Stereochemistry Enhances Potency, Efficacy, and Durability of <i>Malat1</i> Antisense Oligonucleotides In Vitro and In Vivo in Multiple Species

Byrne, Michael; Vathipadiekal, Vinod; Apponi, Luciano H.; Iwamoto, Naoki; Pachamuthu, Kandasamy; Longo, Kenneth A.; Liu, Fangjun; Looby, Richard; Norwood, Lauren; Shah, Anee; Shelke, Juili Dilip; Shivalila, Chikdu Shakti; Yang, Hailin; Yin, Yuan; Guo, Lankai; Bowman, Keith; Vargeese, Chandra

doi:10.1167/tvst.10.1.23

Cited by 22 publications

(12 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The inclusion of PN-1 linkages generally does not substantially alter the thermal stability of RNA-oligonucleotide heteroduplexes compared with stereorandom and stereopure PS/PO-modified oligonucleotides with the same sequence and 2′-ribose modification pattern (Figure 2A ), which is consistent with other reports ( 21 , 23 ). As expected based on our previous work ( 5 ), stereopure MALAT1-200 was more active in biochemical RNase H assays than stereorandom MALAT1-181 (Figure 2B ). The introduction of PN-1 linkages in the wings did not alter on this biochemical activity.…”

Section: Resultssupporting

confidence: 90%

“…We have previously reported a stereopure Malat1-targeting PS/PO oligonucleotide (MALAT1-200) that demonstrated superior activity in the eye than a stereorandom PS/PO oligonucleotide (MALAT1-181) with the same sequence and 2′-ribose modification pattern ( 5 ). To assess whether incorporation of the PN backbone linkages based on (1,3-dimethylimidazolidin-2-ylidene) phosphoramidate ( 1 ), (denoted PN-1, Supplementary Figure S1 ) can further improve on this activity, we generated a series of chimeric oligonucleotides derived from MALAT-200 containing three consecutive stereopure or stereorandom PN-1 backbone linkages in the 5′-wing, the 3′-wing, or both (Figure 2A ).…”

Section: Resultsmentioning

confidence: 99%

“…To assess whether incorporation of the PN backbone linkages based on (1,3-dimethylimidazolidin-2-ylidene) phosphoramidate ( 1 ), (denoted PN-1, Supplementary Figure S1 ) can further improve on this activity, we generated a series of chimeric oligonucleotides derived from MALAT-200 containing three consecutive stereopure or stereorandom PN-1 backbone linkages in the 5′-wing, the 3′-wing, or both (Figure 2A ). We initially positioned the PN-1 linkages in the wings where PO is often incorporated ( 5 , 6 ).…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS

Pachamuthu

Liu

Aduda

et al. 2022

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

Attaining sufficient tissue exposure at the site of action to achieve the desired pharmacodynamic effect on a target is an important determinant for any drug discovery program, and this can be particularly challenging for oligonucleotides in deep tissues of the CNS. Herein, we report the synthesis and impact of stereopure phosphoryl guanidine-containing backbone linkages (PN linkages) to oligonucleotides acting through an RNase H-mediated mechanism, using Malat1 and C9orf72 as benchmarks. We found that the incorporation of various types of PN linkages to a stereopure oligonucleotide backbone can increase potency of silencing in cultured neurons under free-uptake conditions 10-fold compared with similarly modified stereopure phosphorothioate (PS) and phosphodiester (PO)-based molecules. One of these backbone types, called PN-1, also yielded profound silencing benefits throughout the mouse brain and spinal cord at low doses, improving both the potency and durability of response, especially in difficult to reach brain tissues. Given these benefits in preclinical models, the incorporation of PN linkages into stereopure oligonucleotides with chimeric backbone modifications has the potential to render regions of the brain beyond the spinal cord more accessible to oligonucleotides and, consequently, may also expand the scope of neurological indications amenable to oligonucleotide therapeutics.

show abstract

Section: Resultssupporting

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS

Pachamuthu

Liu

Aduda

et al. 2022

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…Nevertheless, the difference between blocking the new acceptor site and donor site should be noted due to recognition by the different spliceosome complexes at the 5′ or 3′ intronic regions [ 42 ], as the involved mechanism might have an impact on splicing modulation approaches. Recently, it has been shown that stereochemistry of the PS linkage can increase the potency of AONs [ 43 , 44 ]. In general, stereopure AONs can be more efficacious at a lower concentration.…”

Section: Discussionmentioning

confidence: 99%

Antisense Oligonucleotide-Based Rescue of Aberrant Splicing Defects Caused by 15 Pathogenic Variants in ABCA4

Tomkiewicz

Suárez-Herrera

Cremers

et al. 2021

IJMS

View full text Add to dashboard Cite

The discovery of novel intronic variants in the ABCA4 locus has contributed significantly to solving the missing heritability in Stargardt disease (STGD1). The increasing number of variants affecting pre-mRNA splicing makes ABCA4 a suitable candidate for antisense oligonucleotide (AON)-based splicing modulation therapies. In this study, AON-based splicing modulation was assessed for 15 recently described intronic variants (three near-exon and 12 deep-intronic variants). In total, 26 AONs were designed and tested in vitro using a midigene-based splice system. Overall, partial or complete splicing correction was observed for two variants causing exon elongation and all variants causing pseudoexon inclusion. Together, our results confirm the high potential of AONs for the development of future RNA therapies to correct splicing defects causing STGD1.

show abstract

“…Recent examples from Wave Life Sciences Ltd. have shown that incorporation of select PO2 linkages into a stereodefined P(S) backbone generated more potent and selective oligonucleotides when compared to previously published candidates. 4,5 Similarly, work by Roche and Silence Therapeutics have shown that judicious incorporation of PS2 linkages into a stereorandom P(S) backbone generates more potent and stable leads. 6,7 The opportunity to install broader combinations and variations, in any order, at will thus presents a new step in the evolution of oligonucleotide therapeutics and requires the invention of enabling science, one such step is described herein.…”

Section: Introductionmentioning

confidence: 99%

A P(V)-Platform for Oligonucleotide Synthesis

Baran¹,

Knouse²,

Huang³

et al. 2021

Preprint

View full text Add to dashboard Cite

<div><div><div><p>The early promise of gene-based therapies is currently being realized at an accelerated pace with over 155 active clinical trials for antisense compounds and multiple FDA-approved oligonucleotide therapeutics. Fundamental advances in this area are vital and present an unprecedented opportunity to both address disease states that have been resistant to other common modalities and improve the significant sustainability challenges associated with production of these complex molecules on a commercial scale. The advent of phosphoramidite coupling chemistry and solid-phase synthesis 40 years ago democratized oligonucleotide synthesis to the scientific community, paving the way for many of these stunning developments. The reliability and generality of this approach for the preparation of native phosphate-diesters is attributed to the high reactivity of phosphorus when in the P(III)-oxidation state versus the desired P(V), as it enables rapid P-heteroatom bond formation. However, the growing demand for more diverse phosphorus-based linkages has challenged the limits of this technology. For example, the phosphorothioate (PS) linkage, which stabilizes oligonucleotides towards nuclease cleavage, is universally employed in current oligonucleotide therapeutics but is generally incorporated in racemic form. Stereodefined PS oligonucleotides may have desirable biological and physical properties but are accessed with difficulty using phosphoramidite chemistry. Here we report a flexible and efficient [P(V)]-based platform that can install a wide variety of phosphate linkages at will into oligonucleotides. This approach uses readily accessible reagents and can efficiently install not only stereodefined or racemic thiophosphates, but can install any combination of (S, R or rac)-PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotides. Importantly this platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable, P(V) reagents.</p></div></div></div>

show abstract

Stereochemistry Enhances Potency, Efficacy, and Durability of Malat1 Antisense Oligonucleotides In Vitro and In Vivo in Multiple Species

Cited by 22 publications

References 22 publications

Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS

Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS

Antisense Oligonucleotide-Based Rescue of Aberrant Splicing Defects Caused by 15 Pathogenic Variants in ABCA4

A P(V)-Platform for Oligonucleotide Synthesis

Contact Info

Product

Resources

About