# Patent

## Title
Compositions and methods for treating cancer with aberrant lipogenic signaling

## Abstract

The technology described herein relates to pinacolyl boronate substituted stilbenes for the treatment of cancers, e.g. cancers expressing abnormally high levels of SREBP1. Exemplary pinacolyl boronate stilbenes include the following:

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a 35 U.S.C. §371 National Phase Entry Application of International Application No. PCT/US2013/044887 filed Jun. 10, 2013, which designates the U.S., and which claims benefit under 35 U.S.C. §119(e) of U.S. Provisional Application No. 61/663,875 filed Jun. 25, 2012, the contents of which are incorporated herein by reference in their entirety.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jun. 7, 2013, is named 003252-071731-PCT_SL.txt and is 104,058 bytes in size.
TECHNOLOGICAL FIELD
Embodiments of the technology described herein relate to treatments for cancer.
BACKGROUND
A hallmark of rapidly proliferating tumor cells is increased lipogenesis, i.e. increased production of lipids. Although most normal cells acquire the bulk of their fatty acids from circulation, tumor cells synthesize more than 90% of their own required lipids. The perturbed lipogenesis regulation of cancer cells thus offers targets for the development of new cancer therapies.
The regulation of lipogenesis in relation to cancer is also of importance due to the link between obesity and cancer. For example, epidemiological studies have identified obesity as the most common risk factor for endometrial cancer. Obese women have a 2-4 times greater risk of developing endometrial cancer compared to women of normal weight. As the number of people affected by obesity is expectedly growing, particularly in developing countries, endometrial cancer will continue to be a serious public health problem.
SUMMARY
Therapies that can target the aberrant lipogenesis of tumor cells and/or cells predisposed to become tumor cells will be of use in treating and preventing, e.g., the growing concern of endometrial cancer. Embodiments of the technology described herein are based on the inventors' discovery that pinacolyl boronate substituted stilbenes inhibit sterol regulatory binding protein 1 (SREBP1) and can be used to treat cancers expressing abnormally high levels of SREBP1.
Accordingly, in one aspect, provided herein are compounds which inhibit SREBP1. In some embodiments, the compounds can be selected from the group consisting of:













In some embodiments, the compounds can be selected from the group consisting of:













In some embodiments, the compounds can be selected from the group consisting of:













In some embodiments, the compounds can be selected from the group consisting of:













In one aspect, the technology described herein relates to a method of treating cancer in a subject, the method comprising administering to the subject an inhibitor of sterol regulatory binding protein 1 (SREBP1) as described herein. In some embodiments, the method can further comprise a first step of selecting a subject having cancer cells which express abnormal levels of sterol regulatory binding protein 1 (SREBP1). In some embodiments, the cells which express abnormal levels of sterol regulatory binding protein 1 (SREBP1) can be cells which have abnormal levels of SREBP1 polypeptide.
In some embodiments, the method can further comprise a first step of selecting a subject having cancer cells which express abnormal amounts of Erb2. In some embodiments, the method can further comprise a first step of selecting a subject having cancer cells which express abnormal amounts of at least one gene selected from the group consisting of: FASN, SCD1 or ACLY.
In some embodiments, the subject can have an endometrial cancer. In some embodiments, the cancer can be selected from the group consisting of: prostate cancer; breast cancer; colorectal cancer; colorectal carcinoma; hepatocarcinoma; endometrial adenocarcinoma; uterine cancer; leukemia; lung cancer; central nervous system cancer; melanoma; ovarian cancer; renal cancer; and pancreatic cancer.
In one aspect, the technology described herein relates to a pharmaceutical composition comprising an inhibitor of SREBP1 as described herein. In some embodiments, the composition can further comprise a pharmaceutically acceptable carrier.
In one aspect, the technology described herein relates to the use of an inhibitor of sterol regulatory binding protein 1 (SREBP1) to treat cancer. In some embodiments, the cancer can be comprised of cells expressing abnormal levels of sterol regulatory binding protein 1 (SREBP1). In some embodiments, the cells which express abnormal levels of sterol regulatory binding protein 1 (SREBP1) can be cells which have abnormal levels of SREBP1 polypeptide.
In some embodiments, the cancer can be comprised of cells expressing abnormal amounts of Erb2. In some embodiments, the cancer can be comprised of cells expressing abnormal amounts of at least one gene selected from the group consisting of: FASN, SCD1 or ACLY.
In some embodiments, the cancer can be an endometrial cancer. In some embodiments, the cancer can be selected from the group consisting of: prostate cancer; breast cancer; colorectal cancer; colorectal carcinoma; hepatocarcinoma; endometrial adenocarcinoma; uterine cancer; leukemia; lung cancer; central nervous system cancer; melanoma; ovarian cancer; renal cancer; and pancreatic cancer.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A-1B demonstrate SREBP1 expression in endometrial cancer (EC) determined by IHC. FIG. 1A depicts boxplots of IHC staining score for SREBP1 in normal tissue and endometrial cancer. FIG. 1B depicts a graph of quantitative RT-PCR analysis of mRNA abundance of lipogenic genes including SREBP1a, SREBP1c, SREBP2, and SCD1. The relative expression levels of lipogenic gene were calculated as fold change compared to normal where the mRNA abundance was set as 1.
FIGS. 2A-2F demonstrate SREBP1 is required for expression of lipogenic genes, cell proliferation, and cell migration in endometrial cancer cells. (FIG. 2A). Western blot (WB) analysis of lipogenic gene expression in commonly used endometrial cancer cell lines. Actin serves as protein loading control. (FIG. 2B). Quantitative RT-PCR analysis of mRNA abundance of SREBP1a and SREBP1c in endometrial cancer cells. RNA abundance was shown as fold change relative to that in ECC-1 cells. (FIG. 2C). AN3-CA cells were transiently transfected with shRNA targeting human SREBP1 (shSREBP1). The cells stably expressing shSREBP1 were selected by antibiotics. WB showed reduced protein expression of SREBP1. (FIG. 2D). Quantitative RT-PCR analysis of mRNA abundance of SREBP1a and its target genes including FASN and SCD1. (FIG. 2E). AN3-CA cells knockdown of endogenous SREBP1 are partially defective for cell growth. Cellular growth was determined by counting the cells at different time points. (FIG. 2F) Boyden chamber assays were performed to determine the cell migration ability. Transwell assays were performed to determine cell migration. 1×105 cells were seeded in upper chamber. After 6 hrs, the medium in upper chamber was replaced with serum-free medium. The lower chamber contains medium supplemented with 10% FBS which serves as chemo-attractant. 48 hrs post cell seeding, cells that migrate across the pore were counted and plotted.
FIGS. 3A-3E demonstrate pharmacological inhibition by BF175 represses lipid formation and lipogenic gene expression. (FIG. 3A). Drosophila larvae fed with BF175. The fat body was separated and stained with Oil-Red O. Signaling was quantified. (FIG. 3B). AN3-CA cells were treated with increasing doses of BF175. Cells were lysed after 24 hrs and then subjected to Western blot to detect the protein abundance of SREBP1 and its target genes. GDI served as protein loading control. (FIG. 3C). AN3-CA cells were treated with increasing doses of BF175 as indicated. Cells were lysed after 24 hrs and then subjected to qRT-PCR to detect the mRNA expression of SREBP1 and its target genes as indicated. (FIG. 3D, 3E). FASN (FIG. 3D) and Scd (FIG. 3E) promoter-driven luciferase reporter activity was included as surrogate measure of SREBP1 transcriptional activity. HEK 293T cells transfected with reporter plasmid together with a vector encoding nSREBP1 were treated with increasing doses of BF175.
FIGS. 4A-4C demonstrate that cellular proliferation is repressed by BF175 in SREBP1 expressing cells. (FIG. 4A). Endometrial cancer cells were seeded 24 hrs prior to treatment with increasing doses of BF175. 48 hrs post treatment, cells were subjected to MTT assays to determine the cell viability. BF175 significantly represses the proliferation of RL95-2 and AN3-CA cells, where SREBP1 expression is relatively high. (FIG. 4B). 5×105 cells were seeded per well in 6-well plate and treated with increased dose of BF175. The cell number was counted 48 hrs post-treatment. (FIG. 4C). AN3-CA cells were starved with serum-free medium and released by adding 10% serum to the medium in the presence of BrdU. Cells were either treated with BF175 or vehicle control. The BrdU was stained after 6 hrs and BrdU-positive cells were counted.
FIGS. 5A-5B demonstrate that BF175 induces cell death. (FIG. 5A). AC3-CA cells were seeded 24 hrs prior to treatment with increased dose of BF175 for 48 hrs. Cells were subjected to flow cytometry assays to determine the percentage of apoptotic cell death (cells in sub-G1 phase). (FIG. 5B).
FIGS. 6A-6D demonstrate that BF175 targets SREBP1 and inhibits SREBP1-dependent gene transcription. (6A, 6C). Schematic maps of luciferase reporters driven by SREBP1 promoters. (6B, 6D). AN3-CA cells were transiently transfected with SREBP1 promoter reporter plasmids and treated with increasing doses of BF175 for 24 hrs before the luciferase activity was measured.
FIG. 7 depicts a schematic of SREBP1-related pathways in lipogenesis.
FIG. 8 depicts a mean graph of the percent growth of cells treated with BF175 when compared to control cells.



DETAILED DESCRIPTION
Embodiments of the technology described herein are based on the discovery that compounds as described herein can inhibit sterol regulatory binding protein 1 (SREBP1), a gene which is upregulated in certain cancers, e.g. endometrial cancers, and which thereby contributes to the increased level of lipogenesis displayed by those cancers. Accordingly, provided herein are compositions and methods relating to the treatment of cancers by administering SREBP1 inhibitors. In some embodiments, the cancer is an endometrial cancer. In some embodiments, the cancer is comprised of cells which express abnormal levels of SREBP1.
For convenience, certain terms employed herein, in the specification, examples and appended claims are collected here. Unless stated otherwise, or implicit from context, the following terms and phrases include the meanings provided below. Unless explicitly stated otherwise, or apparent from context, the terms and phrases below do not exclude the meaning that the term or phrase has acquired in the art to which it pertains. The definitions are provided to aid in describing particular embodiments, and are not intended to limit the claimed invention, because the scope of the invention is limited only by the claims. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.
The terms “decrease,” “reduce,” “reduced”, “reduction”, “decrease,” and “inhibit” are all used herein generally to mean a decrease by a statistically significant amount relative to a reference. However, for avoidance of doubt, “reduce,” “reduction” or “decrease” or “inhibit” typically means a decrease by at least 10% as compared to a reference and can include, for example, a decrease by at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, up to and including, for example, the complete absence of the given entity or parameter as compared to the reference, or any decrease between 10-99% as compared to the absence of a given treatment.
The terms “increase”, “increased” or “enhance” or “activate” are all used herein to generally mean an increase by a statically significant amount; for the avoidance of doubt, the terms “increased”, “increase” or “enhance” or “activate” typically means an increase of at least 10% as compared to a reference, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or up to and including a 100% increase or any increase between 10-100% as compared to a reference, or at least about a 2-fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference.
The term “biological sample” as used herein denotes a sample taken or isolated from a biological organism, e.g., cancer biopsy sample, blood sample, cell lysate, a homogenate of a tissue sample from a subject, or a fluid sample from a subject. Exemplary biological samples include, but are not limited to, cancer tissue biopsies or blood and/or serum samples. In some embodiments, the sample is from a resection, biopsy, or core needle biopsy. In addition, fine needle aspirate samples can be used. In some embodiments, samples can be either paraffin-embedded or frozen tissue. The term “biological sample” can also include untreated or pretreated (or pre-processed) biological samples. In some embodiments, the biological sample can be an untreated biological sample. As used herein, the phrase “untreated biological sample” refers to a biological sample that has not had any prior sample pre-treatment except for dilution and/or suspension in a solution. Exemplary methods for treating a biological sample include, but are not limited to, centrifugation, filtration, sonication, homogenization, heating, freezing and thawing, and any combinations thereof. The skilled practitioner is aware of methods and processes appropriate for pre-processing of biological samples required for determination of levels of polypeptides or nucleotides as described herein.
The sample can be obtained by removing a sample of cells from a subject, but can also be accomplished by using previously isolated cells (e.g. isolated at a prior timepoint and isolated by the same or another person). In addition, the biological sample can be freshly collected or a previously collected sample. In some embodiments, a biological sample is a biological fluid. Examples of biological fluids include, but are not limited to, saliva, blood, sputum, an aspirate, and any combinations thereof. In some embodiments, the biological sample is a frozen biological sample, e.g., a frozen tissue or fluid sample such as blood. The frozen sample can be thawed before employing methods, assays and systems of the invention. After thawing, a frozen sample can be centrifuged before being subjected to methods, assays and systems of the invention. In some embodiments, the biological sample can be treated with at least one chemical reagent, such as a protease inhibitor. Chemical and/or biological reagents can be employed to protect and/or maintain the stability of the sample, including biomolecules (e.g., nucleic acid and protein) therein, during processing. One exemplary reagent is a protease inhibitor, which is generally used to protect or maintain the stability of protein during processing. In addition, or alternatively, chemical and/or biological reagents can be employed to release nucleic acid or protein from the sample. A biological sample can contain cells, but the term can also refer to non-cellular biological material, such as non-cellular fractions that can be used to measure gene expression levels.
As used herein, a “subject” means a human or animal. Usually the animal is a vertebrate such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon. Patient or subject includes any subset of the foregoing, e.g., all of the above, but excluding one or more groups or species such as humans, primates or rodents. In certain embodiments, the subject is a mammal, e.g., a primate, e.g., a human. The terms, “patient”, “individual” and “subject” are used interchangeably herein.
Preferably, the subject is a mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but is not limited to these examples. Mammals other than humans can be advantageously used, for example, as subjects that represent animal models of, for example, cancer. In addition, the methods described herein can be used to treat domesticated animals and/or pets. A subject can be male or female.
A subject can be one who has been previously diagnosed with or identified as suffering from or having a condition in need of treatment (e.g. cancer) or one or more complications related to such a condition, and optionally, have already undergone treatment for cancer or the one or more complications related to cancer. Alternatively, a subject can also be one who has not been previously diagnosed as having cancer or one or more complications related to cancer. For example, a subject can be one who exhibits one or more risk factors for cancer or one or more complications related to cancer or a subject who does not exhibit risk factors. A “subject in need” of treatment for a particular condition can be a subject having that condition, diagnosed as having that condition, or being at risk of developing that condition.
As used herein, the term “proteins” and “polypeptides” are used interchangeably herein to designate a series of amino acid residues connected to each other by peptide bonds between the alpha-amino and carboxy groups of adjacent residues. The terms “protein”, and “polypeptide” refer to a polymer of amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, etc.) and amino acid analogs, regardless of their size or function. “Protein” and “polypeptide” are often used in reference to relatively large polypeptides, whereas the term “peptide” is often used in reference to small polypeptides, but usage of these terms in the art overlaps. The terms “protein” and “polypeptide” are used interchangeably herein when referring to a gene product and fragments thereof. Thus, exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs, orthologs, paralogs, fragments and other equivalents, variants, fragments, and analogs of the foregoing.
As used herein, the term “nucleic acid” or “nucleic acid sequence” refers to any molecule, preferably a polymeric molecule, incorporating units of ribonucleic acid, deoxyribonucleic acid or an analog thereof. The nucleic acid can be either single-stranded or double-stranded. A single-stranded nucleic acid can be one strand nucleic acid of a denatured double-stranded DNA. Alternatively, it can be a single-stranded nucleic acid not derived from any double-stranded DNA. In one aspect, the template nucleic acid is DNA. In another aspect, the template is RNA. Suitable nucleic acid molecules are DNA, including genomic DNA or cDNA. Other suitable nucleic acid molecules are RNA, including mRNA.
As used herein, the terms “treat,” “treatment,” “treating,” or “amelioration” refer to therapeutic treatments, wherein the object is to reverse, alleviate, ameliorate, inhibit, slow down or stop the progression or severity of a condition associated with a disease or disorder, e.g. cancer. The term “treating” includes reducing or alleviating at least one adverse effect or symptom of a condition, disease or disorder associated with a cancer. Treatment is generally “effective” if one or more symptoms or clinical markers are reduced. Alternatively, treatment is “effective” if the progression of a disease is reduced or halted. That is, “treatment” includes not just the improvement of symptoms or markers, but also a cessation of, or at least slowing of, progress or worsening of symptoms compared to what would be expected in the absence of treatment. Beneficial or desired clinical results include, but are not limited to, alleviation of one or more symptom(s), diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, remission (whether partial or total), and/or decreased mortality, whether detectable or undetectable. The term “treatment” of a disease also includes providing relief from the symptoms or side-effects of the disease (including palliative treatment).
As used herein, the terms “alkyl,” “alkenyl” and the prefix “alk-” are inclusive of both straight chain and branched chain groups and of cyclic groups, i.e. cycloalkyl and cycloalkenyl. Unless otherwise specified, these groups contain from 1 to 20 carbon atoms, with alkenyl groups containing from 2 to 20 carbon atoms. Preferred groups have a total of up to 10 carbon atoms. Cyclic groups can be monocyclic or polycyclic and preferably have from 3 to 10 ring carbon atoms. Exemplary cyclic groups include cyclopropyl, cyclopentyl, cyclohexyl, cyclopropylmethyl, adamantly, norbornane, and norbornene. This is also true of groups that include the prefix “alkyl-,” such as alkylcarboxylic acid, alkyl alcohol, alkylcarboxylate, alkylaryl, and the like. Examples of suitable alkylcarboxylic acid groups are methylcarboxylic acid, ethylcarboxylic acid, and the like. Examples of suitable alkylacohols are methylalcohol, ethylalcohol, isopropylalcohol, 2-methylpropan-1-ol, and the like. Examples of suitable alkylcarboxylates are methylcarboxylate, ethylcarboxylate, and the like. Examples of suitable alkyl aryl groups are benzyl, phenylpropyl, and the like.
These may be straight chain or branched, saturated or unsaturated aliphatic hydrocarbon, which may be optionally inserted with N, O, or S. Representative saturated straight chain alkyls include methyl, ethyl, n-propyl, n-butyl, n-pentyl, n-hexyl, and the like; while saturated branched alkyls include isopropyl, sec-butyl, isobutyl, tert-butyl, isopentyl, and the like.
As used herein, the term “alkenyl” means an alkyl, as defined above, containing at least one double bond between adjacent carbon atoms. Alkenyls include both cis and trans isomers. Representative straight chain and branched alkenyls include ethylenyl, propylenyl, 1-butenyl, 2-butenyl, isobutylenyl, 1-pentenyl, 2-pentenyl, 3-methyl-1-butenyl, 2-methyl-2-butenyl, 2,3-dimethyl-2-butenyl, and the like.
As used herein, the term “alkynyl” means any alkyl or alkenyl, as defined above, which additionally contains at least one triple bond between adjacent carbons. Representative straight chain and branched alkynyls include acetylenyl, propynyl, 1-butynyl, 2-butynyl, 1-pentynyl, 2-pentynyl, 3-methyl-1 butynyl, and the like.
The term “aryl” as used herein includes carbocyclic aromatic rings or ring systems. As used herein, the term “aryl” refers to an aromatic 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system. Examples of aryl groups include phenyl, naphthyl, biphenyl, fluorenyl and indenyl.
The term “heteroaryl” includes aromatic rings or ring systems that contain at least one ring hetero atom (e.g., O, S, N). As used herein, the term “heteroaryl” refers to an aromatic 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system having 1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, said heteroatoms selected from O, N, or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N, O, or S if monocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2, 3, or 4 atoms of each ring may be substituted by a substituent. Examples of heteroaryl groups include pyridyl, furyl or furanyl, imidazolyl, thiazolyl, benzimidazolyl, pyrimidinyl, thiophenyl or thienyl, quinolinyl, indolyl, oxazolyl, isoquinolinyl, isoindolyl, thiazolyl, pyrrolyl, tetrazolyl, pyrazolyl, oxazolyl, thiazolyl, benzofuranyl, benzothiophenyl, carbazolyl, benzoxazolyl, benzimidazolyl, quinoxalinyl, benzothiazolyl, naphthyridinyl, isoxazolyl, isothiazolyl, purinyl, quinazolinyl, and the like.
The aryl, and heteroaryl groups can be unsubstituted or substituted by one or more substituents independently selected from the group consisting of alkyl, alkoxy, methylenedioxy, ethylenedioxy, alkylthio, haloalkyl, haoalkoxy, haloalkylthio, halogen, nitro, hydroxy, mercapto, cyano, carboxy, formyl, aryl, aryloxy, arylthio, arylalkoxy, arylalkylthio, heteroaryl, heteroaryloxy, heteroarylalkoxy, heteroarylalkylthio, amino, alkylamino, dialkylamino, heterocyclyl, heterocycloalkyl, alkylcarbonyl, alkenylcarbonyl, alkoxycarbonyl, haloalkylcarbonyl, haloalkoxycarbonyl, alkylthiocarbonyl, arylcarbonyl, heteroarylcarbonyl, aryloxycarbonyl, heteroaryloxycarbonyl, arylthiocarbonyl, heteroarylthiocarbonyl, alkanoyloxy, alkanoylthio, alkanoylamino, arylcarbonyloxy, arylcarbonythio, alkylaminosulfonyl, alkylsulfonyl, arylsulfonyl, heteroarylsulfonyl, aryldiazinyl, alkylsulfonylamino, arylsulfonylamino, arylalkylsulfonylamino, alkylcarbonylamino, alkenylcarbonylamino, arylcarbonylamino, arylalkylcarbonylamino, arylcarbonylaminoalkyl, heteroarylcarbonylamino, heteroarylalkycarbonylamino, alkylsulfonylamino, alkenylsulfonylamino, arylsulfonylamino, arylalkylsulfonylamino, heteroarylsulfonylamino, heteroarylalkylsulfonylamino, alkylaminocarbonylamino, alkenylaminocarbonylamino, arylaminocarbonylamino, arylalkylaminocarbonylamino, heteroarylaminocarbonylamino, heteroarylalkylaminocarbonylamino and, in the case of heterocyclyl, oxo. If other groups are described as being “substituted” or “optionally substituted,” then those groups can also be substituted by one or more of the above enumerated substituents.
The term “arylalkyl,” as used herein, refers to a group comprising an aryl group attached to the parent molecular moiety through an alkyl group.
As used herein, the term “cyclyl” refers to a nonaromatic 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system, which can be saturated or partially unsaturated. Representative saturated cyclyl groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, cyclooctyl, and the like; while unsaturated cyclyl groups include cyclopentenyl and cyclohexenyl, and the like.
The terms “heterocycle”, “heterocyclyl” and “heterocyclic group” are recognized in the art and refer to nonaromatic 3- to about 14-membered ring structures, such as 3- to about 7-membered rings, whose ring structures include one to four heteroatoms, 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system having 1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, said heteroatoms selected from O, N, or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N, O, or S if monocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2 or 3 atoms of each ring may be substituted by a substituent. The heterocycle may include portions which are saturated or unsaturated. In some embodiments, the heterocycle may include two or more rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls) in which two or more carbons are common to two adjoining rings, e.g., the rings are “fused rings.” In some embodiments, the heterocycle may be a “bridged” ring, where rings are joined through non-adjacent atoms, e.g., three or more atoms are common to both rings. Each of the rings of the heterocycle may be optionally substituted. Examples of heterocyclyl groups include, for example, thiophene, thianthrene, furan, pyran, isobenzofuran, chromene, xanthene, phenoxathin, pyrrole, imidazole, pyrazole, isothiazole, isoxazole, pyridine, pyrazine, pyrimidine, pyridazine, indolizine, isoindole, indole, indazole, purine, quinolizine, isoquinoline, quinoline, phthalazine, naphthyridine, quinoxaline, quinazoline, cinnoline, pteridine, carbazole, carboline, phenanthridine, acridine, pyrimidine, phenanthroline, phenazine, phenarsazine, phenothiazine, furazan, dioxane, morpholine, tetrahydrofurane, phenoxazine, pyrrolidine, oxolane, thiolane, oxazole, piperidine, piperazine, morpholine, lactones, lactams such as azetidinones and pyrrolidinones, sultams, sultones, and the like. The heterocyclic ring may be substituted at one or more positions with substituents including, for example, halogen, aryl, heteroaryl, alkyl, heteroalkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, CF3, CN, or the like.
As used herein, the term “halogen” refers to iodine, bromine, chlorine, and fluorine.
As used herein, the terms “optionally substituted alkyl,” “optionally substituted cyclyl,” “optionally substituted heterocyclyl,” “optionally substituted aryl,” and “optionally substituted heteroaryl” means that, when substituted, at least one hydrogen atom in said alkyl, cyclyl, heterocylcyl, aryl, or heteroaryl is replaced with a substituent. In the case of an oxo substituent (═O) two hydrogen atoms are replaced. In this regard, substituents include oxo, halogen, alkyl, cyclyl, heterocyclyl, aryl, heteroaryl, —CN, —ORx, —NRxRy, —NRxC(═O)Ry, —NRxSO2Ry, —C(═O)Rx, —C(═O)ORx, —C(═O)NRxRy, —SOnRx and —SOnNRxRy, wherein n is 0, 1 or 2, Rx and Ry are the same or different and independently hydrogen, alkyl, cyclyl, heterocyclyl, aryl or heterocycle, and each of said alkyl, cyclyl, heterocyclyl, aryl and heterocycle substituents may be further substituted with one or more of oxo, halogen, —OH, —CN, alkyl, —ORx, heterocycle, —NRxRy, —NRxC(═O)Ry, —NRxSO2Ry, —C(═O)Rx, —C(═O)ORx, —C(═O)NRxRy, —SOnRx and —SOnNRxRy.
The term “carbonyl,” as used herein, refers to “C(═O)”.
The terms “acyl,” “carboxyl group,” or “carbonyl group” are recognized in the art and can include such moieties as can be represented by the general formula:




wherein W is ORw, N(Rw)2, SRw, or Rw, Rw being hydrogen, alkyl, heteroalkyl, alkenyl, heteroalkenyl, alkynyl, heteroalkynyl, aryl, heteroaryl, heterocycle, substituted derivatives thereof, or a salt thereof. For example, when W is O-alkyl, the formula represents an “ester,” and when W is OH, the formula represents a “carboxylic acid.” When W is alkyl, the formula represents a “ketone” group, and when W is hydrogen, the formula represents an “aldehyde” group. Those of ordinary skill in the art will understand the use of such terms.

As used herein, the term “substituted” is contemplated to include all permissible substituents of organic compounds, “permissible” being in the context of the chemical rules of valence known to those of ordinary skill in the art. In some cases, “substituted” may generally refer to replacement of a hydrogen with a substituent as described herein. However, “substituted,” as used herein, does not encompass replacement and/or alteration of a key functional group by which a molecule is identified, e.g., such that the “substituted” functional group becomes, through substitution, a different functional group. For example, a “substituted phenyl” must still comprise the phenyl moiety and cannot be modified by substitution, in this definition, to become, e.g., a heteroaryl group such as pyridine. In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and nonaromatic, fused, and bridged substituents of organic compounds. Illustrative substituents include, for example, those described herein. The permissible substituents can be one or more and the same or different for appropriate organic compounds. For purposes of this invention, the heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valencies of the heteroatoms. This invention is not intended to be limited in any manner by the permissible substituents of organic compounds.
As used herein the term “comprising” or “comprises” is used in reference to compositions, methods, and respective component(s) thereof, that are essential to the method or composition, yet open to the inclusion of unspecified elements, whether essential or not.
The term “consisting of” refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.
As used herein the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment.
As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Thus for example, references to “the method” includes one or more methods, and/or steps of the type described herein and/or which will become apparent to those persons skilled in the art upon reading this disclosure and so forth. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below. The abbreviation, “e.g.” is derived from the Latin exempli gratia, and is used herein to indicate a non-limiting example. Thus, the abbreviation “e.g.” is synonymous with the term “for example.”
Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used in connection with percentages can mean±1%.
The term “statistically significant” or “significantly” refers to statistical significance and generally means a two standard deviation (2SD) difference, above or below a reference value. Additional definitions are provided in the text of individual sections below.
Definitions of common terms in cell biology and molecular biology can be found in “The Merck Manual of Diagnosis and Therapy”, 19th Edition, published by Merck Research Laboratories, 2006 (ISBN 0-911910-19-0); Robert S. Porter et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); The ELISA guidebook (Methods in molecular biology 149) by Crowther J. R. (2000); Immunology by Werner Luttmann, published by Elsevier, 2006. Definitions of common terms in molecular biology can also be found in Benjamin Lewin, Genes X, published by Jones & Bartlett Publishing, 2009 (ISBN-10: 0763766321); Kendrew et al. (eds.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8) and Current Protocols in Protein Sciences 2009, Wiley Intersciences, Coligan et al., eds.
Unless otherwise stated, the present invention was performed using standard procedures, as described, for example in Sambrook et al., Molecular Cloning: A Laboratory Manual (3 ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2001) and Davis et al., Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (1995) which are both incorporated by reference herein in their entireties.
Other terms are defined herein within the description of the various aspects of the invention.
The methods and compositions described herein relate to the treatment of cancer by inhibiting the activity of sterol regulatory binding protein 1 (SREBP1). As used herein, “sterol regulatory binding protein 1” or “SREBP1” (e.g. NCBI Gene ID: 6720) refers to a transcription factor involved in the regulation of lipid homeostasis which is synethized as an inactive precursor bound to the endoplasmic reticulum and upon a decrease in cellular sterol levels, undergoes a sequential two-step cleavage process to release the NH2-terminal active domain in the nucleus (designated nSREBPs), and then transactivating SREBP target genes to maintain cholesterol and FAs homeostasis. Targets of SREBP1 activity include enzymes required for cholesterol and fatty acids (FAs) synthesis, e.g. FASN and SCD. Two SREBP1 human isoforms exist; SREBP1a (protein: SEQ ID NO: 1; mRNA: SEQ ID NO: 2) and SREBP1c (protein: SEQ ID NO: 3; mRNA: SEQ ID NO: 4). In some embodiments, SREBP1 can refer to SREBP1a and SREBP1c. In some embodiments, SREBP1 can be SREBP1a. In some embodiments, SREBP1 can be SREBP1c. SREBP1 can be expressed at abnormally high levels in certain cancers and is believed to have a correlation with, e.g. malignant transformation, cancer progression, proliferation, and metastasis for several cancer types, particularly hormone-responsive tissues including breast and prostate cancers.
Given the broad range of tumor types which display growth inhibition in response to inhibitors of SREBP1, (e.g. leukemias, CNS cancers, non-small cell lung cancers, prostate cancers, melanomas, colon cancers, ovarian cancers, renal cancers, and breast cancers, as described in Example 3), it is contemplated herein that the inhibitors and methods described herein can treat any cancer comprising cells with increased or high levels of SREBP1 expression and/or activity.
In some embodiments, the technology described herein relates to methods of treating cancer by inhibiting the lipogenesis characteristic of cancer by inhibiting SREBP1. In some embodiments, SREBP1 can be inhibited by administering to a subject an inhibitor of SREBP1. As used herein, the term “inhibitor of SREBP1” or “SREBP1 inhibitor” refers to an agent which reduces the expression and/or activity of SREBP1 by at least 10%, e.g. by 10% or more, 20% or more, 30% or more, 50% or more, 75% or more, 90% or more, 95% or more, 98% or more, or 99% or more. The term “agent” refers generally to any entity which is normally not present or not present at the levels being administered to a cell, tissue or subject. An agent can be selected from a group comprising: polynucleotides; polypeptides; small molecules; antibodies; or functional fragments thereof. In some embodiments, the SREBP1 inhibitor can be a pinacolyl boronate-substituted stilbene.
In some embodiments, the inhibitor of SREBP1 can be a compound having the formula of I, II, III or IV, wherein formulae I, II, III, and IV are:




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;
R3 is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R4 and R5 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —CN; halogen; or hydroxyl;
R6 is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl;
R7 are independently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
n is an integer 0-4 inclusive; and
m is an integer 0-5 inclusive;




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;
R3, R4, R5, R6, R7 and R8 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; B(O)R1R2; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R9 is independently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo; and wherein R9 and R5 or R6 can be taken together to form a substituted or unsubstituted five or six membered ring; and
n is an integer 0 to 5, inclusive;




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring; and
R3, R4, R5, R6, R7, R8, R9, R10 and R11 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; B(O)R1R2; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;
R3 halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R4 is optionally substituted aryl, or optionally substituted heteroaryl; and
n is an integer 0-4 inclusive.
In some embodiments, provided herein are SREBP1 inhibitors of formula I:




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;
R3 is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R4 and R5 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —CN; halogen; or hydroxyl;
R6 is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl;
R7 are independently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
n is an integer 0-4 inclusive; and
m is an integer 0-5 inclusive.
In some embodiments R1 and R2 are the different. In some embodiments, R1 and R2 are the same. In some embodiments, at least R1 or R2 is C1-4 alkyl. In some embodiments, both R1 and R2 are methyl, ethyl, propyl, or butyl. In some embodiments R1 and R2 are taken together to form an unsubstituted five membered ring. In some embodiments R1 and R2 are taken together to form a substituted five membered ring. In some embodiments R1 and R2 are taken together to form an unsubstituted six membered ring. In some embodiments R1 and R2 are taken together to form a substituted six membered ring. In some embodiments, R1 and R2 are taken together to form




In some embodiments, R3 and R6 are independently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
In some embodiments, n is 0. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4.
In some embodiments, all R3 are different. In some embodiments, all R3 are the same. In some embodiments, at least two R3 are the same. In some embodiments, at least three R3 are the same. In some embodiments, at least one R3 is C1-4 alkyl. In some embodiments, at least one R3 is C2-4 alkenyl. In some embodiments, at least one R3 is C2-4 alkynyl. In some embodiments, at least one R3 is C1-4 alkoxy. In some embodiments, at least one R3 is CN. In some embodiments, at least one R3 is halogen. In some embodiments, at least one R3 is F, Cl, Br, or I. In some embodiments, at least one R3 is CF3. In some embodiments, at least one R3 is NO2. In some embodiments, at least one R3 is substituted aryl. In some embodiments, at least one R3 is unsubstituted aryl. In some embodiments, at least one R3 is substituted phenyl. In some embodiments, at least one R3 is unsubstituted phenyl.
In some embodiments, R4 and R5 are independently hydrogen, —CN, halogen, hydroxyl, alkoxy, aryloxy, alkylthioxy, arylthioxy, amino, alkylamino, dialkylamino, heteroaryloxy, heteroarylthioxy, or alkylhalo. In some embodiments, R4 and R5 are the same. In some embodiments, R4 and R5 are different. In some embodiments, at least R4 is hydrogen. In some embodiments, at least R5 is hydrogen. In some embodiments, both R4 and R5 are hydrogen. In some embodiments, R4 is C1-4 alkyl. In some embodiments, R4 is C2-4 alkenyl. In some embodiments, R4 is C2-4 alkynyl. In some embodiments, R4 is CN. In some embodiments, R4 is substituted aryl. In some embodiments, R4 is unsubstituted aryl. In some embodiments, R4 is substituted phenyl. In some embodiments, R4 is unsubstituted phenyl. In some embodiments, R5 is C1-4 alkyl. In some embodiments, R5 is C2-4 alkenyl. In some embodiments, R5 is C2-4 alkynyl. In some embodiments, R5 is CN. In some embodiments, R5 is substituted aryl. In some embodiments, R5 is unsubstituted aryl. In some embodiments, R5 is substituted phenyl. In some embodiments, R5 is unsubstituted phenyl. In some embodiments, R4 is CN and R5 is phenyl.
In some embodiments, R6 is C1-4 alkyl. In some embodiments, R6 is methyl, ethyl, n-propyl, propyl, n-butyl, i-butyl or t-butyl. In some embodiments, R6 is C2-4 alkenyl. In some embodiments, R6 is C2-4 alkynyl. In some embodiments, R6 is substituted or unsubstituted aryl. In some embodiments, R6 is




In some embodiments, m is 0. In some embodiments, m is 1. In some embodiments, m is 2. In some embodiments, m is 3. In some embodiments, m is 4. In some embodiments, m is 5.
In some embodiments, all R7 are different. In some embodiments, all R7 are the same. In some embodiments, at least two R7 are the same. In some embodiments, at least three R7 are the same. In some embodiments, at least one R7 is C1-4 alkyl. In some embodiments, at least one R7 is C2-4 alkenyl. In some embodiments, at least one R7 is C2-4 alkynyl. In some embodiments, at least one R7 is C1-4 alkoxy. In some embodiments, at least one R7 is CN. In some embodiments, at least one R7 is halogen. In some embodiments, at least one R7 is F, Cl, Br, or I. In some embodiments, at least one R7 is CF3. In some embodiments, at least one R7 is NO2. In some embodiments, at least two R7 are NO2. In some embodiments, at least three R7 are NO2. In some embodiments, at least one R7 is substituted aryl. In some embodiments, at least one R7 is unsubstituted aryl. In some embodiments, at least one R7 is substituted phenyl. In some embodiments, at least one R7 is unsubstituted phenyl. In some embodiments, R7 is OH-phenyl.
In some embodiments, formula I can be




In some embodiments, provided herein are SREBP1 inhibitors of formula II:




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;
R3, R4, R5, R6, R7 and R8 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; B(O)R1R2; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R9 is independently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo; and wherein R9 and R5 or R6 can be taken together to form a substituted or unsubstituted five or six membered ring; and
n is an integer 0 to 5, inclusive.
In some embodiments R1 and R2 are the different. In some embodiments, R1 and R2 are the same. In some embodiments, at least R1 or R2 is C1-4 alkyl. In some embodiments, both R1 and R2 are methyl, ethyl, propyl, or butyl. In some embodiments R1 and R2 are taken together to form an unsubstituted five membered ring. In some embodiments R1 and R2 are taken together to form a substituted five membered ring. In some embodiments R1 and R2 are taken together to form an unsubstituted six membered ring. In some embodiments R1 and R2 are taken together to form a substituted six membered ring. In some embodiments, R1 and R2 are taken together to form




In some embodiments, R1 and R2 are taken together to form





In some embodiments, each one of R3, R4, R5, R6, R7 and R8 are different. In some embodiments, all of R3, R4, R5, R6, R7 and R8 are the same. In some embodiments, at least two of R3, R4, R5, R6, R7 and R8 are the same. In some embodiments, at least three of R3, R4, R5, R6, R7 and R8 are the same. In some embodiments, at least four of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are the same. In some embodiments, at least five of R3, R4, R5, R6, R7 and R8 are the same. In some embodiments, at least one of R3, R4, R5, R6, R7 and R8 is hydrogen. In some embodiments, each one of R3, R4, R5, R6, R7 and R8 is hydrogen. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is C1-4 alkyl. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is methyl, ethyl, n-propyl, i-propyl, n-butyl, i-butyl, or t-butyl. In some embodiments, at least one of R3, R4, R5, R6, R7 and R8 is C2-4 alkenyl. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is C2-4 alkynyl. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is C1-4 alkoxy. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is CN. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is halogen. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is F, Cl, Br, or I. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is CF3. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is NO2. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is substituted aryl. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is unsubstituted aryl. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is substituted phenyl. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 unsubstituted phenyl. In some embodiments, at least one R3, R4, R5, R6, R7 and R8 is B(O)R1R2.
In some embodiments, n is 0. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4.
In some embodiments, all R9 are different. In some embodiments, all R9 are the same. In some embodiments, at least two R9 are the same. In some embodiments, at least three R9 are the same. In some embodiments, at least one R9 is C1-4 alkyl. In some embodiments, at least one R9 is methyl, ethyl, n-propyl, i-propyl, n-butyl, i-butyl, or t-butyl. In some embodiments, at least one R9 is C2-4 alkenyl. In some embodiments, at least one R9 is C2-4 alkynyl. In some embodiments, at least one R9 is C1-6 alkoxy. In some embodiments, at least one R9 is C1-6 alcohol. In some embodiments, at least one R9 is C1-6 diol. In some embodiments, at least one R9 is O—C1-6 alcohol. In some embodiments, at least one R9 is O—C1-6 diol. In some embodiments, at least one R9 is a substituted or unsubstituted cyclic aliphatic. In some embodiments, at least one R9 is a monocyclic. In some embodiments, at least one R9 is a bicyclic. In some embodiments, at least one R9 is a tricyclic. In some embodiments, at least on R9 is a six membered ring system. In some embodiments, at least one R9 is a seven membered ring system. In some embodiments, at least on R9 is an eight membered ring system. In some embodiments, at least on R9 is a nine membered ring system. In some embodiments, at least on R9 is a ten membered ring system. In some embodiments, at least on R9 is an eleven membered ring system. In some embodiments, at least on R9 is a twelve membered ring system. In some embodiments, at least one R9 is S—C1-12 alkyl. In some embodiments, at least one R9 is S—C1-12 alkyl, wherein C1-12 alkyl is a monocyclic, bicyclic, or tricyclic ring system. In some embodiments, at least one R9 is CN. In some embodiments, at least one R9 is halogen. In some embodiments, at least one R9 is F, Cl, Br, or I. In some embodiments, at least one R9 is CF3. In some embodiments, at least one R9 is NO2. In some embodiments, at least one R9 is substituted aryl. In some embodiments, at least one R9 is unsubstituted aryl. In some embodiments, at least one R9 is substituted phenyl. In some embodiments, at least one R9 is unsubstituted phenyl.
In some embodiments, R9 is at the ortho position. In some embodiments, R9 is at the meta position. In some embodiments, R9 is at the para position. In some embodiments, one R9 is at the meta position and one R9 is at the para position. In some embodiments, one R9 is at the ortho position and one R9 is at the para position. In some embodiments, one R9 is at the ortho position, one R9 is at the meta position, and one R9 is at the para position.
In some embodiments, formula II can be







In some embodiments, provided herein are SREBP1 inhibitors of formula III:




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring; and
R3, R4, R5, R6, R7, R8, R9, R10 and R11 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; B(O)R1R2; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo.
In some embodiments R1 and R2 are the different. In some embodiments, R1 and R2 are the same. In some embodiments, at least R1 or R2 is C1-4 alkyl. In some embodiments, both R1 and R2 are methyl, ethyl, propyl, or butyl. In some embodiments R1 and R2 are taken together to form an unsubstituted five membered ring. In some embodiments R1 and R2 are taken together to form a substituted five membered ring. In some embodiments R1 and R2 are taken together to form an unsubstituted six membered ring. In some embodiments R1 and R2 are taken together to form a substituted six membered ring. In some embodiments, R1 and R2 are taken together to form




In some embodiments, each one of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are different. In some embodiments, all of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are the same. In some embodiments, at least two of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are the same. In some embodiments, at least three of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are the same. In some embodiments, at least four of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are the same. In some embodiments, at least five of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are the same. In some embodiments, at least six of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are the same. In some embodiments, at least seven of R3, R4, R5, R6, R7, R8, R9, R10 and R11 are the same. In some embodiments, at least one of R3, R4, R5, R6, R7, R8, R9, R10 and R11 is hydrogen. In some embodiments, each one of R3, R4, R5, R6, R7, R8, R9, R10 and R11 is hydrogen. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is Cm alkyl. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is methyl, ethyl, n-propyl, i-propyl, n-butyl, i-butyl, or t-butyl. In some embodiments, at least one of R3, R4, R5, R6, R7, R8, R9, R10 and R11 is C2-4 alkenyl. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is C2-4 alkynyl. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is Cm alkoxy. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is CN. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is halogen. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is F, Cl, Br, or I. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is CF3. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is NO2. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is substituted aryl. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is unsubstituted aryl. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is substituted phenyl. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 unsubstituted phenyl. In some embodiments, at least one R3, R4, R5, R6, R7, R8, R9, R10 and R11 is B(O)R1R2.
In some embodiments, formula III can be




In some embodiments, provided herein are SREBP1 inhibitors of formula IV:




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;

R3 halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R4 is optionally substituted aryl, or optionally substituted heteroaryl; and
n is an integer 0-4 inclusive.
In some embodiments R1 and R2 are the different. In some embodiments, R1 and R2 are the same. In some embodiments, at least R1 or R2 is C1-4 alkyl. In some embodiments, both R1 and R2 are methyl, ethyl, propyl, or butyl. In some embodiments R1 and R2 are taken together to form an unsubstituted five membered ring. In some embodiments R1 and R2 are taken together to form a substituted five membered ring. In some embodiments R1 and R2 are taken together to form an unsubstituted six membered ring. In some embodiments R1 and R2 are taken together to form a substituted six membered ring. In some embodiments, R1 and R2 are taken together to form




In some embodiments, R3 is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
In some embodiments, n is 0. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4.
In some embodiments, all R3 are different. In some embodiments, all R3 are the same. In some embodiments, at least two R3 are the same. In some embodiments, at least three R3 are the same. In some embodiments, at least one R3 is C1-4 alkyl. In some embodiments, at least one R3 is C2-4 alkenyl. In some embodiments, at least one R3 is C2-4 alkynyl. In some embodiments, at least one R3 is C1-4 alkoxy. In some embodiments, at least one R3 is CN. In some embodiments, at least one R3 is halogen. In some embodiments, at least one R3 is F, Cl, Br, or I. In some embodiments, at least one R3 is CF3. In some embodiments, at least one R3 is NO2. In some embodiments, at least one R3 is substituted aryl. In some embodiments, at least one R3 is unsubstituted aryl. In some embodiments, at least one R3 is substituted phenyl. In some embodiments, at least one R3 is unsubstituted phenyl.
In some embodiments, R4 is unsubstituted aryl. In some embodiments, R2 is substituted aryl. In some embodiments, R4 is substituted or unsubstituted monocyclic aryl. In some embodiments, R4 is substituted or unsubstituted bicyclic aryl. In some embodiments, R4 is substituted or unsubstituted tricyclic aryl. In some embodiments, R4 is unsubstituted heteroaryl. In some embodiments, R2 is substituted heteroaryl. In some embodiments, R4 is substituted or unsubstituted monocyclic heteroaryl. In some embodiments, R4 is substituted or unsubstituted bicyclic heteroaryl. In some embodiments, R4 is substituted or unsubstituted tricyclic heteroaryl. Is some embodiments, R4 is




In some embodiments, R4 is substituted. In some embodiments, R4 is substituted at more than one position. In some embodiments, R4 is substituted with C1-4 alkyl. In some embodiments, R4 is substituted with C2-4 alkenyl. In some embodiments, R4 is substituted with C2-4 alkynyl. In some embodiments, R4 is substituted with C1-4 alkoxy. In some embodiments, R4 is substituted with CN. In some embodiments, R4 is substituted with halogen. In some embodiments, R4 is substituted with F, Cl, Br, or I. In some embodiments, R4 is substituted with CF3. In some embodiments, R4 is substituted with NO2. In some embodiments, R4 is substituted with substituted aryl. In some embodiments, R4 is substituted with unsubstituted aryl.
In some embodiments, formula IV can be




Whether a given compound reduces the expression and/or activity of SREBP1 can be determined in vitro or in vivo, e.g. in in vitro assays or in an animal model of, for example, breast cancer. Methods of determining the expression of SREBP1 are described below herein. A non-limiting example can be immunohistochemical analysis of tumor tissue as described in the Examples herein. Briefly, 5-μm thick sections of tumor tissue are de-paraffinized with xylene and rehydrated through a graded alcohol series. Endogenous peroxidase activity can be blocked by incubation in a 3% hydrogen peroxide solution for 15 minutes. Antigen retrieval can be carried out by immersing the slides in 10 mM sodium citrate buffer (pH 6.0) and maintaining them at a sub-boiling temperature for 5 minutes. The slides can be rinsed in phosphate-buffered saline and incubated with 10% normal serum to block non-specific staining. The slides can then be incubated with the primary antibody (anti-SREBP1, K-10, Santa Cruz) overnight at 4° C. in a humidified chamber. Staining can be assessed e.g., using a semi-quantitative method such as, e.g., the German semi-quantitative scoring system as described in the Examples herein. Where SREBP1 is a transcription factor, its activity can be determined by monitoring the activity of one or more genes that is transactivates, e.g., ACLY and SCD1 or FASN. SREPB1 target gene expression can be monitored, e.g. via RT-PCR or at the protein level, e.g. by Western blot of other immuno-chemical approaches. Alternatively, the promoters for these SREBP1 target genes (or other target genes) can be ligated to a reporter gene, e.g. GFP, to provide a read-out in cultured cells for SREBP1 activity under given conditions. In some embodiments, if SREBP1 activity is decreased, expression of both SREBP1 isoforms, SREBP2, ACLY, and SCD1 will be decreased, while FASN expression will be decreased to a lesser extent, and PKLR expression will not be altered.
In some embodiments, the methods described herein relate to selecting a subject to be treated for cancer with the inhibitors of SREBP1 described herein. A subject selected for treatment according to the methods described herein should be one having a cancer comprised of cells which are or are likely to be sensitive to the inhibitors of SREBP1 described herein, e.g. a cancer having cells which express abnormal (e.g. high) levels of SREBP1. Whether a cancer is likely to be sensitive to inhibitors of SREBP1 can be determined, for example, by determining whether the cancer cells are of a type of cancer cell that typically express abnormal levels of SREBP1 or by determining if they express abnormal levels of SREBP1.
In some embodiments, the subject can have cancer cells which express abnormal levels of SREBP1. As used herein, the term “abnormal level” of SREBP1 can refer to amounts of SREBP1 expression products and/or activity that are significantly greater than the amounts of SREBP1 expression products and/or activity in a control reference sample representative of the levels of SREBP1 expression products and/or activity in cells of the same type from a healthy individual.
In some embodiments, a subject expressing an abnormal level of SREBP1 can be a subject having a cancer which has an H-score of greater than 1. An H-score can be calculated based upon immunohistochemical staining of a sample of a cancer obtained from a subject and stained as described herein for SREBP1 polypeptide expression. The expression levels of SREBP1 in such clinical specimens can be scored (H-score) based on the total percentage of positive cells and the intensity of the staining (1+, 2+, or 3+), where H=(%“1+”×1)+(%“2+”×2)+(%“3+”×3). A score of 0-1 can be a normal level of SREBP1 expression, while a score of greater than 1 can be an abnormal level of SREBP1 expression, e.g. a score of 1.1 or greater, 1.5 or greater, 2.0 or greater, or 2.5 or greater.
In some embodiments, the control reference sample can comprise healthy cells of the same type as the cells for which SREBP1 levels are to be determined. In some embodiments, the cells of the control reference sample can be of similar age, developmental status, sex, and/or cell type as the cells for which the level of SREBP1 expression and/or activity is to be determined. In some embodiments, the control reference sample can be obtained from a healthy organism of similar age, developmental status, and/or sex as the subject organism for which the level of SREBP1 expression and/or activity is to be determined. In some embodiments, the test sample and control reference sample are of the same type, that is, obtained from the same biological source, and comprising the same composition, e.g. the same number and type of cells. In some embodiments, the control reference sample can be non-cancerous cells from the subject organism which are of the cell type from which the cancerous cells descended, e.g. if the cancerous cells are breast cancer cells, the control reference sample can be healthy breast cells from the same subject.
In some embodiments, a subject is a candidate for treatment according to the methods described herein if the levels of SREBP1 expression products and/or activity in the cells of a subject are significantly greater than the levels of SREBP1 expression products and/or activity present in the control reference sample. In some embodiments, a subject is a candidate for treatment according to the methods described herein if the levels of SREBP1 expression products and/or activity in the cells of a subject are at least 2-fold greater than the levels of SREBP1 expression products and/or activity present in the control reference sample, e.g. 2-fold or greater, 3-fold or greater, 4-fold or greater, 5-fold or greater, or 6-fold or more or greater.
The expression of a given gene can be determined by measuring the level of any of the expression products of that gene, e.g. the mRNA or polypeptide encoded by that gene. In some embodiments, a cell which expresses an abnormal level of a gene can be a cell that expresses an abnormal level of mRNA encoded by that gene. In some embodiments, a cell which expresses an abnormal level of a gene can be a cell that expresses an abnormal level of polypeptide encoded by that gene.
In some embodiments, a cell which expresses an abnormal level of SREBP1 can be a cell that expresses an abnormal level of SREBP1 polypeptide.
The level of expression of, e.g. SREBP1, can be determined by measuring the level of an mRNA and/or a polypeptide encoded by SREBP1 in a biological sample obtained from the subject. In some embodiments, the biological sample comprises cancer cells. In some embodiments, the biological sample comprises a biopsy sample.
Methods for determining the level of an mRNA and/or polypeptide in a subject or a sample obtained from a subject are well known in the art. Methods of determining the level of a SREBP1 polypeptide include, but are not limited to, Western blot; immunoprecipitation; enzyme-linked immunosorbent assay (ELISA); radioimmunological assay (RIA); sandwich assay; fluorescence in situ hybridization (FISH); immunohistological staining; radioimmunometric assay; mass spectroscopy and/or immunoelectrophoresis assay. In certain embodiments determining the level of SREBP1 polypeptide involves the use of an antibody, an antibody fragment, a monoclonal antibody, and/or a monoclonal antibody fragment. Antibodies specific for SREBP1 are commercially available, e.g. Cat. No. 3259 from Abeam; Cambridge, Mass. Methods of determining the level of a SREBP1 mRNA include, but are not limited to RT-PCR, quantitative RT-PCR, hybridization assays, RNA-Seq, Northern blot, high-throughput sequencing, and/or microarray based expression analysis.
When certain genes are expressed at abnormally high levels in a cell, SREBP1 is likely expressed at abnormal levels in the same cell, i.e. there are genes whose expression can serve as a proxy for the direct measurement of SREBP1 expression. Non-limiting examples of such genes include, Erb2 (NCBI Gene ID: 2100, e.g. SEQ ID NO: 05 (mRNA), SEQ ID NO: 06 (protein); FASN (NCBI Gene ID: 2194, e.g. SEQ ID NO: 07 (mRNA), SEQ ID NO: 08 (protein); SCD1 (NCBI Gene ID: 6319, e.g. SEQ ID NO: 09 (mRNA), SEQ ID NO: 10 (protein); or ACLY (NCBI Gene ID: 47, e.g. SEQ ID NO: 11 (mRNA), SEQ ID NO: 12 (protein). In some embodiments, a subject in need of treatment according to the methods described herein can have cancer cells which express abnormal levels of genes which are correlated with expression of abnormal levels of SREBP1. In some embodiments, a subject in need of treatment according the methods described herein can have cancer cells which express abnormal levels of an mRNA of one or more genes correlated with expression of abnormal levels of SREBP1. In some embodiments, a subject in need of treatment according the methods described herein can have cancer cells which express abnormal levels of a polypeptide of one or more genes correlated with expression of abnormal levels of SREBP1. Expression of these genes in the cancer cells of a subject can be determined as described above herein for SREBP1. Antibodies specific for Erb2, FASN, SCD1, and ACLY are commercially available, e.g., respectively, Cat. Nos. ab3576, ab22759, ab19862, and ab40793 from Abeam; Cambridge, Mass.
In some embodiments, determining the expression level of SREBP1 and/or one or more genes correlated with expression of abnormal levels of SREBP1 involves determining the expression of no more than 20 genes, e.g. 20 or fewer genes, 15 or fewer genes, 10 or fewer genes, or 5 or fewer genes.
Certain cancers are known to be characterized and/or likely to be characterized by abnormal expression of SREBP1. Non-limiting examples of such cancers can include endometrial cancer; prostate cancer; breast cancer; colorectal cancer; colorectal carcinoma; hepatocarcinoma; endometrial adenocarcinoma; uterine cancer; leukemia; lung cancer; central nervous system cancer; melanoma; ovarian cancer; renal cancer; and pancreatic cancer. In some embodiments, the subject treated according to the methods described herein can have a cancer likely to be sensitive to the inhibitors of SREBP1 described herein. In some embodiments, the subject selected for treatment according to the methods described herein can have a cancer likely to be sensitive to the inhibitors of SREBP1 described herein. A cancer likely to be sensitive to the inhibitors of SREBP1 described herein can be a type of cancer known to have abnormal expression of SREBP1.
In some embodiments, a cancer treated according to the methods described herein comprises a poorly-differentiated or moderately-differentiated tumor. In some embodiments, a cancer treated according to the methods described herein does not comprise a well-differentiated tumor. The level of differentiation of a tumor can be determined by methods well known to one of skill in the art, e.g. Gleason scores, wherein a Grade 1 tumor is well-differentiated, a Grade 2 tumor is moderately-differentiated, and a Grade 3 or higher tumor is poorly-differentiated (see, e.g. Gleason, Donald F; Mellinger George T. J. Urol. 2002 167:953-8; which is incorporated by reference herein in its entirety).
In some embodiments, the methods described herein relate to treating a subject having or diagnosed as having cancer with a SREBP1 inhibitor. Subjects having cancer can be identified by a physician using current methods of diagnosing cancer. Symptoms and/or complications of cancer which characterize these conditions and aid in diagnosis are well known in the art and include but are not limited to, for example, in the case of breast cancer a lump or mass in the breast tissue, swelling of all or part of a breast, skin irritation, dimpling of the breast, pain in the breast or nipple, nipple retraction, redness, scaliness, or irritation of the breast or nipple, and nipple discharge. Tests that may aid in a diagnosis of, e.g. breast cancer include, but are not limited to, mammograms, x-rays, MRI, ultrasound, ductogram, a biopsy, and ductal lavage. A family history of cancer, or exposure to risk factors for cancer (e.g. smoke, radiation, pollutants, BRCA1 mutation, etc.) can also aid in determining if a subject is likely to have cancer or in making a diagnosis of cancer. The terms “malignancy,” “malignant condition,” “cancer,” or “tumor,” as used herein, refer to an uncontrolled growth of cells which interferes with the normal functioning of the bodily organs and systems.
The compositions and methods described herein can be administered to a subject having or diagnosed as having cancer. In some embodiments, the methods described herein comprise administering an effective amount of compositions described herein, e.g. a SREBP1 inhibitor to a subject in order to alleviate a symptom of a cancer. As used herein, “alleviating a symptom of a cancer” is ameliorating any condition or symptom associated with the cancer. As compared with an equivalent untreated control, such reduction is by at least 5%, 10%, 20%, 40%, 50%, 60%, 80%, 90%, 95%, 99% or more as measured by any standard technique. A variety of means for administering the compositions described herein to subjects are known to those of skill in the art. Such methods can include, but are not limited to oral or parenteral routes, including intravenous, intramuscular, subcutaneous, transdermal, airway (aerosol), pulmonary, or intratumoral. Administration can be local or systemic.
The term “effective amount” as used herein refers to the amount of a SREBP1 inhibitor needed to alleviate at least one or more symptom of the disease or disorder, and relates to a sufficient amount of pharmacological composition to provide the desired effect. The term “therapeutically effective amount” therefore refers to an amount of a SREBP1 inhibitor that is sufficient to cause a particular anti-cancer effect when administered to a typical subject. An effective amount as used herein, in various contexts, would also include an amount sufficient to delay the development of a symptom of the disease, alter the course of a symptom disease (for example but not limited to, slow the progression of a symptom of the disease), or reverse a symptom of the disease. Thus, it is not generally practicable to specify an exact “effective amount”. However, for any given case, an appropriate “effective amount” can be determined by one of ordinary skill in the art using only routine experimentation.
Effective amounts, toxicity, and therapeutic efficacy can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dosage can vary depending upon the dosage form employed and the route of administration utilized. The dose ratio between toxic and therapeutic effects is the therapeutic index and can be expressed as the ratio LD50/ED50. Compositions and methods that exhibit large therapeutic indices are preferred. A therapeutically effective dose can be estimated initially from cell culture assays. Also, a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the SREBP1 inhibitor, which achieves a half-maximal inhibition of symptoms) as determined in cell culture, or in an appropriate animal model. Levels in plasma can be measured, for example, by high performance liquid chromatography. The effects of any particular dosage can be monitored by a suitable bioassay, e.g., assay for inhibition of SREBP1 activity or for inhibition of cancer cell proliferation, among others. The dosage can be determined by a physician and adjusted, as necessary, to suit observed effects of the treatment.
In certain embodiments, an effective dose of a composition comprising a SREBP1 inhibitor as described herein can be administered to a patient once. In certain embodiments, an effective dose of a composition comprising a SREBP1 inhibitor can be administered to a patient repeatedly. Patients can be administered a therapeutic amount of a composition comprising a SREBP1 inhibitor, such as, e.g. 0.1 mg/kg, 0.5 mg/kg, 1.0 mg/kg, 2.0 mg/kg, 2.5 mg/kg, 5 mg/kg, 10 mg/kg, 15 mg/kg, 20 mg/kg, 25 mg/kg, 30 mg/kg, 40 mg/kg, 50 mg/kg, or more. A composition comprising a SREBP1 inhibitor can be administered over a period of time, such as over a 5 minute, 10 minute, 15 minute, 20 minute, or 25 minute period. If warranted, the administration can be repeated, for example, on a regular basis, such as hourly for 3 hours, 6 hours, 12 hours or longer or such as biweekly (i.e., every two weeks) for one month, two months, three months, four months or longer. In some instances, after an initial treatment regimen, the treatments can be administered on a less frequent basis. For example, after administration biweekly for three months, administration can be repeated once per month, for six months or a year or longer. Administration of a composition comprising a SREBP1 inhibitor can reduce levels of a marker or symptom of cancer, e.g. the size of a tumor or the rate of growth of a tumor by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80 or at least 90% or more.
The dosage of a composition as described herein can be determined by a physician and adjusted, as necessary, to suit observed effects of the treatment. With respect to duration and frequency of treatment, it is typical for skilled clinicians to monitor subjects in order to determine when the treatment is providing therapeutic benefit, and to determine whether to increase or decrease dosage, increase or decrease administration frequency, discontinue treatment, resume treatment, or make other alterations to the treatment regimen. The dosing schedule can vary from once a week to daily depending on a number of clinical factors, such as the subject's sensitivity to the SREBP1 inhibitor.
In some embodiments, the technology described herein relates to a pharmaceutical composition comprising a SREBP1 inhibitor as described herein, and optionally a pharmaceutically acceptable carrier. Pharmaceutically acceptable carriers and diluents include saline, aqueous buffer solutions, solvents and/or dispersion media. The use of such carriers and diluents is well known in the art. Some non-limiting examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, sunflower oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents, such as polypeptides and amino acids (23) serum component, such as serum albumin, HDL and LDL; (22) C2-C12 alcohols, such as ethanol; and (23) other non-toxic compatible substances employed in pharmaceutical formulations. Wetting agents, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservative and antioxidants can also be present in the formulation. The terms such as “excipient”, “carrier”, “pharmaceutically acceptable carrier” or the like are used interchangeably herein. In some embodiments, the carrier inhibits the degradation of the active agent, e.g. a SREBP1 inhibitor as described herein.
The methods described herein can further comprise administering a second agent and/or treatment to the subject, e.g. as part of a combinatorial therapy. Non-limiting examples of a second agent and/or treatment can include radiation therapy, surgery, gemcitabine, cisplastin, paclitaxel, carboplatin, bortezomib, AMG479, vorinostat, rituximab, temozolomide, rapamycin, ABT-737, PI-103; alkylating agents such as thiotepa and CYTOXAN® 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 gammal I and calicheamicin omegall (see, e.g., Agnew, Chem. Intl. Ed. Engl., 33: 183-186 (1994)); dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, ADRIAMYCIN® doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), 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 (JHS Natural Products, Eugene, Oreg.); 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., TAXOL® paclitaxel (Bristol-Myers Squibb Oncology, Princeton, N.J.), ABRAXANE® Cremophor-free, albumin-engineered nanoparticle formulation of paclitaxel (American Pharmaceutical Partners, Schaumberg, Ill.), and TAXOTERE® doxetaxel (Rhone-Poulenc Rorer, Antony, France); chloranbucil; GEMZAR® gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin, oxaliplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; NAVELBINETM vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (Camptosar, CPT-11) (including the treatment regimen of irinotecan with 5-FU and leucovorin); topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids such as retinoic acid; capecitabine; combretastatin; leucovorin (LV); oxaliplatin, including the oxaliplatin treatment regimen (FOLFOX); lapatinib (TykerbTM); inhibitors of PKC-alpha, Raf, H-Ras, EGFR (e.g., erlotinib (Tarceva®)) and VEGF-A that reduce cell proliferation and pharmaceutically acceptable salts, acids or derivatives of any of the above.
In addition, the methods of treatment can further include the use of radiation or radiation therapy. Further, the methods of treatment can further include the use of surgical treatments.
In some embodiments, the pharmaceutical composition comprising a SREBP1 inhibitor as described herein can be a parenteral dose form. Since administration of parenteral dosage forms typically bypasses the patient's natural defenses against contaminants, parenteral dosage forms are preferably sterile or capable of being sterilized prior to administration to a patient. Examples of parenteral dosage forms include, but are not limited to, solutions ready for injection, dry products ready to be dissolved or suspended in a pharmaceutically acceptable vehicle for injection, suspensions ready for injection, and emulsions. In addition, controlled-release parenteral dosage forms can be prepared for administration of a patient, including, but not limited to, administration DUROS®-type dosage forms, and dose-dumping.
Suitable vehicles that can be used to provide parenteral dosage forms of the SREBP1 inhibitor as disclosed within are well known to those skilled in the art. Examples include, without limitation: sterile water; water for injection USP; saline solution; glucose solution; aqueous vehicles such as but not limited to, sodium chloride injection, Ringer's injection, dextrose Injection, dextrose and sodium chloride injection, and lactated Ringer's injection; water-miscible vehicles such as, but not limited to, ethyl alcohol, polyethylene glycol, and propylene glycol; and non-aqueous vehicles such as, but not limited to, corn oil, cottonseed oil, peanut oil, sesame oil, ethyl oleate, isopropyl myristate, and benzyl benzoate. Compounds that alter or modify the solubility of a pharmaceutically acceptable salt of a SREBP1 inhibitor as disclosed herein can also be incorporated into the parenteral dosage forms of the disclosure, including conventional and controlled-release parenteral dosage forms.
Pharmaceutical compositions comprising a SREBP1 inhibitor can also be formulated to be suitable for oral administration, for example as discrete dosage forms, such as, but not limited to, tablets (including without limitation scored or coated tablets), pills, caplets, capsules, chewable tablets, powder packets, cachets, troches, wafers, aerosol sprays, or liquids, such as but not limited to, syrups, elixirs, solutions or suspensions in an aqueous liquid, a non-aqueous liquid, an oil-in-water emulsion, or a water-in-oil emulsion. Such compositions contain a predetermined amount of the pharmaceutically acceptable salt of the disclosed compounds, and may be prepared by methods of pharmacy well known to those skilled in the art. See generally, Remington: The Science and Practice of Pharmacy, 21st Ed., Lippincott, Williams, and Wilkins, Philadelphia Pa. (2005).
In some embodiments, a SREBP1 inhibitor as described herein can be administered by controlled- or delayed-release means. Controlled-release pharmaceutical products have a common goal of improving drug therapy over that achieved by their non-controlled release counterparts. Ideally, the use of an optimally designed controlled-release preparation in medical treatment is characterized by a minimum of drug substance being employed to cure or control the condition in a minimum amount of time. Advantages of controlled-release formulations include: 1) extended activity of the drug; 2) reduced dosage frequency; 3) increased patient compliance; 4) usage of less total drug; 5) reduction in local or systemic side effects; 6) minimization of drug accumulation; 7) reduction in blood level fluctuations; 8) improvement in efficacy of treatment; 9) reduction of potentiation or loss of drug activity; and 10) improvement in speed of control of diseases or conditions. Kim, Cherng-ju, Controlled Release Dosage Form Design, 2 (Technomic Publishing, Lancaster, Pa.: 2000).
Conventional dosage forms generally provide rapid or immediate drug release from the formulation. Depending on the pharmacology and pharmacokinetics of the drug, use of conventional dosage forms can lead to wide fluctuations in the concentrations of the drug in a patient's blood and other tissues. These fluctuations can impact a number of parameters, such as dose frequency, onset of action, duration of efficacy, maintenance of therapeutic blood levels, toxicity, side effects, and the like. Advantageously, controlled-release formulations can be used to control a drug's onset of action, duration of action, plasma levels within the therapeutic window, and peak blood levels. In particular, controlled- or extended-release dosage forms or formulations can be used to ensure that the maximum effectiveness of a drug is achieved while minimizing potential adverse effects and safety concerns, which can occur both from under-dosing a drug (i.e., going below the minimum therapeutic levels) as well as exceeding the toxicity level for the drug.
Most controlled-release formulations are designed to initially release an amount of drug (active ingredient) that promptly produces the desired therapeutic effect, and gradually and continually release other amounts of drug to maintain this level of therapeutic or prophylactic effect over an extended period of time. In order to maintain this constant level of drug in the body, the drug must be released from the dosage form at a rate that will replace the amount of drug being metabolized and excreted from the body. Controlled-release of an active ingredient can be stimulated by various conditions including, but not limited to, pH, ionic strength, osmotic pressure, temperature, enzymes, water, and other physiological conditions or compounds.
A variety of known controlled- or extended-release dosage forms, formulations, and devices can be adapted for use with the salts and compositions of the disclosure. Examples include, but are not limited to, those described in U.S. Pat. Nos. 3,845,770; 3,916,899; 3,536,809; 3,598,123; 4,008,719; 5,674,533; 5,059,595; 5,591,767; 5,120,548; 5,073,543; 5,639,476; 5,354,556; 5,733,566; and 6,365,185 B1; each of which is incorporated herein by reference. These dosage forms can be used to provide slow or controlled-release of one or more active ingredients using, for example, hydroxypropylmethyl cellulose, other polymer matrices, gels, permeable membranes, osmotic systems (such as OROS® (Alza Corporation, Mountain View, Calif. USA)), or a combination thereof to provide the desired release profile in varying proportions.
The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. For example, while method steps or functions are presented in a given order, alternative embodiments may perform functions in a different order, or functions may be performed substantially concurrently. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. These and other changes can be made to the disclosure in light of the detailed description.
Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure.
All patents and other publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.
This invention is further illustrated by the following examples which should not be construed as limiting.
Some embodiments of the technology described herein can be defined according to any of the following numbered paragraphs:

    
    
        1. A compound of formula I, II, III or IV, wherein formulae I, II, III, and IV are:
    
    






wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;
R3 is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R4 and R5 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —CN; halogen; or hydroxyl;
R6 is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl;
R7 are independently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
n is an integer 0-4 inclusive; and
m is an integer 0-5 inclusive;




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;
R3, R4, R5, R6, R7 and R8 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; B(O)R1R2; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R9 is independently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo; and wherein R9 and R5 or R6 can be taken together to form a substituted or unsubstituted five or six membered ring; and
n is an integer 0 to 5, inclusive;




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring; and
R3, R4, R5, R6, R7, R8, R9, R10 and R11 are independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; B(O)R1R2; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;




wherein R1 and R2 are unsubstituted branched or straight chain alkyl, and R1 and R2 can be taken together to form a substituted or unsubstituted five or six membered ring;

R3 halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —C(═O)RB; —CO2RB; -; —CN; —SCN; —SRB; —SORB; —SO2RB; —NO2; —N(RB)2; —NHC(O)RB; or —C(RB)3; wherein each occurrence of RB is independently hydrogen; halogen; a protecting group; aliphatic; heteroaliphatic; acyl; aryl moiety; heteroaryl; hydroxyl; alkoxy; aryloxy; alkylthioxy; arylthioxy; amino; alkylamino; dialkylamino; heteroaryloxy; heteroarylthioxy; or alkylhalo;
R4 is optionally substituted aryl, or optionally substituted heteroaryl; and
n is an integer 0-4 inclusive.

    
    
        2. A compound of paragraph 1, wherein the compound is selected from the group consisting of:
    
    















    
    
        3. A method of treating cancer in a subject, the method comprising administering to the subject an inhibitor of sterol regulatory binding protein 1 (SREBP1) of any of paragraphs 1-2.
        4. The method of paragraph 3, further comprising a first step of selecting a subject having cancer cells which express abnormal levels of sterol regulatory binding protein 1 (SREBP1).
        5. The method of paragraph 4, wherein the cells which express abnormal levels of sterol regulatory binding protein 1 (SREBP1) are cells which have abnormal levels of SREBP1 polypeptide.
        6. The method of paragraph 3, further comprising a first step of selecting a subject having cancer cells which express abnormal amounts of Erb2.
        7. The method of paragraph 3, further comprising a first step of selecting a subject having cancer cells which express abnormal amounts of at least one gene selected from the group consisting of:
        
            FASN, SCD1 or ACLY.
        
        
        8. The method of any of paragraphs 3-7, wherein the subject has an endometrial cancer.
        9. The method of any of paragraphs 3-8, wherein the cancer is selected from the group consisting of:
        
            prostate cancer; breast cancer; colorectal cancer; colorectal carcinoma; hepatocarcinoma; endometrial adenocarcinoma; uterine cancer; leukemia; lung cancer; central nervous system cancer; melanoma; ovarian cancer; renal cancer; and pancreatic cancer.
        
        
        10. A pharmaceutical composition comprising a compound of any of paragraphs 1-2.
        11. The composition of paragraph 10, further comprising a pharmaceutically acceptable carrier.
        12. The use of an inhibitor of sterol regulatory binding protein 1 (SREBP1) of any of paragraphs 1-2 to treat cancer.
        13. The use of paragraph 12, wherein the cancer is comprised of cells expressing abnormal levels of sterol regulatory binding protein 1 (SREBP1).
        14. The use of paragraph 13, wherein the cells which express abnormal levels of sterol regulatory binding protein 1 (SREBP1) are cells which have abnormal levels of SREBP1 polypeptide.
        15. The use of paragraph 12, wherein the cancer is comprised of cells expressing abnormal amounts of Erb2.
        16. The use of paragraph 12, wherein the cancer is comprised of cells expressing abnormal amounts of at least one gene selected from the group consisting of:
        
            FASN, SCD1 or ACLY.
        
        
        17. The use of any of paragraphs 12-16, wherein the cancer is an endometrial cancer.
        18. The use of paragraph 17, wherein the cancer is selected from the group consisting of:
        
            prostate cancer; breast cancer; colorectal cancer; colorectal carcinoma; hepatocarcinoma; endometrial adenocarcinoma; uterine cancer; leukemia; lung cancer; central nervous system cancer; melanoma; ovarian cancer; renal cancer; and pancreatic cancer.
        
        
    
    


EXAMPLES
Example 1
Targeting Lipogenic Signaling to Repress Endometrial Cancer Cell Growth
Significantly enhanced lipogenesis is a metabolic hallmark of rapidly proliferating tumor cells. Although most normal cells acquire the bulk of their fatty acids from circulation, tumor cells synthesize more than 90% of required lipids de novo. The sterol regulatory element-binding protein 1 (SREBP1), encoded by SREBP1 gene, is a master regulator of lipogenic gene expression. Although it is known that SREBP1 and its target genes are overexpressed in a variety of cancers, the role of SREBP1 in endometrial cancer (EC) is largely unknown. Herein, a panel of endometrial cancer specimens was screened for their lipogenic gene expression by quantitative PCR and a significant increase in mRNA abundance of SREBP1, SREBP2, and FASN genes was found in cancer compared to normal endometrium Immunohistochemical staining confirmed SREBP1 protein overexpression and further demonstrated increased nuclear distribution of SREBP1 in EC. SREBP1 promotes cellular proliferation in cell culture and enhances tumor growth in a xenograft model. Knockdown of endogenous SREBP1 gene impaired the viability of cells cultured in medium supplemented with lipid-depleted serum. The small molecule BF175 repressed SREBP1-dependent gene expression and cell growth and induced EC cell death. All together, the results presented herein established a role of SREBP1 in EC cell growth and validated BF175 for its therapeutic effectiveness in targeting SREBP1 and lipogenesis to block EC proliferation.
INTRODUCTION
The number of women with newly diagnosed endometrial cancer (EC) increased by 20% from 1987; however the number of deaths posted a 168% increase during the same time period. Estimated new cases and deaths from EC in the United States in 2011 are 46,470 and 8,120, respectively (data available on the world wide web at http://www.cancer.gov/cancertopics/types/endometrial). Epidemiological studies have identified obesity as the most common risk factor for EC. Obese women have a 2-4 times greater risk of developing EC compared to women of normal weight, regardless of menopausal status (1-5). As population size affected by this disease is expected to grow, particularly in developing countries, EC will continue to be a serious public health problem. Sterol regulatory element binding proteins (SREBPs) are a family of transcription factors that regulate lipid homeostasis by controlling the expression of multiple enzymes required for cholesterol and fatty acids (FAs) synthesis. The three SREBP isoforms, SREBP1a, SREBP1c and SREBP2, have different roles in lipid synthesis (6,7). In vivo studies using transgenic and knockout mice suggest that SREBP1c is involved in FA synthesis and insulin-induced glucose metabolism (particularly in lipogenesis), whereas SREBP2 is relatively specific in controlling cholesterol synthesis. The SREBP1a isoform is implicated in regulating both cholesterol and FA pathways. SREBP transcription factors are synthesized as inactive precursors bound to the endoplasmic reticulum (ER) membranes and their processing is mainly controlled by cellular sterol content. When sterol level decreases, the precursor undergoes a sequential two-step cleavage process to release the NH2-terminal active domain in the nucleus (designated nSREBPs), which then activate SREBP target genes to maintain cholesterol and FAs homeostasis (8-15). The major SREBP targets include FASN (16,17) and stearoyl-CoA desaturase (SCD) (18-21). This sterol-sensitive process appears to be a major point of regulation for the SREBP1a and SREBP2 isoforms but not for SREBP1c. Moreover, the SREBP1c isoform is mainly regulated at the transcriptional level by insulin. The unique regulation and activation properties of each SREBP isoform facilitate the co-ordinate regulation of lipid metabolism. At a minimum, SREBP1 activity refers to the ability of the amino-terminal active domain of SREBP1a to transactive expression from an SRE-containing gene or reporter gene construct. As noted, SREBP targets include FASN and SCD. Accordingly, an inhibitor of SREPB1 activity will inhibit SRE-mediated transactivation by the amino-terminal active domain of SREBP1a. A reporter construct comprising, for example, a regulatory element comprising one or more SREs can be used to monitor that effect of an SREBP1 inhibitor on SREBP1-mediated transactivation. Examples of suitable reporter constructs include the FASN and SCD promoter-driven luciferase reporter constructs described herein in Example 1 and the reporter constructs (e.g. the FAS, ACLY, LDLR, HMG, and FPP reporters) described in Amemiya-Kudo et al. Journal of Lipid Research 2002 43:1220-1235, which is incorporated by reference herein in its entirety.
Lipogenesis is a highly active process in many human cancers. The regulatory function of SREBP1 suggests a role in sensing and regulating cancer-associated lipogenesis. Increased expression of SREBP1 has been reported in colorectal carcinoma, breast and prostate cancer, and hepatocarcinoma. Moreover, elevated expression of SREBP1 coincided with malignant transformation, cancer progression, and metastasis for several cancer types, particularly hormone-responsive tissues including breast and prostate cancers (22-25). SREBP1 expression correlates with FASN and Ki-67 expression in colorectal cancer, indicating a role for SREBP1 in supporting rapid cellular proliferation (25). SREBP1 is elevated in clinical prostate cancer samples compared to benign prostatic hypertrophy (26). Gene expression profiling of hepatocellular carcinoma (HCC) tissue and non-cancerous liver tissue showed increased lipogenic signaling in HCC. Enhanced SREBP1 expression in hepatocellular carcinoma predicts an increased mortality (22,23). Over-expression of SREBP1 in human hepatoma HuH7 and Hep3B cells enhanced cellular proliferation and foci formation while siRNA knockdown of SREBP1 in these cells reduced cell replication and anchorage-independent cell growth (22). A dramatic increase of SREBP1 has been correlated with the progression of prostate cancer towards androgen-independence (26). Oncogene transformation of normal breast epithelial cells was accompanied by SREBP1 and FASN over-expression, consistent with the observation of increased SREBP1 abundance in human breast cancers (27-29). Previous studies have established that SREBP1, through induction of FASN and subsequent fatty acids production, regulates PPARγ trans-activation (16,30).
Despite the relatively clear understanding of enhanced lipogenic signaling, the role of SREBP1 in endometrial cancer is still largely unknown. Given the evidence of elevated expression of SREBP1 transcriptional target genes, the primary focus of this study was to determine the SREBP1 expression status in, for example, endometrial cancer. Demonstrated herein is increased nuclear staining for SREBP1 in higher grade tumors, suggesting that enhanced SREBP1 transactivation may contribute to endometrial cancer progression through induction of lipogenic gene expression and lipogenesis. Knockdown of endogenous SREBP1 expression using a shRNA approach results in a reduction of SREBP1 target gene expression as well as impaired cellular proliferation and migration. Furthermore, a small molecule inhibitor of lipogenic signaling, BF175, is demonstrated to repress tumor cell growth by targeting SREBP1-mediated signaling.
Results
Increased SREBP1 Expression in Endometrial Cancer.
Previous studies indicated that lipogenic genes such as FASN are overexpressed in endometrial cancers. The underlying mechanisms through which EC cells overexpress FASN are not well understood. SREBP1 is the major transcription factor which binds to FASN gene promoter and positively regulates FASN expression. It was hypothesized that elevated SREBP1 expression and/or activity may contribute to enhanced FASN expression in EC. In order to determine the levels of SREBP1 expression, immunohistochemical staining was performed on formalin-fixed, paraffin-embedded sections using anti-SREBP1 antibody. Nuclear and cytoplasmic SREBP1 abundance was scored for both matured and precursor forms, respectively. SREBP1 was detected in both normal and cancerous tissues. SREBP1 was found to be overexpressed in poorly-differentiated EC. Nuclear localization of SREBP1 was frequently seen in poorly-differentiated tumors (grade 2-3), but not in well-differentiated tumors (grade 1) (FIG. 1A and data not shown). The majority of SREBP1 was found in the cytoplasm of epithelial cells of normal endometrium and well-differentiated tumors, while nuclear SREBP1 was detected in high-grade from moderately differentiated to poorly differentiated tumors (FIGS. 2A-2F). These observations suggest a role of activated SREBP1 in endometrial cancer progression.
SREBP1 abundance was regulated at either transcriptional or post-translational levels (31,32). The increased protein expression may be due to enhanced gene expression. To confirm this, quantitative real-time PCR (qRT-PCR) analysis was performed on a panel of cDNA samples prepared from surgically resected samples and the transcript levels of SREBPs and SCD1, a transcriptional target of SREBPs, was compared between normal and cancerous tissues. As shown in FIG. 1A, cancer tissue exhibited markedly reduced SREBP1a and SREBP2. No significant difference of SREBP1c expression was observed. Meanwhile, the mRNA levels of SCD1 were significantly increased in cancer, which keeps in line with increased SREBP1 protein expression and activation as evidenced by nuclear translocation. Reduced mRNA expression and increased protein abundance suggest mechanisms by which SREBP1 protein is stabilized in cancer.
SREBP1 is Responsible for Lipogenic Gene Expression in Endometrial Cancer Cells.
Having established the correlation between SREBP1 expression and endometrial cancer progression, it was determined whether SREBP1 contributes to tumorigenesis. In order to do so, an initial screening for SREBP1 expression was performed in five commonly used endometrial cell lines including ECC, HEC-1-A, RL95-2, KLE, and AN3-CA. SREBP1 expression was undetectable in the well-differentiated ECC-1 cells and highly expressed in medium and poorly differentiated RL95-2 and AN3-CA cells (data not shown). Since SREBP1 antibody cannot differentiate SREBP1a and SREBP1c, qRT-PCR was performed to determine which SREBP1 isoform was predominantly expressed. As shown in FIG. 2B, the RL95-2 cells express both isoforms at relatively high levels. AN3-CA expresses SREBP1a, but not SREBP1c. The expression levels of SREBP target genes including FASN, SCD, and ACLY were also determined Relatively high expression of FASN, SCD1, and ACLY were detected in AN3-CA cells (FIG. 2A). AN3-CA cells were chosen for most experiments in this study due to the relatively high levels of lipogenic gene expressions. To test whether the endogenous SREBP1 is required for lipogenic gene expression, SREBP1 gene expression was knocked-down using a shRNA approach (33). Over 90% knockdown efficiency was achieved at both protein and mRNA levels (FIG. 2C). The expression of SREBP1 target genes was also significantly reduced (FIG. 2D), indicating a partial SREBP1 dependency of these genes.
SREBP1 is Required for Cellular Proliferation and Migration.
Cell proliferation is tightly controlled by mitogenic signaling and requires the activation of biosynthetic pathways for the generation of macromolecules, including proteins and lipids. Given the evidence that SREBP1 regulates lipogenesis, the metabolic process that supplies cells with lipids, it was expected that the knockdown of endogenous SREBP1 would reduce cellular proliferation and cell growth. In order to determine the functional consequences of SREBP1 inactivity in cell culture, cells with either knockdown of SREBP1 by shRNA or vector control were compared. The same number of each group of cells were seeded and counted for 5 days. Reduced cell number was observed in shSREBP1 expressing cells (FIG. 2E). It has been previously shown that suppression of lipogenic signaling reduces cellular migration. To test whether SREBP1 is involved in cell migration, transwell assays were conducted, in which the knockdown of endogenous SREBP1 significantly inhibited the cell migration (FIG. 2F).
BF175, a Small Molecule Inhibitor, Represses Lipogenesis In Vivo.
To further examine whether BF175 has any effect in regulating lipid homeostasis, Drosophila larvae were fed fly food containing 100 μM of BF175 from hatching to the third instar larvae. Lipids were then stained and quantified with Oil Red O. As shown in FIG. 3A, the wild-type larvae fed with 100 μM of BF175 in food have 20 ̃25% reduction of the fat levels compared to the control food with DMSO. Similar results were observed with 50 uM or 200 uM of BF175, or BF102, a compound similar to BF175. These results suggest that BF175 (and BF102) has a conserved role in inhibiting lipogenesis in whole organisms. At 200 μM, both compounds do not affect the Drosophila development and viability, and adult flies fed with food mixed with these compounds also do not have any obvious effect on life span (data not shown), suggesting that these compounds are not toxic to Drosophila. 
BF175 Represses SREBP1 Activity and Lipogenic Gene Expression.
It was investigated whether that inhibition of lipogenic signaling could provide therapeutic intervention of endometrial cancer progression. BF175 repression of lipogenesis suggests that tumor cell growth might be alleviated by this agent. AC3-CA cells were treated with increased doses of BF175. BF175 markedly reduced the protein expression of ACLY and SCD1, as well as FASN to a lesser extent (FIG. 3B). This is consistent with the observation made above herein, that the knockdown of SREBP1 only led to 30% reduction of FASN mRNA levels (FIG. 2D). Previous reports also showed that FASN gene expression is controlled by multiple signaling pathways (16,25,27,35-38). qRT-PCR assays were conducted to determine the mRNA levels of these genes in cells treated with BF175. All three forms of SREBPs were significantly repressed. The expression of FASN, SCD and ACLY genes were also inhibited (FIG. 3C). The pyruvate kinase (PK) encoded by the PKLR gene is involved in lipogenesis, but not regulated by SREBP1. No change in PKLR gene expression was observed in cells exposed to BF175, suggesting SREBP1-specific signaling is targeted. It is no surprise to see that the mRNA expression of SREBPs was also repressed since SREBP1 positively regulates its gene expression through a feed-forward mechanism (31).
Both SCD and FASN are transcriptional targets of SREBP1. Using the FASN or SCD promoter-driven luciferase reporter as surrogate measures of SREBP1 activity (FIG. 3D, 3E), it was determined whether BF175 regulates the gene expression by targeting their transcription. Experiments were conducted in AN3-CA and human embryonic kidney HEK 293 cells showing that BF175 potently represses FASN and SCD reporter activity in a dose-dependent manner (FIG. 3D, 3E).
BF175 Inhibits Endometrial Cancer Cell Growth.
Since the results described above herein demonstrate that SREBP1 is required for cellular proliferation and BF175 targeted SREBP1 for repression, it was next tested whether BF175 inhibition of SREBP1 could reduce cell growth. Five cell lines were incubated with different doses of BF175 for 24 hrs, and MTT assays were conducted to measure cell viability. BF175 treatment significantly inhibited the growth of AN3-CA and RL95-2 cells. Little or no effect was observed in ECC1, HEC1A and KLE cells, where lower SREBP1 expression was detected (FIG. 4A). These results further confirmed that BF175 functions in an SREBP1-dependent manner. Cell growth was also determined by the total cell number in BF175 treated cells, showing a significant reduction of cells in a dose dependent manner (FIG. 4B)
To better understand the mechanisms by which BF175 inhibition of SREBP1 impairs cell growth, AN3-CA cells were starved with serum-free medium for 48 hrs, then released by supplying cells with 10% serum and BrdU in the presence and absence of BF175. After 6 hrs, cells were stained for BrdU incorporated in the newly synthesized DNA. BrdU-positive cells were counted and calculated as a percentage of total cell number. No significant change in the number of BrdU-positive cells was found between BF175 treated and control groups (FIG. 4C), indicating that SREBP1 inhibition by BF175 does not block DNA synthesis in response to mitogen signaling.
BF175-Dependent Induction of Apoptotic and Autophagic Cell Death.
It has been previously shown that inhibition of SREBP1 sensitizes cells to death ligand and evasion of cell death contributes to the net cell growth (39). It has been hypothesized that BF175 inhibition of cell growth could also be due to the enhanced cell death. To test this idea, several approaches were used. First, the sub-G1 population of cells treated with BF175 or control were analyzed. Cells treated with BF175 for 24 hrs were subjected to flow cytometry assays, showing that BF175 markedly increased the cells in sub-G1 cell population (FIG. 5A). BF175-treated cells were also analyzed by Annexin V staining to determine the apoptotic cell death. Cells that are in early apoptosis are Annexin V positive and 7-AAD negative; while cells that are in late apoptosis are both Annexin V and 7-AAD positive. As demonstrated in FIG. 5B, the percentage of early apoptotic cells increased from 1.81% to 5.92%, a three-time induction of cell death by BF175. This observation was further confirmed by TUNEL staining showing a dramatic increase of apoptotic cell death in the presence of BF175 (data not shown). A primary cellular response to nutrient deprivation is the induction of autophagy. Whether blockage of SREBP1 induces cells to undergo autophagy was examined. AN3-CA cells were transduced with retroviral vector encoding GFP-LC3 or GFP as previously described (40). GFP-positive cells enriched by FACs sorting were treated with BF175. An increased number of punctate dots, indicative of autophagosome accumulation, were found in BF175 treated cells (data not shown).
BF175 Represses SREBP1-Dependent Transcription.
To understand mechanistically how BF175 regulates SREBP1 activity, an assay using SREBP1 gene promoter driven luciferase reporter as described previously (41) was conducted. The truncated promoter reporter was first tested for responsiveness to BF175 (FIG. 6A). The minimal promoter (90-bp) reporter activity was repressed equally well as the full-length (2,600-bp), suggesting the responsive element was restricted to the 90 base pairs of SREBP1 promoter region. As previously identified, Ebox, SRE and Sp1 were main sites within this region. Using promoter reporter with mutation of each individual site as illustrated in FIG. 6C, it was demonstrated that SRE mutant reporter is less responsive to BF175 repression, suggesting that SREBPs, rather than Ebox or Sp1 binding proteins, were targeted by BF175 (FIG. 6D).
DISCUSSION
The results described herein establish a role of SREBP1 in endometrial cancer cell proliferation Enhanced lipogenic gene expression and lipogenesis are required for cancer cell proliferation. It has been previously established that lipogenic signaling controls cellular proliferation. By targeting SREBP1 expression and/or activity using shRNA and pharmacological approaches, it is possible to block the cell growth. The SREBP1 gene knockdown experiment described herein established a role of SREBP1 in supporting cellular proliferation and migration.
Tumor growth is the net gain of cell population, which is contributed to by both cell proliferation and cell death. BF175 treatment reduced cell viability and total cells numbers as measured by MTT assay. BF175 did not inhibit BrdU incorporation into newly synthesized DNA, suggesting that BF175 may not block the G1/S transition, which is a critical step for rapidly proliferating cells. Knockdown of SREBP1 expression sensitizes cells to lipid depletion and leads to cell death under lipid-free culture condition (data not shown). This is in complete agreement with the observation that BF175 induces cell death.
The current study addressed an important question of whether SREBP1 is responsible for enhanced lipogenesis in tumors, which contributes to cancer progression. Targeting SREBP1 activity provides an approach to repress cell growth. It is demonstrated herein that synthetic SREBP1 inhibitors are effective in blocking cancer cell growth by inhibiting cellular proliferation and by inducing cell death. BF175 and its analogs can serve as lead compounds for pharmacological intervention in cancer progression.
Materials and Methods
Endometrial Cancer Specimens and Immunohistochemistry (IHC) Staining.
Formalin-fixed and paraffin-embedded tumor specimens used in this study were from a commercial source (Creative Biolabs, Shirley, N.Y.) and from the tissue bank of the 90th Hospital of Jinan, China. All tumors were primary and untreated before surgery with complete clinicopathological information. All patients received radical mastectomy or modified radical mastectomy; the axillary lymph nodes were routinely dissected, and lymph node metastasis was determined based on histological examination. Tumor size was defined as the maximum tumor diameter measured on the tumor specimens at the time of operation. Endometrial cancer tissues from the 90th Hospital of Jinan were built into a 60-core array with 2 mm diameter of the core size. Adjacent normal tissues were included for some cancer tissues.
IHC staining for SREBP1 was performed on the paraffin-embedded tissue blocks in the Kimmel Cancer Center Pathology Core Facility at Thomas Jefferson University. Hematoxylin and eosin (H&E) staining were reviewed to ensure the cancer tissue and normal epithelia. IHC staining for these markers was performed on 5-μm thick sections. Briefly, tissue slides were de-paraffinized with xylene and rehydrated through a graded alcohol series. The endogenous peroxidase activity was blocked by incubation in a 3% hydrogen peroxide solution for 15 minutes. Antigen retrieval was carried out by immersing the slides in 10 mM sodium citrate buffer (pH 6.0) and maintained at a sub-boiling temperature for 5 minutes. The slides were rinsed in phosphate-buffered saline and incubated with 10% normal serum to block non-specific staining. The slides were then incubated with the primary antibody (anti-SREBP1, K-10, Santa Cruz) overnight at 4° C. in a humidified chamber.
All staining was assessed by pathologists blinded to the origination of the samples using a semi-quantitative method. The widely accepted German semi-quantitative scoring system in considering the staining intensity and area extent was used. Each specimen was assigned a score according to the intensity of the nucleic and cytoplasmic staining (no staining=0; weak staining=1, moderate staining=2, strong staining=3) and the extent of stained cells (0%=0, 1-10%=1, 11-50%=2, 51-80%=3, 81-100%=4). The final immunoreactive score was determined by multiplying the intensity score with the extent of score of stained cells, ranging from 0 (the minimum score) to 12 (the maximum score). SREBP1 expression was defined as low (scored 0-4), medium (score 5-8), and high (9-12).
Plasmids, Antibodies, and Reagents.
shRNA targeting human SREBP1 was described previously (33). The 1000-bp promoter of FASN was amplified from genomic DNA of AN3-CA cells and subcloned into Kpn I/Bgl II of pGL3-basic vector (Promega). Mouse Scd1 promoter-driven luciferase reporter was described previously (42). pcDNA3-FLAG-SREBP1a was obtained from Addgene (43). All the mutant constructs for SREBP1 promoter-driven luciferase reporter were described previously (41). The retroviral vector (MSCV-IRES-GFP) expressing GFP-LC3 was described previously by the inventors (40). Anti-SREBP1 (K-10 and H-160), anti-FASN (H300), anti-actin (C4) were purchased from Santa Cruz Biotechnology (Santa Cruz, Calif.). Anti-SCD (MC38) was purchased from Cell Signaling Technology (Danvers, Mass.). Anti-ACLY was from Abcam (Cat. # ab40993, Cambridge, Mass.).
Cell Culture.
The human embryonic kidney 293T cells (HEK293T) were maintained in DMEM containing 1% penicillin/streptomycin and supplemented with 10% fetal bovine serum (FBS). Endometrial cancer cell lines including ECC-1, HEC-1A, RL95-2, KLE, and AN3-CA were purchased from the American Type Culture Collection (ATCC). The basal culture medium are: RPMI-1640 (ECC-1), McCoy's 5a (HEC-1A), DMEM:F12 (RL95-2, KLE), and Eagle's Minimum Essential Medium (AN3-CA). For cell maintenance, the basal medium was supplemented with 10% fetal bovine serum (FBS). Under lipid-free culture condition as indicated, the basal medium was supplemented with 5% lipid-depleted FBS purchased from Cocalico Biologicals (Reamstown, Pa.) (Cat. #55-0116).
Transfection, Transduction and Luciferase Reporter Assays.
For transient transfection, SUPERFECTTM transfection reagent was used following manufacturer's protocol (Qiagen, Valencia, Calif.). For cell transduction, retroviruses were prepared by transient co-transfection with helper virus into HEK 293T cells using calcium phosphate precipitation. HEK 293T cells were transfected with plasmid DNA and cultured at 37° C. for 6 hrs, the medium was replaced and after 36 h the supernatant was collected and filtered through a 0.45 μm filter. Cells were infected at approximately 70% confluence in DMEM supplemented with 8 μg/ml of polybrene. The following day the medium was changed to basal medium supplemented with 10% FBS and cultured for further assay.
Luciferase assays were performed as previously described (44). Briefly, cells were seeded at 50% confluence in a 24-well plate on the day prior to transfection. Cells were transiently transfected with the appropriate combination of the reporter (300 ng per well), expression vectors (calculated as molar concentration equal to 300 ng of control vector), and control vector (300 ng per well) via calcium phosphate precipitation for HEK 293T or LIPOFECTAMINE 2000TM (Invitrogen, Carlsbad, Calif.) for remaining cell lines according to the manufacturer's instructions. 24 hours post transfection, luciferase assays were performed at room temperature using an AUTOLUMAT LB 953TM (EG&G Berthold). The data are shown as mean±SEM from at least two separate experiments with triplicate samples each.
RNA Isolation, Quantitative Real-Time PCR.
Total RNA was prepared using TRIZOLTM reagent (Invitrogen, Carlsbad, Calif.) following manufacturer's instructions. 5 μg of total RNA was subjected to reverse transcription to synthesize cDNA using the SUPERSCRIPTTM Reverse Transcriptase Kit (Invitrogen, Carlsbad, Calif.). A 25 μl volume reaction consisted of 1 μl reverse transcription product and 100 nM of each primer. The primers used for qRT-PCR are listed as below:












TABLE 1







Seq

SEQ



Gene
Forward primer
ID
Reverse primer
ID
Amplicon


symbol
sequence
No:
sequence
No:
size







SREBP1
5′-
13
5′-
22
104 bp


a
CGGCGCTGCTGACCGACAT

CCCTGCCCCACTCCCAGC





C

AT




 


SREBP1
5′-
14
5′-
23
116 bp


c
GCGCAGATCGCGGAGCCAT

CCCTGCCCCACTCCCAGC







AT




 


SREBP2
5′-
15
5′-
24
140 bp



CAAGCTTCTAAAGGGCATC

AGTAGGGAGAGAAGCCAG





G

CC




 


FANS
5′-
16
5′-
25
 97 bp



CACAGGGACAACCTGGAGT

ACTCCACAGGTGGGAACA





T

AG




 


SCD1
5′-
17
5′-
26
 70 bp



CGACGTGGCTTTTTCTTCTC

CCTTCTCTTTGACAGCTGG







G




 


ACLY
5′-
18
5′-
27
137 bp



GCCCATCCCCAACCAGCCA

TTGCAGGCGCCACCTCATC





C

G




 


ADIPOQ
5′-
19
5′-
28
168 bp



TCCTGCCAGTAACAGGGAA

AGGGGAAGTGTCAGTACC





G

CG




 


aP2
5′-
20
5′-
29
122 bp



CTCTCCGTTCAGATTGAAG

AATCCCGCCTCCATCCTAA





GGG

CT




 


GAPDH
5′-
21
5′-
30
103 bp



GAGTCAACGGATTTGGTCG

TTGAGGTCAATGAAGGGG





T

TC









Cellular Proliferation, Migration and Apoptosis Assays.
Cells were stably transfected with shRNA targeting SREBP1 and control were subjected to TRANSWELLTM migration assays. Cells were seeded on an 8 μm-pore size TRANSWELLTM filter insert (Costar) coated with ECM (Sigma, St. Louis, Mo.) at a density of 1×104 cells in each well in DMEM containing 10% FBS. After 6 h of incubation at 37° C. and 5% CO2, cells adherent to the upper surface of the filter were removed using a cotton applicator. Cells were stained with 0.4% crystal violet dissolved in methanol, and the numbers of cells on the bottom were counted. Data are from at least three experiments done in triplicate (mean±SEM).
TRANSWELLTM migration assays were described in our prior publications (45,46). 2.5×10^4 cells were seeded on an 8 μm-pore size TRANSWELLTM filter insert (Corning Inc., Corning, N.Y.) coated with ECM (1:7.5) (Sigma, St. Louis, Mo.). After 6 h of incubation at 37° C. and 5% CO2, cells adherent to the upper surface of the filter were removed using a cotton applicator. Cells were stained with 0.4% crystal violet dissolved in methanol, and the numbers of cells on the bottom were counted.
Cell death was determined by PE Annexin V Apoptosis Detection Kit (BD Biosciences) and TACS 2 TdT-DAB In Situ Apoptosis Detection Kit (Trevigen, Gaithersburg, Md.) following manufacturer's instructions.
Mixing the BF175 in the Drosophila Food,
1M stock solution of BF175, or BF102 are made in DMSO, and further diluted and mixed in melted fly food for the final concentrations of 50 uM, 100 uM and 200 uM, and the control food was mixed with the equivalent amount of DMSO. Wild-type (w1118) flies were allowed to embryos on these food and female larvae at the third instar wandering stage were analyzed for the Oil Red O staining.
Oil Red O Staining and Quantification.
Drosophila larvae were dissected in PBS and then fixed in 4% formalin in PBS for 15 min at room temperature. They were stained with 5 ml of 0.036% Oil Red O for 25 min, rinsed once with 70% isopropanol and distilled water. After being dried overnight, the Oil Red O from each larva was extracted in 0.3 ml of isopropanol and the O.D. at 510 nm was measured. One-tailed t-test was used for statistical analysis.
REFERENCES


    1. Bratos, K., Roszak, A., Cikowska-Wozniak, E., and Niecewicz, P. (2002) Ginekol Pol 73, 945-950
    2. Gull, B., Karlsson, B., Milsom, I., and Granberg, S. (2001) Am J Obstet Gynecol 185, 386-391
    3. Weiderpass, E., Persson, I., Adami, H. O., Magnusson, C., Lindgren, A., and Baron, J. A. (2000) Cancer Causes Control 11, 185-192
    4. Shoff, S. M., and Newcomb, P. A. (1998) Am J Epidemiol 148, 234-240
    5. Goodman, M. T., Hankin, J. H., Wilkens, L. R., Lyu, L. C., McDuffie, K., Liu, L. Q., and Kolonel, L. N. (1997) Cancer Res 57, 5077-5085
    6. Hua, X., Wu, J., Goldstein, J. L., Brown, M. S., and Hobbs, H. H. (1995) Genomics 25, 667-673
    7. Edwards, P. A., Tabor, D., Kast, H. R., and Venkateswaran, A. (2000) Biochim Biophys Acta 1529, 103-113
    8. Wang, X., Zelenski, N. G., Yang, J., Sakai, J., Brown, M. S., and Goldstein, J. L. (1996) EMBO J 15, 1012-1020
    9. Wang, X., Sato, R., Brown, M. S., Hua, X., and Goldstein, J. L. (1994) Cell 77, 53-62
    10. Hua, X., Yokoyama, C., Wu, J., Briggs, M. R., Brown, M. S., Goldstein, J. L., and Wang, X. (1993) Proc Natl Acad Sci USA 90, 11603-11607
    11. Yokoyama, C., Wang, X., Briggs, M. R., Admon, A., Wu, J., Hua, X., Goldstein, J. L., and Brown, M. S. (1993) Cell 75, 187-197
    12. Briggs, M. R., Yokoyama, C., Wang, X., Brown, M. S., and Goldstein, J. L. (1993) J Biol Chem 268, 14490-14496
    13. Wang, X., Briggs, M. R., Hua, X., Yokoyama, C., Goldstein, J. L., and Brown, M. S. (1993) J Biol Chem 268, 14497-14504
    14. Shimano, H. (2001) Prog Lipid Res 40, 439-452
    15. Horton, J. D., and Shimomura, I. (1999) Curr Opin Lipidol 10, 143-150
    16. Kim, J. B., and Spiegelman, B. M. (1996) Genes Dev 10, 1096-1107
    17. Liang, G., Yang, J., Horton, J. D., Hammer, R. E., Goldstein, J. L., and Brown, M. S. (2002) J Biol Chem 277, 9520-9528
    18. Bene, H., Lasky, D., and Ntambi, J. M. (2001) Biochem Biophys Res Commun 284, 1194-1198
    19. Ntambi, J. M. (1999) J Lipid Res 40, 1549-1558
    20. Tabor, D. E., Kim, J. B., Spiegelman, B. M., and Edwards, P. A. (1999) J Biol Chem 274, 20603-20610
    21. Shimomura, I., Shimano, H., Korn, B. S., Bashmakov, Y., and Horton, J. D. (1998) J Biol Chem 273, 35299-35306
    22. Yamashita, T., Honda, M., Takatori, H., Nishino, R., Minato, H., Takamura, H., Ohta, T., and Kaneko, S. (2009) J Hepatol 50, 100-110
    23. Yahagi, N., Shimano, H., Hasegawa, K., Ohashi, K., Matsuzaka, T., Najima, Y., Sekiya, M., Tomita, S., Okazaki, H., Tamura, Y., Iizuka, Y., Nagai, R., Ishibashi, S., Kadowaki, T., Makuuchi, M., Ohnishi, S., Osuga, J., and Yamada, N. (2005) Eur J Cancer 41, 1316-1322
    24. Yang, Y. A., Morin, P. J., Han, W. F., Chen, T., Bornman, D. M., Gabrielson, E. W., and Pizer, E. S. (2003) Exp Cell Res 282, 132-137
    25. Li, J. N., Mahmoud, M. A., Han, W. F., Ripple, M., and Pizer, E. S. (2000) Exp Cell Res 261, 159-165
    26. Ettinger, S. L., Sobel, R., Whitmore, T. G., Akbari, M., Bradley, D. R., Gleave, M. E., and Nelson, C. C. (2004) Cancer Res 64, 2212-2221
    27. Furuta, E., Pai, S. K., Zhan, R., Bandyopadhyay, S., Watabe, M., Mo, Y. Y., Hirota, S., Hosobe, S., Tsukada, T., Miura, K., Kamada, S., Saito, K., Iiizumi, M., Liu, W., Ericsson, J., and Watabe, K. (2008) Cancer Res 68, 1003-1011
    28. Yoon, S., Lee, M. Y., Park, S. W., Moon, J. S., Koh, Y. K., Ahn, Y. H., Park, B. W., and Kim, K. S. (2007) J Biol Chem 282, 26122-26131
    29. Yang, Y. A., Han, W. F., Morin, P. J., Chrest, F. J., and Pizer, E. S. (2002) Exp Cell Res 279, 80-90
    30. Kim, J. B., Wright, H. M., Wright, M., and Spiegelman, B. M. (1998) Proc Natl Acad Sci USA 95, 4333-4337
    31. Chen, G., Liang, G., Ou, J., Goldstein, J. L., and Brown, M. S. (2004) Proc Natl Acad Sci USA 101, 11245-11250
    32. Walker, A. K., Yang, F., Jiang, K., Ji, J. Y., Watts, J. L., Purushotham, A., Boss, O., Hirsch, M. L., Ribich, S., Smith, J. J., Israelian, K., Westphal, C. H., Rodgers, J. T., Shioda, T., Elson, S. L., Mulligan, P., Najafi-Shoushtari, H., Black, J. C., Thakur, J. K., Kadyk, L. C., Whetstine, J. R., Mostoslaysky, R., Puigserver, P., Li, X., Dyson, N. J., Hart, A. C., and Naar, A. M. (2010) Genes Dev 24, 1403-1417
    33. Taghibiglou, C., Martin, H. G., Lai, T. W., Cho, T., Prasad, S., Kojic, L., Lu, J., Liu, Y., Lo, E., Zhang, S., Wu, J. Z., Li, Y. P., Wen, Y. H., Imm, J. H., Cynader, M. S., and Wang, Y. T. (2009) Nat Med 15, 1399-1406
    34. Das, B. C., Zhao, X., Tang, X. Y., and Yang, F. (2011) Bioorg Med Chem Lett 21, 5638-5641
    35. Van de Sande, T., De Schrijver, E., Heyns, W., Verhoeven, G., and Swinnen, J. V. (2002) Cancer Res 62, 642-646
    36. Porstmann, T., Griffiths, B., Chung, Y. L., Delpuech, O., Griffiths, J. R., Downward, J., and Schulze, A. (2005) Oncogene 24, 6465-6481
    37. Bennett, M. K., Lopez, J. M., Sanchez, H. B., and Osborne, T. F. (1995) J Biol Chem 270, 25578-25583
    38. Choi, W. I., Jeon, B. N., Park, H., Yoo, J. Y., Kim, Y. S., Koh, D. I., Kim, M. H., Kim, Y. R., Lee, C. E., Kim, K. S., Osborne, T. F., and Hur, M. W. (2008) J Biol Chem 283, 29341-29354
    39. Eberhard, Y., Gronda, M., Hurren, R., Datti, A., MacLean, N., Ketela, T., Moffat, J., Wrana, J. L., and Schimmer, A. D. (2011) Oncotarget 2, 186-196
    40. Zhou, J., Zhang, W., Liang, B., Casimiro, M. C., Whitaker-Menezes, D., Wang, M., Lisanti, M. P., Lanza-Jacoby, S., Pestell, R. G., and Wang, C. (2009) Int J Biochem Cell Biol 41, 2334-2342
    41. Amemiya-Kudo, M., Shimano, H., Yoshikawa, T., Yahagi, N., Hasty, A. H., Okazaki, H., Tamura, Y., Shionoiri, F., Iizuka, Y., Ohashi, K., Osuga, J., Harada, K., Gotoda, T., Sato, R., Kimura, S., Ishibashi, S., and Yamada, N. (2000) J Biol Chem 275, 31078-31085
    42. Chu, K., Miyazaki, M., Man, W. C., and Ntambi, J. M. (2006) Mol Cell Biol 26, 6786-6798
    43. Toth, J. I., Datta, S., Athanikar, J. N., Freedman, L. P., and Osborne, T. F. (2004) Mol Cell Biol 24, 8288-8300
    44. Wang, C., Fu, M., D'Amico, M., Albanese, C., Zhou, J. N., Brownlee, M., Lisanti, M. P., Chatterjee, V. K., Lazar, M. A., and Pestell, R. G. (2001) Mol Cell Biol 21, 3057-3070
    45. Zhou, J., Liu, Y., Zhang, W., Popov, V. M., Wang, M., Pattabiraman, N., Sune, C., Cvekl, A., Wu, K., Jiang, J., Wang, C., and Pestell, R. G. (2010) J Biol Chem
    46. Meng, H., Tian, L., Zhou, J., Li, Z., Jiao, X., Li, W. W., Plomann, M., Xu, Z., Lisanti, M. P., Wang, C., and Pestell, R. G. (2011) Cell Cycle 10, 73-81


Example 2
According to the statistics published by American Cancer Society, about 1,596,670 new cancer cases were expected to be diagnosed in 2011. The National Cancer Institute estimates that approximately 11.7 million Americans with a history of cancer were alive in 2007. Epidemiological studies have identified obese and obesity as the most common risk factors for cancer. Obese patients have a 2-4 times greater risk of developing endometrial, breast and colon and liver cancers compared to population of normal weight. As population size affected by obese and obesity is expected to grow, particularly in developing countries, cancer will continue to be a serious public health problem. The significantly enhanced lipogenesis is a metabolic hallmark of rapidly proliferating tumor cells. Further, there is currently no effective therapy to target both obesity and cancer. Although most normal cells acquire the bulk of their fatty acids from circulation, tumor cells synthesize more than 90% of required lipids de novo. The sterol regulatory element-binding protein 1 (SREBP1), encoded by SREBP1 gene, as described herein, is a master regulator of lipogenic gene expression. The inventors' work has strongly associated altered lipogenic signaling in cancer with oncogene ErbB2 and estrogen receptor status in breast cancer.
To broadly explore possible targets of BF175, a microarray expression analysis of cells treated with BF175 compared to control was conducted. The microarray analyses detected that the mRNA expression of 472 genes was differentially increased, while that of 542 was decreased in BF175 treated cells. INGENUITYTM analysis of these BF175-regulated genes revealed “Lipid Metabolism” as the most significant function (Table 2). Of those BF175 down-regulated genes, 48 genes were directly involved in catalyzing and converting the glucose to produce either lipids or cholesterol (FIGS. 6A-6D, and Table 2). A considerable number of these BF175 genes have been reported as SREBP1 targets, including SREBP1 and SREBP2, suggesting that BF175 directly regulates SREBP1 activity. Furthermore, the significant overlap between this dataset and those from previously published SREBP1 gene signature again confirmed the specificity of BF175.
Example 3
NCI60 testing was performed in 59 cell lines with BF175 at a single dose of 10^−5 molar. The one-dose data was reported as a mean graph of the percent growth of treated cells. The number reported for the one-dose assay is growth relative to the no-drug control, and relative to the time zero number of cells. This allows detection of both growth inhibition (values between 0 and 100) and lethality (values less than 0). For example, a value of 100 means no growth inhibition. A value of 40 would mean 60% growth inhibition. A value of 0 means no net growth over the course of the experiment. A value of −40 would mean 40% lethality. A value of −100 means all cells are dead.
The human tumor cell lines of the cancer screening panel were grown in RPMI 1640 medium containing 5% fetal bovine serum and 2 mM L-glutamine Cells were inoculated into 96 well microtiter plates in 100 μL at plating densities ranging from 5,000 to 40,000 cells/well depending on the doubling time of individual cell lines. After cell inoculation, the microtiter plates were incubated at 37° C., 5% CO2, 95% air and 100% relative humidity for 24 h prior to addition of BF175. After 24 h, two plates of each cell line were fixed in situ with TCA, to represent a measurement of the cell population for each cell line at the time of drug addition (Tz). BF175 was solubilized in dimethyl sulfoxide at 400-fold the desired final maximum test concentration and stored frozen prior to use. At the time of drug addition, an aliquot of frozen concentrate was thawed and diluted to twice the desired final maximum test concentration with complete medium containing 50 μg/ml gentamicin. Aliquots of 100 μl of these drug dilutions were added to the appropriate microtiter wells already containing 100 μl of medium, resulting in the required final drug concentrations.
Following drug addition, the plates were incubated for an additional 48 h at 37° C., 5% CO2, 95% air, and 100% relative humidity. For adherent cells, the assay is terminated by the addition of cold TCA. Cells were fixed in situ by the gentle addition of 50 μl of cold 50% (w/v) TCA (final concentration, 10% TCA) and incubated for 60 minutes at 4° C. The supernatant was discarded, and the plates are washed five times with tap water and air dried. Sulforhodamine B (SRB) solution (100 μl) at 0.4% (w/v) in 1% acetic acid was added to each well, and plates were incubated for 10 minutes at room temperature. After staining, unbound dye was removed by washing five times with 1% acetic acid and the plates were air dried. Bound stain was subsequently solubilized with 10 mM trizma base, and the absorbance was read on an automated plate reader at a wavelength of 515 nm.
For suspension cells, the methodology is the same except that the assay was terminated by fixing settled cells at the bottom of the wells by gently adding 50 μl of 80% TCA (final concentration, 16% TCA). Using the absorbance measurements [time zero, (Tz), control growth, (C), and test growth in the presence of drug at 10^−5 molar concentration of BF175 (Ti)], the percentage growth is calculated as: [(Ti−Tz)/(C−Tz)]×100 for concentrations for which Ti>/=Tz and [(Ti−Tz)/Tz]×100 for concentrations for which Ti<Tz.











TABLE 2





Entrez
Gene





ID
symbol
Description
Fold change
P-value



















3156
HMGCR
3-hydroxy-3-methylglutaryl-CoA reductase
−1.96
0.0003


7108
TM7SF2
transmembrane 7 superfamily member 2/C-14 sterol reductase
−1.94
0.0000


3638
INSIG1
insulin induced gene 1
−1.86
0.0000


1717
DHCR7
7-dehydrocholesterol reductase
−1.79
0.0000


6576
SLC25A1
solute carrier family 25 (mitochondrial carrier: citrate transporter). member 1
−1.78
0.0000


4598
MVK
mevalonate kinase
−1.76
0.0013


6319
SCD
stearoyl-CoA desaturase (delta-9-desaturase)
−1.74
0.0000


9415
FADS2
fatty acid desaturase 2
−1.71
0.0004


1384
CRAT
carnitine O-acetyltransferase
−1.71
0.0000


6307
SC4MOL
sterol-C4-methyl oxidase-like
−1.71
0.0000


54947
LPCAT2
lysophosphatidylcholine acyltransferase 2
−1.68
0.0009


3638
INSIG1
insulin induced gene 1
−1.67
0.0007


3949
LDLR
low density lipoprotein receptor
−1.67
0.0000


6721
SREBF2
sterol regulatory element binding transcription factor 2
−1.67
0.0002


51181
DCXR
dicarbonyl/L-xylulose reductase
−1.67
0.0000


2222
FDFT1
farnesyl-diphosphate farnesyltransferase 1
−1.64
0.0000


6720
SREBF1
sterol regulatory element binding transcription factor 1
−1.64
0.0144


29988
SLC2A8
solute carrier family 2 (facilitated glucose transporter), member 8
−1.62
0.0000


11182
SLC2A6
solute carrier family 2 (facilitated glucose transporter), member 6
−1.61
0.0000


30
ACAA1
acetyl-CoA acyltransferase 1
−1.59
0.0000


4597
MVD
mevalonate (diphospho) decarboxylase
−1.58
0.0001


10682
EBP
emopamil binding protein (sterol isomerase)
−1.57
0.0201


6713
SQLE
squalene epoxidase
−1.54
0.0000


79602
ADIPOR2
adiponectin receptor 2
−1.54
0.0001


10162
LPCAT3
lysophosphatidylcholine acyltransferase 3
−1.48
0.0004


10999
SLC27A4
solute carrier family 27 (fatty acid transporter), member 4
−1.48
0.0063


3422
IDI1
isopentenyl-diphosphate delta isomerase 1
−1.47
0.0001


1431
CS
citrate synthase
−1.47
0.0058


6720
SREBF1
sterol regulatory element binding transcription factor 1
−1.46
0.0002


1737
DLAT
dihydrolipoamide S-acetyltransferase
−1.45
0.0015


47
ACLY
ATP citrate lyase
−1.45
0.0017


3422
IDI1
isopentenyl-diphosphate delta isomerase 1
−1.44
0.0000


2194
FASN
fatty acid synthase
−1.44
0.0000


1595
CYP51A1
cytochrome P450, family 51, subfamily A, polypeptide 1
−1.43
0.0241


55326
AGPAT5
1-acylglycerol-3-phosphate O-acyltransferase 5
−1.40
0.0018


2542
SLC37A4
solute carrier family 37 (glucose-6-phosphate transporter), member 4
−1.40
0.0112


2224
FDPS
farnesyl diphosphate synthase
−1.40
0.0010


10423
CDIPT
CDP-diacylglycerol-inositol 3-phosphatidyltransferase
−1.38
0.0111


31
ACACA
acetyl-CoA carboxylase alpha
−1.38
0.0001


27349
MCAT
malonyl CoA: ACP acyltransferase (mitochondrial)
−1.37
0.0000


2639
GCDH
glutaryl-CoA dehydrogenase
−1.36
0.0281


9926
LPGAT1
lysophosphatidylglycerol acyltransferase 1
−1.35
0.0297


3795
KHK
ketohexokinase (fructokinase)
−1.35
0.0010


11332
ACOT7
acyl-CoA thioesterase 7
−1.34
0.0003


8310
ACOX3
acyl-CoA oxidase 3, pristanoyl
−1.34
0.0238


3417
IDH1
isocitrate dehydrogenase 1 (NADP+), soluble
−1.34
0.0003


4047
LSS
lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)
−1.33
0.0033


3988
LIPA
lipase A, lysosomal acid, cholesterol esterase
−1.30
0.0015

## Claims

1. A method of treating endometrial cancer in a subject, the method comprising administering to the subject an inhibitor of sterol regulatory binding protein 1 (SREBP1) selected from the group consisting of: