Methods for modulating splicing

Abstract

Described herein are methods of use of small molecule splicing modulator compounds that modulate splicing of mRNA, such as pre-mRNA, encoded by genes, and methods of treating diseases and conditions associated with gene expression or activity of proteins encoded by genes.

1 .- 20 . (canceled) 
     
     
         21 . A pharmaceutical composition comprising:
 (a) a small molecule splicing modulator (SMSM) that does not comprise a phosphodiester linkage and that has a molecular weight of from 100 Daltons to 2000 Daltons,
 wherein the SMSM binds to a pre-mRNA that encodes a target protein and that comprises a splice site sequence thereby modulating splicing of the pre-mRNA at the splice site to generate a spliced product of the pre-mRNA that comprises a poison exon, 
 wherein the spliced product of the pre-mRNA undergoes nonsense-mediated mRNA decay (NMD), and 
 wherein expression of the target protein encoded by the spliced product is decreased in a cell contacted with the SMSM compared to expression of the target protein encoded by the pre-mRNA in a cell that has not been contacted with the SMSM; and 
   (b) a pharmaceutically acceptable excipient.   
     
     
         22 . The pharmaceutical composition of  claim 21 , wherein the splice site sequence comprises a bulged nucleotide. 
     
     
         23 . The pharmaceutical composition of  claim 22 , wherein the bulged nucleotide is located at position that is a −1 position relative to the splice site of the splice site sequence. 
     
     
         24 . The pharmaceutical composition of  claim 21 , wherein the splice site sequence is a 5′ splice site sequence, a 3′ splice site sequence, a branch point splice site sequence, an exonic splicing enhancer (ESE) sequence, an exonic splicing silencer (ESS) sequence, an intronic splicing enhancer (ISE) sequence, an intronic splicing silencer (ISS) sequence, a polypyrimidine tract sequence, or a cryptic splice site sequence. 
     
     
         25 . The pharmaceutical composition of  claim 21 , wherein the splice site sequence is GAguaag. 
     
     
         26 . The pharmaceutical composition of  claim 21 , wherein the SMSM has a carbon composition of between 63% and 68%. 
     
     
         27 . The pharmaceutical composition of  claim 26 , wherein the SMSM has a nitrogen composition of between 18% and 26%. 
     
     
         28 . The pharmaceutical composition of  claim 27 , wherein the SMSM has a hydrogen composition of between 5% and 8%. 
     
     
         29 . The pharmaceutical composition of  claim 28 , wherein the SMSM has an oxygen composition of between 3% and 8%. 
     
     
         30 . The pharmaceutical composition of  claim 29 , wherein the SMSM has a topological polar surface area of between 86 and 103 Å 2 . 
     
     
         31 . The pharmaceutical composition of  claim 30 , wherein the SMSM has a sulfur composition of between 0% and 9%. 
     
     
         32 . The pharmaceutical composition of  claim 31 , wherein the SMSM has a ratio of hydrogen bond donors to hydrogen bond acceptors between 1:1.6 and 1:5. 
     
     
         33 . A method of treating, preventing, and/or delaying progression of a disease or a condition in a subject in need thereof, the method comprising administering a therapeutically effective amount of the pharmaceutical composition of  claim 21  to the subject. 
     
     
         34 . The method of  claim 33 , wherein the disease or the condition is a disease or a condition associated with expression level, over-expression, or gain-of-function of a protein encoded by a mutation in a gene encoding the pre-mRNA. 
     
     
         35 . The method of  claim 34 , wherein the disease or the condition is associated with expression level, over-expression, or gain-of-function of a protein encoded by the gene. 
     
     
         36 . The method of  claim 33 , wherein the disease or the condition is a cancer, a degenerative disease, a genetic disorder, an inherited disease, or a brain disease. 
     
     
         37 . The method of  claim 33 , wherein the disease or the condition is selected from the group consisting of ischemic heart disease, dilated cardiomyopathy, cystinosis, myasthenic syndrome, congenital, 6, presynaptic (CMS6); dyslexia; reading disorder; leukemia; colon cancer; Lynch syndrome; Werner syndrome; prostate cancer; an MSI-related cancer; ovarian cancer; breast cancer; endometrial cancer; neuroblastoma; Coffin-Siris syndrome; or autism spectrum disorder; Robinow syndrome; brachydactyly type B; von Willebrand disease; Becker disease; Leber congenital amaurosis; Thomsen disease factor X deficiency; β-thalassemia; retinitis pigmentosa and blindness; Schmid metaphyseal chondrodysplasia; Sandhoff disease; Marfan syndrome; multiple cancers; triosphosphate isomerase (TPI) deficiency; autism; prior-induced neurodegeneration; Huntington's disease; Parkinson's disease; Alzheimer's disease; demyelinating neuropathy; central dysmyelinating leukodystrophy; Waardenburg syndrome and Hirschsprung disease (PCWH); congenital hypomyelinating neuropathy (MPZ); Dejerine-Sottas neuropathy (DNS); Charcot-Marie-Tooth disease type 1B (CMT1B); supravalvular aortic stenosis (SVAC); congential cutis laxa; Ehlers-Danlos syndrome (EDS); osteogenesis imperfecta (OI); small vessel brain disease and Hereditary angiopathy with nephropathy; aneurysms; and muscle cramps (HANAC) syndrome; Leigh syndrome and respiratory complex I deficiency; spherocytosis and renal tubular acidosis; amyotrophic lateral sclerosis (ALS) and infantile-onset ascending spastic paralysis; Greig Cephalopolysyndactyly syndrome (GCS); Pallister-Hall syndrome (PHS) and acrocallosal syndrome. 
     
     
         38 . The method of  claim 33 , wherein the subject is a human subject. 
     
     
         39 . The method of  claim 38 , wherein the method comprises administering the pharmaceutical composition to the human subject orally. 
     
     
         40 . The method of  claim 39 , wherein the method comprises administering from 0.001 mg/kg/day to 500 mg/kg/day to the human subject.