Diastereoselective amplification of an induced-fit receptor from a dynamic combinatorial library

Social Self-Sorting of Quasi-Racemates: A Unique Approach for Dual-Pore Molecular Crystals

Despite recent advances in porous organic molecular crystals, the engineering of dual-pore systems within the intermolecular voids remains a significant challenge. In this study, we have achieved the crystallization-induced social self-sorting of "quasi-racemic" dialdehydes into a macrocyclic imine. X-ray crystallographic analysis unambiguously characterizes the resulting structure as incorporating two quasi-racemate pairs with four diamine molecules. Notably, different alkyl substituents on the quasi-racemates afford two types of one-dimensional pores within the macrocyclic imine crystal. The different adsorption properties of these pores were substantiated through adsorption experiments. An intriguing helical arrangement of guest molecules was observed within one of the pores. This study provides pioneering evidence that the social self-sorting of quasi-racemates offers a new methodology for creating dual-functional supramolecular materials.

Self-assembly of achiral building blocks into chiral cyclophanes using non-directional interactions

The diastereoselective assembly of achiral constituents through a single spontaneous process into complex covalent architectures bearing multiple stereogenic elements still remains a challenge for synthetic chemists. Here, we show that such an extreme level of control can be achieved by implementing stereo-electronic information on synthetic organic building blocks and templates and that non-directional interactions (i.e., electrostatic and steric interactions) can transfer this information to deliver, after self-assembly, high-molecular weight macrocyclic species carrying up to 16 stereogenic elements. Beyond the field of supramolecular chemistry, this proof of concept should stimulate the on-demand production of highly structured polyfunctional architectures.

Heterochiral Diastereomer-Discriminative Diphanes That Form Hierarchical Superstructures with Nonlinear Optical Properties

In order to study the emergence of homochirality during complex molecular systems, most works mainly concentrated on the resolution of a pair of enantiomers. However, the preference of homochiral over heterochiral isomers has been overlooked, with very limited examples focusing only on noncovalent interactions. We herein report on diastereomeric discrimination of twin-cavity cages (denoted as diphanes) against heterochiral tris-(2-aminopropyl)amine (TRPN) bearing triple stereocenters. This diastereomeric selectivity results from distinct spatial orientation of reactive secondary amines on TRPN. Homochiral TRPNs with all reactive moieties rotating in the same way facilitate the formation of homochiral and achiral meso diphanes with low strain energy, while heterochiral TRPNs with uneven orientation of secondary amines preclude the formation of cage-like entity, since the virtual diphanes exhibit considerably high strain. Moreover, homochiral diphanes self-assemble into an acentric superstructure composed of single-handed helices, which exhibits interesting nonlinear optical behavior. Such a property is a unique occurrence for organic cages, which thus showcases their potential to spawn novel materials with interesting properties and functions.

Recent trends in organic cage synthesis: push towards water-soluble organic cages

Research on organic cages has blossomed over the past few years into a mature field of study which can contribute to solving some of the challenging problems. In this review we aim to showcase the recent trends in synthesis of organic cages including a brief discussion on their use in catalysis, gas sorption, host-guest chemistry and energy transfer. Among the organic cages, water-soluble analogues are a special class of compounds which have gained renewed attention in recent times. Due to their advantage of being compatible with water, such cages have the potential of showing biomimetic activities and can find use in drug delivery and also as hosts for catalysis in aqueous medium. Hence, the synthetic strategies for the formation of water-soluble organic cages shall be discussed along with their potential applications.

Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix

The CW domain binds to histone tail modifications found in different protein families involved in epigenetic regulation and chromatin remodeling. CW domains recognize the methylation state of the fourth lysine on histone 3 and could, therefore, be viewed as a reader of epigenetic information. The specificity toward different methylation states such as me1, me2, or me3 depends on the particular CW subtype. For example, the CW domain of ASHH2 methyltransferase binds preferentially to H3K4me1, and MORC3 binds to both H3K4me2 and me3 modifications, while ZCWPW1 is more specific to H3K4me3. The structural basis for these preferential bindings is not well understood, and recent research suggests that a more complete picture will emerge if dynamical and energetic assessments are included in the analysis of interactions. This study uses fold assessment by NMR in combination with mutagenesis, ITC affinity measurements, and thermal denaturation studies to investigate possible couplings between ASHH2 CW selectivity toward H3K4me1 and the stabilization of the domain and loops implicated in binding. The key elements of the binding site—the two tryptophans and the α1-helix form and maintain the binding pocket— were perturbed by mutagenesis and investigated. Results show that the α1-helix maintains the overall stability of the fold via the I915 and L919 residues and that the correct binding consolidates the loops designated as η1 and η3, as well as the C-terminal. This consolidation is incomplete for H3K4me3 binding to CW, which experiences a decrease in overall thermal stability on binding. Loop mutations not directly involved in the binding site, nonetheless, affect the equilibrium positions of the key residues.

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.

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).

Dynamic Covalent Chemistry as a Facile Route to Unusual Main-Group Thiolate Assemblies and Disulfide Hoops and Cages

Dynamic Covalent Chemistry (DCC) - combining the robustness of covalent bonds with the self-correcting nature of supramolecular chemistry - facilitates the modular synthesis of complex molecular assemblies in high yields. Although numerous reactions form covalent bonds, only a small set of chemical transformations affect covalent bond formation reversibly under suitable conditions for DCC. Further progress in this area still requires the identification of dynamic motifs and greater insights into their reversibility. We have fruitfully employed DCC of both thiolate coordination to main-group elements and disulfide formation for the facile self-assembly of: (1) metal/metalloid-thiolate assemblies, and (2) purely organic cyclic and caged disulfides, thioethers, and even hydrocarbons, many of which have remained elusive by traditional stepwise synthesis yet form readily through our methods. In this Minireview, we highlight the approaches to prepare these unusual compounds and the factors inducing structural transformations or favoring the formation of certain products over others, given a set of external stimuli or reaction conditions.

Guest-mediated chirality transfer in the host–guest complexes of an atropisomeric perylene bisimide cyclophane host

Chirality transfer upon preferential binding of homochiral guests to one stereoisomer of a conformationally equilibrated atropisomeric cyclophane is reported.

Endo- and Exocyclic Coordination of a 20-Membered N2O2S2-Macrocycle and Cascade Complexation of a 40-Membered N4O4S4-Macrocycle

A 20-membered N₂O₂S₂-macrocycle (L¹) and a 40-membered N₄O₄S₄-macrocycle (L²) were employed as a [1:1] and a [2:2] cyclization product, respectively, for the preparation of diverse types of supramolecular complexes including a cascade complex. Six complexes (1-6) of the smaller macrocycle L¹ including discrete to continuous forms, mono- to heteronuclear, and endo- to exo- and endo/exocoordination were prepared and their coordination modes were discussed systemically. First, the reaction of L¹ with CuI in the presence of trifluoroacetic acid afforded an exocyclic 1-D coordination polymer {[(μ₄-Cu₄I₄)(HL¹)₂](CF₃COO)₂} _n (1). Meanwhile, the reaction of L¹ with Cu(ClO₄)₂·6H₂O afforded a typical endocyclic mononuclear complex [Cu^II(L¹)](ClO₄)₂·H₂O (2). In the reactions of L¹ with CdX₂ (X = Br and I), isostructural sandwich-type complexes [Cd(L¹)₂Br₂] (3) and [Cd(L¹)₂I₂] (4) were isolated. The treatment of L¹ with Hg(ClO₄)₂ also afforded a sandwich-type complex [Hg(L¹)₂](ClO₄)₂ (5). One-pot reaction of L¹ with a mixture of HgI₂ and CdI₂ afforded a dumbbell-type heteronuclear complex {[Cd(L¹)]₂(μ-Hg₂I₆)}[Hg₂I₆] (6), in which the Cd(II) ion occupies the macrocyclic cavity. Further, such two endocyclic Cd(II) complex units are bridged by a square-type (μ-Hg₂I₆)^2- cluster remaining another same cluster separately. The comparative NMR data exhibited a higher affinity of Cd(II) over Hg(II) toward L¹, in the parallel to the situation occurred in the solid state. Meanwhile, complexations of the extra-large macrocycle L² is more challenging to afford some interesting dimercury(II) coordination products including a cascade complex. In solution, the dimercury(II) perchlorato complex of L² as a metalloligand shows a preferential binding of dabco (1,4-diazabicyclo[2,2,2]octane), but its dimercury(II) iodo complex has a much smaller affinity for dabco. In order to explain these results, the solid dimercury(II) complexes with different anions [Hg₂(L²)X₄] (7: X = I, 8: X = ClO₄) were prepared and characterized. Further, the dimercury(II) perchlorato complex 8 reacts with dabco to forms a cascade complex [Hg₂(L²)(μ-dabco)(ClO₄)₂](ClO₄)₂·2DMF·2ether (9), exhibiting its formation being metal-driven and coordinated anion-regulated. The observed cascade complexation both in solution and solid states is an example of the adaptive guest binding.

One-step Access to Resorcinsalens-Solvent-Dependent Synthesis, Tautomerism, Self-sorting and Supramolecular Architectures of Chiral Polyimine Analogues of Resorcinarene

Substituted 2,4- and 4,6-dihydroxyisophthalaldehydes were condensed with optically pure and racemic trans-1,2-diaminocyclohexane to form resorcinarene-like polyimine macrocycles (resorcinsalens), the structure and stoichiometry of which were controlled by the choice of the reaction medium. Particularly, the cyclocondensation reactions were driven by the solubility, tautomerization, or by social self-sorting. The resorcinsalens crystallized as inclusion compounds, in which the guest molecules were situated either in channels or in voids. In the highly hydrated crystals of one of the [2+2] macrocycles and chloroform-solvated crystals of a [4+4] product the channels were interconnected, as in zeolites, enabling possible migration of loosely bound solvent molecules in three dimensions. The association mode depended on the structural modification of the host molecule and the type of included solvent molecule(s).

Making a Right or Left Choice: Chiral Self-Sorting as a Tool for the Formation of Discrete Complex Structures

This review discusses chiral self-sorting-the process of choosing an interaction partner with a given chirality from a complex mixture of many possible racemic partners. Chiral self-sorting (also known as chiral self-recognition or chiral self-discrimination) is fundamental for creating functional structures in nature and in the world of chemistry because interactions between molecules of the same or the opposite chirality are characterized by different interaction energies and intrinsically different resulting structures. However, due to the similarity between recognition sites of enantiomers and common conformational lability, high fidelity homochiral or heterochiral self-sorting poses a substantial challenge. Chiral self-sorting occurs among natural and synthetic molecules that leads to the amplification of discrete species. The review covers a variety of complex self-assembled structures ranging from aggregates made of natural and racemic peptides and DNA, through artificial functional receptors, macrocyles, and cages to catalytically active metal complexes and helix mimics. The examples involve a plethora of reversible interactions: electrostatic interactions, π-π stacking, hydrogen bonds, coordination bonds, and dynamic covalent bonds. A generalized view of the examples collected from different fields allows us to suggest suitable geometric models that enable a rationalization of the observed experimental preferences and establishment of the rules that can facilitate further design.

Protein-ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling

In the last three decades, protein and nucleic acid structure determination and comprehension of the mechanisms, leading to their physiological and pathological functions, have become a cornerstone of biomedical sciences. A deep understanding of the principles governing the fates of cells and tissue at the molecular level has been gained over the years, offering a solid basis for the rational design of drugs aimed at the pharmacological treatment of numerous diseases. Historically, affinity indicators (i.e. Kd and IC50/EC50) have been assumed to be valid indicators of the in vivo efficacy of a drug. However, recent studies pointed out that the kinetics of the drug-receptor binding process could be as important or even more important than affinity in determining the drug efficacy. This eventually led to a growing interest in the characterisation and prediction of the rate constants of protein-ligand association and dissociation. For instance, a drug with a longer residence time can kinetically select a given receptor over another, even if the affinity for both receptors is comparable, thus increasing its therapeutic index. Therefore, understanding the molecular features underlying binding and unbinding processes is of central interest towards the rational control of drug binding kinetics. In this review, we report the theoretical framework behind protein-ligand association and highlight the latest advances in the experimental and computational approaches exploited to investigate the binding kinetics.

Entropy-driven homochiral self-sorting of a dynamic library

The efficient homochiral self-sorting of pseudopeptidic macrocycles, observed from a simple dynamic library, is driven by entropy.

Chiral Self-Sorting of [2+3] Salicylimine Cage Compounds

An inherently chiral C₃ -symmetric triaminotribenzotriquinacene was condensed in racemic and enantiomerically pure form with a bis(salicylaldehyde) to form [2+3] salicylimine cage compounds. Investigations on the chiral self-sorting revealed that while entropy favors narcissistic self-sorting in solution, selective social self-sorting can be achieved by exploiting the difference in solubility between the homochiral and heterochiral cages. Gas sorption measurements further showed that seemingly small structural differences can have a significant impact on the surface area of microporous covalent cage compounds.

Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods

Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed.

Self-Assembly Process of Dodecanuclear Pt(II)-Linked Cyclic Hexagon

The self-assembly process of a Pt(II)-linked hexagonal macrocycle consisting of six linear dinuclear Pt(II) units and six organic ditopic bent ligands was investigated. The process was monitored by (1)H NMR, and the intermediates in the self-assembly were analyzed by the n-k analysis. It was found that a 1:2 complex of a dinuclear Pt(II) unit and an organic ditopic ligand was exclusively observed as an intermediate with a certain lifetime and that the reaction of the 1:2 complex is the rate-determining step in the supramolecular macrocycle formation. The key 1:2 complex was unambiguously characterized by (1)H and DOSY NMR and ESI-TOF mass measurement.

Introducing a static receptor to compete with a dynamic combinatorial library in template binding

Association constants can be obtained from HPLC analysis of a system comprising a dynamic combinatorial library and a static host.

Discovery of potent inhibitors of human β-tryptase from pre-equilibrated dynamic combinatorial libraries

Pre-equilibrated combinatorial libraries based on multivalent peptide acyl hydrazones were used to find potent inhibitors of β-tryptase. The best inhibitors bind to the protein surface, and inhibit β-tryptase with nanomolar affinity (K_ica. 10 nM) and high selectivity in a reversible and non-competitive way.

Pre-equilibrated dynamic combinatorial libraries based on acyl hydrazone interchange of peptide-derived hydrazides and di- and tri-aldehydes have been used to discover potent inhibitors with nanomolar affinities for β-tryptase. To identify potent inhibitors the activity of the full library containing 95 members was compared with those of sub-libraries in which individual building blocks were missing. The most active library members contain a rigid central aromatic scaffold with three cationic peptide arms. The arms of the best inhibitors also contained a tailor-made GCP oxoanion binding motif attached to a lysine side chain. The most potent tri-armed hydrazones with peptide arms GKWR or GKWK(GCP) were shown to inhibit β-tryptase (K_ica. 10–20 nM) reversibly, non-competitively and selectively (compared to related serine proteases, e.g. trypsin and chymotrypsin), most likely by binding to the protein surface, also in agreement with molecular modelling calculations. These new inhibitors are one order of magnitude more efficient than related tetravalent inhibitors obtained from previous work on a split-mix-combinatorial library and were identified with significantly less effort, demonstrating the usefulness of this approach for the identification of enzyme inhibitors in general.

Disulfide exchange: exposing supramolecular reactivity through dynamic covalent chemistry

A Tutorial Review of the subtle supramolecular interactions influencing the outcomes of equilibrating systems, focusing on the dynamic covalent chemistry (DCC) of disulfide exchange reactions, is presented. We discuss the topics of cation-π interactions (2.1), hydrophobic effects (2.2), hydrogen bonding interactions (2.3) aromatic donor-acceptor interactions (2.4), and metal-ligand interactions (2.5) in the context of dynamic disulfide chemistry.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

"Choose-a-size" approach in dynamic combinatorial chemistry: a single substrate dynamic combinatorial library of oligomacrocycles that adapts to the size and shape of carboxylates

A neutral anion binding receptor based on dipicolinic acid diamide was equipped with thiol groups in the amidic side arms. After the thiol was oxidized to disulfide groups with I2, a mixture of cyclic oligomers (a library) was obtained. The distribution of macrocycles can be controlled kinetically during the oxidation process or thermodynamically at basic conditions via disulfide bond exchange. The library proved to be very sensitive to templation with various carboxylates in DMSO. The amplification pattern reflects the structural features of the anionic template and is sensitive to changes in the template's geometry. The application of carboxylates with multiple functional groups resulted in very strong amplification of the large penta- and hexameric macrocycles. The thermodynamic parameters of some templation effects were rationalized using a simple model and confirmed using competitive NMR titration.

Evolution of dynamic combinatorial chemistry

Since its inception in the mid-1990s, dynamic combinatorial chemistry (DCC), the chemistry of complex systems under thermodynamic control, has proved valuable in identifying unexpected molecules with remarkable binding properties and in providing effective synthetic routes to complex species. Essentially, in this approach, one designs the experiment rather than the molecule. DCC has also provided us with insights into how some chemical systems respond to external stimuli. Using examples from the work of our laboratory and others, this Account shows how the concept of DCC, inspired by the evolution of living systems, has found an increasing range of applications in diverse areas and has evolved conceptually and experimentally. A dynamic combinatorial library (DCL) is a thermodynamically controlled mixture of interconverting species that can respond to various stimuli. The Cambridge version of dynamic combinatorial chemistry was initially inspired by the mammalian immune system and was conceived as a way to create and identify new unpredictable receptors. For example, an added template can select and stabilize a strongly binding member of the library which is then amplified at the expense of the unsuccessful library members, minimizing the free energy of the system. But researchers have exploited DCC in a variety of other ways: over the past two decades, this technique has contributed to the evolution of chemistry and to applications in the diverse fields of catalysis, fragrance release, and responsive materials. Among these applications, researchers have built intricate and well-defined architectures such as catenanes or hydrogen-bonded nanotubes, using the ability of complex chemical systems to reach a high level of organization. In addition, DCC has proved a powerful tool for the study of complex molecular networks and systems. The use of DCC is improving our understanding of chemical and biological systems. The study of folding or self-replicating macrocycles in DCLs has served as a model for appreciating how complex organisations such as life can emerge from a pool of simple chemicals. Today, DCC is no longer restricted to thermodynamic control, and new systems have recently appeared in which kinetic and thermodynamic control coexist. Expanding the realm of DCC to unexplored and promising new territories, these hybrid systems show that the concept of dynamic combinatorial chemistry continues to evolve.

Dynamic molecular networks: from synthetic receptors to self-replicators

Dynamic combinatorial libraries (DCLs) are molecular networks in which the network members exchange building blocks. The resulting product distribution is initially under thermodynamic control. Addition of a guest or template molecule tends to shift the equilibrium towards compounds that are receptors for the guest. This Account gives an overview of our work in this area. We have demonstrated the template-induced amplification of synthetic receptors, which has given rise to several high-affinity binders for cationic and anionic guests in highly competitive aqueous solution. The dynamic combinatorial approach allows for the identification of new receptors unlikely to be obtained through rational design. Receptor discovery is possible and more efficient in larger libraries. The dynamic combinatorial approach has the attractive characteristic of revealing interesting structures, such as catenanes, even when they are not specifically targeted. Using a transition-state analogue as a guest we can identify receptors with catalytic activity. Although DCLs were initially used with the reductionistic view of identifying new synthetic receptors or catalysts, it is becoming increasingly apparent that DCLs are also of interest in their own right. We performed detailed computational studies of the effect of templates on the product distributions of DCLs using DCLSim software. Template effects can be rationalized by considering the entire network: the system tends to maximize global host-guest binding energy. A data-fitting analysis of the response of the global position of the DCLs to the addition of the template using DCLFit software allowed us to disentangle individual host-guest binding constants. This powerful procedure eliminates the need for isolation and purification of the various individual receptors. Furthermore, local network binding events tend to propagate through the entire network and may be harnessed for transmitting and processing of information. We demonstrated this possibility in silico through a simple dynamic molecular network that can perform AND logic with input and output in the form of molecules. Not only are dynamic molecular networks responsive to externally added templates, but they also adjust to internal template effects, giving rise to self-replication. Recently we have started to explore scenarios where library members recognize copies of themselves, resulting in a self-assembly process that drives the synthesis of the very molecules that self-assemble. We have developed a system that shows unprecedented mechanosensitive self-replication behavior: depending on whether the solution is shaken, stirred or not agitated, we have obtained a hexameric replicator, a heptameric replicator or no replication, respectively. We rationalize this behavior through a mechanism in which replication is promoted by mechanically-induced fragmentation of self-assembled replicator fibers. These results represent a new mode of self-replication in which mechanical energy liberates replicators from a self-inhibited state. These systems may also be viewed as self-synthesizing, self-assembling materials. These materials can be captured photochemically, converting a free-flowing fiber solution into a hydrogel through photo-induced homolytic disulfide exchange.