Cysteine specific bioconjugation with benzyl isothiocyanates

Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents

Penicillin-binding proteins (PBPs) contribute to bacterial cell wall biosynthesis and are targets of antibacterial agents. Here, we investigated PBP1b inhibition by boronic acid derivatives. Chemical starting points were identified by structure-based virtual screening and aliphatic boronic acids were selected for further investigations. Structure-activity relationship studies focusing on the branching of the boron-connecting carbon and quantum mechanical/molecular mechanical simulations showed that reaction barrier free energies are compatible with fast reversible covalent binding and small or missing reaction free energies limit the inhibitory activity of the investigated boronic acid derivatives. Therefore, covalent labelling of the lysine residue of the catalytic dyad was also investigated. Compounds with a carbonyl warhead and an appropriately positioned boronic acid moiety were shown to inhibit and covalently label PBP1b. Reversible covalent labelling of the catalytic lysine by imine formation and the stabilisation of the imine by dative N-B bond is a new strategy for PBP1b inhibition.

Site-Selective Antibody Conjugation with Dibromopyrazines

In recent years, antibody conjugates have evolved as state-of-the-art options for diagnostic and therapeutic applications. During site-selective antibody conjugation, incomplete rebridging of antibody chains limits the homogeneity of conjugates and calls for the development of new rebridging agents. Herein, we report a dibromopyrazine derivative optimized to reach highly homogeneous conjugates rapidly and with high conversion on rebridging of trastuzumab, even providing a feasible route for antibody modification in acidic conditions. Furthermore, coupling a fluorescent dye and a cytotoxic drug resulted in effective antibody conjugates with excellent serum stability and in vitro selectivity, demonstrating the utility of the dibromopyrazine rebridging agent to produce on-demand future antibody conjugates for diagnostic or therapeutic applications.

Enzyme-Responsive Fluorescent Labeling Strategy for In Vivo Imaging of Gut Bacteria

Myrosinase (Myr), as a unique β-thioglucosidase enzyme capable of converting natural and gut bacterial metabolite glucosinolates into bioactive agents, has recently attracted a great deal of attention because of its essential functions in exerting homeostasis dynamics and promoting human health. Such nutraceutical and biomedical significance demands unique and reliable strategies for specific identification of Myr enzymes of gut bacterial origin in living systems, whereas the dearth of methods for bacterial Myr detection and visualization remains a challenging concern. Herein, we present a series of unique molecular probes for specific identification and imaging of Myr-expressing gut bacterial strains. Typically, an artificial glucosinolate with an azide group in aglycone was synthesized and sequentially linked with the probe moieties of versatile channels through simple click conjugation. Upon gut bacterial enzymatic cleavage, the as-prepared probe molecules could be converted into reactive isothiocyanate forms, which can further act as reactive electrophiles for the covalent labeling of gut bacteria, thus realizing their localized fluorescent imaging within a wide range of wavelength channels in live bacterial strains and animal models. Overall, our proposed method presents a novel technology for selective gut bacterial Myr enzyme labeling in vitro and in vivo. We envision that such a rational probe design would serve as a promising solution for chemoprevention assessment, microflora metabolic mechanistic study, and gut bacterium-mediated physiopathological exploration.

Chemical technology principles for selective bioconjugation of proteins and antibodies

Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.

Effective synthesis, development and application of a highly fluorescent cyanine dye for antibody conjugation and microscopy imaging

An asymmetric cyanine-type fluorescent dye was designed and synthesized via a versatile, multi-step process, aiming to conjugate with an Her2+ receptor specific antibody by an azide-alkyne click reaction. The aromaticity and the excitation and relaxation energetics of the fluorophore were characterized by computational methods. The synthesized dye exhibited excellent fluorescence properties for confocal microscopy, offering efficient applicability in in vitro imaging due to its merits such as a high molar absorption coefficient (36 816 M-1 cm-1), excellent brightness, optimal wavelength (627 nm), larger Stokes shift (26 nm) and appropriate photostability compared to cyanines. The conjugated cyanine-trastuzumab was constructed via an effective, metal-free, strain-promoted azide-alkyne click reaction leading to a regulated number of dyes being conjugated. This novel cyanine-labelled antibody was successfully applied for in vitro confocal imaging and flow cytometry of Her2+ tumor cells.

Substituent Effects of Fluorescein on Photoredox Initiating Performance under Visible Light

We demonstrated the effects of substituents in fluorescein on the photoredox catalytic performance under visible light. For the systematic investigation, the phenyl ring of fluorescein was substituted with six different functional groups (i.e., amine, amide, isothiocyanate, aminomethyl, bromo, or nitro group) at the 5- or 6-position. The fluorescein derivatives were carefully characterized through photophysical and electrochemical analyses. The substituent effects were estimated by comparing the photopolymerization of poly(ethylene glycol) diacrylate (PEGDA) and N-vinylpyrrolidone (VP) in the presence of triethanolamine (TEOA) under aerobic conditions to that of intact fluorescein. As a result, the amine and nitro groups exhibited the lowest performances, presumably due to intramolecular photoinduced electron transfer (PET) promoted by the strong electron push-pull effect. The others, representative moderate or weak deactivators and activators, exhibited inferior performances than intact fluorescein, presumably owing to the more negative ΔGPET values, resulting in a decreased rate of intermolecular PET. These results are crucial for understanding the structure-performance relationship and the development of visible-light photoredox catalysts with improved performance and functionality.

Engineering Alkaline-Stable Barley Stripe Mosaic Virus-Like Particles for Efficient Surface Modification

Viruses and virus-like particles are powerful templates for materials synthesis because of their capacity for precise protein engineering and diverse surface functionalization. We recently developed a recombinant bacterial expression system for the production of barley stripe mosaic virus-like particles (BSMV VLPs). However, the applicability of this biotemplate was limited by low stability in alkaline conditions and a lack of chemical handles for ligand attachment. Here, we identify and validate novel residues in the BSMV Caspar carboxylate clusters that mediate virion disassembly through repulsive interactions at high pH. Point mutations of these residues to create attractive interactions that increase rod length ~2 fold, with an average rod length of 91 nm under alkaline conditions. To enable diverse chemical surface functionalization, we also introduce reactive lysine residues at the C-terminus of BSMV coat protein, which is presented on the VLP surface. Chemical conjugation reactions with this lysine proceed more quickly under alkaline conditions. Thus, our alkaline-stable VLP mutants are more suitable for rapid surface functionalization of long nanorods. This work validates novel residues involved in BSMV VLP assembly and demonstrates the feasibility of chemical functionalization of BSMV VLPs for the first time, enabling novel biomedical and chemical applications.

Synthesis and Application of Two-Photon Active Fluorescent Rhodol Dyes for Antibody Conjugation and In Vitro Cell Imaging

A novel family of julolidine-containing fluorescent rhodols equipped with a wide variety of substituents was synthesized in a versatile two-step process. The prepared compounds were fully characterized and exhibited excellent fluorescence properties for microscopy imaging. The best candidate was conjugated to the therapeutic antibody trastuzumab through a copper-free strain-promoted azide-alkyne click reaction. The rhodol-labeled antibody was successfully applied for in vitro confocal and two-photon microscopy imaging of Her2+ cells.

Bacterial detoxification of plant defence secondary metabolites mediates the interaction between a shrub and frugivorous birds

Many plants produce fleshy fruits, attracting fruit-eating animals that disperse the seeds in their droppings. Such seed dispersal results in a conflict between the plant and the animal, as digestion of seeds can be highly beneficial to the animal but reduces plant fitness. The plant Ochradenus baccatus uses the myrosinase-glucosinolates system to protect its seeds. We show that hydrolysis of the O. baccatus fruit glucosinolates by the myrosinase enzyme inhibited digestive enzymes and hampered digestion in naïve individuals of the bird Pycnonotus xanthopygos. However, digestion in birds regularly feeding on O. baccatus fruits was unaffected. We find that Pantoea bacteria, dominating the gut of these experienced birds as well as the fruits, thrive on glucosinolates hydrolysis products in culture. Augmentation of Pantoea protects both naïve birds and plant seedlings from the effects of glucosinolates hydrolysis products. Our findings demonstrate a tripartite interaction, where the plant-bird mutually beneficial interactions are mediated by a communal bacterial tenant.

Rational Design of Self-Assembling Supramolecular Protein Nanostructures Utilizing the Cucurbit[8]Uril Macrocyclic Host

Self-assembly is a phenomenon that governs molecular structural organization in nature, therefore raising research interest for the fabrication of novel nanomaterials with diverse applications in biocatalysis, biomedicine, material templating, and biosensor development. In this chapter we provide protocols for the development of supramolecular protein complexes based on host-guest interactions in the presence of the macrocyclic host, cucurbit[8]uril (CB[8]). CB[8] is reported to exhibit high binding affinity towards the tripeptide Phe-Gly-Gly (FGG), therefore it can be utilized as a selective adhesive of protein molecules, after fusion of FGG to an accessible protein surface.

Optimized Production of Fc Fusion Proteins by Sortase Enzymatic Ligation

Fc fusions are a growing class of drugs comprising an antibody Fc domain covalently linked to a protein or peptide and can pose manufacturing challenges. In this study we evaluated three synthetic approaches to generate Fc fusions, using Fc-insulin as a model drug candidate. Engineered human IgG1 was digested with HRV3C to produce an Fc fragment with a C-terminal sortase tag (Fc-LPETGGH6). The synthesis of Fc-insulin2 from Fc-LPETGGH6 was evaluated with direct sortase-mediated ligation (SML) and two chemoenzymatic strategies. Direct SML was performed with triglycine-insulin, and chemoenzymatic strategies used to SML fuse either triglycine-azide or triglycine-DBCO prior to linking insulin with copper-catalyzed or strain-promoted azidealkyne cycloaddition. Reaction conditions were optimized by evaluating reagent concentrations, relative equivalents, temperature, and time. Direct SML provided the most effective reaction yields, converting 60-70% of Fc-LPETGGH6 to Fc-insulin2, whereas our optimized chemoenzymatic synthesis converted 30-40% of Fc-LPETGGH6 to Fc-insulin2. Here we show that SML is a practical and efficient method to synthesize Fc fusions and provide an optimized pathway for fusion drug synthesis.

Recent developments in chemical conjugation strategies targeting native amino acids in proteins and their applications in antibody-drug conjugates

Many fields in chemical biology and synthetic biology require effective bioconjugation methods to achieve their desired functions and activities. Among such biomolecule conjugates, antibody-drug conjugates (ADCs) need a linker that provides a stable linkage between cytotoxic drugs and antibodies, whilst conjugating in a biologically benign, fast and selective fashion. This review focuses on how the development of novel organic synthesis can solve the problems of traditional linker technology. The review shall introduce and analyse the current developments in the modification of native amino acids on peptides or proteins and their applicability to ADC linker. Thereafter, the review shall discuss in detail each endogenous amino acid's intrinsic reactivity and selectivity aspects, and address the research effort to construct an ADC using each conjugation method.

Recent Advances in the Synthesis of Isothiocyanates Using Elemental Sulfur

Isothiocyanates (ITCs) are biologically active molecules found in several natural products and pharmaceutical ingredients. Moreover, due to their high and versatile reactivity, they are widely used as intermediates in organic synthesis. This review considers the best practices for the synthesis of ITCs using elemental sulfur, highlighting recent developments. First, we summarize the in situ generation of thiocarbonyl surrogates followed by their transformation in the presence of primary amines leading to ITCs. Second, carbenes and amines afford isocyanides, and the further reaction of this species with sulfur readily generates ITCs under thermal, catalytic or basic conditions. Additionally, we also reveal that in the catalyst-free reaction of isocyanides and sulfur, two—until this time overlooked and not investigated—different mechanistic pathways exist.

Green and Healthier Alternatives to Chemical Additives as Cheese Preservative: Natural Antimicrobials in Active Nanopackaging/Coatings

The side effects and potential impacts on human health by traditional chemical additives as food preservatives (i.e., potassium and sodium salts) are the reasons why novel policies are encouraged by worldwide public health institutes. More natural alternatives with high antimicrobial efficacy to extend shelf life without impairing the cheese physicochemical and sensory quality are encouraged. This study is a comprehensive review of emerging preservative cheese methods, including natural antimicrobials (e.g., vegetable, animal, and protist kingdom origins) as a preservative to reduce microbial cheese contamination and to extend shelf life by several efforts such as manufacturing ingredients, the active ingredient for coating/packaging, and the combination of packaging materials or processing technologies. Essential oils (EO) or plant extracts rich in phenolic and terpenes, combined with packaging conditions and non-thermal methods, generally showed a robust microbial inhibition and prolonged shelf life. However, it impaired the cheese sensory quality. Alternatives including EO, polysaccharides, polypeptides, and enzymes as active ingredients/nano-antimicrobials for an edible film of coating/nano-bio packaging showed a potent and broad-spectrum antimicrobial action during shelf life, preserving cheese quality parameters such as pH, texture, color, and flavor. Future opportunities were identified in order to investigate the toxicological effects of the discussed natural antimicrobials' potential as cheese preservatives.

Chemical Conjugation Strategies for the Development of Protein-Based Subunit Nanovaccines

The production of subunit nanovaccines relies heavily on the development of a vaccine delivery system that is safe and efficient at delivering antigens to the target site. Nanoparticles have been extensively investigated for vaccine delivery over the years, as they often possess self-adjuvanting properties. The conjugation of antigens to nanoparticles by covalent bonds ensures co-delivery of these components to the same subset of immune cells in order to trigger the desired immune responses. Herein, we review covalent conjugation strategies for grafting protein or peptide antigens onto other molecules or nanoparticles to obtain subunit nanovaccines. We also discuss the advantages of chemical conjugation in developing these vaccines.

Synthesis and characterization of new fluorescent boro-β-carboline dyes

The first representatives of the new fluorescent boro-β-carboline family were synthesized by the insertion of the difluoroboranyl group into the oxaza or diaza core. The resulting compounds showed good photophysical properties with fine Stokes-shifts in the range of 38-85 nm with blue and green emission. The energetics of the excitation states and molecular orbitals of two members were investigated by quantum chemical computations suggesting effects for the improved properties of diazaborinino-carbolines over oxazaborolo-carbolines. These properties nominated this chemotype as a new fluorophore for the development of fluorescent probes. As an example, diazaborinino-carbolines were used for the specific labeling of anti-Her2 antibody trastuzumab. The fluorescent conjugate showed a high fluorophore-antibody ratio and was confirmed as a useful tool for labeling and confocal microscopy imaging of tumour cells in vitro together with the ex vivo two-photon microscopy imaging of tumour slices.

Silicon-based fluorescent platforms for copper(ii) detection in water

The potential of silicon-based fluorescent platforms for the detection of trace toxic metal ions was investigated in an aqueous environment. To this aim, silicon chips were first functionalized with amino groups, and fluorescein organic dyes, used as sensing molecules, were then covalently linked to the surface via formation of thiourea groups. The obtained hybrid heterostructures exhibited high sensitivity and selectivity towards copper(ii), a limit of detection compatible with the recommended upper limits for copper in drinking water, and good reversibility using a standard metal–chelating agent. The fluorophore–analyte interaction mechanism at the basis of the reported fluorescence quenching, as well as the potential of performance improvement, were also studied. The herein presented sensing architecture allows, in principle, tailoring of the selectivity towards other metal ions by proper fluorophore selection, and provides a favorable outlook for integration of fluorescent chemosensors with silicon photonics technology.

Covalent linkage of fluorescein to silanized silicon chips yields solid-state platforms for detection of copper(ii) in water. This architecture represents a step forward towards the fabrication of sensors for remote water analysis applications.

Fluorescein Derivatives as Fluorescent Probes for pH Monitoring along Recent Biological Applications

Potential of hydrogen (pH) is one of the most relevant parameters characterizing aqueous solutions. In biology, pH is intrinsically linked to cellular life since all metabolic pathways are implicated into ionic flows. In that way, determination of local pH offers a unique and major opportunity to increase our understanding of biological systems. Whereas the most common technique to obtain these data in analytical chemistry is to directly measure potential between two electrodes, in biological systems, this information has to be recovered in-situ without any physical interaction. Based on their non-invasive optical properties, fluorescent pH-sensitive probe are pertinent tools to develop. One of the most notorious pH-sensitive probes is fluorescein. In addition to excellent photophysical properties, this fluorophore presents a pH-sensitivity around neutral and physiologic domains. This review intends to shed new light on the recent use of fluorescein as pH-sensitive probes for biological applications, including targeted probes for specific imaging, flexible monitoring of bacterial growth, and biomedical applications.

Radiotracers for positron emission tomography (PET) targeting tumour-associated carbonic anhydrase isoforms

The tumour-associated, cell membrane-bound isoforms IX and XII of human carbonic anhydrase (CA, EC 4.2.1.1) are overexpressed in cancer cells contributing to the hypoxic tumour pH/metabolism regulating machinery and as thus, can serve as markers of malignant neoplastic tissue. Inhibitors of CAs can be employed both for the treatment of hypoxic tumours and in the design of radiotracers for positron emission tomography and imaging of such cancers. The present review provides a comprehensive summary of the progress achieved to-date in the field of developing PET-tracers based on monoclonal antibodies, biomolecules, and small-molecule ligands of CA IX and XII.