Nanogels: Smart tools to enlarge the therapeutic window of gene therapy

Gene therapy can potentially treat a great number of diseases, from cancer to rare genetic disorders. Very recently, the development and emergency approval of nucleic acid-based COVID-19 vaccines confirmed its strength and versatility. However, gene therapy encounters limitations due to the lack of suitable carriers to vectorize therapeutic genetic material inside target cells. Nanogels are highly hydrated nano-size crosslinked polymeric networks that have been used in many biomedical applications, from drug delivery to tissue engineering and diagnostics. Due to their easy production, tunability, and swelling properties they have called the attention as promising vectors for gene delivery. In this review, nanogels are discussed as vectors for nucleic acid delivery aiming to enlarge gene therapy's therapeutic window. Recent works highlighting the optimization of inherent transfection efficiency and biocompatibility are reviewed here. The importance of the monomer choice, along with the internal structure, surface decoration, and responsive features are outlined for the different transfection modalities. The possible sources of toxicological endpoints in nanogels are analyzed, and the strategies to limit them are compared. Finally, perspectives are discussed to identify the remining challenges for the nanogels before their translation to the market as transfection agents.

Molecular Features for Probing Small Amphiphilic Molecules with Self-Assembled Monolayer-Protected Nanoparticles

The sensing of small molecules poses the challenge of developing devices able to discriminate between compounds that may be structurally very similar. Here, attention has been paid to the use of self-assembled monolayer (SAM)-protected gold nanoparticles since they enable a modular approach to tune single-molecule affinity and selectivity simply by changing functional moieties (i.e., covering ligands), along with multivalent molecular recognition. To date, the discovery of monolayers suitable for a specific molecular target has relied on trial-and-error approaches, with ligand chemistry being the main criterion used to modulate selectivity and sensitivity. By using molecular dynamics, we showcase that either individual molecular characteristics and/or collective features such as ligand flexibility, monolayer organization, ligand local ordering, and interfacial solvent properties can also be exploited conveniently. The knowledge of the molecular mechanisms that drive the recognition of small molecules on SAM-covered nanoparticles will critically expand our ability to manipulate and control such supramolecular systems.

Chemical sensors for selective and quantitative heparin sensing

In this review article, chemical sensors for selective and quantitative heparin sensing are discussed with detailed examples.

Lost in (Clinical) Translation: Recent Advances in Heparin Neutralization and Monitoring

The heparin family, which includes unfractionated heparin, low-molecular heparin, and fondaparinux, is a class of drugs clinically used as intravenous blood thinners. To date, issues related to both the reversal of anticoagulation and the blood level determination of the anticoagulant at the point-of-care remain: while the only U.S. Food and Drug Administration (FDA) approved antidote for heparin displays serious efficacy and safety drawbacks, the current assays for heparin monitoring are indirect measurements subject to their own limitations and variations. Herein, we provide an update on the numerous recent chemical approaches to tackle these issues, from which it is clear that some new antidotes and sensors for heparin certainly have the potential to exceed current clinical standards. This review aims to review a field that requires close collaborations between physicians, biologists, and chemists in order to foster advances toward clinical translation.

Self-assembled multivalent (SAMul) ligand systems with enhanced stability in the presence of human serum

Self-assembled cationic micelles are an attractive platform for binding biologically-relevant polyanions such as heparin. This has potential applications in coagulation control, where a synthetic heparin rescue agent could be a useful replacement for protamine, which is in current clinical use. However, micelles can have low stability in human serum and unacceptable toxicity profiles. This paper reports the optimisation of self-assembled multivalent (SAMul) arrays of amphiphilic ligands to bind heparin in competitive conditions. Specifically, modification of the hydrophobic unit kinetically stabilises the self-assembled nanostructures, preventing loss of binding ability in the presence of human serum - cholesterol hydrophobic units significantly outperform systems with a simple aliphatic chain. It is demonstrated that serum albumin disrupts the binding thermodynamics of the latter system. Molecular simulation shows aliphatic lipids can more easily be removed from the self-assembled nanostructures than the cholesterol analogues. This agrees with the experimental observation that the cholesterol-based systems undergo slower disassembly and subsequent degradation via ester hydrolysis. Furthermore, by stabilising the SAMul nanostructures, toxicity towards human cells is decreased and biocompatibility enhanced, with markedly improved survival of human hepatoblastoma cells in an MTT assay.

Unchain My Blood: Lessons Learned from Self-Assembled Dendrimers as Nanoscale Heparin Binders

This review work reports a collection of coupled experimental/computational results taken from our own experience in the field of self-assembled dendrimers for heparin binding. These studies present and discuss both the potentiality played by this hybrid methodology to the design, synthesis, and development of possible protamine replacers for heparin anticoagulant activity reversal in biomedical applications, and the obstacles this field has still to overcome before these molecules can be translated into nanomedicines available in clinical settings.

Polymerization-like kinetics of the self-assembly of colloidal nanoparticles into supracolloidal polymers

The self-assembly of colloidal nanoparticles is conceptually analogous to the polymerization of reactive monomers in molecular systems. However, less is known about the polymerization of colloidal nanoparticles into supracolloidal polymers. Herein, using coarse-grained molecular dynamics and theoretical analysis, we reveal the self-assembly mechanism and kinetics of colloidal nanoparticles constructed from triblock terpolymers. The results show that the formation pathway of supracolloidal polymers involves monomer condensation and oligomer coalescence through the manner of end-to-end collisions. In contrast to the polymerization kinetics of molecular systems, the simulations and theoretical analysis definitely demonstrate that the growth of supracolloidal polymers obeys diffusion-controlled step-growth polymerization kinetics with a variable rate coefficient, where the growth rate is dependent upon the concentration of colloidal nanoparticles and the molecular information of triblock terpolymers. Our findings possess wide implications for understanding the growth of supracolloidal polymers, which is important for the rational and precise design of one-dimensional self-assembled superstructures with new horizons for biomedical applications.

From fundamental supramolecular chemistry to self-assembled nanomaterials and medicines and back again – how Sam inspired SAMul

Personal inspiration led to the development of a programme of research targeting the use of self-assembled systems in nanomedicine, which in the process of approaching a range of applications has uncovered new fundamental concepts in supramolecular science.

Multi-component hybrid hydrogels - understanding the extent of orthogonal assembly and its impact on controlled release

This paper reports self-assembled multi-component hybrid hydrogels including a range of nanoscale systems and characterizes the extent to which each component maintains its own unique functionality, demonstrating that multi-functionality can be achieved by simply mixing carefully-chosen constituents. Specifically, the individual components are: (i) pH-activated low-molecular-weight gelator (LMWG) 1,3;2,4-dibenzylidenesorbitol-4',4''-dicarboxylic acid (DBS-COOH), (ii) thermally-activated polymer gelator (PG) agarose, (iii) anionic biopolymer heparin, and (iv) cationic self-assembled multivalent (SAMul) micelles capable of binding heparin. The LMWG still self-assembles in the presence of PG agarose, is slightly modified on the nanoscale by heparin, but is totally disrupted by the micelles. However, if the SAMul micelles are bound to heparin, DBS-COOH self-assembly is largely unaffected. The LMWG endows hybrid materials with pH-responsive behavior, while the PG provides mechanical robustness. The rate of heparin release can be controlled through network density and composition, with the LMWG and PG behaving differently in this regard, while the presence of the heparin binder completely inhibits heparin release through complexation. This study demonstrates that a multi-component approach can yield exquisite control over self-assembled materials. We reason that controlling orthogonality in such systems will underpin further development of controlled release systems with biomedical applications.

Morphological control of self-assembled multivalent (SAMul) heparin binding in highly competitive media

Shape control – self-assembly of ligands into different morphologies directs their ability to bind heparin.

Emergence of highly-ordered hierarchical nanoscale aggregates on electrostatic binding of self-assembled multivalent (SAMul) cationic micelles with polyanionic heparin

Self assembled cationic micelles form well-defined structurally ordered hierarchical nanoscale aggregates on interaction with polyanionic heparin in solution.

Effect of buffer at nanoscale molecular recognition interfaces – electrostatic binding of biological polyanions

The electrostatic binding of polyanionic heparin by cationic receptors is highly dependent on the buffer in which the binding assay is carried out.

Using L-STM to directly visualize enzymatic self-assembly/disassembly of nanofibers

Self-assembly/disassembly is ubiquitous in nature and plays an important role in many biological events. But noninvasive characterization of this process in real time at molecular resolution remains challenging. Herein, using homebuilt liquid-phase scanning tunneling microscopy (L-STM) with ultrahigh stability, we directly visualized enzymatic self-assembly/disassembly of oligopeptide nanofibers in real time for the first time. Static high-resolution L-STM images clearly showed the molecular packing details in the supramolecular nanofiber and the diameter of the nanofiber was consistent with that of cryo transmission electron microscopy (cryo-TEM) observations. Moreover, the self-repairing behavior of the supramolecular nanofibers was also directly observed at high resolution for the first time. This work unprecedentedly revealed new insights into Nature-mimic self-assembly and disassembly at the molecular level. It also illustrates the potential of our homebuilt L-STM in studying delicate biological processes in physiological solution with high resolution.

Electrostatic binding of polyanions using self-assembled multivalent (SAMul) ligand displays - structure-activity effects on DNA/heparin binding

This paper reports that modifying the ligands in self-assembled multivalent (SAMul) displays has an impact on apparent binding selectivity towards two nanoscale biological polyanions - heparin and DNA. For the nanostructures assayed here, spermidine ligands are optimal for heparin binding but spermine ligands are preferred for DNA. Probing subtle differences in such nanoscale binding interfaces is a significant challenge, and as such, several experimental binding assays - competition assays and isothermal calorimetry - are employed to confirm differences in affinity and provide thermodynamic insights. Given the dynamic nature and hierarchical binding processes involved in SAMul systems, we employed multiscale modelling to propose reasons for the origins of polyanion selectivity differences. The modelling results, when expressed in thermodynamic terms and compared with the experimental data, suggest that DNA is a shape-persistent polyanion, and selectivity originates only from ligand preferences, whereas heparin is more flexible and adaptive, and as such, actively reinforces ligand preferences. As such, this study suggests that inherent differences between polyanions may underpin subtle binding selectivity differences, and that even simple electrostatic interfaces such as these can have a degree of tunability, which has implications for biological control and regulation on the nanoscale.

Cationic Peptides and Peptidomimetics Bind Glycosaminoglycans as Potential Sema3A Pathway Inhibitors

Semaphorin3A (Sema3A) is a vertebrate-secreted protein that was initially characterized as a repulsive-guidance cue. Semaphorins have crucial roles in several diseases; therefore, the development of Sema3A inhibitors is of therapeutic interest. Sema3A interacts with glycosaminoglycans (GAGs), presumably through its C-terminal basic region. We used different biophysical techniques (i.e., NMR, surface plasmon resonance, isothermal titration calorimetry, fluorescence, and UV-visible spectroscopy) to characterize the binding of two Sema3A C-terminus-derived basic peptides (FS2 and NFS3) to heparin and chondroitin sulfate A. We found that these peptides bind to both GAGs with affinities in the low-micromolar range. On the other hand, a peptoid named SICHI (semaphorin-induced chemorepulsion inhibitor), which is positively charged at physiological pH, was first identified by our group as being able to block Sema3A chemorepulsion and growth-cone collapse in axons at the extracellular level. To elucidate the direct target for the reported SICHI inhibitory effect in the Sema3A signaling pathway, we looked first to the protein-protein interaction between secreted Sema3A and the Nrp1 receptor. However, our results show that SICHI does not bind directly to the Sema3A sema domain or to Nrp1 extracellular domains. We evaluated a new, to our knowledge, hypothesis, according to which SICHI binds to GAGs, thereby perturbing the Sema3A-GAG interaction. By using the above-mentioned techniques, we observed that SICHI binds to GAGs and competes with Sema3A C-terminus-derived basic peptides for binding to GAGs. These data support the ability of SICHI to block the biologically relevant interaction between Sema3A and GAGs, thus revealing SICHI as a new, to our knowledge, class of inhibitors that target the GAG-protein interaction.

Chiral recognition at self-assembled multivalent (SAMul) nanoscale interfaces – enantioselectivity in polyanion binding

We investigate structure–activity effect relationships at the nanoscale chiral molecular recognition interface between enantiomeric self-assembled multivalent (SAMul) systems and biological polyanions, heparin and DNA.

Pyrene-based heparin sensors in competitive aqueous media – the role of self-assembled multivalency (SAMul)

Simple functionalised pyrene derivatives can achieve ratiometric sensing of heparin with the precise sensing mechanism depending on whether the sensor self-assembles into a multivalent ligand display.

Synthesis and evaluation of a desymmetrised synthetic lectin: an approach to carbohydrate receptors with improved versatility

A new design for carbohydrate receptors features unmatched apolar surfaces, and could lead to selectivities for a broader range of substrates.

Monitoring clinical levels of heparin in human blood samples with an indicator-displacement assay

We report that a "tree-like" polymer of lysine is able to form a multi-ligand complex with a fluorescently labelled peptide, leading to the almost complete extinction of the optical signal that can be restored upon the introduction of heparin. This simple system allows, for the first time, the turn-ON fluorescent sensing of the anticoagulant in human blood at clinically relevant levels.

Resonance Rayleigh scattering detection of heparin with concanavalin A

Stepwise macromolecular interactions observed between conA and heparin, which are accompanied by RRS changes.

The marriage of endo-cavity and exo-wall complexation provides a facile strategy for supramolecular polymerization

The marriage of exo-wall interactions and endo-cavity inclusion provides a new strategy for the construction of supramolecular polymers from unfunctionalized neutral receptors.

Structure–activity relationship study of dendritic polyglycerolamines for efficient siRNA transfection

Structure–activity relationship studies were performed through in vitro, in silico, and in vivo analysis in order to evaluate the gene transfection potential of dendritic polyglycerolamines with different amine loadings.

Ultra-sensitive detection of heparin via aPTT using plastic antibodies on QCM-D platform

One of the challenges faced by today's clinics is unavailability of practical, precise and accurate determination of the most commonly used anti-coagulant ‘heparin’ in human blood/plasma in surgery.