Design, Synthesis, and Cellular Uptake of Oligonucleotides Bearing Glutathione-Labile Protecting Groups

Advances in structural-guided modifications of siRNA

To date, the US Food and Drug Administration (FDA) has approved six small interfering RNA (siRNA) drugs: patisiran, givosiran, lumasiran, inclisiran, vutrisiran, and nedosiran, serving as compelling evidence of the promising potential of RNA interference (RNAi) therapeutics. The successful implementation of siRNA therapeutics is improved through a combination of various chemical modifications and diverse delivery approaches. The utilization of chemically modified siRNA at specific sites on either the sense strand (SS) or antisense strand (AS) has the potential to enhance resistance to ribozyme degradation, improve stability and specificity, and prolong the efficacy of drugs. Herein, we provide comprehensive analyses concerning the correlation between chemical modifications and structure-guided siRNA design. Various modifications, such as 2'-modifications, 2',4'-dual modifications, non-canonical sugar modifications, and phosphonate mimics, are crucial for the activity of siRNA. We also emphasize the essential strategies for enhancing overhang stability, improving RISC loading efficacy and strand selection, reducing off-target effects, and discussing the future of targeted delivery.

RNA Control via Redox-Responsive Acylation

Incorporating stimuli-responsive components into RNA constructs provides precise spatiotemporal control over RNA structures and functions. Despite considerable advancements, the utilization of redox-responsive stimuli for the activation of caged RNAs remains scarce. In this context, we present a novel strategy that leverages post-synthetic acylation coupled with redox-responsive chemistry to exert control over RNA. To achieve this, we design and synthesize a series of acylating reagents specifically tailored for introducing disulfide-containing acyl adducts into the 2'-OH groups of RNA ("cloaking"). Our data reveal that these acyl moieties can be readily appended, effectively blocking RNA catalytic activity and folding. We also demonstrate the traceless release and reactivation of caged RNAs ("uncloaking") through reducing stimuli. By employing this strategy, RNA exhibits rapid cellular uptake, effective distribution and activation in the cytosol without lysosomal entrapment. We anticipate that our methodology will be accessible to laboratories engaged in RNA biology and holds promise as a versatile platform for RNA-based applications.

Thiol-Mediated Uptake

This Perspective focuses on thiol-mediated uptake, that is, the entry of substrates into cells enabled by oligochalcogenides or mimics, often disulfides, and inhibited by thiol-reactive agents. A short chronology from the initial observations in 1990 until today is followed by a summary of cell-penetrating poly(disulfide)s (CPDs) and cyclic oligochalcogenides (COCs) as privileged scaffolds in thiol-mediated uptake and inhibitors of thiol-mediated uptake as potential antivirals. In the spirit of a Perspective, the main part brings together topics that possibly could help to explain how thiol-mediated uptake really works. Extreme sulfur chemistry mostly related to COCs and their mimics, cyclic disulfides, thiosulfinates/-onates, diselenolanes, benzopolysulfanes, but also arsenics and Michael acceptors, is viewed in the context of acidity, ring tension, exchange cascades, adaptive networks, exchange affinity columns, molecular walkers, ring-opening polymerizations, and templated polymerizations. Micellar pores (or lipid ion channels) are considered, from cell-penetrating peptides and natural antibiotics to voltage sensors, and a concise gallery of membrane proteins, as possible targets of thiol-mediated uptake, is provided, including CLIC1, a thiol-reactive chloride channel; TMEM16F, a Ca-activated scramblase; EGFR, the epithelial growth factor receptor; and protein-disulfide isomerase, known from HIV entry or the transferrin receptor, a top hit in proteomics and recently identified in the cellular entry of SARS-CoV-2.

Engineering Aptamer Switches for Multifunctional Stimulus-Responsive Nanosystems

Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" process, performing complex functions such as signaling or controlled payload release in response to external stimuli including light, pH, ligand-binding and other microenvironmental cues. Although this field is still in its infancy, these efforts offer exciting potential for the development of biologically based "smart materials". Herein, ongoing progress in the use of nucleic acids as an externally controllable switching material is reviewed. The diverse range of mechanisms that can trigger a stimulus response, and strategies for engineering those functionalities into nucleic acid materials are explored. Finally, recent progress is discussed in incorporating aptamer switches into more complex synthetic nucleic acid-based nanostructures and functionalized smart materials.

Chemical synthesis and biochemical characterization of cyclic oligonucleotides containing acyl groups at both 5'- and 3'-terminal positions

Modified oligonucleotides, whose ON-OFF switch of hybridization can be controlled by an external stimulus, are important to understanding life phenomena and efficient treatment of diseases. The ON-OFF switch can be completely controlled by chemical modification of the oligonucleotide such as cyclization. However, their chemical modifications of the previous cyclic oligonucleotides remain after the addition of an external stimulus. To overcome this problem, we carried out the first synthesis of cyclic oligonucleotides containing acyl groups at both 5'- and 3'-terminal positions, which can be hydrolyzed by intracellular esterase. The cyclic oligonucleotides were successfully synthesized via disulfide bond formation and the phosphoramidite method without base protection on polymer supports containing a silyl linker. Subsequently, we were able to introduce a functional group into the cyclic oligonucleotide using the corresponding isothiocyanate reagent. Additionally, a cyclic oligonucleotide with acyl groups was found to have a much lower binding ability than the corresponding linear oligonucleotide. Moreover, we demonstrated its structural conversion to the corresponding linear oligonucleotide with two thiol groups under reducing conditions using dithiothreitol. It was also confirmed that the two terminal acyl groups of the linear oligonucleotide were hydrolyzed by pig liver esterase. These results indicate that hybridization of cyclic acylated nucleic acid drugs with high nuclease resistance is regulated by intracellular esterase under the reducing conditions in the cell cytoplasm.

Development of Bioreduction Labile Protecting Groups for the 2'-Hydroxyl Group of RNA

Protection and deprotection of the 2'-hydroxyl group of RNAs are critical for RNA-based drug discovery. This paper reports development of a bioreduction labile protecting group of the 2'-hydroxyl group in RNA. After the reduction of the nitro group in a chemical or enzymatic manner, the protecting groups were removed spontaneously. The attachment of electron-donating groups to the benzene ring or benzylic carbon enabled fast and controllable deprotection of the 2'-hydroxyl protecting group under physiological conditions.