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EP-4735602-A2 - COMPOSITIONS AND METHODS OF USING PRKAG2-TARGETING ANTIBODY-OLIGONUCLEOTIDE CONJUGATES ABSTRACT

EP4735602A2EP 4735602 A2EP4735602 A2EP 4735602A2EP-4735602-A2

Abstract

Disclosed herein are polynucleic acid molecules, pharmaceutical compositions, and methods of use for PRKAG2 antibody oligonucleotide conjugates (AOC).

Inventors

  • MISSINATO, Maria Azzurra
  • KARAMANLIDIS, Georgios
  • ABDULKADIR, Sami Abdulwahab
  • NALLAGATLA, Subbarao
  • JORDAN, Maryam

Assignees

  • Atrium Therapeutics, Inc.

Dates

Publication Date
20260506
Application Date
20240626

Claims (20)

  1. 1. A polynucleotide conjugate comprising an anti-transferrin receptor antibody or antigenbinding fragment thereof conjugated to a polynucleotide that hybridizes to a target sequence of PRKAG2 mRNA and mediates RNA interference against PRKAG2 mRNA preferentially in a muscle cell.
  2. 2 The polynucleotide conjugate of claim 1, wherein the target sequence is a PPKAG2 mRNA having a mutation.
  3. 3 The polynucleotide conjugate of claim 2, wherein the mutation is a gain of function mutation.
  4. 4 The polynucleotide conjugate of any one of claims 1-3, wherein the polynucleotide hybridizes to at least 8 contiguous bases of the target sequence of the PPKAG2 mRNA.
  5. 5 The polynucleotide conjugate of any one of claims 1-4, wherein the polynucleotide is from about 8 to about 50 nucleotides in length or from about 10 to about 30 nucleotides in length.
  6. 6 The polynucleotide conjugate of any one of claims 1-5, wherein the polynucleotide is a single- stranded antisense polynucleotide or a double-stranded polynucleotide.
  7. 7 The polynucleotide conjugate of claim 6, wherein the single-stranded polynucleotide is an antisense oligonucleotide (ASO).
  8. 8 The polynucleotide conjugate of claim 7, wherein the ASO comprises a nucleic acid sequence having at least 80%, 85%, 90%, 95%, or 100% homology with a sequence selected from SEQ ID NOs: 1-102.
  9. 9 The polynucleotide conjugate of claim 7, wherein the ASO comprises a nucleic acid sequence having at least 14, 15, 16, 17, 18 consecutive nucleotides from a sequence selected from SEQ ID NOs: 1-102, with no more than 1, 2, 3 mismatches.
  10. 10 The polynucleotide conjugate of claim 7, wherein the ASO comprises a nucleic acid sequence selected from SEQ ID NOs: 233-236.
  11. 11 The polynucleotide-antibody conjugate of claim 6, wherein the double-stranded polynucleotide is a small interfering RNA (siRNA) comprising a guide strand and a passenger strand.
  12. 12 The polynucleotide conjugate of claim 11, wherein the passenger strand comprises a nucleic acid sequence having at least 80%, 85%, 90%, 95%, or 100% homology with a sequence selected from SEQ ID NOs: 103-204.
  13. 13. The polynucleotide conjugate of claim 11, wherein the guide strand of comprises a nucleic acid sequence having at least 80%, 85%, 90%, 95%, or 100% homology with a sequence selected from SEQ ID NOs: 1-102.
  14. 14. The polynucleotide conjugate of claim 11, wherein the passenger strand comprises a nucleic acid sequence having at least 16, 17, 18, or 19 consecutive nucleotides from a sequence selected from SEQ ID NOs: 103-204, with no more than 1, 2, 3 mismatches.
  15. 15. The polynucleotide conjugate of claim 11, wherein the guide strand comprises a nucleic acid sequence having at least 16, 17, 18, or 19 consecutive nucleotides from a sequence selected from SEQ ID NOs: 1-102, with no more than 1, 2, 3 mismatches.
  16. 16. The polynucleotide conjugate of any one of claims 1-15, wherein the polynucleotide comprises at least one 2’ modified nucleotide, at least one modified internucleotide linkage, or at least one inverted abasic moiety.
  17. 17. The polynucleotide conjugate of claim 16, wherein the at least one 2’ modified nucleotide comprises 2’-O-methyl, 2’-O-methoxyethyl (2’-0-M0E), 2’-O-aminopropyl, 2'-deoxy, 2’-deoxy-2'-fluoro, 2'-O-aminopropyl (2'-O-AP), 2'-O-dimethylaminoethyl (2'- O-DMAOE), 2'-O-dimethylaminopropyl (2'-O-DMAP), 2’-O- dimethylaminoethyloxyethyl (2'-O-DMAEOE), or 2'-O-N-methylacetamido (2'-0-NMA) modified nucleotide; comprises locked nucleic acid (LNA) or ethylene nucleic acid (ENA); or comprises a combination thereof.
  18. 18. The polynucleotide conjugate of any one of claims 16-17, wherein the at least one modified intemucleotide linkage comprises a phosphorothioate linkage or a phosphorodithioate linkage.
  19. 19. The polynucleotide conjugate of any one of claims 1-18, wherein the polynucleotide comprises a 5 ’-terminal vinylphosphonate modified nucleotide.
  20. 20. The polynucleotide conjugate of any one of claims 11-19, wherein the passenger strand comprises a nucleic acid sequence having at least 80%, 85%, 90%, 95%, or 100% homology with a sequence selected from SEQ ID NOs: 221-232.

Description

COMPOSITIONS AND METHODS OF USING PRKAG2-TARGETING ANTIBOD Y- OLIGONUCLEOTIDE CONJUGATES CROSS-REFERENCE [0001] This application claims the benefit of U.S. Provisional Application No. 63/510,531 filed June 27, 2023, which is incorporated herein by reference in its entirety. BACKGROUND OF THE DISCLOSURE [0002] Gene suppression by RNA-induced gene silencing provides several levels of control: transcription inactivation, small interfering RNA (siRNA)-induced mRNA degradation, and siRNA-induced transcriptional attenuation. In some instances, RNA interference (RNAi) provides long lasting effects over multiple cell divisions. As such, RNAi represents a viable method useful for drug target validation, gene function analysis, pathway analysis, and disease therapeutics. [0003] AMP-activated protein kinase (AMPK) is an energy sensor kinase, composed of 3 subunits: a catalytic subunit (al or a2) and 2 regulatory subunits (pi or P2 subunit and yl, y2, or y3 subunit). The Protein Kinase AMP -Activated Non-Catalytic Subunit Gamma 2 (PRKAG2) gene encodes the y2 regulatory subunit of the AMPK, which responds to AMP/ ATP fluctuations. PRKAG2 is predominantly a cardiac isoform and the human PRKAG2 gene shares high homology (-90%) with the non-human primate and murine PRKAG2 gene. Binding of AMP to the y2 regulatory subunit encoded by PPKAG2 activates AMPK and induces its conformational changes. As such, mutations in PPKAG2 result in decreased affinity to ATP to so maintain AMPK inactive such that the AMPK loses its ability to sense AMP and ATP levels. Elevated AMPK activity promotes glucose transporter 4 (GLUT4) shuttling to the plasma membrane and increases glucose uptake and intracellular glucose 6-phosphate (G6P) concentration. This leads to an allosteric activation of glycogen synthase (GS), which overrides the inhibitory effect of AMPK on GS, resulting in a net increase in GS activity and excess glycogen storage in muscle cells. [0004] PPKAG2 cardiac syndrome is an autosomal dominant metabolic heart disease characterized by left ventricular hypertrophy (LVH), progressive conduction abnormalities, and ventricular pre-excitation. PPKAG2 cardiac syndrome causes cardiac hypertrophy and electrophysiologic abnormalities, particularly preexcitation (Wolff-Parkinson-White syndrome) and atrioventricular conduction block, glycogen storage disease of the heart. The prevalence of PPKAG2 syndrome is 0.23-1% in patients with suspected HCM. The glycogen accumulation is often associated with an eccentric pattern of hypertrophy and conduction abnormalities that characterize the PRKAG2 cardiac syndrome. Cardiomyopathies caused by glycogen storage diseases including PRKAG2 mutations are distinguished from other types of hypertrophic cardiomyocyte (HCM) by the formation of glycogen filled vacuoles in myocytes. Most of the mutations on PPKAG2 are gain of function (GOF) mutations. Numerous human PPKAG2 GOF mutations have been identified and each of these mutations is associated with a point mutation within the PPKAG2 gene resulting in an amino acid substitution of the PPKAG2 protein. Most commonly identified amino acid substitutions of the PRKAG2 protein include H142R, R302Q, L341S, H383R, R384T, T400N, H401D, K475E, K485I, Y487H, N488I, S548P, and R531G. These PPKAG2 GOF mutations in cardiac cells result in glycogen accumulation in the heart muscle cells, leading to glycogen storage cardiomyopathy. [0005] Current treatments for PPKAG2 cardiac syndrome that include standard heart failure and anti arrhythmic treatment, pacemaker, defibrillator implantation and surgical ablation alleviate the symptoms but do not treat the genetic cause of the cardiac abnormalities. However, there are no specific treatments available that target PPKAG2 mRNA. There is a need to develop therapeutics for treating cardiomyopathy caused by PPKAG2 cardiac syndrome. INCORPORATION BY REFERENCE [0006] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. SUMMARY OF THE DISCLOSURE [0007] In the present disclosure, methods and compositions of antibody-oligonucleotide conjugates (AOC) targeting PPKAG2 mRNA are provided to inhibit the expression of PPKAG2. In addition, the present disclosure provides methods and compositions to treat cardiomyopathy caused by mutations of PPKAG2 with antibody oligonucleotide conjugates to deliver nucleic acids that target the expression of PPKAG2 in tissue. In addition, the present disclosure provides methods and compositions to treat cardiomyopathy caused by PPKAG2 cardiac syndrome with antibody-oligonucleotide conjugates to deliver nucleic acids that target the expression of PPKAG2 in cardiac tissue. [0008] Disclosed herein, in certain embodiments, are polynucleotides and pharmaceutical compositions comprising the