Synthesis of PS/PO-chimeric oligonucleotides using mixed oxathiaphospholane and phosphoramidite chemistry

Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies

Phosphate linkages govern life as we know it. Their unique properties provide the foundation for many natural systems from cell biology and biosynthesis to the backbone of nucleic acids. Phosphates are ideal natural moieties; existing as ionized species in a stable P(V)-oxidation state, they are endowed with high stability but exhibit enzymatically unlockable potential. Despite intense interest in phosphorus catalysis and condensation chemistry, organic chemistry has not fully embraced the potential of P(V) reagents. To be sure, within the world of chemical oligonucleotide synthesis, modern approaches utilize P(III) reagent systems to create phosphate linkages and their analogs. In this Outlook, we present recent studies from our laboratories suggesting that numerous exciting opportunities for P(V) chemistry exist at the nexus of organic synthesis and biochemistry. Applications to the synthesis of stereopure antisense oligonucleotides, cyclic dinucleotides, methylphosphonates, and phosphines are reviewed as well as chemoselective modification to peptides, proteins, and nucleic acids. Finally, an outlook into what may be possible in the future with P(V) chemistry is previewed, suggesting these examples represent just the tip of the iceberg.

A P(V) platform for oligonucleotide synthesis

The promise of gene-based therapies is being realized at an accelerated pace, with more than 155 active clinical trials and multiple U.S. Food and Drug Administration approvals for therapeutic oligonucleotides, by far most of which contain modified phosphate linkages. These unnatural linkages have desirable biological and physical properties but are often accessed with difficulty using phosphoramidite chemistry. 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 install not only stereodefined or racemic thiophosphates but any combination of (S, R or rac)–PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotide polymers. This platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable P(V) reagents.

P-stereocontrolled synthesis of oligo(nucleoside N3'→O5' phosphoramidothioate)s - opportunities and limitations

3'-N-(2-Thio-1,3,2-oxathiaphospholane) derivatives of 5'-O-DMT-3'-amino-2',3'-dideoxy-ribonucleosides (NOTP-N), that bear a 4,4-unsubstituted, 4,4-dimethyl, or 4,4-pentamethylene substituted oxathiaphospholane ring, were synthesized. Within these three series, NOTP-N differed by canonical nucleobases (i.e., AdeBz, CytBz, GuaiBu, or Thy). The monomers were chromatographically separated into P-diastereomers, which were further used to prepare NNPSN' dinucleotides (3), as well as short P-stereodefined oligo(deoxyribonucleoside N3'→O5' phosphoramidothioate)s (NPS-) and chimeric NPS/PO- and NPS/PS-oligomers. The condensation reaction for NOTP-N monomers was found to be 5-6 times slower than the analogous OTP derivatives. When the 5'-end nucleoside of a growing oligomer adopts a C3'-endo conformation, a conformational 'clash' with the incoming NOTP-N monomer takes place, which is a main factor decreasing the repetitive yield of chain elongation. Although both isomers of NNPSN' were digested by the HINT1 phosphoramidase enzyme, the isomers hydrolyzed at a faster rate were tentatively assigned the R P absolute configuration. This assignment is supported by X-ray analysis of the protected dinucleotide DMTdGiBu NPSMeTOAc, which is P-stereoequivalent to the hydrolyzed faster P-diastereomer of dGNPST.

Efficient Conjugation to Phosphorothioate Oligonucleotides by Cu-Catalyzed Huisgen 1,3-Dipolar Cycloaddition

Improving oligonucleotide delivery is critical for the further development of oligonucleotide-based therapeutics. Covalent attachment of reporter molecules is one of the most promising approaches toward efficient oligonucleotide-based therapies. An efficient methods for the attachment of a variety of reporter groups is Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition. However, the majority of potential oligonucleotide (ON) therapeutics in clinical trials are carrying phosphorothioate (PS) linkages, and this robust conjugation method is not yet established for these ONs due to a general concern of Cu-S interaction. Here, we developed a method allowing for efficient conjugation of peptides to PS oligonucleotides. The method utilizes solid supported oligonucleotides that can be readily transformed into "clickable ONs" by simple linker conjugation and further reacted with an azido containing moiety (e.g., a peptide) using the CuBr × Me₂S complex as a superior catalyst in that reaction. This study opens the way for further development of PS oligonucleotide-conjugates by means of efficient Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition.

Determination of silyl peroxides by ultra-performance liquid chromatography/electrospray ionisation mass spectrometry

RATIONALE

Residual initiators in polymers are a concern in the case of products that come directly into contact with the human body or food. Due to low concentrations and difficulties in the sample preparation, highly sensitive and selective methods are required.

METHODS

A series of bis-silyl- and alkyl-silyl peroxides were analysed by electrospray ionisation mass spectrometry (ESI-MS) on an ultra-performance liquid chromatography/time-of-flight (UPLC/TOF) instrument. Li, Na, K, and NH₄ acetates were used to promote the formation of [M + Me]⁺ ions. The sample preparation involved only dissolution of the polymer sample in 0.1 mL of acetonitrile, followed by precipitation with 1 mL of water. A portion of 0.1-1 μL of the solution was then analysed without further treatment by UPLC/ESI-MS.

RESULTS

Limits of detection (LODs) were in the range of 0.06-9 pmol, depending on the peroxide structure. On average, the signal intensity increased with the number of phenyl groups in a peroxide and decreased in the order Na > Li > K > NH₄ . Peroxides that did not contain phenyl groups could not be detected. Collision-induced dissociation experiments can be used for structural investigations of alkyl-silyl peroxides. It was possible to detect 2 × 10^-4 % (LOD = 7 × 10^-5 %) of unreacted Ph₃ SiOOt-Bu in the poly(methyl methacrylate) sample.

CONCLUSIONS

The method is suitable for the analysis of trace peroxide initiators in polymers and for other purposes where LODs in the pmol range are required.