Facile Synthesis, Geometry, and 2'-Substituent-Dependent in Vivo Activity of 5'-(E)- and 5'-(Z)-Vinylphosphonate-Modified siRNA Conjugates

J Med Chem. 2018 Feb 8;61(3):734-744. doi: 10.1021/acs.jmedchem.7b01147. Epub 2018 Jan 27.

Abstract

(E)-Vinylphosphonate ((E)-VP), a metabolically stable phosphate mimic at the 5'-end of the antisense strand, enhances the in vivo potency of siRNA. Here we describe a straightforward synthetic approach to incorporate a nucleotide carrying a vinylphosphonate (VP) moiety at the 5'-end of oligonucleotides under standard solid-phase synthesis and deprotection conditions by utilizing pivaloyloxymethyl (POM) protected VP-nucleoside phosphoramidites. The POM protection enhances scope and scalability of 5'-VP-modified oligonucleotides and, in a broader sense, the synthesis of oligonucleotides modified with phosphonate moieties. Trivalent N-acetylgalactosamine-conjugated small interfering RNA (GalNAc-siRNA) comprising (E)-geometrical isomer of VP showed improved RISC loading with robust RNAi-mediated gene silencing in mice compared to the corresponding (Z)-isomer despite similar tissue accumulation. We also obtained structural insights into why bulkier 2'-ribosugar substitutions such as 2'-O-[2-(methylamino)-2-oxoethyl] are well tolerated only when combined with 5'-(E)-VP.

MeSH terms

  • Animals
  • Argonaute Proteins / chemistry
  • Argonaute Proteins / deficiency
  • Argonaute Proteins / genetics
  • Base Sequence
  • Chemistry Techniques, Synthetic
  • Gene Silencing
  • Mice
  • Models, Molecular
  • Organophosphonates / chemical synthesis*
  • Organophosphonates / chemistry*
  • Protein Domains
  • RNA, Small Interfering / chemistry*
  • RNA, Small Interfering / genetics
  • Stereoisomerism

Substances

  • Ago2 protein, mouse
  • Argonaute Proteins
  • Organophosphonates
  • RNA, Small Interfering