Small molecules targeting repeat r(CGG) sequences
The invention provides a series of bioactive small molecules that target expanded r(CGG) repeats, termed r(CGG) exp , that causes Fragile X-associated Tremor Ataxia Syndrome (FXTAS). The compound was identified by using information on the chemotypes and RNA motifs that interact. Specifically, 9-hydroxy-5,11-dimethyl-2-(2-(piperidin-1-yl)ethyl)-6H-pyrido[4,3-b]carbazol-2-ium, binds the 5′C G G/3′G G C motifs in r(CGG) exp and disrupts a toxic r(CGG) exp -protein complex. Specifically, dimeric compounds incorporating two 9-hydroxyellipticine analog structures can even more potently bind the 5′C G G/3′G G C motifs in r(CGG) exp and disrupts a toxic r(CGG) exp -protein complex. Structure-activity relationships (SAR) studies determined that the alkylated pyridyl and phenolic side chains are important chemotypes that drive molecular recognition of r(CGG) repeats, such as r(CGG) exp . Importantly, the compound is efficacious in FXTAS model cellular systems as evidenced by its ability to improve FXTAS-associated pre-mRNA splicing defects and to reduce the size and number of r(CGG) exp -protein aggregates.
1. A dimeric r(CGG) binding compound of formula (II)
wherein
R 1 is H, (C1-C6)alkyl, or (C1-C6)alkanoyl;
R 2 is H, (C1-C6)alkyl, or (C1-C6)alkanoyl;
R 3 and R 4 are independently H, (C1-C6)alkyl, (C1-C6)haloalkyl, (C1-C6)alkoxyalkyl (C1-C6)haloalkoxyalkyl, or (C6-C10)aryl, wherein any alkyl, alkanoyl, alkoxy, or aryl group can be substituted with 0-3 J groups;
wherein J is any of halo, (C1-C6)alkyl, (C1-C6)alkoxy, (C1-C6)haloalkyl, hydroxy(C1-C6)alkyl, alkoxy(C1-C6)alkyl, (C1-C6)alkanoyl, (C1-C6)alkanoyloxy, cyano, nitro, azido, R 2 N, R 2 NC(O), R 2 NC(O)O, R 2 NC(O)NR, (C1-C6)alkenyl, (C1-C6)alkynyl, (C6-C10)aryl, (C6-C10)aryloxy, (C6-C10)aroyl, (C6-C10)aryl(C1-C6)alkyl, (C6-C10)aryl(C1-C6)alkoxy, (C6-C10)aryloxy(C1-C6)alkyl, (C6-C10)aryloxy(C1-C6)alkoxy, (3- to 9-membered)heterocyclyl, (3- to 9-membered)heterocyclyl(C1-C6)alkyl, (3- to 9-membered)heterocyclyl(C1-C6)alkoxy, (5- to 10-membered)heteroaryl, (5- to 10-membered)heteroaryl(C1-C6)alkyl, (5- to 10-membered)heteroaryl(C1-C6)alkoxy, or (5- to 10-membered)heteroaroyl;
R is independently at each occurrence H, (C1-C6)alkyl, or (C6-C10)aryl, wherein any alkyl or aryl group is substituted with 0-3 J;
and wherein L is a linker comprising a polypeptide backbone bonded by two respective nitrogen atoms thereof to a nitrogen atom of a respective 1,2,3-triazole group via a respective (C1-C6)alkylene group optionally further comprising a glycyl residue, each respective triazole group being bonded via a (C1-C6)alkylene group to the respective pyridinium nitrogen atom of each ellipticine scaffold; or a pharmaceutically acceptable salt thereof.
2. The compound of claim 1 wherein for the dimeric r(CGG) binding compound of formula (II), linker group L is a linker of formula (LI)
wherein n=1, 2, 3, 4, 5, 6, 7, or 8; each independently selected n1=0, 1, 2, 3, 4, or 5; and
each independently selected n2=1, 2, 3, 4, 5, or 6; and wherein a wavy line indicates a position of bonding to the respective pyridinium nitrogen atom of formula (II).
3. A pharmaceutical composition comprising a compound of claim 1 or 2 and a pharmaceutically acceptable excipient.
4. A method of inhibiting a messenger RNA molecule with a repeat r(CGG) sequence from binding to a protein with a binding affinity for a RNA hairpin loop comprising a non-Watson-Crick G-G nucleotide pair, comprising contacting the messenger RNA molecule having the repeat r(CGG) sequence and
an effective amount or concentration of a dimeric r(CGG) binding compound of formula (II)
wherein
R 1 is H, (C1-C6)alkyl, or (C1-C6)alkanoyl;
R 2 is H, (C1-C6)alkyl, or (C1-C6)alkanoyl;
R 3 and R 4 are independently H, (C1-C6)alkyl, (C1-C6)haloalkyl, (C1-C6)alkoxyalkyl (C1-C6)haloalkoxyalkyl, or (C6-C10)aryl, wherein any alkyl, alkanoyl, alkoxy, or aryl group can be substituted with 0-3 J groups;
wherein J is any of halo, (C1-C6)alkyl, (C1-C6)alkoxy, (C1-C6)haloalkyl, hydroxy(C1-C6)alkyl, alkoxy(C1-C6)alkyl, (C1-C6)alkanoyl, (C1-C6)alkanoyloxy, cyano, nitro, azido, R 2 N, R 2 NC(O), R 2 NC(O)O, R 2 NC(O)NR, (C1-C6)alkenyl, (C1-C6)alkynyl, (C6-C10)aryl, (C6-C10)aryloxy, (C6-C10)aroyl, (C6-C10)aryl(C1-C6)alkyl, (C6-C10)aryl(C1-C6)alkoxy, (C6-C10)aryloxy(C1-C6)alkyl, (C6-C10)aryloxy(C1-C6)alkoxy, (3- to 9-membered)heterocyclyl, (3- to 9-membered)heterocyclyl(C1-C6)alkyl, (3- to 9-membered)heterocyclyl(C1-C6)alkoxy, (5- to 10-membered)heteroaryl, (5- to 10-membered)heteroaryl(C1-C6)alkyl, (5- to 10-membered)heteroaryl(C1-C6)alkoxy, or (5- to 10-membered)heteroaroyl;
R is independently at each occurrence H, (C1-C6)alkyl, or (C6-C10)aryl, wherein any alkyl or aryl group is substituted with 0-3 J;
and wherein L is a linker comprising a polypeptide backbone bonded by two respective nitrogen atoms thereof to a nitrogen atom of a respective 1,2,3-triazole group via a respective (C1-C6)alkylene group optionally further comprising a glycyl residue, each respective triazole group being bonded via a (C1-C6)alkylene group to the respective pyridinium nitrogen atom of each ellipticine scaffold; or a pharmaceutically acceptable salt thereof.
5. The method of claim 4 wherein the repeat r(CGG) sequence is a r(CGG) exp sequence.
6. The method of claim 4 wherein R 1 is H, or wherein R 2 is H, or both.
7. The method of claim 4 wherein R 3 and R 4 are each methyl.
8. The method of claim 4 wherein for the dimeric r(CGG) binding compound of formula (II), linker group L is a linker of formula (LI)
wherein p1 =1, 2, 3, 4, 5, 6, 7, or 8; each independently selected p2=0, 1, 2, 3, 4, or 5; and
each independently selected p3=1, 2, 3, 4, 5, or 6; and wherein a wavy line indicates a position of bonding to the respective pyridinium nitrogen atom of the compound of formula (II).
9. The method of claim 8 wherein the compound of formula (II) is of formula 2E-nNME
wherein n=1, 2, 3, 4, 5, 6, 7 or 8;
or a pharmaceutically acceptable salt thereof.
10. The method of claim 9 wherein the contacting is in vivo in a patient wherein the inhibiting is medically indicated for treatment of a condition.
11. The method of claim 10 wherein the patient is suffering from Fragile X-associated Tremor Ataxia Syndrome.
12. A method of treatment of Fragile X-associated Tremor Ataxia Syndrome, comprising administering to a patient afflicted therewith an effective amount or concentration of a dimeric r(CGG) binding compound of formula (II)
wherein
R 1 is H, (C1-C6)alkyl, or (C1-C6)alkanoyl;
R 2 is H, (C1-C6)alkyl, or (C1-C6)alkanoyl;
R 3 and R 4 are independently H, (C1-C6)alkyl, (C1-C6)haloalkyl, (C1-C6)alkoxyalkyl (C1-C6)haloalkoxyalkyl, or (C6-C10)aryl; wherein any alkyl, alkanoyl, alkoxy, or aryl group can be substituted with 0-3 J groups;
wherein J is any of halo, (C1-C6)alkyl, (C1-C6)alkoxy, (C1-C6)haloalkyl, hydroxy(C1-C6)alkyl, alkoxy(C1-C6)alkyl, (C1-C6)alkanoyl, (C1-C6)alkanoyloxy, cyano, nitro, azido, R 2 N, R 2 NC(O), R 2 NC(O)O, R 2 NC(O)NR, (C1-C6)alkenyl, (C1-C6)alkynyl, (C6-C10)aryl, (C6-C10)aryloxy, (C6-C10)aroyl, (C6-C10)aryl(C1-C6)alkyl, (C6-C10)aryl(C1-C6)alkoxy, (C6-C10)aryloxy(C1-C6)alkyl, (C6-C10)aryloxy(C1-C6)alkoxy, (3- to 9-membered)heterocyclyl, (3- to 9-membered)heterocyclyl(C1-C6)alkyl, (3- to 9-membered)heterocyclyl(C1-C6)alkoxy, (5- to 10-membered)heteroaryl, (5- to 10-membered)heteroaryl(C1-C6)alkyl, (5- to 10-membered)heteroaryl(C1-C6)alkoxy, or (5- to 10-membered)heteroaroyl;
R is independently at each occurrence H, (C1-C6)alkyl, or (C6-C10)aryl, wherein any alkyl or aryl group is substituted with 0-3 J;
and wherein L is a linker comprising a polypeptide backbone bonded by two respective nitrogen atoms thereof to a nitrogen atom of a respective 1,2,3-triazole group via a respective (C1-C6)alkylene group optionally further comprising a glycyl residue, each respective triazole group being bonded via a (C1-C6)alkylene group to the respective pyridinium nitrogen atom of each ellipticine scaffold; or a pharmaceutically acceptable salt thereof.
13. The method of claim 12 wherein R 1 is H.
14. The method of claim 12 wherein R 2 is H.
15. The method of claim 12 wherein R 3 and R 4 are each methyl.
16. The method of claim 12 wherein for the dimeric r(CGG) binding compound of formula (II), linker group L is a linker of formula (LI)
wherein p1=1, 2, 3, 4, 5, 6, 7, or 8; each independently selected p2=0, 1, 2, 3, 4, or 5; and
each independently selected p3=1, 2, 3, 4, 5, or 6; and wherein a wavy line indicates a position of bonding to the respective pyridinium nitrogen atom of the compound of formula (II).
17. The method of claim 16 wherein the compound of formula (II) is of formula 2E-nNME
wherein n=1, 2, 3, 4, 5, 6, 7 or 8;
or a pharmaceutically acceptable salt thereof.