Enzyme-mediated dynamic combinatorial chemistry allows out-of-equilibrium template-directed synthesis of macrocyclic oligosaccharides

Triple Adaptation of Constitutional Dynamic Networks of Imines in Response to Micellar Agents: Internal Uptake-Interfacial Localization-Shape Transition

Understanding the behavior of complex chemical reaction networks and how environmental conditions can modulate their organization as well as the associated outcomes may take advantage of the design of related artificial systems. Microenvironments with defined boundaries are of particular interest for their unique properties and prebiotic significance. Dynamic covalent libraries (DCvLs) and their underlying constitutional dynamic networks (CDNs) have been shown to be appropriate for studying adaptation to several processes, including compartmentalization. However, microcompartments (e.g., micelles) provide specific environments for the selective protection from interfering reactions such as hydrolysis and an enhanced chemical promiscuity due to the interface, governing different processes of network modulation. Different interactions between the micelles and the library constituents lead to dynamic sensing, resulting in different expressions of the network through pattern generation. The constituents integrated into the micelles are protected from hydrolysis and hence preferentially expressed in the network composition at the cost of constitutionally linked members. In the present work, micellar integration was observed for two processes: internal uptake based on hydrophobic forces and interfacial localization relying on attractive electrostatic interactions. The latter drives a complex triple adaptation of the network with feedback on the shape of the self-assembled entity. Our results demonstrate how microcompartments can enforce the expression of constituents of CDNs by reducing the hydrolysis of uptaken members, unravelling processes that govern the response of reactions networks. Such studies open the way toward using DCvLs and CDNs to understand the emergence of complexity within reaction networks by their interactions with microenvironments.

Quantitative determination of the binding capabilities of individual large-ring cyclodextrins in complex mixtures

Large-ring cyclodextrins (CDs) are a comparatively unexplored family of macrocycles. We use high-resolution 1H-13C HSQC NMR experiments to resolve the anomeric signals of at least 13 different size CDs in a mixture. Using a single titration experiment, we can quantify the individual binding capabilites of these structurally-related hosts, avoiding the need for cumbersome isolation.

Dynamic covalent synthesis

Dynamic covalent synthesis aims to precisely control the assembly of simple building blocks linked by reversible covalent bonds to generate a single, structurally complex, product. In recent years, considerable progress in the programmability of dynamic covalent systems has enabled easy access to a broad range of assemblies, including macrocycles, shape-persistent cages, unconventional foldamers and mechanically-interlocked species (catenanes, knots, etc.). The reversibility of the covalent linkages can be either switched off to yield stable, isolable products or activated by specific physico-chemical stimuli, allowing the assemblies to adapt and respond to environmental changes in a controlled manner. This activatable dynamic property makes dynamic covalent assemblies particularly attractive for the design of complex matter, smart chemical systems, out-of-equilibrium systems, and molecular devices.

Large anion binding in water

Large water-soluble anions with chaotropic character display surprisingly strong supramolecular interactions in water, for example, with macrocyclic receptors, polymers, biomembranes, and other hydrophobic cavities and interfaces. The high affinity is traced back to a hitherto underestimated driving force, the chaotropic effect, which is orthogonal to the common hydrophobic effect. This review focuses on the binding of large anions with water-soluble macrocyclic hosts, including cyclodextrins, cucurbiturils, bambusurils, biotinurils, and other organic receptors. The high affinity of large anions to molecular receptors has been implemented in several lines of new applications, which are highlighted herein.

Light-controlled enzymatic synthesis of γ-CD using a recyclable azobenzene template

Cyclodextrins (CDs) are important molecular hosts for hydrophobic guests in water and extensively employed in the pharmaceutical, food and cosmetic industries to encapsulate drugs, flavours and aromas. Compared with α- and β-CD, the wide-scale use of γ-CD is currently limited due to costly production processes. We show how the yield of γ-CD in the enzymatic synthesis of CDs can be increased 5-fold by adding a tetra-ortho-isopropoxy-substituted azobenzene template irradiated at 625 nm (to obtain the cis-(Z)-isomer) to direct the synthesis. Following the enzymatic reaction, the template can then be readily recovered from the product mixture for use in subsequent reaction cycles. Heating induces thermal cis-(Z) to trans-(E) relaxation and consequent dissociation from γ-CD whereupon the template can then be precipitated by acidification. For this study we designed and synthesised a set of three water-soluble azobenzene templates with different ortho-substituents and characterised their photoswitching behaviour using UV/vis and NMR spectroscopy. The templates were tested in cyclodextrin glucanotransferase-mediated dynamic combinatorial libraries (DCLs) of cyclodextrins while irradiating at different wavelengths to control the cis/trans ratios. To rationalise the behaviour of the DCLs, NMR titrations were carried out to investigate the binding interactions between α-, β- and γ-CD and the cis and trans isomers of each template.

Templated Enzymatic Synthesis of δ-Cyclodextrin

While α-, β-, and γ-cyclodextrin (CD) are ubiquitous hosts employed by supramolecular chemists, δ-CD (formed from nine α-1,4-linked glucopyranose units) has received very little attention. α-, β-, and γ-CD are the major products of the enzymatic breakdown of starch by cyclodextrin glucanotransferase (CGTase), but δ-CD forms only transiently in this reaction, as a minor component of a complex mixture of linear and cyclic glucans. In this work, we show how δ-CD can be synthesized in unprecedented yields by employing a bolaamphiphile template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that δ-CD can thread up to three bolaamphiphiles forming [2]-, [3]-, or [4]-pseudorotaxanes, depending on the size of the hydrophilic headgroup and the length of the alkyl chain axle. Threading of the first bolaamphiphile occurs in fast exchange on the NMR chemical shift time scale, while subsequent threading occurs in slow exchange. To extract quantitative information for 1:2 and 1:3 binding events occurring in mixed exchange regimes, we derived equations for nonlinear curve fitting that take into consideration both the chemical shift changes for species in fast exchange and the integrals for species in slow exchange to determine K_a1, K_a2, and K_a3. Template T1 could be used to direct the enzymatic synthesis of δ-CD due to the cooperative formation of a 1:2 complex─the [3]-pseudorotaxane δ-CD·T1₂. Importantly, T1 is recyclable. It can be readily recovered from the enzymatic reaction by precipitation and reused in subsequent syntheses enabling preparative-scale synthesis of δ-CD.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.

Anion-assisted amidinium exchange and metathesis

Dynamic covalent chemistry has become an invaluable tool for the design and preparation of adaptable yet robust molecular systems. Herein we explore the scope of a largely overlooked dynamic covalent reaction – amidinium exchange – and report on conditions that allow formal amidinium metathesis reactions.

In this article, we explore the scope of a largely overlooked dynamic covalent reaction – amidinium exchange – and report on conditions that allow formal amidinium metathesis reactions.

pH-Responsive templates modulate the dynamic enzymatic synthesis of cyclodextrins

Product selection in the dynamic enzymatic synthesis of cyclodextrins can be controlled by changing the pH. Using cyclodextrin glucanotransferase to make labile the glycosidic linkages in cyclodextrins (CDs), we generate a dynamic combinatorial library of interconverting linear and cyclic α-1,4-glucans. Templates can be employed to favour the selective production of specific CDs and, herein, we show that by using ionisable templates, the synthesis of α-CD or β-CD can be favoured by simply changing the pH. Using 4-nitrophenol as the template, β-CD is the preferred product at low pH, while α-CD is the preferred product at high pH. Furthermore, a new methodology is described for the simulation of product distributions in dynamic combinatorial libraries with ionisable templates at any given pH.

Chaotropic Effect as an Assembly Motif to Construct Supramolecular Cyclodextrin-Polyoxometalate-Based Frameworks

In aqueous solution, low-charged polyoxometalates (POMs) exhibit remarkable self-assembly properties with nonionic organic matter that have been recently used to develop groundbreaking advances in host-guest chemistry, as well as in soft matter science. Herein, we exploit the affinity between a chaotropic POM and native cyclodextrins (α-, β-, and γ-CD) to enhance the structural and functional diversity of cyclodextrin-based open frameworks. First, we reveal that the Anderson-Evans type polyoxometalate [AlMo₆O₁₈(OH)₆]^3- represents an efficient inorganic scaffold to design open hybrid frameworks built from infinite cyclodextrin channels connected through the disk-shaped POM. A single-crystal X-ray analysis demonstrates that the resulting supramolecular architectures contain large cavities (up to 2 nm) where the topologies are dictated by the rotational symmetry of the organic macrocycle, generating honeycomb (bnn net) and checkerboard-like (pcu net) networks for α-CD (C₆) and γ-CD (C₈), respectively. On the other hand, the use of β-CD, a macrocycle with C₇ ideal symmetry, led to a distorted-checkerboard-like network. The cyclodextrin-based frameworks built from an Anderson-Evans type POM are easily functionalizable using the molecular recognition properties of the macrocycle building units. As a proof of concept, we successfully isolated a series of compartmentalized functional frameworks by the entrapment of polyiodides or superchaotropic redox-active polyanions within the macrocyclic host matrix. This set of results paves the way for designing multifunctional supramolecular frameworks whose pore dimensions are controlled by the size of inorganic entities.

Unnatural cyclodextrins can be accessed from enzyme-mediated dynamic combinatorial libraries

Dynamic systems of cyclodextrins (CDs) enabled by a native cyclodextrin glucanotransferase (CGTase) can incorporate unnatural glucopyranose-derived building blocks, expanding the applicability of enzyme-mediated dynamic combinatorial chemistry by using synthetically modified substrates. Starting dynamic combinatorial libraries from CDs with a single 6-modified glucopyranose results in a dynamic mixture of CDs containing several modified glucopyranoses. The relative concentrations of modified α, β or γ-CDs can be controlled by the addition of templates, providing a novel way to access modified CDs.

Identification of potent α-amylase inhibitors via dynamic combinatorial chemistry

In this study, we report for the first time the discovery of potent α-amylase inhibitors using principle of dynamic combinatorial chemistry. The best compound identified exhibited not only high inhibitory efficiency but also low cytotoxicity. The binding mode and possible mechanism are determined in the subsequent kinetic and molecular docking studies.

Chaotropic and Kosmotropic Anions Regulate the Outcome of Enzyme-Mediated Dynamic Combinatorial Libraries of Cyclodextrins in Two Different Ways

We demonstrate how different anions from across the Hofmeister series can influence the behavior of enzyme-mediated dynamic combinatorial libraries of cyclodextrins (CDs). Using cyclodextrin glucanotransferase to catalyze reversible transglycosylation, dynamic mixtures of interconverting cyclodextrins can be formed wherein the relative concentrations of α-CD, β-CD and γ-CD is determined by their intrinsic stabilities and any stabilizing influences of added template (guest) molecules. Here, we find that addition of high concentrations of kosmotropic anions can be used to enhance the effects of added hydrophobic templates, while chaotropic anions can themselves act as templates, causing predictable and significant changes in the cyclodextrin composition due to weak, but specific, binding interactions with α-CD.

Oligosaccharides from Traditional Chinese Herbal Medicines: A Review of Chemical Diversity and Biological Activities

Most of traditional Chinese herbal medicine (TCHM) substances come from medicinal plants, among which oligosaccharides have gradually attracted widespread attention at home and abroad due to their important biological activities and great medicinal potential. Numerous in vitro and in vivo experiments exhibited that oligosaccharides possess various activities, such as antitumor, anti-oxidation, modulate the gut microflora, anti-inflammatory, anti-infection, and immune-regulatory activities. Generally, biological activities are closely related to chemical structures, including molecular weight, monosaccharide composition, glycosidic bond connection, etc. The structural analysis of oligosaccharides is an important basis for studying their structure-activity relationship, but the structural diversity and complexity of carbohydrate compounds limit the study of oligosaccharides activities. Understanding the structures and biological functions of oligosaccharides is important for the development of new bioactive substances with natural oligosaccharides. This review provides a systematic introduction of the current knowledge of the chemical structures and biological activities of oligosaccharides. Most importantly, the reported chemical characteristics and biological activities of the famous TCHM oligosaccharides were briefly summarized, including Morinda officinalis, Rehmannia glutinosa, Arctium lappa, Polygala tenuifolia, Panax ginseng, Lycium barbarum and Astragalus membranaceus. TCHM oligosaccharides play an important role in nutrition, health care, disease diagnosis and prevention as well as have broad application prospects in the field of medicine.

Building up cyclodextrins from scratch - templated enzymatic synthesis of cyclodextrins directly from maltose

Cyclodextrins (CDs) are commercially produced via enzymatic breakdown of starch or amylose. In contrast, we show that cyclodextrins can be synthesised directly from the disaccharide maltose in good yields by exploiting the use of templates to favour the enzymatic build-up of cyclodextrins. Using cyclodextrin glucanotransferase to catalyse reversible transglycosylation, and 1-adamantane carboxylic acid as the template, we can synthesise β-CD from maltose in approximately 70% yield. This work represents a step towards supramolecular control over enzymatic production of complex oligosaccharides from simple building blocks.

Reaction Tracking and High-Throughput Screening of Active Compounds in Combinatorial Chemistry by Tandem Mass Spectrometry Molecular Networking

Combinatorial synthesis has been widely used as an efficient strategy to screen for active compounds. Mass spectrometry is the method of choice in the identification of hits resulting from high-throughput screenings due to its high sensitivity, specificity, and speed. However, manual data processing of mass spectrometry data, especially for structurally diverse products in combinatorial chemistry, is extremely time-consuming and one of the bottlenecks in this process. In this study, we demonstrated the effectiveness of a tandem mass spectrometry molecular networking-based strategy for product identification, reaction dynamics monitoring, and active compound targeting in combinatorial synthesis. Molecular networking connects compounds with similar tandem mass spectra into a cluster and has been widely used in natural products analysis. We show that both the expected and side products can be readily characterized using molecular networking based on their mass spectrometry fragmentation patterns. Additionally, time-dependent molecular networking was integrated to track reaction dynamics to determine the optimal reaction time to maximize target product yields. We also present a proof-of-concept experiment that successfully identified and isolated active molecules from a dynamic combinatorial library. These results demonstrated the potential of using molecular networking for identifying, tracking, and high-throughput screening of active compounds in combinatorial synthesis.

Tuning the Outcome of Enzyme-Mediated Dynamic Cyclodextrin Libraries to Enhance Template Effects

Enzyme-mediated dynamic combinatorial chemistry combines the concept of thermodynamically controlled covalent self-assembly with the inherent biological relevance of enzymatic transformations. A system of interconverting cyclodextrins has been explored, in which the glycosidic linkage is rendered dynamic by the action of cyclodextrin glucanotransferase (CGTase). External factors, such as pH, temperature, solvent, and salinity are reported to modulate the composition of the dynamic cyclodextrin library. Dynamic libraries of cyclodextrins (CDs) could be obtained in wide ranges of pH (5.0-9.0), temperature (5-37 °C), and salinity (up to 7.5 m NaNO₃ ), and with high organic solvent content (50 % by volume of ethanol), showing that enzyme-mediated dynamic systems can be robust and not limited to physiological conditions. Furthermore, it is demonstrated how strategic choice of reaction conditions can enhance template effects, in this case, to achieve highly selective production of α-CD, an otherwise challenging target due to competition from the structurally similar β-CD.

Template effects of vesicles in dynamic covalent chemistry

Vesicle lipid bilayers have been employed as templates to modulate the product distribution in a dynamic covalent library of Michael adducts formed by mixing a Michael acceptor with thiols. In methanol solution, all possible Michael adducts were obtained in similar amounts. Addition of vesicles to the dynamic covalent library led to the formation of a single major product. The equilibrium constants for formation of the Michael adducts are similar for all of the thiols used in this experiment, and the effect of the vesicles on the composition of the library is attributed to the differential partitioning of the library members between the lipid bilayer and the aqueous solution. The results provide a quantitative approach for exploiting dynamic covalent chemistry within lipid bilayers.

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

Small peptides are involved in countless biological processes. Hence selective binding motifs for peptides can be powerful tools for labeling or inhibition. Finding those binding motifs, especially in water which competes for intermolecular H-bonds, poses an enormous challenge. A dynamic combinatorial library can be a powerful method to overcome this issue. We previously reported artificial receptors emerging form a dynamic combinatorial library of peptide building blocks. In this study we aimed to broaden this scope towards recognition of small peptides. Employing CXC peptide building blocks, we found that cyclic dimers of oxidized CFC bind to the aromatic peptides FF and YY (K ≈ 229–702 M⁻¹), while AA binds significantly weaker (K ≈ 65–71 M⁻¹).

A p-tert-Tutyldihomooxacalix[4]arene Based Soft Gel for Sustained Drug Release in Water

P-tert-butyldihomooxacalix[4]arene is a well-known calix[4]arene analog in which one CH₂ bridge is replaced by one -O- group. Thus, dihomooxacalix[4]arene has a slightly larger cavity than that of calix[4]arene and usually possesses a more flexible cone conformation, and the bridged oxygen atom might provide additional binding sites. Here, we synthesized a new functional p-tert-butyldihomooxacalix[4]arene 1 through Ugi reaction with good yield (70%), starting from condensed p-tert-butyldihomooxacalix[4]arene O-alkoxy-substituted benzaldehydes, benzoic acid, benzylamine, and cyclohexyl isocyanide. Proton nuclear magnetic resonance spectroscopy (¹H NMR), ¹³C NMR, IR, and diffusion-ordered ¹H NMR spectroscopy (DOSY) methods were used to characterize the structure of 1. Then soft gel was prepared by adding 1 into cyclohexane directly. It shows remarkable thermoreversibility and can be demonstrated for several cycles. As is revealed by scanning electron microscopy (SEM) images, xerogel showed highly interconnected and homogeneous porous network structures, and hence, the gel is suitable for storage and controlled release.

Light-controlled out-of-equilibrium assembly of cyclodextrins in an enzyme-mediated dynamic system

We show that the selective enzymatic synthesis of specific cyclodextrins can be modulated using light. We use enzyme-mediated dynamic combinatorial chemistry to generate a mixture of interconverting linear and cyclic α-1,4-glucans, and employ an azobenzene photoswitch as a template. Using UV or blue light to switch between photostationary states with different azobenzene cis/trans isomeric ratios, we can promote the out-of-equilibrium assembly of either α-cyclodextrin or β-cyclodextrin.