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EP-3587432-B1 - NUCLEIC ACID COMPOUND AND OLIGONUCLEOTIDE

EP3587432B1EP 3587432 B1EP3587432 B1EP 3587432B1EP-3587432-B1

Inventors

  • OBIKA, SATOSHI
  • ITO, KOSUKE
  • HABUCHI, Takaaki
  • HORIBA, Masahiko

Dates

Publication Date
20260506
Application Date
20180220

Claims (10)

  1. A compound represented by the following formula (I) or the following formula (II), or a salt thereof: wherein X 1 and X 2 are each independently S or Se, Y is O, S, an -N(R 19 )- group, a -C(=O)-O- group, a-C(=O)-N(R 20 )-group (R 19 and R 20 are each independently H or a C 1-6 alkyl group), and Z is a cyclopropyl group represented by the following formula (VII): wherein R 21 and R 22 are each independently H, a C 1-6 alkyl group, or R 21 and R 22 are optionally joined to form a C 1-4 alkylene group, R 1 is H or a C 1-6 alkyl group, R 2 and R 3 are each independently H, a hydroxyl-protecting group, or a phosphate group represented by the following formula (VIII): wherein Q is O or S, R 23 is H, a hydroxyl group, or a C 1-6 alkoxy group optionally substituted by a cyano group; R 24 is a hydroxyl group, a C 1-6 alkoxy group optionally substituted by a cyano group or an NR 25 R 26 group wherein R 25 and R 26 are each independently H, a C 1-6 alkyl group or a 2-cyanoethyl group; and n is 0 or 1, and R 4 is H, a C 1-6 alkyl group or a 2-cyanoethyl group.
  2. The compound according to claim 1 wherein Y is O, or a salt thereof.
  3. The compound according to claim 1 or 2 wherein R 1 is a methyl group, or a salt thereof.
  4. An oligonucleotide having one or more residues with a structure represented by the following formula (IX), or a pharmacologically acceptable salt thereof: wherein X 1 is S or Se, Y is O, S, an -N(R 19 )- group, a -C(=O)-O- group, a-C(=O)-N(R 20 )-group (R 19 and R 20 are each independently H or a C 1-6 alkyl group), and Z is a cyclopropyl group represented by the following formula (VII): wherein R 21 and R 22 are each independently H, a C 1-6 alkyl group, or R 21 and R 22 are optionally joined to form a C 1-4 alkylene group, and R 1 is H or a C 1-6 alkyl group.
  5. The oligonucleotide according to claim 4 wherein Y is O, or a pharmacologically acceptable salt thereof.
  6. The oligonucleotide according to claim 4 or 5 wherein R 1 is a methyl group, or a pharmacologically acceptable salt thereof.
  7. process for reducing side effects of an oligonucleotide due to an off-target effect characterized by bridging the 2'-position and 4'-position of the residue(s) thereof with a -Y-Z- group to form an oligonucleotide according to claim 4, wherein said process is not performed on the human or animal body.
  8. The method according to claim 7 wherein Y is O.
  9. A method of manufacturing an oligonucleotide according to claim 4, wherein one or more compounds according to any one of claims 1 to 3 are selected, and the oligonucleotide is prepared using said compounds as a monomer.
  10. The method according to claim 9 wherein Y is O.

Description

[Technical Field] The present invention relates to a nucleic acid compound that hardly forms non-Watson-Crick base pairs and an oligonucleotide containing the nucleic acid compound and showing reduced non-specific binding with nucleic acids other than the target nucleic acid. [Background Art] It has been clarified by Watson and Crick that the chromosome is composed of DNA double strands. In addition, a double strand is partially formed in the mRNA molecule. Furthermore, various therapeutic methods utilizing interaction between nucleic acids have been developed in recent years. For example, an antisense oligonucleotide binds to a single-stranded portion of RNA related to a disease to form a double strand and inhibits its action. Typically, a method is known in which complementary DNA is bound to a single-stranded portion of mRNA to form a double strand, and this part is hydrolyzed and cleaved with RNaseH. In addition, a method is also known in which a triplex strand is formed by an antigene complementary to a gene related to a disease and a DNA double strand of the gene, and transcription from DNA to mRNA is inhibited. siRNA specifically cleaves target mRNA by RNA interference. The above-mentioned interaction between nucleic acid strands is based on hydrogen bonds between nucleic acid bases. For example, the interaction between adenosine adenine and thymidine thymine is shown below. However, since the interaction between thymine and guanine described below is also relatively stable thermodynamically, a non-Watson-Crick base pair called a wobble base pair is sometimes formed. Such wobble base pair may cause binding of the above-mentioned antisense oligonucleotide or the like to a nucleic acid other than the original target nucleic acid, and may lead to unexpected expression of gene or suppression of expression of important gene. Such phenomenon is called an off-target effect and may cause serious side effects (non-patent document 1). Thus, it has been clarified that the hydrogen binding strength with guanine can be reduced by converting the 2-position carbonyl group of thymine to a thiocarbonyl group, whereby formation of G-T non-Watson-Crick base pair can be suppressed (non-patent document 2). While nucleic acid drugs such as the above-mentioned antisense oligonucleotide and the like have an advantage of high specificity, they have a problem of insufficient stability in vivo since they serve as nuclease substrates. In addition, the nucleoside moiety in the nucleic acid has an N-type or S-type structure, and this structure also affects the interaction between nucleic acid bases. Therefore, the present inventors' research group has developed a technique for bridging the 2' - position and the 4' -position of the nucleic acid, stabilizing the nucleic acid conformation, increasing the nuclease resistance, and increasing the affinity for the target nucleic acid (patent documents 1 - 5). Masahiko Horiba et al., J. Org. Chem. 2016, 81, 11000-11008 describes the synthesis of scpBNA-mC, -A, and -G monomers and evaluation of the binding Affinities of scpBNA-modified oligonucleotides toward complementary ssRNA and ssDNA. Aiko Yahara et al., ChemBioChem 2012, 13, 2513-2516 describes the synthesis, duplex stability, nuclease resistance, and in vitro antisense potency of amido-bridged nucleic acids. WO 2017/018360 describes an artificial nucleoside or artificial nucleotide. WO 2004/044245 describes oligomeric compounds having modified bases for binding to adenine and guanine and their use in gene modulation. WO 2004/035819 describes oligonucleotides said to be useful for detecting and analyzing nucleic acids of interest. Curtis B. Hughesman et al., Biochemistry 2011, 50, 5354-5368 describes the role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified locked nucleic acid. US 2004/033973 describes nucleoside compositions comprising nucleobases that are said to be novel and oligomeric compounds comprising at least one such nucleoside. These oligomeric compounds are said typically to have enhanced binding affinity properties compared to oligomeric compounds without the modification. The oligomeric compounds are said to be useful for investigative and therapeutic purposes. [Document List] [Patent documents] patent document 1: WO 2011/052436patent document 2: WO 2014/046212patent document 3: WO 2014/112463patent document 4: WO 2015/125783patent document 5: WO 2016/017422 [non-patent document] non-patent document 1: Obika, S et al., Nucleic Acids Res., 37, pp.1225-1238 (2009)non-patent document 2: Herman O. Sintim et al., J. Am. Chem. Soc., 128, pp.396-397 (2006) [SUMMARY OF THE INVENTION] [Problems to be Solved by the Invention] As described above, it was known that formation of G-T non-Watson-Crick base pair can be suppressed by functionally converting the 2-position carbonyl group of thymine to a thiocarbonyl group. However, non-