Rotaxane-based architectures for biological applications

A Platform Approach to Cleavable Macrocycles for the Controlled Disassembly of Mechanically Caged Molecules

Inspired by interlocked oligonucleotides, peptides and knotted proteins, synthetic systems where a macrocycle cages a bioactive species that is "switched on" by breaking the mechanical bond have been reported. However, to date, each example uses a bespoke chemical design. Here we present a platform approach to mechanically caged structures wherein a single macrocycle precursor is diversified at a late stage to include a range of trigger units that control ring opening in response to enzymatic, chemical, or photochemical stimuli. We also demonstrate that our approach is applicable to other classes of macrocycles suitable for rotaxane and catenane formation.

Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry

The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.

Molecular Machines For The Control Of Transmembrane Transport

Nature embeds some of its molecular machinery, including ion pumps, within lipid bilayer membranes. This has inspired chemists to attempt to develop synthetic analogues to exploit membrane confinement and transmembrane potential gradients, much like their biological cousins. In this perspective, we outline the various strategies by which molecular machines─molecular systems in which a nanomechanical motion is exploited for function─have been designed to be incorporated within lipid membranes and utilized to mediate transmembrane ion transport. We survey molecular machines spanning both switches and motors, those that act as mobile carriers or that are anchored within the membrane, mechanically interlocked molecules, and examples that are activated in response to external stimuli.

Stimuli-Responsive Catenane-Based Catalysts

Rotaxanes and molecular knots exhibit particular properties resulting from the presence of a mechanical bond within their structure that maintains the molecular components interlocked in a permanent manner. On the other hand, the disassembly of the interlocked architecture through the breakdown of the mechanical bond can activate properties which are masked in the parent compound. Herein, we present the development of stimuli-responsive Cu^I -complexed [2]catenanes as OFF/ON catalysts for the copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The encapsulation of the Cu^I ion inside the [2]catenanes inhibits its ability to catalyze the formation of triazoles. In contrast, the controlled opening of the two macrocycles induces the breaking of the mechanical bond, thereby restoring the catalytic activity of the Cu^I ion for the CuAAC reaction. Such OFF/ON catalysts can be involved in signal amplification processes with various potential applications.

Supramolecular Rotaxane‐Based Multi‐Modal Probes for Cancer Biomarker Imaging**

Mechanically interlocked molecules present opportunities to construct therapeutic drugs and diagnostic imaging agents but harnessing supramolecular chemistry to make biologically active probes in water is a challenge. Here, we describe a rotaxane‐based approach to synthesise radiolabelled proteins and peptides for molecular imaging of cancer biomarkers in vivo. Host–guest chemistry using β‐cyclodextrin‐ and cucurbit[6]uril‐catalysed cooperative capture synthesis produced gallium‐68 or zirconium‐89 radiolabelled metallo[4]rotaxanes. Photochemical conjugation to trastuzumab led to a viable positron emission tomography (PET) radiotracer. The rotaxane architecture can be tuned to accommodate different radiometal ion complexes, other protein‐ or peptide‐based drugs, and fluorophores for optical detection. This technology provides a platform to explore how mechanical bonding can improve drug delivery, enhance tumour specificity, control radiotracer pharmacokinetics, and reduce dosimetry.

[3]Foldarotaxane-mediated synthesis of an improbable [2]rotaxane

The wrapping of an aromatic oligoamide helix around an active ester-containing [2]rotaxane enforced the sliding and the sequestration of the surrounding macrocycle around a part of the axle for which it has no formal affinity. The foldamer-mediated compartmentalization of the [2]rotaxane shuttle was subsequently used to prepare an improbable rotaxane.

BINOL as a chiral element in mechanically interlocked molecules

In this minireview we present the use of the axially chiral 1,1'-binaphthyl-2,2'-diol (BINOL) unit as a stereogenic element in mechanically interlocked molecules (MIMs). We describe the synthesis and properties of such BINOL-based chiral MIMs, together with their use in further diastereoselective modifications, their application in asymmetric catalysis, and their use in stereoselective chemosensing. Given the growing importance of mechanically interlocked molecules and the key advantages of the privileged chiral BINOL backbone, we believe that this research area will continue to grow and deliver many useful applications in the future.

Controlling catalyst activity, chemoselectivity and stereoselectivity with the mechanical bond

Mechanically interlocked molecules, such as rotaxanes and catenanes, are receiving increased attention as scaffolds for the development of new catalysts, driven by both their increasing accessibility and high-profile examples of the mechanical bond delivering desirable behaviours and properties. In this Review, we survey recent advances in the catalytic applications of mechanically interlocked molecules organized by the effect of the mechanical bond on key catalytic properties, namely, activity, chemoselectivity and stereoselectivity, and focus on how the mechanically bonded structure leads to the observed behaviour. Our aim is to inspire future investigations of mechanically interlocked catalysts, including those outside of the supramolecular community.

Weinreb Amide, Ketone and Amine as Potential and Competitive Secondary Molecular Stations for Dibenzo-[24]Crown-8 in [2]Rotaxane Molecular Shuttles

This paper reports the synthesis and study of new pH-sensitive DB24C8-based [2]rotaxane molecular shuttles that contain within their axle four potential sites of interaction for the DB24C8: ammonium, amine, Weinreb amide, and ketone. In the protonated state, the DB24C8 lay around the best ammonium site. After either deprotonation or deprotonation-then-carbamoylation of the ammonium, different localizations of the DB24C8 were seen, depending on both the number and nature of the secondary stations and steric restriction. Unexpectedly, the results indicated that the Weinreb amide was not a proper secondary molecular station for the DB24C8. Nevertheless, through its methoxy side chain, it slowed down the shuttling of the macrocycle along the threaded axle, thereby partitioning the [2]rotaxane into two translational isomers on the NMR timescale. The ketone was successfully used as a secondary molecular station, and its weak affinity for the DB24C8 was similar to that of a secondary amine.

Nanohoop Rotaxane Design to Enhance the Selectivity of Reaction-Based Probes: A Proof-of-Principle Study

Mechanical interlocking of a nanohoop fluorophore and a reactive thread couples the benefits of a reaction-based probe with a sterically congested active site for enhanced selectivity. Advantageously, the thread design uses dual function stoppers that act as both a quencher and a trigger for sensing. In progress toward expanding this approach to biologically relevant analytes, this system is used to demonstrate steric differentiation and provide a selective turn-on fluorescent response with size selectivity for HS^- rather than larger thiolates.

Rotaxanes as Cages to Control DNA Binding, Cytotoxicity, and Cellular Uptake of a Small Molecule*

The efficacy of many drugs can be limited by undesirable properties, such as poor aqueous solubility, low bioavailability, and "off-target" interactions. To combat this, various drug carriers have been investigated to enhance the pharmacological profile of therapeutic agents. In this work, we demonstrate the use of mechanical protection to "cage" a DNA-targeting metallodrug within a photodegradable rotaxane. More specifically, we report the synthesis of rotaxanes incorporating as a stoppering unit a known G-quadruplex DNA binder, namely a Pt^II -salphen complex. This compound cannot interact with DNA when it is part of the mechanically interlocked assembly. The second rotaxane stopper can be cleaved by either light or an esterase, releasing the Pt^II -salphen complex. This system shows enhanced cell permeability and limited cytotoxicity within osteosarcoma cells compared to the free drug. Light activation leads to a dramatic increase in cytotoxicity, arising from the translocation of Pt^II -salphen to the nucleus and its binding to DNA.

Concentration-dependent supramolecular self-assembly of A1/A2-asymmetric-difunctionalized pillar[5]arene

A series of A1/A2-bromoalkoxy-and-hydroxy-difunctionalized pillar[5]arenes were synthesized by the removal of the pillar[5]arene-bearing benzyl group using catalytic hydrogenation. The difunctionalized pillar[5]arene bearing 8-bromooctoxy and benzyloxy substituents at the A1/A2 positions formed pseudo[1]rotaxane at low concentration and double-threaded supramolecular dimer at high concentration. The supramolecular self-assembly behavior has been probed with multiple methods including varying (variable) concentration ¹H NMR spectroscopy, diffusion-ordered spectroscopy (DOSY), dynamic light scattering (DLS) measurements, isothermal titration calorimetry (ITC), and single-crystal X-ray analysis.

Concentration-dependent supramolecular self-assembly of A1/A2-asymmetric-difunctionalized pillar[5]arene was synthesized by co-cyclization strategy. This approach enables wide range of structural manipulations to regulate the supramolecular assembly.

Synthesis, structures and properties of Cd(II) supramolecular compound based on nitrogen heterocyclic cation

A novel supramolecular compound {(L1) [CdI4]} (L1 = 1-(3-(((1 s,3R,5S)-1,3,5,7,tetraazaadamantan-1-ium-1-yl)methyl)benzyl)-1,3,5,7,-tetraazaadamantan-1-ium) was synthesized from CdI2 and L1 by self-assembly reaction in solution. Its structure was analyzed by X-ray diffraction, and X-ray crystallography showed that the crystal was mononuclear. The compound was characterized by UV, TG, photocatalysis and adsorption.

Lanthanide-Containing Rotaxanes, Catenanes, and Knots

The valuable luminescence, magnetic, and catalytic properties of lanthanide cations are beginning to be exploited in conjunction with structurally exotic mechanically interlocked molecules (MIMs) such as rotaxanes, catenanes and knots. This Minireview provides an account of this rapidly developing research area commencing with the use of lanthanides in extended MIM-containing frameworks. Then, attention turns to discrete lanthanide-containing pseudorotaxanes, followed by fully interlocked rotaxanes, catenanes and knots - where lanthanides have not only been incorporated into MIM architectures but have also been used to template formation of the interlocked structure. Particular focus is paid to examples where the lanthanide MIMs have been put to useful applications, in what is still a relatively youthful avenue of research in both lanthanide coordination chemistry and the chemistry of mechanically interlocked molecules.

AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides

We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.

Can aromaticity be a kinetic trap? Example of mechanically interlocked aromatic [2-5]catenanes built from cyclo[18]carbon

Aromaticity serves as a kinetic trap for mechanically interlocked cyclo[18]carbon rings.

Locked and Loaded: Ruthenium(II)-Capped Cucurbit[n]uril-Based Rotaxanes with Antimetastatic Properties

We report here the first coupling of Ru(II) units with cucurbit[6/7]uril-based pseudorotaxane ligands meant for biological application. The resulting ruthenium-capped rotaxanes were fully characterized, and a structure of one supramolecular system was determined by X-ray diffraction. Because the biological properties of Ru-based metallodrugs are tightly linked to the ligand-exchange processes, the effect of salt concentration on the hydrolysis of chlorides from the Ru(II) center was monitored by using ¹H NMR spectroscopy. The biological activity of Ru(II)-based rotaxanes was evaluated for three selected mammalian breast cell lines, HBL-100, MCF-7, and MDA-MB-231. The antimetastatic activity of the assembled cationic Ru(II)-rotaxane systems, evaluated in migration assays against MCF-7 and MDA-MB-231 cell lines, is notably enhanced compared to that of RAPTA-C, a reference that was used. The indicated synergistic effect of combining Ru(II) with a pseudorotaxane unit opens a new direction in searching for anticancer supramolecular metallodrugs.

Stepwise, Protecting Group Free Synthesis of [4]Rotaxanes

Despite significant advances in the last three decades towards high yielding syntheses of rotaxanes, the preparation of systems constructed from more than two components remains a challenge. Herein we build upon our previous report of an active template copper-catalyzed azide-alkyne cycloaddition (CuAAC) rotaxane synthesis with a diyne in which, following the formation of the first mechanical bond, the steric bulk of the macrocycle tempers the reactivity of the second alkyne unit. We have now extended this approach to the use of 1,3,5-triethynylbenzene in order to successively prepare [2]-, [3]- and [4]rotaxanes without the need for protecting group chemistry. Whilst the first two iterations proceeded in good yield, the steric shielding that affords this selectivity also significantly reduces the efficacy of the active template (AT)-CuAAC reaction of the third alkyne towards the preparation of [4]rotaxanes, resulting in severely diminished yields.