A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy.

Nature-inspired molecular machines can exert mechanical forces by controlling and varying the distance between two molecular subunits in response to different inputs. Here, we present an automated molecular linear actuator composed of T7 RNA polymerase (T7RNAP) and a DNA [2]rotaxane. A T7 promoter region and terminator sequences are introduced into the rotaxane axle to achieve automated and iterative binding and detachment of T7RNAP in a self-controlled fashion. Transcription by T7RNAP is exploited to control the release of the macrocycle from a single-stranded (ss) region in the T7 promoter to switch back and forth from a static state (hybridized macrocycle) to a dynamic state (movable macrocycle). During transcription, the T7RNAP keeps restricting the movement range on the axle available for the interlocked macrocycle and prevents its return to the promotor region. Since this range is continuously depleted as T7RNAP moves along, a directional and active movement of the macrocycle occurs. When it reaches the transcription terminator, the polymerase detaches, and the system can reset as the macrocycle moves back to hybridize again to the ss-promoter docking site. The hybridization is required for the initiation of a new transcription cycle. The rotaxane actuator runs autonomously and repeats these self-controlled cycles of transcription and movement as long as NTP-fuel is available.

Construction of pH sensitive smart glutathione peroxidase (GPx) mimics based on pH responsive pseudorotaxanes.

Two organoselenium compounds, both of which were modified with two primary amine groups, were designed and synthesized to mimic the catalytic properties of glutathione peroxidase (GPx). It was demonstrated that the catalytic mechanism of the diselenide organoselenium compound (compound 1) was a ping-pong mechanism while that of the selenide organoselenium compound (compound 2) was a sequential mechanism. The pH-controlled switching of the catalytic activities was achieved by controlling the formation and dissociation of the pseudorotaxanes based on the organoselenium compounds and cucurbit[6]uril (CB[6]). Moreover, the switching was reversible at pH between 7 and 9 for compound 1 or between 7 and 10 for compound 2.

A Complex Comprising a Cyanine Dye Rotaxane and a Porphyrin Nanoring as a Model Light-Harvesting System.

A nanoring-rotaxane supramolecular assembly with a Cy7 cyanine dye (hexamethylindotricarbocyanine) threaded along the axis of the nanoring was synthesized as a model for the energy transfer between the light-harvesting complex LH1 and the reaction center in purple bacteria photosynthesis. The complex displays efficient energy transfer from the central cyanine dye to the surrounding zinc porphyrin nanoring. We present a theoretical model that reproduces the absorption spectrum of the nanoring and quantifies the excitonic coupling between the nanoring and the central dye, thereby explaining the efficient energy transfer and demonstrating similarity with structurally related natural light-harvesting systems.

An Artificial Molecular Shuttle Operates in Lipid Bilayers for Ion Transport.

Inspired by natural biomolecular machines, synthetic molecular-level machines have been proven to perform well-defined mechanical tasks and measurable work. To mimic the function of channel proteins, we herein report the development of a synthetic molecular shuttle, [2]rotaxane 3, as a unimolecular vehicle that can be inserted into lipid bilayers to perform passive ion transport through its stochastic shuttling motion. The [2]rotaxane molecular shuttle is composed of an amphiphilic molecular thread with three binding stations, which is interlocked in a macrocycle wheel component that tethers a K+ carrier. The structural characteristics enable the rotaxane to transport ions across the lipid bilayers, similar to a cable car, transporting K+ with an EC50 value of 1.0 µM (3.0 mol % relative to lipid). We expect that this simple molecular machine will provide new opportunities for developing more effective and selective ion transporters.

Allosteric Control of Oxidative Catalysis by a DNA Rotaxane Nanostructure.

DNA is a versatile construction material for the bottom-up assembly of structures and functional devices in the nanoscale. Additionally, there are specific sequences called DNAzymes that can fold into tertiary structures that display catalytic activity. Here we report the design of an interlocked DNA nanostructure that is able to fine-tune the oxidative catalytic activity of a split DNAzyme in a highly controllable manner. As scaffold, we employed a double-stranded DNA rotaxane for its ability to undergo programmable and predictable conformational changes. Precise regulation of the DNAzyme's oxidative catalysis can be achieved by external stimuli (i.e., addition of release oligos) that modify the spatial arrangement within the system, without interfering with the catalytic core, similar to structural rearrangements that occur in allosterically controlled enzymes. We show that multiple switching steps between the active and inactive conformations can be performed consistent with efficient regulation and robust control of the DNA nanostructure.

Crosslinked Network with Rotatable Binding Sites Based on Monocarboxylated α-Cyclodextrin [2]Rotaxane Capable of Angiotensin†III Recognition.

Synthetic receptors selective for target peptides or proteins have received attention because of their potential applications in the separation of biomolecules and biomedical diagnostics. Herein, a [2]rotaxane-based functional monomer containing monocarboxylated α-cyclodextrin (α-CD) was synthesized, and its crosslinked polymers were evaluated to determine their binding ability to a model peptide, angiotensin III (Arg-Val-Tyr-Ile-His-Pro-Phe), containing an arginine (Arg) residue. The binding ability of the resulting polymers toward angiotensin III, angiotensin IV (Val-Tyr-Ile-His-Pro-Phe), and FMRF-amide (Phe-Met-Arg-Phe) was examined by the batch-binding assay and compared with that of control polymers, in which maleic acid-introduced α-CD was chemically crosslinked. The results suggest that the [2]rotaxane-based functional monomer in the crosslinked polymer contributes to the high affinity toward angiotensin III. The α-CD motion and rotation within the [2]rotaxane-based crosslinked polymer may be applicable for designing molecular recognition materials.

A Protein Rotaxane Controls the Translocation of Proteins Across a ClyA Nanopore.

Rotaxanes, pseudorotaxanes, and catenanes are supramolecular complexes with potential use in nanomachinery, molecular computing, and single-molecule studies. Here we constructed a protein rotaxane in which a polypeptide thread is encircled by a Cytolysin A (ClyA) nanopore and capped by two protein stoppers. The rotaxane could be switched between two states. At low negative applied potentials (<-50 mV) one of the protein stoppers resided inside the nanopore indefinitely. Under this configuration the rotaxane prevents the diffusion of protein molecules across the lipid bilayer and provides a useful platform for single-molecule analysis. High negative applied potentials (-100 mV) dismantled the interlocked rotaxane system by the forceful translocation of the protein stopper, allowing new proteins to be trapped inside or transported across the nanopore. The observed voltage threshold for the translocation of the protein stopper through the nanopore related well to the biphasic voltage dependence of the residence time measured for the freely diffusing protein stopper. We propose a model in which molecules translocate through a nanopore when the average dwell time decreases with the applied potential.

The Role of Galectin-1 in Cancer Progression, and Synthetic Multivalent Systems for the Study of Galectin-1.

This review discusses the role of galectin-1 in the tumor microenvironment. First, the structure and function of galectin-1 are discussed. Galectin-1, a member of the galectin family of lectins, is a functionally dimeric galactoside-binding protein. Although galectin-1 has both intracellular and extracellular functions, the defining carbohydrate-binding role occurs extracellularly. In this review, the extracellular roles of galectin-1 in cancer processes are discussed. In particular, the importance of multivalent interactions in galectin-1 mediated cellular processes is reviewed. Multivalent interactions involving galectin-1 in cellular adhesion, mobility and invasion, tumor-induced angiogenesis, and apoptosis are presented. Although the mechanisms of action of galectin-1 in these processes are still not well understood, the overexpression of galectin-1 in cancer progression indicates that the role of galectin-1 is significant. To conclude this review, synthetic frameworks that have been used to modulate galectin-1 processes are reviewed. Small molecule oligomers of carbohydrates, carbohydrate-functionalized pseudopolyrotaxanes, cyclodextrins, calixarenes, and glycodendrimers are presented. These synthetic multivalent systems serve as important tools for studying galectin-1 mediated cancer cellular functions.

Xanthomonins†I-III: a new class of lasso peptides with a seven-residue macrolactam ring.

Lasso peptides belong to the class of ribosomally synthesized and post-translationally modified peptides. Their common distinguishing feature is an N-terminal macrolactam ring that is threaded by the C-terminal tail. This lasso fold is maintained through steric interactions. The isolation and characterization of xanthomonins I-III, the first lasso peptides featuring macrolactam rings consisting of only seven amino acids, is now presented. The crystal structure of xanthomonin I and the NMR structure of xanthomonin II were also determined. A total of 25 variants of xanthomonin II were generated to probe different aspects of the biosynthesis, stability, and fold maintenance. These mutational studies reveal the limits such a small ring imposes on the threading and show that every plug amino acid larger than serine is able to maintain a heat-stable lasso fold in the xanthomonin II scaffold.

Enhanced Tumor Targeting and Antitumor Activity of Methylated ß-Cyclodextrin-Threaded Polyrotaxanes by Conjugating Cyclic RGD Peptides.

We previously reported that acid-degradable methylated ß-cyclodextrins (Me-ß-CDs)-threaded polyrotaxanes (Me-PRXs) can induce autophagic cell death through endoplasmic reticulum (ER) stress-related autophagy, even in apoptosis-resistant cells. Hence, Me-PRXs show great potential as anticancer therapeutics. In this study, peptide-supermolecule conjugates were designed to achieve the targeted delivery of Me-PRX to malignant tumors. Arg-Gly-Asp peptides are well-known binding motifs of integrin αvß3, which is overexpressed on angiogenic sites and many malignant tumors. The tumor-targeted cyclic Arg-Gly-Asp (cRGD) peptide was orthogonally post-modified to Me-PRX via click chemistry. Surface plasmon resonance (SPR) results indicated that cRGD-Me-PRX strongly binds to integrin αvß3, whereas non-targeted cyclic Arg-Ala-Glu (cRGE) peptide conjugated to Me-PRX (cRGE-Me-PRX) failed to interact with integrins αvß3. In vitro, cRGD-Me-PRX demonstrated enhanced cellular internalization and antitumor activity in 4T1 cells than that of unmodified Me-PRX and non-targeted cRGE-Me-PRX, due to its ability to recognize integrin αvß3. Furthermore, cRGD-Me-PRX accumulated effectively in tumors, leading to antitumor effects, and exhibited excellent biocompatibility and safety in vivo. Therefore, cRGD conjugation to enhance selectivity for integrin αvß3-positive cancer cells is a promising design strategy for Me-PRXs in antitumor therapy.

A rotaxane turing machine for peptides.

A ringing belt: An artificial molecular machine was invented to build up a programmable peptidic sequence. By molecular movements, the rotaxane-based machine progressively introduces amino acids to form a short peptide chain. The journey towards an artificial ribosome is still quite long, but a conceivable future can be envisaged.

Synthesis of 2-hydroxypropyl-ß-cyclodextrin/pluronic-based polyrotaxanes via heterogeneous reaction as potential Niemann-Pick type C therapeutics.

Five polyrotaxanes were synthesized by threading 2-hydroxypropyl-ß-cyclodextrin (HP-ß-CD) onto a variety of α,ω-ditriethylenediamino-N-carbamoyl-poly-(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (Pluronic) triblock copolymers using a two-pot strategy under heterogeneous, nonaqueous conditions. The threaded HP-ß-CD units were retained on the pseudopolyrotaxane precursors by end-capping the branched diamine termini with sodium 2,4,6-trinitrobenzene sulfonate. Inclusion of the Pluronic copolymers within the HP-ß-CD cavities was more favorable in nonpolar solvents, such as diethyl ether and n-hexane, both of which gave better coverage ratios than polar solvents. (1)H NMR and MALDI-TOF were used to estimate the average molecular weights of the purified polyrotaxane products. A globular morphology of aggregated polyrotaxanes was observed by tapping-mode AFM imaging of dried samples. Treatment of Niemann-Pick C (NPC) type 2-deficient fibroblasts with the polyrotaxane derivatives produced substantial reductions in sterol accumulation, as seen by diminished filipin staining in these cells, suggesting that Pluronic-based polyrotaxanes may be promising vehicles for delivery of HP-ß-CD to cells with abnormal cholesterol accumulation.

Differences in the Intracellular Localization of Methylated ß-Cyclodextrins-Threaded Polyrotaxanes Lead to Different Cellular States.

Activation of autophagy represents a potential therapeutic strategy for the treatment of diseases that are caused by the accumulation of defective proteins and the formation of abnormal organelles. Methylated ß-cyclodextrins-threaded polyrotaxane (Me-PRX), a supramolecular structured polymer, induces autophagy by interacting with the endoplasmic reticulum. We previously reported on the successful activation of mitochondria-targeted autophagy by delivering Me-RRX to mitochondria using a MITO-Porter, a mitochondria-targeted nanocarrier. The same level of autophagy induction was achieved at one-twentieth the dosage for the MITO-Porter (Me-PRX) compared to the naked Me-PRX. We report herein on the quantitative evaluation of the intracellular organelle localization of both naked Me-PRX and the MITO-Porter (Me-PRX). Mitochondria, endoplasmic reticulum and lysosomes were selected as target organelles because they would be involved in autophagy induction. In addition, organelle injury and cell viability assays were performed. The results showed that the naked Me-PRX and the MITO-Porter (Me-PRX) were localized in different intracellular organelles, and organelle injury was different, depending on the route of administration, indicating that different organelles contribute to autophagy induction. These findings indicate that the organelle to which the autophagy-inducing molecules are delivered plays an important role in the level of induction of autophagy.

Water-soluble, deep-red fluorescent squaraine rotaxanes.

Eight fluorescent squaraine rotaxanes with deep-red absorption/emission wavelengths were prepared and assessed for chemical stability and suitability as water-soluble, fluorescent tracers. The most stable squaraine rotaxanes have four large stopper groups attached to the ends of the encapsulated squaraine, and two members of this structural class have promise as highly fluorescent tracers with rapid renal clearance and very low tissue uptake in living mice.

Poly-ε-caprolactone/poly(rotaxane) seeded with human dental pulp stem cells or osteoblasts promotes angiogenesis: a chorioallantoic membrane assay.

Biomaterials used for tissue regeneration should ideally provide a favorable environment for cell proliferation and differentiation. Angiogenesis is crucial for supplying oxygen and nutrients necessary for cellular survival at implantation sites. The aim of this study was to evaluate the overall angiogenesis response of a poly ε-caprolactone/poly (rotaxane) blend (poly-blend) carried by human dental pulp stem cells (hDPSCs) or osteoblasts (OB) seeded in the chorioallantoic membranes (CAM) of fertilized chicken eggs on embryonic day 7. They were classified into the following intervention groups: (a) poly(polymeric blend disks free of cells); (b) hDPSC seeded onto CAM; (c) poly/hDPSC (where hDPSCs were seeded onto poly-blend); (d) poly/OB (where osteoblasts were seeded onto poly); (e) OB (where hDPSCs differentiated into osteoblasts were seeded onto CAM); and (f) a negative control when a sterilized silicone ring free of cells or polymer was inserted into CAM. On embryonic day 14, the quantitative and qualitative characteristics of the blood vessels in the CAMs were analyzed macroscopically and microscopically. Macroscopic examination showed that the Poly/hDPSC samples exhibited an increased medium vessel density. Additionally, microscopic observations showed that the Poly/hDPSC group and poly alone resulted in a large lumen area of vascularization. Thus, poly ε-caprolactone/poly (rotaxane) did not impair angiogenesis. Furthermore, poly-blend carried by stem cells of dental pulp origin shows a better vasculogenic potential, which is essential for regenerative therapies.

Development of a multi-arm polyrotaxanes modified mesoporous silica-coated gold nanoplatform for protecting endothelial progenitor cells against high glucose environment.

Recent study reported that endothelial progenitor cells (EPCs) have potential to treat diabetic macroangiopathy. High glucose environment of diabetes can affect the adhesion of EPCs by decreasing the expression of CXC chemokine receptor 4 (CXCR4) and affect the proliferation of EPCs by decreasing the expression of miR-126. The results showed that the cytotoxicity of GNR@MSNs@PEI to EPCs was significantly lower than PEI; the temperature of GNR@MSNs@PEI solution can be controlled between 38-40°C under 808 nm laser irradiation. 25.67 µg of pcDNA3.1-GFP-CXCR4 and 5.36 µg of FITC-miR-126 could be loaded in 1 mg of GNR@MSNs@PEI; GNR@MSNs@PEI has gene transfection almost the same as Lipofectamine 3000. Subsequent in vitro studies showed that pcDNA3.1-GFP-CXCR4 and miR-126 loaded GNR@MSNs@PEI can significantly increase the adhesion and proliferation and decrease the apoptosis of EPCs treated with high glucose under 808 nm laser irradiation. In conclusion, nano-carriers (GNR@MSNs@PEI) with high pcDNA3.1-CXCR4 and miR-126 loading capacity, high biocompatibility, well cell internalization, and controllable release ability were constructed to transfer CXCR4 expression plasmid (pcDNA3.1-CXCR4) and miR-126 into EPCs efficiently. Further in vitro studies indicated that pcDNA3.1-CXCR4 and miR-126-loaded GNR@MSNs@PEI could protect EPCs against high glucose-induced injury.

Cografting of Zwitterionic Sulfobetaines and Cationic Amines on ß-Cyclodextrin-Threaded Polyrotaxanes Facilitates Cellular Association and Tissue Accumulation with High Biocompatibility.

ß-Cyclodextrins (ß-CDs) and ß-CD-containing polymers have attracted considerable attention as potential candidates for the treatment of cholesterol-related metabolic and intractable diseases. We have advocated the use of ß-CD-threaded acid-degradable polyrotaxanes (PRXs) as intracellular delivery carriers for ß-CDs. As unmodified PRXs are insoluble in aqueous solutions, chemical modification of PRXs is an essential process to improve their solubility and impart novel functionalities. In this study, we investigated the effect of the modification of zwitterionic sulfobetaines on PRXs due to their excellent solubility, biocompatibility, and bioinert properties. Sulfobetaine-modified PRXs were synthesized by converting the tertiary amino groups of precursor 2-(N,N-dimethylamino)ethyl carbamate-modified PRXs (DMAE-PRXs) using 1,3-propanesultone. The resulting sulfobetaine-modified PRXs showed high solubility in aqueous solutions and no cytotoxicity, while their intracellular uptake levels were low. To further improve this system, we designed PRXs cografted with zwitterionic sulfobetaine and cationic DMAE groups via partial betainization of the DMAE groups. Consequently, the interaction with proteins, intracellular uptake levels, and liver accumulation of partly betainized PRXs were found to be higher than those of completely betainized PRXs. Additionally, partly betainized PRXs showed no toxicity in vitro or in vivo despite the presence of residual cationic DMAE groups. Furthermore, partly betainized PRXs ameliorated the abnormal free cholesterol accumulation in Niemann-Pick type C disease patient-derived cells at lower concentrations than ß-CD derivatives and previously designed PRXs. Overall, the cografting of sulfobetaines and amines on PRXs is a promising chemical modification for therapeutic applications due to the high cholesterol-reducing ability and biocompatibility of such modified PRXs. In addition, modification with both zwitterionic and cationic groups can be used for the design of various polymeric materials exhibiting both bioinert and bioactive characteristics.

Post-Cross-Linking of Collagen Hydrogels by Carboxymethylated Polyrotaxanes for Simultaneously Improving Mechanical Strength and Cell Proliferation.

To improve the mechanical properties of collagen hydrogels, which are widely utilized as biomaterials, post-cross-linking of collagen hydrogels was performed using polyrotaxane (PRX) as a cross-linker. Herein, carboxymethyl group-modified PRXs (CMPRs) composed of carboxymethylated α-cyclodextrins (α-CDs) threaded along poly(ethylene glycol) (PEG) capped with bulky stoppers were used to cross-link via reaction with the amino groups in the collagen. Four series of CMPRs with different α-CD threading ratios and axle PEG molecular weights were used for the post-cross-linking of the collagen hydrogels to verify the optimal CMPR chemical compositions. The post-cross-linking of the collagen hydrogels with CMPRs improved the swelling ratios and mechanical properties, such as viscoelasticity and tensile strength. Among the tested CMPRs, CMPRs with an axle PEG molecular weight of 35,000 (PEG35k) resulted in better mechanical properties than CMPRs with a PEG10k axis. Additionally, the cell adhesion and proliferation were greatly improved on the surface of the collagen hydrogels post-cross-linked with CMPRs with the PEG35k axle. These findings suggest that the molecular weight of an axle polymer in CMPRs is a more important parameter than the α-CD threading ratios. Accordingly, the post-cross-linking of hydrogels with PRXs is promising for improving the mechanical properties and biomaterial functions of collagen hydrogels.

Structure-function relationships of cholesterol mobilization from the endo-lysosome compartment of NPC1-deficient human cells by ß-CD polyrotaxanes.

Niemann-Pick Type C is a rare metabolic disorder characterized by the cellular accumulation of cholesterol within endosomal and lysosomal compartments. 2-Hydroxypropyl-ß-cyclodextrin (HP-ß-CD) containing polyrotaxanes represent an attractive approach for treating this disease due to their ability to circulate in the blood stream for longer periods of time as a prodrug form of HP-ß-CD. Once inside the cell, the macromolecular structure is thought to break down into the Pluronic precursor and the active cyclodextrin agent that promotes cholesterol mobilization from the aberrant accumulations within NPC-deficient cells. We now report that both cholesterol and decaarginine (R10) endcapped polyrotaxanes are able to remove cholesterol from NPC1 patient fibroblasts. R10 endcapped materials enter these cells and are localized within endosomes after 16 h. The cholesterol mobilization from endo-lysosomal compartments of NPC1 cells by the polyrotaxanes was directly related to their extent of endcapping and their threading efficiency. Incorporation of 4-sulfobutylether-ß-cyclodextrin (SBE-ß-CD) significantly improved cholesterol mobilization due to the improved solubility of the compounds. Additionally, in our efforts to scale-up the synthesis for preclinical studies, we prepared a library of polyrotaxanes using a solid phase synthesis method. These compounds also led to significant cholesterol mobilization from the cells, however, cytotoxicity studies showed that they were substantially more toxic than those prepared by the solvent-assisted method, thus limiting the therapeutic utility of agents prepared by this expedited method. Our findings demonstrate that complete endcapping of the polyrotaxanes and improved solubility are important design features for delivering high copy numbers of therapeutic ß-CD to promote enhanced sterol clearance in human NPC1-deficient cells.