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CN-122029279-A - Oligonucleotides for modulating KCNT expression

CN122029279ACN 122029279 ACN122029279 ACN 122029279ACN-122029279-A

Abstract

The present disclosure provides antisense oligonucleotides for modulating the expression of potassium-sodium activated channel T subfamily member 1 (KCNT) encoded by KCNT gene and their use for treating Developmental Epileptic Encephalopathy (DEE).

Inventors

  • H. TRAN
  • G. Das Dores
  • B. Shangliweng

Assignees

  • 法国施维雅药厂

Dates

Publication Date
20260512
Application Date
20240814
Priority Date
20230816

Claims (20)

  1. 1. An antisense oligonucleotide for reducing KCNT1 expression, wherein the antisense oligonucleotide has a nucleobase sequence comprising at least 12 consecutive nucleobases of the nucleobase sequence of any one of SEQ ID NOs 4-12.
  2. 2. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide has a nucleobase sequence comprising at least 15 consecutive nucleobases of the nucleobase sequence of any one of SEQ ID NOs 4-12.
  3. 3. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide has a nucleobase sequence of any one of SEQ ID NOs 4-12.
  4. 4. The antisense oligonucleotide of claim 3, wherein the antisense oligonucleotide has a nucleobase sequence of any one of SEQ ID NOs 7, 8 and 9.
  5. 5. The antisense oligonucleotide of any one of claims 1-4, wherein the antisense oligonucleotide has 18 to 20 linked nucleosides.
  6. 6. The antisense oligonucleotide of any one of claims 1-5, wherein at least one internucleoside linkage is a modified internucleoside linkage.
  7. 7. The antisense oligonucleotide of claim 6, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.
  8. 8. The antisense oligonucleotide of claim 7, wherein the phosphorothioate internucleoside linkages are preferably located at positions 1-2, 5-16 and 19-20.
  9. 9. The antisense oligonucleotide of any one of claims 1-8, wherein at least one nucleoside of the antisense oligonucleotide comprises a modified sugar moiety.
  10. 10. The antisense oligonucleotide of claim 9, wherein the modified sugar moiety comprises a 2' -O-methoxyethyl group.
  11. 11. An oligonucleotide comprising the structure: i) Aes Teo mCeo mCeo mCes Ads Gds Gds Tds Tds Tds Ads mCds mCds mCds Geo Aeo Teo Tes mCe (SEQ ID NO： 7); ii) Tes mCeo mCeo mCeo Aes Gds Gds Tds Tds Tds Ads mCds mCds mCds Gds Aeo Teo Teo mCes Ae (SEQ ID NO： 8); iii) Tes Aeo Teo mCeo mCes mCds Ads Gds Gds Tds Tds Tds Ads mCds mCds mCeo Geo Aeo Tes Te (SEQ ID NO： 9); iv) Aes Teo mCeo mCeo mCes Ads Gds Gds Tds Tds Tds Ads Cds Cds Cds Geo Aeo Teo Tes mCe (SEQ ID NO： 10); v) Tes mCeo mCeo mCeo Aes Gds Gds Tds Tds Tds Ads Cds Cds Cds Gds Aeo Teo Teo mCes Ae (SEQ ID NO： 11); vi) Tes Aeo Teo mCeo mCes Cds Ads Gds Gds Tds Tds Tds Ads Cds Cds mCeo Geo Aeo Tes Te (SEQ ID NO： 12) Wherein: A = adenine C=cytosine Mc=5-methylcytosine G=guanine T=thymine E=2' -O-methoxyethyl ribose D=2' -deoxyribose S=phosphorothioate internucleoside linkage O = phosphodiester internucleoside linkage.
  12. 12. An oligonucleotide comprising the structural formula: 。
  13. 13. An oligonucleotide comprising the structural formula: 。
  14. 14. An oligonucleotide comprising the structural formula: 。
  15. 15. a conjugate comprising an antisense oligonucleotide according to any one of claims 1-14 and at least one conjugate moiety covalently linked to said oligonucleotide.
  16. 16. A pharmaceutical composition comprising the oligonucleotide of any one of claims 1-14 or the conjugate of claim 15 and a pharmaceutically acceptable excipient.
  17. 17. A method of reducing KCNT1 expression in a mammalian cell, comprising contacting the cell with an antisense oligonucleotide of any one of claims 1-14, a conjugate of claim 15, or a pharmaceutical composition of claim 16, thereby reducing KCNT1 expression in the cell.
  18. 18. The method of claim 17, wherein the cell is a cell in the central nervous system, optionally a cell in the human brain.
  19. 19. A method of treating developmental epileptic brain Disease (DEE) in a subject in need thereof (optionally, a human subject), the method comprising administering to the subject a therapeutically effective amount of an antisense oligonucleotide of any one of claims 1-14, a conjugate of claim 15, or a pharmaceutical composition of claim 16.
  20. 20. The method of claim 19, wherein the oligonucleotide is injected intrathecally or intracranially into the subject.

Description

Oligonucleotides for modulating KCNT expression Background The KCNT gene encodes an intracellular sodium-activated potassium channel (Potassium sodium activated channel T subfamily member 1-UNIPOTID Q5JUK 3-3) that is expressed in the central nervous system. KCNT 1A1, also known as Slack, is a member of the Slo-type potassium channel gene family, and may be co-assembled with other Slo channel subunits. These channels can mediate a sodium-sensitive potassium current that is triggered by the influx of sodium channels or neurotransmitter receptors. Delayed outward currents may be involved in regulating neuronal excitability. Pathogenic variations in the KCNT gene encoding potassium sodium activated channel T subfamily member 1 are associated with a range of epilepsy and neurodevelopmental disorders (Barcia et al., neurol genet. (2019) 5 (6): e 363). They cause Developmental Epileptic Encephalopathy (DEEs), including infant epileptic with wandering focal seizures (EIMFS) and early epileptic encephalopathy (EOEE). DEEs associated with KCNT pathogenic variations is characterized by normal prenatal development and birth. EIMFS is the most common and severe DEE phenotype, usually seen in early infancy, characterized by an extremely high seizure burden. Similarly to EIMFS, EOEE patients often develop symptoms before one year of age and have a high seizure burden, almost daily onset, and these patients also have severe developmental delays and early deaths (Bonardi et al., brain (2021) 144 (12): 3635-3650). A recent review of the literature reports 189 individuals affected by KCNT related DEEs (Bonardi, supra), but the actual patient population may be higher, with the KCNT foundation reporting 3,000 cases worldwide. This incidence makes DEE a class of very rare diseases. Typically, the progression of DEE disease is divided into three phases, sporadic onset, storm and chronic. During the storm phase, patients may experience hundreds of seizures per day, typically occurring between three and six months after birth. This stage is characterized by frequent and/or prolonged seizures or status epilepticus, leading to severe developmental delays and increased risk of mortality. The chronic phase usually occurs around the age of 1-2 years, with fewer seizures in the patient. However, higher clinical heterogeneity was observed, some patients entered storm phase without sporadic seizure phase, and the time course of the different phases may vary greatly among affected children (Kuchenbuch et al., brain (2019) 142 (10): 2996-3008). Death may occur at any stage of the disease process. Death may have different causes, including heart failure and other co-diseases, but sudden epileptic death, which is not expected, has been reported as the most prominent cause of death in EIMFS. Epileptic seizures are predominantly focal motor seizures with varying degrees of secondary generalization including tonic, clonic, tonic-clonic, myoclonus, and epileptic spasticity. In the chronic phase, seizures are predominantly tonic seizures, with manifestations of autonomic dysfunction. For example, perioral cyanosis and apneas are common. A characteristic manifestation of electroencephalogram (EEG) is focal episodic discharges, which can migrate across adjacent cortical areas, and can occur independently at multiple sites. Other neurological characteristics of these patients include hypotonia, microcephaly, and severe developmental disorders. Different degrees of myelination delay, hippocampal volume reduction, and cerebellar atrophy have been observed on brain Magnetic Resonance Imaging (MRI). Attempts have been made to control seizures using a variety of interventions, including benzodiazepine (benzodiazepines), vigabatrin (vigabatrin), settop alcohol (stiripentol), phenobarbital (phenobarbital), topiramate (topiramate), quinidine (quinidine) and ketogenic diet (ketogenic diet). However, it has been widely reported to lack efficacy (LANDMARK ET al., epilepia (2021) 62 (4): 857-873). Seizures may rapidly develop resistance to drugs. Quinidine is an antiarrhythmic drug that has been explored as an antiepileptic treatment for DEE, but in some patients it exacerbates the disease or even leads to serious side effects (e.g., prolongation of QT interval) (Liu et al, neurol sci. (2023) 44 (4): 1201-1206). VALERIASEN is an antisense oligonucleotide intended to degrade KCNT1 mRNA, which has been administered in children with two KCNT mutations carried by them, the number of seizures in these children being reduced. However, treatment has to be suspended due to serious adverse events including hydrocephalus. DEE associated with KCNT pathogenic variations is a devastating childhood neurological disorder with prognosis ranging from severe encephalopathy to early death. This dull prognosis and lack of effective therapies highlight the urgent medical need for the disease. Summary of The Invention The present disclosure provides antisense oligonucleotides (ASOs)