Supramolecular Chemistry Targeting Proteins

Photomodulation of ultrastable host–guest complexes in water and their application in light-controlled steroid release

Host–guest complexation of dithienylethene photoswitches with cucurbit[8]uril leads to photoresponsive binding pairs with picomolar affinity in water.

Theoretical Study of Macrocyclic Host Molecules: From Supramolecular Recognition to Self-Assembly

Supramolecular chemistry focuses on molecular recognition and self-assembly of various building blocks through weak non-covalent interactions, including anion-π, hydrogen bond (HB), hydrophobic interactions, van der Waals (vdW) interactions, etc, which...

Construction of nano receptors for ubiquitin and ubiquitinated proteins based on the region-specific interactions between ubiquitin and polydopamine

Ubiquitination is a prevalent post-translational modification that controls a multitude of important biological processes. Due to the low abundance of ubiquitinated proteins, highly efficient separation and enrichment approaches are required...

Asymmetric patterning drives the folding of a tripodal DNA nanotweezer

DNA tweezers have emerged as powerful devices for a wide range of biochemical and sensing applications; however, most DNA tweezers consist of single units activated by DNA recognition, limiting their range of motion and ability to respond to complex stimuli. Herein, we present an extended, tripodal DNA nanotweezer with a small molecule junction. Simultaneous, asymmetric elongation of our molecular core is achieved using polymerase chain reaction (PCR) to produce length- and sequence-specific DNA arms with repeating DNA regions. When rigidified, our DNA tweezer can be addressed with streptavidin-binding ligands. Full control over the number, separation, and location of these ligands enables site-specific streptavidin recognition; all three arms of the DNA nanotweezer wrap around multiple streptavidin units simultaneously. Our approach combines the simplicity of DNA tile arrays with the size regime normally provided by DNA origami, offering an integrated platform for the use of branched DNA scaffolds as structural building blocks, protein sensors, and dynamic, stimuli-responsive materials.

Advanced protein drugs and formulations

For a long time, proteins were a subset of molecules rarely applied as therapeutically active molecules. Some of the first applications of proteins as drugs have been insulin and vaccines for supply a physiological deficiency and the prevention of diseases, respectively. Nowadays, proteins have increased their range of application, not only as drugs but also as drug delivery systems to be administered by different routes. Due to their nature, proteins show different behavior while the conditions of the environment are modified. For this reason, it has been necessary to study their behavior for predicting the correct manufacturing, storing, or combination with other possible molecules in a formulation or into the body. The application of techniques for predicting the behavior of proteins in different environments has led to associate this type of behavior into the body with the occurrence of diseases such as celiac disease or Alzheimer's disease. Thus, this work shows an overview of the main types of proteins applied as active therapeutically molecules, proteins-based drug delivery systems, and techniques for predicting their stability into the storing container and the body.

29th Annual GP2A Medicinal Chemistry Conference

The 29th Annual GP₂A (Group for the Promotion of Pharmaceutical chemistry in Academia) Conference was a virtual event this year due to the COVID-19 pandemic and spanned three days from Wednesday 25 to Friday 27 August 2021. The meeting brought together an international delegation of researchers with interests in medicinal chemistry and interfacing disciplines. Abstracts of keynote lectures given by the 10 invited speakers, along with those of the 8 young researcher talks and the 50 flash presentation posters, are included in this report. Like previous editions, the conference was a real success, with high-level scientific discussions on cutting-edge advances in the fields of pharmaceutical chemistry.

Natural and Synthetic Flavylium-Based Dyes: The Chemistry Behind the Color

Flavylium compounds are a well-known family of pigments because they are prevalent in the plant kingdom, contributing to colors over a wide range from shades of yellow-red to blue in fruits, flowers, leaves, and other plant parts. Flavylium compounds include a large variety of natural compound classes, namely, anthocyanins, 3-deoxyanthocyanidins, auronidins, and their respective aglycones as well as anthocyanin-derived pigments (e.g., pyranoanthocyanins, anthocyanin-flavan-3-ol dimers). During the past few decades, there has been increasing interest among chemists in synthesizing different flavylium compounds that mimic natural structures but with different substitution patterns that present a variety of spectroscopic characteristics in view of their applications in different industrial fields. This Review provides an overview of the chemistry of flavylium-based compounds, in particular, the synthetic and enzymatic approaches and mechanisms reported in the literature for obtaining different classes of pigments, their physical-chemical properties in relation to their pH-dependent equilibria network, and their chemical and enzymatic degradation. The development of flavylium-based systems is also described throughout this Review for emergent applications to explore some of the physical-chemical properties of the multistate of species generated by these compounds.

When Supramolecular Chemistry Meets Chemical Biology: New Strategies to Target Proteins through Host-Guest Interactions

Supramolecular chemistry for targeting proteins is of great interest for the development of novel approaches to recognize, isolate and control proteins. Taking advantage of chemical biology approaches, such as genetic-code expansion and enzyme-mediated ligation, guest recognition elements can be built into proteins of interest, allowing supramolecular control of protein function and regulation. In this viewpoint article, we will discuss the methods, applications, limitations, and future perspectives of supramolecular chemistry for targeting proteins in a site-specific manner.

A Supramolecular Antidote to Macromolecular Toxins Prepared through Coassembly of Macrocyclic Amphiphiles

Poisoning is a leading cause of admission to medical emergency departments and intensive care units. Supramolecular detoxification, which involves injecting supramolecular receptors that bind with toxins to suppress their biological activity, is an emerging strategy for poisoning treatment; it has few requirements and a broad application scope. However, it is still a formidable challenge to design supramolecular therapeutic materials as an antidote to macromolecular toxins, because the large size, flexible conformation, and presence of multiple and diverse binding sites of biomacromolecules hinder their recognition. Herein, a supramolecular antidote to macromolecular toxins is developed through the coassembly of macrocyclic amphiphiles, relying on heteromultivalent recognition between the coassembled components and toxic macromolecules. The coassembly of amphiphilic cyclodextrin and calixarene strongly and selectively captures melittin, a toxin studied herein; this imparts various therapeutic effects such as inhibiting the interactions of melittin with cell membranes, alleviating melittin cytotoxicity and hemolytic toxicity, reducing the mortality rate of melittin-poisoned mice, and mitigating damage to major organs. The use of the proposed antidote overcomes the limitation of supramolecular detoxification applicability to only small-molecular toxins. The antidote can also detoxify other macromolecular toxins as long as selective and strong binding is achieved because of the coassembling tunability.

Substrate Protection in Controlled Enzymatic Transformation of Peptides and Proteins

Proteins are involved in practically every single biological process. The many enzymes involved in their synthesis, cleavage, and posttranslational modification (PTM) carry out highly specific tasks with no usage of protecting groups. Yet, the chemists' strategy of protection/deprotection potentially can be highly useful, for example, when a specific biochemical reaction catalyzed by a broad-specificity enzyme needs to be inhibited, during infection of cells by enveloped viruses, in the invasion and spread of cancer cells, and upon mechanistic investigation of signal-transduction pathways. Doing so requires highly specific binding of peptide substrates in aqueous solution with biologically competitive affinities. Recent development of peptide-imprinted cross-linked micelles allows such protection and affords previously impossible ways of manipulating peptides and proteins in enzymatic transformations.

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.