Compounds and methods for modulating frataxin expression

Patent metadata

Field	Value
Publication number	US-10517877-B2
Application number	US-201715472852-A
Country	US
Kind code	B2
Filing date	Mar 29, 2017
Priority date	Mar 30, 2016
Publication date	Dec 31, 2019
Grant date	Dec 31, 2019

Abstract

The present technology relates to compositions and methods for modulating expression of genes, which include a target oligonucleotide sequence, such as repeats of a particular oligonucleotide sequence containing 3 to 10 nucleotides. In particular aspects, the present technology relates to agents having a formula A-L-B, wherein -L- is a linker; A- is a Brd4 binding moiety; and -B is a nucleic acid binding moiety, such as a polyamide or complementary oligonucleotide, that specifically binds to the target oligonucleotide sequence.

First claim

What is claimed is:

1. An agent having a formula A-L-B wherein -L- is a linker; A- is a bromodomain-containing protein 4 (Brd4) binding moiety having a structure of a bromodomain inhibitor; and -B is a nucleic acid binding moiety that specifically binds to one or more repeats of a GAA oligonucleotide sequence.

2. The agent of claim 1 , wherein the -B is a polyamide that specifically binds to one or more repeats of a GAA oligonucleotide sequence.

3. The agent of claim 1 , wherein the agent is capable of increasing frataxin (FXN) mRNA levels in a GM15850 Friedreich's ataxia (FRDA) patient cell line relative to an untreated GM15850 cell.

4. The agent of claim 1 , wherein the -B comprises one or more of the following subunits:

wherein Z is hydrogen, amino, or amido group.

5. The agent of claim 4 , wherein the -B comprises -X-(β-Py-Im) n -β-Py-TRM;
X is -β-Im-, -β-Py-, -β-, or a bond;
n is 1-10; and -TRM is -ImT or -CTh.

6. The agent of claim 4 , wherein the -B comprises -X-(β-Py-Im) n -β-Py-TRM;
X is -β-Im-, -β-Py-, -β-, or a bond;
n is 1-10; and -TRM is -ImT or -CTh;
wherein one of the -β-Py-Im- trimers is replaced by a -β-Im-Im- trimer.

7. The agent of claim 5 , wherein the -B comprises -(β-Py-Im) n -β-Py-ImT; Z is hydrogen; and n is 1 or 2.

8. The agent of claim 5 , wherein the -B comprises -β-Py-β-Py-Im-β-Py-ImT or -β-Py-β-Py-Im-β-Py-CTh; and Z is hydrogen.

9. The agent of claim 1 , wherein -L- is a linker having a backbone chain which comprises at least about 10 continuous atoms.

10. The agent of claim 9 , wherein -L- comprises a combination of one or more linking moieties selected from the group consisting of arylene, cycloalkylene, heteroarylene, heterocycloalkylene, —O—, —(CH 2 ) x —, —(OCH 2 CH 2 ) y —, —C(O)NR′—, —NR′C(O)—, —C(O)—, —NR*—, —(CH 2 CH 2 CH 2 O) y —, —(OCH 2 CH 2 CH 2 ) y —, and

wherein R′ and R* are each independently a hydrogen or C 1 -C 6 alkyl; and x and y are each independently an integer from 1-10.

11. The agent of claim 9 , wherein -L- comprises
—(CH 2 ) X —C(O)NH—(CH 2 CH 2 O) Y —(CH 2 ) Q —C(O)NH—(CH 2 ) Z —N(CH 3 )—(CH 2 ) P —NH—, —(CH 2 ) X —C(O)NH—(CH 2 ) R —(OCH 2 CH 2 ) Y —O—(CH 2 ) Q —C(O)NH—(CH 2 ) Z —N(CH 3 )—(CH 2 ) P —NH—, or —(CH 2 ) X —C(O)NH—(CH 2 ) Z —N(CH 3 )—(CH 2 ) P —C(O)NH—(CH 2 CH 2 O) Y —(CH 2 ) Q —NH—;
x is an integer from 1 to 5; z, p, R and Q are each independently an integer from 2 to 5; and y is an integer from 1 to 10.

12. The agent of claim 9 , wherein -L- comprises
—(CH 2 )—C(O)NH—(CH 2 CH 2 O) Y —(CH 2 ) 2 —C(O)NH—(CH 2 ) 3 —N(CH 3 )—(CH 2 ) 3 —NH—; and y is an integer from 3 to 10.

13. The agent of claim 9 , wherein -L- comprises one or more linking moieties selected from (Gly-Ser-Gly)v and (Gly-Gly-Ser)w , where v and w are an integer from 1 to 10.

14. The agent of claim 1 , wherein the A- is a triazolodiazepine Brd4 binding moiety.

15. The agent of claim 14 , wherein the A- is a triazolodiazepine Brd4 binding moiety having a formula

J is N, O or CR 11 ; K is N, O or CR 11 ; with the proviso that J and K cannot both be —O—; P is N, except when one of J or K is O, P is C;
wherein R 11 is a hydrogen or substituted or unsubstituted alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl group;
R 1 is a hydrogen or substituted or unsubstituted alkyl, hydroxyalkyl, aminoalkyl, alkoxyalkyl, halogenated alkyl, hydroxyl, alkoxy, or —COOR 4 ;
wherein R 4 is a hydrogen, substituted or unsubstituted arylene, aralkylene, cycloalkylene, heteroarylene, heteroaralkylene, heterocycloalkylene, alkylene, alkenylene, alkynylene, cycloalkylalkylene, or cycloalkylalkylene group interrupted by one or more heteroatoms;

R 2 is a substituted or unsubstituted aryl, alkyl, cycloalkyl, or aralkyl group;
R 3 is a hydrogen, halogen, or substituted or unsubstituted alkyl group; and
Ring E is a substituted or unsubstituted aryl or heteroaryl ring.

16. The agent of claim 14 , wherein the A- is a thienotriazolodiazepine Brd4 binding moiety having a formula

wherein R 3 is hydrogen or —CH 3 ; R 1 , R 5 , and R 7 are each independently hydrogen, methyl, ethyl, or halomethyl group; and R 8 is a halogen.

17. The agent of claim 1 , wherein -L- is a linker having a backbone chain which comprises about 15 to 30 continuous atoms;
the -B comprises -X-(β-Py-Im) n -β-Py-TRM; X is -β-Im-, -β-Py-, -β-, or a bond; n is 1 or 2; -TRM is -ImT or -CTh; and
the A- is a thienotriazolodiazepine Brd4 binding moiety having a formula:

wherein R 3 is hydrogen or -CH3; R 1 , R 5 , and R 7 are methyl; and R 8 is a halogen.

18. The agent of claim 17 , wherein the -L- is a linker comprising
—(CH 2 ) X —C(O)NH—(CH 2 CH 2 O) Y —(CH 2 ) Q —C(O)NH—(CH 2 ) Z —N(CH 3 )—(CH 2 ) P —NH—, —(CH 2 ) X —C(O)NH—(CH 2 ) R —(OCH 2 CH 2 ) Y —O—(CH 2 ) Q —C(O)NH—(CH 2 ) Z —N(CH 3 )—(CH 2 ) P —NH—or —(CH 2 ) X —C(O)NH—(CH 2 ) Z —N(CH 3 )—(CH 2 ) P —C(O)NH—(CH 2 CH 2 O) Y —(CH 2 ) Q —NH—;
x is an integer from 1 to 5; z, p, R and Q are each independently an integer from 2 to 5; and y is an integer from 1 to 10.

19. The agent of claim 17 , wherein the -B comprises a polyamide sequence selected from the group consisting of:

β-Im-β-Py-Im-β-Py-ImT,

β-Py-β-Py-Im-β-Py-ImT,

β-β-Py-Im-β-Py-ImT,

β-Py-Im-β-Py-ImT,

β-Im-β-Py-Im-β-Py-Im-β-Py-ImT,

β-Py-β-Py-Im-β-Py-Im-β-Py-ImT,

β-Py-Im-β-Py-Im-β-Py-ImT,

-β-β-Py-Im-β-Py-Im-β-Py-ImT,

β-Py-Im-β-Py-CTh

and

β-Py-β-Py-Im-β-Py-CTh.

Assignees

• Wisconsin Alumni Res Found

Inventors

• Ansari Aseem
• Erwin Graham
• Grieshop Matthew

Classifications

• A61P25/28

  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 title

• C07D495/14 Primary

  Ortho-condensed systems · CPC title

• A61K47/545

  Heterocyclic compounds (A61K47/558 takes precedence) · CPC title

• A61K47/55

  the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug · CPC title

• C08L77/00

  Compositions of polyamides obtained by reactions forming a carboxylic amide link in the main chain (of polyhydrazides C08L79/06; of polyamideimides or polyamide acids C08L79/08); Compositions of derivatives of such polymers · CPC title