Thiol Nucleophiles Research Articles

Click-PEGylation – A mobility shift approach to assess the redox state of cysteines in candidate proteins

The redox state of cysteine thiols is critical for protein function. Whereas cysteines play an important role in the maintenance of protein structure through the formation of internal disulfides, their nucleophilic thiol groups can become oxidatively modified in response to diverse redox challenges and thereby function in signalling and antioxidant defences. These oxidative modifications occur in response to a range of agents and stimuli, and can lead to the existence of multiple redox states for a given protein. To assess the role(s) of a protein in redox signalling and antioxidant defence, it is thus vital to be able to assess which of the multiple thiol redox states are present and to investigate how these alter under different conditions. While this can be done by a range of mass spectrometric-based methods, these are time-consuming, costly, and best suited to study abundant proteins or to perform an unbiased proteomic screen. One approach that can facilitate a targeted assessment of candidate proteins, as well as proteins that are low in abundance or proteomically challenging, is by electrophoretic mobility shift assays. Redox-modified cysteine residues are selectively tagged with a large group, such as a polyethylene glycol (PEG) polymer, and then the proteins are separated by electrophoresis followed by immunoblotting, which allows the inference of redox changes based on band shifts. However, the applicability of this method has been impaired by the difficulty of cleanly modifying protein thiols by large PEG reagents. To establish a more robust method for redox-selective PEGylation, we have utilised a Click chemistry approach, where free thiol groups are first labelled with a reagent modified to contain an alkyne moiety, which is subsequently Click-reacted with a PEG molecule containing a complementary azide function. This strategy can be adapted to study reversibly reduced or oxidised cysteines. Separation of the thiol labelling step from the PEG conjugation greatly facilitates the fidelity and flexibility of this approach. Here we show how the Click-PEGylation technique can be used to interrogate the redox state of proteins.

Mechanistic understanding of the cysteine capping modifications of antibodies enables selective chemical engineering in live mammalian cells

Protein modifications by intricate cellular machineries often redesign the structure and function of existing proteins to impact biological networks. Disulfide bond formation between cysteine (Cys) pairs is one of the most common modifications found in extracellularly-destined proteins, key to maintaining protein structure. Unpaired surface cysteines on secreted mammalian proteins are also frequently found disulfide-bonded with free Cys or glutathione (GSH) in circulation or culture, the mechanism for which remains unknown. Here we report that these so-called Cys-capping modifications take place outside mammalian cells, not in the endoplasmic reticulum (ER) where oxidoreductase-mediated protein disulfide formation occurs. Unpaired surface cysteines of extracellularly-arrived proteins such as antibodies are uncapped upon secretion before undergoing disulfide exchange with cystine or oxidized GSH in culture medium. This observation has led to a feasible way to selectively modify the nucleophilic thiol side-chain of cell-surface or extracellular proteins in live mammalian cells, by applying electrophiles with a chemical handle directly into culture medium. These findings provide potentially an effective approach for improving therapeutic conjugates and probing biological systems.

Methylmercury-Induced Neurotoxicity: Focus on Pro-oxidative Events and Related Consequences.

Methylmercury (MeHg) is a highly neurotoxic environmental pollutant. Even though molecular mechanisms mediating MeHg toxicity are not completely understood, several lines of evidence indicate that the neurotoxic effects resultant from MeHg exposure represent a consequence of its pro-oxidative properties. In this regard, MeHg is a soft electrophile that preferentially interacts with (and oxidize) nucleophilic groups (mainly thiols and selenols) from biomolecules, including proteins and low-molecular-weight molecules. Such interaction contributes to the occurrence of oxidative stress and impaired function of several molecules [proteins (receptors, transporters, enzymes, structural proteins), lipids (i.e., membrane constituents and intracellular messengers), and nucleic acids (i.e., DNA)], culminating in neurotoxicity.In this chapter, an initial background on the general aspects regarding the neurotoxicology of MeHg, with a particular focus on its pro-oxidative properties and its interaction with nucleophilic thiol- and selenol-containing molecules, is provided. Even though experimental evidence indicates that symptoms (i.e., motor impairment) resultant from MeHg exposure are linked to its pro-oxidative properties, as well as to their molecular consequences (lipid peroxidation, disruption of glutamate and/or calcium homeostasis, etc.), data concerning the relationship between molecular parameters and behavioral impairment others that those related to the motor function (i.e., visual impairment, cognitive skills, etc.) are scarce. Thus, even though scientific research has provided a significant amount of knowledge concerning the mechanisms mediating MeHg-induced neurotoxicity in the last decades, the whole scenario is far from being completely understood, and further research in this area is well warranted.

A dual-channel responsive near-infrared fluorescent probe for multicolour imaging of cysteine in living cells.

Aberrant levels of cysteine (Cys) in living cells are closely related to some diseases; thus in situ visualization of intracellular Cys is very helpful for the investigation of physiological and pathological processes. Herein, we report a dual-channel responsive near-infrared (NIR) fluorescent probe for multicolour imaging of Cys in living cells. The probe was constructed with a NIR BODIPY attached to 7-nitrobenzofurazan (NBD) via an ether bond. Upon substitution of the ether with the nucleophilic thiolate of Cys, a NIR BODIPY fluorophore was released to produce a significant fluorescence-enhanced signal at 735 nm. Moreover, Cys induced an intramolecular rearrangement reaction on the electrophilic site of NBD, resulting in another emission band at 540 nm. This probe exhibited some favorable properties including a dual-channel response, high fluorescence brightness, good photostability, fast response, low detection limit (22 nM) and low cytotoxicity. Furthermore, the probe was successfully applied for multicolour imaging of Cys in living cells.

The STIM-Orai Pathway: Regulation of STIM and Orai by Thiol Modifications.

Cysteines are among the least abundant amino acids found in proteins. Due to their unique nucleophilic thiol group, they are able to undergo a broad range of chemical modifications besides their known role in disulfide formation, such as S-sulfenylation (-SOH), S-sulfinylation (-SO(2)H), S-sufonylation (-SO(3)H), S-glutathionylation (-SSG), and S-sulfhydration (-SSH), among others. These posttranslational modifications can be irreversible and act as transitional modifiers or as reversible on-off switches for the function of proteins. Disturbances of the redox homeostasis, for example, in situations of increased oxidative stress, can contribute to a range of diseases. Because Ca2+ signaling mediated by store-operated calcium entry (SOCE) is involved in a plethora of cellular responses, the cross-talk between reactive oxygen species (ROS) and Ca2+ is critical for homeostatic control. Identification of calcium regulatory protein targets of thiol redox modifications is needed to understand their role in biology and disease.

Thiol–ene polymerization of oligospiroketal rods

The nucleophilic thiol–ene (thia-Michael) reaction between molecular rods bearing terminal thiols and bis-maleimides was investigated.

Structural and Biochemical Characterization of Chlamydia trachomatis DsbA Reveals a Cysteine-Rich and Weakly Oxidising Oxidoreductase.

The Gram negative bacteria Chlamydia trachomatis is an obligate intracellular human pathogen that can cause pelvic inflammatory disease, infertility and blinding trachoma. C. trachomatis encodes a homolog of the dithiol oxidoreductase DsbA. Bacterial DsbA proteins introduce disulfide bonds to folding proteins providing structural bracing for secreted virulence factors, consequently these proteins are potential targets for antimicrobial drugs. Despite sharing functional and structural characteristics, the DsbA enzymes studied to date vary widely in their redox character. In this study we show that the truncated soluble form of the predicted membrane anchored protein C. trachomatis DsbA (CtDsbA) has oxidase activity and redox properties broadly similar to other characterized DsbA proteins. However CtDsbA is distinguished from other DsbAs by having six cysteines, including a second disulfide bond, and an unusual dipeptide sequence in its catalytic motif (Cys-Ser-Ala-Cys). We report the 2.7 Å crystal structure of CtDsbA revealing a typical DsbA fold, which is most similar to that of DsbA-II type proteins. Consistent with this, the catalytic surface of CtDsbA is negatively charged and lacks the hydrophobic groove found in EcDsbA and DsbAs from other enterobacteriaceae. Biochemical characterization of CtDsbA reveals it to be weakly oxidizing compared to other DsbAs and with only a mildly destabilizing active site disulfide bond. Analysis of the crystal structure suggests that this redox character is consistent with a lack of contributing factors to stabilize the active site nucleophilic thiolate relative to more oxidizing DsbA proteins.

Synthesis of New 1‐Hydroxyindole‐2‐Carboxylates and Mechanistic Studies on Reaction Pathways

Synthesis of new 1‐hydroxyindole‐2‐carboxylates 1 and mechanistic studies on the reaction pathways were described. The substrates 2, prepared through two‐step synthetic sequences, were treated with nucleophiles in the presence of SnCl2 · 2H2O to obtain compounds 1. In particular, the mechanistic studies led to a significant finding that reactions with thiol nucleophiles occur through a newly proposed pathway (path B: 1,4‐addition followed by reduction/condensation) rather than through a previously assumed pathway (path A: reduction/condensation followed by 1,5‐addition). Further mechanistic investigations revealed steric effects of o‐substituents in 2 governing the ratio of products (1i/7).

Identification of Covalent Binding Sites Targeting Cysteines Based on Computational Approaches.

Covalent drugs have attracted increasing attention in recent years due to good inhibitory activity and selectivity. Targeting noncatalytic cysteines with irreversible inhibitors is a powerful approach for enhancing pharmacological potency and selectivity because cysteines can form covalent bonds with inhibitors through their nucleophilic thiol groups. However, most human kinases have multiple noncatalytic cysteines within the active site; to accurately predict which cysteine is most likely to form covalent bonds is of great importance but remains a challenge when designing irreversible inhibitors. In this work, FTMap was first applied to check its ability in predicting covalent binding site defined as the region where covalent bonds are formed between cysteines and irreversible inhibitors. Results show that it has excellent performance in detecting the hot spots within the binding pocket, and its hydrogen bond interaction frequency analysis could give us some interesting instructions for identification of covalent binding cysteines. Furthermore, we proposed a simple but useful covalent fragment probing approach and showed that it successfully predicted the covalent binding site of seven targets. By adopting a distance-based method, we observed that the closer the nucleophiles of covalent warheads are to the thiol group of a cysteine, the higher the possibility that a cysteine is prone to form a covalent bond. We believe that the combination of FTMap and our distance-based covalent fragment probing method can become a useful tool in detecting the covalent binding site of these targets.

Cinchona Urea-Catalyzed Asymmetric Sulfa-Michael Reactions: The Brønsted Acid-Hydrogen Bonding Model.

The cinchona alkaloid-derived urea-catalyzed asymmetric conjugate addition of aromatic thiols to cycloalkenones was studied using density functional theory (DFT). Deprotonation of the thiol gives a protonated amine that activates the electrophile by Brønsted acid catalysis, while the urea group binds the nucleophilic thiolate by hydrogen bonding. These results demonstrate the generality of the Brønsted acid-hydrogen bonding transition state (TS) model for cinchona alkaloid catalysis that we recently showed to be favored over Wynberg's widely accepted ion pair-hydrogen bonding model and represent the first detailed mechanistic study of a cinchona urea-catalyzed reaction. The conformation of the catalyst methoxy group has a strong effect on the TS, an effect overlooked in previous mechanistic studies of reactions catalyzed by cinchona alkaloids.

Phase-Separated Thiol–Epoxy–Acrylate Hybrid Polymer Networks with Controlled Cross-Link Density Synthesized by Simultaneous Thiol–Acrylate and Thiol–Epoxy Click Reactions

Thiol–epoxy–acrylate hybrid polymer networks (HPNs) are formed by the combination of nucleophilic thiol–acrylate Michael addition and thiol–epoxy coupling reactions catalyzed by 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in a one-pot synthesis. A stoichiometric balance between thiol groups (multifunctional thiols with a thiol functionality greater than two) and the addition of epoxide (difunctional epoxy) and acrylate groups (difunctional acrylate) is applied in the reactant mixture. Full conversion is achieved based on the disappearance of the thiol absorbance peak from Fourier transform infrared spectroscopy, demonstrating the high efficiency of thiol–click reactions. With relatively high molecular weight (MW = 2000 g mol–1) acrylates, novel phase-separated, thiol-based hybrid materials are obtained, as evidenced by the presence of two glass transition temperatures from both differential scanning calorimetry and dynamic mechanical analysis as well as morphology characterization by scanning electron micros...

In Situ Observation of Thiol Michael Addition to a Reversible Covalent Drug in a Crystalline Sponge.

A reversible Michael addition reaction between thiol nucleophiles and cyanoenones has been previously postulated to be the mechanism-of-action of a new family of reversible covalent drugs. However, the hypothetical Michael adducts in this mechanism have only been detected by spectroscopic methods in solution. Herein, the crystallographic observation of reversible Michael addition with a potent cyanoenone drug candidate by means of the crystalline-sponge method is reported. After inclusion of the cyanoenone substrate, the sponge crystal was treated with a thiol solution. Subsequent crystallographic analysis confirmed the single-crystal-to-single-crystal transformation of the substrate into the impermanent Michael adduct.

In Situ Observation of Thiol Michael Addition to a Reversible Covalent Drug in a Crystalline Sponge

AbstractA reversible Michael addition reaction between thiol nucleophiles and cyanoenones has been previously postulated to be the mechanism‐of‐action of a new family of reversible covalent drugs. However, the hypothetical Michael adducts in this mechanism have only been detected by spectroscopic methods in solution. Herein, the crystallographic observation of reversible Michael addition with a potent cyanoenone drug candidate by means of the crystalline‐sponge method is reported. After inclusion of the cyanoenone substrate, the sponge crystal was treated with a thiol solution. Subsequent crystallographic analysis confirmed the single‐crystal‐to‐single‐crystal transformation of the substrate into the impermanent Michael adduct.

Octa(3-mercaptopropyl)octasilsesquioxane – A reactive nanocube of unique self-assembled packing morphology

The synthesis of octa(3-mercaptopropyl)octasilsesquioxane (γHS-POSS) was studied with a special regard to factors determining the yield of octahedral product (acidity of the reaction medium and solvation of primary oligomeric species). The role of thiol moieties as effective acidic catalysts accelerating the hydrolysis of (MeO)3SiCH2CH2CH2SH was explained. Nucleophilic thiol groups were also found to be appreciably reactive towards polar aprotic solvents (acetone, acetonitrile). Isolation of γHS-POSS by preparative size exclusion chromatography (SEC) was proposed as an effective and safe purification method.Orthogonal alignment of side 3-mercaptopropyl substituents yields a rod-like geometry of the molecule and affects the packing morphology of crystalline γHS-POSS as revealed by X-ray diffraction. Self-assembling of side groups allows for the formation of a specific nanostructure of a long-range order. Several specific solid-solid (rotor phase and crystallographic transition) and solid-liquid phase transitions were detected for γHS-POSS using thermal (DSC) as well as optical (POM) techniques.

Multifunctional Homopolymers: Postpolymerization Modification via Sequential Nucleophilic Aromatic Substitution

Despite recent progress for efficient and precise synthesis of functional polymers, few reports describe postpolymerization functionalization strategies for the controlled incorporation of multiple pendent groups per repeat unit. Cyanuric chloride, or 2,4,6-trichloro-1,3,5-triazine (TCT), offers a facile method to introduce distinct pendent functionalities. An acrylamide monomer containing a triazine ring with two electrophilic sites was prepared from TCT and polymerized via reversible addition–fragmentation chain transfer (RAFT) polymerization. Subsequent nucleophilic aromatic substitution reactions using a combination of amine and thiol nucleophiles introduced two functionalities into each repeat unit of the RAFT-derived polymers. The success of each postpolymerization modification reaction was confirmed by 1H NMR spectroscopy and size-exclusion chromatography, and small molecule model studies corroborated the high chemoselectivity of the nucleophilic aromatic substitution reactions. This postpolymeriza...

Cinchona Alkaloid-Catalyzed Asymmetric Conjugate Additions: The Bifunctional Brønsted Acid-Hydrogen Bonding Model.

Wynberg's report from 1977 that natural cinchona alkaloids catalyze the asymmetric conjugate addition of aromatic thiols to cycloalkenones is a landmark discovery in hydrogen bonding organocatalysis. Wynberg proposed that this reaction proceeded via the formation of a thiolate-alkylammonium tight ion pair and activation of the enone electrophile by a hydrogen bond from the catalyst's hydroxyl group. This reaction model provided the mechanistic basis for understanding Wynberg's reaction and many other asymmetric transformations since. Our quantum mechanical calculations reveal a different model should be used to explain the results: the alkylammonium ion activates the enone by Brønsted acid catalysis, and the catalyst's hydroxyl group orients the thiolate nucleophile. The new model rationalizes the stereoselective outcome of Wynberg's reaction and provides a new, general model for asymmetric cinchona organocatalysis.

Rapid biocompatible macrocyclization of peptides with decafluoro-diphenylsulfone.

In this manuscript, we describe modification of Cys-residues in peptides and proteins in aqueous solvents via aromatic nucleophilic substitution (SNAr) with perfluoroarenes (fAr). Biocompatibility of this reaction makes it attractive for derivatization of proteins and peptide libraries comprised of 20 natural amino acids. Measurement of the reaction rates for fAr derivatives by 19F NMR with a model thiol donor (β-mercaptoethanol) in aqueous buffers identified decafluoro-diphenylsulfone (DFS) as the most reactive SNAr electrophile. Reaction of DFS with thiol nucleophiles is >100 000 faster than analogous reaction of perfluorobenzene; this increase in reactivity enables application of DFS at low concentrations in aqueous solutions compatible with biomolecules and protein complexes irreversibly degraded by organic solvents (e.g., bacteriophages). DFS forms macrocycles when reacted with peptides of the general structure X n -Cys-X m -Cys-X l , where X is any amino acid and m = 1-15. It formed cyclic peptides with 6 peptide hormones-oxytocin, urotensin II, salmon calcitonin, melanin-concentrating hormone, somatostatin-14, and atrial natriuretic factor (1-28) as well as peptides displayed on M13 phage. Rates up to 180 M-1 s-1 make this reaction one of the fastest Cys-modifications to-date. Long-term stability of macrocycles derived from DFS and their stability toward oxidation further supports DFS as a promising method for modification of peptide-based ligands, cyclization of genetically-encoded peptide libraries, and discovery of bioactive macrocyclic peptides.

ChemInform Abstract: Chemical Biology Protein Modification in a Trice

AbstractReview: 10 refs.

PEG-based hydrogels prepared by catalyst-free thiol-yne addition and their post-antibacterial modification.

PEG-based hydrogels possess tissue-like mechanical elasticity, solute permeability, cytocompatibility and biocompatibility. In this work, PEG-based hydrogels were prepared via nucleophilic thiol-yne addition between a 4-arm PEG functionalized with thiols (PEG10k-4-SH) and an electron-deficient alkyne (PEG10k-4-PP). The as-fabricated hydrogels still possess residual functionalities, enabling a second nucleophilic thiol-yne addition on the gel matrix. A thiol-containing fluorescent dye was conjugated with the electron-deficient alkyne appended hydrogels. A thiol-containing antimicrobial peptide (AMP-SH) was also embedded into the gel matrix via nucleophilic thiol-yne addition. The inhibition of bacterial growth in suspensions and contaminated substrate surfaces by the AMP-embedded hydrogels was studied. The cytotoxicity of unmodified and AMP-embedded PEG-based hydrogels against 3T3 fibroblasts was investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) viability assay.

Penicillamine prevents ram sperm agglutination in media that support capacitation.

Ram spermatozoa are difficult to capacitate in vitro. Here we describe a further complication, the unreported phenomenon of head-to-head agglutination of ram spermatozoa following dilution in the capacitation medium Tyrodes plus albumin, lactate and pyruvate (TALP). Sperm agglutination is immediate, specific and persistent and is not associated with a loss of motility. Agglutination impedes in vitro sperm handling and analysis. So the objectives of this study were to investigate the cause of sperm agglutination and potential agents which may reduce agglutination. The percentage of non-agglutinated, motile spermatozoa increased when bicarbonate was omitted from complete TALP suggesting that bicarbonate ions stimulate the agglutination process. d-penicillamine (PEN), a nucleophilic thiol, was highly effective at reducing agglutination. The inclusion of 250 μM PEN in TALP reduced the incidence of motile, agglutinated spermatozoa from 76.7 ± 2.7% to 2.8 ± 1.4%. It was then assessed if PEN (1 mM) could be included in existing ram sperm capacitation protocols (TALP +1 mM dibutyryl cAMP, caffeine and theophylline) to produce spermatozoa that were simultaneously capacitated and non-agglutinated. This protocol resulted in a sperm population which displayed high levels of tyrosine phosphorylated proteins and lipid disordered membranes (merocyanine-540) while remaining motile, viable, acrosome-intact and non-agglutinated. In summary, PEN (1 mM) can be included in ram sperm capacitation protocols to reduce sperm agglutination and allow for the in vitro assessment of ram sperm capacitation.