PI Session 1, PI Session
PI1-013

A Streamlined Strategy for the Construction of Oligonucleotide Phosphoramidate Libraries

S. Dana1, C. Bon1, C. Sparr1
1Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland

Oligonucleotides and cyclic dinucleotides (CDNs) are emerging therapeutic modalities for the treatment of many previously untreatable diseases. Typically, (oligo)nucleotide backbones are constituted by nucleoside units that are hinged together by phosphate linkages. The strong negative charge of canonical phosphate linkages constrains the therapeutic utility of nucleotide-based modalities by restricting cellular uptake, compromising metabolic stability, and impeding efficient systemic delivery. In this context, the internucleoside phosphoramidate linkages exhibit promising pharmacokinetic properties. Yet, their conventional synthesis has remained a challenge owing to the poor scope of amine nucleophiles and the overreliance on azide-based Staudinger reaction. Developing a divergent platform for the construction of diverse internucleoside linkages across different nucleoside base pairs and suitable for industrial solidphase oligonucleotide synthesis is essential for the advancement of oligonucleotide therapeutics. Here, we present a straightforward and cost-effective synthetic route for the rapid generation of phosphoramidate libraries from commercial reagents. The synthetic protocol provides a divergent platform for the efficient insertion of diverse chemical handles into the dinucleotide backbone, giving access to charged and charge-neutral internucleoside linkages. A diverse array of previously inaccessible phosphorus linkages can now be accessed while avoiding the use of unstable reagents and complex protecting-group manipulations. The current transformative tool allows the synthesis of phosphoramidates in one-pot, both in linear and parallel fashion, starting from commercially accessible nucleosides and avoiding the purification of sensitive phosphoramidite and phosphite intermediates. The strategy is also operative in standard solid-phase oligonucleotide synthetic platform. These findings enable efficient modulation of a range of dinucleotide chimeras for biological evaluation, thereby expediting their advancement as therapeutic agents and biological probes toward clinical translation.