Compositions and methods for selective delivery of oligonucleotide molecules to cell types

• US 9,938,525 B2
• Filed: 10/25/2013
• Issued: 04/10/2018
• Est. Priority Date: 10/26/2012
• Status: Active Grant

• Current Assignee: Nlife Therapeutics, S.L.
• Original Assignee: Nlife Therapeutics, S.L.
• Inventors: Carmona Orozco, Maria del Carmen, Montefeltro, Andrs Pablo, Alvarado, Gabriel G., Bortolozzi, Analia, Revilla-Sanchez, Raquel
• Primary Examiner(s): VIVLEMORE, TRACY ANN
• Application Number:
  US14/438,869
• Publication Number:
  US 20150315575A1
• Time in Patent Office: 1,628 Days
• Field of Search: None
• CPC Class Codes: A61K 31/165 having aromatic rings, e.g. colchicine, atenolol, progabide
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61K 31/711 Natural deoxyribonucleic acids, i.e. containing only 2'-deoxyriboses attached to adenine, guanine, cytosine or thymine and having 3'-5' phosphodiester links
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61K 47/54 the modifying agent being an organic compound
• CPC Class Codes: A61K 47/55 the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug, i.e. a dimer, oligomer or polymer of pharmacologically or therapeutically active compounds
• CPC Class Codes: A61K 47/64 Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent peptidic linkers A61K47/65
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/06 Antimigraine agents
• CPC Class Codes: A61P 25/14 for treating abnormal movements, e.g. chorea, dyskinesia
• CPC Class Codes: A61P 25/16 Anti-Parkinson drugs
• CPC Class Codes: A61P 25/18 Antipsychotics, i.e. neuroleptics; Drugs for mania or schizophrenia
• CPC Class Codes: A61P 25/20 Hypnotics; Sedatives
• CPC Class Codes: A61P 25/22 Anxiolytics
• CPC Class Codes: A61P 25/24 Antidepressants
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• CPC Class Codes: A61P 3/04 Anorexiants; Antiobesity agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07K 5/06078 and aromatic or cycloaliphatic
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 15/1137 : against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 2310/11 : Antisense
• CPC Class Codes: C12N 2310/14 : interfering N.A.
• CPC Class Codes: C12N 2310/315 : Phosphorothioates
• CPC Class Codes: C12N 2310/321 : 2'-O-R Modification
• CPC Class Codes: C12N 2310/346 : having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3513 : Protein; Peptide

Abstract

The invention provides a conjugate comprising (i) a nucleic acid which is complementary to a target nucleic acid sequence and which expression prevents or reduces expression of the target nucleic acid and (ii) a selectivity agent which is capable of binding with high affinity to a receptor which can be internalized by the cell in response to the binding of said selectivity agent. The conjugates of the present invention are useful for the delivery of the nucleic acid to cell of interests and thus, for the treatment of diseases which require a down-regulation of the protein encoded by the target nucleic acid as well as for the delivery of contrast agents to the cells for diagnostic purposes.

Claims

1. A conjugate comprising:

(i) at least one selectivity agent which binds specifically to a receptor which is internalized by the cell upon binding of said selectivity agent, wherein the selectivity agent is a compound having the structure

2. The conjugate according to claim 1 wherein the target molecule is a polypeptide or a mRNA.

3. The conjugate according to claim 2 wherein the inhibition of the target molecule is an inhibition of the activity of the polypeptide if the target polypeptide is a polypeptide or is the silencing of the mRNA if the target polypeptide is a mRNA.

4. The conjugate according to claim 1 wherein the target molecule is a polypeptide selected from the group consisting of the polypeptides defined in the left-hand column of Table 3 or its corresponding mRNAs.

5. The conjugate according to claim 4 wherein the target molecule is the growth hormone secretagogue receptor.

6. A method of treating a disease selected from the group consisting of the diseases shown in the right-hand column of Table 3, wherein the disease is to be treated with the conjugate according to claim 4 directed to a target polypeptide shown in the left-hand column of the same row as the diseases in Table 3.

7. A conjugate according to claim 1 wherein the receptor which is expressed in the mesencephalon is selected from the group consisting of the growth hormone secretagogue receptor, the bombesin BB1 receptor, the bradykinin B2 receptor, the galanin GAL2 receptor, neuropeptide FF/B NPBW2 receptor, the neuropeptide FF/B NPFF2 receptor, the neuropeptide Y Y1 receptor, the neurotensin NTSR1 receptor, the neurotensin NTSR2 receptor, the neuropeptide S receptor, the orexin OX2 receptor, the 5-HT1D receptor, the angiotensin AT2a receptor, the angiotensin AT2b receptor, the calcitonin AM2 receptor, the calcitonin AMY3 receptor, the frizzled FZD6 receptor, the kisspeptin receptor, the melatonin MT1 receptor, the neuropeptide FF/B NPBW1 receptor and the opioid mu receptor.

8. The conjugate according to claim 7 wherein the target molecule is a polypeptide selected from the group consisting of the polypeptides defined in the left-hand column of Table 4 or its corresponding mRNAs.

9. A method of treating a disease selected from the group consisting of the diseases shown in the right-hand column of Table 4, wherein the disease is to be treated with the conjugate of claim 8 directed to a target polypeptide shown in the left-hand column of the same row as the diseases in Table 4.

10. The conjugate according to claim 1 wherein the receptor which is expressed in the brainstem is selected from the group consisting of the 5-HT₃ receptor, the galanin receptor 1, the melanocortin MC1 receptor, the melanocortin MC2 receptor, the melanocortin MC3 receptor, the melanocortin MC4 receptor, the calcitonin receptor-like, the CRF2 receptor, the neuropeptide FF/B NPBW2 receptor, the 5-HT1_A receptor, the neuropeptide Y Y2 receptor, the neurotensin NTSR1 receptor, the opioid mu receptor, the orexin OX1 receptor, the orexin OX2 receptor and the dopamine D2 receptor.

11. The conjugate according to claim 10 wherein the target molecule is a polypeptide selected from the group consisting of the polypeptides defined in the left-hand column of Table 5 or its corresponding mRNAs.

12. A method of treating a disease selected from the group consisting of the diseases shown in the right-hand column of Table 5, wherein the disease is to be treated with the conjugate of claim 11 directed to a target polypeptide shown in the left-hand column of the same row as the disease in Table 5.

13. The conjugate according to claim 1 wherein the receptor which is expressed in the cortex is selected from the group consisting of the 5-HT₃ receptor, the melanocortin MC1 receptor, the CRF1 receptor, the 5-HT2_A receptor, the alpha1 adrenergic receptor, the bombesin BB1 receptor, the frizzled FZD3 receptor, the bombesin BB3 receptor, the bradykinin B2 receptor, the calcitonin receptor-like receptor, the cholecystokinin CCK2 receptor, the CRF1 receptor, the CRF2 receptor, the galanin GAL2 receptor, the galanin GAL3 receptor, the neuropeptide FF/B NPBW2 receptor, the neuropeptide FF/B NPFF2 receptor, the neuropeptide Y Y1 receptor, the neuropeptide Y Y5 receptor, the neuropeptide Y Y2 receptor, the neurotensin NTSR2 receptor, the opioid kappa receptor, the opioid delta receptor, the somatostatin sst2 receptor, the somatostatin sst3 receptor, the somatostatin sst4 receptor, the 5-HT1A receptor, the endothelin ETa receptor, the endothelin ETb receptor, the melanocortin MC3 receptor, the neuropeptide S NPS receptor, the neurotensin NTSR1 receptor, the orexin OX1 receptor, the orexin OX2 receptor, the vasopressin V1B receptor, the kisspeptin receptor, the melatonin MT1 receptor, the tachykinin NK1 receptor, the tachykinin NK2 receptor and the tachykinin NK3 receptor.

14. The conjugate according to claim 13 wherein the target molecule is a polypeptide selected from the group consisting of the polypeptides defined in the left-hand column of Table 6 or its corresponding mRNAs.

15. A method of treating a disease selected from the group consisting of the diseases shown in the right-hand column of Table 6, wherein the disease is to be treated with the conjugate of claim 14 directed to a target polypeptide shown in the left-hand column of the same row as the disease in Table 6.

16. A conjugate according to claim 1 wherein the receptor which is expressed in the cerebellum is selected from the group consisting of the CRF1 receptor, the 5-HT_1B receptor, the frizzled FZD4 receptor, the frizzled FZD10 receptor, the frizzled FZD7 receptor, the bradikinin B2 receptor, the galanin GAL3 receptor, the neurotensin NTSR2 receptor, the endothelin ETb receptor, the formylpeptide FPR1 receptor, the formylpeptide FPR2 receptor, the melatonin MT2 receptor, the vasopressin V1A receptor, the angiotensin AT2a receptor, the angiotensin AT2b receptor, the kisspeptin receptor and the melatonin MT1 receptor.

17. The conjugate according to claim 16 wherein the target molecule is a polypeptide selected from the group consisting of the polypeptides defined in the left-hand column of Table 7 or its corresponding mRNAs.

18. A method of treating a disease selected from the group consisting of the diseases shown in the right-hand column of Table 7, wherein the disease is to be treated with the conjugate of claim 17 directed to a target polypeptide shown in the left-hand column of the same row as the diseases in Table 7.

19. A conjugate according to claim 1 wherein the receptor which is expressed in the striatum is selected from the group consisting of the 5-HT2A receptor, the cholecystokinin CCK2 receptor, the CRF1 receptor, the neuropeptide FF/B NPBW2 receptor, the neuropeptide FF/B NPFF2 receptor, the somatostatin sst5 receptor, the vasopressin V1B receptor, the 5-HT6 receptor, the adenosine A2 receptor, the adenosine A2A receptor, the dopamine D1 receptor, the dopamine D2 receptor, the peptide P518 receptor, the tachykinin NK1 receptor, the tachykinin NK2 receptor and the tachykinin NK3 receptor.

20. The conjugate according to claim 19 wherein the target molecule is a polypeptide selected from the group consisting of the polypeptides defined in the left-hand column of Table 8 or its corresponding mRNAs.

21. A method of treating a disease selected from the group consisting of the diseases shown in the right-hand column of Table 8, wherein the disease is to be treated with the conjugate of claim 20 directed to a target polypeptide shown in the left-hand column of the same row as the diseases in Table 8.

22. A conjugate according to claim 1 wherein the receptor which is expressed in the hippocampus is selected from the group consisting of the 5-HT₃ receptor, the bradykinin B2 receptor, the CRF2 receptor, the frizzled FZD3 receptor, the galanin GAL3 receptor, the neuropeptide FF/B NPBW2 receptor, the neuropeptide Y Y1 receptor, the neuropeptide Y Y5 receptor, the neurotensin NTSR2 receptor, the opioid delta receptor, the somatostatin sst3 receptor, the somatostatin sst5 receptor, the 5-HT1A receptor, the adenosine A1 receptor, the endothelin ETa receptor, the endothelin ETb receptor, the formylpeptide FPR1 receptor, the formylpeptide FPR3 receptor, the frizzled FZD8 receptor, the frizzled FZD9 receptor, the melatonin MT2 receptor, the neuropeptide FF/B NPBW2 receptor, the neuropeptide Y Y2 receptor, the neuropeptide FF/B NPFF1 receptor, the neuropeptide Y Y4 receptor, the neurotensin NTSR1 receptor, the orexin OX1 receptor, the orexin OX2 receptor, the somatostatin sst1 receptor, the somatostatin sst5 receptor, the vasopressin V1A receptor and the vasopressin V1B receptor.

23. The conjugate according to claim 22 wherein the target molecule is a polypeptide selected from the group consisting of the polypeptides defined in the left-hand column of Table 9 or its corresponding mRNAs.

24. A method of treating a disease selected from the group consisting of the diseases shown in the right-hand column of Table 9, wherein the disease is to be treated with the conjugate of claim 23 directed to a target polypeptide shown in the left-hand column of the same row as the diseases in Table 9.

25. The conjugate according to claim 1 wherein the receptor which is expressed in the glia is selected from the group consisting of the formylpeptide FPR1 receptor, the formylpeptide FPR2 receptor, the formylpeptide FPR3 receptor and TLR7.

26. The conjugate according to claim 1 wherein the receptor which is expressed in the medulla is selected from the group consisting of EphA1, EphA2, EphA3, EphA4, EphAB1, EphAB2, EphAB3, the opioid mu receptor, the GlyT1 transported, the DP1 receptor, the neurokinin NK1 receptor, the neurokinin NK2 receptor, the neurokinin NK3 receptor, the CXCR4 chemokine receptor, VEGFR1, VEGFR2 and VEGFR3.

27. The conjugate according to claim 26 wherein the target molecule is a polypeptide selected from the group consisting of the polypeptides defined in the left-hand column of Table 10 or its corresponding mRNAs.

28. A method of treating a disease selected from the group consisting of the diseases shown in the right-hand column of Table 10, wherein the disease is to be treated with the conjugate of claim 27 directed to a target polypeptide shown in the left-hand column of the same row as the diseases in Table 10.

29. The conjugate according to claim 1 further comprising at least one additional selectivity agent.

30. The conjugate according to claim 29 wherein the first and said at least one additional selectivity agent are different.

31. The conjugate according to claim 30 wherein both selectivity agents are specific for receptors which are expressed in the same location of the central nervous system.

32. The conjugate according to claim 31 wherein the locations in the central nervous systems to which the first and the at least one additional selectivity agents bind are selected from the group consisting of:

(i) mesencephalon and striatum,

(ii) cortex and hippocampus,

(iii) brainstem and hippocampus,

(iv) cortex, hippocampus and striatum,

(v) cortex, glia and hippocampus,

(vi) hippocampus and striatum,

(vii) brainstem and hypothalamus

(viii) cortex and striatum

(ix) glia and medulla

(x) brainstem, cortex and mesencephalon,

(xi) brainstem, mesencephalon and striatum,

(xii) brainstem, cortex and hippocampus and

(xiii) cortex, mesencephalon and striatum.

33. The conjugate according to claim 1 wherein the nucleic acid which is capable of specifically binding to a target molecule which is expressed in the same cell as the target molecule is selected from the group consisting of a gapmer, double stranded RNA interference oligonucleotide, double stranded RNA with microRNA activity, an antisense oligonucleotide, an antiMicro RNA oligonucleotide, pre-miRNA, a mRNA coding for microRNAs, or shRNAs, a PNA, a LNA, a ribozyme and an aptamer.

34. The conjugate as defined in claim 1 wherein the selectivity agent is attached to the 5′

end of the nucleic acid or to the 3′

end of the nucleic acid.

35. The conjugate of claim 1 further comprising a nucleic acid which is complementary to the first nucleic acid.

36. A conjugate as defined in claim 35 wherein the nucleic acid is an interfering RNA.

37. The conjugate according to claim 1 wherein, if the conjugate comprises a second selectivity agent, then

(xiv) if the nucleic acid is a single stranded polynucleotide, the second selectivity agent is attached to the opposite end of the nucleic acid to which the first selectivity agent is attached or to the same end to which the first selectivity agent is attached by means of a bifunctional linker or

(xv) if the nucleic acid is a double stranded polynucleotide, the second selectivity agent is attached either to the opposite end of the strand wherein the first selectivity agent is attached, to either end of the strand which is complementary to the strand wherein the first selectivity agent is attached or to the same end as the end which is attached to the first selectivity agent via a bifunctional linker.

38. The conjugate of claim 1 wherein at least one of the selectivity agents is connected to the nucleic acid by a linking group.

39. A conjugate according to claim 38 wherein the linking group has the structure

-L1_d-[(A-L2)_a-(B-L3)_b]_c-

wherein:

A and B represent monomer units independently selected from the group consisting of a monosaccharide, an C₁-C₅₀ alkyl chain and a (C₂-C₂₀) alkylene glycol;

a and b are integers ranging from 0 to 50;

c is an integer ranging from 0 and 30;

L1, L2 and L3 are linking compounds independently selected from the group consisting of phosphodiester, phosphorothioate, carbonyl, carbamate, methylphosphonate, carbonyl, guanidinium, sulfamate, sulfamide, formacetal, thioformacetal, sulfone, amide and mixtures thereof;

d is 0 or 1.

40. The conjugate according to claim 39 wherein b and d are 0, c is 1, A is an alkyl chain and L2 is a phosphodiester bond.

41. The conjugate according to claim 1 further comprising a protecting group attached to the end or ends of the polynucleotide which is not attached to the selectivity agent.

42. The conjugate according to claim 1 further comprising a group which facilitates transport across biological membranes.

43. The conjugate according to claim 1 further comprising an endosomolytic peptide.

45. The conjugate of claim 1, wherein the selectivity agent is tabimorelin or tabimorelin hemifumarate.

44. A conjugate comprising

(xvi) at least one selectivity agent which binds specifically to a receptor which is internalized by the cell upon binding of said selectivity agent wherein the selectivity agent is a compound having the structure