox modifications in complex proteomes. Here, we review chemical proteomic strategies used to expand the landscape of thiol redox modifications.

A Chemical Approach for the Detection of Protein Sulfinylation

Protein sulfinic acids are formed by the reaction of reactive oxygen species with protein thiols. Sulfinic acid formation has long been considered an irreversible state of oxidation and is associated with high cellular oxidative stress. Increasing evidence, however, indicates that cysteine is oxidized to sulfinic acid in cells to a greater extent, and is more controlled, than first thought. The discovery of sulfiredoxin has demonstrated that cysteine sulfinic acid can be reversed, pointing to a vast array of potential implications for redox biology. Identification of the site of protein sulfinylation is crucial in clarifying the physiological and pathological effects of post-translational modifications. Currently, the only methods for detection of sulfinic acids involve mass spectroscopy and the use of specific antibodies. However, these methodologies are not suitable for proteomic studies. Herein, we report the first probe for detection of protein sulfinylation, NO-Bio, which combines a C-nitroso warhead for rapid labeling of sulfinic acid with a biotin handle. Based on this new tool, we developed a selective two-step approach. In the first, a sulfhydryl-reactive compound is introduced to selectively block free cysteine residues. Thereafter, the sample is treated with NO-Bio to label sulfinic acids. This new technology represents a rapid, selective, and general technology for sulfinic acid detection in biological samples. As proof of our concept, we also evaluated protein sulfinylation levels in various human lung tumor tissue lysates. Our preliminary results suggest that cancer tissues generally have higher levels of sulfinylation in comparison to matched normal tissues. A new ability to monitor protein sulfinylation directly should greatly expand the impact of sulfinic acid as a post-translational modification.

Characterization of Peroxidases Expressed in Human Antigen Presenting Cells and Analysis of the Covalent Binding of Nitroso Sulfamethoxazole to Myeloperoxidase

Drug hypersensitivity remains a major concern, as it causes high morbidity and mortality. Understanding the mechanistic basis of drug hypersensitivity is complicated by the multiple risk factors implicated. This study utilized sulfamethoxazole (SMX) as a model drug to (1) relate SMX metabolism in antigen presenting cells (APCs) to the activation of T-cells and (2) characterize covalent adducts of SMX and myeloperoxidase, which might represent antigenic determinants for T-cells. The SMX metabolite nitroso-SMX (SMX-NO) was found to bind irreversibly to APCs. Time- and concentration-dependent drug-protein adducts were also detected when APCs were cultured with SMX. Metabolic activation of SMX was significantly reduced by the oxygenase/peroxidase inhibitor methimazole. Similarly, SMX-NO-specific T-cells were activated by APCs pulsed with SMX, and the response was inhibited by pretreatment with methimazole or glutaraldehyde, which blocks antigen processing. Western blotting, real-time polymerase chain reaction (RT-PCR), and mass spectrometry analyses suggested the presence of low concentrations of myeloperoxidase in APCs. RT-PCR revealed mRNA expression for flavin-containing monooxygenases (FMO1-5), thyroid peroxidase, and lactoperoxidase, but the corresponding proteins were not detected. Mass spectrometric characterization of SMX-NO-modified myeloperoxidase revealed the formation of N-hydroxysulfinamide adducts on Cys309 and Cys398. These data show that SMX's metabolism in APCs generates antigenic determinants for T-cells. Peptides derived from SMX-NO-modified myeloperoxidase may represent one form of functional antigen.

Effects of ionizing radiation on biological molecules--mechanisms of damage and emerging methods of detection

SIGNIFICANCE

The detrimental effects of ionizing radiation (IR) involve a highly orchestrated series of events that are amplified by endogenous signaling and culminating in oxidative damage to DNA, lipids, proteins, and many metabolites. Despite the global impact of IR, the molecular mechanisms underlying tissue damage reveal that many biomolecules are chemoselectively modified by IR.

RECENT ADVANCES

The development of high-throughput "omics" technologies for mapping DNA and protein modifications have revolutionized the study of IR effects on biological systems. Studies in cells, tissues, and biological fluids are used to identify molecular features or biomarkers of IR exposure and response and the molecular mechanisms that regulate their expression or synthesis.

CRITICAL ISSUES

In this review, chemical mechanisms are described for IR-induced modifications of biomolecules along with methods for their detection. Included with the detection methods are crucial experimental considerations and caveats for their use. Additional factors critical to the cellular response to radiation, including alterations in protein expression, metabolomics, and epigenetic factors, are also discussed.

FUTURE DIRECTIONS

Throughout the review, the synergy of combined "omics" technologies such as genomics and epigenomics, proteomics, and metabolomics is highlighted. These are anticipated to lead to new hypotheses to understand IR effects on biological systems and improve IR-based therapies.

Accurate predictions of C–SO2R bond dissociation enthalpies using density functional theory methods

M06-2X/6-31G(d) was found to be accurate in calculating C–S BDEs, and preliminary mechanistic studies were performed using it.