Synthesis and study of neutral backbones for therapeutic antisense oligonucleotides

Thesis

Antisense oligonucleotides (ASOs) are a therapeutic modality which represent a transformative approach to drug development. By altering RNA processing through Watson-Crick base-pairing and therefore modulating down-stream protein expression, ASOs have provided heretofore undruggable diseases such as Duchenne muscular dystrophy with first-of-its-kind treatment. However, many ASOs rely solely upon chemical modifications to attain drug-like properties. This doctoral thesis focuses on expanding the chemical space of ASOs by combining neutral backbones and the locked nucleic acid (LNA) ribose modification to enhance their drug-like properties and therapeutic potential.

The work detailed in this thesis includes the synthesis of various dinucleotide and monomer phosphoramidites featuring neutral linkages, such as the amide (Chapter 2), carbamate (Chapter 3), and alkyl triester (Chapter 4), in combination with LNA. Biophysical studies such as thermal melting stability and circular dichroism reveal that linkages which are both flexible and good bioisosteres of the native phosphodiester adopt stable ASO:RNA heteroduplexes. Splice-switching was chosen as the therapeutic mechanism of action to evaluate these chemical modifications, as these ASOs have the capability to restore or up-regulate protein expression which is historically di fficult to achieve using traditional small molecule discovery. The LNA-amide and LNA-isopropyl triester linkages were found to be more active than the clinically-validated 2’OMe ribose and phosphorothioate (PS) backbone modifications, indicating their potential in enhancing the drug-like properties of ASOs. Finally, the protein-binding profiles of the most promising ASOs were investigated (Chapter 5), offering preliminary insights into their enhanced activity. This thesis hopes that by developing and investigating LNA-neutral backbones, it may contribute to the medicinal chemistry of ASOs, an area in which continual innovation may improve their clinical success.

Authors: Lie, L

• DOI: 10.5287/ora-yergzzvy2
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: neutral backbones; antisense oligonucleotides; locked nucleic acid
• Subjects: Antisense nucleic acids; Nucleic acids--Synthesis