Autosomal dominant polycystic kidney disease therapy

Abstract

Disclosed herein are methods for treating polycystic kidney disease (PKD), including autosomaldominant polycystic kidney disease (ADPKD). The disclosure further relates to methods of administering pharmaceutical compositions that include compounds targeting Hippo-Yap signaling, thereby blocking apical constriction and shrinking kidney cysts.

Description

AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE THERAPYFIELD OF THE INVENTION

[0001] This disclosure generally relates to methods of treating a cystic kidney disease, such as autosomal-dominant polycystic kidney disease (ADPKD). The disclosure further relates to methods of blocking apical constriction and shrinking kidney cysts, such as by administering pharmaceutical compositions that include inhibitors of Hippo-YAPl signaling.BACKGROUND

[0002] Autosomal dominant polycystic kidney disease (ADPKD) is a relatively common genetic disease associated with kidney enlargement due to the formation of cysts that progressively expand in size until end-stage kidney disease results. Substantial progress has been made in identifying and understanding causative mutations in ADPKD, as well as the role that the failure of cilia assembly or that cilia signaling plays in initiating renal cysts. However, lumen expansion is the primary kidney damaging process in cystogenesis, and the subsequent cellular signaling pathway changes that underlie cystogenesis have not been fully elucidated.

[0003] While in vitro modelling of renal cysts can recapitulate cyst initiation from loss of contact inhibition, failure to produce cysts that have large lumens undermines representation of a critical clinical feature of ADPKD. For example, cadherin 8 has been shown to initiate cyst emergence, but the resultant cysts lack enlarged lumens. Elements of the Hippo- Yap pathway have also been shown to play a critical role in cystogenesis, specifically in promoting the lumen expansion characteristic of ADPKD. Whereas cell signalling events related to apical lumen size have been explored, there exists a need to exploit the cellular events related to apical constriction, a critical driver in reducing renal cyst size. Additionally, improved methods of treating cystic kidney disease are needed, which not only inhibit cyst formation but reduce the surface area of existing cysts. Aspects of the invention disclosed herein address these needs.1DMSJJS.367066309.1INCORPORATION BY REFERENCE

[0004] Each patent, publication, and non-patent literature cited in the application is hereby incorporated by reference in its entirety as if each was incorporated by reference individually, and as if each is fully set forth herein. However, where such reference is made, and whether to patents, publications, non-patent literature, or other sources of information, it is for the general purpose of providing context for discussing features of the invention. Accordingly, unless specifically stated otherwise, the reference is not to be construed as an admission that the document or underlying information, in any jurisdiction, is prior art, or forms part of the common general knowledge in the art.SUMMARY OF THE INVENTION

[0005] The present invention provides method of treating a cystic kidney disease in a subject comprising administering a Hippo-YAPl pathway inhibitor to the subject. In some aspects, the Hippo-YAPl pathway inhibitor is a YAP-l-TEAD inhibitor. In some aspects, the Hippo-YAPl pathway inhibitor is a sulfonamide.

[0006] In another aspect, the present invention provides a method for slowing expansion of or reducing the size of renal cysts in a subject. In some aspects, administering the Hippo-YAPl pathway inhibitor to the subject slows the expansion and / or reduces the size of a kidney cyst in the subject.

[0007] In further aspects of the invention, the Hippo-YAPl pathway inhibitor administered comprises compound 4, compound 22, compound 59, compound 1991, compound 1993, compound 1994, compound 1995, an analog thereof, a pharmaceutical salt thereof, or a combination thereof.

[0008] In further aspects, the cystic kidney disease is autosomal dominant polycystic kidney disease.

[0009] In a further aspect, the size of the kidney cyst is reduced by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to the size of the kidney cyst before administering the Hippo-YAPl pathway inhibitor to the subject as measured by surface area, volume, or mean cross-sectional area.2DMSJJS.367066309.1BRIEF DESCRIPTION OF THE FIGURES

[0010] The accompanying drawings are included to provide a further understanding of the disclosure and are incorporated in and constitute a part of this specification, illustrate embodiments, and together with the description serve to explain the principles of the disclosure.

[0011] FIG. 1 shows a schematic representation of the Hippo Signaling Pathway.DETAILED DESCRIPTION

[0012] Applicant previously reported that expression of Cadherin 8, a type II Cadherin, is sufficient to induce cyst emergence from HK-2 cells grown as tubule arrays in collagen matrix (Wells et al., bioRxiv 2022.03.01.482118). However, emergent cysts did not exhibit the luminal enlargement observed in autosomal-dominant polycystic kidney disease (ADPKD). Applicant has reconstituted cyst emergence with consequent cyst lumen expansion in 3D culture by stable coexpression of Cadherin 8 in combination with a constitutively active mutant of yes-associated protein 1 (YAP1), the key effector of the HIPPO pathway. Specifically, immortalized cells derived from ADPKD cyst epithelia formed cysts with substantially larger lumen sizes when transduced with YAP1-5SA. Conversely, expression of the YAP1 inhibitor, AMOTL1, in these cells resulted in their forming cysts with smaller lumens than control cells. Data showed that cyst formation results from a sequential two-step process consisting of cyst initiation and subsequent cyst expansion.

[0013] Taken together, cyst initiation induced by Cadherin 8 expression is proposed to result from decreased cell-cell adhesion while cyst expansion is driven by increased YAP1 activity. See Wells et al., bioRxiv 2022.03.01.482118. Applicants work highlighted a fundamental role of apical constriction in the pathogenesis of renal cyst formation and revealed the unexpected involvement of the Hippo YAP1 pathway as a significant driver of abnormal biology. This finding was especially surprising because the Hippo YAP1 pathway is typically implicated in growth but not morphology.

[0014] FIG. 1 shows a diagram of the Hippo Signaling Pathway, including interactions between YAP and TEAD. When phosphorylated by LATS Kinases, YAP1 is sequestered in the cytoplasm and is eventually degraded by ubiquitin mediated proteasomal degradation. YAP1 can enter the nucleus and bind TEAD when not phosphorylated, activating genes involved in cell3DMSJJS.367066309.1proliferation, survival, and differentiation. Hippo signaling is linked to mechano-sensation, and active Hippo signaling silences the growth and pro-survival actions of YAP / TAZ transcriptional co-activators at TEAD bound enhancers. The Hippo signaling network and its biological functions are described, e.g., by Misra & Irvine, Annu Rev Genet. 2018 Nov 23; 52: 65-87; Meng et al., Genes Dev. 2016 Jan 1; 30(1): 1-17.

[0015] YAP1 is a key transcription factor in the Hippo signaling pathway and is negatively regulated by this pathway. YAP1 has been implicated in the development of several medical conditions, including cancer, cardiovascular diseases, and skin conditions. See, e.g., Huang, Int J Mol Set. 2023 Jan 14;24(2): 1666, Zhang et al., J Exp Clin Cancer Res. 2018 Sep 4;37(1):216, and Jia et al., Skin Res Technol. 2023 Mar;29(3):el3285. The TEAD family of transcription factors mediate YAP-dependent gene expression. TEAD is also required for YAP -induced cell growth, oncogenic transformation, and epithelial-mesenchymal transition. See, e.g., Zhao et al., Genes Dev. 2008 Jul 15; 22(14): 1962-1971.

[0016] The Hippo / YAPl signaling pathway is an evolutionarily conserved signaling pathway that is primarily involved in the regulation of stem cell self-renewal, organ size, and tissue regeneration. The biology of the Hippo- Yap 1 pathway has been described, e.g., by Xie et al., Front Cell Dev Biol. 2020; 8: 573455. In the context of kidney conditions, YAP1 has been implicated in kidney dysfunction, lupus nephritis, and kidney fibrosis. See, e.g., Xie et al., Pathobiology . 2021;88(6):412-423; Allison, Nat Rev Nephrol. 2021 May;17(5):297; and Muller and Schermer, Pediatr Nephrol 35, 1143-1152 (2020). Regarding polycystic kidney disease, the RhoA-YAP-c- Myc signaling axis has been identified as integral to PKD1 deficiency in ADPKD pathogenesis. See, e.g., Ma & Guan, Genes Dev. 2018 Jun 1;32(11-12):737-739; Cai, et al., Genes Dev. 2018 Jun 1;32(11-12):781-793; and Lee et al., Proc Natl Acad Sci USA. 2020 Nov 17;117(46):29001- 29012. As discovered by Applicant and described herein, the field has not recognized methods of treatment nor compounds that leverage the Hippo-YAPl pathway to shrink kidney cysts.

[0017] As used herein, the term “inhibitor” means a molecule that impedes or decreases a biological action. For the purpose of the present disclosure, an inhibitor generally has a specific target in the cell that it inhibits but inhibition of that specific target will have indirect effects on other biological molecules or processes that are regulated by the specific target. This inhibition may happen directly or indirectly.4DMSJJS.367066309.1

[0018] As used herein, the terms “treating” or “treatment” refer to a desired biological or pharmacological effect as described herein, as well as any one or more of: (a) preventing a disorder from occurring in a subject who may be predisposed to the disorder but has not yet been diagnosed with it; (b) inhibiting a disorder, e.g., arresting the development of kidney cysts; and (c) relieving a disorder, e.g., causing regression thereof, such as kidney cyst shrinkage. Other such measurements, benefits, and surrogate or clinical endpoints, alone or in combination, will be understood to one of ordinary skill based on the teachings herein and the knowledge in the art.

[0019] “Therapeutically effective amount” or “therapeutically effective dose” of a composition (e.g,. a composition comprising an agent) refers to an amount that is effective to achieve a desired therapeutic result (e.g., reducing the size of kidney cysts). Therapeutically effective amounts will typically depend upon the IC50 and safety profile of the specific agent being administered.

[0020] Method of Treatment

[0021] In some aspects, provided herein are methods of treating a cystic kidney disease. In some embodiments, disclosed methods comprise administering a therapeutically effective amount of a Hippo-YAPl pathway inhibitor to a subject having a cystic kidney disease.

[0022] In some embodiments, disclosed methods include inhibiting the growth of a kidney cyst by administering a Hippo-YAPl pathway inhibitor to a subject having a cystic kidney disease. In some embodiments, disclosed methods include shrinking or reducing the size of a kidney cyst by administering a Hippo-YAPl pathway inhibitor to a subject having a cystic kidney disease. Size may be determined by measuring surface area, volume, cross-sectional area, or other dimensions available to one of skill in the art.

[0023] Disease progression correlates with cyst volume, i.e., cyst growth is a major driver of kidney damage, and the rate of cyst growth varies from subject to subject. While inhibition of cyst growth is a validated FDA biomarker by FDA, methods that result in shrinking kidney cysts, such as the disclosed methods, are unexpected and extremely useful. To date, no compound has ever been shown to shrink kidney cysts. At best, known therapeutics slow down cyst growth.

[0024] In some embodiments, the Hippo-YAPl pathway inhibitor inhibits the interaction between YAP1 and TEAD, such as a YAP1-TEAD inhibitor. Exemplary YAP1-TEAD inhibitors include compound 22 and compound 59. YAP1-TEAD inhibition can be determined to methods available to one of skill in the art, e.g., TEAD reporter assays, peptide labelling, and fluorescent5DMSJJS.367066309.1polarization assays. In some examples, the Hippo-YAPl pathway inhibitor has an IC50 value of less than 50 pm, 25 pm, 10 pm, 5 pm, 1 pm, in a TEAD reporter assay. Such methods are described, e.g., by A. Thompson, 2020, “Identification Of Novel Small Molecule Inhibitors Of YAP-TEAD Binding Within The Hippo Signaling Pathway,” Masters Thesis, Indiana University.

[0025] In some embodiments, the Hippo-YAPl pathway inhibitor is a sulfonamide. In some embodiments, the Hippo-YAPl pathway inhibitor is selected from Table I Compounds, including analogs thereof, pharmaceutical salts thereof, and combinations thereof.Table I Compounds6DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1DMSJJS.367066309.1

[0026] In some embodiments, the Hippo-YAPl pathway inhibitor comprises compound 4, compound 22, compound 59, compound 1989, compound 1991, compound 1993, compound 1994, compound 1995, or a combination thereof.18DMSJJS.367066309.1

[0027] In some embodiments, disclosed methods comprise administering compound 4, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.

[0028] In some embodiments, disclosed methods comprise administering compound 22, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.Compound 22

[0029] In some embodiments, disclosed methods comprise administering compound 59, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.Compound 59

[0030] In some embodiments, disclosed methods comprise administering compound 1989, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.19DMSJJS.367066309.1

[0031] In some embodiments, disclosed methods comprise administering compound 1990, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.1990

[0032] In some embodiments, disclosed methods comprise administering compound 1991, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.1991

[0033] In some embodiments, disclosed methods comprise administering compound 1993, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.20DMSJJS.367066309.1

[0034] In some embodiments, disclosed methods comprise administering compound 1994, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.

[0035] In some embodiments, disclosed methods comprise administering compound 1995, an analog thereof, or a pharmaceutical salt thereof to a subject that has a cystic kidney disease.

[0036] Other Hippo-YAP pathway inhibitors that may be used in accordance with the present disclosure are available to one of skill in the art, and described, e.g., in W02021 / 021607 A2, CN110863001A, JP2020164539A, US2022 / 0280590A1, CN110257380 A, WO 2015 / 073813 A2, EP 3882242A1, WO 2020 / 096416A1, CN108913654A, WO 2018 / 085275A1, and CN114292849A.21DMSJJS.367066309.1

[0037] In some embodiments, disclosed methods comprise co-administering a renal cyst agent and a Hippo-YAP pathway inhibitor to a subject in need thereof. In some embodiments, the renal cyst agent is fascaplysin, an inhibitor of mitogen-activated protein kinase-interacting serine / threonine-protein kinase 1 (MNK1), PD98059, RO-3306, a dual inhibitor of Cdc7 / Cdk9, 4- cyano-3 -methylisoquinoline, IKK-2 inhibitor VI ((5-phenyl-2-ureido)thiophene-3-carboxamide), IKK inhibitor VII, UCN-01 (7-Hydroxystaurosporine), UCN-02 (7-epi-hydroxystaurosporine), celastrol, staurosporine, carfilzomib, or a combination thereof.

[0038] In some embodiments, disclosed methods involve administering a pharmaceutical composition comprising the Hippo-YAP pathway inhibitor to a subject via a suitable route of administration. In some embodiments, the Hippo-YAP pathway inhibitor is administered locally or systemically. In some embodiments, the Hippo-YAP pathway inhibitor is administered via oral, buccal, parenteral (e.g., intravenous, intraarterial, subcutaneous), intraperitoneal (i.e., into the body cavity), inhalation or aeration (i.e., through the mouth or nose), or rectally systemic (i.e., affecting the entire body). The pharmaceutical composition may be formulated with a pharmaceutically acceptable carrier, adjuvant, or vehicle.

[0039] In some embodiments, the pharmaceutical composition comprising the Hippo-YAP pathway inhibitor is in unit dosage form. In some embodiments, the unit dosage form is an immediate release, controlled release, sustained release, extended release, or modified release formulation.

[0040] In preferred embodiments, disclosed methods involve orally administering the Hippo- YAP pathway inhibitor to a subject in need thereof. According, the Hippo-YAP pathway inhibitor can be provided to the subject as an oral dosage form. Oral dosage forms include oral liquid dosage forms (such as tinctures, drops, emulsions, syrups, elixirs, suspensions, and solutions, and the like) and oral solid dosage forms. The disclosed pharmaceutical compositions also may be prepared as formulations suitable for intramuscular, subcutaneous, intraperitoneal, or intravenous injection, comprising physiologically acceptable sterile aqueous or non-aqueous solutions, dispersions, suspensions or emulsions, liposomes, and sterile powders for reconstitution into sterile injectable solutions or dispersions.

[0041] In some embodiments, disclosed methods involve administering the Hippo-YAP pathway inhibitor to the subject in a total amount of about 1 and 500 mg, 5 and 250 mg, 10 and 75 mg, or 15 and 50 mg, wherein each range is inclusive.22DMSJJS.367066309.1IU-2024-019-02-WG

[0042] The subject treated in accordance with disclosed methods may have a cystic kidney disease with one of many underlying causes, such as an inherited single-gene disorder, a syndromic disorder associated with kidney cysts, and a non-genetic form of renal cystic disease. In some embodiments, the cystic kidney disease involves any of acquired cystic kidney disease, multicystic dysplastic kidney, medullary sponge kidney, polycystic kidney disease, autosomal dominant polycystic kidney disease, autosomal recessive polycystic kidney disease, tuberous sclerosis complex, simple kidney cysts, glomerulocystic kidney disease (GCKD), medullary cystic kidney disease (MCKD), and nephronophthisis.

[0043] The molecular pathogenesis, diagnostic evaluation, clinical characteristics, and management of renal cystic diseases are described, e.g., by Cramer and Guay -Woodford, Adv Chronic Kidney Dis. 2015 Jul;22(4):297-305. In some examples, imaging techniques, such as MRI, CT, and ultrasound can be used to determine the size or the change in size, such as shrinkage, of kidney cysts. In other examples, treatment of a cystic kidney disease according to the disclosure involves administering a kidney function test. The kidney function test may assess glomerular filtration rate (GFR), which relates to kidney filtration, creatinine levels, a muscle waste product that the kidneys remove from blood, or the presence of albumin in urine, a sign of kidney damage.

[0044] In some embodiments, disclosed methods reduce the number of kidney cysts in a subject. Disclosed methods may result in a reduction of 1 kidney cyst, 1-3 kidney cysts, 1-5 kidney cysts, 1-7 kidney cysts, or 1-10 kidney cysts. Cyst volumes decrease along with surface areas based on standard geometric formulas. In some examples, disclosed methods reduce the total surface area of kidney cyst(s) in a subject. In some examples, disclosed methods reduce the total volume of kidney cyst(s) in a subject. In some examples, disclosed methods reduce the mean cross- sectional area of kidney cyst(s) in a subject. The reduction in kidney cyst size can be determined relative to the size of the kidney cyst prior to administration of the Hippo-YAPl pathway inhibitor.

[0045] Disclosed methods may reduce the size of kidney cyst by at least about 25%, 50%, 75%, 100%, 125%, 150%, 175%, 200%, 225%, 250%, 275%, 300%, 325%, 350%, 375%, 400%, 425%, 450%, 475%, or 500% relative to the size of the kidney cyst prior to administration of the Hippo-YAPl pathway inhibitor to the subject. In other examples, disclosed methods may reduce the size of kidney cyst by at least about 1-5%, 1-10%, 1-15%, 1-20%, 1-25%, 1-50%, 1-75%, 1- 100%, 1-125%, 1-150%, 1-175%, 1-200%, 1-225%, 1-250%, 1-275%, 1-300%, 1-325%, 1-350%, 1-375%, 1-400%, 1-425%, 1-450%, 1-475%, 1-500%, 1-1000%, 1-1500%, or 1-2000% relative to23DMSJJS.367066309.1the size of the kidney cyst prior to administration of the Hippo-YAPl pathway inhibitor to the subject. Disclosed methods may reduce the size of kidney cyst by about 25%, 50%, 75%, 100%, 125%, 150%, 175%, 200%, 225%, 250%, 275%, 300%, 325%, 350%, 375%, 400%, 425%, 450%, 475%, or 500% relative to the size of the kidney cyst prior to administration of the Hippo-YAPl pathway inhibitor to the subject.

[0046] In some embodiments, the subject is a mammal. In some embodiments, the subject is a dog, a cat, a ferret, a sheep, a rabbit, a pig, a cow, or a human. In preferred embodiments, the subject is human.EXAMPLES

[0047] Example 1: Evaluation of Hippo-YAPl pathway inhibitor on renal cyst size

[0048] Six samples were evaluated for cyst size before and after treatment. Samples 1-3 were treated with compound 59, while samples 4-6 were vehicle treated for use as controls. As shown in Table II below, not only was there a delay in the increase in the % of area of the cysts in the treated samples, but the samples treated with compound 59 also showed decrease in the cyst size following treatment.Table II24DMSJJS.367066309.125DMSJJS.367066309.1

[0049] The change in % area was determined using T-test, paired, 2 tail. The change in % cyst area for treated samples 1-3, was 0.000596 and the change for untreated samples 4-6, 0.915453.26DMSJJS.367066309.1

Claims

CLAIMSI claimClaim 1. A method of treating a cystic kidney disease in a subject comprising administering a Hippo- YAP 1 pathway inhibitor to the subject.Claim 2. The method of claim 1, wherein the Hippo- YAP 1 pathway inhibitor is a YAP-l-TEAD inhibitor.Claim 3. The method of claim 1 or 2, wherein the Hippo- YAP 1 pathway inhibitor is a sulfonamide.Claim 4. The method of any one of claims 1 to 3, wherein the Hippo- YAP 1 pathway inhibitor comprises compound 4, compound 22, compound 59, compound 1991, compound 1993, compound 1994, compound 1995, an analog thereof, a pharmaceutical salt thereof, or a combination thereof.Claim 5. The method of any one of claims 1 to 4, wherein the Hippo- YAP 1 pathway inhibitor comprises compound 22, compound 59, or a combination thereof.Claim 6. The method of any one of claims 1 to 5, wherein the Hippo- YAP1 pathway inhibitor is orally administered to the subject.Claim 7. The method of any one of claims 1 to 6, wherein the cystic kidney disease is autosomal dominant polycystic kidney disease.Claim 8. The method of any one of claims 1 to 7, wherein administering the Hippo- YAP1 pathway inhibitor to the subject reduces the size of a kidney cyst in the subject.27DMSJJS.367066309.1Claim 9. The method of claim 8, wherein the size of the kidney cyst is reduced by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to the size of the kidney cyst before administering the Hippo- YAP 1 pathway inhibitor to the subject.Claim 10. The method of claim 8 or 9, wherein the size of the kidney cyst is measured as surface area, volume, or mean cross-sectional area.Claim 11. The method of any one of claims 1 to 10, wherein the subject is human.Claim 12. The method of any one of claims 1 to 11, wherein administering the Hippo-YAP pathway inhibitor to the subject include a total amount of about 1 and 500 mg, 5 and 250 mg, 10 and 75 mg, or 15 and 50 mg.28DMSJJS.367066309.1

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