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Advanced Drug Delivery Reviews Aug 2023Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases,... (Review)
Review
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
Topics: Humans; Nucleic Acids; COVID-19; Oligonucleotides; Oligonucleotides, Antisense; Technology
PubMed: 37244354
DOI: 10.1016/j.addr.2023.114872 -
The Analyst Jan 2024Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile,...
Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile, affordable, and simpler than classical "open-close" and strand displacement-based aptamer switches. Recently, many new aptamers with an overall hairpin structure have been reported. In this study, intramolecular aptamer switches were developed by adding new base pairs to the end of aptamers. The additional nucleotides can pair with the internal domains of the aptamer, causing a change in its conformation from the original secondary structure without a target. When a target binds to an aptamer, a marked change in the structure of the aptamer is expected. As models for testing this intramolecular aptamer switch idea, aptamers of oxytetracycline (OTC), 17β-estradiol (E2), and adenosine were employed. When the additional base pairs are too long, binding the target to the aptamer becomes more challenging. This research offers valuable insights into the development of intramolecular aptamer switches and their potential applications in biosensor design.
Topics: Aptamers, Nucleotide; Oxytetracycline; Nucleic Acid Conformation; Adenosine; Biosensing Techniques
PubMed: 38193253
DOI: 10.1039/d3an02022c -
ACS Nano Jan 2024Unraveling the complexities of brain function, which is crucial for advancing human health, remains a grand challenge. This endeavor demands precise monitoring of small... (Review)
Review
Unraveling the complexities of brain function, which is crucial for advancing human health, remains a grand challenge. This endeavor demands precise monitoring of small molecules such as neurotransmitters, the chemical messengers in the brain. In this Perspective, we explore the potential of aptamers, selective synthetic bioreceptors integrated into electronic affinity platforms to address limitations in neurochemical biosensing. We emphasize the importance of characterizing aptamer thermodynamics and target binding to realize functional biosensors in biological systems. We focus on two label-free affinity platforms spanning the micro- to nanoscale: field-effect transistors and nanopores. Integration of well-characterized structure-switching aptamers overcame nonspecific binding, a challenge that has hindered the translation of biosensors from the lab to the clinic. In a transformative era driven by neuroscience breakthroughs, technological innovations, and multidisciplinary collaborations, an aptamer renaissance holds the potential to bridge technological gaps and reshape the landscape of diagnostics and neuroscience.
Topics: Humans; Aptamers, Nucleotide; Nanopores; Biosensing Techniques; Thermodynamics
PubMed: 38236046
DOI: 10.1021/acsnano.3c09576 -
International Journal of Molecular... Apr 2024As a follow-up to the previous Special Issue "Aptamers: Functional-Structural Studies and Biomedical Applications" [...].
As a follow-up to the previous Special Issue "Aptamers: Functional-Structural Studies and Biomedical Applications" [...].
Topics: Aptamers, Nucleotide; Humans; SELEX Aptamer Technique
PubMed: 38673864
DOI: 10.3390/ijms25084279 -
Science (New York, N.Y.) Apr 2024Therapeutic oligonucleotides are a powerful drug modality with the potential to treat many diseases. The rapidly growing number of therapies that have been approved and... (Review)
Review
Therapeutic oligonucleotides are a powerful drug modality with the potential to treat many diseases. The rapidly growing number of therapies that have been approved and that are in advanced clinical trials will place unprecedented demands on our capacity to manufacture oligonucleotides at scale. Existing methods based on solid-phase phosphoramidite chemistry are limited by their scalability and sustainability, and new approaches are urgently needed to deliver the multiton quantities of oligonucleotides that are required for therapeutic applications. The chemistry community has risen to the challenge by rethinking strategies for oligonucleotide production. Advances in chemical synthesis, biocatalysis, and process engineering technologies are leading to increasingly efficient and selective routes to oligonucleotide sequences. We review these developments, along with remaining challenges and opportunities for innovations that will allow the sustainable manufacture of diverse oligonucleotide products.
Topics: Oligonucleotides; Chemistry Techniques, Synthetic
PubMed: 38603508
DOI: 10.1126/science.adl4015 -
Nucleic Acids Research Sep 2023Sensors to measure the abundance and signaling of intracellular molecules are crucial for understanding their physiological functions. Although conventional fluorescent...
Sensors to measure the abundance and signaling of intracellular molecules are crucial for understanding their physiological functions. Although conventional fluorescent protein-based sensors have been designed, RNA-based sensors are promising imaging tools. Numerous RNA-based sensors have been developed. These sensors typically contain RNA G-quadruplex (RG4) motifs and thus may be suboptimal in living cells. Here we describe RNA-based sensors based on Pepper, a fluorogenic RNA without an RG4 motif. With Pepper, we engineered various sensors for metabolites, synthetic compounds, proteins and metal ions in vitro and in living cells. In addition, these sensors show high activation and selectivity, demonstrating their universality and robustness. In the case of sensors responding to S-adenosylmethionine (SAM), a metabolite produced by methionine adenosyltransferase (MATase), we showed that our sensors exhibited positively correlated fluorescence responding to different SAM levels. Importantly, we revealed the SAM biosynthesis pathway and monitored MATase activity and gene expression spatiotemporally in living individual human cells. Additionally, we constructed a ratiometric SAM sensor to determine the inhibition efficacy of a MATase inhibitor in living cells. Together, these sensors comprising Pepper provide a useful platform for imaging diverse cellular targets and their signaling pathway.
Topics: Humans; RNA; Aptamers, Nucleotide; Fluorescent Dyes; Fluorescence
PubMed: 37486780
DOI: 10.1093/nar/gkad620 -
Polish Journal of Veterinary Sciences Sep 2023Viral infections are common causes of diseases in animals and appropriate methods are increasingly being required to detect viral pathogens in animals. In this regard,... (Review)
Review
Viral infections are common causes of diseases in animals and appropriate methods are increasingly being required to detect viral pathogens in animals. In this regard, similar to antigen- -antibody interactions, aptamers have high affinity and specificity for their respective target molecules, and can be selected using the Systematic Evolution of Ligands by EXponential enrichment (SELEX) technique. Recently, significant progress has been made in the development of aptamer selection and aptamer-based sensors for viral detection, and here we review some of the recent advances in aptamer-based detection of viral infections in animals. This review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics.
Topics: Animals; Virus Diseases; SELEX Aptamer Technique; Aptamers, Nucleotide
PubMed: 37727988
DOI: 10.24425/pjvs.2023.145056 -
ACS Chemical Biology Oct 2023New technologies are required to combat the challenges faced with manufacturing commercial quantities of oligonucleotide drug substances which are required for treating...
New technologies are required to combat the challenges faced with manufacturing commercial quantities of oligonucleotide drug substances which are required for treating large patient populations. Herein we report a convergent biocatalytic synthesis strategy for an Alnylam model siRNA. The siRNA chemical structure includes several of the unnatural modifications and conjugations typical of siRNA drug substances. Using Almac's 3-2-3-2 hybrid RNA ligase enzyme strategy that sequentially ligates short oligonucleotide fragments (blockmers), the target siRNA was produced to high purity at 1 mM concentration. Additional strategies were investigated including the use of polynucleotide kinase phosphorylation and the use of crude blockmer starting materials without chromatographic purification. These findings highlight a path toward a convergent synthesis of siRNAs for large-scale manufacture marrying both enzymatic liquid and classical solid-phase synthesis.
Topics: Humans; RNA, Small Interfering; Biocatalysis; Oligonucleotides; Phosphorylation
PubMed: 37061926
DOI: 10.1021/acschembio.3c00071 -
The Journal of Biological Chemistry Aug 2023Human neutrophil elastase (HNE) plays a pivotal role in innate immunity, inflammation, and tissue remodeling. Aberrant proteolytic activity of HNE contributes to organ...
Human neutrophil elastase (HNE) plays a pivotal role in innate immunity, inflammation, and tissue remodeling. Aberrant proteolytic activity of HNE contributes to organ destruction in various chronic inflammatory diseases including emphysema, asthma, and cystic fibrosis. Therefore, elastase inhibitors could alleviate the progression of these disorders. Here, we used the systematic evolution of ligands by exponential enrichment to develop ssDNA aptamers that specifically target HNE. We determined the specificity of the designed inhibitors and their inhibitory efficacy against HNE using biochemical and in vitro methods, including an assay of neutrophil activity. Our aptamers inhibit the elastinolytic activity of HNE with nanomolar potency and are highly specific for HNE and do not target other tested human proteases. As such, this study provides lead compounds suitable for the evaluation of their tissue-protective potential in animal models.
Topics: Humans; Cystic Fibrosis; Emphysema; Leukocyte Elastase; Neutrophils; Serine Proteinase Inhibitors; Aptamers, Nucleotide; Sensitivity and Specificity; Enzyme Activation; Proteolysis; Cells, Cultured
PubMed: 37286041
DOI: 10.1016/j.jbc.2023.104889 -
Nature Communications Feb 2024Drugs that target pre-mRNA splicing hold great therapeutic potential, but the quantitative understanding of how these drugs work is limited. Here we introduce...
Drugs that target pre-mRNA splicing hold great therapeutic potential, but the quantitative understanding of how these drugs work is limited. Here we introduce mechanistically interpretable quantitative models for the sequence-specific and concentration-dependent behavior of splice-modifying drugs. Using massively parallel splicing assays, RNA-seq experiments, and precision dose-response curves, we obtain quantitative models for two small-molecule drugs, risdiplam and branaplam, developed for treating spinal muscular atrophy. The results quantitatively characterize the specificities of risdiplam and branaplam for 5' splice site sequences, suggest that branaplam recognizes 5' splice sites via two distinct interaction modes, and contradict the prevailing two-site hypothesis for risdiplam activity at SMN2 exon 7. The results also show that anomalous single-drug cooperativity, as well as multi-drug synergy, are widespread among small-molecule drugs and antisense-oligonucleotide drugs that promote exon inclusion. Our quantitative models thus clarify the mechanisms of existing treatments and provide a basis for the rational development of new therapies.
Topics: Humans; RNA Splicing; Azo Compounds; Oligonucleotides; Oligonucleotides, Antisense; RNA Splice Sites; Muscular Atrophy, Spinal; Pyrimidines
PubMed: 38424098
DOI: 10.1038/s41467-024-46090-5