Treatment of autophagy-based disorders and related pharmaceutical compositions, diagnostic and screening assays and kits

Abstract

In one embodiment, the invention provides a method of treating a subject suffering from a Mycobacterium infection by administering to the subject a therapeutically-effective amount of a degradative autophagy agonist or a secretory autophagy antagonist. In another embodiment, the invention provides a method of treating a subject suffering from one or more diseases selected from the group consisting of a Mycobacterium infection, an inflammatory disorder, an immune disorder, a cancer and a neurodegenerative disorder by administering to the subject a therapeutically-effective amount of a TBK-1 antagonist (e.g. BX795 or amlexanox). Related pharmaceutical compositions, diagnostic and screening assays and kits are also provided.

1 . A method of inhibiting, reducing the likelihood or treating a  tuberculosis  infection in a patient or subj ect comprising administering to a patient in need an effective amount of an autophagy modulator. 
     
     
         2 . The method according to  claim 1  wherein said moldulator is an autophagy agonist. 
     
     
         3 . The method according to  claim 1  wherein said modulator is flubendazole, hexachlorophene, propidium iodide, bepridil, clomiphene citrate (Z,E), GBR 12909, propafenone, metixene, dipivefrin, fluvoxamine, dicyclomine, dimethisoquin, ticlopidine, memantine, bromhexine, norcyclobenzaprine, diperodon, nortriptyline, a mixture thereof or a pharmaceutically acceptable salt thereof. 
     
     
         4 . The method according to  claim 1  wherein said modulator is benzethonium, niclosamide, monensin, bromperidol, levobunolol, dehydroisoandosterone 3-acetate, sertraline, tamoxifen, reserpine, hexachlorophene, dipyridamole, harmaline, prazosin, lidoflazine, thiethylperazine, dextromethorphan, desipramine, mebendazole, canrenone, chlorprothixene, maprotiline, homochlorcyclizine, loperamide, nicardipine, dexfenfluramine, nilvadipine, dosulepin, biperiden, denatonium, etomidate, toremifene, tomoxetine, clorgyline, zotepine, beta-escin, tridihexethyl, ceftazidime, methoxy-6-harmalan, melengestrol, albendazole, rimantadine, chlorpromazine, pergolide, cloperastine, prednicarbate, haloperidol, clotrimazole, nitrofural, iopanoic acid, naftopidil, Methimazole, Trimeprazine, Ethoxyquin, Clocortolone, Doxycycline, Pirlindole mesylate, Doxazosin, Deptropine, Nocodazole, Scopolamine, Oxybenzone, Halcinonide, Oxybutynin, Miconazole, Clomipramine, Cyproheptadine, Doxepin, Dyclonine, Salbutamol, Flavoxate, Amoxapine, Fenofibrate, Pimethixene, or a pharmaceutically acceptable salt or mixture thereof. 
     
     
         5 . (canceled) 
     
     
         6 . (canceled) 
     
     
         7 . A pharmaceutical composition in aerosol delivery form for delivery to patient or subject in need of treatment for a  tuberculosis  infection comprising an effective amount flubendazole, hexachlorophene, propidium iodide, bepridil, clomiphene citrate (Z,E), GBR 12909, propafenone, metixene, dipivefrin, fluvoxamine, dicyclomine, dimethisoquin, ticlopidine, memantine, bromhexine, norcyclobenzaprine, diperodon, nortriptyline, benzethonium, niclosamide, monensin, bromperidol, levobunolol, dehydroisoandosterone 3-acetate, sertraline, tamoxifen, reserpine, hexachlorophene, dipyridamole, harmaline, prazosin, lidoflazine, thiethylperazine, dextromethorphan, desipramine, mebendazole, canrenone, chlorprothixene, maprotiline, homochlorcyclizine, loperamide, nicardipine, dexfenfluramine, nilvadipine, dosulepin, biperiden, denatonium, etomidate, toremifene, tomoxetine, clorgyline, zotepine, beta-escin, tridihexethyl, ceftazidime, methoxy-6-harmalan, melengestrol, albendazole, rimantadine, chlorpromazine, pergolide, cloperastine, prednicarbate, haloperidol, clotrimazole, nitrofural, iopanoic acid, naftopidil, Methimazole, Trimeprazine, Ethoxyquin, Clocortolone, Doxycycline, Pirlindole mesylate, Doxazosin, Deptropine, Nocodazole, Scopolamine, Oxybenzone, Halcinonide, Oxybutynin, Miconazole, Clomipramine, Cyproheptadine, Doxepin, Dyclonine, Salbutamol, Flavoxate, Amoxapine, Fenofibrate, Pimethixene, or a pharmaceutically acceptable salt or mixture thereof. 
     
     
         8 . A pharmaceutical composition according to  claim 7  wherein said compound or compounds are further formulated in combination with an additional anti- tuberculosis  agent. 
     
     
         9 . The pharmaceutical composition according to  claim 7  wherein said additional anti- tuberculosis  agent is aminosalicylic acid, isoniazid, ethionamide, myambutol, rifampin, rifabutin, rifapentine, carpeomycin, cycloserine, or a pharmaceutically acceptable salt or a mixture thereof. 
     
     
         10 . (canceled) 
     
     
         11 . (canceled) 
     
     
         12 . A method of treating a subject suffering from a  Mycobacterium  infection, the method comprising administering to the subject a therapeutically-effective amount of a secretory autophagy antagonist. 
     
     
         13 . The method of  claim 12 , wherein the secretory autophagy antagonist is selected from the group consisting of an IL-1RA antagonist, an IL-1β antagonist, an IL-18 (IL-1F4) antagonist, a TSG101 antagonist, a HMGB1 antagonist, a Rab GTPase antagonist and a GRASP55 or GRASP65 antagonist. 
     
     
         14 . The method of  claim 12 , wherein the IL-1RA antagonist and IL-1β antagonist are Anakinra; the TSG101 antagonist is a TSG101 siRNA; the HMGB1 antagonist is selected from the group consisting of anti-HMGB1 antibody, ethyl pyruvate, a high mobility group box (HMGB) A box or a biologically active fragment thereof, an antibody to HMGB or an antigen-binding fragment thereof, an HMGB small molecule antagonist, an antibody to TLR2 or an antigen-binding fragment thereof, a soluble TLR2 polypeptide, an antibody to RAGE or an antigen-binding fragment thereof, a soluble RAGE polypeptide and a RAGE small molecule antagonist; the Rab GTPase antagonist is 2-(benzoylcarbarnothioylamino)-5,5-dimethyl-4,7-dihydrothieno[2,3-c]pyran-3-carboxylic acid and the GRASP55 or GRASP65 antagonist is a GRASP55 or GRASP65 siRNA. 
     
     
         15 . The method of  claim 13 , wherein the HMGB 1 antagonist is glycyrrhizin. 
     
     
         16 . A method of treating a subject suffering from one or more diseases selected from the group consisting of a  Mycobacterium  infection, an inflammatory disorder, an immune disorder, a cancer and a neurodegenerative disorder, the method comprising administering a therapeutically-effective amount of a TBK-1 antagonist to the subject. 
     
     
         17 . The method of  claim 16 , wherein the TBK-1 antagonist is BX795 or amlexanox. 
     
     
         18 . (canceled) 
     
     
         19 . (canceled) 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . (canceled) 
     
     
         24 . (canceled) 
     
     
         25 . A method of determining whether a subject suffers from, or is likely to develop, one or more autophagy-related disorders selected from the group consisting of an inflammatory disorder, an immune disorder, a cancer and a neurodegenerative disorder, the method comprising measuring expression levels in a cell sample obtained from the subject of one or more biomarkers selected from the group consisting of vimentin, galectin-1, galectin-3, ASC, ferritin and thioredoxin and comparing measured expression levels of the one or more biomarkers to expression levels of corresponding biomarkers in a control cell sample, wherein elevated expression levels of the one or more biomarkers when compared to control levels indicates that the subject suffers from, or is likely to develop, one or more of the autophagy-related disorders. 
     
     
         26 . A method of determining whether a subject suffers from, or is likely to develop, a  Mycobacterium  infection, the method comprising measuring expression levels in a cell sample obtained from the subject of one or more biomarkers selected from the group consisting of Atg8 (LC3A, B and C, and GABARAP, GABARAPL1 and L2), Rab8a, Atg9, FIP200, VMP1, WIPIs 91, DFCP-1 69, [L-1RA, IL-1β, IL-18 (IL-1F4), TSG101, HMGB1, a Rab GTPase, GRASP55 and GRASP65 and comparing measured expression levels of the one or more biomarkers to expression levels of corresponding biomarkers in a control cell sample, wherein elevated expression levels of the one or more biomarkers when compared to control levels indicates that the subject suffers from one or more of the autophagy-related disorders. 
     
     
         27 . (canceled) 
     
     
         28 . (canceled) 
     
     
         29 . (canceled) 
     
     
         30 . (canceled) 
     
     
         31 . A pharmaceutical composition comprising:
 (a) an amount of a TBK-1 antagonist which is effective in treating one or more diseases selected from the group consisting of a  Mycobacterium  infection, an inflammatory disorder, an immune disorder, a cancer and a neurodegenerative disorder; and optionally   (b) a pharmaceutically-acceptable excipient.   
     
     
         32 . The pharmaceutical composition of  claim 31 , wherein the TBK-1 antagonist is BX795 or amlexanox. 
     
     
         33 . (canceled) 
     
     
         34 . A kit comprising:
 (a) at least one reagent which is selected from the group consisting of:   (i) reagents that detect a transcription product of the gene coding for one or more biomarkers selected from the group consisting of IL-1RA, IL-1β, IL-18 (IL-1F4A), TSG101, HMGB1, Rab GTPase, GRASP55 , GRASP65, Atg8 (LC3A, B and C, and GABARAP, GABARAPL1 and L2), Rab8a, Atg9, FIP200, VMP1, WIPIs 91, DFCP-1 69, vimentin, galectin-1, galectin-3, ASC, ferritin and thioredoxin;   (ii) reagents that detect a translation product of the gene coding for the one or more biomarkers, and/or reagents that detect a fragment or derivative or variant of said transcription or translation product;   (b) instructions for diagnosing, or prognosticating a  Mycobacterium  infection, or determining the propensity or predisposition of a subject to develop such a disease or of monitoring the effect of a treatment by determining a level, or an activity, or both said level and said activity, and/or expression of said transcription product and/or said translation product and/or of fragments, derivatives or variants of the foregoing, in a sample obtained from said subject; and   (1) comparing said level and/or said activity and/or expression of said transcription product and/or said translation product and/or fragments, derivatives or variants thereof to a reference value representing a known  Mycobacterium  infection status (patient) and/or to a reference value representing a known health status (control) and/or to a reference value; and   (2) analyzing whether said level and/or said activity and/or expression is varied compared to a reference value representing a known health status, and/or is similar or equal to a reference value representing a known disease status or a reference value; and   (3) diagnosing or prognosticating a  Mycobacterium  infection, or determining the propensity or predisposition of said subject to develop such a disease, wherein a varied or altered level, expression or activity, or both said level and said activity, of said transcription product and/or said translation product and/or said fragments, derivatives or variants thereof compared to a reference value representing a known health status (control) and/or wherein a level, or activity, or both said level and said activity, of said transcription product and/or said translation product and/or said fragments, derivatives or variants thereof is similar or equal to a reference value and/or to a reference value representing a known  Mycobacterium  infection stage, indicates a diagnosis or prognosis of a disease, or an increased propensity or predisposition of developing such a disease, a high risk of developing signs and symptoms of a disease.   
     
     
         35 . (canceled) 
     
     
         36 . A method of treating or reducing the likelihood of a disease state or condition selected from the group consisting of sepsis, an inflammatory disease state or disorder or cancer in a patient in need comprising administering to said patient a composition selected from the group consisting of a HMGB1 modulator, an IL-1β modulator, an IL-18 modulator, an IL-33 modulator, a galectin modulator or mixtures thereof. 
     
     
         37 . The method according to  claim 36  wherein said HMGB1 modulator is an inhibitor selected from the group consisting of an anti-HMGB 1 antibody or an antigen binding fragment thereof, ethyl pyruvate, a HMGB 1 peptide, an HMGB small molecule antagonist, an anti-TLR2 antibody or an antigen-binding fragment thereof, a soluble TLR2 polypeptide, an antibody to RAGE or an antigen-binding fragment thereof, a soluble RAGE polypeptide, a RAGE small molecule antagonist and mixtures thereof. 
     
     
         38 . The method according to  claim 37  wherein said HMGB small molecule antagonist is glycyrrhizin. 
     
     
         39 . The method according to  claim 36  wherein said IL-1β modulator is an anti-IL-1β antibody or anakinra. 
     
     
         40 . The method according to  claim 36  wherein said IL-18 modulator is an anti-IL-18 antibody or IL-18 binding protein (IL-18BP). 
     
     
         41 . The method according to  claim 36  wherein said IL-33 modulator is an anti-IL-33 antibody or ST2. 
     
     
         42 . The method according to  claim 36  wherein said galectin modulator is a galectin inhibitor selected from the group consisting of GM-CT-01, GR-MD-02, GCS-100, taloside, pectin or a mixture thereof. 
     
     
         43 . The method according to  claim 36  whererin said inflammatory disease state or disorder is a lung disease, diabetes type I and type II, severe insulin resistance, hyperinsulinemia, dyslipidemia, elevated low-density lipoprotein (LDL), depressed high-density lipoprotein (HDL), elevated triglycerides, Mendenhall's Syndrome, Werner Syndrome, leprechaunism, lipoatrophic diabetes, acute and chronic renal insufficiency, end-stage chronic renal failure, glomerulonephritis, interstitial nephritis, pyelonephritis, glomerulosclerosis, Kimmelstiel-Wilson disease in diabetic patients, kidney failure after kidney transplantation, obesity, GH-deficiency, GH resistance, Turner's syndrome, Laron's syndrome, short stature, increased fat mass-to-lean ratios, immunodeficiencies including decreased CD 4   +  T cell counts and decreased immune tolerance or chemotherapy-induced tissue damage, bone marrow transplantation, diseases or insufficiencies of cardiac structure or function such as heart dysfunctions and congestive heart failure, neuronal, neurological, or neuromuscular disorders, e.g., diseases of the central nervous system including Alzheimer's disease, or Parkinson's disease or multiple sclerosis, and diseases of the peripheral nervous system and musculature including peripheral neuropathy, muscular dystrophy, or myotonic dystrophy, and catabolic states, including those associated with wasting caused by any condition, including, e.g., mental health condition (e.g., anorexia nervosa), trauma or wounding or infection such as with a bacterium or human virus such as HIV, wounds, skin disorders, gut structure and function that need restoration. 
     
     
         44 . The method according to  claim 36  wherein said inflammatory disease state or disorder is an infectious disease, a disorder of bone or cartilage growth in children, arthritis, osteoporosis, heart dysfunction, kidney disorder, a neurological disorder, a bone disorder, a whole body growth disorder or an immunological disorder. 
     
     
         45 . The method according to  claim 44  wherein said neurological disorder is Alzheimer's Dementia (AD), amyotrophic lateral sclerosis, depression, epilepsy, Huntington's Disease, multiple sclerosis, neurological complications of AIDS, spinal cord injury, glaucoma and Parkinson's disease. 
     
     
         46 . An assay for determining whether a compound of unknown activity is an inhibitor or inducer of autophagy secretion comprising two populations of cells, the first population of cells expressing a sequestome-like receptor (SLR) and a galectin-GFP fusion protein and emitting a green fluorescent signal in the absence of a test compound (a first cell population control signal) wherein said SLR and said galectin-GFP fusion protein interact to secrete said galectin-GFP fusion protein from said first population of cells, said second population of cells expressing a red fluorescent protein and galectin receptors on the surface of the cells which are capable of binding galectin-GFP secreted from said first population of cells