Tandem MS analysis of selenamide-derivatized peptide ions

Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins

Chemoproteomic profiling of sulfhydryl-containing proteins has consistently been an attractive research hotspot. However, there remains a dearth of probes that are specifically designed for sulfhydryl-containing proteins, possessing sufficient reactivity, specificity, distinctive isotopic signature, as well as efficient labeling and evaluation capabilities for proteins implicated in the regulation of redox homeostasis. Here, the specific selenium-containing probes (Se-probes) in this work displayed high specificity and reactivity toward cysteine thiols on small molecules, peptides and purified proteins and showed very good competitive effect of proteins labeling in gel-ABPP. We identified more than 6000 candidate proteins. In TOP-ABPP, we investigated the peptide labeled by Se-probes, which revealed a distinct isotopic envelope pattern of selenium in both the primary and secondary mass spectra. This unique pattern can provide compelling evidence for identifying redox regulatory proteins and other target peptides. Furthermore, our examiation of post-translational modification (PTMs) of the cysteine site residues showed that oxidation PTMs was predominantly observed. We anticipate that Se-probes will enable broader and deeper proteome-wide profiling of sulfhydryl-containing proteins, provide an ideal tool for focusing on proteins that regulate redox homeostasis and advance the development of innovative selenium-based pharmaceuticals.

Ebselen-Agents for Sensing, Imaging and Labeling: Facile and Full-Featured Application in Biochemical Analysis

Phenyl-1,2-benzoselenazol-3(2H)-one (ebselen) is a classical mimic of glutathione peroxidase (GPx). Thioredoxin interaction endows ebselen attractive biological functions, such as antioxidation and anti-infection, as well as versatile therapeutic usage. Accordingly, application of ebselen analogues in biosensing, chemical labeling, imaging analysis, disease pathology, drug development, clinical treatment, etc. have been widely developed, in which mercaptans, reactive oxygen species, reactive sulfur species, peptides, and proteins were involved. Herein, focusing on the application of ebselen-agents in biochemistry, we have made a systematic summary and comprehensive review. First, we summarized both the classical and the innovative methods for preparing ebselen-agents to present the synthetic strategies. Then we discussed the full functional applicability of ebselen analogues in three fields of biochemical analysis including the fluorescence sensing and bioimaging, derivatization for high throughput fluorescence analysis, and the labeling gents for proteomics. Finally, we discussed the current challenges and perspectives for ebselen-agents as analytical tools in biological research. By presenting the multifunctional applicability of ebselen, we hope this review could appeal researchers to design the ebselen-related biomaterials for biochemical analysis.

Fabrication of a "Selenium Signature" Chemical Probe-Modified Paper Substrate for Simultaneous and Efficient Determination of Biothiols by Paper Spray Mass Spectrometry

Significant efforts have been made to develop robust and reliable methods for simultaneous biothiols determination in different matrices, but there still exist the problems such as easy oxidation, tedious derivatization, and difficulty in discrimination, which brings unsatisfactory results in their accuracy and fast quantification in biological samples. To overcome these problems, a simultaneous biothiols detection method combining a "selenium signature" chemical probe and paper spray mass spectrometry (PS-MS) was proposed. In the strategy, the modified-paper substrate is used to enhance the analytical performance. Chemical probe Ebselen-NH₂ that has a specific response to biothiols was designed and covalently fixed on the surface of an oxidized paper substrate. By the identification of derivatized product with distinctive selenium isotope distribution and employment of the optimized PS-MS method, qualitative and quantitative analysis of five biothiols including glutathione (GSH), cysteine (Cys), cysteinylglycine (CysGly), N-acetylcysteine (Nac), and homocysteine (Hcy) were realized. Biothiols in plasma and cell lysates were measured with satisfactory results. The established method not only provides a novel protocol for simultaneous determination of biothiols, but also is helpful for understanding the biological and clinical roles played by these bioactive small molecules.

Target discovery of ebselen with a biotinylated probe

Despite numerous studies on ebselen over the past decade, its cellular targets remain obscure. Here we synthesized a biotinylated ebselen probe (biotin-ebselen) and characterized ebselen-binding proteins via an efficient activity-based protein profiling (ABPP) method, which allowed for the robust identification of 462 targeted proteins in HeLa cells. This first work of global target profiling of ebselen will be helpful to re-design ebselen-based therapy appropriately in clinical trials.

Characterization of the Cysteine Content in Proteins Utilizing Cysteine Selenylation with 266 nm Ultraviolet Photodissociation (UVPD)

Characterization of the cysteine content of proteins is a key aspect of proteomics. By defining both the total number of cysteines and their bound/unbound state, the number of candidate proteins considered in database searches is significantly constrained. Herein we present a methodology that utilizes 266 nm UVPD to count the number of free and bound cysteines in intact proteins. In order to attain this goal, proteins were derivatized with N-(phenylseleno)phthalimide (NPSP) to install a selectively cleavable Se-S bond upon 266 UVPD. The number of Se-S bonds cleaved upon UVPD, a process that releases SePh moieties, corresponds to the number of cysteine residues per protein. Graphical Abstract ᅟ.

Cysteine-Selective Peptide Identification: Selenium-Based Chromophore for Selective S-Se Bond Cleavage with 266 nm Ultraviolet Photodissociation

The tremendous number of peptides identified in current bottom-up mass spectrometric workflows, although impressive for high-throughput proteomics, results in little selectivity for more targeted applications. We describe a strategy for cysteine-selective proteomics based on a tagging method that installs a S-Se bond in peptides that is cleavable upon 266 nm ultraviolet photodissociation (UVPD). The alkylating reagent, N-(phenylseleno)phthalimide (NPSP), reacts with free thiols in cysteine residues and attaches a chromogenic benzeneselenol (SePh) group. Upon irradiation of tagged peptides with 266 nm photons, the S-Se bond is selectively cleaved, releasing a benzeneselenol moiety corresponding to a neutral loss of 156 Da per cysteine. Herein we demonstrate a new MS/MS scan mode, UVPDnLossCID, which facilitates selective screening of cysteine-containing peptides. A "prescreening" event occurs by activation of the top N peptide ions by 266 nm UVPD. Peptides exhibiting a neutral loss corresponding to one or more SePh groups are reactivated and sequenced by CID. Because of the low frequency of cysteine in the proteome, unique cysteine-containing peptides may serve as surrogates for entire proteins. UVPDnLossCID does not generate as many peptide spectrum matches (PSMs) as conventional bottom-up methods; however, UVPDnLossCID provides far greater selectivity.

Dramatic substituent effects on the mechanisms of nucleophilic attack on Se-S bridges

The reactions of XSeSX, XSeSY, and YSeSX (X, Y = CH3, NH2, OH, F) with F(-) and CN(-) nucleophiles have been investigated by means of B3PW91/6-311+G(2df,p) and G4 calculations. In systems where the two substituents are not identical (XSeSY), the more stable of the two possible isomers corresponds to those in which the most electronegative substituent is attached to Se. Nucleophilic attack takes place at Se, independent of the nature of the nucleophile, with the only exception being XSeSF (X = CH3 , NH2 , OH), in which case the attack occurs at S. In agreement with recent results for disulfide and diselenide linkages, the mechanisms leading to Se-S bond cleavage are not always the more favorable ones because for highly electronegative substituents the most favorable process is fission of the chalcogen-substituent bond. These dissimilarities in the observed reactivity pattern as a function of the electronegativity of the substituents are due to the fact that the σ-type Se-S antibonding orbital, which for low-electronegative substituents is the lowest unnoccupied molecular orbital (LUMO), becomes strongly destabilized when the electronegativity of the substituent increases, and is replaced by an antibonding π-type Se-X (or S-X) orbital. In contrast, however, with what has been found for disulfide and diselenide derivatives, the observed reactivity does not change with the nature of the nucleophile. The activation strain model provides interesting insight into these processes, showing that in most cases the activation barriers are the consequence of subtle differences in the strain or in the interaction energies.

Fast and selective modification of thiol proteins/peptides by N-(phenylseleno)phthalimide

We previously reported that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used to selectively derivatize thiols for mass spectrometric analysis, and the introduced selenium tags are useful as they could survive or removed with collision-induced dissociation (CID). Described herein is the further study of the reactivity of various protein/peptide thiols toward NPSP and its application to derivatize thiol peptides in protein digests. With a modified protocol (i.e., dissolving NPSP in acetonitrile instead of aqueous solvent), we found that quantitative conversion of thiols can be obtained in seconds, using NPSP in a slight excess amount (NPSP:thiol of 1.1-2:1). Further investigation shows that the thiol reactivity toward NPSP reflects its chemical environment and accessibility in proteins/peptides. For instance, adjacent basic amino acid residues increase the thiol reactivity, probably because they could stabilize the thiolate form to facilitate the nucleophilic attack of thiol on NPSP. In the case of creatine phosphokinase, the native protein predominately has one thiol reacted with NPSP while all of four thiol groups of the denatured protein can be derivatized, in accordance with the corresponding protein conformation. In addition, thiol peptides in protein/peptide enzymatic digests can be quickly and effectively tagged by NPSP following tri-n-butylphosphine (TBP) reduction. Notably, all three thiols of the peptide QCCASVCSL in the insulin peptic digest can be modified simultaneously by NPSP. These results suggest a novel and selective method for protecting thiols in the bottom-up approach for protein structure analysis.