Configuration of the 5′-Methyl Group Modulates the Biophysical and Biological Properties of Locked Nucleic Acid (LNA) Oligonucleotides

• Published in: Journal of medicinal chemistry 2010-12, Vol.53 (23), p.8309-8318
• Main Authors: Seth, Punit P, Allerson, Charles R, Siwkowski, Andrew, Vasquez, Guillermo, Berdeja, Andres, Migawa, Michael T, Gaus, Hans, Prakash, Thazha P, Bhat, Balkrishen, Swayze, Eric E
• Format: Article
• Language: English
• Subjects: Biophysics; Nuclear Magnetic Resonance, Biomolecular; Oligonucleotides - chemistry; Oligonucleotides - pharmacology; Structure-Activity Relationship
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm101207e

As part of a program aimed at exploring the structure− activity relationships of 2′,4′-bridged nucleic acid (BNA) containing antisense oligonucleotides (ASOs), we report the synthesis and biophysical and biological properties of R- and S-5′-Me LNA modified oligonucleotides. We show that introduction of a methyl group in the (S) configuration at the 5′-position is compatible with the high affinity recognition of complementary nucleic acids observed with LNA. In contrast, introduction of a methyl group in the (R) configuration reversed the stabilization effect of LNA. NMR studies indicated that the R-5′-Me group changes the orientation around torsion angle γ from the +sc to the ap range at the nucleoside level, and this may in part be responsible for the poor hybridization behavior exhibited by this modification. In animal experiments, S-5′-Me-LNA modified gapmer antisense olignucleotides showed slightly reduced potency relative to the sequence matched LNA ASOs while improving the therapeutic profile.