Superior Silencing by 2',4'-BNA(NC)-Based Short Antisense Oligonucleotides Compared to 2',4'-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors

Overview

Journal J Nucleic Acids

Publisher Wiley

Date 2012 Oct 12

PMID 23056920

Citations 8

Authors

Tsuyoshi Yamamoto

Hidenori Yasuhara

Fumito Wada

Mariko Harada-Shiba

Takeshi Imanishi

Satoshi Obika

Affiliations

Soon will be listed here.

Abstract

The duplex stability with target mRNA and the gene silencing potential of a novel bridged nucleic acid analogue are described. The analogue, 2',4'-BNA(NC) antisense oligonucleotides (AONs) ranging from 10- to 20-nt-long, targeted apolipoprotein B. 2',4'-BNA(NC) was directly compared to its conventional bridged (or locked) nucleic acid (2',4'-BNA/LNA)-based counterparts. Melting temperatures of duplexes formed between 2',4'-BNA(NC)-based antisense oligonucleotides and the target mRNA surpassed those of 2',4'-BNA/LNA-based counterparts at all lengths. An in vitro transfection study revealed that when compared to the identical length 2',4'-BNA/LNA-based counterpart, the corresponding 2',4'-BNA(NC)-based antisense oligonucleotide showed significantly stronger inhibitory activity. This inhibitory activity was more pronounced in shorter (13-, 14-, and 16-mer) oligonucleotides. On the other hand, the 2',4'-BNA(NC)-based 20-mer AON exhibited the highest affinity but the worst IC(50) value, indicating that very high affinity may undermine antisense potency. These results suggest that the potency of AONs requires a balance between reward term and penalty term. Balance of these two parameters would depend on affinity, length, and the specific chemistry of the AON, and fine-tuning of this balance could lead to improved potency. We demonstrate that 2',4'-BNA(NC) may be a better alternative to conventional 2',4'-BNA/LNA, even for "short" antisense oligonucleotides, which are attractive in terms of drug-likeness and cost-effective bulk production.

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References

Honcharenko D, Varghese O, Plashkevych O, Barman J, Chattopadhyaya J . Synthesis and structure of novel conformationally constrained 1',2'-azetidine-fused bicyclic pyrimidine nucleosides: their incorporation into oligo-DNAs and thermal stability of the heteroduplexes. J Org Chem. 2006; 71(1):299-314. DOI: 10.1021/jo052115x. View

Watanabe T, Geary R, Levin A . Plasma protein binding of an antisense oligonucleotide targeting human ICAM-1 (ISIS 2302). Oligonucleotides. 2006; 16(2):169-80. DOI: 10.1089/oli.2006.16.169. View

Miyashita K, Rahman S, Seki S, Obika S, Imanishi T . N-Methyl substituted 2',4'- BNANC: a highly nuclease-resistant nucleic acid analogue with high-affinity RNA selective hybridization. Chem Commun (Camb). 2007; (36):3765-7. DOI: 10.1039/b707352f. View

Swayze E, Siwkowski A, Wancewicz E, Migawa M, Wyrzykiewicz T, Hung G . Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals. Nucleic Acids Res. 2006; 35(2):687-700. PMC: 1802611. DOI: 10.1093/nar/gkl1071. View

Yamamoto T, Harada-Shiba M, Nakatani M, Wada S, Yasuhara H, Narukawa K . Cholesterol-lowering Action of BNA-based Antisense Oligonucleotides Targeting PCSK9 in Atherogenic Diet-induced Hypercholesterolemic Mice. Mol Ther Nucleic Acids. 2013; 1:e22. PMC: 3393380. DOI: 10.1038/mtna.2012.16. View

Mitsuoka Y, Kodama T, Ohnishi R, Hari Y, Imanishi T, Obika S . A bridged nucleic acid, 2',4'-BNA COC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNA COC monomers and RNA-selective nucleic-acid recognition. Nucleic Acids Res. 2009; 37(4):1225-38. PMC: 2651773. DOI: 10.1093/nar/gkn1062. View

Brown D, Kang S, Gryaznov S, DeDionisio L, Heidenreich O, Sullivan S . Effect of phosphorothioate modification of oligodeoxynucleotides on specific protein binding. J Biol Chem. 1994; 269(43):26801-5. View

Seth P, Allerson C, Berdeja A, Siwkowski A, Pallan P, Gaus H . An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. J Am Chem Soc. 2010; 132(42):14942-50. PMC: 2993159. DOI: 10.1021/ja105875e. View

Prakash T, Siwkowski A, Allerson C, Migawa M, Lee S, Gaus H . Antisense oligonucleotides containing conformationally constrained 2',4'-(N-methoxy)aminomethylene and 2',4'-aminooxymethylene and 2'-O,4'-C-aminomethylene bridged nucleoside analogues show improved potency in animal models. J Med Chem. 2010; 53(4):1636-50. DOI: 10.1021/jm9013295. View

10.

Akdim F, Visser M, Tribble D, Baker B, Stroes E, Yu R . Effect of mipomersen, an apolipoprotein B synthesis inhibitor, on low-density lipoprotein cholesterol in patients with familial hypercholesterolemia. Am J Cardiol. 2010; 105(10):1413-9. DOI: 10.1016/j.amjcard.2010.01.003. View

11.

Straarup E, Fisker N, Hedtjarn M, Lindholm M, Rosenbohm C, Aarup V . Short locked nucleic acid antisense oligonucleotides potently reduce apolipoprotein B mRNA and serum cholesterol in mice and non-human primates. Nucleic Acids Res. 2010; 38(20):7100-11. PMC: 2978335. DOI: 10.1093/nar/gkq457. View

12.

Guvakova M, Yakubov L, Vlodavsky I, Tonkinson J, Stein C . Phosphorothioate oligodeoxynucleotides bind to basic fibroblast growth factor, inhibit its binding to cell surface receptors, and remove it from low affinity binding sites on extracellular matrix. J Biol Chem. 1995; 270(6):2620-7. DOI: 10.1074/jbc.270.6.2620. View

13.

Yamamoto T, Nakatani M, Narukawa K, Obika S . Antisense drug discovery and development. Future Med Chem. 2011; 3(3):339-65. DOI: 10.4155/fmc.11.2. View

14.

White P, Anastasopoulos F, Pouton C, Boyd B . Overcoming biological barriers to in vivo efficacy of antisense oligonucleotides. Expert Rev Mol Med. 2009; 11:e10. DOI: 10.1017/S1462399409001021. View

15.

Levin A . A review of the issues in the pharmacokinetics and toxicology of phosphorothioate antisense oligonucleotides. Biochim Biophys Acta. 2000; 1489(1):69-84. DOI: 10.1016/s0167-4781(99)00140-2. View

16.

Rahman S, Seki S, Obika S, Yoshikawa H, Miyashita K, Imanishi T . Design, synthesis, and properties of 2',4'-BNA(NC): a bridged nucleic acid analogue. J Am Chem Soc. 2008; 130(14):4886-96. DOI: 10.1021/ja710342q. View

17.

Seth P, Siwkowski A, Allerson C, Vasquez G, Lee S, Prakash T . Short antisense oligonucleotides with novel 2'-4' conformationaly restricted nucleoside analogues show improved potency without increased toxicity in animals. J Med Chem. 2008; 52(1):10-3. DOI: 10.1021/jm801294h. View

18.

Imanishi T, Obika S . BNAs: novel nucleic acid analogs with a bridged sugar moiety. Chem Commun (Camb). 2002; (16):1653-9. DOI: 10.1039/b201557a. View

19.

Visser M, Kastelein J, Stroes E . Apolipoprotein B synthesis inhibition: results from clinical trials. Curr Opin Lipidol. 2010; 21(4):319-23. DOI: 10.1097/MOL.0b013e32833af4c1. View

20.

Benimetskaya L, Tonkinson J, Koziolkiewicz M, Karwowski B, Guga P, Zeltser R . Binding of phosphorothioate oligodeoxynucleotides to basic fibroblast growth factor, recombinant soluble CD4, laminin and fibronectin is P-chirality independent. Nucleic Acids Res. 1995; 23(21):4239-45. PMC: 307375. DOI: 10.1093/nar/23.21.4239. View