Evolution of dynamic combinatorial chemistry

Isothermal Phase Transitions in Liquid Crystals Driven by Dynamic Covalent Chemistry

The dynamic nature of calamitic liquid crystals is exploited to perform isothermal phase transitions driven by dynamic covalent chemistry. For this purpose, nematic (N) arrays based on aldehyde 1 were treated with different amines (A-E) in an on-surface process, which resulted in different isothermal phase transitions. These phase transformations were caused by in situ imination reactions and are dependent on the nature of the added amine. Transitions from the N to crystal (1A, 1E), isotropic (1B), and smectic (Sm) (1C, 1D) phases were achieved, while the resulting materials feature thermotropic liquid crystal behavior. A sequential transformation from the N 1 to the Sm 1C and then to the N 1B was achieved by coupling an imination to a transimination processes and adjusting the temperature. All of these processes were well characterized by microscopic, spectroscopic, and X-ray techniques, unlocking not only the constitutional but also the structural aspects of the phase transitions. This work provides new insights into designing constitutionally and structurally adaptable liquid crystal systems, paving the way toward the conception of programable evolutive pathways and adaptive materials.

Functionalization of Supramolecular Polymers by Dynamic Covalent Boroxine Chemistry

Molecular scaffolds that enable the combinatorial synthesis of new supramolecular building blocks are promising targets for the construction of functional molecular systems. Here, we report a supramolecular scaffold based on boroxine that enables the formation of chiral and ordered 1D supramolecular polymers, which can be easily functionalized for circularly polarized luminescence. The boroxine monomers are quantitatively synthesized in situ, both in bulk and in solution, from boronic acid precursors and cooperatively polymerize into 1D helical aggregates stabilized by threefold hydrogen-bonding and π-π stacking. We then demonstrate amplification of asymmetry in the co-assembly of chiral/achiral monomers and the co-condensation of chiral/achiral precursors in classical and in situ sergeant-and-soldiers experiments, respectively, showing fast boronic acid exchange reactions occurring in the system. Remarkably, co-condensation of pyrene boronic acid with a hydrogen-bonding chiral boronic acid results in chiral pyrene aggregation with circularly polarized excimer emission and g-values in the order of 10-3. Yet, the electron deficiency of boron in boroxine makes them chemically addressable by nucleophiles, but also sensitive to hydrolysis. With this sensitivity in mind, we provide first insights into the prospects offered by boroxine-based supramolecular polymers to make chemically addressable, functional, and adaptive systems.

Guest-induced narcissistic self-sorting in water via imine formation

Two anionic tetrahedral cages were self-assembled as the only observable products in weakly basic water via imine condensation. The success of the high-yielding formation of the cages in water relies on (i) multivalency enhancing the stability of the imine bond and affording these cages water compatibility and (ii) a guest template with a complementary size and geometry that provides a hydrophobic driving force by occupying the corresponding cage cavity. When all four precursors, namely two trisaldehydes and two trisamines, were combined in water, narcissistic self-sorting occurred when both guest templates were present. In organic media where the hydrophobic effect is absent, narcissistic self-sorting did not occur in the analogous cage systems, confirming the importance of guest templates.

Discovery of selective monosaccharide receptors via dynamic combinatorial chemistry

The molecular recognition of saccharides by synthetic hosts has become an appealing but elusive task in the last decades. Herein, we combine Dynamic Combinatorial Chemistry (DCC) for the rapid self-assembly and screening of virtual libraries of receptors, with the use of ITC and NMR to validate the hits and molecular modelling to understand the binding mechanisms. We discovered a minimalistic receptor, 1F (N-benzyl-L-phenylalanine), with considerable affinity for fructose (Ka = 1762 M-1) and remarkable selectivity (>50-fold) over other common monosaccharides. The approach accelerates the discovery process of receptors for saccharides.

Neighboring Effects of Sulfur Oxidation State on Dynamic Covalent Bonds and Assemblies

The impact of a varied sulfur oxidation state (sulfide, sulfoxide, and sulfone) on imine dynamic covalent chemistry is presented. The role of noncovalent interactions, including chalcogen bonds and CH hydrogen bonds, on aldehyde/imine structures and imine exchange reactions was elucidated through experimental and computational evidence. The change in the sulfur oxidation state and diamine linkage further allowed the regulation of imine macrocycles, providing a platform for controlling molecular assemblies.

Dynamic Covalent Bonds in the Ebselen Class of Antioxidants Probed by X-ray Quantum Crystallography

Dynamic bonds are essential structural ingredients of dynamic covalent chemistry that involve reversible cleavage and formation of bonds. Herein, we explore the electronic characteristics of Se-N bonds in the organo-selenium antioxidant ebselen and its derivatives for their propensity to function as dynamic covalent bonds by employing high-resolution X-ray quantum crystallography and complementary computational studies. An analysis of the experimentally reconstructed X-ray wavefunctions reveals the salient electronic features of the Se-N bonds with very low electron density localized at the bonding region and a positive Laplacian value at the bond critical point. Bond orders and percentage covalency and ionicity estimated from the X-ray wavefunctions, along with localized orbital locator (LOL) and electron localization function (ELF) analyses show that the Se-N bond is unique in its closed shell-like features, despite being a covalent bond. Time-dependent DFT calculations simulate the cleavage of Se-N bonds in ebselen in the excited state, further substantiating their nature as dynamic bonds.

"The Sulfur Dance" Around Arenes and Heteroarenes - the Reversible Nature of Nucleophilic Aromatic Substitutions

We disclose the features of a category of reversible nucleophilic aromatic substitutions in view of their significance and generality in dynamic aromatic chemistry. Exchange of sulfur components surrounding arenes and heteroarenes may occur at 25 °C, in a process that one may call a "sulfur dance". These SN Ar systems present their own features, apart from common reversible reactions utilized in dynamic covalent chemistry (DCC). By varying conditions, covalent dynamics may operate to provide libraries of thiaarenes with some selectivity, or conversion of a hexa(thio)benzene asterisk into another one. The reversible nature of SN Ar is confirmed by three methods: a convergence of the products distribution in reversible SN Ar systems, a related product redistribution between two per(thio)benzenes by using a thiolate promoter, and from kinetic/thermodynamic data. A four-component dynamic covalent system further illustrates the thermodynamically-driven formation of a thiacalix[2]arene[2]pyrimidine by sulfur component exchanges. This work stimulates the implementation of reversible SN Ar in aromatic chemistry and in DCC.

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.

Recent advances in supramolecular fullerene chemistry

Fullerene chemistry has come a long way since 1990, when the first bulk production of C60 was reported. In the past decade, progress in supramolecular chemistry has opened some remarkable and previously unexpected opportunities regarding the selective (multiple) functionalization of fullerenes and their (self)assembly into larger structures and frameworks. The purpose of this review article is to provide a comprehensive overview of these recent developments. We describe how macrocycles and cages that bind strongly to C60 can be used to block undesired addition patterns and thus allow the selective preparation of single-isomer addition products. We also discuss how the emergence of highly shape-persistent macrocycles has opened opportunities for the study of photoactive fullerene dyads and triads as well as the preparation of mechanically interlocked compounds. The preparation of two- or three-dimensional fullerene materials is another research area that has seen remarkable progress over the past few years. Due to the rapidly decreasing price of C60 and C70, we believe that these achievements will translate into all fields where fullerenes have traditionally (third-generation solar cells) and more recently been applied (catalysis, spintronics).

Anion-π catalysis on carbon allotropes

Anion-π catalysis, introduced in 2013, stands for the stabilization of anionic transition states on π-acidic aromatic surfaces. Anion-π catalysis on carbon allotropes is particularly attractive because high polarizability promises access to really strong anion-π interactions. With these expectations, anion-π catalysis on fullerenes has been introduced in 2017, followed by carbon nanotubes in 2019. Consistent with expectations from theory, anion-π catalysis on carbon allotropes generally increases with polarizability. Realized examples reach from enolate addition chemistry to asymmetric Diels-Alder reactions and autocatalytic ether cyclizations. Currently, anion-π catalysis on carbon allotropes gains momentum because the combination with electric-field-assisted catalysis promises transformative impact on organic synthesis.

Dynamic Phosphorus: Thiolate Exchange Cascades with Higher Phosphorothioates

In this study, we introduce phosphorus, a pnictogen, as an exchange center for dynamic covalent chemistry. Cascade exchange of neutral phosphorotri- and -tetrathioates with thiolates is demonstrated in organic solvents, aqueous micellar systems, and in living cells. Exchange rates increase with the pH value, electrophilicity of the exchange center, and nucleophilicity of the exchangers. Molecular walking of the dynamic phosphorus center along Hammett gradients is simulated by the sequential addition of thiolate exchangers. Compared to phosphorotrithioates, tetrathioates are better electrophiles with higher exchange rates. Dynamic phosphorotri- and -tetrathioates are non-toxic to HeLa Kyoto cells and participate in the dynamic networks that account for thiol-mediated uptake into living cells.

Anion-(π)n -π Catalytic Micelles

Anion-π catalysis operates by stabilizing anionic transition states on π-acidic aromatic surfaces. In anion-(π)n -π catalysis, π stacks add polarizability to strengthen interactions. In search of synthetic methods to extend π stacks beyond the limits of foldamers, the self-assembly of micelles from amphiphilic naphthalenediimides (NDIs) is introduced. To interface substrates and catalysts, charge-transfer complexes with dialkoxynaphthalenes (DANs), a classic in supramolecular chemistry, are installed. In π-stacked micelles, the rates of bioinspired ether cyclizations exceed rates on monomers in organic solvents by far. This is particularly impressive considering that anion-π catalysis in water has been elusive so far. Increasing rates with increasing π acidity of the micelles evince operational anion-(π)n -π catalysis. At maximal π acidity, autocatalytic behavior emerges. Dependence on position and order in confined micellar space promises access to emergent properties. Anion-(π)n -π catalytic micelles in water thus expand supramolecular systems catalysis accessible with anion-π interactions with an inspiring topic of general interest and great perspectives.

Dynamic covalent nano-networks comprising antibiotics and polyphenols orchestrate bacterial drug resistance reversal and inflammation alleviation

New antimicrobial strategies are urgently needed to meet the challenges posed by the emergence of drug-resistant bacteria and bacterial biofilms. This work reports the facile synthesis of antimicrobial dynamic covalent nano-networks (aDCNs) composing antibiotics bearing multiple primary amines, polyphenols, and a cross-linker acylphenylboronic acid. Mechanistically, the iminoboronate bond drives the formation of aDCNs, facilitates their stability, and renders them highly responsive to stimuli, such as low pH and high H₂O₂ levels. Besides, the representative A1B1C1 networks, composed of polymyxin B1(A1), 2-formylphenylboronic acid (B1), and quercetin (C1), inhibit biofilm formation of drug-resistant Escherichia coli, eliminate the mature biofilms, alleviate macrophage inflammation, and minimize the side effects of free polymyxins. Excellent bacterial eradication and inflammation amelioration efficiency of A1B1C1 networks are also observed in a peritoneal infection model. The facile synthesis, excellent antimicrobial performance, and biocompatibility of these aDCNs potentiate them as a much-needed alternative in current antimicrobial pipelines.

Transient self-assembly of metal-organic complexes

Implementing transient processes in networks of dynamic molecules holds great promise for developing new functional behaviours. Here we report that trichloroacetic acid can be used to temporarily rearrange networks of dynamic imine-based metal complexes towards new equilibrium states, forcing them to express complexes otherwise unfavourable in their initial equilibrium states. Basic design principles were determined for the creation of such networks. Where a complex distribution of products was obtained in the initial equilibrium state of the system, the transient rearrangement temporarily yielded a simplified output, forcing a more structured distribution of products. Where a single complex was obtained in the initial equilibrium state of the system, the transient rearrangement temporarily modified the properties of this complex. By doing so, the mechanical properties of an helical macrocyclic complex could be temporarily altered by rearranging it into a [2]catenane.

Selection of diverse polymorphic structures from a small dynamic molecular network controlled by the environment

The complex interplay between systems and their environment plays an important role in processes ranging from self-assembly to evolution. Polymorphism, where, from the same ingredients different products can be formed, is likely to be an important enabler for evolutionary adaptation. Environmental pressures may induce polymorphic behaviour, where different pressures result in different structural organisation. Here we show that by combining covalent and non-covalent bond formation three distinct polymorphs can emerge from the same small dynamic molecular network: vesicular aggregates, self-replicating fibres and nanoribbons, depending on the nature of the solvent environment. Additionally, a particular set of conditions allows the transient co-existence of both vesicles and fibres.

An Orthogonal Dynamic Covalent Chemistry Tool for Ring-Opening Polymerization of Cyclic Oligochalcogenides on Detachable Helical Peptide Templates

A model system is introduced as a general tool to elaborate on orthogonal templation of dynamic covalent ring‐opening polymerization (ODC‐TROP). The tool consists of 3₁₀ helical peptides as unprecedented templates and semicarbazones as orthogonal dynamic covalent linkers. With difficult‐to‐control 1,2‐dithiolanes, ODC‐TROP on the level of short model oligomers occurs with high templation efficiency, increasing and diminishing upon helix stabilization and denaturation, respectively. Further, an anti‐templated conjugate with mispositioned monomers gave reduced templation upon helix twisting. Even with the “unpolymerizable” 1,2‐diselenolanes, initial studies already afford mild templation efficiency. These proof‐of‐principle results promise that the here introduced tool, recyclable and enabling late‐stage side chain modification, will be useful to realize ODC‐TROP of intractable or unknown cyclic dynamic covalent monomers for dynamer materials as well as cellular uptake and signaling applications.

Cyclic Thiosulfonates for Thiol-Mediated Uptake: Cascade Exchangers, Transporters, Inhibitors

Thiol-mediated uptake is emerging as a powerful method to penetrate cells. Cyclic oligochalcogenides (COCs) have been identified as privileged scaffolds to enable and inhibit thiol-mediated uptake because they can act as dynamic covalent cascade exchangers, i.e., every exchange produces a new, covalently tethered exchanger. In this study, our focus is on the essentially unexplored COCs of higher oxidation levels. Quantitative characterization of the underlying dynamic covalent exchange cascades reveals that the initial ring opening of cyclic thiosulfonates (CTOs) proceeds at a high speed even at a low pH. The released sulfinates exchange with disulfides in aprotic but much less in protic environments. Hydrophobic domains were thus introduced to direct CTOs into hydrophobic pockets to enhance their reactivity. Equipped with such directing groups, fluorescently labeled CTOs entered the cytosol of living cells more efficiently than the popular asparagusic acid. Added as competitive agents, CTOs inhibit the uptake of various COC transporters and SARS-CoV-2 lentivectors. Orthogonal trends found with different transporters support the existence of multiple cellular partners to account for the diverse expressions of thiol-mediated uptake. Dominant self-inhibition and high activity of dimers imply selective and synergistic exchange in hydrophobic pockets as distinguishing characteristics of thiol-mediated uptake with CTOs. The best CTO dimers with hydrophobic directing groups inhibit the cellular entry of SARS-CoV-2 lentivectors with an IC₅₀ significantly lower than the previous best CTO, below the 10 μM threshold and better than ebselen. Taken together, these results identify CTOs as an intriguing motif for use in cytosolic delivery, as inhibitors of lentivector entry, and for the evolution of dynamic covalent networks in the broadest sense, with reactivity-based selectivity of cascade exchange emerging as a distinguishing characteristic that deserves further attention.

Molecular Cavity for Catalysis and Formation of Metal Nanoparticles for Use in Catalysis

The employment of weak intermolecular interactions in supramolecular chemistry offers an alternative approach to project artificial chemical environments like the active sites of enzymes. Discrete molecular architectures with defined shapes and geometries have become a revolutionary field of research in recent years because of their intrinsic porosity and ease of synthesis using dynamic non-covalent/covalent interactions. Several porous molecular cages have been constructed from simple building blocks by self-assembly, which undergoes many self-correction processes to form the final architecture. These supramolecular systems have been developed to demonstrate numerous applications, such as guest stabilization, drug delivery, catalysis, smart materials, and many other related fields. In this respect, catalysis in confined nanospaces using such supramolecular cages has seen significant growth over the years. These porous discrete cages contain suitable apertures for easy intake of substrates and smooth release of products to exhibit exceptional catalytic efficacy. This review highlights recent advancements in catalytic activity influenced by the nanocavities of hydrogen-bonded cages, metal-ligand coordination cages, and dynamic or reversible covalently bonded organic cages in different solvent media. Synthetic strategies for these three types of supramolecular systems are discussed briefly and follow similar and simplistic approaches manifested by simple starting materials and benign conditions. These examples demonstrate the progress of various functionalized molecular cages for specific chemical transformations in aqueous and nonaqueous media. Finally, we discuss the enduring challenges related to porous cage compounds that need to be overcome for further developments in this field of work.

Recent advances in DNA-encoded dynamic libraries

The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.

Dynamic Combinatorial Optimization of In Vitro and In Vivo Heparin Antidotes

Heparin-like macromolecules are widely used in clinics as anticoagulant, antiviral, and anticancer drugs. However, the search of heparin antidotes based on small synthetic molecules to control blood coagulation still remains a challenging task due to the physicochemical properties of this anionic polysaccharide. Here, we use a dynamic combinatorial chemistry approach to optimize heparin binders with submicromolar affinity. The recognition of heparin by the most amplified members of the dynamic library has been studied with different experimental (SPR, fluorescence, NMR) and theoretical approaches, rendering a detailed interaction model. The enzymatic assays with selected library members confirm the correlation between the dynamic covalent screening and the in vitro heparin inhibition. Moreover, both ex vivo and in vivo blood coagulation assays with mice show that the optimized molecules are potent antidotes with potential use as heparin reversal drugs. Overall, these results underscore the power of dynamic combinatorial chemistry targeting complex and elusive biopolymers.

Using Solid Catalysts in Disulfide-Based Dynamic Combinatorial Solution- and Mechanochemistry

It was shown for the first time that solid amines can act as catalysts for disulfide-based dynamic combinatorial chemistry (DCC) by ball mill grinding. The mechanochemical equilibrium for the two disulfide reactions studied was reached within 1-3 h using ten different amine catalysts. This contrasts with the weeks to months to achieve solution equilibrium for most solid amine catalysts at 2 %mol mol^-1 concentration in a 2 mMolar disulfide dynamic combinatorial library in a suitable solvent. The final mechanochemical equilibrium was independent of the catalyst used but varied with other ball mill grinding factors such as the presence of traces of solvent. The different efficiencies of the amines tested were discussed.

Metal-dependent selective formation of calix[4]arene assemblies based on dynamic covalent chemistry

The reaction of calix[4]arene derivatives 1a and 1b bearing four salicylaldehyde moieties with 1,3-propanediamine gave macrocyclic trimers 5a and 5b, respectively, which have intramolecular bridges formed via the flattened cone conformation. In contrast, a capsular-shaped dimeric cage [7a·2Na]²⁺ was selectively formed when the conformation of the calix[4]arene moiety of 1a was fixed in the spread cone conformation by complexation with Na⁺ at the lower-rim amide groups.

Two-Dimensional Polymers and Polymerizations

Synthetic chemists have developed robust methods to synthesize discrete molecules, linear and branched polymers, and disordered cross-linked networks. However, two-dimensional polymers (2DPs) prepared from designed monomers have been long missing from these capabilities, both as objects of chemical synthesis and in nature. Recently, new polymerization strategies and characterization methods have enabled the unambiguous realization of covalently linked macromolecular sheets. Here we review 2DPs and 2D polymerization methods. Three predominant 2D polymerization strategies have emerged to date, which produce 2DPs either as monolayers or multilayer assemblies. We discuss the fundamental understanding and scope of each of these approaches, including: the bond-forming reactions used, the synthetic diversity of 2DPs prepared, their multilayer stacking behaviors, nanoscale and mesoscale structures, and macroscale morphologies. Additionally, we describe the analytical tools currently available to characterize 2DPs in their various isolated forms. Finally, we review emergent 2DP properties and the potential applications of planar macromolecules. Throughout, we highlight achievements in 2D polymerization and identify opportunities for continued study.

Protein Assembly by Design

Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.

Self-Assembly of Stimuli-Responsive [2]Rotaxanes by Amidinium Exchange

Advances in supramolecular chemistry are often underpinned by the development of fundamental building blocks and methods enabling their interconversion. In this work, we report the use of an underexplored dynamic covalent reaction for the synthesis of stimuli-responsive [2]rotaxanes. The formamidinium moiety lies at the heart of these mechanically interlocked architectures, because it enables both dynamic covalent exchange and the binding of simple crown ethers. We demonstrated that the rotaxane self-assembly follows a unique reaction pathway and that the complex interplay between crown ether and thread can be controlled in a transient fashion by addition of base and fuel acid. Dynamic combinatorial libraries, when exposed to diverse nucleophiles, revealed a profound stabilizing effect of the mechanical bond as well as intriguing reactivity differences between seemingly similar [2]rotaxanes.

Self-assembly of chiral BINOL cages via imine condensation

Condensation of an (S)- or (R)-BINOL-derived dialdehyde and tris(2-aminoethyl)amine produced chiral [2+3] imine cages, which were further reduced to furnish more stable chiral amine cages and applied in the enantioselective recognition of (1R,2R)- and (1S,2S)-1,2-diaminocyclohexane.

Dynamic Catalytic Highly Enantioselective 1,3-Dipolar Cycloadditions

In dynamic covalent chemistry, reactions follow a thermodynamically controlled pathway through equilibria. Reversible covalent‐bond formation and breaking in a dynamic process enables the interconversion of products formed under kinetic control to thermodynamically more stable isomers. Notably, enantioselective catalysis of dynamic transformations has not been reported and applied in complex molecule synthesis. We describe the discovery of dynamic covalent enantioselective metal‐complex‐catalyzed 1,3‐dipolar cycloaddition reactions. We have developed a stereodivergent tandem synthesis of structurally and stereochemically complex molecules that generates eight stereocenters with high diastereo‐ and enantioselectivity through asymmetric reversible bond formation in a dynamic process in two consecutive Ag‐catalyzed 1,3‐dipolar cycloadditions of azomethine ylides with electron‐poor olefins. Time‐dependent reversible dynamic covalent‐bond formation gives enantiodivergent and diastereodivergent access to structurally complex double cycloadducts with high selectivity from a common set of reagents.

Oligonucleotide Phosphorothioates Enter Cells by Thiol-Mediated Uptake

Oligonucleotide phosphorothioates (OPS) are DNA or RNA mimics where one phosphate oxygen is replaced by a sulfur atom. They have been shown to enter mammalian cells much more efficiently than non-modified DNA. Thus, solving one of the key challenges with oligonucleotide technology, OPS became very useful in practice, with several FDA-approved drugs on the market or in late clinical trials. However, the mechanism accounting for this facile cellular uptake is unknown. Here, we show that OPS enter cells by thiol-mediated uptake. The transient adaptive network produced by dynamic covalent pseudo-disulfide exchange is characterized in action. Inhibitors with nanomolar efficiency are provided, together with activators that reduce endosomal capture for efficient delivery of OPS into the cytosol, the site of action.

Thiol-Mediated Uptake

This Perspective focuses on thiol-mediated uptake, that is, the entry of substrates into cells enabled by oligochalcogenides or mimics, often disulfides, and inhibited by thiol-reactive agents. A short chronology from the initial observations in 1990 until today is followed by a summary of cell-penetrating poly(disulfide)s (CPDs) and cyclic oligochalcogenides (COCs) as privileged scaffolds in thiol-mediated uptake and inhibitors of thiol-mediated uptake as potential antivirals. In the spirit of a Perspective, the main part brings together topics that possibly could help to explain how thiol-mediated uptake really works. Extreme sulfur chemistry mostly related to COCs and their mimics, cyclic disulfides, thiosulfinates/-onates, diselenolanes, benzopolysulfanes, but also arsenics and Michael acceptors, is viewed in the context of acidity, ring tension, exchange cascades, adaptive networks, exchange affinity columns, molecular walkers, ring-opening polymerizations, and templated polymerizations. Micellar pores (or lipid ion channels) are considered, from cell-penetrating peptides and natural antibiotics to voltage sensors, and a concise gallery of membrane proteins, as possible targets of thiol-mediated uptake, is provided, including CLIC1, a thiol-reactive chloride channel; TMEM16F, a Ca-activated scramblase; EGFR, the epithelial growth factor receptor; and protein-disulfide isomerase, known from HIV entry or the transferrin receptor, a top hit in proteomics and recently identified in the cellular entry of SARS-CoV-2.

Cell-Selective siRNA Delivery Using Glycosylated Dynamic Covalent Polymers Self-Assembled In Situ by RNA Templating

Dynamic covalent libraries enable exploring complex chemical systems from which bioactive assemblies can adaptively emerge through template effects. In this work, we studied dynamic covalent libraries made of complementary bifunctional cationic peptides, yielding a diversity of species from macrocycles to polymers. Although polymers are typically expressed only at high concentration, we found that siRNA acts as a template in the formation of dynamic covalent polymers at low concentration in a process guided by electrostatic binding. Using a glycosylated building block, we were able to show that this templated polymerization further translates into the multivalent presentation of carbohydrate ligands, which subsequently promotes cell uptake and even cell-selective siRNA delivery.

Biomimetic selenocystine based dynamic combinatorial chemistry for thiol-disulfide exchange

Dynamic combinatorial chemistry applied to biological environments requires the exchange chemistry of choice to take place under physiological conditions. Thiol-disulfide exchange, one of the most popular dynamic combinatorial chemistries, usually needs long equilibration times to reach the required equilibrium composition. Here we report selenocystine as a catalyst mimicking Nature's strategy to accelerate thiol-disulfide exchange at physiological pH and low temperatures. Selenocystine is able to accelerate slow thiol-disulfide systems and to promote the correct folding of an scrambled RNase A enzyme, thus broadening the practical range of pH conditions for oxidative folding. Additionally, dynamic combinatorial chemistry target-driven self-assembly processes are tested using spermine, spermidine and NADPH (casting) and glucose oxidase (molding). A non-competitive inhibitor is identified in the glucose oxidase directed dynamic combinatorial library.

Glucose Binding Drives Reconfiguration of a Dynamic Library of Urea-Containing Metal-Organic Assemblies

A bis-urea-functionalized ditopic subcomponent assembled with 2-formylpyridine and Fe^II , resulting in a dynamic library of metal-organic assemblies: an irregular Fe^II ₄ L₆ structure and three Fe^II ₂ L₃ stereoisomers: left- and right-handed helicates and a meso-structure. This library reconfigured in response to the addition of monosaccharide derivatives, which served as guests for specific library members, and the rate of saccharide mutarotation was also enhanced by the library. The (P) enantiomer of the Fe^II ₂ L₃ helical structure bound β-D-glucose selectively over α-D-glucose. As a consequence, the library collapsed into the (P)-Fe^II ₂ L₃ helicate following glucose addition. The α-D-glucose was likewise transformed into the β-D-anomer during equilibration and binding. Thus, β-D-glucose and (P)-3 amplified each other in the product mixture, as metal-organic and saccharide libraries geared together into a single equilibrating system.

A water-soluble naphthalenediimide-containing hexacationic cage

A water-soluble cage containing three naphthalenediimide (NDI) units was synthesized in a one-pot manner without chromatographic purification, during which six irreversible C-N bonds formed simultaneously via an SN2 reaction. The cage was observed to be capable of accommodating a variety π-electron rich guests in a peripheral manner in water. However, for linear guests including I3- and I2, the cage is able to form an inclusion complex. Besides, in the solid state, the cage can absorb vapor of I2.

Efficient one-pot synthesis of [3]catenanes based on Pt(ii) metallacycles with a flexible building block

Three [3]catenanes were fabricated in high efficiency through the self-assembly of a 90° platinum(ii) receptor, a flexible bis(4,4′-bipyridinium) donor and a crown ether (DB24C8 or DB30C10).

Dynamic Covalent Chemistry Approach toward 18-Membered P4N2 Macrocycles and Their Nickel(II) Complexes

A dynamic covalent chemistry approach was used for the stereoselective synthesis of 1,10-diaza-3,8,12,17-tetraphosphacyclooctadecanes via condensation reaction of 1,4-bis(organylphosphino)butane, formaldehyde, and primary amines. The obtained 18-membered P₄N₂ macrocycles were isolated in pure form as meso- (R_PS_PS_PR_P) or rac- (R_PR_PR_PR_P/S_PS_PS_PS_P) isomers. The structural features of the individual stereoisomers were revealed by NMR spectroscopy and X-ray structure analysis. All P₄N₂ macrocycles form square-planar nickel(II) complexes with the R_PS_PS_PR_P isomer only, in which the orientation of the lone pairs of electrons at phosphorus favors this coordination mode, independent of the initial configuration of the ligand, indicating the ability of the 18-membered P₄N₂ macrocycles to stereoisomerize in the course of the complexation.

Medical Applications Based on Supramolecular Self-Assembled Materials From Tannic Acid

Polyphenol, characterized by various phenolic rings in the chemical structure and an abundance in nature, can be extracted from vegetables, grains, chocolates, fruits, tea, legumes, and seeds, among other sources. Tannic acid (TA), a classical polyphenol with a specific chemical structure, has been widely used in biomedicine because of its outstanding biocompatibility and antibacterial and antioxidant properties. TA has tunable interactions with various materials that are widely distributed in the body, such as proteins, polysaccharides, and glycoproteins, through multimodes including hydrogen bonding, hydrophobic interactions, and charge interactions, assisting TA as important building blocks in the supramolecular self-assembled materials. This review summarizes the recent immense progress in supramolecular self-assembled materials using TA as building blocks to generate different materials such as hydrogels, nanoparticles/microparticles, hollow capsules, and coating films, with enormous potential medical applications including drug delivery, tumor diagnosis and treatment, bone tissue engineering, biofunctional membrane material, and the treatment of certain diseases. Furthermore, we discuss the challenges and developmental prospects of supramolecular self-assembly nanomaterials based on TA.

Naphthalenediimides with Cyclic Oligochalcogenides in Their Core

Naphthalenediimides (NDIs) are privileged scaffolds par excellence, of use in functional systems from catalysts to ion channels, photosystems, sensors, ordered matter in all forms, tubes, knots, stacks, sheets, vesicles, and colored over the full visible range. Despite this extensively explored chemical space, there is still room to discover core-substituted NDIs with fundamentally new properties: NDIs with cyclic trisulfides (i.e., trisulfanes) in their core absorb at 668 nm, emit at 801 nm, and contract into disulfides (i.e., dithietes) upon irradiation at <475 nm. Intramolecular 1,5-chalcogen bonds account for record redshifts with trisulfides, ring-tension mediated chalcogen-bond-mediated cleavage for blueshifts to 492 nm upon ring contraction. Cyclic oligochalcogenides (COCs) in the NDI core open faster than strained dithiolanes as in asparagusic acid and are much better retained on thiol exchange affinity columns. This makes COC-NDIs attractive not only within the existing multifunctionality, particularly artificial photosystems, but also for thiol-mediated cellular uptake.

Polyether Natural Product Inspired Cascade Cyclizations: Autocatalysis on π-Acidic Aromatic Surfaces

Anion-π catalysis functions by stabilizing anionic transition states on aromatic π surfaces, thus providing a new approach to molecular transformation. The delocalized nature of anion-π interactions suggests that they serve best in stabilizing long-distance charge displacements. Aiming therefore for an anionic cascade reaction that is as charismatic as the steroid cyclization is for conventional cation-π biocatalysis, reported here is the anion-π-catalyzed epoxide-opening ether cyclizations of oligomers. Only on π-acidic aromatic surfaces having a positive quadrupole moment, such as hexafluorobenzene to naphthalenediimides, do these polyether cascade cyclizations proceed with exceptionally high autocatalysis (rate enhancements k_auto /k_cat >10⁴  m^-1 ). This distinctive characteristic adds complexity to reaction mechanisms (Goldilocks-type substrate concentration dependence, entropy-centered substrate destabilization) and opens intriguing perspectives for future developments.

Discovery of an all-donor aromatic [2]catenane

We report herein the first all-donor aromatic [2]catenane formed through dynamic combinatorial chemistry, using single component libraries. The building block is a benzo[1,2-b:4,5-b′]dithiophene derivative, a π-donor molecule, with cysteine appendages that allow for disulfide exchange. The hydrophobic effect plays an essential role in the formation of the all-donor [2]catenane. The design of the building block allows the formation of a quasi-fused pentacyclic core, which enhances the stacking interactions between the cores. The [2]catenane has chiro-optical and fluorescent properties, being also the first known DCC-disulphide-based interlocked molecule to be fluorescent.

An all-donor [2]catenane has been synthesised via dynamic combinatorial chemistry. It features stacked benzodithiophenes which are quasi-pentacyclic through hydrogen bonding.