Multifunctional chiral bis(amidine) organocatalysts enable stereoselective synthesis of phosphorothioate oligonucleotides

Abstract

Phosphorothioate oligonucleotides (PS-ODNs) and cyclic dinucleotides are important therapeutic agents whose activity depends critically on phosphorus stereochemistry. However, existing strategies largely rely on chiral auxiliaries that require multistep installation and removal. Although chiral phosphoric acid catalysis enables diastereoselective synthesis of P-stereogenic dinucleotides via P(III)-phosphoramidite chemistry, this approach fails to access long-chain stereodefined PS-ODNs. Here we report a catalytic asymmetric P(V)-based strategy that enables stereocontrolled synthesis of PS-ODNs and cyclic dinucleotides using chiral organocatalysts. This platform integrates a catalyst-controlled nucleoside loading step with a stereospecific coupling process under mild, redox-neutral conditions. The method exhibits broad substrate scope, enabling efficient construction of diverse P–O, P–S, P–C and P–N linkages with high stereochemical fidelity. Notably, the method enables the stereocontrolled synthesis of PS-ODNs under both 5′ → 3′ and standard 3′ → 5′ solid-phase oligonucleotide synthesis workflows. Mechanistic studies support a cooperative activation mode involving hydrogen bonding, nucleophilic activation and general base catalysis. Existing methodologies for the stereocontrolled synthesis of phosphorothioate oligonucleotides and cyclic dinucleotides generally rely on chiral auxiliaries and are not catalytic. This study reports a catalytic asymmetric P(V)-based strategy, enabled by a C2-symmetric multifunctional chiral bis(amidine) organocatalyst, for the stereoselective synthesis of these classes of compounds.