Conjugation and Evaluation of Small Hydrophobic Molecules to Triazole-Linked siRNAs

Recent advances in the synthesis of cholesterol-based triazoles and their biological applications

Double-headed warheads focusing on the pharmacological aspects as well as membrane permeability can contribute a lot to medicinal chemistry. Over the past few decades, a lot of research has been conducted on steroid-heterocycle conjugates as possible therapeutic agents against a variety of disorders. In the second half of the 20th century, successful research was conducted on cholesterol-based heterocyclic moieties. Keeping in view the biological significance of various triazoles, research on fusion with cholesterol has emerged. This review has been designed to explore the chemistry of cholesterol-based triazoles for the duration from 2010 to 2023 and their significance in medicinal chemistry.

Effective carrier-free gene-silencing activity of sphingosine-modified siRNAs

RNA interference (RNAi) is a natural cellular process that silences the expression of target genes in a sequence-specific way by mediating targeted mRNA degradation. One of the main challenges in RNAi research is developing an effective career-free delivery system and targeting cells in the central nervous system (CNS). Recently, lipid-conjugated systems involving fatty acids have shown promising potential as safe and effective delivery systems of oligonucleotides to CNS cells due to their hydrophobic tails and interactions with the cell's hydrophobic membrane. Therefore, in this study, we are interested in creating career-free siRNA therapeutics for potential applications in drug delivery to the CNS. Here we explore different synthetic pathways of conjugating sphingolipids containing long-carbon chains to siRNA and assess their effectiveness as career-free delivery systems. In this project, a library of sphingosine-modified siRNAs was created, and their gene-silencing effect was evaluated in both the presence and absence of a transfection carrier. siRNAs modified with one or two sphingosine moieties resulted in dose-dependent gene knockdown while demonstrating promising results for their use as carrier-free agents. The IC₅₀ values of single-modified siRNAs ranged from 49.9 nM to 670.7 nM, whereas double-modified siRNAs had IC₅₀ values in the range of 49.9 nM to 66.4 nM. In conclusion, sphingosine-modified siRNAs show promising results in advancing carrier-free siRNA therapeutics.

SiRNAs with Neutral Phosphate Triester Hydrocarbon Tails Exhibit Carrier-Free Gene-Silencing Activity

Short interfering RNAs (siRNAs) show promise as gene-silencing therapeutics, but their cellular uptake remains a challenge. We have recently shown the synthesis of siRNAs bearing a single neutral phenylethyl phosphotriester linkage within the sense strand. Here, we report the synthesis of siRNAs bearing three different hydrophobic phosphate triester linkages at key positions within the sense strand and assess their gene silencing in the absence of a transfection carrier. The best siRNAs bearing hydrophobic phosphate triester tails were not aromatic and exhibited effective gene silencing (IC₅₀ ≈ 56-141 nM), whereas the aromatic derivative with three hydrophobic tails did not exhibit carrier-free gene silencing.

Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides

In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.

Synthesis, Derivatization and Photochemical Control of ortho-Functionalized Tetrachlorinated Azobenzene-Modified siRNAs

We report the chemical synthesis and derivatization of an ortho-functionalized tetrachlorinated azobenzene diol. A 4',4-dimethoxytrityl (DMT) phosphoramidite was synthesized for its site-specific incorporation within the sense strand of an siRNA duplex to form ortho-functionalized tetrachlorinated azobenzene-containing siRNAs (Cl-siRNAzos). Compared to a non-halogenated azobenzene, ortho-functionalized tetrachlorinated azobenzenes are capable of red-shifting the π→π* transition from the ultraviolet (UV) portion of the electromagnetic spectrum into the visible range. Within this visible range, the azobenzene molecule can be reliably converted from trans to cis with red light (660 nm), and converted back to trans with violet wavelength light (410 nm) and/or thermal relaxation. We also report the gene-silencing ability of these Cl-siRNAzos in cell culture as well as their reversible control with visible light for up to 24 hours.

Effective carrier-free gene-silencing activity of cholesterol-modified siRNAs

The use of short interfering RNAs (siRNAs) as therapeutics holds great promise, but chemical modifications must first be employed to improve their pharmacokinetic properties. This study evaluates the in vitro cellular uptake and knock-down efficacy of cholesterol-modified triazole-linked siRNAs targeting firefly luciferase in the absence of a transfection carrier. These siRNAs displayed low cytotoxicity and excellent dose-dependent knockdown in HeLa cells in the 500 to 3000 nM concentration range, with a 70–80% reduction in firefly luciferase activity. Our results indicate that this modification is compatible with the RNA interference pathway, and is less cytotoxic and more effective than a commercially-available triethylene glycol (TEG) cholesterol modification.

The use of short interfering RNAs (siRNAs) as therapeutics holds great promise, but chemical modifications must first be employed to improve their pharmacokinetic properties.

Effective gene-silencing of siRNAs that contain functionalized spacer linkages within the central region

Short-interfering RNAs containing a variety of functional groups at the central region of the sense strand were synthesized and evaluated.

siRNAmod: A database of experimentally validated chemically modified siRNAs

Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.

Synthesis and in vitro assessment of chemically modified siRNAs targeting BCL2 that contain 2′-ribose and triazole-linked backbone modifications

Short-interfering RNAs (siRNAs) are naturally occurring biomolecules used for post-transcriptional gene regulation, and therefore hold promise as a future therapeutic by silencing gene expression of overexpressed deleterious genes.