Synthesis and evaluation of (S)-5′-C-aminopropyl and (S)-5′-C-aminopropyl-2′-arabinofluoro modified DNA oligomers for novel RNase H-dependent antisense oligonucleotides

Abstract

We designed and synthesized two novel thymidine analogs: (S)-5′-C-aminopropyl-thymidine and (S)-5′-C-aminopropyl-2′-β-fluoro-thymidine.

Antisense Gapmers with LNA-Wings and (S)-5′-C-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of KNTC2

“…The incorporation of 5ara -modified analogs in the gap region showed moderate effects on T m values, while the replacement of LNAs in the wing region with 5ara-T or 5ara- Me C resulted in thermal destabilization. These results are consistent with previous studies showing that the thermal stability of 5ara modification is comparable to that of natural DNA but lower than that of LNA [ 27 ]. Furthermore, the T m value of KN5ara-9 was similar to the addition of KN5ara-7 and KN5ara-8, indicating that the continuous introduction of modified analogs might not have an additional impact on thermal stability.…”

“…The accurate binding of ASOs to target mRNA is necessary for RNase H recognition and the following antisense mechanism. As reported before, although PS linkages negatively affected thermal stability, LNAs could significantly increase RNA binding affinity and a single ( S )-5ʹ- C -Aminopropyl-2ʹ-arabinofluoro modification caused few changes to the 50% melting temperature ( T m ) values of ASO/RNA duplexes [ 27 , 28 , 29 ]. Therefore, we hypothesized that the series of KN5ara gapmers would have sufficient RNA binding affinity for therapeutic application.…”

“…In previous studies, our group designed and synthesized various chemically modified nucleoside analogs containing an aminoalkyl sidechain, which is expected to strengthen nuclease resistance and improve the intracellular internalization of oligonucleotides [ 21 , 22 , 23 , 24 , 25 , 26 , 27 ]. As a result of evaluating ( S )-5ʹ- C -aminopropyl- ( 5deo ) and ( S )-5ʹ- C -aminopropyl-2ʹ-arabinofluoro- ( 5ara ) modified ASOs, it was revealed that ASOs with several 5ara modifications could significantly enhance the nuclease resistance and show a superior ability to activate the RNase H-dependent antisense mechanism compared with the 5deo -modified ones, although the cleavage of the complementary RNA strands would be obviously impeded compared with the natural DNAs [ 27 ].…”

Synthesis, gene silencing activity, thermal stability, and serum stability of siRNA containing four (S)-5′-C-aminopropyl-2′-O-methylnucleosides (A, adenosine; U, uridine; G, guanosine; and C, cytidine)

“…The congurations of the 5-carbons in 6 and 7 were determined by nuclear overhauser effect spectroscopy (NOESY). 21,24,25 To x the conformations of the sugar moieties of 6 and 7, the 3and 5-hydroxy groups of 6 and 7 were protected by cyclic silyl groups. Aer removing the 3-O-tert-butyldiphenylsilyl (TBDPS) groups of 6 and 7, the resulting 3, 5-dihydroxy derivatives were treated with 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane (TIPDSCl 2 ) in pyridine to afford 3,5-O-TIPDS derivatives 34 and 35 in 81% and 79% yields, respectively (Scheme 4).…”

“…The crude material was puried by column chromatography (33% ethyl acetate in hexane) to afford desired product 24 as a white solid (7.03 g, 9.86 mmol, 93%). 1 (25). CH 3 I (1.84 mL, 29.58 mmol) and NaH (0.43 g, 10.85 mmol) were added to a solution of 24 (7.03 g, 9.86 mmol) and molecular sieve 3 A (7.0 g) in DMF (70 mL) at 0 C under argon atmosphere.…”