The role of chemistry in the success of oligonucleotides as therapeutics

• Pawan Kumar and
• Tom Brown

Beilstein J. Org. Chem. 2022, 18, 197–199, doi:10.3762/bjoc.18.22

• nucleotides; siRNAs; RNA-targeting oligonucleotides (e.g., antisense, siRNA, and anti-miR) are widely explored as fundamental research tools and are gaining increasing promise as therapeutic agents, particularly against diseases of genetic origin. The idea of treating a disease by targeting the molecular

• , both of them target mRNA to disrupt protein synthesis. In the following text we will refer both antisense oligonucleotides and siRNAs collectively as therapeutic oligonucleotides. More than 10 oligonucleotide drugs have received regulatory approval by the FDA and are now helping patients suffering from

• antisense and siRNAs) to the liver. Currently, there are three siRNA-GalNAc conjugates approved by the FDA and many others are in late-stage clinical trials. The success of GalNAc-oligonucleotide conjugates highlights the power of therapeutic oligonucleotides in treating previously untreatable conditions

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

• improved liver targeting [22][23] and ASO–glucagon-like peptide-1 (GLP1) conjugation for improved delivery to pancreatic β-cells [24]. Previously, Menzi et al. reviewed the impact of cationic modifications and conjugations for ONs and siRNAs biophysical and biological activities until 2015 [25]. In this

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• increase in silencing activity for AM1-modified siRNAs with amide linkages at specific sites [75]. Structural insight into this observation was obtained using the crystal structure of the complex between Bacillus halodurans RNase H and the r(GAC ACC UGA UAM1UC) - d(GAA TCA GGT GTC) hybrid duplex [73

• structural distortions caused by A/B junctions within the helical structures [207]. 2',4'-diF-modified siRNA sequences were capable of triggering RNAi with high efficiency, and the incorporation of multiple residues in the guide (antisense) strand yielded more potent siRNAs than those containing LNA or FANA

• -methyluridine (GMU) (Figure 9K) has shown that functionalizing the C4' position with guanidinium leads to siRNAs with increased thermal stability (1–3 °C/mod) and improved stability in human serum [215]. These guanidinium-modified siRNAs also lead to sustained gene silencing with only picomolar concentrations

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• interfering RNA (siRNA), through a stick bridge motif, to deliver siRNAs into the respective target cells. The G-3 siRNA conjugate had the highest efficacy with 70% delivery into target T-cells, while the A-1 siRNA conjugate showed a 20% delivery into target gp160-expressing cells [34][35]. Thus, both

• –maleimide–PEG into their LNPs to target epidermal growth factor receptor (EGFR)-positive cancer cells. The authors showed an increased delivery of siRNAs and fluorescent quantum dot nanocrystals both in vitro and in EGFR-positive tumor xenografts in mice [48]. In 2020, Chandra et al. used a maleimide–PEG in

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• strategies include antisense oligonucleotides (AONs), ribozymes, DNAzymes, small interfering RNAs (siRNAs) and micro RNAs (miRNAs) that specifically target the complementary mRNA sequence of the relevant undesired gene before translation. AONs are single-stranded DNA of 15 to 25 nucleotides in length that

• , more potent than AONs or ribozymes for gene knockdown, is centered on the RNA interference (RNAi) mechanism, which uses two natural pathways for gene silencing. One is guided by double-stranded siRNAs of 19–23 nucleotides in length that are fully complementary to the mRNA targets, and the other is

• cells or tissues, off-target effects and toxicity hamper the path to success of ON-based therapeutics and need to be solved. Fortunately, various chemical modifications of ONs have been designed to address these issues [9]. The most common modification in AONs and siRNAs is the phosphorothioate (PS

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• and limitations of the different strategies and – if available – will show ways to circumvent them. This review focuses strictly on mRNA cap analogues (and some non-natural modifications); for preparation of other capped biomolecules such as capped siRNAs [21], peptidyl capped oligonucleotides [22

Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2015, 11, 913–929, doi:10.3762/bjoc.11.103

• the amphiphilic head group but preserved the oligonucleotide DNA sequence. This sequence [5’-d(NL-(Cy5) TAG GTC AAT ACT); NL = nucleolipid] was chosen because it forms neither a hairpin structure nor a self-complementary duplex [9]. Particularly, for a successful delivery of siRNAs [10][11][12] their

Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• an ever-greater focus [5][6][8][9][10][11]. The study of the interactions of single- and double-stranded nucleic acids with lipid bilayers is, therefore, of significant importance, particularly for the following reasons: 1. for the optimization of the in vivo delivery of lipophilic siRNAs [12][13][14