The Medicinal Chemistry of Antisense Oligonucleotides

Watts, Jonathan K.

doi:10.1002/9781119070153.ch2

Cited by 9 publications

(12 citation statements)

References 299 publications

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“…This is in accordance with previous results in adult rodents, NHPs, and humans for the blood compartment [ 56 , 68 ], liver [ 69 , 70 , 71 ], and kidney [ 72 ]. PO ASOs are degraded within minutes in the blood and tissue compartments by endogenous nucleases, and thus, chemistry modifications of the phosphate bonds and sugar moiety of the oligonucleotide sequence are warranted to improve nuclease stability [ 6 , 22 , 73 , 74 , 75 ]. In addition to ASO chemistry modifications, sequence length also influences the rate of metabolism, as shorter sequences are digested more slowly [ 71 ].…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, once inside the cell, ASOs could bind to specific proteins and get sequestered away from the target RNA and RNase H [ 121 , 132 , 133 , 134 , 135 ]. More broadly, aside from binding to ASOs inside the cell, some proteins also contribute to their activity [ 22 , 136 ]. Therefore, we hypothesize that the specific proteins involved in the uptake and trafficking [ 137 ] of ASO are also under-expressed in the neonate.…”

Section: Discussionmentioning

confidence: 99%

“…Unmodified ASOs containing P-O bonds are inherently susceptible to nucleolytic degradation and have poor intrinsic binding affinity and biodistribution, which make these ASOs not suitable as therapeutic agents. This led to the development of first-generation ASOs with backbone chemistry modifications, e.g., phosphorothioate (PS), so-called phosphorothioate antisense oligonucleotides (PTOs) [ 22 , 23 ]. PTOs later included additional modifications of the nucleotide sugar moiety, e.g., locked-nucleic acids (LNAs) in the flanking regions.…”

Section: Introductionmentioning

confidence: 99%

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Safety Testing of an Antisense Oligonucleotide Intended for Pediatric Indications in the Juvenile Göttingen Minipig, including an Evaluation of the Ontogeny of Key Nucleases

Valenzuela

Tardiveau²,

Ayuso

et al. 2021

Pharmaceutics

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The adult Göttingen Minipig is an acknowledged model for safety assessment of antisense oligonucleotide (ASO) drugs developed for adult indications. To assess whether the juvenile Göttingen Minipig is also a suitable nonclinical model for pediatric safety assessment of ASOs, we performed an 8-week repeat-dose toxicity study in different age groups of minipigs ranging from 1 to 50 days of age. The animals received a weekly dose of a phosphorothioated locked-nucleic-acid-based ASO that was assessed previously for toxicity in adult minipigs. The endpoints included toxicokinetic parameters, in-life monitoring, clinical pathology, and histopathology. Additionally, the ontogeny of key nucleases involved in ASO metabolism and pharmacologic activity was investigated using quantitative polymerase chain reaction and nuclease activity assays. Similar clinical chemistry and toxicity findings were observed; however, differences in plasma and tissue exposures as well as pharmacologic activity were seen in the juvenile minipigs when compared with the adult data. The ontogeny study revealed a differential nuclease expression and activity, which could affect the metabolic pathway and pharmacologic effect of ASOs in different tissues and age groups. These data indicate that the juvenile Göttingen Minipig is a promising nonclinical model for safety assessment of ASOs intended to treat disease in the human pediatric population.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Safety Testing of an Antisense Oligonucleotide Intended for Pediatric Indications in the Juvenile Göttingen Minipig, including an Evaluation of the Ontogeny of Key Nucleases

Valenzuela

Tardiveau²,

Ayuso

et al. 2021

Pharmaceutics

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“…Progress in chemical modification of oligonucleotides has been profoundly important in enabling clinical success. [22][23][24] Further improvements in modification and formulation of ASOs, as well as increased mechanistic understanding of the factors defining efficacy and toxicity, is essential to expand the therapeutic use of gapmer ASOs in the CNS.…”

Section: Introductionmentioning

confidence: 99%

Quantifying and Mitigating Motor Phenotypes Induced by Antisense Oligonucleotides in the Central Nervous System

Moazami

Rembetsy-Brown

Wang

et al. 2021

Preprint

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Antisense oligonucleotides (ASOs) are emerging as a promising class of therapeutics for neurological diseases. When injected directly into the cerebrospinal fluid, ASOs distribute broadly across brain regions and exert long-lasting therapeutic effects. However, many phosphorothioate (PS)-modified gapmer ASOs show transient motor phenotypes when injected into the cerebrospinal fluid, ranging from reduced motor activity to ataxia or acute seizure-like phenotypes. The effect of sugar and phosphate modifications on these phenotypes has not previously been systematically studied. Using a behavioral scoring assay customized to reflect the timing and nature of these effects, we show that both sugar and phosphate modifications influence acute motor phenotypes. Among sugar analogues, PS-DNA induces the strongest motor phenotype while 2'-substituted RNA modifications improve the tolerability of PS-ASOs. This helps explain why gapmer ASOs have been more challenging to develop clinically relative to steric blocker ASOs, which have a reduced tendency to induce these effects. Reducing the PS content of gapmer ASOs, which contain a stretch of PS-DNA, improves their toxicity profile, but in some cases also reduces their efficacy or duration of effect. Reducing PS content improved the acute tolerability of ASOs in both mice and sheep. We show that this acute toxicity is not mediated by the major nucleic acid sensing innate immune pathways. Formulating ASOs with calcium ions before injecting into the CNS further improved their tolerability, but through a mechanism at least partially distinct from the reduction of PS content. Overall, our work identifies and quantifies an understudied aspect of oligonucleotide toxicology in the CNS, explores its mechanism, and presents platform-level medicinal chemistry approaches that improve tolerability of this class of compounds.

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“…Four Food and Drug Administration-approved ASOs are on the market, and dozens more are in clinical trials. This has largely been made possible by the evolution of ASO chemistry. − A key enabling modification has been the phosphorothioate (PS) backbone, which increases both nuclease stability and its rate of cellular uptake . Nevertheless, the PS backbone is also associated with toxicity .…”

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confidence: 99%

Next-Generation Peptide Nucleic Acid Chimeras Exhibit High Affinity and Potent Gene Silencing

et al. 2018

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We present a new design of mixed-backbone antisense oligonucleotides (ASOs) containing both DNA and peptide nucleic acid (PNA). Previous generations of PNA− DNA chimeras showed low binding affinity, reducing their potential as therapeutics. The addition of a 5′-wing of locked nucleic acid as well as the combination of a modified nucleotide and a PNA monomer at the junction between PNA and DNA yielded high-affinity chimeras. The resulting ASOs demonstrated high serum stability and elicited robust RNase H-mediated cleavage of complementary RNA. These properties allowed the chimeric ASOs to demonstrate high gene silencing efficacy and potency in cells, comparable with those of LNA gapmer ASOs, via both lipid transfection and gymnosis.

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The Medicinal Chemistry of Antisense Oligonucleotides

Cited by 9 publications

References 299 publications

Safety Testing of an Antisense Oligonucleotide Intended for Pediatric Indications in the Juvenile Göttingen Minipig, including an Evaluation of the Ontogeny of Key Nucleases

Safety Testing of an Antisense Oligonucleotide Intended for Pediatric Indications in the Juvenile Göttingen Minipig, including an Evaluation of the Ontogeny of Key Nucleases

Quantifying and Mitigating Motor Phenotypes Induced by Antisense Oligonucleotides in the Central Nervous System

Next-Generation Peptide Nucleic Acid Chimeras Exhibit High Affinity and Potent Gene Silencing

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