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Systems chemistry aims to develop molecular systems that display emerging properties arising from their network and absent in their individual constituents. Employing reversible chemistry under thermodynamic control represents a valuable tool for generating dynamic combinatorial libraries of interconverting molecules, which may exhibit intriguing collective behaviour. A simple dynamic combinatorial library was prepared using dithioacetal/thiol/disulfide exchanges. Because of the relative reactivities of these reversible reactions, the library constitutes a two‐layer dynamic system with one layer active in an acid medium (thiol/dithioacetal exchange) and one layer active in a basic medium (thiol/disulfide exchange). This property enables the system to respond to momentary changes in acidity of the medium by activating different network regions, channeling some building blocks from one layer to another through shared thiol reagents (nodes). This momentaneous change in wiring affects the final steady state composition of the library, measured the next day, even though the event that caused it vanishes without leaving any residue. Therefore, the final composition of this dynamic system provides information about this transient past perturbation in the environment such as: when it occurred, how long it was, or how intense it was. [ABSTRACT FROM AUTHOR]

The intricate interplay of metabolic reactions and molecular assembly in living systems enables spatiotemporally organization and gives rise to diverse dynamic behaviors that characterize life. Over the last decades, research efforts have increasingly focused on replicating the remarkable properties and characteristics of living systems, driving the rapid growth of systems chemistry. This young discipline which generally studies interacting molecular networks and emergent system‐level properties, behaviors, and functions, offers new concepts and tools to tackle the complexity of life. In this review paper, we have explored seminal research and recent advancements in recreating dynamic behaviors of life with systems chemistry. We believe that the recreation of the dynamic behaviors of life through systems chemistry would set the initial steps to obtain synthetic life de novo. [ABSTRACT FROM AUTHOR]

Mutualisms are interactions that benefit all species involved. It has been widely investigated in neighbouring subjects, such as biology, ecology, sociology, and economics. However, such a reciprocal relationship in synthetic chemical systems has rarely been studied. Here, we demonstrate a mutualistic synthesis where byproducts from two orthogonal chemical reactions aid each other′s production. Disulfide exchange and hydrazone exchange were chosen to generate two dynamic combinatorial libraries. A minor tetrameric macrocycle from the active disulfide library was quantitatively amplified in the presence of the hydrazone library. This incorporation also turned on the previously inert hydrazone reaction, producing a linear species that formed a "handcuffs" catenane with the disulfide tetramer. These findings not only lend robust support to the hypothesis of "RNA‐peptide coevolution" for the origin of life but also broaden the scope of synthetic chemistry, highlighting the untapped potential of minor products from different reactions. Additionally, the co‐self‐assembly of these mutualistic entities to form supramolecular structures opens new avenues for future development of composite nanosystems with synergistic properties. [ABSTRACT FROM AUTHOR]

Peptide folding is a dynamic process driven by non‐covalent cross‐linking leading to functional nanostructures for essential biochemical activities. However, replicating this process in synthetic systems is challenging due to the difficulty in mimicking nature's real‐time regulation of non‐covalent crosslinking for single‐chain polymer folding. Here, we address this by employing anionic dithiol building blocks to create macrocyclic disulfides as non‐covalent crosslinkers that adapted to the folding process. Initially, small macrocycles facilitated a low degree folding of a polycation. Then, this preorganized structure catalysed the production of larger macrocycles that enhanced the folding conversely. The self‐adaptive synthesis was verified through the encapsulation of an anticancer drug, showing an updated production distribution of non‐covalent crosslinkers and maximizing drug‐loading efficiency against drug‐resistant cancer in vitro. Our research advances the understanding of molecular systems by exploring species evolution via the structural dynamics of polymer folding. Additionally, adaptive synthesis enables controlled, sequential folding of synthetic polymers, with the potential to mimic protein functions. [ABSTRACT FROM AUTHOR]

Base‐filling, i. e., post‐synthetic furnishing of an oligonucleotide scaffold with base moieties or their analogues, is an interesting alternative to the conventional approach of sequential coupling of building blocks (modified or otherwise). Reversible attachment of the base moieties is particularly attractive as it allows the use of dynamic combinatorial chemistry and usually leads to higher fidelity. This concept article summarizes the various backbones and coupling reactions used for base‐filling over the past fifteen years, discusses the impact of base stacking and pairing on efficiency and fidelity and highlights potential and realized applications. [ABSTRACT FROM AUTHOR]

A bis-ferrocene macrocycle was synthesized by reversible acylhydrazone formation under thermodynamic control, starting from a ferrocene functionalized with hydrazide and protected aldehyde moieties. A hydrogen sulfate anion acts as a template to direct the synthesis specifically toward the macrocyclic dimer, due to a weak but selective binding interaction. This work highlights the utility of dynamic combinatorial chemistry as an approach to macrocycle synthesis. [ABSTRACT FROM AUTHOR]

Dynamic combinatorial chemistry (DCC) leverages a reversible reaction to generate compound libraries from constituting building blocks under thermodynamic control. The position of this equilibrium can be biased by addition of a target macromolecule towards enrichment of bound ligands. While DCC has been applied to select ligands for a single target protein, its application to identifying chimeric molecules inducing proximity between two proteins is unprecedented. In this proof‐of‐concept study, we develop a DCC approach to select bifunctional proteolysis targeting chimeras (PROTACs) based on their ability to stabilize the ternary complex. We focus on VHL‐targeting Homo‐PROTACs as model system, and show that the formation of a VHL2 : Homo‐PROTAC ternary complex reversibly assembled using thiol‐disulfide exchange chemistry leads to amplification of potent VHL Homo‐PROTACs with degradation activities which correlated well with their biophysical ability to dimerize VHL. Ternary complex templated dynamic combinatorial libraries allowed identification of novel Homo‐PROTAC degraders. We anticipate future applications of ternary‐complex directed DCC to early PROTAC screenings and expansion to other proximity‐inducing modalities beyond PROTACs. [ABSTRACT FROM AUTHOR]

Darwinian evolution, including the selection of the fittest species under given environmental conditions, is a major milestone in the development of synthetic living systems. In this regard, generalist or specialist behavior (the ability to replicate in a broader or narrower, more specific food environment) are of importance. Here we demonstrate generalist and specialist behavior in dynamic combinatorial libraries composed of a peptide‐based and an oligo(ethylene glycol) based building block. Three different sets of macrocyclic replicators could be distinguished based on their supramolecular organization: two prepared from a single building block as well as one prepared from an equimolar mixture of them. Peptide‐containing hexamer replicators were found to be generalists, i. e. they could replicate in a broad range of food niches, whereas the octamer peptide‐based replicator and hexameric ethyleneoxide‐based replicator were proven to be specialists, i. e. they only replicate in very specific food niches that correspond to their composition. However, sequence specificity cannot be demonstrated for either of the generalist replicators. The generalist versus specialist nature of these replicators was linked to their supramolecular organization. Assembly modes that accommodate structurally different building blocks lead to generalist replicators, while assembly modes that are more restrictive yield specialist replicators. [ABSTRACT FROM AUTHOR]

A strong revival of interest has been dedicated to peptides over the last few years, in different fields including drug discovery, biosensing and material sciences. The use of dynamic covalent chemistry has allowed the development of self‐adaptative peptides or peptidomimetics, responsive to their environment. The development of methods allowing the building, screening or deconvolution of libraries of peptides is a highly active research area and dynamic combinatorial chemistry represents an innovative and underexploited method in this field. This Review gives an overview of the use of dynamic covalent chemistry as a tool to produce peptides or peptidomimetics, with particular attention to applications in dynamic combinatorial chemistry. [ABSTRACT FROM AUTHOR]

Abstract Understanding dynamic systems is a crucial step toward the design of complex matter. Here, we aim to study the behavior of Constitutional Dynamic Networks (CDNs) in conditions of dynamic competition, taking cryptands and metal cations as a test bed. The CDNs of cryptates were analyzed by NMR spectroscopy. The experimental results were complemented by extensive numerical simulations, based on a large amount of thermodynamic and kinetic data available in the literature for cryptates. Although the CDN′s output is a result of the interplay between the individual stability constants of the complexes in a mixture, the overall effect may be governed by only one – the most thermodynamically stable member of a network. Significantly, these findings indicate that an increase in complexity (multiplicity and connectivity) of a system may, in conditions of dynamic competition, result in “simplexity”, i. e. a simplification of the output of the system.

Acylhydrazone‐based (macro)molecules display an increasingly broad spectrum of applications, from small therapeutic molecules and metal‐ions probes to self‐healing films and biorelevant dynamic polymers. The acylhydrazone function is indeed of prime interest since its unique design combines hydrogen bonds, pH‐dependent reversibility, ability to undergo molecular exchanges, and a possible polyvalency. However, a key parameter of its use in aqueous media is the associated water‐solubility of the resulting (macro)molecule. This property can indeed become a limitation for applications requiring high concentrations or no organic cosolvent. This review first focuses on describing the acylhydrazone function, its properties, and its relevancy in dynamic combinatorial chemistry. Then it details the synthesis strategies (molecular design, cosolvent, reaction conditions) reported in the literature to ensure a sufficient solubilization of both single‐bond and multiple‐bond acylhydrazone (macro)molecules, together with their various applications. [ABSTRACT FROM AUTHOR]

Dynamic combinatorial chemistry is a method widely used for generating responsive libraries of compounds, with applications ranging from chemical biology to materials science. It relies on dynamic covalent bonds that are able to form in a reversible manner in mild conditions, and therefore requires the discovery of new types of these bonds in order to progress. Amides, due to their high stability, have been scarcely used in this field and typically require an external catalyst or harsh conditions for exchange. Compounds able to undergo uncatalysed transamidation at room temperature are still rare exceptions. In this work, we describe reversible amide formation and transamidation in a class of compounds known as maleamic acids. Due to the presence of a carboxylic acid in β‐position, these compounds are in equilibrium with their anhydride and amine precursors in organic solvents at room temperature. First, we show that this equilibrium is responsive to external stimuli: by alternating the additions of a Brønsted acid and a base, we can switch between amide and anhydride several times without side‐reactions. Next, we prove that this equilibrium provides a pathway for reversible transamidation without any added catalyst, leading to thermodynamic distributions of amides at room temperature. Lastly, we use different preparation conditions and concentrations of Brønsted acid to access different library distributions, easily controlling the transition between kinetic and thermodynamic regimes. Our results show that maleamic acids can undergo transamidation in mild conditions in a reversible and tunable way, establishing them as a new addition to the toolbox of dynamic combinatorial chemistry. [ABSTRACT FROM AUTHOR]

Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur‐based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs. [ABSTRACT FROM AUTHOR]

An efficient strategy for the synthesis of large libraries of conformationally defined peptides is reported, using dynamic combinatorial chemistry as a tool to graft amino acid side chains on a well‐ordered 3D (3‐dimension) peptide backbone. Combining rationally designed scaffolds with combinatorial side chains selection represents an alternative method to access peptide libraries for structures that are not genetically encodable. This method would allow a breakthrough for the discovery of protein mimetic for unconventional targets for which little is known. [ABSTRACT FROM AUTHOR]

Among the key characteristics of living systems are their ability to self‐replicate and the fact that they exist in an open system away from equilibrium. Herein, we show how the outcome of the competition between two self‐replicators, differing in size and building block composition, is different depending on whether the experiments are conducted in a closed vial or in an open and out‐of‐equilibrium replication–destruction regime. In the closed system, the slower replicator eventually prevails over the faster competitor. In a replication‐destruction regime, implemented through a flow system, the outcome of the competition is reversed and the faster replicator dominates. The interpretation of the experimental observations is supported by a mass‐action‐kinetics model. These results represent one of the few experimental manifestations of selection among competing self‐replicators based on dynamic kinetic stability and pave the way towards Darwinian evolution of abiotic systems. [ABSTRACT FROM AUTHOR]

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).

Dyn[n]arenes are the strict polydisulfide‐based analogues of pillar[n]arenes. Although less famous than their static homologues, these dynamic cavitands possess unique (stereo)chemical features. The disulfide bridge between monomeric units not only provides these architectures with constitutional lability but is also an additional stereogenic element. As a result, the covalent assembling process can be guided by supramolecular interactions with or without a targeted partner, enabling to decipher supramolecular at work from the synthetic stage. Not only can the size and functions be chosen on demand, but the stereochemical features can be precisely controlled by careful choice on the assembling conditions. Eventually, deciphering the interactions at work during self‐assembly opens the way toward innovative applications such as biomolecules sensing. This account describes the synergistic interplay between covalent and noncovalent bounds found in dyn[n]arenes. [ABSTRACT FROM AUTHOR]

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.

A conceptual approach for the synthesis of quasi‐heteroleptic complexes with properly endo‐functionalized cages as ligands is presented. The cage ligand reported here is of a covalent organic nature, it has been synthesized via a dynamic combinatorial chemistry approach, making use of a masked amine. Inspired by enzymatic active sites, the described system bears one carboxylate and two imidazole moieties as independent ligating units through which it is able to coordinate to transition metals. Analysis of the iron(II) complex in solution and the solid state validates the structure and shows that no undesired but commonly observed dimerization process takes place. The solid‐state structure shows a five‐coordinate metal center with the carboxylate bidentately bound to iron, which makes Fe@2 an unprecedentedly detailed structural model complex for this kind of non‐heme iron oxygenases. As, as confirmed by the crystal structure, sufficient space for other organic ligands is available, the biologically relevant ligand α‐ketoglutarate is implemented. We observe biomimetic reaction behavior towards dioxygen that opens studies investigating Fe@2 as a functional model complex. [ABSTRACT FROM AUTHOR]

Nature segregates fundamental tasks such as information storage/transmission and catalysis between two different compound classes (e.g. polynucleotides for replication and folded polyamides for catalysis). This division of labor is likely a product of evolution, raising the question of how simpler systems in which replicators and folded macromolecules co‐exist may emerge in the transition from chemistry to biology. In synthetic systems, achieving co‐existence of replicators and foldamers in a single molecular network remains an unsolved problem. Previous work on dynamic molecular networks has given rise to either self‐replicating fibers or well‐defined foldamer structures (or completely un‐sorted complex systems). We report a system in which two cross‐reactive dithiol (nucleobase‐ and peptide‐based) building blocks self‐sort into a replicator fiber and foldamer that both emerge spontaneously and co‐exist. The self‐sorting behavior remains prevalent across different building block ratios as two phases of emergence occur: replicator growth followed by foldamer formation. This is attributed to the autocatalytic formation of the replicator fiber, followed by enrichment of the system in the remaining building block, which is subsequently incorporated into a foldamer. [ABSTRACT FROM AUTHOR]

Molecular self‐assembly has been widely used to develop nanocarriers for drug delivery. However, most of them have unsatisfactory drug loading capacity (DLC) and the dilemma between stimuli‐responsiveness and stability, stagnating their translational process. Herein, we overcame these drawbacks using dynamic combinatorial chemistry. A carrier molecule was spontaneously and quantitatively synthesized, aided by co‐self‐assembly with a template molecule and an anti‐cancer drug doxorubicin (DOX) from a dynamic combinatorial library that was operated by disulfide exchange under thermodynamic control. The highly selective synthesis guaranteed a stable yet pH‐ and redox‐ responsive nanocarrier with a maximized DLC of 40.1 % and an enhanced drug potency to fight DOX resistance in vitro and in vivo. Our findings suggested that harnessing the interplay between synthesis and self‐assembly in complex chemical systems could yield functional nanomaterials for advanced applications. [ABSTRACT FROM AUTHOR]

G-quadruplexes (G4s) are guanine rich and i-motifs are cytosine rich non-canonical four-stranded DNA secondary structures present throughout the genome. Their presence in important regulatory regions of the genome marks their significance in biology. This perspective discusses the importance of both G-quadruplex and i-motif structures and highlights their discovery, structural uniqueness, prevalence, and role in the biological system. Herein, we discuss the ligands developed in our laboratory that target G-quadruplexes and i-motifs and modulate gene expression in cancer cells. We also shed light on some recent techniques developed by us to simplify the synthesis and screening of G4 and i-motif specific ligands and their importance in anti-cancer therapeutics. Synopsis: G-quadruplexes and i-motifs are non-canonical DNA secondary structures prevalent in the telomeric region as well as in the regulatory regions of proto-oncogenes. We have described selective targeting of DNA secondary structures by small molecules and their functional role in the regulation of gene expression. [ABSTRACT FROM AUTHOR]

Dynamic covalent chemistry combines in a single step the screening and synthesis of ligands for biomolecular recognition. In order to do that, a chemical entity is used as template within a dynamic combinatorial library of interconverting species, so that the stronger binders are amplified due to the efficient interaction with the target. Here we employed whole A549 living cells as template in a dynamic mixture of imines, for which amplification reflects the efficient and selective interaction with the corresponding extracellular matrix. The amplified polyamine showed strong interaction with the A549 extracellular matrix in on‐cell NMR experiments, while combination of NMR, SPR, and molecular dynamics simulations in model systems provided insights on the molecular recognition event. Notably, our work pioneers the use of whole living cells in dynamic combinatorial chemistry, which paves the way towards the discovery of new bioactive molecules in a more biorelevant environment. [ABSTRACT FROM AUTHOR]

Dynamic combinatorial chemistry (DCC) is a powerful approach for creating complex chemical systems, giving access to the studies of complexity and exploration of functionality in synthetic systems. However, compared with more advanced living systems, the man‐made chemical systems are still less functional, due to their limited complexity and insufficient kinetic control. Here we start by introducing strategies to enrich the complexity of dynamic combinatorial libraries (DCLs) for exploiting unexpected functions by increasing the species of building blocks and/or templates used. Then, we discuss how dynamic isomerization of photo‐switchable molecules help DCLs increase and alter the systemic complexity in‐situ. Multi‐phase DCLs will also be reviewed to thrive complexity and functionality across the interfaces. Finally, there will be a summary and outlook about remote kinetic control in DCLs that are realized by applying exogenous physical transduction signals of stress, light, heat and ultrasound. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this study, we report the generation of a polymer based dynamic combinatorial library (DCL) using aldehyde-functionalized linear poly(glycidol) and hydrazide derivatives as initial building blocks. In combination with tetrameric acetylcholinesterase (AChE), a certain type of amplified acylhydrazone side chain is identified and further used for the synthesis of a multivalent AChE inhibitor. The cytotoxicity and inhibition properties of the multivalent inhibitor are evaluated, and the results indicate superior bioactivity compared to the commercial reference Edrophonium chloride. [ABSTRACT FROM AUTHOR]

Modern drug discovery is mainly based on the de novo synthesis of a large number of compounds with a diversity of chemical functionalities. Though the introduction of combinatorial chemistry enabled the preparation of large libraries of compounds from so-called building blocks, the problem of successfully identifying leads remains. The introduction of a dynamic combinatorial chemistry method served as a step forward due to the involvement of biological macromolecular targets (receptors) in the synthesis of high affinity products. The major breakthrough was a synthetic method in which building blocks are irreversibly combined due to the presence of a receptor. Here we present various receptor-based combinatorial chemistry approaches. Huisgen’s cycloaddition (1,3-dipolar cycloaddition of azides and alkynes) forms stabile 1,2,3-triazoles with very high receptor affinity that can reach femtomolar levels, as the case with acetylcholinesterase inhibitors shows. Huisgen’s cycloaddition can be applied to various receptors including acetylcholinesterase, acetylcholine binding protein, carbonic anhydrase-II, serine/threonine-protein kinase and minor groove of DNA.

Graphical abstract Abstract Generation and screening of oxime libraries by competitive MS Binding Assays represents a powerful tool for the identification of new compounds, with affinity to mGAT1, the most abundant plasma membrane bound GABA transporter in the CNS. By screening a guvacine derived oxime library, new potent inhibitors of mGAT1 had been revealed. In the present study, oxime libraries generated by reaction of a large excess of a rac -nipecotic acid derivative displaying a hydroxylamine functionality in which various aldehydes under suitable conditions, were examined for new potent inhibitors of mGAT1. The p K i values obtained of the best hits were compared with those of related compounds displaying a guvacine instead of a nipecotic acid subunit as hydrophilic moiety. Amongst the new compounds one of the most affine ligands of mGAT1 known so far (p K i = 8.55 ± 0.04) was found. [ABSTRACT FROM AUTHOR]

Dynamic combinatorial chemistry (DCC) is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80%) was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue.

The kinetic and thermodynamic selectivity of acylhydrazone formation in dynamic combinatorial libraries (DCL) is described. Competition reactions were generated from hydrazides: isoniazid, 4-nitro-benzohydrazide, 4-dimethylamino-benzohydrazide, and nicotinic hydrazide; as well as the aldehyde derivatives: benzaldehyde and 2-pyridine-carboxaldehyde. The obtained species and the distribution of the DCLs were monitored by 1H-NMR spectroscopy finding that those acylhydrazones containing the 4-dimethylamino-benzohydrazide are both the kinetic and thermodynamic product of their respective libraries. Configurational and coordination dynamics for some of these libraries were also investigated. The obtained results allowed the study of the redistribution of components and the amplification of one or more products using light and metal ions as physical and chemical templates, respectively.

This review highlights the author’s indirect path to research at the interface of supramolecular chemistry and chemical biology.

We report a new class of building blocks for Dynamic Combinatorial Chemistry (DCC) based on the pyrroloindole scaffold. The attachment of l-cysteine on the α, α′ positions of the core makes the molecule suitable for disulfide exchange in aqueous dynamic combinatorial libraries (DCLs). The synthesis of the core follows a modified version of the Knoevenagel–Hemetsberger approach. The new building block (l-PI) is fluorescent (Φ = 48%) and relatively stable towards thermal and photodegradation. The chirality of the cysteine is transferred to the electron-rich pyrroloindole core. Homo- and heterochiral DCLs of l-PI with electron-deficient l- and d-naphthalenediimide (NDI) lead to similar library distributions regardless of the enantiomer used. When no salt is present, the major component is a dimer, while dimers and tetramers are obtained at increased ionic strength.

Target-directed dynamic combinatorial chemistry is a very attractive strategy for the discovery of bioactive peptides. However, its application has not yet been demonstrated, presumably due to analytical challenges that arise from the diversity of a peptide library with combinatorial side-chains. We previously reported an efficient method to generate, under biocompatible conditions, large dynamic libraries of cyclic peptides grafted with amino acid's side-chains, by thiol-to-thioester exchanges. In this work, we present analytical tools to easily characterize such libraries by HPLC and mass spectrometry, and in particular to simplify the isomers' distinction requiring sequencing by MS/MS fragmentations. After structural optimization, the cyclic scaffold exhibits a UV-tag, absorbing at 415 nm, and an ornithine residue which favors the regioselective ring-opening and simultaneous MS/MS fragmentation, in the gas-phase., (© 2023 The Authors. ChemBioChem published by Wiley-VCH GmbH.)

Dynamic combinatorial chemistry (DCC) has repeatedly proven to be an effective approach to generate directed ligand libraries for macromolecular targets. In the absence of an external stimulus, a dynamic library forms from reversibly reacting building blocks and reaches a stable thermodynamic equilibrium. However, upon addition of a macromolecular host which can bind and stabilize certain components of the library, the equilibrium composition changes and induces an evolution‐like selection and enrichment of high‐affinity ligands. A valuable application of this so‐called target‐directed DCC (tdDCC) is the identification of potent ligands for pharmacologically relevant targets. Over time, the term tdDCC has been applied to describe a number of different experimental setups, leading to some ambiguity concerning its definition. This article systematically classifies known procedures for tdDCC and related approaches, with a special focus on the methods used for analysis and evaluation of experiments. Dynamic combinatorial chemistry (DCC) describes the generation of adaptive compound libraries from reversibly reacting building blocks. Upon addition of a target protein, high‐affinity constituents are amplified, making the approach ideally suited for drug discovery. Here, various DCC setups are systematically classified and differentiated from related methodologies, yielding a thorough overview of the potential of DCC. [ABSTRACT FROM AUTHOR]

Abstract: Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self‐assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic “thermal tag” with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily‐selective probes against two clinically important epigenetic enzymes: FTO (7; IC50=2.6 μ m) and ALKBH3 (8; IC50=3.7 μ m). To date, this is the first report of a subfamily‐selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest. [ABSTRACT FROM AUTHOR]

Abstract: The study of the interplay between different self‐replicating molecules constitutes an important new phase in the synthesis of life and in unravelling the origin of life. Here we show how existing replicators can direct the nature of a newly formed replicator. Starting from the same building block, 6‐ring replicators formed when the mixture was exposed to pre‐existing 6‐membered replicators, while pre‐formed 8‐membered replicators funneled the building block into 8‐ring replicators. Not only ring size, but also the mode of assembly of the rings into stacks was inherited from the pre‐existing replicators. These results show that the nature of self‐replicating molecules can be strongly influenced by the interplay between different self‐replicators, overriding preferences innate to the structure of the building block. [ABSTRACT FROM AUTHOR]