Design, synthesis and evaluation of constrained methoxyethyl (cMOE) and constrained ethyl (cEt) nucleoside analogs.
Antisense drug discovery technology is a powerful method to modulate gene expression in animals and represents a novel therapeutic platform.(1) We have previously demonstrated that replacing 2'O-methoxyethyl (MOE, 2) residues in second generation antisense oligonucleotides (ASOs) with LNA (3) nucleosides improves the potency of some ASOs in animals. However, this was accompanied with a significant increase in the risk for hepatotoxicity.(2) We hypothesized that replacing LNA with novel nucleoside monomers that combine the structural elements of MOE and LNA might mitigate the toxicity of LNA while maintaining potency. To this end we designed and prepared novel nucleoside analogs 4 (S-constrained MOE, S-cMOE) and 5 (R-constrained MOE, R-cMOE) where the ethyl chain of the 2'O-MOE moiety is constrained back to the 4' position of the furanose ring. As part of the SAR series, we also prepared nucleoside analogs 7 (S-constrained ethyl, S-cEt) and 8 (R-constrained Ethyl, R-cEt) where the methoxymethyl group in the cMOE nucleosides was replaced with a methyl substituent. A highly efficient synthesis of the nucleoside phosphoramidites with minimal chromatography purifications was developed starting from cheap commercially available starting materials. Biophysical evaluation revealed that the cMOE and cEt modifications hybridize complementary nucleic acids with the same affinity as LNA while greatly increasing nuclease stability. Biological evaluation of oligonucleotides containing the cMOE and cEt modification in animals indicated that all of them possessed superior potency as compared to second generation MOE ASOs and a greatly improved toxicity profile as compared to LNA.
Seth
Punit P
PP
Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1891 Rutherford Road, Carlsbad, CA 92008, USA. pseth@isisph.com
Siwkowski
Andrew
A
Allerson
Charles R
CR
Vasquez
Guillermo
G
Lee
Sam
S
Prakash
Thazha P
TP
Kinberger
Garth
G
Migawa
Michael T
MT
Gaus
Hans
H
Bhat
Balkrishen
B
Swayze
Eric E
EE
D015195:Drug Design; D009705:Nucleosides / Q000138:chemical synthesis* / Q000737:chemistry; D016376:Oligonucleotides, Antisense / Q000138:chemical synthesis* / Q000737:chemistry; D009943:Organophosphorus Compounds / Q000138:chemical synthesis
D009705:Nucleosides; D016376:Oligonucleotides, Antisense; D009943:Organophosphorus Compounds; C434331:phosphoramidite