Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
Bioorg Med Chem. 2024 Feb 15;100:117616. doi: 10.1016/j.bmc.2024.117616. Epub 2024 Jan 28.
Herein, we report the synthesis of 2'-O-alkyl/2'-fluoro-N-methyluridine (2'-O-alkyl/2'-F-mU) phosphoramidites and their incorporation in DNA and RNA oligonucleotides. The duplex binding affinity and base discrimination studies showed that all 2'-O-alkyl/2'-F-mU modifications significantly decreased the thermal stability and base-pairing discrimination ability. Serum stability study of dT with 2'-O-alkyl-mU modification exhibited excellent nuclease resistance when incubated with 3'-exonucleases (SVPD) or 5'-exonucleases (PDE-II) as compared to mU, 2'-F, 2'-OMe modified oligonucleotides. MD simulation studies with RNA tetradecamer duplexes illustrated that the mU and 2'-O-methyl-mU modifications reduce the duplex stabilities by disrupting the Watson-Crick hydrogen bonding and base-stacking interactions. Further molecular modelling investigations demonstrated that the 2'-O-propyl-mU modification exhibits steric interactions with amino acid residues in the active site of 3'- and 5'-exonuclease, leading to enhanced stability. These combined data indicate that the 2'-modified-mU nucleotides can be used as a promising tool to enhance the stability, silencing efficiency, and drug-like properties of antisense/siRNA-based therapeutics.
本文报道了 2'-O-烷基/2'-氟-N-甲基尿苷（2'-O-烷基/2'-F-mU）的磷酰胺的合成及其在 DNA 和 RNA 寡核苷酸中的掺入。双链结合亲和力和碱基区分研究表明，所有 2'-O-烷基/2'-F-mU 修饰均显著降低了热稳定性和碱基配对区分能力。与 mU、2'-F、2'-OMe 修饰的寡核苷酸相比，2'-O-烷基-mU 修饰的 dT 具有出色的核酸酶抗性，当与 3'-核酸外切酶（SVPD）或 5'-核酸外切酶（PDE-II）孵育时，血清稳定性研究表明。RNA 十四聚体双链的 MD 模拟研究表明，mU 和 2'-O-甲基-mU 修饰通过破坏 Watson-Crick 氢键和碱基堆积相互作用降低了双链稳定性。进一步的分子建模研究表明，2'-O-丙基-mU 修饰与 3'-和 5'-核酸外切酶活性位点中的氨基酸残基发生空间相互作用，导致稳定性增强。这些综合数据表明，2'-修饰-mU 核苷酸可用作增强反义/siRNA 治疗剂的稳定性、沉默效率和类药性的有前途的工具。
