Synthesis, RNA selective hybridization and high nuclease resistance of an oligonucleotide containing novel bridged nucleic acid with cyclic urea structure

Development of nucleic acid medicines based on chemical technology

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.

Synthesis of scpBNA-mC, -A, and -G Monomers and Evaluation of the Binding Affinities of scpBNA-Modified Oligonucleotides toward Complementary ssRNA and ssDNA

We previously reported the synthesis and evaluation of 2'-O,4'-C-spirocyclopropylene-bridged nucleic acid (scpBNA) bearing a thymine (T) nucleobase. Oligonucleotides (ONs) modified with scpBNA-T exhibited strong binding affinity to complementary single-stranded RNA (ssRNA) and high enzymatic stability. These biophysical properties suggest that scpBNAs are well suited for use in antisense strategies. Herein, we describe the synthesis of scpBNA monomers bearing 5-methylcytosine (^mC), adenine (A), and guanine (G) nucleobases for use in a variety of sequences. The prepared scpBNA monomers were incorporated into ONs at various positions. The scpBNA-modified ONs exhibited excellent duplex-forming ability with the complementary ssRNA comparable to ONs modified with 2'-O,4'-C-methylene-bridged nucleic acid (2',4'-BNA/LNA). Moreover, ON modified with scpBNA-^mC, -A, and -G showed higher enzymatic stability than the corresponding 2',4'-BNA/LNA-modified ON. These results demonstrated a promising role for the incorporation of scpBNA monomers into therapeutic antisense ONs.

The Medicinal Chemistry of Therapeutic Oligonucleotides

Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.

Synthesis and properties of 2'-O,4'-C-spirocyclopropylene bridged nucleic acid (scpBNA), an analogue of 2',4'-BNA/LNA bearing a cyclopropane ring

2'-O,4'-C-Spirocyclopropylene bridged nucleic acid (scpBNA), an analogue of 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA/LNA) bearing a cyclopropane ring at the 6'-position, was synthesized and successfully incorporated into oligonucleotides. The scpBNA-modified oligonucleotides showed excellent duplex-forming ability with complementary single-stranded RNA and exhibited increased enzymatic stability as compared to the corresponding natural and 2',4'-BNA/LNA-modified oligonucleotides. Our results demonstrate the potential of scpBNA for gene therapeutics, such as antisense technology.

Amido-bridged nucleic acids with small hydrophobic residues enhance hepatic tropism of antisense oligonucleotides in vivo

High scalability of a novel bicyclic nucleoside building block, amido-bridged nucleic acid (AmNA), to diversify pharmacokinetic properties of therapeutic antisense oligonucleotides is described. N2'-functionalization of AmNA with a variety of hydrophobic groups is straightforward. Combinations of these modules display similar antisense knockdown effects and improve cellular uptake, relative to sequence-matched conventional 2',4'-bridged nucleic acid (2',4'-BNA) in vivo.

Synthesis and Properties of the 5-Methyluridine Derivative of 3,4-Dihydro-2H-pyran-Bridged Nucleic Acid (DpNA)

A novel 2'-O,4'-C-bridged nucleic acid, 3,4-dihydro-2H-pyran bridge moiety (DpNA), with a dioxabicyclo[3.2.1]oct-3-ene ring was designed. Construction of the dihydropyran bridge was achieved by dehydration of a six-membered hemiacetal ring, and the DpNA monomer was synthesized in 10 steps from 5-methyluridine (total yield 9%). The synthesized DpNA monomer was incorporated into oligonucleotides to examine the properties of the modified oligonucleotides. The DpNA-modified oligonucleotides possessed high affinity toward ssRNA and were more resistant to nucleases compared to the corresponding natural oligonucleotide.

Sulfonamide-bridged nucleic acid: synthesis, high RNA selective hybridization, and high nuclease resistance

2'-N,4'-C-(N-methylamino)sulfonylmethylene-bridged thymidine (SuNA), which has a six-membered linkage including a sulfonamide moiety, was synthesized and introduced into oligonucleotides. The oligonucleotides containing SuNA exhibited excellent nuclease resistance, a high affinity toward single-stranded RNA, and a low affinity toward single-stranded DNA compared to the natural oligonucleotide.

Skipping multiple exons of dystrophin transcripts using cocktail antisense oligonucleotides

Duchenne muscular dystrophy (DMD) is one of the most common and lethal genetic disorders, with 20,000 children per year born with DMD globally. DMD is caused by mutations in the dystrophin (DMD) gene. Antisense-mediated exon skipping therapy is a promising therapeutic approach that uses short DNA-like molecules called antisense oligonucleotides (AOs) to skip over/splice out the mutated part of the gene to produce a shortened but functional dystrophin protein. One major challenge has been its limited applicability. Multiple exon skipping has recently emerged as a potential solution. Indeed, many DMD patients need exon skipping of multiple exons in order to restore the reading frame, depending on how many base pairs the mutated exon(s) and adjacent exons have. Theoretically, multiple exon skipping could be used to treat approximately 90%, 80%, and 98% of DMD patients with deletion, duplication, and nonsense mutations, respectively. In addition, multiple exon skipping could be used to select deletions that optimize the functionality of the truncated dystrophin protein. The proof of concept of systemic multiple exon skipping using a cocktail of AOs has been demonstrated in dystrophic dog and mouse models. Remaining challenges include the insufficient efficacy of systemic treatment, especially for therapies that target the heart, and limited long-term safety data. Here we review recent preclinical developments in AO-mediated multiple exon skipping and discuss the remaining challenges.

Guanidine bridged nucleic acid (GuNA): an effect of a cationic bridged nucleic acid on DNA binding affinity

A novel 2',4'-BNA/LNA analog bridged by guanidine, termed as guanidine bridged nucleic acid (GuNA), was synthesized and incorporated into oligonucleotides. Thermal stabilities and nuclease resistance of GuNA-modified oligonucleotides were investigated and compared with those of 2',4'-BNA/LNA and natural DNA oligonucleotides. GuNA exhibited interestingly high binding affinity towards complementary ssDNA than 2',4'-BNA/LNA.

Synthesis and properties of 2'-O,4'-C-ethyleneoxy bridged 5-methyluridine

2'-O,4'-C-Ethyleneoxy bridged 5-methyluridine (EoNA-T), possessing a seven-membered linkage and an anomeric 4'-carbon, was synthesized and introduced into oligonucleotides by using an automated DNA synthesizer. The EoNA-modified oligonucleotides significantly stabilized the duplexes with single-stranded RNA and triplexes with double-stranded DNA relative to the natural oligonucleotide and oligonucleotides modified by another seven-membered bridged 5-methyluridine, 2',4'-BNA(COC)-T. In addition, EoNA-T showed excellent nuclease resistance.

Synthesis and properties of a bridged nucleic acid with a perhydro-1,2-oxazin-3-one ring

A novel derivative of 2',4'-bridged nucleic acid, named hydroxamate-bridged nucleic acid (HxNA), containing a six-membered perhydro-1,2-oxazin-3-one ring, was designed and synthesized. The introduction of a carbonyl function along with an N-O linkage in the six-membered bridged structure is the unique structural feature of the novel 2',4'-bridged nucleic acid analogue. The design was carried out to restrict the flexibility of the sugar moiety through the trigonal planarity of carbonyl function, which would improve the properties of the modification. The synthesized monomer was incorporated into oligonucleotides, and their properties were examined. The HxNA-modified oligonucleotides exhibited selectively high affinity toward complementary ssRNA. Furthermore, the nuclease resistance of the HxNA-modified oligonucleotide was found to be higher than that of the corresponding natural and 2',4'-BNA/LNA-modified oligonucleotides. Interestingly, exposure of HxNA modified oligonucleotide to 3'-exonuclease resulted in gradual opening of the bridge, which stopped further digestion. Moreover, ring-opening of only one modification at the 3'-end of the oligonucleotides was observed, even if two or three HxNA modifications were present in the sequence. The results demonstrate the strong potential of the HxNA modification as a switch for the generation of highly nuclease-resistant RNA selective oligonucleotide in situ, which could have potential applications in antisense technology.

Bridged nucleic acid conjugates at 6'-thiol: synthesis, hybridization properties and nuclease resistances

The bridged nucleic acid (BNA) containing a thiol at the 6'-position in the bridged structure was synthesized from the disulfide-type BNA and conjugated with various functional molecules via the thioether or the disulfide linkage post-synthetically and efficiently in solution phase. The disulfide-linked conjugate was cleaved under reductive conditions derived from glutathione and an oligonucleotide bearing a free thiol was released smoothly. Conjugated functional molecules had great effects on duplex stability with the DNA complement. In contrast, the molecules little influenced the stability with the RNA complement. Moreover, the oligonucleotides with functional groups at the 6'-position had as high or higher resistances against 3'-exonuclease than phosphorothioate oligonucleotide (S-oligo).

Benzylidene acetal type bridged nucleic acids: changes in properties upon cleavage of the bridge triggered by external stimuli

Four classes of benzylidene acetal type bridged nucleic acids (BA-BNAs) were designed with 2',4'-bridged structures that cleaved upon exposure to appropriate external stimuli. Cleavage of 6-nitroveratrylidene and 2-nitrobenzylidene acetal type BNA bridges occurred upon photoirradiation and subsequent treatment with thiol caused changes in secondary structure to afford 4'-C-hydroxymethyl RNA. Benzylidene and 4-nitrobenzylidene acetal type BNA responded to acids and reducing agents, respectively, resulting in hydrolysis of the acetal-bridged structure. Cleavage of the bridge removed sugar conformational restrictions and changed the duplex- and triplex-forming properties of the BNA-modified oligonucleotides. Moreover, oligonucleotides incorporating a single BA-BNA modification had considerably improved stability toward 3'-exonuclease, which was lost upon cleavage of the bridge. Thus, these new BNAs may be useful as therapeutic and detection tools by sensing various environments.

[Design, syntheses and properties of nucleic Acid switch in response to external stimuli]

The control of molecular properties using external stimuli is an attractive research area that offers the potential for regulation of various biological phenomena. This review summarizes the concept, design, syntheses and properties of nucleic acid switches in response to external stimuli, namely, "external-stimuli-responsive bridged nucleic acids monomer". From (1)H-NMR experiments, every external-stimuli-responsive bridged nucleic acid monomer was found to have an N-conformation, while an S-conformation was predominantly observed after exposure to a proper stimulus. Each bridged nucleic acid monomer was effectively introduced into oligodeoxynucleotides using an automated DNA synthesizer. Moreover, oligonucleotides modified with these bridged nucleic acid monomer were changed in their hybridization property and tolerance to enzymatic digestion in response to each stimulus. These results clearly showed that external-stimuli-responsive bridged nucleic acids monomers should work as a nucleic acid switch, and have the potential for regulation of various biological phenomena.