Methods and pharmaceutical compositions for modulating autophagy in a subject in need thereof

Abstract

The present invention provides novel methods for the modulation of autophagy and the treatment of autophagy-related diseases, including cancer, neurodegenerative diseases, liver diseases, muscle diseases and pancreatitis.

1 . A method of inducing autophagy in a subject comprising administering the subject with an amount of at least one AcCoA depleting agent. 
     
     
         2 . The method of  claim 1  wherein the subject suffers from a disease selected from the group consisting of cancer diseases, neurodegenerative diseases, cardiovascular diseases such as ischemia, infectious diseases, auto-immune disease and/or inflammatory diseases such as pancreatitis, proteinopathies, metabolic diseases such as obesity and insulin resistance. 
     
     
         3 . The method of  claim 1  wherein the AcCoA depleting agent is selected from the group consisting of inhibitors of inhibitors of the glycolytic or lipolytic pathways, inhibitors of the mitochondrial export of AcCoA, or inhibitors of cytosolic AcCoA synthase. 
     
     
         4 . The method of  claim 1  wherein the AcCoA depleting agent is an inhibitor of mitochondrial pyruvate carrier complex (MPC) such as UK5099 (2-Cyano-3-(1-phenyl-1H-indol-3-yl)-2-propenoic acid). 
     
     
         5 . The method of  claim 1  wherein the AcCoA depleting agent is an inhibitor of mitochondrial carnitine palmitoytransferase-1 (CTP1) such as perhexiline (PHX) or an inhibitor of CTP1c expression. 
     
     
         6 . The method of  claim 1  wherein the AcCoA depleting agent is an inhibitor of mitochondrial citrate carrier (CiC), such as benzenetricarboxylate (BTC). 
     
     
         7 . The method of  claim 1  wherein the AcCoA depleting agent is an inhibitor of ATP-citratre lyase (ACLY) such as hydroxycitrate, (R,S)—S-(3,4-dicarboxy-3-hydroxy-3-methyl-butyl)-CoA, and S-carboxymethyl-CoA. 
     
     
         8 . The method of  claim 1  wherein the AcCoA depleting agent is an EP300 acetyltransferase inhibitor such as aspirin, acetylate derivatives and C646. 
     
     
         9 . The method of  claim 1  wherein the AcCoA depleting agent is an inhibitor of acyl-CoA synthetase short-chain family member 2 (ACCS2). 
     
     
         10 . A method of inhibiting autophagy in a subject comprising administering the subject with a therapeutically effective amount AcCoA and/or at least one AcCoA replenishing agent. 
     
     
         11 . The method of  claim 10  wherein the subject suffers from a disease selected from the group consisting of cardiovascular diseases such as surgical thoracic constriction (TAC), infectious diseases such as bacterial infections, cancer such as cancer with an advanced stage (stage II or IV), pulmonary diseases such as chronic obstructive pulmonary disease (COPD), hepatic diseases such as liver fibrosis, lysosomal impairment diseases, such as Danon disease, X-linked myopathy with excessive autophagy (XMEA), Glycogen Storage Type II (GSDII), Pompe disease, muscular diseases such as muscular atrophy. 
     
     
         12 . The method of  claim 10  wherein the AcCoA-replenishing agent is selected from the group consisting of dicholoroacetate (DCA), lipoic acid (LA), ketoisocaproic acid (KIC), butyrate and dimethy-α-ketoglutarate (DMKG). 
     
     
         13 . A method for treating a cancer in a subject in need thereof comprising administering the subject with a therapeutically effective amount of AcCoA depleting agent and a therapeutically effective amount of a chemotherapeutic agent wherein the AcCoA depleting agent is administered prior to the chemotherapeutic agent. 
     
     
         14 . The method of  claim 13  wherein the AcCoA depleting agent is administered 12; 13; 14; 15; 16; 17; 18; 19; 20; 21; 22; 23; 24; 25; 26; 27; 28; 29; 30; 31; 32; 33; 34; 35; 36; 37; 38; 39; 40; 41; 42; 43; 44; 45; 46; 47; 48; 49; 50; 51; 52; 53; 54; 55; or 56 h before the administration of the chemotherapeutic agent. 
     
     
         15 . The method of  claim 14  wherein the cancer is selected from the group consisting of cancer cells from the bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, gastrointestine, gum, head, kidney, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, testis, tongue, or uterus. In addition, the cancer may specifically be of the following histological type, though it is not limited to these: neoplasm, malignant; carcinoma; carcinoma, undifferentiated; giant and spindle cell carcinoma; small cell carcinoma; papillary carcinoma; squamous cell carcinoma; lymphoepithelial carcinoma; basal cell carcinoma; pilomatrix carcinoma; transitional cell carcinoma; papillary transitional cell carcinoma; adenocarcinoma; gastrinoma, malignant; cholangiocarcinoma; hepatocellular carcinoma; combined hepatocellular carcinoma and cholangiocarcinoma; trabecular adenocarcinoma; adenoid cystic carcinoma; adenocarcinoma in adenomatous polyp; adenocarcinoma, familial polyposis coli; solid carcinoma; carcinoid tumor, malignant; branchiolo-alveolar adenocarcinoma; papillary adenocarcinoma; chromophobe carcinoma; acidophil carcinoma; oxyphilic adenocarcinoma; basophil carcinoma; clear cell adenocarcinoma; granular cell carcinoma; follicular adenocarcinoma; papillary and follicular adenocarcinoma; nonencapsulating sclerosing carcinoma; adrenal cortical carcinoma; endometroid carcinoma; skin appendage carcinoma; apocrine adenocarcinoma; sebaceous adenocarcinoma; ceruminous; adenocarcinoma; mucoepidermoid carcinoma; cystadenocarcinoma; papillary cystadenocarcinoma; papillary serous cystadenocarcinoma; mucinous cystadenocarcinoma; mucinous adenocarcinoma; signet ring cell carcinoma; infiltrating duct carcinoma; medullary carcinoma; lobular carcinoma; inflammatory carcinoma; paget's disease, mammary; acinar cell carcinoma; adenosquamous carcinoma; adenocarcinoma w/squamous metaplasia; thymoma, malignant; ovarian stromal tumor, malignant; thecoma, malignant; granulosa cell tumor, malignant; and roblastoma, malignant; Sertoli cell carcinoma; leydig cell tumor, malignant; lipid cell tumor, malignant; paraganglioma, malignant; extra-mammary paraganglioma, malignant; pheochromocytoma; glomangiosarcoma; malignant melanoma; amelanotic melanoma; superficial spreading melanoma; malig melanoma in giant pigmented nevus; epithelioid cell melanoma; blue nevus, malignant; sarcoma; fibrosarcoma; fibrous histiocytoma, malignant; myxosarcoma; liposarcoma; leiomyosarcoma; rhabdomyosarcoma; embryonal rhabdomyosarcoma; alveolar rhabdomyo sarcoma; stromal sarcoma; mixed tumor, malignant; mullerian mixed tumor; nephroblastoma; hepatoblastoma; carcinosarcoma; mesenchymoma, malignant; brenner tumor, malignant; phyllodes tumor, malignant; synovial sarcoma; mesothelioma, malignant; dysgerminoma; embryonal carcinoma; teratoma, malignant; struma ovarii, malignant; choriocarcinoma; mesonephroma, malignant; hemangiosarcoma; hemangioendothelioma, malignant; kaposi's sarcoma; hemangiopericytoma, malignant; lymphangiosarcoma; osteosarcoma; juxtacortical osteosarcoma; chondrosarcoma; chondroblastoma, malignant; mesenchymal chondrosarcoma; giant cell tumor of bone; ewing's sarcoma; odontogenic tumor, malignant; ameloblastic odontosarcoma; ameloblastoma, malignant; ameloblastic fibrosarcoma; pinealoma, malignant; chordoma; glioma, malignant; ependymoma; astrocytoma; protoplasmic astrocytoma; fibrillary astrocytoma; astroblastoma; glioblastoma; oligodendroglioma; oligodendroblastoma; primitive neuroectodermal; cerebellar sarcoma; ganglioneuroblastoma; neuroblastoma; retinoblastoma; olfactory neurogenic tumor; meningioma, malignant; neurofibrosarcoma; neurilemmoma, malignant; granular cell tumor, malignant; malignant lymphoma; Hodgkin's disease; Hodgkin's lymphoma; paragranuloma; malignant lymphoma, small lymphocytic; malignant lymphoma, large cell, diffuse; malignant lymphoma, follicular; mycosis fungoides; other specified non-Hodgkin's lymphomas; malignant histiocytosis; multiple myeloma; mast cell sarcoma; immunoproliferative small intestinal disease; leukemia; lymphoid leukemia; plasma cell leukemia; erythroleukemia; lymphosarcoma cell leukemia; myeloid leukemia; basophilic leukemia; eosinophilic leukemia; monocytic leukemia; mast cell leukemia; megakaryoblastic leukemia; myeloid sarcoma; and hairy cell leukemia. 
     
     
         16 . The method of  claim 14  wherein the cancer is KRAS mutated cancer. 
     
     
         17 . The method of  claim 13  wherein the chemotherapeutic agent is selected from the group consisting of 1. alkylating agents such as thiotepa and cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammall and calicheamicin omegall; dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromophores, aclacinomysins, actinomycin, authrarnycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxy doxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK polysaccharide complex); razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonic acid; triaziquone; 2,2′,2″-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide; thiotepa; taxoids, e.g., paclitaxel and doxetaxel; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum coordination complexes such as cisplatin, oxaliplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-1 1); topoisomerase inhibitor RFS 2000; difluoromethylomithine (DMFO); retinoids such as retinoic acid; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above. 
     
     
         18 . A kit-of-parts comprising at least one AcCoA depleting agent and at least one chemotherapeutic agent for use in the treatment of cancer. 
     
     
         19 . A method for screening a plurality of test substances useful for inducing autophagy in a cell comprising the steps of (a) testing each of the test substances for its ability to deplete AcCoA in the cell and b) positively selecting the test substances capable of depleting AcCoA in the cell. 
     
     
         20 . The method of  claim 19  which further comprises the steps of (a) testing each of the test substances for its ability to inhibit the activity or expression of a autophagy-related gene product selected from the group consisting of mitochondrial pyruvate carrier complex, mitochondrial carnitine palmitoytransferase-1, mitochondrial citrate carrier (CiC), ATP-citratre lyase (ACLY), EP300 acetyltransferase, acyl-CoA synthetase short-chain family member 2 (ACCS2) and b) positively selecting the test substances capable of inhibiting the autophagy-related gene product.