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US-12616714-B2 - Enhanced oligonucleotides for modulating FUBP1 expression

US12616714B2US 12616714 B2US12616714 B2US 12616714B2US-12616714-B2

Abstract

The present invention relates to enhanced antisense oligonucleotides that are complementary to the Far Upstream Element-Binding Protein 1 (FUBP1) and are capable of reducing a FUBP1 target nucleic acid, such as FUBP1 mRNA. The invention relates to enhanced antisense oligonucleotides targeting FUBP1 or conjugates thereof for use in treating and/or preventing a hepatitis B virus (HBV) infection, in particular a chronic HBV infection. The invention in particular relates to the use of the enhanced antisense oligonucleotides targeting FUBP1 or conjugates thereof for destabilizing cccDNA, such as HBV cccDNA. The invention further relates to enhanced antisense oligonucleotides targeting FUBP1 or conjugates thereof for use in treating cancer. A pharmaceutical composition and its use in the treatment and/or prevention of an HBV infection, or its use in the treatment of cancer is also disclosed.

Inventors

  • Sabine Sewing
  • Susanne MOHR
  • Valentina D'ARIENZO
  • Søren OTTOSEN
  • Jacob Ravn
  • Lykke Pedersen
  • Souphalone Luangsay
  • Erich Koller
  • Johanna Marie WALTHER
  • Helene Maria GYLLING
  • Natascha HRUSCHKA

Assignees

  • HOFFMANN-LA ROCHE INC.

Dates

Publication Date
20260505
Application Date
20210625
Priority Date
20200626

Claims (19)

  1. 1 . An antisense oligonucleotide selected from the group of antisense oligonucleotides consisting of (SEQ ID NO: 7) CTtAtgctttttatGgTT, and (SEQ ID NO: 18) AcCAAttttcatttCtAC, wherein capital letters are beta-D-oxy LNA nucleosides, lowercase letters are DNA nucleosides, all LNA C are 5-methyl cytosine, and all internucleoside linkages are phosphorothioate internucleoside linkages.
  2. 2 . A conjugate comprising the antisense oligonucleotide of claim 1 , and at least one conjugate moiety covalently attached to said antisense oligonucleotide.
  3. 3 . The conjugate of claim 2 , wherein the at least one conjugate moiety is capable of binding to an asialoglycoprotein receptor.
  4. 4 . The conjugate of claim 2 , wherein the conjugate moiety is selected from one of the-trivalent GalNAc moieties in FIG. 9 as follows:
  5. 5 . The conjugate of claim 4 , wherein the conjugate moiety is the trivalent GalNAc moiety in FIG. 9 D 1 , or 9 D 2 or a mixture thereof as follows:
  6. 6 . A conjugate of claim 2 , comprising a linker positioned between the antisense oligonucleotide and the conjugate moiety.
  7. 7 . The conjugate of claim 6 , wherein the linker comprises 2 to 5 consecutive phosphodiester linked nucleosides.
  8. 8 . A conjugate as shown in FIG. 8 or FIG. 8 . 1 as follows:
  9. 9 . A pharmaceutically acceptable salt of the oligonucleotide of claim 1 .
  10. 10 . A pharmaceutical composition comprising the antisense oligonucleotide of claim 1 , and a pharmaceutically acceptable diluent, solvent, carrier, salt and/or adjuvant.
  11. 11 . A method for modulating FUBP1 expression in a target cell which is expressing FUBP1, the method comprising administering the antisense oligonucleotide of claim 1 in an effective amount to the cell.
  12. 12 . A method for treating a disease comprising administering a therapeutically or prophylactically effective amount of the antisense oligonucleotide of claim 1 to a subject suffering from or susceptible to the disease, wherein the disease is hepatitis B virus (HBV) infection and/hepatocellular cancer.
  13. 13 . An antiviral or antitumor medicine comprising the antisense oligonucleotide of claim 1 .
  14. 14 . A method of treating hepatitis B virus (HBV) infection and/or hepatocellular cancer, comprising the antisense oligonucleotide of claim 1 .
  15. 15 . A medicament, comprising the antisense oligonucleotide of claim 1 , for the treatment of a hepatitis B virus (HBV) infection and/or hepatocellular cancer.
  16. 16 . The method of claim 12 , wherein the disease is a hepatitis B virus (HBV) infection.
  17. 17 . The method of claim 12 , wherein the disease is hepatocellular cancer.
  18. 18 . A method for treating a disease comprising administering a therapeutically or prophylactically effective amount of the antisense oligonucleotide of claim 1 to a subject suffering from or susceptible to the disease, wherein the disease is a chronic HBV infection.
  19. 19 . A method for treating a disease comprising administering a therapeutically or prophylactically effective amount of the antisense oligonucleotide of claim 1 to a subject suffering from or susceptible to the disease, wherein the disease is a hepatocellular carcinoma.

Description

CROSS-REFERENCE TO RELATED APPLICATION This application is a continuation of and claims the benefit of European Patent Application No. 20182437.2, filed 26 Jun. 2020, the disclosure of which is incorporated, in its entirety, by this reference. FIELD OF INVENTION The present invention relates to enhanced antisense oligonucleotides that are complementary to the Far Upstream Element-Binding Protein 1 (FUBP1) and are capable of reducing a FUBP1 target nucleic acid, such as FUBP1 mRNA. The invention relates to enhanced antisense oligonucleotides targeting FUBP1 or conjugates thereof for use in treating and/or preventing a hepatitis B virus (HBV) infection, in particular a chronic HBV infection. The invention in particular relates to the use of the enhanced antisense oligonucleotides targeting FUBP1 or conjugates thereof for destabilizing cccDNA, such as HBV cccDNA. The invention further relates to enhanced antisense oligonucleotides targeting FUBP1 or conjugates thereof for use in treating cancer. Also comprised in the present invention is a pharmaceutical composition and its use in the treatment and/or prevention of a HBV infection, or its use in the treatment of cancer. BACKGROUND Far Upstream Element-Binding Protein 1 (FUBP1 or FBP1) is a single stranded DNA-binding protein that binds to multiple DNA elements. This protein is also thought to bind RNA and contains 3′-5′ helicase activity with in vitro activity on both DNA-DNA and RNA-RNA duplexes. FUBP1 is known to activate the transcription of the proto-oncogene c-myc by binding to far upstream element (FUSE) located upstream of c-myc in undifferentiated cells. The protein is primarily present in the nucleus of the cell. Upregulation of FUBP1 has been observed in many types of cancers. Furthermore, FUBP1 can bind to and mediate replication of RNA from Hepatitis C virus and Enterovirus (Zhang and Chen 2013 Oncogene vol 32 p. 2907-2916). FUBP1 has also been identified in Hepatocellular carcinoma (HCC) where it has been suggested to be involved in HCC tumorigenesis (Ramdzan et al 2008 Proteomics Vol 8 p. 5086-5096) and that FUBP1 is required for HCC tumour growth as illustrated using lentivirus-expressed shRNA targeting FUBP1 (Rabenhorst et al 2009 Hepatology vol 50 p 1121-1129). It has been demonstrated that knock-down of FUBP1 with lentivirus-expressed shRNA's enhances treatment response in ovarian cancer (Zhang et al 2017 Oncology Letters Vol 14 p. 5819-5824). WO 2004/027061 disclose a screening method, which involves the step of analyzing whether or not a test substance inhibits FBP (FBP is now referred to as FUBP) and a medicinal composition for treating a proliferative disease, which contains as the active ingredient(s) a substance inhibiting FBP. Poly(U) Binding Splicing Factor 60 (PUF60) is a potentially regulator of both transcriptional and post-transcriptional steps of HBV pregenome expression. PUF60 is known to form a complex with FUBP1 in relation to c-myc repression. However, FUBP1 does not participate in the PUF60 dependent regulation of HBV pregenome expression (Sun et al 2017 Scientific Reports 7:12874). HBV infection remains a major health problem worldwide affecting an estimated 350 million chronically infected carriers. Approximately 25% of carriers ultimately die from chronic hepatitis, cirrhosis, or liver cancer. Hepatitis B virus is the second most significant carcinogen behind tobacco, causing from 60% to 80% of all primary liver cancer. HBV is 100 times more contagious than HIV. The hepatitis B virus (HBV) is an enveloped, partially double-stranded DNA virus. The compact 3.2 kb HBV genome consists of four overlapping open reading frames (ORF), which encode for the core, polymerase (Pol), envelope and X-proteins respectively. The Pol ORF is the longest and the envelope ORF is located within it, while the X and core ORFs overlap with the Pol ORF. The replicative cycle of the HBV genome has two main events: 1) generation of closed circular DNA (cccDNA) from relaxed circular (RC DNA), and 2) reverse transcription of pregenomic RNA (pgRNA) to produce RC DNA. The RC DNA may stem from an infecting viral particle, or as an intracellular replication intermediate. HBsAg quantification is a significant biomarker for prognosis and treatment response in chronic hepatitis B with the loss of circulating HBsAg in the chronically infected patient seen as a key event in achieving cure. However, the achievement of HBsAg loss and seroconversion (functional cure) is rarely observed in chronically infected patients. Hepatitis B e-antigen (also called HBV envelope antigen or HBeAg) is a viral protein that is secreted by hepatitis B infected cells. HBeAg is associated with chronic hepatitis B infections and is used as a marker of active viral disease and a patient's degree of infectiousness. Accordingly, reducing secretion of HBeAg in addition to secretion of HBsAg would lead to an improved inhibition of development of a chronic HBV infection as compared to the