Supramolecular Chemistry Targeting Proteins

Supramolecular Enhancement of a Natural 14-3-3 Protein Ligand

Rational design of protein-protein interaction (PPI) inhibitors is challenging. Connecting a general supramolecular protein binder with a specific peptidic ligand provides a novel conceptual approach. Thus, lysine-specific molecular tweezers were conjugated to a peptide-based 14-3-3 ligand and produced a strong PPI inhibitor with 100-fold elevated protein affinity. X-ray crystal structure elucidation of this supramolecular directed assembly provides unique molecular insight into the binding mode and fully aligns with Molecular Dynamics (MD) simulations. This new supramolecular chemical biology concept opens the path to novel chemical tools for studying PPIs.

A medium-firm drug-candidate library of cryptand-like structures on T7 phage: design and selection of a strong binder for Hsp90

We designed and synthesized a medium-firm drug-candidate library of cryptand-like structures possessing a randomized peptide linker on the bacteriophage T7. From the macrocyclic library with a 109 diversity, we obtained a binder toward a cancer-related protein (Hsp90) with an antibody-like strong affinity (KD = 62 nM) and the binding was driven by the enthalpy. The selected supramolecular ligand inhibited Hsp90 activity by site-specific binding outside of the well-known ATP-binding pocket on the N-terminal domain (NTD).

Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages

The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.

Sequence-selective recognition of cationic amphipathic tripeptides with similar structures in aqueous solutions by cucurbit[7]uril

Sequence-selective recognition of cationic amphipathic peptides by synthetic receptors is significant to biological applications, but it is still a great challenging task. Here we first study the binding characteristics of receptor cucurbit[7]uril (CB[7]) to the smallest aromatic tripeptides X1GG (X1 = tryptophan (W), phenylalanine (F), and tyrosine (Y)) and basic tripeptides X2GG (X2 = arginine (R), lysine (K), and histidine (H)) by molecular dynamics simulations. The study indicates that the sidechains of aromatic X1 residues can be encapsulated into the CB[7] cavity, while the sidechains of basic X2 residues prefer to locate at the CB[7] portal. Based on that, we consider hydrophobic aromatic residues as the N-terminus, the smallest glycine (G) as the 2nd-residue and basic residues as the C-terminus, and design nine tripeptides X1GX2 (X1 = F, Y, W and X2 = H, K, R). We found that there is a great influence of the C-terminal basic residue of X1GX2 on binding with CB[7] due to the introduction of a new binding site between CB[7] and the sidechain of the C-terminal residue. Interestingly, CB[7] can differentiate WGR and WGK with similar structures efficiently because of their eight orders of magnitude difference in the association constant (Ka). Besides, for WGR, YGR, and YGK with a nanomolar binding affinity (Ka > 109 M-1), on reversing the sequence order of the 2nd-residue and 3rd-residue, their Ka reduces by about at least 1000-fold, implying the sequence dependence of CB[7] on recognizing these tripeptides. These results predict the potential applications of CB[7] in recognizing cationic amphipathic peptides.

Toward Light-Controlled Supramolecular Peptide Dimerization

The selective photodeprotection of the NVoc-modified FGG tripeptide yields the transformation of its 1:1 receptor-ligand complex with cucurbit[8]uril into a homoternary FGG₂@CB8 assembly. The resulting light-induced dimerization of the model peptide provides a tool for the implementation of stimuli-responsive supramolecular chemistry in biologically relevant contexts.

Cucurbit[8]uril facilitated Michael addition for regioselective cysteine modification

Utilizing the interactions between tryptophan, methyl viologen and cucurbit[8]uril, we found that the distance between the targeted peptides/protein and the reactive peptide was shortened, which facilitated the Michael addition reaction between cysteine and dehydroalanine. The highest acceleration was observed on cysteines with suitable pKa and spatial location to tryptophan, suggesting that our system can be used for regioselective cysteine modification.

Redefining Protein Interfaces within Protein Single Crystals with DNA

Proteins are exquisite nanoscale building blocks: molecularly pure, chemically addressable, and inherently selective for their evolved function. The organization of proteins into single crystals with high positional, orientational, and translational order results in materials where the location of every atom can be known. However, controlling the organization of proteins is challenging due to the myriad interactions that define protein interfaces within native single crystals. Recently, we discovered that introducing a single DNA-DNA interaction between protein surfaces leads to changes in the packing of proteins within single crystals and the protein-protein interactions (PPIs) that arise. However, modifying specific PPIs to effect deliberate changes to protein packing is an unmet challenge. In this work, we hypothesized that disrupting and replacing a highly conserved PPI with a DNA-DNA interaction would enable protein packing to be modulated by exploiting the programmability of the introduced oligonucleotides. Using concanavalin A (ConA) as a model protein, we circumvent potentially deleterious mutagenesis and exploit the selective binding of ConA toward mannose to noncovalently attach DNA to the protein surface. We show that DNA association eliminates the major PPI responsible for crystallization of native ConA, thereby allowing subtle changes to DNA design (length, complementarity, and attachment position) to program distinct changes to ConA packing, including the realization of three novel crystal structures and the deliberate expansion of ConA packing along a single crystallographic axis. These findings significantly enhance our understanding of how DNA can supersede native PPIs to program protein packing within ordered materials.

Sequence-Selective Protection of Peptides from Proteolysis

Proteolysis of proteins and peptides is involved in the infection of cells by enveloped viruses and also in the invasion and spread of cancer cells. Shutting down broad‐specificity proteases, however, is problematic because normal functions by these proteases will be affected. Herein, nanoparticle receptors were prepared from molecular imprinting for complex biological peptides. Their strong and selective binding enabled them to protect their targeted sequences from proteolysis in aqueous solution at stoichiometric amounts. Generality of the method was demonstrated by the protection of hydrophobic and hydrophilic peptides from different proteases, selective protection of a segment of a long peptide, and selective protection of a targeted peptide in a mixture. Most interestingly, two receptors targeting different parts of a long peptide could work in cooperation to protect the overall sequence, highlighting the versatility of the method.

A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition

Regulation of specific protein function is of great importance for both research and therapeutic development. Many small or large molecules have been developed to control specific protein function, but there is a lack of a universal approach to regulate the function of any given protein. We report a general host-guest molecular recognition approach involving modification of the protein functional surfaces with genetically encoded unnatural amino acids bearing guest side chains that can be specifically recognized by cucurbit[7]uril. Using two enzymes and a cytokine as models, we showed that the activity of proteins bearing unnatural amino acid could be turned off by host molecule binding, which blocked its functional binding surface. Protein activity can be switched back by treatment with a competitive guest molecule. Our approach provides a general tool for reversibly regulating protein function through molecular recognition and can be expected to be valuable for studying protein functions.

Supramolecular Interaction of Molecular Cage and β-Galactosidase: Application in Enzymatic Inhibition, Drug Delivery and Antimicrobial Activity

Enzyme inhibitors play a crucial role in diagnosis of a wide spectrum of diseases related to bacterial infections. We report here the effect of a water-soluble self-assembled Pd^II ₈ molecular cage towards β-galactosidase enzyme activity. The molecular cage is composed of a tetrapyridyl donor (L) and cis-[(en)Pd(NO₃ )₂ ] (en=ethane-1,2-diamine) acceptor and it has a hydrophobic internal cavity. We have observed that the acceptor moiety mainly possesses the ability to inactivate the β-galactosidase enzyme activity. Kinetic investigation revealed the mixed mode of inhibition. This inhibition strategy was extended to control the growth of methicillin-resistant Staphylococcus aureus. The internalization of the Pd(II) cage inside the bacteria was confirmed when bacterial solutions were incubated with curcumin loaded cage. The intrinsic green fluorescence of curcumin made the bacteria glow when put under an optical microscope. Furthermore, this curcumin loaded molecular cage shows an enhanced antibacterial activity. Thus, Pd^II ₈ molecular cage is quite attractive due to its dual role as enzyme inhibitor and drug carrier.

Understanding the binding properties of phosphorylated glycoluril-derived molecular tweezers and selective nanomolar binding of natural polyamines in aqueous solution

A modular synthetic platform for the construction of flexible glycoluril-derived molecular tweezers was developed. The binding properties of four exemplary supramolecular hosts obtained via this approach towards 16 organic amines were investigated by means of 1H NMR titration. In this work, we compare the Ka values obtained this way with those of three structurally related molecular tweezers and provide a computational approach towards an explanation of the observed behavior of those novel hosts. The results showcase that certain structural modifications lead to very potent and selective binders of natural polyamines, with observed binding of spermine below 10 nM.

Pillararene-based self-assemblies for electrochemical biosensors

The ingenious design and synthesis of novel macrocycles bring out renewed vigor of supramolecular chemistry in the past decade. As an intriguing class of macrocycles, pillararene and pillararene-based functional materials that are constructed through the noncovalent bond self-assembly approach have been undergoing a rapid growth, benefiting from their unique structures and physiochemical properties. This review elaborates recent significant advances of electrochemical studies based on pillararene systems. Fundamental electrochemical behavior of pillar[n]arene[m]quinone and pillararene-based self-assemblies as well as their applications in electrochemical biosensors are highlighted. In addition, the advantages and functions of pillararene self-assembly systems resulted from the unique molecular architectures are analyzed. Finally, current challenges and future development tendency in this burgeoning field are discussed from the viewpoint of both fundamental research and applications. Overall, this review not only manifests the main development vein of pillararene-based electrochemical systems, but also conquers a solid foundation for their further bioelectrochemical applications.

Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers

Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.

Reversible Control of DNA Binding with Cucurbit[8]uril-Induced Supramolecular 4,4'-Bipyridinium-Peptide Dimers

Many cellular processes in living organisms are regulated by complex regulatory networks, built from noncovalent interactions between relatively few proteins that perform their functions by switching between homo- and heterooligomeric assemblies or mono- and bivalent states. Herein, we demonstrate that the conjugation of a 4,4'-bipyridinium scaffold to the basic region of the GCN4 bZip transcription factor can be exploited to control the dimerization of the conjugate by formation of a supramolecular complex with cucurbit[8]uril. Importantly, this supramolecular complex is able to specifically recognize its target dsDNA, and this binding can be reversibly switched by the application of external stimuli.

Noncovalent Protein-Pseudorotaxane Assembly Incorporating an Extended Arm Calix[8]arene with α-Helical Recognition Properties

Water-soluble, anionic calix[n]arenes are useful receptors for protein recognition and assembly. For example, sulfonato-calix[8]arene (sclx ₈ ) can encapsulate proteins and direct their assembly into porous frameworks. In this work, we turned our attention to an "extended arm" calixarene with 16 phenyl rings. We hypothesized that this larger receptor would have increased capacity for protein masking/encapsulation. A cocrystal structure of p-benzyl-sulfonato-calix[8]arene (b-sclx ₈ ) and cytochrome c (cyt c) revealed a surprising assembly. A pseudorotaxane comprising a stack of three b-sclx ₈ molecules threaded by polyethylene glycol (PEG) was bound to the protein. The trimeric b-sclx ₈ stack, a tubelike structure with a highly charged surface, mediated assembly via a new mode of protein recognition. The calixarene stack presents four hydrophobic grooves, each of which binds to one cyt c by accommodating the N-terminal α-helix. This unprecedented binding mode suggests new possibilities for supramolecular protein chemistry.

Peptide-Protein Interactions: From Drug Design to Supramolecular Biomaterials

The self-recognition and self-assembly of biomolecules are spontaneous processes that occur in Nature and allow the formation of ordered structures, at the nanoscale or even at the macroscale, under thermodynamic and kinetic equilibrium as a consequence of specific and local interactions. In particular, peptides and peptidomimetics play an elected role, as they may allow a rational approach to elucidate biological mechanisms to develop new drugs, biomaterials, catalysts, or semiconductors. The forces that rule self-recognition and self-assembly processes are weak interactions, such as hydrogen bonding, electrostatic attractions, and van der Waals forces, and they underlie the formation of the secondary structure (e.g., α-helix, β-sheet, polyproline II helix), which plays a key role in all biological processes. Here, we present recent and significant examples whereby design was successfully applied to attain the desired structural motifs toward function. These studies are important to understand the main interactions ruling the biological processes and the onset of many pathologies. The types of secondary structure adopted by peptides during self-assembly have a fundamental importance not only on the type of nano- or macro-structure formed but also on the properties of biomaterials, such as the types of interaction, encapsulation, non-covalent interaction, or covalent interaction, which are ultimately useful for applications in drug delivery.

Porous assembly of an antifungal protein mediated by zinc and sulfonato-calix[8]arene

Controlled protein assembly holds great potential in the fabrication of biohybrid materials. However, the structural diversity and complexity of proteins present an obstacle to controlled assembly. Supramolecular chemistry is a possible solution as it offers tools to mediate self-assembly with molecular precision. This paper deals with the calixarene- and zinc-mediated assembly and crystallization of the histidine-rich Penicillium chrysogenum antifungal protein B (PAFB). We report crystal structures of pure PAFB, PAFB in complex with Zn²⁺, and the ternary complex of PAFB, Zn²⁺ and sulfonato-calix[8]arene (sclx₈). A comparison of the three crystal structures revealed the structural plasticity of PAFB. While the flexible and highly anionic sclx₈ resulted in large molecular weight aggregates of PAFB in solution, diffraction-quality crystals of PAFB-sclx₈ were not obtained. We report crystals of PAFB-Zn²⁺-sclx₈ in which a trinuclear zinc cluster occurred adjacent to a calixarene binding site. Interestingly, the combination of sclx₈ complexation and zinc coordination resulted in a porous framework with channels of circa 2 nm diameter. Detailed analysis of the crystal structure highlighted novel molecular recognition features. This research enriches the set of supramolecular interactions available to promote protein assembly.

Targeting the Surface of the Protein 14-3-3 by Ultrasmall (1.5 nm) Gold Nanoparticles Carrying the Specific Peptide CRaf

The surface of ultrasmall gold nanoparticles with an average diameter of 1.55 nm was conjugated with a 14-3-3 protein-binding peptide derived from CRaf. Each particle carries 18 CRaf peptides, leading to an overall stoichiometry of Au(115)Craf(18). The binding to the protein 14-3-3 was probed by isothermal titration calorimetry (ITC) and fluorescence polarization spectroscopy (FP). The dissociation constant (K_D ) was measured as 5.0 μM by ITC and 0.9 μM by FP, which was close to the affinity of dissolved CRaf to 14-3-3σ. In contrast to dissolved CRaf, which alone did not enter HeLa cells, CRAF-conjugated gold nanoparticles were well taken up by HeLa cells, opening the opportunity to target the protein inside a cell.

Protein recognition by cucurbit[6]uril: high affinity N-terminal complexation

The donut-shaped cucurbit[n]urils (Qn, n = 6-8) are rigid macrocyclic receptors with widespread use in protein recognition. To date, most applications have centred on the encapsulation of N-terminal aromatic residues by Q7 or Q8. Less attention has been placed on Q6, which can recognize lysine side chains due to its high affinity for alkylamines. In this work, we investigated protein-Q6 complexation by using NMR spectroscopy. Attempts to crystallize protein-Q6 complexes were thwarted by the crystallization of Q6. We studied four proteins that vary in size, net charge, and lysine content. In addition to Q6 interactions with specific Lys or dimethylated Lys residues, we report striking evidence for N-terminal recognition. High affinity (micromolar) binding occurred with the N-terminal Met-Lys motif present in one of the four model proteins. Engineering this feature into another model protein yielded a similar high affinity site. We also present evidence for Q8 binding at this N-terminal feature. These data expand the cucurbituril toolkit for protein sensing.

Conformational switch in the crystal states of a calix[4]arene

Two distinct conformational switches were observed in the crystals of calix[4]arene molecule: closed-I crystals transform to the open polymorph spontaneously; temperature induced reversible transformation of closed-I to a closed-II polymorph.

Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors

To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.

Cucurbiturils in nucleic acids research

During the past ten years, the importance of cucurbiturils (CB[n]) as macrocyclic hosts in supramolecular assemblies with various types of natural and synthetic nucleic acids (NAs) has increased explosively. As a component of such systems, CB[n] macrocycles can play a wide spectrum of roles from drug and gene delivery vehicles to catalysts/inhibitors of biochemical reactions and even building blocks for NA-based materials. The aim of this highlight article is to describe the development of the CB[n] applications in nucleic acids research and to outline the current situation and perspectives of this fascinating synergistic combination of supramolecular chemistry of CB[n] and NAs.

A New Mechanically-Interlocked [Pd2 L4 ] Cage Motif by Dimerization of two Peptide-based Lemniscates

Most metallo-supramolecular assemblies of low nuclearity adopt simple topologies, with bridging ligands spanning neighboring metal centers in a direct fashion. Here we contribute a new structural motif to the family of host compounds with low metal count (two) that consists of a pair of doubly-interlocked, Figure-eight-shaped subunits, also termed "lemniscates". Each metal is chelated by two chiral bidentate ligands, composed of a peptidic macrocycle that resembles a natural product with two pyridyl-terminated arms. DFT calculation results suggest that dimerization of the mononuclear halves is driven by a combination of 1) Coulomb interaction with a central anion, 2) π-stacking between intertwined ligand arms and 3) dispersive interactions between the structure's compact inner core bedded into an outer shell composed of the cavitand-type macrocycles. The resulting cage-like architecture was characterized by NMR, MS and X-ray structure analyses. This new mechanically bonded system highlights the scope of structural variety accessible in metal-mediated self-assemblies composed of only a few constituents.

Molecular Dynamics Approach for Capturing Calixarene-Protein Interactions: The Case of Cytochrome C

Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonated calix-[8]-arenes to cytochrome c starting from initially distant proteins and ligands. We characterize two main binding sites for the sulfonated calixarene on the cytochrome c surface which are in perfect agreement with the previous experiments with regard to the structure (comparison with the X-ray structure PDB 6GD8) and the binding free energies [comparison between the molecular mechanics Poisson-Boltzmann surface area analysis and the isothermal titration calorimetry measurements]. The per-residue decomposition of the interaction energies reveals the detailed picture of this electrostatically driven association and notably the role of arginine R13 as a bridging residue between the two main anchoring sites. In addition, the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of a hydrogen bond network far from the binding sites, increasing the rigidity of the protein. This study paves the way toward an automated procedure to predict the supramolecular protein-cage association, with the possibility of a computational screening of new promising derivatives for controlled protein assembly and protein surface recognition processes.

Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays

We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.

Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins

Since the discovery of fullerene, carbon-based nanomolecules sparked a wealth of research across biological, medical and material sciences. Understanding the interactions of these materials with biological samples at the atomic level is crucial for improving the applications of nanomolecules and address safety aspects concerning their use in medicine. Protein crystallography provides the interface view between proteins and carbon-based nanomolecules. We review forefront structural studies of nanomolecules interacting with proteins and the mechanism underlying these interactions. We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. Carbon-based nanomolecules modulate protein surface electrostatic and, by forming ordered clusters, could modify protein quaternary structures. Lessons learned from structural studies are exemplary and will guide new projects for bioimaging tools, tuning of intrinsically disordered proteins, and design assembly of precise hybrid materials.

Dynamic modulation of proximity-induced enzyme activity using supramolecular polymers

Synthetic supramolecular polymers are used as dynamic nanoscaffolds for the activation of the apoptotic signalling enzyme caspase-9. Recruitment of caspase-9 to the nanoscaffold results in an increase in enzymatic activity due to enhanced proximity, with a bell-shaped response as a function of nanoscaffold concentration. The modularity of the system allows for dynamic regulation of enzyme activity through variation of the recruitment-motif density along the supramolecular polymer.

An Azobenzene-Based Single-Component Supramolecular Polymer Responsive to Multiple Stimuli in Water

One of the most appealing features of supramolecular assemblies is their ability to respond to external stimuli due to their noncovalent nature. This provides the opportunity to gain control over their size, morphology, and chemical properties and is key toward some of their applications. However, the design of supramolecular systems able to respond to multiple stimuli in a controlled fashion is still challenging. Here we report the synthesis and characterization of a novel discotic molecule, which self-assembles in water into a single-component supramolecular polymer that responds to multiple independent stimuli. The building block of such an assembly is a C₃-symmetric monomer, consisting of a benzene-1,3,5-tricarboxamide core conjugated to a series of natural and non-natural functional amino acids. This design allows the use of rapid and efficient solid-phase synthesis methods and the modular implementation of different functionalities. The discotic monomer incorporates a hydrophobic azobenzene moiety, an octaethylene glycol chain, and a C-terminal lysine. Each of these blocks was chosen for two reasons: to drive the self-assembly in water by a combination of H-bonding and hydrophobicity and to impart specific responsiveness. With a combination of microscopy and spectroscopy techniques, we demonstrate self-assembly in water and responsiveness to temperature, light, pH, and ionic strength. This work shows the potential to integrate independent mechanisms for controlling self-assembly in a single-component supramolecular polymer by the rational monomer design and paves the way toward the use of multiresponsive systems in water.

Kinetics and Mechanism of Cation-Induced Guest Release from Cucurbit[7]uril

The release of two organic guests from cucurbit[7]uril (CB7) was selectively monitored by the stopped‐flow method in aqueous solutions of inorganic salts to reveal the mechanistic picture in detail. Two contrasting mechanisms were identified: The symmetric dicationic 2,7‐dimethyldiazapyrenium shows a cation‐independent complex dissociation mechanism coupled to deceleration of the ingression in the presence of alkali and alkaline earth cations (Mⁿ⁺) due to competitive formation of CB7–Mⁿ⁺ complexes. A much richer, unprecedented kinetic behaviour was observed for the ingression and egression of the monocationic and non‐symmetric berberine (B⁺). The formation of ternary complex B⁺–CB7–Mⁿ⁺ was unambiguously revealed. A difference of more than two orders of magnitude was found in the equilibrium constants of Mⁿ⁺ binding to B⁺–CB7 inclusion complex. Large cations, such as K⁺ and Ba²⁺, also promoted B⁺ expulsion from the ternary complex in a bimolecular process. This study reveals a previously hidden mechanistic picture and motivates systematic kinetic investigations of other host–guest systems.

Induced CD of iron(ii) clathrochelates: sensing of the structural and conformational alterations of serum albumins

An ability of inherently achiral macrobicyclic metal complexes iron(ii) clathrochelates to acquire an induced CD (ICD) output in the visible spectral range upon interaction with bovine serum albumin (BSA) was recently discovered. In the present work, the CD-reporting properties of iron(ii) clathrochelates to proteins and the thermodynamic parameters of their binding to albumins are evaluated. It is shown that iron(ii) clathrochelates functionalized by six ribbed carboxyphenylsulfide groups are able to discriminate between serum albumins of relative structure (here human and bovine albumins) by giving distinct ICD spectra. Besides, by the variation of the shape and intensity of CD bands, these cage metal complexes reflect the pH-triggered alterations of the tertiary structure of albumins. The constitutional isomerism (ortho-, meta- or para-isomers) of terminal carboxyphenylsulfide groups of iron(ii) clathrochelates strongly affects both the character of their ICD output upon binding with proteins and the parameters of the formed guest-host associates. Using isothermal titration calorimetry, it was determined that cage metal complexes bearing meta- and ortho-isomers of carboxyphenylsulfide groups possess higher association constants (Ka ∼ 2 × 104 M-1) and clathrochelate-to-BSA binding ratios (n = 2) than the para-isomer (Ka ∼ 5 × 103 M-1, n = 1). The iron(ii) clathrochelates are suggested to be potential molecular three-dimensional scaffolds for the design of CD-sensitive reporters able to recognize specific elements of protein surfaces.

Exploring and Controlling the Polymorphism in Supramolecular Assemblies of Carbohydrates and Proteins

In biology, polymorphism is a well-known phenomenon by which a discrete biomacromolecule can adopt multiple specific conformations in response to its environment. This term can be extended to the ability of biomacromolecules to pack into different ordered patterns. Thus, exploration and control of the polymorphism of biomacromolecules via supramolecular methods have been key steps in achieving bioinspired structures, developing bioinspired functional materials, and exploring the mechanisms of these self-assembly processes, which are models for more complex biological systems. This task could be difficult for proteins and carbohydrates due to the complicated multiple noncovalent interactions of these two species which can hardly be manipulated.In this account, dealing with the structural polymorphisms from biomacromolecular assemblies, we will first briefly comment on the problems that carbohydrate/protein assemblies are facing, and then on the basis of our long-term research on carbohydrate self-assemblies, we will summarize the new strategies that we have developed in our laboratory in recent years to explore and control the polymorphism of carbohydrate/protein assemblies.Considering the inherent ability of carbohydrates to recognize lectin, we proposed the "inducing ligand" strategy to assemble natural proteins into various nanostructures with highly ordered packing patterns. The newly developed inducing ligand approach opened a new window for protein assembly where dual noncovalent interactions (i.e., carbohydrate-protein interactions and dimerization of rhodamine) instead of the traditionally used protein-protein interactions direct the assembly pattern of proteins. As a result, various polymorphisms of protein assemblies have been constructed by simply changing the ligand chemical structure and/or the rhodamine dimerization.Another concept that we proposed for glycopolymer self-assembly is DISA (i.e., deprotection-induced glycopolymer self-assembly). It is well known that protection-deprotection chemistry has been employed to construct complex oligosaccharide structures. However, its application in glycopolymer self-assembly has been overlooked. We initiated this new strategy with diblock copolymers. Such copolymers with a carbohydrate block having protected pendent groups exist as single chains in organic media. The self-assembly can be initiated by the deprotection of the pendent groups. The process was nicely controlled by introducing various protective groups with different deprotection rates. Later on, the DISA process has been proven practical in water and even in the cellular environment, which opens a new avenue for the development of polymeric glycomaterials.Finally, the resultant polymeric glyco-materials, as a new type of biomimetic materials, provide a nice platform for investigating the functions of glycocalyx. The glycocalyx-mimicking nanoparticles achieved unprecedent functions which exceed their carbohydrate precursors. Here, the reversion of tumor-associated macrophages induced by glycocalyx-mimicking nanoparticles will be discussed with potential applications in cancer immunotherapy, where such a reversion effect could be combined with other methods (e.g., tumor checkpoint blockade).

Supramolecular Metallacycles and Their Binding of Fullerenes

The synthesis of a new triaminoguanidinium-based ligand with three tris-chelating [NNO]-binding pockets and C3 symmetry is described. The reaction of tris-(2-pyridinylene-N-oxide)triaminoguanidinium salts with zinc(II) formate leads to the formation of cyclic supramolecular coordination compounds which in solution bind fullerenes in their spherical cavities. The rapid encapsulation of C60 can be observed by NMR spectroscopy and single-crystal X-ray diffraction and is verified using computation.

A Supramolecular Approach to Structure-Based Design with A Focus on Synthons Hierarchy in Ornithine-Derived Ligands: Review, Synthesis, Experimental and in Silico Studies

The success of innovative drugs depends on an interdisciplinary and holistic approach to their design and development. The supramolecular architecture of living systems is controlled by non-covalent interactions to a very large extent. The latter are prone to extensive cooperation and like a virtuoso play a symphony of life. Thus, the design of effective ligands should be based on thorough knowledge on the interactions at either a molecular or high topological level. In this work, we emphasize the importance of supramolecular structure and ligand-based design keeping the potential of supramolecular H-bonding synthons in focus. In this respect, the relevance of supramolecular chemistry for advanced therapies is appreciated and undisputable. It has developed tools, such as Hirshfeld surface analysis, using a huge data on supramolecular interactions in over one million structures which are deposited in the Cambridge Structure Database (CSD). In particular, molecular interaction surfaces are useful for identification of macromolecular active sites followed by in silico docking experiments. Ornithine-derived compounds are a new, promising class of multi-targeting ligands for innovative therapeutics and cosmeceuticals. In this work, we present the synthesis together with the molecular and supramolecular structure of a novel ornithine derivative, namely N-α,N-δ)-dibenzoyl-(α)-hydroxymethylornithine, 1. It was investigated by modern experimental and in silico methods in detail. The incorporation of an aromatic system into the ornithine core induces stacking interactions, which are vital in biological processes. In particular, rare C=O…π intercontacts have been identified in 1. Supramolecular interactions were analyzed in all structures of ornithine derivatives deposited in the CSD. The influence of substituent was assessed by the Hirshfeld surface analysis. It revealed that the crystal packing is stabilized mainly by H…O, O…H, C…H, Cl (Br, F)…H and O…O interactions. Additionally, π…π, C-H…π and N-O…π interactions were also observed. All relevant H-bond energies were calculated using the Lippincott and Schroeder H-bond model. A library of synthons is provided. In addition, the large synthons (Long-Range Synthon Aufbau Module) were considered. The DFT optimization either in vacuo or in solutio yields very similar molecular species. The major difference with the relevant crystal structure was related to the conformation of terminal benzoyl C15-C20 ring. Furthermore, in silico prediction of the extensive physicochemical ADME profile (absorption, distribution, metabolism and excretion) related to the drug-likeness and medicinal chemistry friendliness revealed that a novel ornithine derivative 1 has the potential to be a new drug candidate. It has shown good in silico absorption and very low toxicity.

Boron-Nitrogen Double Tweezers Comprising Arylboronic Esters and Diamines: Self-Assembly in Solution and Adaptability as Hosts for Aromatic Guests in the Solid State

The thermodynamic stability of 1 : 1 and 2 : 1 boron-nitrogen (B←N) adducts formed between aromatic boronic esters with mono- and diamines was studied in solution by NMR and UV-vis spectroscopy with association energies (ΔG°) ranging from -11 to -28 kJ mol^-1 . The effect of different substituents in the boronic ester, the nature of the diamine linker, and the effect of the solvent was explored. Stable 2 : 1 B←N adducts with diamines such as 1,3-diaminopropane were produced in solutions of hydrogen-bonding acceptor solvents (acetonitrile and ethyl acetate), which can be isolated in the solid state as crystalline solvates, whereas the use of noncoordinating solvents such as 1,2-dichloroethane afforded mainly 1 : 1 B←N adducts. In suitable combinations, aromatic bis-pyridyl diamines produced stable 2 : 1 B←N adducts that were isolated either as solvent-free solids, solvates, or cocrystals. In these crystalline forms, double-tweezer hosts were observed with an exceptional syn/anti conformational guest-adaptability driven by simultaneous donor-acceptor and C-H⋅⋅⋅π interactions in the tweezer cavities, resembling preorganized covalent tweezer hosts. Interestingly, cocrystals with electron-rich guests such as tetrathiafulvalene and pyrene showed non-centrosymmetric crystal lattices with infinite π-stacked donor-acceptor columns.

Supramolecular dimerization of a hexameric hemoprotein via multiple pyrene-pyrene interactions

Protein assemblies are being investigated as a new-class of biomaterials. A supramolecular assembly of a mutant hexameric tyrosine coordinated hemoprotein (HTHP) modified with a pyrene derivative is described. Cysteine was first introduced as a site-specific reaction point at position V44 which is located at the bottom surface of the cylindrical structure of HTHP. [Formula: see text]-(1-pyrenyl)maleimide was then reacted with the mutant. The modification was confirmed by MALDI-TOF mass spectrometry and UV-vis absorption spectroscopy, indicating that approximately 90% cysteine residues are attached via the pyrene derivative. Size exclusion chromatography (SEC) measurements for pyrene-attached HTHP include a single peak which elutes earlier than the unmodified HTHP. Further investigation by SEC and dynamic light scattering (DLS) measurements indicate the desired size corresponding to the dimer of the hemoprotein hexamers. The multivalent effect of pyrene–pyrene interactions including hydrophobic and [Formula: see text]–[Formula: see text] stacking interactions appears to be responsible for including formation of the stable dimer of the hexamers. Interestingly, the assembly dissociates to the hexamer by removal of heme. In the case of the apo-form of pyrene-attached HTHP, the pyrene moiety appears to be incorporated into the heme pocket because the modification point is located at the adjacent residue of the Tyr45 coordinating to heme in the holo-form of HTHP. Subsequent addition of heme into the apo-form of pyrene-attached HTHP regenerates the dimer of the hexamers. The present study demonstrates a unique heme-dependent system in which HTHP is assembled to form a dimer of hexamers in the presence of heme and disassembled by removal of heme.