Removal of the 5-nitro-2-pyridine-sulfenyl protecting group from selenocysteine and cysteine by ascorbolysis

New Role for Radical SAM Enzymes in the Biosynthesis of Thio(seleno)oxazole RiPP Natural Products

Ribosomally synthesized post-translationally modified peptides (RiPPs) are ubiquitous and represent a structurally diverse class of natural products. The ribosomally encoded precursor polypeptides are often extensively modified post-translationally by enzymes that are encoded by coclustered genes. Radical S-adenosyl-l-methionine (SAM) enzymes catalyze numerous chemically challenging transformations. In RiPP biosynthetic pathways, these transformations include the formation of C-H, C-C, C-S, and C-O linkages. In this paper, we show that the Geobacter lovleyi sbtM gene encodes a radical SAM protein, SbtM, which catalyzes the cyclization of a Cys/SeCys residue in a minimal peptide substrate. Biochemical studies of this transformation support a mechanism involving H-atom abstraction at the C-3 of the substrate Cys to initiate the chemistry. Several possible cyclization products were considered. The collective biochemical, spectroscopic, mass spectral, and computational observations point to a thiooxazole as the product of the SbtM-catalyzed modification. To our knowledge, this is the first example of a radical SAM enzyme that catalyzes a transformation involving a SeCys-containing peptide and represents a new paradigm for formation of oxazole-containing RiPP natural products.

Cysteine protecting groups: applications in peptide and protein science

Protecting group chemistry for the cysteine thiol group has enabled a vast array of peptide and protein chemistry over the last several decades. Increasingly sophisticated strategies for the protection, and subsequent deprotection, of cysteine have been developed, facilitating synthesis of complex disulfide-rich peptides, semisynthesis of proteins, and peptide/protein labelling in vitro and in vivo. In this review, we analyse and discuss the 60+ individual protecting groups reported for cysteine, highlighting their applications in peptide synthesis and protein science.

Chemistry and Chemical Biology of Selenenyl Sulfides and Thioseleninic Acids

Significance: Selenenyl sulfides (RSeSRs) and thioseleninic acids (RSeSHs) are the monoselenium (Se) analogs of disulfides and persulfides that contain Se-S bonds. These bonds are found in several antioxidant-regenerating enzymes as derivatives of selenocysteine, making them an important player in redox biology as it pertains to sulfur redox regulation. Recent Advances: Mechanistic studies of redox-regulating selenoenzymes such as thioredoxin reductase and glutathione peroxidase suggest crucial Se-S bonds in the active sites. Peptide models and small-molecule mimics of these active sites have been prepared to study their fundamental chemistry. These advances help pave the road to better understand the functions of the Se-S bond in the body. Critical Issues: The Se-S bond is unstable at atmospheric temperatures and pressures. Therefore, studying their properties proposes a major challenge. Currently, there are no trapping reagents specific to RSeSRs or RSeSHs, making their presence, identity, and fates in biological environments difficult to track. Future Directions: Further understanding of the fundamental chemistry/biochemistry of RSeSRs and RSeSHs is needed to understand what their intracellular targets are and to what extent they impact signaling. Besides antioxidant regeneration and peroxide radical reduction, the roles of RSeSR and RSeSHs in other systems need to be further explored.

2,2'-Dipyridyl diselenide: A chemoselective tool for cysteine deprotection and disulfide bond formation

There are many examples of bioactive, disulfide-rich peptides and proteins whose biological activity relies on proper disulfide connectivity. Regioselective disulfide bond formation is a strategy for the synthesis of these bioactive peptides, but many of these methods suffer from a lack of orthogonality between pairs of protected cysteine (Cys) residues, efficiency, and high yields. Here, we show the utilization of 2,2'-dipyridyl diselenide (PySeSePy) as a chemical tool for the removal of Cys-protecting groups and regioselective formation of disulfide bonds in peptides. We found that peptides containing either Cys(Mob) or Cys(Acm) groups treated with PySeSePy in trifluoroacetic acid (TFA) (with or without triisopropylsilane (TIS) were converted to Cys-S-SePy adducts at 37 °C and various incubation times. This novel Cys-S-SePy adduct is able to be chemoselectively reduced by five-fold excess ascorbate at pH 4.5, a condition that should spare already installed peptide disulfide bonds from reduction. This chemoselective reduction by ascorbate will undoubtedly find utility in numerous biotechnological applications. We applied our new chemistry to the iodine-free synthesis of the human intestinal hormone guanylin, which contains two disulfide bonds. While we originally envisioned using ascorbate to chemoselectively reduce one of the formed Cys-S-SePy adducts to catalyze disulfide bond formation, we found that when pairs of Cys(Acm) residues were treated with PySeSePy in TFA, the second disulfide bond formed spontaneously. Spontaneous formation of the second disulfide is most likely driven by the formation of the thermodynamically favored diselenide (PySeSePy) from the two Cys-S-SePy adducts. Thus, we have developed a one-pot method for concomitant deprotection and disulfide bond formation of Cys(Acm) pairs in the presence of an existing disulfide bond.

Marie EJ, Mose G, Ruggles EL, Hondal RJ. Facile removal of 4-methoxybenzyl protecting group from selenocysteine

Historically, methods to remove the 4-methoxybenzyl (Mob)-protecting group from selenocysteine (Sec) in peptides have used harsh and toxic reagents. The use of 2,2'-dithiobis-5-nitropyridine (DTNP) is an improvement over these methods; however, many wash steps are required to remove the by-product contaminant 5-nitro-2-thiopyridine. Even with many washes, excess DTNP adheres to the peptide. The final product needs excess purification to remove these contaminants. It was recently discovered by our group that hindered hydrosilanes could be used to reduce Cys(Mob). We sought to apply a similar methodology to reduce Sec(Mob), which we expected to be even more labile. Here, we present a gentle and facile method for deprotection of Sec(Mob) using triethylsilane (TES), phenol, and a variety of other scavengers often used in deprotection cocktails. The different cocktails were all incubated at 40 °C for 4 hours. The combination of TFA/TES/thioanisole (96:2:2) appeared to be the most efficient of the cocktails tested, providing complete deprotection and yielded peptide that was mainly in the diselenide form. This cocktail also showed no evidence of side reactions or significant contaminants in the high-performance liquid chromatography (HPLC) and mass spectral (MS) analyses. We envision that our new method will allow for a simple and gentle "one-pot" deprotection of Sec(Mob) following solid-phase peptide synthesis and will minimize the need for extensive purification steps.

Synthesis of alpha-methyl selenocysteine and its utilization as a glutathione peroxidase mimic

Selenocysteine (Sec) is the 21st amino acid in the genetic code where this amino acid is primarily involved in redox reactions in enzymes because of its high reactivity toward oxygen and related reactive oxygen species. Sec has found wide utility in synthetic peptides, especially as a replacement for cysteine. One limitation of using Sec in synthetic peptides is that it can undergo β-syn elimination reactions after oxidation, rendering the peptide inactive due to loss of selenium. This limitation can be overcome by substituting Cα-H with a methyl group. The resulting Sec derivative is α-methylselenocysteine ((αMe)Sec). Here, we present a new strategy for the synthesis of (αMe)Sec by alkylation of an achiral methyl malonate through the use of a selenium-containing alkylating agent synthesized in the presence of dichloromethane. The seleno-malonate was then subjected to an enzymatic hydrolysis utilizing pig liver esterase followed by a Curtius rearrangement producing a protected derivative of (αMe)Sec that could be used in solid-phase peptide synthesis. We then synthesized two peptides: one containing Sec and the other containing (αMe)Sec, based on the sequence of glutathione peroxidase. This is the first reported incorporation of (αMe)Sec into a peptide as well as the first reported biochemical application of this unique amino acid. The (αMe)Sec-containing peptide had superior stability as it could not undergo β-syn elimination and it also avoided cleavage of the peptide backbone, which we surprisingly found to be the case for the Sec-containing peptide when it was incubated for 96 hours in oxygenated buffer at pH 8.0.

Synthesis and semisynthesis of selenopeptides and selenoproteins

The versatile chemistry of the genetically encoded amino acid selenocysteine (Sec) is employed in Nature to expand the reactivity of enzymes. In addition to, its role in biology, Sec is used in protein engineering to modify folding, stability, and reactivity of proteins, to introduce conjugations and to facilitate reactions. However, due to limitations related to Sec's insertion mechanism in Nature, much of the production of Sec containing peptides and proteins relies on synthesis and semisynthesis. Here, we review recent advances that have enabled the assembly of complicated selenoproteins, including novel uses of protecting groups for solid phase peptide synthesis, rapid selenoester driven chemical ligations and versatile expressed protein ligations.

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 synthesis of membrane proteins: a model study on the influenza virus B proton channel

NCL results in the quantitative yield of a membrane protein, where a thioester peptide is formed from an oxo-ester with an in situ cleavable solubilizing tag.

In the present study we have developed and optimized a robust strategy for the synthesis of highly hydrophobic peptides, especially membrane proteins, exemplarily using the influenza B M2 proton channel (BM2(1–51)). This strategy is based on the native chemical ligation of two fragments, where the thioester fragment is formed from an oxo-ester peptide, which is synthesized using Fmoc-SPPS, and features an in situ cleavable solubilizing tag (ADO, ADO₂ or ADO-Lys₅). The nearly quantitative production of the ligation product was followed by an optimized work up protocol, resulting in almost quantitative desulfurization and Acm-group cleavage. Circular dichroism analysis in a POPC lipid membrane revealed that the synthetic BM2(1–51) construct adopts a helical structure similar to that of the previously characterized BM2(1–33).