Patent Application
20180258123
This invention relates to therapeutic compounds and compositions, and methods for their use in the treatment or amelioration of various indications, including medical conditions associated with premature termination codons (PTCs) in RNA, including various cancers. In particular the invention relates to therapies and methods of treatment that would at least partially restore translation of full-length protein products.
This application claims the benefit of U.S. Provisional Patent Application Ser. No. 62/232,789 filed 25 Sep. 2015.
Genomics advances will soon make it routine to identify the precise molecular lesions responsible for many of the rare genetic diseases that afflict our population. Unfortunately, most of these diseases have no treatments, in Canada about 30% of patients die in childhood, and it is exceedingly difficult to develop disease-specific treatments because of the small number of patients for each disease and the high cost of developing new drugs. About 10% of disease-causing mutations are nonsense mutations that introduce a PTC.
The European Organization for Rare Diseases estimates that there are at least 5,000 rare genetic diseases, defined as affecting less than 1 in 2,000 people and the genes for about 4,000 have been identified (Online Mendelian Inheritance in Man database). Rare genetic diseases are believed to affect 5-6% of the population, or about 25 million people in the EU, 16 million in the USA and 1.8 million in Canada. It is estimated that 95% of rare genetic diseases have no specific treatment. Furthermore, genetic diseases that would not have the rare classification, also have nonsense mutations. It is estimated that 20.3% of the ˜43,000 disease-associated single-base pair substitutions affecting gene coding regions that are cataloged in the Human Gene Mutation Database (HGMD 2007-Mort M. et al. 2008) are PTCs.
For nearly all these diseases, about 10-11% of patients have nonsense point mutations. These mutations change an amino acid codon to a PTC (i.e. UAA, UAG and UGA). PTCs may result in decreased mRNA stability via nonsense-mediated mRNA decay (NMD), as well as production of some truncated non-functional protein, if any protein is produced. Compounds that allow insertion of an amino acid at a PTC, without affecting normal termination codons, can enable production of functional full-length protein. This approach, termed both nonsense mutation suppression and PTC read-through, offers the possibility of developing a single treatment for large numbers of patients across multiple diseases. In reality, a proportion of these patients would likely not benefit from such a therapy, for example those children born with irreversible neurological damage. Nevertheless, for 50% of rare genetic diseases, the onset of disease occurs in childhood and progressively worsens, and these patients are the ones who stand to benefit most from nonsense suppression therapy.
The therapeutic potential of nonsense suppression is not limited to inherited disorders. Nonsense mutations also occur in tumour suppressor genes in about 10% of cases of sporadic cancer, which affects 40% of the population and is far from rare. To illustrate, the R213X mutation in protein p53 is present in 1% of all human cancers. This corresponds to about 220,000 cases worldwide (Hoe, K. K. Verma, C. S. and Lane, D. P. 2014) that could theoretically benefit from nonsense suppression therapy. A further 70 cancer-driver tumour suppressor genes have been identified (Vogelstein B, et al. 2013). Tumour sequencing and mutation analysis is not yet routine for cancer diagnosis. However, the concept of personalized medicine has taken huge steps in the cancer field and it is anticipated that identifying nonsense mutations in cancer will become routine in the next decade.
Accordingly, the targeting of nonsense mutations could eliminate the “rare” element of rare genetic diseases in some cases where the genetic disease is caused at least in part by a nonsense mutation and nonsense suppression may also be of use in the treatment of some cancers.
Compounds that enable PTC read-through, offer the possibility of using the same treatment for large numbers of patients across multiple diseases based on the mechanism of the PTC and not the particular gene having the PTC.
High concentrations of aminoglycoside antibiotics were shown 30 years ago to induce PTC read-through in some yeast genes (Singh A et al. 1979) and in a reporter gene in mammalian cells (Burke J F and Mogg A E. 1985). The potential for using gentamicin to treat cystic fibrosis patients with a PTC in the CFTR gene was shown when gentamicin was used to induce CFTR protein expression from the endogenous gene in a patient-derived bronchial epithelial cell line (Bedwell D M et al. 1997), recovery of function in mice bearing the human CFTR G542X transgene (Du M et al. 2002) and increases in CFTR chloride conductance in patients (Clancy J P et al. 2001; and Wilschanski M et al. 2003). Similarly, paromomycin, geneticin (G418) and PTC124 (3-[5-(2-fluorophenyl)-[1,2,4]oxadiazole-3-yl]-benzoic acid) are all reported to have nonsense suppressive properties (Karijolich J, and Yu, Y-T 2014). In all cases the improvement was small and patient response was variable (Linde L et al. 2007). The lack of potency, the recognized renal and otic toxicities of high dose gentamicin and the need for intravenous or intramuscular administration likely limited its further development.
Read-through by gentamicin was demonstrated in mdx mice (Barton-Davis E R et al. 1999) with a PTC introduced into the mouse dystrophin gene to model human Duchenne Muscular Dystrophy (DMD). The first small trial in DMD patients showed no effect of gentamicin. Two others showed dystrophin expression in some patients (Malik V et al. 2010) but the level of expression was insufficient for patient improvement. Again, dose-limiting toxicities prevented further development.
Major efforts have been put into developing aminoglycoside derivatives with reduced toxicity e.g. (Shulman E et al. 2014; and Xue X et al. 2014) and discovering non-aminoglycoside RT compounds such as RTC13, RTC14, GJ71, GJ72 and PTC124 (Gatti R A. 2012; and Welch E M et al. 2007). These compounds increased protein production in several cell culture and animal disease models, but often at the limit of detection by western blotting for endogenous gene expression and with variable responses between genes, cell lines, and PTC mutations.
Furthermore, there are numerous approaches to read-through therapy. For example, read-through drugs, suppressor tRNAs, PTC pseudouridylation, and inhibition of nonsense-mediated mRNA decay (Keeling, K. M. et al. 2104).
PTC124 (Translarna™) is the sole new compound to have entered clinical trials. It is orally bioavailable and has a good safety profile compared with aminoglycosides. PTC124's PTC RT activity has been challenged based on artifactual activity in luciferase reporter assays of the type used for its discovery and lack of demonstrable RT activity in other reporter assays (McElroy S P et al. 2013). Nevertheless, it has shown activity in higher model systems, including increased dystrophin expression and muscle function in the mdx mouse (Welch E M et al. 2007) and CFTR protein expression and improved chloride conductance in the intestine of the G542X-hCFTR mouse (Du M et al. 2008). Recently, a phase 3 clinical trial in CFTR (Kerem E. 2014) and a phase 2b trial in DMD patients (Bushby K et al. 2014) both failed to reach statistical significance. However, retrospective analyses hinted at signs of efficacy in subgroups of authorization for DMD treatment in the European Union, conditional upon completion of a phase 3 trial (mid-2015) and submission of additional safety and efficacy data (Ryan N J. 2014).
Overall, currently available RT compounds suffer two major limitations: they display low activity, typically inducing less than 5% of wild-type (wt) protein levels; and they show unpredictable activity in only a small subset of genetic disease systems tested.
This invention is based in part on the discovery that compounds described herein suppress premature termination codons. Specifically, compounds identified herein, show the ability to read through premature stop codons.
In accordance with one embodiment, there is provided a pharmaceutical composition including 1) a compound, or a pharmaceutically acceptable salt thereof, in an amount effective for treating or ameliorating a medical condition associated with premature termination codons (PTCs) in RNA, wherein the compound has the structure of Formula II:
wherein M may be
and 2) a pharmaceutically acceptable excipient or pharmaceutically acceptable carrier.
In accordance with a further embodiment, there is provided a pharmaceutical composition including i) a compound, or a pharmaceutically acceptable salt thereof, in an amount effective for treating or ameliorating a medical condition associated with premature termination codons (PTCs) in RNA, wherein the compound has the structure of Formula I:
wherein R may be OH or NH2;
M may be
when R is OH and M may be
when R is NH2; and 2) a pharmaceutically acceptable excipient or pharmaceutically acceptable carrier.
In accordance with a further embodiment, there is provided a method of treating or ameliorating a medical condition associated with premature termination codons (PTCs) in RNA, the method including administering a compound, or a pharmaceutically acceptable salt thereof, in an amount effective for treating or ameliorating a medical condition associated with a PTC in RNA, wherein the compound has the structure of Formula II:
wherein M may be
to a subject in need thereof. Alternatively, the method may have a compound of Formula I.
In accordance with a further embodiment, there is provided a method of promoting read-through of a premature termination codon (PTC) in a RNA sequence, the method including administering a compound, or a pharmaceutically acceptable salt thereof, in an amount effective for treating or ameliorating a medical condition associated with a PTC in RNA, wherein the compound has the structure of Formula II:
wherein M may be
to a subject in need thereof. Alternatively, the compound may be of Formula I.
In accordance with a further embodiment, there is provided a method of promoting production of a functional protein in a cell, the protein encoded by a nucleotide sequence comprising a premature termination codon (PTC), the method comprising contacting the cell with an effective amount of a compound having the structure of Formula II:
wherein M may be
to a subject in need thereof. Alternatively, the compound may be of Formula I.
In accordance with a further embodiment, there is provided a compound, wherein the compound has the structure:
In accordance with a further embodiment, there is provided a pharmaceutical composition, the pharmaceutical composition comprising: a compound having the structure
and a steroid.
In accordance with a further embodiment, there is provided a method of treating or ameliorating a medical condition associated with premature termination codons (PTCs) in RNA, the method including administering a compound, or a pharmaceutically acceptable salt thereof, in an amount effective to treat or ameliorate a medical condition associated with a PTC in RNA, wherein the compound has the structure of
in combination with a steroid, to a subject in need thereof.
In accordance with a further embodiment, there is provided a use of a compound, or a pharmaceutically acceptable salt thereof, in an amount effective for treating or ameliorating a medical condition associated with premature termination codons (PTCs) in RNA, wherein the compound has the structure of Formula II:
wherein M may be
Alternatively, the compound may be of Formula I.
In accordance with a further embodiment, there is provided a use of a compound in the manufacture of a medicament for treatment or amelioration of a medical condition associated with premature termination codons (PTCs) in RNA, wherein the compound has the structure of Formula II:
and wherein M may be
Alternatively, the compound may be of Formula I.
In accordance with a further embodiment, there is provided a commercial package comprising: (a) a compound having the structure of Formula II:
wherein M may be
and (b) instructions for treating or ameliorating a medical condition associated with premature termination codons (PTCs) in RNA. Alternatively, the compound ma be of Formula I.
The compound may be selected from one or more of the following:
The compound may be selected from one or more of the following:
The compound may be selected from one or more of the following:
The medical condition may be selected from one or more of the conditions listed in TABLE 1 or TABLE 2. The medical condition may be selected from TABLE 1 or TABLE 2. The medical condition may be selected from TABLE 1. The medical condition may be selected from TABLE 2.
The medical condition may be selected from the group consisting of: central nervous system disease; peripheral nervous system disease; neurodegenerative disease; autoimmune disease; DNA repair disease; inflammatory disease; collagen disease; kidney disease; pulmonary disease; eye disease; cardiovascular disease; blood disease; metabolic disease; neuromuscular diseases; neoplastic disease; and any genetic disorder caused by nonsense mutation(s).
The medical condition may be selected from the group consisting of: ataxia-telangiectasia; muscular dystrophy; Duchenne muscular dystrophy; Dravet syndrome; myotonic dystrophy; multiple sclerosis; infantile neuronal ceroid lipofuscinosis; Alzheimer's disease; Tay-Sachs disease; neural tissue degeneration; Parkinson's disease; chronic rheumatoid arthritis; lupus erythematosus; graft-versus-host disease; primary immunodeficiencies; severe combined immunodeficiency; DNA Ligase IV deficiency; Nijmegen breakage disorders; xeroderma pigmentosum (XP); rheumatoid arthritis; hemophilia; von Willebrand disease; thalassemia (for example; β-thalassemia); familial erythrocytosis; nephrolithiasis; osteogenesis imperfecta; cirrhosis; neurofibroma; bullous disease; lysosomal storage diseases; Hurler's disease; familial cholesterolemia; cerebellar ataxia; tuberous sclerosis; immune deficiency; cystic fibrosis; familial hypercholesterolemia; pigmentary retinopathy; retinitis pigmentosa; amyloidosis; atherosclerosis; giantism; dwarfism; hypothyroidism; hyperthyroidism; aging; obesity; diabetes mellitus; familial polycythemia; Niemann-Pick disease; epidermolysis bullosa; Marfan syndrome; Becker muscular dystrophy (BMD); spinal muscular atrophy; cancer; and any genetic disorder caused by nonsense mutation(s).
The medical condition may be cancer. The cancer may be of the head and neck, eye, skin, mouth, throat, esophagus, chest, bone, blood, lung, colon, sigmoid, rectum, stomach, prostate, breast, ovaries, kidney, liver, pancreas, brain, intestine, heart or adrenals. The cancer may be sarcoma, carcinoma, fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, Kaposi's sarcoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, melanoma, neuroblastoma, retinoblastoma, a blood-born tumor or multiple myeloma. The cancer may be acute lymphoblastic leukemia, acute lymphoblastic B-cell leukemia, acute lymphoblastic T-cell leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute monoblastic leukemia, acute erythroleukemic leukemia, acute megakaryoblastic leukemia, acute myelomonocytic leukemia, acute nonlymphocyctic leukemia, acute undifferentiated leukemia, chronic myelocytic leukemia, chronic lymphocytic leukemia, hairy cell leukemia, or multiple myeloma.
The premature termination codon may be UGA or UAG. The premature termination codon may be UGA. The premature termination codon may be UAG. The premature termination codon may be UAA.
The method may further include the administration of a steroid to the subject. The steroid may be selected from one or more of the following: Medroxyprogesterone; Betamethasone; Dexamethasone; Beclomethasone; Budesonide; Clobetasol propionate; Cortisone acetate; Flumethasone Pivalate; Fluticasone Propionate; Hydrocortisone; Methylprednisolone; Paramethasone; Prednisolone; Prednisone; Triamcinolone; Danazol; Fludrocortisone; Mifepristone; Megestrol acetate; and Progesterone.
The compound may be
The compound may be
The compound may be
The compound may be
The compound may be
The compound may be
The compound may be
The compound may be
The compound may be
The compound may be
The compound may be
The compound may be
In some embodiments, the compounds described herein may be used to treat or ameliorate various indications, including medical conditions associated with premature termination codons (PTCs) in RNA, including various cancers. The various conditions may be found in TABLE 1.
The codon changes resulting in all of the above medical conditions are well known in the art and new codon changes that result in PTC are still being discovered. Nevertheless, there is an expectation that the compounds described herein will have some degree of readthrough activity for all such PTCs.
Compounds as described herein may be in the free form or in the form of a salt thereof. In some embodiment, compounds as described herein may be in the form of a pharmaceutically acceptable salt, which are known in the art (Berge S. M. et al., J. Pharm. Sci. (1977) 66(1):1-19). Pharmaceutically acceptable salt as used herein includes, for example, salts that have the desired pharmacological activity of the parent compound (salts which retain the biological effectiveness and/or properties of the parent compound and which are not biologically and/or otherwise undesirable). Compounds as described herein having one or more functional groups capable of forming a salt may be, for example, formed as a pharmaceutically acceptable salt. Compounds containing one or more basic functional groups may be capable of forming a pharmaceutically acceptable salt with, for example, a pharmaceutically acceptable organic or inorganic acid. Pharmaceutically acceptable salts may be derived from, for example, and without limitation, acetic acid, adipic acid, alginic acid, aspartic acid, ascorbic acid, benzoic acid, benzenesulfonic acid, butyric acid, cinnamic acid, citric acid, camphoric acid, camphorsulfonic acid, cyclopentanepropionic acid, diethylacetic acid, digluconic acid, dodecylsulfonic acid, ethanesulfonic acid, formic acid, fumaric acid, glucoheptanoic acid, gluconic acid, glycerophosphoric acid, glycolic acid, hemisulfonic acid, heptanoic acid, hexanoic acid, hydrochloric acid, hydrobromic acid, hydriodic acid, 2-hydroxyethanesulfonic acid, isonicotinic acid, lactic acid, malic acid, maleic acid, malonic acid, mandelic acid, methanesulfonic acid, 2-napthalenesulfonic acid, naphthalenedisulphonic acid, p-toluenesulfonic acid, nicotinic acid, nitric acid, oxalic acid, pamoic acid, pectinic acid, 3-phenylpropionic acid, phosphoric acid, picric acid, pimelic acid, pivalic acid, propionic acid, pyruvic acid, salicylic acid, succinic acid, sulfuric acid, sulfamic acid, tartaric acid, thiocyanic acid or undecanoic acid. Compounds containing one or more acidic functional groups may be capable of forming pharmaceutically acceptable salts with a pharmaceutically acceptable base, for example, and without limitation, inorganic bases based on alkaline metals or alkaline earth metals or organic bases such as primary amine compounds, secondary amine compounds, tertiary amine compounds, quaternary amine compounds, substituted amines, naturally occurring substituted amines, cyclic amines or basic ion-exchange resins. Pharmaceutically acceptable salts may be derived from, for example, and without limitation, a hydroxide, carbonate, or bicarbonate of a pharmaceutically acceptable metal cation such as ammonium, sodium, potassium, lithium, calcium, magnesium, iron, zinc, copper, manganese or aluminum, ammonia, benzathine, meglumine, methylamine, dimethylamine, trimethylamine, ethylamine, diethylamine, triethylamine, isopropylamine, tripropylamine, tributylamine, ethanolamine, diethanolamine, 2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, hydrabamine, choline, betaine, ethylenediamine, glucosamine, glucamine, methylglucamine, theobromine, purines, piperazine, piperidine, procaine, N-ethylpiperidine, theobromine, tetramethylammonium compounds, tetraethylammonium compounds, pyridine, N,N-dimethylaniline, N-methylpiperidine, morpholine, N-methylmorpholine, N-ethylmorpholine, dicyclohexylamine, dibenzylamine, N,N-dibenzylphenethylamine, 1-ephenamine, N,N′-dibenzylethylenediamine or polyamine resins. In some embodiments, compounds as described herein may contain both acidic and basic groups and may be in the form of inner salts or zwitterions, for example, and without limitation, betaines. Salts as described herein may be prepared by conventional processes known to a person skilled in the art, for example, and without limitation, by reacting the free form with an organic acid or inorganic acid or base, or by anion exchange or cation exchange from other salts. Those skilled in the art will appreciate that preparation of salts may occur in situ during isolation and purification of the compounds or preparation of salts may occur by separately reacting an isolated and purified compound.
In some embodiments, compounds and all different forms thereof (e.g. free forms, salts, polymorphs, isomeric forms) as described herein may be in the solvent addition form, for example, solvates. Solvates contain either stoichiometric or non-stoichiometric amounts of a solvent in physical association the compound or salt thereof. The solvent may be, for example, and without limitation, a pharmaceutically acceptable solvent. For example, hydrates are formed when the solvent is water or alcoholates are formed when the solvent is an alcohol.
In some embodiments, compounds and all different forms thereof (e.g. free forms, salts, solvates, isomeric forms) as described herein may include crystalline and amorphous forms, for example, polymorphs, pseudopolymorphs, conformational polymorphs, amorphous forms, or a combination thereof. Polymorphs include different crystal packing arrangements of the same elemental composition of a compound. Polymorphs usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability and/or solubility. Those skilled in the art will appreciate that various factors including recrystallization solvent, rate of crystallization and storage temperature may cause a single crystal form to dominate.
A PTC read-through compound may provide a therapeutic benefit if the compound permits read-through of a PTC in a protein coding sequence to produce the full length protein. Wherein the full length protein may have sequence variations and may not be the same as the native protein. Generally, the full length protein produced by the read-through is functional and can stand in for the wild-type protein. In some cases, as little as 5% of the normal total amount of the full length protein, wherein the total amount of protein, is what a subject not having the medical condition associated with the PTC would normally produce. However, depending on the medical condition associated with the PTC, as little as 1% of the normal total amount of the full length protein may be sufficient to have a therapeutic benefit. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 1% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 2% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 3% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 4% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 5% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 6% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 7% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 8% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 9% of the normal total amount of the full length protein a therapeutic benefit may be achieved. Provided that the PTC read-through compound provides read-through of a PTC in a protein coding sequence to produce at least about 10% of the normal total amount of the full length protein a therapeutic benefit may be achieved.
Alternatively, a PTC read-through compound may provide a therapeutic benefit if the compound permits sufficient read-through of a PTC in a protein coding sequence to provide some therapeutic benefit to the subject or achieve some therapeutic result. The therapeutic benefit may be determined functionally by measuring some therapeutic result. A therapeutic result may result from a therapeutically effective amount or a prophylactically effective amount of the compound, and may include, for example, reduced tumor size, increased life span, a delay of symptom onset or disease onset, increase metabolic efficiency or increased life expectancy. A therapeutically effective amount of a compound or a prophylactically effective amount of a compound may vary according to the disease state, age, sex, other health factors unrelated to or related to the disease and weight of the subject, and the ability of the compound to elicit a desired response in the subject.
Furthermore, the read-through efficiently may be greater at TGA than TAG, and in some circumstances there may be no read-through at TAA. Accordingly, treatments may be tailored to particular stop codons.
In some embodiments, compounds and all different forms thereof (e.g. free forms, salts, solvates, polymorphs, protonated forms) as described herein include isomers such as geometrical isomers, optical isomers based on asymmetric carbon, stereoisomers, tautomers, individual enantiomers, individual diastereomers, racemates, diastereomeric mixtures and combinations thereof, and are not limited by the description of the formula illustrated for the sake of convenience.
For example, Gentamicin B1 may be represented as follows:
In some embodiments, compounds may include analogs, isomers, stereoisomers, or related derivatives. In some embodiments the compounds may be used in conjunction with another compound to form a pharmaceutical composition.
In some embodiments, pharmaceutical compositions as described herein may comprise a salt of such a compound, preferably a pharmaceutically or physiologically acceptable salt. Pharmaceutical preparations will typically comprise one or more carriers, excipients or diluents acceptable for the mode of administration of the preparation, be it by injection, inhalation, topical administration, lavage, or other modes suitable for the selected treatment. Suitable carriers, excipients or diluents (used interchangeably herein) are those known in the art for use in such modes of administration.
Suitable pharmaceutical compositions may be formulated by means known in the art and their mode of administration and dose determined by the skilled practitioner. For parenteral administration, a compound may be dissolved in sterile water or saline or a pharmaceutically acceptable vehicle used for administration of non-water soluble compounds such as those used for vitamin K. For enteral administration, the compound may be administered in a tablet, capsule or dissolved in liquid form. The tablet or capsule may be enteric coated, or in a formulation for sustained release. Many suitable formulations are known, including, polymeric or protein microparticles encapsulating a compound to be released, ointments, pastes, gels, hydrogels, or solutions which can be used topically or locally to administer a compound. A sustained release patch or implant may be employed to provide release over a prolonged period of time. Many techniques known to one of skill in the art are described in Remington: the Science & Practice of Pharmacy by Alfonso Gennaro, 20th ed., Lippencott Williams & Wilkins, (2000). Formulations for parenteral administration may, for example, contain excipients, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated naphthalenes. Biocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compounds. Other potentially useful parenteral delivery systems for modulatory compounds include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation may contain excipients, for example, lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate and deoxycholate, or may be oily solutions for administration in the form of nasal drops, or as a gel.
Compounds or pharmaceutical compositions as described herein or for use as described herein may be administered by means of a medical device or appliance such as an implant, graft, prosthesis, stent, etc. Also, implants may be devised which are intended to contain and release such compounds or compositions. An example would be an implant made of a polymeric material adapted to release the compound over a period of time.
An “effective amount” of a pharmaceutical composition as described herein includes a therapeutically effective amount or a prophylactically effective amount. A “therapeutically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result, such as reduced tumor size, increased life span or increased life expectancy. A therapeutically effective amount of a compound may vary according to factors such as the disease state, age, sex, and weight of the subject, and the ability of the compound to elicit a desired response in the subject. Dosage regimens may be adjusted to provide the optimum therapeutic response. A therapeutically effective amount is also one in which any toxic or detrimental effects of the compound are outweighed by the therapeutically beneficial effects. A “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result (for example, smaller tumors, increased life span, increased life expectancy or prevention of the progression of the medical condition associated with premature termination codons). Typically, a prophylactic dose is used in subjects prior to or at an earlier stage of disease, so that a prophylactically effective amount may be less than a therapeutically effective amount.
It is to be noted that dosage values may vary with the severity of the condition to be alleviated. For any particular subject, specific dosage regimens may be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions. Dosage ranges set forth herein are exemplary only and do not limit the dosage ranges that may be selected by medical practitioners. The amount of active compound(s) in the composition may vary according to factors such as the disease state, age, sex, and weight of the subject. Dosage regimens may be adjusted to provide the optimum therapeutic response. For example, a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It may be advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage.
In some embodiments, compounds and all different forms thereof as described herein may be used, for example, and without limitation, in combination with other treatment methods for at least one indication selected from the group set out in TABLE 1 or TABLE 2.
In general, compounds as described herein should be used without causing substantial toxicity. Toxicity of the compounds as described herein can be determined using standard techniques, for example, by testing in cell cultures or experimental animals and determining the therapeutic index, i.e., the ratio between the LD50 (the dose lethal to 50% of the population) and the LD100 (the dose lethal to 100% of the population). In some circumstances however, such as in severe disease conditions, it may be appropriate to administer substantial excesses of the compositions. Some compounds as described herein may be toxic at some concentrations. Titration studies may be used to determine toxic and non-toxic concentrations. Toxicity may be evaluated by examining a particular compound's or composition's specificity across cell lines or in an animal model.
Compounds as described herein may be administered to a subject. As used herein, a “subject” may be a human, non-human primate, rat, mouse, cow, horse, pig, sheep, goat, dog, cat, etc. The subject may be suspected of having or at risk of having a medical condition associated with premature termination codons (PTCs).
As used herein, a “medical condition associated with premature termination codons” may be defined as any medical condition caused in whole or in part by a nonsense codon, which may result in decreased mRNA stability as well as protein truncation resulting in a non-functional protein, which in turn may directly or indirectly result in the medical condition. For example, the medical condition associated with premature termination codons may be selected from TABLE 1 or TABLE 2.
There are about 5000 or so such genetic diseases which may be grouped into broad categories, as follows: an autoimmune disease; a blood disease; a collagen disease; diabetes; a neurodegenerative disease; a cardiovascular disease; a pulmonary disease; or an inflammatory disease; a neoplastic disease or central nervous system disease. One third of the cases of genetic inherited diseases involve a premature termination codon (PTC) (Frischmeyer P A and Dietz H C 1999). In most cases, the primary mechanism whereby a nonsense mutation has an effect is through the degradation of that mRNA by a surveillance mechanism called nonsense-mediated mRNA decay (NMD) (see: Chang Y F et al. 2007; Isken O and Maquat L E 2007; Rebbapragada I and Lykke-Andersen J 2009; Rehwinkel J et al. 2006; and Muhlemann 0 et al. 2008).
Diagnostic methods for various medical conditions associated with premature termination codons are known in the art. Depending on the condition genetic diagnostics may be readily available or may be determined with directed sequencing. For example, the medical condition may be selected from the group consisting of central nervous system diseases, ataxia-telangiectasia, muscular dystrophy, Duchenne muscular dystrophy, Dravet syndrome, myotonic dystrophy, multiple sclerosis, infantile neuronal ceroid lipofuscinosis, Alzheimer's disease, Tay-Sachs disease, neural tissue degeneration, Parkinson's disease, autoimmune diseases, chronic rheumatoid arthritis, lupus erythematosus, graft-versus-host disease, primary immunodeficiencies, severe combined immunodeficiency, DNA Ligase IV deficiency, DNA repair disorders, Nijmegen breakage disorders, xeroderma pigmentosum (XP), inflammatory diseases, rheumatoid arthritis, blood diseases, hemophilia, von Willebrand disease, thalassemia (for example, β-thalassemia), familial erythrocytosis, nephrolithiasis, collagen diseases, osteogenesis imperfecta, cirrhosis, neurofibroma, bullous disease, lysosomal storage disease, Hurler's disease, familial cholesterolemia, cerebellar ataxia, tuberous sclerosis, immune deficiency, kidney disease, lung disease, cystic fibrosis, familial hypercholesterolemia, pigmentary retinopathy, retinitis pigmentosa, amyloidosis, atherosclerosis, giantism, dwarfism, hypothyroidism, hyperthyroidism, aging, obesity, diabetes mellitus, familial polycythemia, Niemann-Pick disease, epidermolysis bullosa, Marfan syndrome, neuromuscular diseases, Becker muscular dystrophy (BMD), spinal muscular atrophy, cancer, and any genetic disorder caused by nonsense mutation(s). Furthermore, where the medical condition associated with a premature termination codon is a cancer, the cancer may be selected from one or more of cancer is of the head and neck, eye, skin, mouth, throat, esophagus, chest, bone, blood, lung, colon, sigmoid, rectum, stomach, prostate, breast, ovaries, kidney, liver, pancreas, brain, intestine, heart or adrenals. Alternatively, the cancer may be selected from sarcoma, carcinoma, fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, Kaposi's sarcoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, melanoma, neuroblastoma, retinoblastoma, a blood-born tumor or multiple myeloma. Tests for determining whether a PTC is involved in the condition are known to those of ordinary skill in the art.
Compounds tested and to be tested are set out below in TABLES A and B respectively.
The Gentamicin complex or Gentamicin C complex as used herein includes gentamicin C1, gentamicin C1a, and gentamicin C2 (˜80% of complex) and are reported to have the most significant antibacterial activity. The remaining ˜20% of the complex is made up of Gentamicins A, B, X, et al. The exact compositions may vary between different production runs and based on the producer.
Various alternative embodiments and examples of the invention are described herein. These embodiments and examples are illustrative and should not be construed as limiting the scope of the invention.
Compounds were tested for PTC read-through in human cells, wherein mammary carcinoma HDQ-P1 cells homozygous for TGA (R213X) in exon 6 of the TP53 gene (Wang et al., 2000) were selected on the basis of convincing evidence of read-through by the aminoglycoside G418 (Floquet, C. et al. 2011). Western analysis using a quantitative automated capillary electrophoresis system showed that HDQ-P1 cells express very low levels of truncated p53 and no full-length p53 and that 50 μM G418 induces the formation of full-length p53 while also increasing truncated p53 levels as reported (Floquet, C. et al. 2011).
Nuclear localization sequences and a tetramerization domain located in the p53 C-terminus contribute to retaining p53 in the nucleus (Shaulsky, G et al. 1990; Liang, S. H and Clark, M. F. 2001) and p53 truncated at R213 lacks these sequences. To enable analysis of p53 R213X read-through at high throughput an automated 96-well fluorescence microscopy assay was established to detect and quantitate nuclear p53 signal. G418 induced a concentration-dependent increase in nuclear p53 consistent with read-through induction. During 72 h exposure, 50 μM G418 induced nuclear 53 expression in 9% of cells while 250 μM G418 induced nuclear p53 expression in nearly all cells.
HDQ-P1 cells cultured in DMEM containing 10% FBS and 1× Gibco™ antibioticantimicotic were seeded at 4000 per well of PerkinElmer View™ 96-well plates. The next day, the medium was replaced with fresh culture medium containing the compounds to be tested. After 72 h, the culture medium was removed by aspiration, the cells were fixed with 3% paraformaldehyde, 0.3% Triton X-100 and 1.5 μg/ml Hoechst 33323 in phosphate-buffered saline pH 7.2 (PBS) for 20 min at room temp. The cells were rinsed once with PBS and incubated for 2 h at room temp with a blocking solution of 3% BSA in PBS. The blocking solution was removed by aspiration and cells were incubated with 0.1 μg/ml DO-1 p53 mouse monoclonal p53 antibody (Santa Cruz™) in blocking solution for 90 min at room temp. The wells were washed once with PBS for 5 min and the cells were incubated with Alexa 488-conjugated goat anti-mouse antibody (Invitrogen Life Technologies A11029™) in blocking buffer for 90 min at room temp. The wells were washed once with PBS for 5 min, 75 μl PBS was added, the plates were covered with a black adherent membrane and stored at 4° C. overnight. Nuclear p53 immunofluorescence intensity was measured using a Cellomics ArrayScan VTI™ automated fluorescence imager.
Briefly, images were acquired with a 20× objective in the Hoechst™ and GFP (XF53) channels. Images of 15 fields were acquired for each well, corresponding to ˜2000 cells.
The Compartment Analysis bioapplication was used to identify the nuclei and define their border. The nuclear Alexa 488™ fluorescence intensity was then measured and expressed as average nuclear fluorescence intensity or % positive nuclei, using as a threshold the fluorescence intensity of nuclei from untreated cells (50-75, depending on experiment).
HDQ-P1 cells were seeded at 100,000 cells per well of TC-treated 6-well plates. The next day, the medium was replaced with fresh medium containing compounds to be tested and were incubated for 48 to 96 h. The medium was removed by aspiration, cell monolayers were rinsed with 1 ml ice-cold PBS. Cells were lysed in 80 μl lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% (v/v) Triton X100™, 2.5 mM sodium pyrophosphate, 1 mM beta-glycerophosphate supplemented with fresh 1 mM Na3VO4, 1 mM dithiothreitol and 1× complete protease inhibitor cocktail (Roche Molecular Biochemicals™)). Lysates were pre-cleared by centrifugation at 18,000 g for 15 min at 4° C. Supernatants were collected, protein was quantitated using the Bradford assay and lysates were adjusted to 1 mg/ml protein. Capillary electrophoresis and western analysis conditions were carried out with manufacturer's reagents according to the user manual (ProteinSimple WES™). Briefly, 5.6 μl of cell lysate was mixed with 1.4 μl fluorescent master mix and heated at 95° C. for 5 min. The samples, blocking reagent, wash buffer, DO-1 p53 antibody (0.5 μg/ml) and vinculin antibody (1:2000, R&D clone 728526), secondary antibody and chemiluminescent substrate were dispensed into the microplate provided by the manufacturer. The electrophoretic separation and immunodetection was performed automatically using default settings. The data was analyzed with inbuilt Compass™ software (Proteinsimple™). The truncated and full-length p53 peak intensities were normalized to that of the vinculin peak, used as a loading control. Results are shown as pseudo blots and as electropherograms.
In some instances, a traditional western blotting procedure was used (e.g.
Gentamicin, gentamicin A, B, B1, C1, C1a, C2, C2a, C2b, X2, sisomicin, as well as gentamicin fragments garamine and ring C (see
Methods for
Premature Stop Codon Testing with Genatamicin B1
Methods for
Premature Stop Codon Testing with Genatamicin B1
Methods for
Methods for
Induction of PTC Readthrough by Gentamicin B1 in Cells Derived from Patients with Rare Genetic Diseases.
Methods for
Panel C: HSK001 myoblasts derived from a Duchenne Muscular Dystrophy patient with nonsense mutation (DMD: E2035X) were differentiated into myotubes and exposed to the indicated concentrations of gentamicin B1 or gentamicin for 3 days and dystrophin expression level was determined by automated capillary electrophoresis western analysis using Abeam™ ab1527 α-dystrophin antibody. Extracts from WT myotubes were also analyzed, using 5% of the amount of protein used for DMD cells. Beta-actin was used as a loading control.
Panel D: SD123 fibroblasts from a patient with Schimke Immuno-Osseous Dysplasia, with a homozygous SMARCAL1 nonsense mutation (R17X) were exposed to the indicated concentrations of gentamicin B1 or gentamicin for 6 days and SMARCAL1 levels were determined by western blotting using an anti SMARCAL1 antibody provided by Dr. Cornelius Boerkoel (University of British Columbia). Extracts from WT fibroblasts were also analyzed, using 10% of the amount of protein used for SIOD cells. Beta-actin was used as a loading control.
Panel E: EB14 keratinocytes from a patient with Recessive Dystrophic Epidermolysis Bullosa, with a homozygous Q251X nonsense mutation on the COL7A1 gene were incubated with the indicated concentrations of gentamicin B1 or gentamicin for 72 h and cellular collagen 7 was measured by western blotting using EMD Millipore 234192 collagen 7 antibody. Extracts from WT keratinocytes were also analyzed, using 10% of the amount of protein used for EB14 cells.
Synthesis of the gentamicin analogues (i.e. see Table B) is proposed via α-glycosylation of the pseudo-disaccharide comprising garosamine linked to deoxystreptamine, either chemically or enzymatically. This would require access to the selectively protected disaccharide in which the alcohol to be glycosylated is free while the other alcohols and amines are protected. One route to this disaccharide would involve first protection of all amines with a suitable blocking group known to one skilled in the art (Cbz, Boc etc), then protection of the syn-diol within the streptamine moiety using Ley's reagent. Subsequent protection of the remaining alcohols and selective removal of the Ley protecting group would leave the pseudo-disaccharide with two free alcohols. Glycosylation of this under conditions for generating 1,2-syn linked product (α-gluco in this case) would likely generate a mixture of the two glycosides from which the one of interest could be separated and protecting groups removed.
Alternatively the direct enzymatic glycosylation of the pseudo-disaccharide comprising garosamine linked to deoxystreptamine may be carried out using a variety of α-glycoside phosphorylases, α-glucosidases (run in trans-glycosylation mode) or available α-glucosyl transferases may prove successful. Large libraries of such enzymes are being assembled making such “screening approaches” feasible. If successful this synthesis may provide a remarkably simple and scalable synthetic route.
Gentamicin, gentamicin A, B, B1, C1, C1a, C2, C2a, C2b, X2, sisomicin, as well as gentamicin fragments garamine and ring C (see
As shown in
The 96-well plate assay results were confirmed using western analysis as shown in
This result is important for medical applications of PTC read-through. Gentamicin is known to be nephrotoxic and ototoxic. (Kohlhepp S. J. et al. 1984) have examined the nephrotoxicity of the major gentamicins C, C1a and C2 and found that nephrotoxicity was caused mainly by C2. Although it is not yet know to what extent gentamicin B1 might be nephrotoxic or ototoxic, it is anticipated that treatment of patients with gentamicin B1 would induce PTC read-through at lower doses than treatment with gentamicin, which typically contains only 0.5-3% B1 (MicroCombiChem™, personal communication). Treatment with gentamicin B1 instead of gentamicin should achieve both higher PTC read-through and lower toxicity via omission of toxic gentamicin C2.
Monitoring of gentamicin plasma concentrations is recommended to avoid toxicity. A cursory search indicates that plasma levels of gentamicin are typically between 1 and 12 μg/ml (2-24 μM) and that concentrations above about 10 μM should be avoided during long-term treatment. The concentrations of gentamicin B1 showing read-through (3 μM and higher) are within this range.
As shown in
The results presented in
The results in
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Although various embodiments of the invention are disclosed herein, many adaptations and modifications may be made within the scope of the invention in accordance with the common general knowledge of those skilled in this art. Such modifications include the substitution of known equivalents for any aspect of the invention in order to achieve the same result in substantially the same way. Numeric ranges are inclusive of the numbers defining the range. The word “comprising” is used herein as an open-ended term, substantially equivalent to the phrase “including, but not limited to”, and the word “comprises” has a corresponding meaning. As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a thing” includes more than one such thing. Citation of references herein is not an admission that such references are prior art to an embodiment of the present invention. The invention includes all embodiments and variations substantially as hereinbefore described and with reference to the examples and drawings.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2016/000240 | 9/23/2016 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62232789 | Sep 2015 | US |
