Nucleic-Acid-Templated Synthesis of Smart Polymer Vectors for Gene Delivery

Nucleic acids are information-rich and readily available biomolecules, which can be used to template the polymerization of synthetic macromolecules. Here, we highlight the control over the size, composition, and sequence one can nowadays obtain by using this methodology. We also highlight how templated processes exploiting dynamic covalent polymerization can, in return, result in therapeutic nucleic acids fabricating their own dynamic delivery vector - a biomimicking concept that can provide original solutions for gene therapies.

[1,2,4]triazolo[4,3-a]quinoxaline as Novel Scaffold in the Imiqualines Family: Candidates with Cytotoxic Activities on Melanoma Cell Lines

Cutaneous melanoma is one of the most aggressive human cancers and is the deadliest form of skin cancer, essentially due to metastases. Novel therapies are always required, since cutaneous melanoma develop resistance to oncogenic pathway inhibition treatment. The Imiqualine family is composed of heterocycles diversely substituted around imidazo[1,2-a]quinoxaline, imidazo[1,2-a]pyrazine, imidazo[1,5-a]quinoxaline, and pyrazolo[1,5-a]quinoxaline scaffolds, which display interesting activities on a panel of cancer cell lines, especially melanoma cell lines. We have designed and prepared novel compounds based on the [1,2,4]triazolo[4,3-a]quinoxaline scaffold through a common synthetic route, using 1-chloro-2-hydrazinoquinoxaline and an appropriate aldehyde. Cyclization is ensured by an oxidation-reduction mechanism using chloranil. The substituents on positions 1 and 8 were chosen based on previous structure-activity relationship (SAR) studies conducted within our heterocyclic Imiqualine family. Physicochemical parameters of all compounds have also been predicted. A375 melanoma cell line viability has been evaluated for 16 compounds. Among them, three novel [1,2,4]triazolo[4,3-a]quinoxalines display cytotoxic activities. Compounds 16a and 16b demonstrate relative activities in the micromolar range (respectively, 3158 nM and 3527 nM). Compound 17a shows the best EC₅₀ of the novel series (365 nM), even if EAPB02303 remains the lead of the entire Imiqualine family (3 nM).

Complexation Preferences of Dynamic Constitutional Frameworks as Adaptive Gene Vectors

The growing applications of therapeutic nucleic acids requires the concomitant development of vectors that are optimized to complex one type of nucleic acid, forming nanoparticles suitable for further trafficking and delivery. While fine-tuning a vector by molecular engineering to obtain a particular nanoscale organization at the nanoparticle level can be a challenging endeavor, we turned the situation around and instead screened the complexation preferences of dynamic constitutional frameworks toward different types of DNAs. Dynamic constitutional frameworks (DCF) are recently-identified vectors by our group that can be prepared in a versatile manner through dynamic covalent chemistry. Herein, we designed and synthesized 40 new DCFs that vary in hydrophilic/hydrophobic balance, number of cationic headgroups. The results of DNA complexation obtained through gel electrophoresis and fluorescent displacement assays reveal binding preferences of different DCFs toward different DNAs. The formation of compact spherical architectures with an optimal diameter of 100-200 nm suggests that condensation into nanoparticles is more effective for longer PEG chains and PEI groups that induce a better binding performance in the presence of DNA targets.

Structure-Activity Relationships in Nucleic-Acid-Templated Vectors Based on Peptidic Dynamic Covalent Polymers

The use of nucleic acids as templates, which can trigger the self-assembly of their own vectors represent an emerging, simple and versatile, approach toward the self-fabrication of tailored nucleic acids delivery vectors. However, the structure-activity relationships governing this complex templated self-assembly process that accompanies the complexation of nucleic acids remains poorly understood. Herein, the class of arginine-rich dynamic covalent polymers (DCPs) composed of different monomers varying the number and position of arginines were studied. The combinations that lead to nucleic acid complexation, in saline buffer, using different templates, from short siRNA to long DNA, are described. Finally, a successful peptidic DCP featuring six-arginine repeating unit that promote the safe and effective delivery of siRNA in live cancer cells was identified.

Traceless pH-Sensitive Antibody Conjugation Inspired by Citraconic Anhydride

We introduce a pH-sensitive amide bond, inspired by citraconic anhydride, for the reversible conjugation of polymers to the lysine residues of proteins and antibodies. The pH sensitivity arises from a conformation lock at the end of the polymer, which we introduce by means of a Diels-Alder reaction, that positions a carboxylic acid close to the amide after conjugation occurs. The amide is stable over weeks at pH 7.4 but sensitive to hydrolysis at pH 5.5 and below, returning the amine to its original state. The pH sensitivity can be tuned by positioning secondary amide groups nearby. We use this approach to PEGylate an antibody to human serum albumin at high dilution and demonstrate successful recovery of the activity after hydrolysis at pH 5.5. These results offer a convenient and traceless approach to protein and antibody functionalization.

Fluorescent Dynamic Covalent Polymers for DNA Complexation and Templated Assembly

Dynamic covalent polymers (DCPs) offer opportunities as adaptive materials of particular interest for targeting, sensing and delivery of biological molecules. In this view, combining cationic units and fluorescent units along DCP chains is attractive for achieving optical probes for the recognition and delivery of nucleic acids. Here, we report on the design of acylhydrazone-based DCPs combining cationic arginine units with π-conjugated fluorescent moieties based on thiophene-ethynyl-fluorene cores. Two types of fluorescent building blocks bearing neutral or cationic side groups on the fluorene moiety are considered in order to assess the role of the number of cationic units on complexation with DNA. The (chir)optical properties of the building blocks, the DCPs, and their complexes with several types of DNA are explored, providing details on the formation of supramolecular complexes and on their stability in aqueous solutions. The DNA-templated formation of DCPs is demonstrated, which provides new perspectives on the assembly of fluorescent DCP based on the nucleic acid structure.

Hierarchical self-assembly of aromatic peptide conjugates into supramolecular polymers: it takes two to tango

Supramolecular polymers are self-assembled materials displaying adaptive and responsive "life-like" behaviour which are often made of aromatic compounds capable of engaging in π-π interactions to form larger assemblies. Major advances have been made recently in controlling their mode of self-assembly, from thermodynamically-controlled isodesmic to kinetically-controlled living polymerization. Dynamic covalent chemistry has been recently implemented to generate dynamic covalent polymers which can be seen as dynamic analogues of biomacromolecules. On the other hand, peptides are readily-available and structurally-rich building blocks that can lead to secondary structures or specific functions. In this context, the past decade has seen intense research activity in studying the behaviour of aromatic-peptide conjugates through supramolecular and/or dynamic covalent chemistries. Herein, we review those impressive key achievements showcasing how aromatic- and peptide-based self-assemblies can be combined using dynamic covalent and/or supramolecular chemistry, and what it brings in terms of the structure, self-assembly pathways, and function of supramolecular and dynamic covalent polymers.

Cell-Selective siRNA Delivery Using Glycosylated Dynamic Covalent Polymers Self-Assembled In Situ by RNA Templating

Dynamic covalent libraries enable exploring complex chemical systems from which bioactive assemblies can adaptively emerge through template effects. In this work, we studied dynamic covalent libraries made of complementary bifunctional cationic peptides, yielding a diversity of species from macrocycles to polymers. Although polymers are typically expressed only at high concentration, we found that siRNA acts as a template in the formation of dynamic covalent polymers at low concentration in a process guided by electrostatic binding. Using a glycosylated building block, we were able to show that this templated polymerization further translates into the multivalent presentation of carbohydrate ligands, which subsequently promotes cell uptake and even cell-selective siRNA delivery.

Dynamic Covalent Polymers for Biomedical Applications

The rapid development of supramolecular polymer chemistry and constitutional dynamic chemistry over the last decades has made tremendous impact on the emergence of dynamic covalent polymers. These materials are formed through reversible covalent bonds, endowing them with adaptive and responsive features that have resulted in high interest throughout the community. Owing to their intriguing properties, such as self-healing, shape-memory effects, recyclability, degradability, stimuli-responsiveness, etc., the materials have found multiple uses in a wide range of areas. Of special interest is their increasing use for biomedical applications, and many examples have been demonstrated in recent years. These materials have thus been used for the recognition and sensing of biologically active compounds, for the modulation of enzyme activity, for gene delivery, and as materials for cell culture, delivery, and wound-dressing. In this review, some of these endeavors are discussed, highlighting the many advantages and unique properties of dynamic covalent polymers for use in biology and biomedicine.

Exploiting complexity to implement function in chemical systems

This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.

Cationic dynamic covalent polymers for gene transfection

Dynamic covalent polymers have revealed strong potential in gene delivery, thanks to their versatile self-assembly, adaptive and responsive behaviors.

Growing Prospects of Dynamic Covalent Chemistry in Delivery Applications

Delivery remains a major obstacle restricting the potential action of small molecular drugs as well as novel biologics which cannot readily enter cells without the help of a vector. A successful active delivery process involves three steps: (a) tagging the drug with a vector, (b) effective trafficking of this [drug-vector] conjugate through biological barriers, and finally (c) controlled drug release. While covalent bond formation and/or supramolecular association is involved in the making of the [drug-vector] conjugate, the final step requires precisely a controlled dissociation in order to trigger drug release. Therefore, in pursuit of smart, effective, and nontoxic delivery systems, it has become widely recognized that control over dynamic self-assembly could unleash the efficacy of artificial vectors. In this Account, I discuss our endeavors, and those of colleagues, in the recent implementation of Dynamic Covalent Chemistry (DCvC) in delivery applications. DCvC exploits reversible covalent reactions to generate covalent systems that can self-fabricate, adapt, respond, and fall apart in a controlled fashion. A privileged set of reversible covalent reactions has emerged in the community working on delivery applications and is based on condensation reactions (imine, acylhydrazone, oxime), and disulfide and boronate ester formations. The latest developments making this chemistry particularly attractive for such a DCvC approach are discussed. The rational justifying the potential of DCvC in delivery is based on the principle that using such reversible covalent reactions afford transient [drug-vector] conjugates which form spontaneously and chemoselectively, then adapt and self-correct their structure during self-assembly and trafficking thanks to the dynamic nature of the reversible covalent bonds, and finally respond to physicochemical stimuli such as pH and redox changes, thereby enabling controlled dissociation and concomitant drug release. For these reasons, DCvC has recently emerged as a leverage tool with growing prospects for advancing toward smarter delivery systems. The implementation of DCvC can follow three approaches that are discussed herein: (1) dynamic covalent bioconjugates, involving the transient covalent conjugation with a vector, (2) dynamic covalent vectors, involving the controlled dynamic and adaptive assembly and disassembly of vectors that complex drugs through supramolecular association, and (3) dynamic covalent targeting, involving the transient chemoselective formation of covalent bonds with the constituents of cell membranes. While DCvC has already attracted interest in material sciences, the recent results described in this Account showcase the vast potential of DCvC in biological sciences, and in particular in delivery applications where self-fabricated, adaptive, and responsive devices are of utmost importance.

Conjugated Polyimine Dynamers as Phase-Sensitive Membrane Probes

In this report, dynamic polyimines are introduced as multifunctional sensors of lipid bilayer phases. Under mildly acidic conditions, self-condensation of push-pull amino formyl fluorenes into polyimines occurs in solid- or liquid-ordered phases but not in liquid-disordered phases of vesicular membranes. The obtained conjugated polymers are characterized by a progressive red shift of the absorption maxima, the appearance of exciton-coupled circular dichroism (CD) bands, and fluorescence quenching. These characteristics allow multiple modes of detection of membrane phases, which are known to change under membrane tension.

Multivalent Dendrimers and their Differential Recognition of Short Single-Stranded DNAs of Various Length and Sequence

Polycationic dendrimers were generated through simple and versatile reversible amine/aldehyde-imine chemistry. The inherent CD spectroscopic signal arising from the helical structures of single-stranded DNA (ssDNA) undergoes a dramatic amplification in the presence of the synthesised polycationic dendrimers. Compared to the first-generation core molecule, the second-generation dendrimer shows high spectroscopic responses upon chiral recognition of short ssDNA, owing to the combination of self-assembly and multivalency effects. The maximum signal variation is reached at the molar ratio at which the ratio between the negative charges in ssDNA balance the positive charges of the dendrimers, thus the approach enables differential recognition of ssDNAs of different lengths. Altogether, these results accelerate the simple and systematic discovery of efficient adaptive molecules for biomimetic recognition of ssDNA with high accuracy.

Self-assembly and chiroptical properties in supramolecular complexes of adenosine phosphates and guanidinium-bispyrene

Supramolecular systems that respond to the hydrolysis of adenosine phosphates (APs) are attractive for biosensing and to fabricate bioinspired self-assembled materials. Here, we report on the formation of supramolecular complexes between an achiral guanidinium derivative bearing two pyrene moieties, with each of the three adenosine phosphates: AMP, ADP, and ATP. By combining results from circular dichroism spectroscopy and molecular modeling simulations, we explore the induced chirality, the dynamics of the complexes, and the interactions at play, which altogether provide insights into the supramolecular self-assembly between APs and the guanidinium-bispyrene. Finally, we identify the chiroptical signals of interest in mixtures of the guanidinium derivative with the three APs in different proportions. This study constitutes a basis to evolve toward a chiroptical detection of the hydrolysis of APs based on organic supramolecular probes.

A review on cationic lipids with different linkers for gene delivery

Cationic lipids have become known as one of the most versatile tools for the delivery of DNA, RNA and many other therapeutic molecules, and are especially attractive because they can be easily designed, synthesized and characterized. Most of cationic lipids share the common structure of cationic head groups and hydrophobic portions with linker bonds between both domains. The linker bond is an important determinant of the chemical stability and biodegradability of cationic lipid, and further governs its transfection efficiency and cytotoxicity. Based on the structures of linker bonds, they can be grouped into many types, such as ether, ester, amide, carbamate, disulfide, urea, acylhydrazone, phosphate, and other unusual types (carnitine, vinyl ether, ketal, glutamic acid, aspartic acid, malonic acid diamide and dihydroxybenzene). This review summarizes some research results concerning the nature (such as the structure and orientation of linker groups) and density (such as the spacing and the number of linker groups) of linker bond for improving the chemical stability, biodegradability, transfection efficiency and cytotoxicity of cationic lipid to overcome the critical barriers of in vitro and in vivo transfection.

Biomolecular dynamic covalent polymers for DNA complexation and siRNA delivery

Dynamic covalent polymers made from modified amino acids complex nucleic acids and deliver siRNA in living cells.

Dynamic covalent polymers

This Highlight presents an overview of the rapidly growing field of dynamic covalent polymers. This class of polymers combines intrinsic reversibility with the robustness of covalent bonds, thus enabling formation of mechanically stable, polymer-based materials that are responsive to external stimuli. It will be discussed how the inherent dynamic nature of the dynamic covalent bonds on the molecular level can be translated to the macroscopic level of the polymer, giving access to a range of applications, such as stimuli-responsive or self-healing materials. A primary distinction will be made based on the type of dynamic covalent bond employed, while a secondary distinction will be based on the consideration whether the dynamic covalent bond is used in the main chain of the polymer or whether it is used to allow side chain modification of the polymer. Emphasis will be on the chemistry of the dynamic covalent bonds present in the polymer, in particular in relation to how the specific (dynamic) features of the bond impart functionality to the polymer material, and to the conditions under which this dynamic behavior is manifested. © 2016 The Authors. Journal of Polymer Science Part A: Polymer Chemistry Published by Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 3551-3577.

Synthetic multivalency for biological applications

Current directions and emerging possibilities under investigation for the integration of synthetic and semi-synthetic multivalent architectures with biology are discussed. Attention is focussed around multivalent interactions, their fundamental role in biology, and current and potential approaches in emulating them in terms of structure and functionality using synthetic architectures.

Injectable and pH-Responsive Silk Nanofiber Hydrogels for Sustained Anticancer Drug Delivery

Silk is useful as a drug carrier due to its biocompatibility, tunable degradation, and outstanding capacity in maintaining the function of drugs. Injectable silk hydrogels could deliver doxorubicin (DOX) for localized chemotherapy for breast cancer. To improve hydrogel properties, thixotropic silk nanofiber hydrogels in an all-aqueous solution were prepared and used to locally deliver DOX. The silk hydrogels displayed thixotropic capacity, allowing for easy injectability followed by solidification in situ. The hydrogels were loaded with DOX and released the drug over eight weeks with pH- and concentration-dependent release kinetics. In vitro and in vivo studies demonstrated that DOX-loaded silk hydrogels had good antitumor response, outperforming the equivalent dose of free DOX administered intravenously. Thixotropic silk hydrogels provide improved injectability to support sustained release, suggesting promising applications for localized chemotherapy.

From nucleobase to DNA templates for precision supramolecular assemblies and synthetic polymers

In this minireview, we report on the recent advances of utilization of nucleobases and DNA as templates to achieve well-defined supramolecular polymers, synthetic polymers, and sequence-controlled polymers.

Bioactive clusters promoting cell penetration and nucleic acid complexation for drug and gene delivery applications: from designed to self-assembled and responsive systems

Recent developments in the (self-)assembly of cationic clusters promoting nucleic acids complexation and cell penetration open the door to applications in drug and gene delivery.

Supramolecular rulers enabling selective detection of pure short ssDNA via chiral self-assembly

TPA propellers appear to be compatible with the general requirements for amplified chiral supramolecular rulers used to determine the number of base pairs of short ssDNAs.

Dynamic constitutional frameworks for DNA biomimetic recognition

Linear and cross-linked dynamic constitutional frameworks generated from reversibly interacting linear PEG/core constituents and cationic sites shed light on the dominant coiling versus linear DNA binding behaviours, closer to the histone DNA binding wrapping mechanism.

Dynamic constitutional frameworks (DCFs) as nanovectors for cellular delivery of DNA

We introduce Dynamic Constitutional Frameworks (DCFs), macromolecular structures that efficiently bind and transfect double stranded DNA. DCFs are easily synthesizable adaptive 3D networks consisting of core connection centres reversibly linked via labile imine bonds both to linear polyethyleneglycol (PEG, ∼1500 Da) and to branched polyethyleneimine (bPEI, ∼800 Da). DCFs bind linear and plasmid DNA, forming particulate polyplexes of 40-200 nm in diameter. The polyplexes are stable during gel electrophoresis, well tolerated by cells in culture, and exhibit significant transfection activity. We show that an optimal balance of PEG and bPEI components is important for building DCFs that are non-toxic and exhibit good cellular transfection activity. Our study demonstrates the versatility and effectiveness of DCFs as promising new vectors for DNA delivery.

Injectable and Biodegradable pH-Responsive Hydrogels for Localized and Sustained Treatment of Human Fibrosarcoma

Injectable hydrogels are an important class of biomaterials, and they have been widely used for controlled drug release. This study evaluated an injectable hydrogel formed in situ system by the reaction of a polyethylene glycol derivative with α,β-polyaspartylhydrazide for local cancer chemotherapy. This pH-responsive hydrogel was used to realize a sol-gel phase transition, where the gel remained a free-flowing fluid before injection but spontaneously changed into a semisolid hydrogel just after administration. As indicated by scanning electron microscopy images, the hydrogel exhibited a porous three-dimensional microstructure. The prepared hydrogel was biocompatible and biodegradable and could be utilized as a pH-responsive vector for drug delivery. The therapeutic effect of the hydrogel loaded with doxorubicin (DOX) after intratumoral administration in mice with human fibrosarcoma was evaluated. The inhibition of tumor growth was more obvious in the group treated by the DOX-loaded hydrogel, compared to that treated with the free DOX solution. Hence, this hydrogel with good syringeability and high biodegradability, which focuses on local chemotherapy, may enhance the therapeutic effect on human fibrosarcoma.

A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies

DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.

DyNAvectors: dynamic constitutional vectors for adaptive DNA transfection

A dynamic constitutional strategy presented here, combining easy synthesis and rapid screening, enables the selection of highly effective Dynamic Constitutional Frameworks (DCFs) for DNA transfection.

Emerging trends in enzyme inhibition by multivalent nanoconstructs

This review highlights the recent implementation of multivalent nanoconstructs in enzyme inhibition and discusses the emerging trends in their design and identification.

Multivalent DNA recognition by self-assembled clusters: deciphering structural effects by fragments screening and evaluation as siRNA vectors

Fragment self-assembly was used for producing clusters with a variety of scaffolds and ligands, and an effective siRNA vector was identified.