Racemization-Free Synthesis of S-Alkylated Cysteines via Thiol-ene Reaction

Construction of Peptide Macrocycles via Palladium-Catalyzed Multiple S-Arylation: An Effective Strategy to Expand the Structural Diversity of Cross-Linkers

A simple and versatile method for macrocyclizing unprotected native peptides with a wide range of easily accessible diiodo and triiodoarene reagents via the palladium-catalyzed multiple S-arylation of cysteine residues is developed. Iodoarenes with different arene and heteroarene cores can be incorporated into peptide macrocycles of varied ring sizes and amino acid compositions with high efficiency and selectivity under mild conditions.

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.

Chemically modified and conjugated antimicrobial peptides against superbugs

Antimicrobial resistance (AMR) is one of the greatest threats to human health that, by 2050, will lead to more deaths from bacterial infections than cancer. New antimicrobial agents, both broad-spectrum and selective, that do not induce AMR are urgently required. Antimicrobial peptides (AMPs) are a novel class of alternatives that possess potent activity against a wide range of Gram-negative and positive bacteria with little or no capacity to induce AMR. This has stimulated substantial chemical development of novel peptide-based antibiotics possessing improved therapeutic index. This review summarises recent synthetic efforts and their impact on analogue design as well as their various applications in AMP development. It includes modifications that have been reported to enhance antimicrobial activity including lipidation, glycosylation and multimerization through to the broad application of novel bio-orthogonal chemistry, as well as perspectives on the direction of future research. The subject area is primarily the development of next-generation antimicrobial agents through selective, rational chemical modification of AMPs. The review further serves as a guide toward the most promising directions in this field to stimulate broad scientific attention, and will lead to new, effective and selective solutions for the several biomedical challenges to which antimicrobial peptidomimetics are being applied.

Late-Stage Hydrocarbon Conjugation and Cyclisation in Synthetic Peptides and Proteins

The conventional S-alkylation of cysteine relies upon using activated electrophiles. Here we demonstrate high-yielding and selective S-alkylation and S-lipidation of cysteines in unprotected synthetic peptides and proteins by using weak electrophiles and a Zn²⁺ promoter. Linear or branched iodoalkanes can S-alkylate cysteine in an unprotected 38-residue Myc peptide fragment and in a 91-residue miniprotein Omomyc, thus highlighting selective late-stage synthetic modifications. Metal-assisted cysteine alkylation is also effective for incorporating dehydroalanine into unprotected peptides and for peptide cyclisation via aliphatic thioether crosslinks, including customising macrocycles to stabilise helical peptides for enhanced uptake and delivery to proteins inside cells. Chemoselective and efficient late-stage Zn²⁺ -promoted cysteine alkylation in unprotected peptides and proteins promises many useful applications.

Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design

While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.

Applications of Thiol-Ene Chemistry for Peptide Science

Radical thiol-ene chemistry has been demonstrated for a range of applications in peptide science, including macrocyclization, glycosylation and lipidation amongst a myriad of others. The thiol-ene reaction offers a number of advantages in this area, primarily those characteristic of "click" reactions. This provides a chemical approach to peptide modification that is compatible with aqueous conditions with high orthogonality and functional group tolerance. Additionally, the use of a chemical approach for peptide modification affords homogeneous peptides, compared to heterogeneous mixtures often obtained through biological methods. In addition to peptide modification, thiol-ene chemistry has been applied in novel approaches to biological studies through synthesis of mimetics and use in development of probes. This review will cover the range of applications of the radical-mediated thiol-ene reaction in peptide and protein science.

How Membrane Geometry Regulates Protein Sorting Independently of Mean Curvature

Biological membranes have distinct geometries that confer specific functions. However, the molecular mechanisms underlying the phenomenological geometry/function correlations remain elusive. We studied the effect of membrane geometry on the localization of membrane-bound proteins. Quantitative comparative experiments between the two most abundant cellular membrane geometries, spherical and cylindrical, revealed that geometry regulates the spatial segregation of proteins. The measured geometry-driven segregation reached 50-fold for membranes of the same mean curvature, demonstrating a crucial and hitherto unaccounted contribution by Gaussian curvature. Molecular-field theory calculations elucidated the underlying physical and molecular mechanisms. Our results reveal that distinct membrane geometries have specific physicochemical properties and thus establish a ubiquitous mechanistic foundation for unravelling the conserved correlations between biological function and membrane polymorphism.

Photo-reduction of Ag nanoparticles by using cellulose-based micelles as soft templates: Catalytic and antimicrobial activities

Amphiphilic cellulose derivatives were synthesized from allyl cellulose (AC) and cystein (Cys)/n-dodecyl mercaptan (NDM) via the thiol-ene click reactions. The derivatives were self-assembled into micelles in distilled water, and the micelles sizes increased with an increase of the DS_NDM. The amphiphilic cellulose micelles were served as the soft templates for the controllable synthesis of Ag nanoparticles (NPs) through the photo-reduction. Ag NPs were embedded and stabilized by the amphiphilic cellulose micelles, and their sizes increased from 3.1 to 14.4 nm with an increase of the original template sizes. The catalytic properties of the Ag-loaded micelles were evaluated by the reduction of p-nitropheonl to p-aminophenol. The results demonstrated that the Ag-loaded micelles exhibited excellent catalytic activity. The reduction followed the first-order rate law, and the reaction constant decreased with increasing size of Ag NPs. Moreover, the Ag-loaded micelles displayed good antimicrobial activities to both S. aureus and E. coli. Therefore, the Ag-loaded cellulose-based micelles have potential applications in various fields.

A facile synthesis of cysteine-based diketopiperazine from thiol-protected precursor

l-Cysteine is one of the most promising biomass-based building blocks with great potential applications. Herein, we report a versatile synthetic route to produce cysteine-based 2,5-diketopiperazine (DKP) with good yield from the thiol-ene click reaction of l-cysteine and commercially available acrylates, followed by dimerization of the amino acid intermediates. The achieved DKP diastereomers were successfully separated and fully characterized by spectroscopic methods. Moreover, the chiroptical property of DKP in the presence of various metal ions was investigated by circular dichroism spectroscopy. The potential application of the optically active cysteine-based DKP as a chiral probe for detection of silver ion in water has been demonstrated.

Recent advances in photoinduced glycosylation: oligosaccharides, glycoconjugates and their synthetic applications

Carbohydrates have been demonstrated to perform imperative act in biological processes. This review highlights recent uses of photoinduced glycosylation in carbohydrate chemistry for the synthesis of oligosaccharides, thiosugars, glycoconjugates and glycoprotein.

Chemical Methods for Encoding and Decoding of Posttranslational Modifications

A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full complement of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come.

Synthesis of ST7612AA1, a Novel Oral HDAC Inhibitor, via Radical Thioacetic Acid Addition

Abstract: Background

In the expanding field of anticancer drugs, HDAC inhibitors are playing an increasingly important role. To date, four/five HDAC inhibitors have been approved by FDA. All these compounds fit the widely accepted HDAC inhibitors pharmacophore model characterized by a cap group, a linker chain and a zinc binding group (ZBG), able to bind the Zn²⁺ ion in a pocket of the HDAC active site. Romidepsin, a natural compound, is the only thiol derivative. We have selected a new class of synthetic HDAC inhibitors, the thio-ω(lactam-carboxamide) derivatives, with ST7612AA1 as drug candidate, pan-inhibitor active in the range of single- to two-digit nanomolar concentrations. Preliminary results of a synthetic optimization attempt towards a fast scale-up process are here proposed.

Methods

In the four steps of synthesis, from unsaturated amino acid intermediate to the final product, we explored different synthetic conditions in order to have a transferable process for a scale-up synthetic laboratory.

Results

In the first step, isobutyl chloroformate was used and, after a simple work up with 1M HCl, 2 (96% yield) was obtained as a white solid, which was used directly in the next step. For thioacetic acid addition to the double bond of intermediate 2, two different routes were possible, with addition reaction in the first (D’) or last step (D). Reactions of 2 to give 5 or of 4 to give ST7612AA1 were both performed in dioxane. Reactions were fast and did not need the usually advised radical quenching with cyclohexene. The corresponding products were obtained in good yields (step D’, 89%; step D, 81%) after a flash chromatography.

Conclusion: ST7612AA1

, a thiol derivative prodrug of ST7464AA1, is the first of a new generation of HDAC inhibitors, very potent, orally administered, and well tolerated. Here, we have identified a synthetic route, competitive, versatile and easily transferable to industrial processes.

Design of α-S-Neoglycopeptides Derived from MUC1 with a Flexible and Solvent-Exposed Sugar Moiety

The use of vaccines based on MUC1 glycopeptides is a promising approach to treat cancer. We present herein several sulfa-Tn antigens incorporated in MUC1 sequences that possess a variable linker between the carbohydrate (GalNAc) and the peptide backbone. The main conformations of these molecules in solution have been evaluated by combining NMR experiments and molecular dynamics simulations. The linker plays a key role in the modulation of the conformation of these compounds at different levels, blocking a direct contact between the sugar moiety and the backbone, promoting a helix-like conformation for the glycosylated residue and favoring the proper presentation of the sugar unit for molecular recognition events. The feasibility of these novel compounds as mimics of MUC1 antigens has been validated by the X-ray diffraction structure of one of these unnatural derivatives complexed to an anti-MUC1 monoclonal antibody. These features, together with potential lack of immune suppression, render these unnatural glycopeptides promising candidates for designing alternative therapeutic vaccines against cancer.

The photochemical thiol-ene reaction as a versatile method for the synthesis of glutathione S-conjugates targeting the bacterial potassium efflux system Kef

The thiol-ene coupling reaction is emerging as an important conjugation reaction that is suitable for use in a biological setting. Here, we explore the utility of this reaction for the synthesis of glutathione-S-conjugates (GSX) and present a general, operationally simple, protocol with a wide substrate scope. The GSX afforded are an important class of compounds and provide invaluable molecular tools to study glutathione-binding proteins. In this study we apply the diverse library of GSX synthesised to further our understanding of the structural requirements for binding to the glutathione-binding protein, Kef, a bacterial K⁺ efflux system, found in many bacterial pathogens. This system is vital to the survival of bacteria upon exposure to electrophiles, and plays an essential role in the maintenance of intracellular pH and K⁺ homeostasis. Consequently, Kef is an appealing target for the development of novel antibacterial drugs.

Specificity of Lipoprotein Chaperones for the Characteristic Lipidated Structural Motifs of their Cognate Lipoproteins

Lipoprotein-binding chaperones mediate intracellular transport of lipidated proteins and determine their proper localisation and functioning. Understanding of the exact structural parameters that determine recognition and transport by different chaperones is of major interest. We have synthesised several lipid-modified peptides, representative of different lipoprotein classes, and have investigated their binding to the relevant chaperones PDEδ, UNC119a, UNC119b, and galectins-1 and -3. Our results demonstrate that PDEδ recognises S-isoprenylated C-terminal peptidic structures but not N-myristoylated peptides. In contrast, UNC119 proteins bind only mono-N-myristoylated, but do not recognise doubly lipidated and S-isoprenylated peptides at the C terminus. For galectins-1 and -3, neither binding to N-acylated, nor to C-terminally prenylated peptides could be determined. These results shed light on the specificity of the chaperone-mediated cellular lipoprotein transport systems.

Synthesis of lipidated peptides

One of the main reasons of the high diversity and complexity of the human proteome compared to the human genome is the extensive work performed by the posttranslational machinery to incorporate numerous different functionalities on proteins. The covalent attachment of chemical moieties in proteins after translation is known as posttranslational modification (PTM) and has a crucial role in controlling protein localization and activity. Relevant modifications include phosphorylation, carboxymethylation, glycosylation, acetylation, or lipidation. Despite their essential role on protein function, the synthesis of fully posttranslationally modified proteins has been challenging. However, important advances on chemical biology have enabled the synthesis of fully posttranslationally modified peptides and proteins. As a result of this, peptides bearing, i.e., phosphorylated amino acids, C-terminal methylations, lipid modifications, or nonnatural tags have become accessible. These peptides, as well as the corresponding proteins obtained using ligation techniques, have been invaluable tools in biochemical and biophysical studies. As an example of these advances, this chapter describes the methods developed for the synthesis of lipidated peptides from the Ras and Rab families.

“Click” reactions: a versatile toolbox for the synthesis of peptide-conjugates

Peptides that comprise the functional subunits of proteins have been conjugated to versatile materials (biomolecules, polymers, surfaces and nanoparticles) in an effort to modulate cell responses, specific binding affinity and/or self-assembly behavior.

Chemical modifications of peptide sequences via S-alkylation reaction

A chemoselective, convenient, and mild synthetic strategy to modify peptides on a cysteine sulfhydryl group is described. It simply requires activated molecular sieves to selectively promote S-alkylation in the presence of peptide nucleophilic functionalities. The procedure is easy to perform, fast, and provides high yields even in the case of poor electrophilic groups. Moreover, the method allows an efficient one-pot poly alkylation, proving that the sulfhydryl reactivity does not rely on its specific position within the peptide sequence.

Direct peptide lipidation through thiol-ene coupling enables rapid synthesis and evaluation of self-adjuvanting vaccine candidates

A radical lipidation: Application of a novel thiol-ene lipidation enables the one-step synthesis of self-adjuvanting antigenic peptides as vaccine candidates. The resultant monoacyl lipopeptides are shown to activate monocytes in a robust manner.

Click reactions in protein chemistry: from the preparation of semisynthetic enzymes to new click enzymes

Click-chemistry is an approach based on cycloaddition reactions which has been successfully used as a chemical approach for complex organic molecules and which has recently starred in a boom in the world of protein chemistry. The advantage of the use of this technique in protein chemistry is based on a very high and efficient chemoselectivity, which usually requires simple or no purification and is extremely rate-accelerated in aqueous media. The perspective discusses some of the most recent advances in the application of this reaction in selective enzyme surface modification for the creation of new semisynthetic enzymes (fluorescence labeled enzymes, peptide-enzyme conjugates, glycosylated enzymes), and interestingly, the recent design and creation of "click" enzymes.

Chemoselective immobilization of peptides on abiotic and cell surfaces at controlled densities

We report herein a new and enabling approach for decorating both abiotic and cell surfaces with the extracellular matrix IKVAV peptide in a site-specific manner using strain promoted azide-alkyne cycloaddition. A cyclooctyne-derivatized IKVAV peptide was synthesized and immobilized on the surface of pancreatic islets through strain-promoted azide-alkyne cycloaddition with cell surface azides generated by the electrostatic adsorption of a cytocompatible poly(L-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG) copolymer bearing azido groups (PP-N(3)). Both "one-pot" and sequential addition of PP-N(3) and a cyclooctyne-derivatized IKVAV peptide conjugate enabled efficient modification of the pancreatic islet surface in less than 60 min. The ability to bind peptides at controlled surface densities was demonstrated in a quantitative manner using microarrays. Additionally, the technique is remarkably rapid and highly efficient, opening new avenues for the molecular engineering of cellular interfaces and protein and peptide microarrays.

Preparation of biomolecule microstructures and microarrays by thiol-ene photoimmobilization

A mild, fast and flexible method for photoimmobilization of biomolecules based on the light-initiated thiol-ene reaction has been developed. After investigation and optimization of various surface materials, surface chemistries and reaction parameters, microstructures and microarrays of biotin, oligonucleotides, peptides, and MUC1 tandem repeat glycopeptides were prepared with this photoimmobilization method. Furthermore, MUC1 tandem repeat glycopeptide microarrays were successfully used to probe antibodies in mouse serum obtained from vaccinated mice. Dimensions of biomolecule microstructures were shown to be freely controllable through photolithographic techniques, and features down to 5 microm in size covering an area of up to 75x25 mm were created. Use of a confocal laser microscope with a UV laser as UV-light source enabled further reduction of biotin feature size opening access to nanostructured biochips.

Mechanistic proposal for the formation of specific immunogenic complexes via a radical pathway: a key step in allergic contact dermatitis to olefinic hydroperoxides

The widespread use of scented products causes an increase of allergic contact dermatitis to fragrance compounds in Western countries today. Many fragrance compounds are prone to autoxidation, forming hydroperoxides as their primary oxidation products. Hydroperoxides are known to be strong allergens and to form specific immunogenic complexes. However, the mechanisms for the formation of the immunogenic complexes are largely unknown. We have investigated this mechanism for (5R)-5-isopropenyl-2-methyl-2-cyclohexene-1-hydroperoxide (Lim-2-OOH) by studying the formation of adducts in the reaction between this hydroperoxide and 5,10,15,20-tetraphenyl-21H,23H-porphine iron(III) chloride (Fe(III)TPPCl) in the presence of protected cysteine (NAc-Cys-OMe) or glutathione (GSH). Isolated adducts originate from the addition of the thiol group of NAc-Cys-OMe over the carbon-carbon double bonds of carvone. Furthermore, adducts between NAc-Cys-OMe and carveol as well as between GSH and carvone have been identified. The formation of these adducts most likely proceeds via the radical thiol-ene mechanism. The addition of a terpene moiety to cysteine offers an explanation of the specificity of the immune response to structurally different hydroperoxides. These results also explain the lack of cross-reactivity between carvone and Lim-2-OOH. In conclusion, we propose that immunogenic complexes of olefinic hydroperoxides can be formed via the radical thiol-ene mechanism. These complexes will be specific for the individual olefinic hydroperoxides due to the inclusion of a terpene moiety derived from the hydroperoxide.

Nitrones as dipoles for rapid strain-promoted 1,3-dipolar cycloadditions with cyclooctynes

Strain-promoted cycloadditions of nitrones with cyclooctynes (k(2) = 1.5 M(-1) s(-1) at 25 degrees C) are up to 25 times more rapid than comparable reactions of azides.