Supramolecular assemblies of DNA with neutral nucleoside amphiphiles

Guanosine Nucleolipids: Synthesis, Characterization, Aggregation and X-Ray Crystallographic Identification of Electricity-Conducting G-Ribbons

The lipophilization of β-d-riboguanosine (1) with various symmetric as well as asymmetric ketones is described (→3a-3f). The formation of the corresponding O-2',3'-ketals is accompanied by the appearance of various fluorescent by-products which were isolated chromatographically as mixtures and tentatively analyzed by ESI-MS spectrometry. The mainly formed guanosine nucleolipids were isolated and characterized by elemental analyses, ¹ H-, ¹³ C-NMR and UV spectroscopy. For a drug profiling, static topological polar surface areas as well as ¹⁰ logP_OW values were calculated by an increment-based method as well as experimentally for the systems 1-octanol-H₂ O and cyclohexane-H₂ O. The guanosine-O-2',3'-ketal derivatives 3b and 3a could be crystallized in (D₆ )DMSO - the latter after one year of standing at ambient temperature. X-ray analysis revealed the formation of self-assembled ribbons consisting of two structurally similar 3b nucleolipid conformers as well as integrated (D₆ )DMSO molecules. In the case of 3a ⋅ DMSO, the ribbon is formed by a single type of guanosine nucleolipid molecules. The crystalline material 3b ⋅ DMSO was further analyzed by differential scanning calorimetry (DSC) and temperature-dependent polarization microscopy. Crystallization was also performed on interdigitated electrodes (Au, distance, 5 μm) and visualized by scanning electron microscopy. Resistance and amperage measurements clearly demonstrate that the electrode-bridging 3b crystals are electrically conducting. All O-2',3'-guanosine ketals were tested on their cytostatic/cytotoxic activity towards phorbol 12-myristate 13-acetate (PMA)-differentiated human THP-1 macrophages as well as against human astrocytoma/oligodendroglioma GOS-3 cells and against rat malignant neuroectodermal BT4Ca cells.

DNA-surfactant complexes: self-assembly properties and applications

Over the last few years, DNA-surfactant complexes have gained traction as unique and powerful materials for potential applications ranging from optoelectronics to biomedicine because they self-assemble with outstanding flexibility spanning packing modes from ordered lamellar, hexagonal and cubic structures to disordered isotropic phases. These materials consist of a DNA backbone from which the surfactants protrude as non-covalently bound side chains. Their formation is electrostatically driven and they form bulk films, lyotropic as well as thermotropic liquid crystals and hydrogels. This structural versatility and their easy-to-tune properties render them ideal candidates for assembly in bulk films, for example granting directional conductivity along the DNA backbone, for dye dispersion minimizing fluorescence quenching allowing applications in lasing and nonlinear optics or as electron blocking and hole transporting layers, such as in LEDs or photovoltaic cells, owing to their extraordinary dielectric properties. However, they do not only act as host materials but also function as a chromophore itself. They can be employed within electrochromic DNA-surfactant liquid crystal displays exhibiting remarkable absorptivity in the visible range whose volatility can be controlled by the external temperature. Concomitantly, applications in the biological field based on DNA-surfactant bulk films, liquid crystals and hydrogels are rendered possible by their excellent gene and drug delivery capabilities. Beyond the mere exploitation of their material properties, DNA-surfactant complexes proved outstandingly useful for synthetic chemistry purposes when employed as scaffolds for DNA-templated reactions, nucleic acid modifications or polymerizations. These promising examples are by far not exhaustive but foreshadow their potential applications in yet unexplored fields. Here, we will give an insight into the peculiarities and perspectives of each material and are confident to inspire future developments and applications employing this emerging substance class.

Cytidine- and guanosine-based nucleotide–lipids

A nucleotide–lipids family featuring the four natural nucleobases was explored through their self-assembly properties.

Drug delivery by supramolecular design

Principles rooted in supramolecular chemistry have empowered new and highly functional therapeutics and drug delivery devices. This general approach offers elegant tools rooted in molecular and materials engineered to address the many challenges faced in treating disease.

Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates

The Leloir donors are nucleotide sugars essential for a variety of glycosyltransferases (GTs) involved in the transfer of a carbohydrate to an acceptor substrate, typically a protein or an oligosaccharide. A series of less-polar nucleotide sugar analogues derived from uridine have been prepared by replacing one phosphate unit with an alkyl chain. The methodology is based on the radical hydrophosphonylation of alkenes, which allows coupling of allyl glycosyl compounds with a phosphate unit suitable for conjugation to uridine. Two of these compounds, the GalNAc and galactose derivatives, were further tested on a model GT, such as GalNAc-T2 (an important GT widely distributed in human tissues), to probe that both compounds bound in the medium-high micromolar range. The crystal structure of GalNAc-T2 with the galactose derivative traps the enzyme in an inactive form; this suggests that compounds only containing the β-phosphate could be efficient ligands for the enzyme. Computational studies with GalNAc-T2 corroborate these findings and provide further insights into the mechanism of the catalytic cycle of this family of enzymes.

From nucleobases to nucleolipids: an ITC approach on the thermodynamics of their interactions in aqueous solutions

Hybrid constructions based on nucleosides and lipophilic components, known as nucleolipids, have become an extremely interesting class of molecules, especially for their potential biomedical applications. In this matter, it seemed important to define the nature and estimate the strength of their interaction with polynucleotides by different ways. We report in this work a systematic investigation through isothermal titration calorimetry of the thermodynamics of the association and dissociation of adenine and thymine derivatives, not previously performed. Then we use the results obtained on these simple systems as a basis for comparison with the binding of phospholipids functionalized with adenosine and thymidine to polyadenylic or polyuridylic acids applying the same experimental technique.

Charge-reversal lipids, peptide-based lipids, and nucleoside-based lipids for gene delivery

Twenty years after gene therapy was introduced in the clinic, advances in the technique continue to garner headlines as successes pique the interest of clinicians, researchers, and the public. Gene therapy's appeal stems from its potential to revolutionize modern medical therapeutics by offering solutions to myriad diseases through treatments tailored to a specific individual's genetic code. Both viral and non-viral vectors have been used in the clinic, but the low transfection efficiencies when non-viral vectors are used have lead to an increased focus on engineering new gene delivery vectors. To address the challenges facing non-viral or synthetic vectors, specifically lipid-based carriers, we have focused on three main themes throughout our research: (1) The release of the nucleic acid from the carrier will increase gene transfection. (2) The use of biologically inspired designs, such as DNA binding proteins, to create lipids with peptide-based headgroups will improve delivery. (3) Mimicking the natural binding patterns observed within DNA, by using lipids having a nucleoside headgroup, will produce unique supramolecular assembles with high transfection efficiencies. The results presented in this Account demonstrate that engineering the chemical components of the lipid vectors to enhance nucleic acid binding and release kinetics can improve the cellular uptake and transfection efficacy of nucleic acids. Specifically, our research has shown that the incorporation of a charge-reversal moiety to initiate a shift of the lipid from positive to negative net charge improves transfection. In addition, by varying the composition of the spacer (rigid, flexible, short, long, or aromatic) between the cationic headgroup and the hydrophobic chains, we can tailor lipids to interact with different nucleic acids (DNA, RNA, siRNA) and accordingly affect delivery, uptake outcomes, and transfection efficiency. The introduction of a peptide headgroup into the lipid provides a mechanism to affect the binding of the lipid to the nucleic acid, to influence the supramolecular lipoplex structure, and to enhance gene transfection activity. Lastly, we discuss the in vitro successes that we have had when using lipids possessing a nucleoside headgroup to create unique self-assembled structures and to deliver DNA to cells. In this Account, we state our hypotheses and design elements as well as describe the techniques that we have used in our research to provide readers with the tools to characterize and engineer new vectors.

Lipid conjugated oligonucleotides: a useful strategy for delivery

Oligonucleotides, including antisense oligonucleotides and siRNA, are promising therapeutic agents against a variety of diseases. Effective delivery of these molecules is critical in view of their clinical application. Therefore, cation-based nanoplexes have been developed to improve the stability as well as the intracellular penetration of these short fragments of nucleic acids. However, this approach is clearly limited by the strong interaction with proteins after administration and by the inherent toxicity of these positively charged transfection materials. Neutral lipid-oligonucleotide conjugates have become a subject of considerable interest to improve the safe delivery of oligonucleotides. These molecules have been chemically conjugated to hydrophobic moieties such as cholesterol, squalene, or fatty acids to enhance their pharmacokinetic behavior and trans-membrane delivery. The present review gives an account of the main synthetic methods available to conjugate lipids to oligonucleotides and will discuss the pharmacological efficacy of this approach.

Self-assembled nucleolipids: from supramolecular structure to soft nucleic acid and drug delivery devices

This short review aims at presenting some recent illustrative examples of spontaneous nucleolipids self-assembly. High-resolution structural investigations reveal the diversity and complexity of assemblies formed by these bioinspired amphiphiles, resulting from the interplay between aggregation of the lipid chains and base–base interactions. Nucleolipids supramolecular assemblies are promising soft drug delivery systems, particularly for nucleic acids. Regarding prodrugs, squalenoylation is an innovative concept for improving efficacy and delivery of nucleosidic drugs.

Lipothioureas as Lipids for Gene Transfection: A Review

Non-viral gene therapy requires innovative strategies to achieve higher transfection efficacy. A few years ago, our group proposed bioinspired lipids whose interaction with DNA was not based on ionic interactions, but on hydrogen bonds. We thus developed lipids bearing a thiourea head which allowed an interaction with DNA phosphates through hydrogen bonds. After a proof of concept with a lipid bearing three thiourea functions, a molecular and cellular screening was performed by varying all parts of the lipids: the hydrophobic anchor, the spacer, the linker, and the thiourea head. Two lipothiourea-based structures were identified as highly efficient in vitro transfecting agents. The lipothioureas were shown to reduce non specific interactions with cell membranes and deliver their DNA content intracellularly more efficiently, as compared to cationic lipoplexes. These lipids could deliver siRNA efficiently and allowed specific cell targeting in vitro. In vivo, thiourea lipoplexes presented a longer retention time in the blood and less accumulation in the lungs after an intravenous injection in mice. They also induced luciferase gene expression in muscle and tumor after local administration in mice. Therefore, these novel lipoplexes represent an excellent alternative to cationic lipoplexes as transfecting agents. In this review we will focus on the structure activity studies that permitted the identification of the two most efficient thiourea lipids.

Nucleolipid nanovectors as molecular carriers for potential applications in drug delivery

Novel thymidine- or uridine-based nucleolipids, containing one hydrophilic oligo(ethylene glycol) chain and one or two oleic acid residues (called ToThy, HoThy and DoHu), have been synthesized with the aim to develop bio-compatible nanocarriers for drug delivery and/or produce pro-drugs. Microstructural characterization of their aggregates has been determined in pure water and in pseudo-physiological conditions through DLS and SANS experiments. In all cases stable vesicles, with mean hydrodynamic radii ranging between 120 nm and 250 nm have been revealed. Biological validation of the nucleolipidic nanocarriers was ensured by evaluation of their toxicological profiles, performed by administration of the nanoaggregates to a panel of different cell lines. ToThy exhibited a weak cytotoxicity and, at high concentration, some ability to interfere with cell viability and/or proliferation. In contrast, DoHu and HoThy exhibited no toxicological relevance, behaving similarly to POPC-based liposomes, widely used for systemic drug delivery. Taken together, these results show nucleolipid-based nanocarriers as finely tunable, multi-functional self-assembling materials of interest for the in vivo transport of biomolecules or drugs.

Synthesis, characterization, and in vitro transfection activity of charge-reversal amphiphiles for DNA delivery

A series of charge-reversal lipids were synthesized that possess varying chain lengths and end functionalities. These lipids were designed to bind and then release DNA based on a change in electrostatic interaction with DNA. Specifically, a cleavable ester linkage is located at the ends of the hydrocarbon chains. The DNA release from the amphiphile was tuned by altering the length and position of the ester linkage in the hydrophobic chains of the lipids through the preparation of five new amphiphiles. The amphiphiles and corresponding lipoplexes were characterized by DSC, TEM, and X-ray, as well as evaluated for DNA binding and DNA transfection. For one specific charge-reversal lipid, stable lipoplexes of approximately 550 nm were formed, and with this amphiphile, effective in vitro DNA transfection activities was observed.

Reduction-triggered delivery using nucleoside-lipid based carriers possessing a cleavable PEG coating

A new non-ionic nucleoside based lipid (DOU-SS-PEG(2000), 5'-PEG(2000)-2',3'-dioleoyluridine) featuring uridine (U) as nucleoside and 2',3'-dioleyl (DO), as lipid moieties and a poly(ethylene glycol) (PEG) thiolytic cleavable spacer for in vitro delivery of drugs is described. The PEG detachable nucleotide lipid (DOU-SS-PEG(2000)) was prepared via a convergent synthesis starting from HS-PEG-OMe and uridine. The reduction-triggered delivery using the PEG detachable nucleoside lipid DOU-SS-PEG(2000) was evaluated on both liposomal and micellar objects. The liposomes were prepared from of a mixture of DOTAU (N-[5'-(2',3'-dioleoyl)uridine]-N',N',N'-trimethylammonium tosylate), the PEG detachable nucleoside lipid DOU-SS-PEG(2000) and DOPE-rhodamine (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine B sulfonyl ammonium salt) (60/40/0.1), whereas a mixture of 99.9% of DOU-SS-PEG(2000) and 0.1% of DOPE-rhodamine was used to prepare micelles. In addition, the supramolecular systems underwent a reduction-induced morphology transition from a micellar to vesicular states, which was characterized by DLS, zeta potential and TEM. The disulfide bond of the PEG chain was cleaved, by adding a reducing agent such as dithiothréitol (DTT), to expose the cationic surface of the liposome. The internalization of the resulting liposomes was facilitated as shown by the enhanced fluorescence signal observed in ovarian cancer cells (SKOV3) compared to the pegylated liposome. Likewise, when DTT was added to the mixture of cells incubated in the presence of DOU-SS-PEG(2000)/DOPE-rhodamine micelle, the fluorescence was observed in almost 100% of the SKOV3 cells.

Nanostructured nonionic thymidine nucleolipid self-assembly materials

Three nucleoside lipids have been synthesized: 3'-oleoylthymidine, 3',5'-dioleoylthymidine, and 3'-phytanoylthymidine. Differential scanning calorimetry and X-ray diffraction have been employed to characterize the physical properties of these neat lipids. Polarizing optical microscopy, small-angle X-ray scattering, and cryo-transmission electron microscopy techniques have been used to investigate the phase behavior in aqueous systems. Both oleoyl-based nucleoside lipids adopted a lamellar crystalline phase in the neat form at room temperature, and the phytanoyl derivative exhibited a fluid isotropic phase. Under excess water conditions, the presence of one branched (phytanoyl) or one unsaturated (oleoyl) chain promoted the formation of a liquid-crystalline lamellar phase at physiological temperatures. In contrast, the 3',5'-dioleoylthymidine derivative is nonswelling and does not exhibit lyotropic liquid-crystalline phase behavior. The nucleolipids' propensity for DNA-type binding and recognition has been evaluated by using a monolayer system to measure surface pressure-area isotherms in a Langmuir trough and indicates that the nucleoside base is available for nonspecific hydrogen bonding in the monolayer liquid expanded state for the single-chain nucleolipids but not for the dual-chain amphiphile.

The effect of charge-reversal amphiphile spacer composition on DNA and siRNA delivery

A series of charge-reversal amphiphiles with different spacers separating the headgroup from the hydrophobic chains are described for delivery of DNA and siRNA. Among them, the amphiphiles possessing a glycine spacer (e.g., B-GlyGly) showed effective DNA transfection in CHO and NIH 3T3 cells, as well as siRNA gene knockdown in HepG2 and UASMC cells. Ethidium bromide quenching assays revealed that DNA was released the fastest from the lipoplex of B-GlyGly in the presence of esterase. Also, X-ray diffraction results indicated that the DNA was located between the adjacent lipid bilayers in the lipoplex of B-GlyGly. These distinct features appear to be required for high transfection activity.

Synthesis of novel 5'-uridine-head amphiphiles as model for DNA molecular recognition

Here we describe uridine functionalization in the 5' position, which provides new classes of cationic and nonionic amphiphiles specifically designed as DNA transfection agents. The synthetic procedures developed to obtain the cationic uridine-head surfactants prevented intramolecular cyclization that occurs when uridine is functionalized in this position without using protecting groups in the uracil.

Anionic nucleotide--lipids for in vitro DNA transfection

A family of new anionic nucleotide based lipids featuring thymidine-3'-monophosphate as nucleotide and 1,2-diacyl-sn-glycerol as lipid moiety for in vitro delivery of nucleic acids is described. The nucleotide lipids were prepared in three steps starting from 1,2-diacyl-sn-glycerols and 2'-deoxythymidine-3'-phosphoramidite. Gel electrophoresis experiments show that nucleotide-based lipid-DNA complexes are observed at Ca(2+) concentration higher than 1 mM. The transfection experiments carried out on mammalian Hek cell lines clearly demonstrate that the nucleotide moiety enhances the transfection efficacy of the natural anionic DPPA and DPPG lipids. SAXS studies indicate that the enhancement in transfection for nucleotide-based lipid formulations compared to those of the abasic natural derivative (DPPA) is likely due to the presence of the 2D columnar inverted hexagonal phase (H(II)) with a unit cell parameter a = 69.1 A in the nucleotide lipid formulations. The cytotoxicity studies of lipoplexes, evaluated against Hek cells using an MTS assay, revealed that palmitoyl nucleotide derivative complexes were not toxic even after 4 h of incubation, thus indicating that the anionic nucleotide lipids presented in this work offer an alternative to cationic transfection reagents.

Cationic nucleoside lipids based on a 3-nitropyrrole universal base for siRNA delivery

Cationic nucleoside lipids based on a 3-nitropyrrole universal base were prepared from D-ribose using a straightforward chemical synthesis. Several studies including DLS, TEM, and ethidium bromide (EthBr) assay demonstrated that these amphiphilic molecules form supramolecular organizations of nanometer size in aqueous solutions and are able to bind nucleic acids. siRNA knockdown experiments were performed with these nucleolipids, and we observed protein knockdown activity similar to the siPORT NeoFX positive control. No significant cytotoxicity was found.

Spontaneous self-assembly of water-soluble nucleotide-calixarene conjugates in small micelles coalescing to microspheres

Spontaneous self-assembly of calix[4]arenes bearing four 2'-deoxythymidine or 2'-deoxyadenosine nucleotide pendants is investigated using (1)H NMR, exchange NMR, and diffusion ordered NMR spectroscopies and dynamic light scattering. In aqueous medium, the nucleotide-calixarene conjugates, by noncovalent interactions involving both nucleobases and calixarene skeleton, form dimers which self-organize in micelles by increasing the concentration. Microscopic images (scanning electron microscopy and transmission electron microscopy) show that the nucleobase affects the aggregate morphology in the solid state.

Nucleoside, nucleotide and oligonucleotide based amphiphiles: a successful marriage of nucleic acids with lipids

Amphiphilic molecules based on nucleosides, nucleotides and oligonucleotides are finding more and more biotechnological applications. This Perspective highlights their synthesis, supramolecular organization as well as their applications in the field of biotechnology.