Synthesis and biophysical evaluation of 2',4'-constrained 2'O-methoxyethyl and 2',4'-constrained 2'O-ethyl nucleic acid analogues.
We have recently shown that combining the structural elements of 2'O-methoxyethyl (MOE) and locked nucleic acid (LNA) nucleosides yielded a series of nucleoside modifications (cMOE, 2',4'-constrained MOE; cEt, 2',4'-constrained ethyl) that display improved potency over MOE and an improved therapeutic index relative to that of LNA antisense oligonucleotides. In this report we present details regarding the synthesis of the cMOE and cEt nucleoside phosphoramidites and the biophysical evaluation of oligonucleotides containing these nucleoside modifications. The synthesis of the cMOE and cEt nucleoside phosphoramidites was efficiently accomplished starting from inexpensive commercially available diacetone allofuranose. The synthesis features the use of a seldom used 2-naphthylmethyl protecting group that provides crystalline intermediates during the synthesis and can be cleanly deprotected under mild conditions. The synthesis was greatly facilitated by the crystallinity of a key mono-TBDPS-protected diol intermediate. In the case of the cEt nucleosides, the introduction of the methyl group in either configuration was accomplished in a stereoselective manner. Ring closure of the 2'-hydroxyl group onto a secondary mesylate leaving group with clean inversion of stereochemistry was achieved under surprisingly mild conditions. For the S-cEt modification, the synthesis of all four (thymine, 5-methylcytosine, adenine, and guanine) nucleobase-modified phosphoramidites was accomplished on a multigram scale. Biophysical evaluation of the cMOE- and cEt-containing oligonucleotides revealed that they possess hybridization and mismatch discrimination attributes similar to those of LNA but greatly improved resistance to exonuclease digestion.
Seth
Punit P
PP
Department of Medicinal Chemistry, Isis Pharmaceuticals, 1896 Rutherford Road, Carlsbad, California 92008, USA. pseth@isisph.com
Vasquez
Guillermo
G
Allerson
Charles A
CA
Berdeja
Andres
A
Gaus
Hans
H
Kinberger
Garth A
GA
Prakash
Thazha P
TP
Migawa
Michael T
MT
Bhat
Balkrishen
B
Swayze
Eric E
EE
D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D055592:Biophysical Phenomena; D002384:Catalysis; D003459:Crystallins / Q000138:chemical synthesis* / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009696:Nucleic Acids / Q000138:chemical synthesis* / Q000737:chemistry; D009705:Nucleosides / Q000138:chemical synthesis* / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry*; D013237:Stereoisomerism
D003459:Crystallins; D009696:Nucleic Acids; D009705:Nucleosides; D009841:Oligonucleotides