Nucleic acid therapeutics: a focus on the development of aptamers

Chemistry and Biology of Noncanonical Nucleic Acid Structures: From Physicochemical Properties to Therapeutic Applications

The aim of this Special Issue is to highlight significant and new aspects concerning the chemistry and biology of noncanonical nucleic acid structures, with emphasis on their structure, stability, and conformational equilibria, as well as on the biological relevance of their interactions with proteins and ligands [...].

Developing hydrogels for gene therapy and tissue engineering

Hydrogels are a class of highly absorbent and easily modified polymer materials suitable for use as slow-release carriers for drugs. Gene therapy is highly specific and can overcome the limitations of traditional tissue engineering techniques and has significant advantages in tissue repair. However, therapeutic genes are often affected by cellular barriers and enzyme sensitivity, and carrier loading of therapeutic genes is essential. Therapeutic gene hydrogels can well overcome these difficulties. Moreover, gene-therapeutic hydrogels have made considerable progress. This review summarizes the recent research on carrier gene hydrogels for the treatment of tissue damage through a summary of the most current research frontiers. We initially introduce the classification of hydrogels and their cross-linking methods, followed by a detailed overview of the types and modifications of therapeutic genes, a detailed discussion on the loading of therapeutic genes in hydrogels and their characterization features, a summary of the design of hydrogels for therapeutic gene release, and an overview of their applications in tissue engineering. Finally, we provide comments and look forward to the shortcomings and future directions of hydrogels for gene therapy. We hope that this article will provide researchers in related fields with more comprehensive and systematic strategies for tissue engineering repair and further promote the development of the field of hydrogels for gene therapy.

Novel functional DNA-linked immunosorbent assay for aflatoxin B1 with dual-modality based on hybrid chain reaction

Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins, which is frequently detected in agricultural products. Herein, a novel functional DNA -linked immunosorbent assay (DLISA) with dual-modality based on hybrid chain reaction (HCR) has been successfully developed for ultrasensitive detection of AFB1. The strategy relies on AFB1 immune-bridged occurrence of HCR and the salt-induced aggregation of gold nanoparticles (AuNPs). An aptamer-initiator stand (Apt-Ini stand) is designed for the AFB1 recognition and the activation of HCR, which can recognize the matched hairpins and cause the crossing-opening of H1 and H2, producing a long double-stranded DNA polymer. The addition of SYBR Green I achieves the fluorescent signal output. Remaining less DNA hairpins were added and stuck on the surface of AuNPs, which were insufficient to protect the AuNPs, resulting in the salt-induced aggregation with the color change from red to blue. The dual-modality provides limits of detections of 1.333 × 10-14 g/mL and 2.471 × 10-15 g/mL, respectively. This DLISA with dual-modality provides not only a colorimetry that can meet the needs of on-the-spot preliminary inspection, but also a fluorescence assay that can acquire the precise results.

A homogeneous label-free electrochemical aptasensor based on an omega-like DNA nanostructure for progesterone detection

A novel homogeneous label-free electrochemical aptamer sensor for the detection of progesterone was prepared by combining a well-designed omega (Ω)-like DNA (Ω-DNA) nanostructure, with an isothermal cycling amplification strategy based on the highly efficient exonuclease III (Exo III). The omega-like (Ω) DNA is composed of two oligonucleotide strands: DNA1 and DNA2. The Pro aptamer triggers a chain displacement reaction of Ω-DNA nanostructures, forms a new double-stranded DNA structure (aptamer precursor-DNA2), and releases DNA1. Then, Exo III selectively cleaves the DNA duplex and releases the Pro aptamer to participate in a new displacement reaction. Meanwhile, the released DNA1 strands gain access to the strongly bound hemin, forming a hemin/G-quadruplex (DNAzyme). In the presence of hydrogen peroxide (H2O2), differential pulse voltammetry (DPV) was used to detect the current signal from the oxidation of o-phenylenediamine (OPD) to aminoazobenzene (DAP) catalyzed by DNAzyme. However, the amount of released DNA1 from the Ω-DNA nanostructures is reduced in the presence of the target Pro, and the DPV signal declines because of the small amount of DNAzyme formed. The developed electrochemical aptasensor has a wide dynamic linear relationship in the range of 1 pg mL-1 to 10 ng mL-1 under optimal conditions. Its detection limit is down to 0.3 pg mL-1, providing a potential platform for a sensitive Pro assay among electrochemical assays.

Generation of DNA Aptamers with Functional Activity in Mammalian Cells by Mimicking Retroviruses

DNA aptamers are single-stranded DNA oligonucleotide sequences that bind to specific targets with high affinity. Currently, DNA aptamers can be produced only by in vitro synthesis. It is difficult for DNA aptamers to have a sustained impact on intracellular protein activity, which limits their clinical application. In this study, we developed a DNA aptamer expression system to generate DNA aptamers with functional activity in mammalian cells by mimicking retroviruses. Using this system, DNA aptamers targeting intracellular Ras (Ra1) and membrane-bound CD71 (XQ2) were successfully generated in cells. In particular, the expressed Ra1 not only specifically bound to the intracellular Ras protein but also inhibited the phosphorylation of downstream ERK1/2 and AKT. Furthermore, by inserting the DNA aptamer expression system for Ra1 into a lentivirus vector, the system can be delivered into cells and stably produce Ra1 over time, resulting in the inhibition of lung cancer cell proliferation. Therefore, our study provides a novel strategy for the intracellular generation of DNA aptamers with functional activity and opens a new avenue for the clinical application of intracellular DNA aptamers in disease treatment.

Bifunctional robots inducing targeted protein degradation

The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) and E3-ligase, which induce the ubiquitination of POI. These molecules are based on event-driven pharmacology and are applicable in different conditions such as oncology, antiviral, neurodegenerative disease, acne etc., offering tremendous scope to researchers. In this review, primarily, we attempted to compile the recent works available in the literature on PROTACs for various targeted proteins. We summarized the design and development strategies with a focus on molecular information of protein residues and linker design. Rationalization of the ternary complex formation using Artificial Intelligence including machine & deep learning models and traditionally followed computational tools are also included in this study. Moreover, details describing the optimization of PROTACs chemistry and pharmacokinetic properties are added. Advanced PROTAC designs and targeting complex proteins, is summed up to cover the wide spectrum.

Beneficial effect of TLR4 blockade by a specific aptamer antagonist after acute myocardial infarction

Experimental evidence indicates that the control of the inflammatory response after myocardial infarction is a key strategy to reduce cardiac injury. Cellular damage after blood flow restoration in the heart promotes sterile inflammation through the release of molecules that activate pattern recognition receptors, among which TLR4 is the most prominent. Transient regulation of TLR4 activity has been considered one of the potential therapeutic interventions with greater projection towards the clinic. In this regard, the characterization of an aptamer (4FT) that acts as a selective antagonist for human TLR4 has been investigated in isolated macrophages from different species and in a rat model of cardiac ischemia/reperfusion (I/R). The binding kinetics and biological responses of murine and human macrophages treated with 4FT show great affinity and significant inhibition of TLR4 signaling including the NF-κB pathway and the LPS-dependent increase in the plasma membrane currents (Kv currents). In the rat model of I/R, administration of 4FT following reoxygenation shows amelioration of cardiac injury function and markers, a process that is significantly enhanced when the second dose of 4FT is administered 24 h after reperfusion of the heart. Parameters such as cardiac injury biomarkers, infiltration of circulating inflammatory cells, and the expression of genes associated with the inflammatory onset are significantly reduced. In addition, the expression of anti-inflammatory genes, such as IL-10, and pro-resolution molecules, such as resolvin D1 are enhanced after 4FT administration. These results indicate that targeting TLR4 with 4FT offers new therapeutic opportunities to prevent cardiac dysfunction after infarction.

Recent progress of aptamer‒drug conjugates in cancer therapy

Aptamers are single-stranded DNA or RNA sequences that can specifically bind with the target protein or molecule via specific secondary structures. Compared to antibody-drug conjugates (ADC), aptamer‒drug conjugate (ApDC) is also an efficient, targeted drug for cancer therapy with a smaller size, higher chemical stability, lower immunogenicity, faster tissue penetration, and facile engineering. Despite all these advantages, several key factors have delayed the clinical translation of ApDC, such as in vivo off-target effects and potential safety issues. In this review, we highlight the most recent progress in the development of ApDC and discuss solutions to the problems noted above.

Lipid Nanoparticles as Delivery Vehicles for Inhaled Therapeutics

Lipid nanoparticles (LNPs) have emerged as a powerful non-viral carrier for drug delivery. With the prevalence of respiratory diseases, particularly highlighted by the current COVID-19 pandemic, investigations into applying LNPs to deliver inhaled therapeutics directly to the lungs are underway. The progress in LNP development as well as the recent pre-clinical studies in three main classes of inhaled encapsulated drugs: small molecules, nucleic acids and proteins/peptides will be discussed. The advantages of the pulmonary drug delivery system such as reducing systemic toxicity and enabling higher local drug concentration in the lungs are evaluated together with the challenges and design considerations for improved formulations. This review provides a perspective on the future prospects of LNP-mediated delivery of inhaled therapeutics for respiratory diseases.

Gene therapy to enhance angiogenesis in chronic wounds

Skin injuries and chronic non-healing wounds are one of the major global burdens on the healthcare systems worldwide due to their difficult-to-treat nature, associated co-morbidities, and high health care costs. Angiogenesis has a pivotal role in the wound-healing process, which becomes impaired in many chronic non-healing wounds, leading to several healing disorders and complications. Therefore, induction or promotion of angiogenesis can be considered a promising approach for healing of chronic wounds. Gene therapy is one of the most promising upcoming strategies for the treatment of chronic wounds. It can be classified into three main approaches: gene augmentation, gene silencing, and gene editing. Despite the increasing number of encouraging results obtained using nucleic acids (NAs) as active pharmaceutical ingredients of gene therapy, efficient delivery of NAs to their site of action (cytoplasm or nucleus) remains a key challenge. Selection of the right therapeutic cargo and delivery methods is crucial for a favorable prognosis of the healing process. This article presents an overview of gene therapy and non-viral delivery methods for angiogenesis induction in chronic wounds.

Nucleic acid-based therapeutics for dermal wound healing

Non-healing wounds have long been the subject of scientific and clinical investigations. Despite breakthroughs in understanding the biology of delayed wound healing, only limited advances have been made in properly treating wounds. Recently, research into nucleic acids (NAs) such as small-interfering RNA (siRNA), microRNA (miRNA), plasmid DNA (pDNA), aptamers, and antisense oligonucleotides (ASOs) has resulted in the development of a latest therapeutic strategy for wound healing. In this regard, dendrimers, scaffolds, lipid nanoparticles, polymeric nanoparticles, hydrogels, and metal nanoparticles have all been explored as NA delivery techniques. However, the translational possibility of NA remains a substantial barrier. As a result, different NAs must be identified, and their distribution method must be optimized. This review explores the role of NA-based therapeutics in various stages of wound healing and provides an update on the most recent findings in the development of NA-based nanomedicine and biomaterials, which may offer the potential for the invention of novel therapies for this long-term condition. Further, the challenges and potential for miRNA-based techniques to be translated into clinical applications are also highlighted.

In Vitro Selection of Short DNA Aptamers that Can Inhibit or Alleviate Cocaine and MK-801 Inhibition of Muscle-Type Nicotinic Acetylcholine Receptors

Ligands of high specificity and selectivity have been selected for biological molecules of interest including nicotinic acetylcholine receptor (nAChR) using combinatorial libraries of nucleic acids. The nAChR belongs to a group of structurally related proteins that regulate signal transmission between ~ 10¹² cells of the mammalian nervous system. It is inhibited by both therapeutic agents and abused drugs, including cocaine. A mechanism-based approach to alleviating noncompetitive inhibition of the mucle-type nAChR, including Torpedo, resulted in the selection of very short DNA aptamers only seven nucleotides long. By transient kinetic measurements, these DNA aptamers, which displaced cocaine from its binding site on the muscle-type nAChR, were classified into two groups based on their effects on the nAChR: Class I aptamers inhibit agonist-induced current in the muscle-type nAChR and Class II molecules alleviate inhibition by MK-801 [(+)-dizocilpine] without affecting the receptor function. The most potent Class I DNA aptamer, which inhibits the muscle-type nAChR, has an apparent dissociation constant (K_Iapt) of 5 μM, while the most efficient Class II DNA aptamer, which alleviates MK-801-induced inhibition, has an apparent dissociation constant (K_Apt) of 1.8 μM. An innovative aspect of the work is the identification of very short DNA aptamers with these properties that makes them attractive for therapeutic and diagnostic applications.

Biomaterial-based delivery of nucleic acids for tissue regeneration

Gene therapy is a promising novel method of tissue regeneration by stimulating or inhibiting key signaling pathways. However, their therapeutic applications in vivo are largely limited by several physiological obstacles, such as degradation of nucleases, impermeability of cell membranes, and transport to the desired intracellular compartments. Biomaterial-based gene delivery systems can overcome the problems of stability and local drug delivery, and can temporarily control the overexpression of therapeutic genes, leading to the local production of physiologically relevant levels of regulatory factors. But the gene delivery of biomaterials for tissue regeneration relies on multi-factor design. This review aims to outline the impact of gene delivery methods, therapeutic genes and biomaterials selection on this strategy, emphatically introduce the latest developments in the design of gene delivery vehicles based on biomaterials, summarize the mechanism of nucleic acid for tissue regeneration, and explore the strategies of nucleic acid delivery vehicles for various tissue regeneration.