Oligonucleotide Bioconjugation with Bifunctional Palladium Reagents

Abstract

Organometallic reagents enable practical strategies for bioconjugation. Innovations in the design of water‐soluble ligands and the enhancement of reaction rates have allowed for chemoselective cross‐coupling reactions of peptides and proteins to be carried out in water. There are currently no organometallic‐based methods for oligonucleotide bioconjugation to other biomolecules. Here we report bifunctional palladium(II)‐oxidative addition complexes (OACs) as reagents for high‐yielding oligonucleotide bioconjugation reactions. These bifunctional OACs react chemoselectively with amine‐modified oligonucleotides to generate the first isolable, bench stable oligonucleotide‐palladium(II) OACs. These complexes undergo site‐selective C‐S arylation with a broad range of native thiol‐containing biomolecules at low micromolar concentrations in under one hour. This approach provided oligonucleotide‐peptide, oligonucleotide‐protein, oligonucleotide‐small molecule, and oligonucleotide‐oligonucleotide conjugates in >80 % yield and afforded conjugation of multiple copies of oligonucleotides onto a monoclonal antibody.

Engineering Bioactive Dimeric Transcription Factor Analogs via Palladium Rebound Reagents

“…The use of bifunctional palladium­(II) OACs enabled the synthesis of homo- and heterodimeric TF complexes at milligram scale. In order to dovetail two proteins into a covalent complex, bifunctional reagents proved to be effective. , These reagents have the desired characteristics for macromolecule bioconjugation reaction: a high reaction rate critical for conjugating proteins at low concentrations in reasonable time scales. , The reagents’ chemoselectivity is an essential requirement for the formation of defined complexes. , Furthermore, the ability to obtain stable intermediate protein-OACs allowed for the synthesis of strictly heterodimeric analogs. Finally, the resulting S-aryl linkage between the two monomers did not disrupt the bioactive complex architecture.…”

“…In order to dovetail two proteins into a covalent complex, bifunctional reagents proved to be effective. 23,32 These reagents have the desired characteristics for macromolecule bioconjugation reaction: a high reaction rate critical for conjugating proteins at low concentrations in reasonable time scales. 33,34 The reagents' chemoselectivity is an essential requirement for the formation of defined complexes.…”

Conjugation Approaches for Peptide-Mediated Delivery of Oligonucleotides Therapeutics

“…[72,73] Recently, Jbara et al employed a thioaryl ether linkage to conjugate a DNA oligonucleotide with a cysteine-containing peptide. [74] This strategy utilises an elegant bifunctional conjugation handle with N-hydroxysuccinimide (NHS) and palladium(II)-oxidative addition complex (OAC) moieties for site-selective conjugation (Fig. 8), allowing faster kinetics compared with thiol-maleimide linkages while producing conjugates that are significantly more stable.…”

Convertible and Constrained Nucleotides: The 2’-Deoxyribose 5’-C-Functionalization Approach, a French Touch

“…This expanding field also explored the Sonogashira and the Stille–Migita reactions, their scope and limitations having been recently reviewed [ 65 ]. Although mostly limited to the introduction of small molecules, the Pd-catalyzed conjugation was demonstrated with the selective conjugation of the Z33-N17C protein at the 5’-amino terminal position of ON, through the formation of stable ON-Pd(II) oxidative addition complexes as intermediates [ 66 ]. Buchwald–Hartwig–Migita cross-coupling was also described to occur on a 5-iodo-uracile modification incorporating phosphoramidite chemistry to lead to thioglycosylated oligonucleotides [ 67 ].…”