Macrocyclic Size Research Articles

4-Sulfonatocalixarene-induced nanoparticle formation of methylimidazolium-conjugated dextrans: Utilization for drug encapsulation

Methylimidazolium side groups were grafted via ether linkage to dextran and the self-assembly of these polymers with 4-sulfonato-calix[n]arenes (SCXn) was studied in aqueous solutions. Dynamic light scattering and zeta potential measurements revealed the mixing ratio ranges of the constituents where stable nanoparticles could be created. The macrocycle size of SCXn and the molecular mass of the polymer barely affected the nanoparticle diameter, but the lowering of the imidazolium degree of substitution substantially diminished the stability of the associates. The pH change from neutral to acidic also unfavourably influenced the self-organization owing mainly to the decrease of the SCXn charge. Cryogenic transmission electron microscopy images proved the spherical morphology of the nanoproducts in which the stoichiometry of the constituents was always close to the one corresponding to charge compensation. The flexible and positively charged dextran-chains are compacted by the polyanionic SCXn. Coralyne, a pharmacologically important alkaloid was efficiently embedded by self-assembly in the produced nanoparticles reaching 99% association efficiency.

Calixarene-mediated assembly of a small antifungal protein.

Synthetic macrocycles such as calixarenes and cucurbiturils are increasingly applied as mediators of protein assembly and crystallization. The macrocycle can facilitate assembly by providing a surface on which two or more proteins bind simultaneously. This work explores the capacity of the sulfonato-calix[n]arene (sclx n ) series to effect crystallization of PAF, a small, cationic antifungal protein. Co-crystallization with sclx4, sclx6 or sclx8 led to high-resolution crystal structures. In the absence of sclx n , diffraction-quality crystals of PAF were not obtained. Interestingly, all three sclx n were bound to a similar patch on PAF. The largest and most flexible variant, sclx8, yielded a dimer of PAF. Complex formation was evident in solution via NMR and ITC experiments, showing more pronounced effects with increasing macrocycle size. In agreement with the crystal structure, the ITC data suggested that sclx8 acts as a bidentate ligand. The contributions of calixarene size/conformation to protein recognition and assembly are discussed. Finally, it is suggested that the conserved binding site for anionic calixarenes implicates this region of PAF in membrane binding, which is a prerequisite for antifungal activity.

Delivery of cell membrane impermeable peptides into living cells by using head-to-tail cyclized mitochondria-penetrating peptides.

A series of cyclic Arg-rich mitochondria-penetrating peptides were prepared with variation in the macrocycle size and the chirality of Arg residues. A cyclic heptapeptide was demonstrated to be an efficient mitochondria-specific delivery vector for delivering membrane impermeable peptides.

The influence of metal-complexing macrocycle size on intramolecular movement in rotaxanes.

[2]rotaxanes composed of a dibenzo-24-crown-8 wheel (DB24C8) and an axle containing two metal-complexing tetraazamacrocyclic units linked with a p-xylylene bridge, coordinating the same or different metal ions (Ni and/or Cu) are described. A symmetric di-Ni rotaxane crystallizes in the monoclinic P21/c space group with one rotaxane cation and four PF6- counterions in the asymmetric part of the unit cell. In the crystal, the cations and anions of the investigated compound form an intertwined 3D-framework with C-HF and C-Hπ intermolecular interactions. The NMR ROESY spectrum of the diamagnetic di-Ni rotaxane confirms that at room temperature slow shuttling of the DB24C8 moiety takes place along the symmetric axle. The non-symmetric rotaxane, containing 14- and 16-membered nickel(ii)-complexing macrocycles, exists in solution as an equilibrium mixture of two conformers in the ratio of ca. 1 : 7. This rotaxane behaves as a potential-controlled molecular switch: in the major isomer, the DB24C8 moiety is localized in the vicinity of the 14-membered metal-complexing macrocycle, and moves towards the 16-membered unit upon the first oxidation. Reverse translocation occurs after the subsequent oxidation of the 14-membered complex unit. In contrast, no such movements of the DB24C8 moiety were observed upon investigation of the heteronuclear [2]rotaxane, coordinating copper(ii) and nickel(ii) ions.

Bringing Macrolactamization Full Circle: Self-Cleaving Head-to-Tail Macrocyclization of Unprotected Peptides via Mild N-Acyl Urea Activation.

We establish herein conditions for the cyclization of unprotected N-acyl urea-linked peptides to form macrocyclic peptides mediated by N-terminal cysteine. We report a detailed investigation of the parameters of the reaction, including variation of the reaction conditions, the C-terminal residue, and the macrocycle size. C-Terminal epimerization was not observed. The synthesis of macrocyclic targets ranging from tetrapeptides to the disulfide-linked 14-mer, sunflower trypsin inhibitor 1 are demonstrated. For most substrates, hydrolysis and head-to-tail dimer formation are avoided.

Strain-Promoted Reactivity of Alkyne-Containing Cycloparaphenylenes.

A new class of macrocyclic angle-strained alkynes whose size and reactivity can be precisely tuned by modular organic synthesis is disclosed. Detailed analysis of the size-dependent structural and electronic properties provides evidence for considerable distortion of the alkyne units incorporated into the cycloparaphenylene (CPP)-derived macrocycles. The remarkable increase of the alkyne reactivity with decreasing macrocycle size in [2+2]cycloaddition-retrocyclization was investigated by joint experimental and theoretical studies and the thermodynamic and kinetic parameters that govern this reaction were unraveled. Additionally, even the largest, least strained macrocycle in this series was found to undergo strain-promoted azide-alkyne cycloaddition (SPAAC) efficiently under mild conditions, thereby paving the way to the application of alkyne-containing CPPs as fluorescent "clickable" macrocyclic architectures.

Strain‐Promoted Reactivity of Alkyne‐Containing Cycloparaphenylenes

AbstractA new class of macrocyclic angle‐strained alkynes whose size and reactivity can be precisely tuned by modular organic synthesis is disclosed. Detailed analysis of the size‐dependent structural and electronic properties provides evidence for considerable distortion of the alkyne units incorporated into the cycloparaphenylene (CPP)‐derived macrocycles. The remarkable increase of the alkyne reactivity with decreasing macrocycle size in [2+2]cycloaddition–retrocyclization was investigated by joint experimental and theoretical studies and the thermodynamic and kinetic parameters that govern this reaction were unraveled. Additionally, even the largest, least strained macrocycle in this series was found to undergo strain‐promoted azide–alkyne cycloaddition (SPAAC) efficiently under mild conditions, thereby paving the way to the application of alkyne‐containing CPPs as fluorescent “clickable” macrocyclic architectures.

Building Strain with Large Macrocycles and Using It To Tune the Thermal Half-Lives of Hydrazone Photochromes.

Strain has been used as a tool to modulate the reactivity (e.g., mechanochemistry) and thermal isomerization kinetics of photochromic compounds. Macrocyclization is used to build-up strain in such systems, and in general the reactivity and rates increase with the decrease in macrocycle size. To ascertain the effect of strain on recently reported bistable hydrazone photoswitches, we incorporated them into macrocycles having varying aliphatic linker lengths (C3-C7), and studied their switching behavior, and effect of macrocycle size on the thermal isomerization rate. Surprisingly, while the systems with C3-C5 linkers behave as expected (i.e., the rate is faster with smaller linkers), the isomerization rate in the systems with larger aliphatic linkers (C6-C8) is enhanced up to 4 orders of magnitude. NMR spectroscopy, X-ray crystallography and DFT calculations were used to elucidate this unexpected behavior, which on the basis of our analyses results from the buildup of Pitzer (torsional), Prelog (transannular) and Baeyer (large angle) strain in the longer linkers.

Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors

The design and synthesis of macrocyclic inhibitors of human rhinovirus 3C protease is described. A macrocyclic linkage of the P1 and P3 residues, and the subsequent structure-based optimization of the macrocycle conformation and size led to the identification of a potent biochemical inhibitor 10 with sub-micromolar antiviral activity.

Hexagonal Molecular Tiling by Hexagonal Macrocycles at the Liquid/Solid Interface: Structural Effects on Packing Geometry.

We present here hexagonal tiling using hexagonal phenylene-ethynylene and phenylene-butadiynylene macrocycles attached by alkyl ester groups, PEM-C6 and PBM-C8, respectively, or triethylene glycol ester groups, PEM-TEG and PBM-TEG, respectively, at each vertex of the macrocyclic periphery at the liquid/solid interface. In this study, we focused on the effects of macrocyclic core size and the chemical properties of side chains attached to macrocyclic cores as well as solute concentrations on the hexagonal geometry of self-assembled monolayers. STM observations at the 1,2,4-trichrolobenzene/graphite interface revealed that PEM-C6 formed a honeycomb structure by van der Waals interactions between the interdigitated alkyl chains. However, upon increasing solute concentration, it changed to more dense hexagonal structure (tentatively called loose hexagonal structure I). In contrast, PBM-C8 formed loose hexagonal structure II of a slightly different packing mode at low concentration, while at high concentration it formed a high-density hexagonal structure in which alkyl chains are not adsorbed on the surface (dense hexagonal structure). In the dense hexagonal structure, macrocyclic cores are linked by hydrogen bonds between the ester carbonyl oxygen and the aromatic hydrogen atoms of the neighboring macrocycles. The packing geometries of loose hexagonal structures of PEM-C6 and PBM-C8 are different due to the different distance between the attachment of the alkyl ester groups which are located in confined space. On the other hand, PEM-TEG and PBM-TEG formed dense hexagonal structures, similar to PBM-C8 at high concentration, with their TEG units not adsorbed on the surface.

Emergence of a New Self-Replicator from a Dynamic Combinatorial Library Requires a Specific Pre-Existing Replicator.

Our knowledge regarding the early steps in the formation of evolvable life and what constitutes the minimal molecular basis of life remains far from complete. The recent emergence of systems chemistry reinvigorated the investigation of systems of self-replicating molecules to address these questions. Most of these studies focus on single replicators and the effects of replicators on the emergence of other replicators remains under-investigated. Here we show the cross-catalyzed emergence of a novel self-replicator from a dynamic combinatorial library made from a threonine containing peptide building block, which, by itself, only forms trimers and tetramers that do not replicate. Upon seeding of this library with different replicators of different macrocycle size (hexamers and octamers), we observed the emergence of hexamer replicator consisting of six units of the threonine peptide only when it is seeded with an octamer replicator containing eight units of a serine building block. These results reveal for the first time how a new replicator can emerge in a process that relies critically on the assistance by another replicator through cross-catalysis and that replicator composition is history dependent.

NMR Insights into the Structure-Function Relationships in the Binding of Melanocortin Analogues to the MC1R Receptor.

Linear and cyclic analogues of the α-melanocyte stimulating hormone (α-MSH) targeting the human melanocortin receptor 1 (MC1R) are of pharmacological interest for detecting and treating melanoma. The central sequence of α-MSH (His-Phe-Arg-Trp) has been identified as being essential for receptor binding. To deepen current knowledge on the molecular basis for α-MSH bioactivity, we aimed to understand the effect of cycle size on receptor binding. To that end, we synthesised two macrocyclic isomeric α-MSH analogues, c[NH-NO2-C6H3-CO-His-DPhe-Arg-Trp-Lys]-Lys-NH2 (CycN-K6) and c[NH-NO2-C6H3-CO-His-DPhe-Arg-Trp-Lys-Lys]-NH2 (CycN-K7). Their affinities to MC1R receptor were determined by competitive binding assays, and their structures were analysed by 1H and 13C NMR. These results were compared to those of the previously reported analogue c[S-NO2-C6H3-CO-His-DPhe-Arg-Trp-Cys]-Lys-NH2 (CycS-C6). The MC1R binding affinity of the 22-membered macrocyclic peptide CycN-K6 (IC50 = 155 ± 16 nM) is higher than that found for the 25-membered macrocyclic analogue CycN-K7 (IC50 = 495 ± 101 nM), which, in turn, is higher than that observed for the 19-membered cyclic analogue CycS-C6 (IC50 = 1770 ± 480 nM). NMR structural study indicated that macrocycle size leads to changes in the relative dispositions of the side chains, particularly in the packing of the Arg side chain relative to the aromatic rings. In contrast to the other analogues, the 22-membered cycle’s side chains are favorably positioned for receptor interaction.

P-Phosphonated Calix[n]arene Stabilizes Superparamagnetic Nanoparticles for Nitrate and Phosphate Uptake.

Highly faceted superparamagnetic magnetite nanoparticles roughly 11 nm in diameter are readily accessible in the presence of p-phosphonated calix[n]arenes of different ring sizes (n=4, 5 and 6), through the use of a simple co-precipitation technique. In contrast, the larger calix[8]arene affords spherical particles of comparable size. The maximum magnetization is 70-60 emu g-1 , which decreases with increasing size of the calixarene macrocycle, and the evidence indicates that the calixarenes bind to the surface of the nanoparticles via the phosphonate head groups rather than the phenolic oxygen centers. The stabilized nanoparticles show dual functionality: they remove up to 62 % of nitrate nitrogen and 48 % of phosphate from an aqueous effluent after 24 hours at concentrations of only 1 g L-1 of calixarene-coated nanoparticles.

Rapid synthesis of cyclic oligomeric depsipeptides with positional, stereochemical, and macrocycle size distribution control

Macrocyclic small molecules are attractive tools in the development of sensors, new materials, and therapeutics. Within early-stage drug discovery, they are increasingly sought for their potential to interact with broad surfaces of peptidic receptors rather than within their narrow folds and pockets. Cyclization of linear small molecule precursors is a straightforward strategy to constrain conformationally mobile motifs, but forging a macrocycle bond typically becomes more difficult at larger ring sizes. We report the development of a general approach to discrete collections of oligomeric macrocyclic depsipeptides using an oligomerization/macrocyclization process governed by a series of Mitsunobu reactions of hydroxy acid monomers. Ring sizes of 18, 24, 30, and 36 are formed in a single reaction from a didepsipeptide, whereas sizes of 24, 36, and 60 result from a tetradepsipeptide. The ring-size selectivity inherent to the approach can be modulated by salt additives that enhance the formation of specific ring sizes. Use of chemical synthesis to prepare the monomers suggests broad access to functionally and stereochemically diverse collections of natural product-like oligodepsipeptide macrocycles. Two cyclodepsipeptide natural products were prepared along with numerous unnatural oligomeric congeners to provide rapid access to discrete collections of complex macrocyclic small molecules from medium (18) to large (60) ring sizes.

Effect of Macrocycle Size on the Self-Assembly of Methylimidazolium Surfactant with Sulfonatocalix[n]arenes

The effect of macrocycle size on the association of supramolecular amphiphiles composed of 4-sulfonatocalix[n]arene and 1-methyl-3-tetradecylimidazolium (C14mim+) was studied in aqueous solutions at pH 7. When the cavitand contained four sulfonatophenol units (SCX4), formation of spherical nanoparticles (NPs) was observed. By contrast, both supramolecular micelle (SM) and NP formation could be attained in the presence of NaCl when the larger, more flexible 4-sulfonatocalix[8]arene (SCX8) served as the host compound. The SCX8-promoted self-assembly into the SM was enthalpically more favorable than the NP production, but the molar heat capacity changes in the two processes barely differed. An addition of 50 mM NaCl significantly increased the enthalpy of C14mim+-SCX8 NP formation, thereby making the self-organization into the SM more favorable. The transformation of SM into NP at high temperatures was due to the substantial entropic contribution to the driving force behind the NP formation. The critical micelle concentration (cmc) and the local polarity in the headgroup domain were considerably lower for the SM compared with those of the conventional C14mim+Br- micelle.

Versatile Picklocks To Access All Opioid Receptors: Tuning the Selectivity and Functional Profile of the Cyclotetrapeptide c[Phe-d-Pro-Phe-Trp] (CJ-15,208).

Recently, the tryptophan-containing noncationizable opioid peptides emerged with atypical structure and unexpected in vivo activity. Herein, we describe analogs of the naturally occurring mixed κ/μ-ligand c[Phe-d-Pro-Phe-Trp] 1 (CJ-15,208). Receptor affinity, selectivity, and agonism/antagonism varied upon enlarging macrocycle size, giving the μ-agonist 9 or the δ-antagonist 10 characterized by low nanomolar affinity. In particular, the μ-agonist c[β-Ala-d-Pro-Phe-Trp] 9 was shown to elicit potent antinociception in a mouse model of visceral pain upon systemic administration.

Development of Ion Chemosensors Based on Porphyrin Analogues.

Sensing of metal ions and anions is of great importance because of their widespread distribution in environmental systems and biological processes. Colorimetric and fluorescent chemosensors based on organic molecular species have been demonstrated to be effective for the detection of various ions and possess the significant advantages of low cost, high sensitivity, and convenient implementation. Of the available classes of organic molecules, porphyrin analogues possess inherently many advantageous features, making them suitable for the design of ion chemosensors, with the targeted sensing behavior achieved and easily modulated based on their following characteristics: (1) NH moieties properly disposed for binding of anions through cooperative hydrogen-bonding interactions; (2) multiple pyrrolic N atoms or other heteroatoms for selectively chelating metal ions; (3) variability of macrocycle size and peripheral substitution for modulation of ion selectivity and sensitivity; and (4) tunable near-infrared emission and good biocompatibility. In this Review, design strategies, sensing mechanisms, and sensing performance of ion chemosensors based on porphyrin analogues are described by use of extensive examples. Ion chemosensors based on normal porphyrins and linear oligopyrroles are also briefly described. This Review provides valuable information for researchers of related areas and thus may inspire the development of more practical and effective approaches for designing high-performance ion chemosensors based on porphyrin analogues and other relevant compounds.

Fine-Tuning of Electronic Structure of Cobalt(II) Ion in Nonplanar Porphyrins and Tracking of a Cross-Hybrid Stage: Implications for the Distortion of Natural Tetrapyrrole Macrocycles.

The core size of the porphyrin macrocycles was closely related to their stability of the different electron structure in the central metal ion. Cobalt(II) ions can undergo a conversion in electron configurations upon N4 core contraction of 0.05 Å in nonplanar porphyrins, and these ions still maintain low spin forms after and before conversion. The structural fine-tuning can induce the appearance of a cross-hybrid stage [d(x(2)-y(2))sp(2) ↔ d(z(2))sp(2)] based on quadrilateral coordination of the planar core. The results indicate that the configuration conversion plays a key role in electron transfer in redox catalysis involving cobalt complexes. The electronic properties of six monostrapped cobalt(II) porphyrins were investigated by spectral, paramagnetic, and electrochemical methods. The macrocyclic deformations and size parameters of Co-containing model compounds were directly obtained from their crystal structures.

Macrocyclic Platforms for the Construction of Tetranuclear Oxo and Hydroxo Zinc Clusters

The design of ligands that can act as platforms for the controlled, “bottom-up” synthesis of transition-metal clusters is a promising approach to accessing enzymatic mimics and new small-molecule reaction chemistry. This approach is exemplified here through the coordination chemistry of two compartmental Schiff-base calixpyrroles (H4L) that usually act as dinucleating ligands for transition metals. While reactions between H4L and Zn{N(SiMe3)2}2 form the expected dinuclear Zn “Pacman” complexes Zn2(L), reactions with ZnEt2 result in the tetranuclear Zn alkyl complexes Zn4Et4(THF)4(L), in which open, “bowl-shaped” structures are adopted due to the flexibility of the macrocyclic platform. The outcome of hydrolysis reactions of these tetranuclear complexes is found to depend on the macrocyclic cavity size, with the smaller macrocycle favoring oxo formation in Zn4(μ4-O)Et2(L) and the larger macrocycle favoring complete hydrolysis to form the hydroxide-bridged cluster Zn4(μ2-OH)4(L). This latter complex reacts ...

Competitive formation of homocircuit [3]rotaxanes in synthetically useful yields in the bipyridine-mediated active template CuAAC reaction.

We recently identified competitive formation of doubly interlocked [3]rotaxanes as the origin of the non-linear variation in yield of [2]rotaxane with macrocycle size in the bipyridine-mediated AT-CuAAC reaction. Selection of reaction conditions gave [2]rotaxanes in essentially quantitative yield in all cases and hard to access doubly threaded [3]rotaxanes in up to 50% yield in a single, four component coupling. Based on the effect of macrocycle structure on the reaction outcome we propose a detailed mechanism of [3]rotaxane formation.