US20150259649A1 - Cellular compositions used to restore stem cell or progenitor cell function and methods related thereto - Google Patents

Cellular compositions used to restore stem cell or progenitor cell function and methods related thereto Download PDF

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US20150259649A1
US20150259649A1 US14/438,894 US201314438894A US2015259649A1 US 20150259649 A1 US20150259649 A1 US 20150259649A1 US 201314438894 A US201314438894 A US 201314438894A US 2015259649 A1 US2015259649 A1 US 2015259649A1
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cells
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benzylpiperidin
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Young-Sup Yoon
Ji Woong Han
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Emory University
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06—Animal cells or tissues; Human cells or tissues
    • C12N5/0602—Vertebrate cells
    • C12N5/0652—Cells of skeletal and connective tissues; Mesenchyme
    • C12N5/0662—Stem cells
    • C12N5/0663—Bone marrow mesenchymal stem cells (BM-MSC)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/28—Bone marrow; Haematopoietic stem cells; Mesenchymal stem cells of any origin, e.g. adipose-derived stem cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/44—Vessels; Vascular smooth muscle cells; Endothelial cells; Endothelial progenitor cells
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D239/00—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings
    • C07D239/70—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings condensed with carbocyclic rings or ring systems
    • C07D239/72—Quinazolines; Hydrogenated quinazolines
    • C07D239/95—Quinazolines; Hydrogenated quinazolines with hetero atoms directly attached in positions 2 and 4
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
    • C07D401/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing three or more hetero rings
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2501/00—Active agents used in cell culture processes, e.g. differentation
    • C12N2501/065—Modulators of histone acetylation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2501/00—Active agents used in cell culture processes, e.g. differentation
    • C12N2501/40—Regulators of development

Definitions

  • This disclosure relates to compounds, compositions and methods of epigenetically transforming cells.
  • the disclosure relates to methods of generating epigenetically altered cells comprising mixing isolated cells with compositions disclosed herein under conditions such that epigenetically altered cells are formed.
  • methods of treating or preventing vascular or diabetic diseases or conditions are contemplated.
  • the disclosure contemplates methods of epigenetically modifying stem or progenitor cells comprising mixing the stem or progenitor cells and compositions comprising compounds disclosed wherein such as a quinazoline compound, 5-aza-2′-deoxycytidine, or/and N-Phthalyl-L-tryptophan (RG108), under conditions such that cells with enhanced angiogenic gene expression are produced.
  • the conditions are such that reduced DNA methylation in the promoters of angiogenic genes occurs.
  • the angiogenic genes are one or more or all of the genes selected from Akt1, Hgf, Mapk14, Sphk1, Vegfc, Nudt6, Kdr, Vegfa, and Pten.
  • the stem or progenitor cells are mesenchymal stem cells (MSCs) or endothelial progenitor cells (EPCs), cardiac stem cells, myoblasts, adult bone marrow-derived cells, umbilical cord blood cells, fibroblasts, or peripheral blood CD34 + cells.
  • the endothelial progenitor cells are bone marrow derived.
  • the cells are obtained from a subject diagnosed with diabetes and/or cardiovascular disease.
  • the composition comprise mixtures of compounds disclosed herein.
  • the composition comprises a quinazoline compound optionally in combination with DNA methyltransferase inhibitor, a histone deacetylase (HDAC) inhibitor, DNA methylation inhibitor, a Rho-associated kinase (ROCK) inhibitor, Wnt inhibitor, GSK-3beta inhibitor, and/or a dihydropyridine.
  • the DNA methyltransferase inhibitor is N-phthalyl-L-tryptophan (RG 108).
  • the DNA methylation inhibitor is 5-azacitidine or decitabine.
  • the HDAC inhibitor is vorinostat—suberoylanilide hydroxamic acid (SAHA), trichostatin A (TSA), or valproic acid (VPA).
  • SAHA vorinostat—suberoylanilide hydroxamic acid
  • TSA trichostatin A
  • VPA valproic acid
  • the ROCK inhibitor is 4-(1-aminoethyl)-N-(pyridin-4-yl)cyclohexanecarboxamide (Y-27632) or salt thereof.
  • the dihydropyridine is 1,4-dihydro-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-3-pyridinecarboxylic acid, methyl ester (BayK8644), ester, derivative, or salt thereof.
  • the GSK-3beta inhibitor is 6-[[2-[[4-(2,4-dichlorophenyl)-5-(5-methyl-1H-imidazol-2-yl)-2 pyrimidinyl]amino]ethyl]amino]-3-pyridinecarbonitrile (CHIR99201) or salt thereof.
  • the quinazoline compound has formula I, formula IA, or formula II.
  • the disclosure contemplates methods of treating or preventing vascular disease or condition comprising: mixing progenitor cells from a subject and a composition as provided herein under conditions such that epigenetically modified cells with enhanced angiogenic gene expression are produced; and administering an effective amount of a composition comprising the epigenetically modified cells or cells cultured therefrom to a subject in need thereof.
  • the progenitor cells are bone marrow derived cells, endothelial progenitor cells, or mesenchymal stem cells.
  • the progenitor cells were obtained from the subject receiving the administered composition.
  • the vascular disease or condition is peripheral vascular disease, myocardial ischemia, cardiovascular disease, heart failure, or stroke.
  • the disclosure contemplates methods of treating or preventing a diabetic disease or conditions comprising: mixing progenitor cells from a subject and a composition as provided herein under conditions such that epigenetically modified cells with enhanced angiogenic gene expression are produced; and administering an effective amount of a composition comprising the epigenetically modified cells or cells cultured therefrom to a subject in need thereof.
  • the progenitor cells are bone marrow derived cells, endothelial progenitor cells, or mesenchymal stem cells.
  • the progenitor cells were obtained from the subject receiving the administered composition.
  • the diabetic disease or condition is diabetic wounds or diabetic neuropathy.
  • the epigenetically modified cells may be cultured, expanded, or replicated in order to provide enhanced concentrations upon administration/transplantation and the modified cells may be autologous (i.e., derived from the person on whom they are used) or allogeneic (i.e., originating from another person) in origin.
  • methods include those subjects that are co-morbid with a vascular disease or condition and a diabetic disease or condition.
  • the disclosure contemplates intravenous injection and direct infusion into the coronary arteries.
  • the methods can be used in subject whose blood flow has been restored to their hearts after a heart attack.
  • the compositions are injected directly into the ventricular wall of the subject, i.e., endo-myocardial injection or into the peritoneal cavity, and may be carried out either via a catheter or during open-heart surgery.
  • the disclosure contemplates methods of treating diseases or conditions disclosed herein comprising administering effective amounts of pharmaceutical compositions disclosed herein comprising a compound or mixture of compounds to a subject in need thereof.
  • kidney disease or wound healing by methods disclosed herein are contemplated.
  • FIG. 1 shows data suggesting the restoration of gene expression of angiogenic genes in diabetic MSCs with compounds.
  • FIG. 2 shows data on impaired proliferation of D-MSCs.
  • FIG. 3 shows data on the restoration of impaired proliferation of D-MSCs with compounds.
  • FIG. 4 shows data on the restoration of impaired cell survival of diabetic MSCs with compounds.
  • FIG. 5 shows data on the restoration of impaired adhesion of diabetic MSCs with compounds.
  • FIG. 6 shows data on the restoration of impaired cell movement of diabetic MSCs with compounds.
  • FIG. 7 shows data on the restoration of impaired tube formation of diabetic MSCs with compounds.
  • FIG. 8 shows data on the improvement of hindlimb ischemia by implantation of reprogrammed D-MSCs.
  • FIG. 9 shows data on the increased capillary density by implantation of reprogrammed D-MSCs.
  • FIG. 10 shows data on the increased angiogenic factors by implantation of reprogrammed D-MSCs.
  • FIG. 11A shows data on the restoration of impaired global gene expressions in diabetic MSCs by epigenetic compounds.
  • the color key represents FPKM normalized log 2 transformed counts. Yellow indicates high expression; orange indicates intermediate expression and red indicates no expression.
  • FIG. 11B shows a Bar plot subset of representative 350 genes which are straightforward to identify highly expressed genes in RD-MSCs which were treated with epigenetic drug.
  • Blue bar represented genes expressed in N-MSC, and red bar indicated for genes in D-MSC. And restored gene expressions in RD-MSC were showed with green bar plot.
  • FIG. 12 shows microarray results of mRNA expression of angiogenic genes.
  • FIG. 13 shows gene expression patterns (top) and DNA methylation (bottom) at the promoter regions of angiogenic genes in EPCs.
  • Embodiments of the present disclosure will employ, unless otherwise indicated, techniques of medicine, organic chemistry, biochemistry, molecular biology, pharmacology, and the like, which are within the skill of the art. Such techniques are explained fully in the literature.
  • induced pluripotent stem cells refers to cells induced to a state that can differentiate into at least one cell of the endoderm, mesoderm and ectoderm. Such characteristics include the expression of certain genes and proteins, chromatic methylation patterns, doubling time, embryoid body formation, teratoma formation, and differentiability. Induced pluripotent stem cells typically express alkaline phosphatase, Oct 4, Sox2, Nanog, and other pluripoteny-promoting factors. It is not intended that the cells be entirely identical to embryonic cells. Induced pluripotent stem cells may not necessarily be capable of differentiating into any type of cell.
  • SSEA-1 is a mouse ESC/iPSC specific marker; SSEA-3 and -4 are not expressed in mouse ESC/iPSC. However, human ESC/iPSC express SSEA-3 and SSEA-4, not SSEA-1. SSEA-1 is mouse iPSC specific. SSEA-3, SSEA-4 is human iPSC specific. TRA-1-60 and TRA-1-8 are usually used to identify human PSC.
  • alkyl means a noncyclic straight chain or branched, unsaturated or saturated hydrocarbon such as those containing from 1 to 10 carbon atoms, while the term “lower alkyl” or “C 1-4 alkyl” has the same meaning as alkyl but contains from 1 to 4 carbon atoms. The term “higher alkyl” has the same meaning as alkyl but contains from 7 to 20 carbon atoms.
  • saturated straight chain alkyls include methyl, ethyl, n-propyl, n-butyl, n-pentyl, n-hexyl, n-septyl, n-octyl, n-nonyl, and the like; while saturated branched alkyls include isopropyl, sec-butyl, isobutyl, tert-butyl, isopentyl, and the like.
  • Unsaturated alkyls contain at least one double or triple bond between adjacent carbon atoms (referred to as an “alkenyl” or “alkynyl”, respectively).
  • 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; while representative straight chain and branched alkynyls include acetylenyl, propynyl, 1-butyryl, 2-butynyl, 1-pentynyl, 2-pentynyl, 3-methyl-1-butynyl, and the like.
  • Non-aromatic mono or polycyclic alkyls are referred to herein as “carbocycles” or “carbocyclyl” groups.
  • Representative saturated carbocycles include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like; while unsaturated carbocycles include cyclopentenyl and cyclohexenyl, and the like.
  • Heterocarbocycles or heterocarbocyclyl groups are carbocycles which contain from 1 to 4 heteroatoms independently selected from nitrogen, oxygen and sulfur which may be saturated or unsaturated (but not aromatic), monocyclic or polycyclic, and wherein the nitrogen and sulfur heteroatoms may be optionally oxidized, and the nitrogen heteroatom may be optionally quaternized.
  • Heterocarbocycles include morpholinyl, pyrrolidinonyl, pyrrolidinyl, piperidinyl, hydantoinyl, valerolactamyl, oxiranyl, oxetanyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydropyridinyl, tetrahydroprimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydropyrimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, and the like.
  • Aryl means an aromatic carbocyclic monocyclic or polycyclic ring such as phenyl or naphthyl. Polycyclic ring systems may, but are not required to, contain one or more non-aromatic rings, as long as one of the rings is aromatic.
  • heteroaryl refers an aromatic heterocarbocycle having 1 to 4 heteroatoms selected from nitrogen, oxygen and sulfur, and containing at least 1 carbon atom, including both mono- and polycyclic ring systems.
  • Polycyclic ring systems may, but are not required to, contain one or more non-aromatic rings, as long as one of the rings is aromatic.
  • heteroaryls are furyl, benzofuranyl, thiophenyl, benzothiophenyl, pyrrolyl, indolyl, isoindolyl, azaindolyl, pyridyl, quinolinyl, isoquinolinyl, oxazolyl, isooxazolyl, benzoxazolyl, pyrazolyl, imidazolyl, benzimidazolyl, thiazolyl, benzothiazolyl, isothiazolyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, cinnolinyl, phthalazinyl, and quinazolinyl. It is contemplated that the use of the term “heteroaryl” includes N-alkylated derivatives such as a 1-methylimidazol-5-yl substituent.
  • heterocycle or “heterocyclyl” refers to mono- and polycyclic ring systems having 1 to 4 heteroatoms selected from nitrogen, oxygen and sulfur, and containing at least 1 carbon atom.
  • the mono- and polycyclic ring systems may be aromatic, non-aromatic or mixtures of aromatic and non-aromatic rings.
  • Heterocycle includes heterocarbocycles, heteroaryls, and the like.
  • Alkylthio refers to an alkyl group as defined above attached through a sulfur bridge.
  • An example of an alkylthio is methylthio, (i.e., —S—CH 3 ).
  • Alkoxy refers to an alkyl group as defined above attached through an oxygen bridge.
  • alkoxy include, but are not limited to, methoxy, ethoxy, n-propoxy, i-propoxy, n-butoxy, s-butoxy, t-butoxy, n-pentoxy, and s-pentoxy.
  • Preferred alkoxy groups are methoxy, ethoxy, n-propoxy, i-propoxy, n-butoxy, s-butoxy, t-butoxy.
  • Alkylamino refers an alkyl group as defined above attached through an amino bridge.
  • An example of an alkylamino is methylamino, (i.e., —NH—CH 3 ).
  • Alkanoyl refers to an alkyl as defined above attached through a carbonyl bride (i.e., —(C ⁇ O)alkyl).
  • Alkylsulfonyl refers to an alkyl as defined above attached through a sulfonyl bridge (i.e., —S( ⁇ O) 2 alkyl) such as mesyl and the like, and “Arylsulfonyl” refers to an aryl attached through a sulfonyl bridge (i.e.,—S( ⁇ O) 2 aryl).
  • Alkylsulfinyl refers to an alkyl as defined above attached through a sulfinyl bridge (i.e. —S( ⁇ O)alkyl).
  • substituted refers to a molecule wherein at least one hydrogen atom is replaced with a substituent. When substituted, one or more of the groups are “substituents.” The molecule may be multiply substituted. In the case of an oxo substituent (“ ⁇ O”), two hydrogen atoms are replaced.
  • Example substituents within this context may include halogen, hydroxy, alkyl, alkoxy, nitro, cyano, oxo, carbocyclyl, carbocycloalkyl, heterocarbocyclyl, heterocarbocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, —NR a R b , —NR a C( ⁇ O)R b , —NR a C( ⁇ O)NR a NR b , —NR a C( ⁇ O)OR b , —NR a SO 2 R b , —C( ⁇ O)R a , —C( ⁇ O)OR a , —C( ⁇ O)NR a R b , —OC( ⁇ O)NR a R b , —OR a , —SR a , —SOR a , —S( ⁇ O) 2 R a , —OS( ⁇
  • R a and R b in this context may be the same or different and independently hydrogen, halogen hydroxyl, alkyl, alkoxy, alkyl, amino, alkylamino, dialkylamino, carbocyclyl, carbocycloalkyl, heterocarbocyclyl, heterocarbocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl.
  • salts refer to derivatives of the disclosed compounds where the parent compound is modified making acid or base salts thereof.
  • salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines, alkylamines, or dialkylamines; alkali or organic salts of acidic residues such as carboxylic acids; and the like.
  • the salts are conventional nontoxic pharmaceutically acceptable salts including the quaternary ammonium salts of the parent compound formed, and non-toxic inorganic or organic acids.
  • Preferred salts include those derived from inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like; and the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicylic, sulfanilic, 2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isethionic, and the like.
  • inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like
  • organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic,
  • Subject refers any animal, preferably a human patient, livestock, rodent, monkey or domestic pet.
  • the term “derivative” refers to a structurally similar compound that retains sufficient functional attributes of the identified analogue.
  • the derivative may be structurally similar because it is lacking one or more atoms, substituted, a salt, in different hydration/oxidation states, or because one or more atoms within the molecule are switched, such as, but not limited to, replacing an oxygen atom with a sulfur or nitrogen atom or replacing an amino group with a hydroxyl group or vice versa.
  • the derivative may be a prodrug.
  • Derivatives may be prepare by any variety of synthetic methods or appropriate adaptations presented in synthetic or organic chemistry text books, such as those provide in March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, Wiley, 6th Edition (2007) Michael B. Smith or Domino Reactions in Organic Synthesis, Wiley (2006) Lutz F. Tietze hereby incorporated by reference.
  • the term “combination with” when used to describe administration with an additional treatment means that the agent may be administered prior to, together with, or after the additional treatment, or a combination thereof.
  • Chromatin is the complex of DNA and the histone proteins. Chromatin remodeling occurs through post translational modification of the histone proteins. Chromatic remodeling may also occur with the addition of methyl groups to the DNA. Cytosines are often converted to 5-methylcytosine in CG sequences of DNA, often referred to as methylated “CpGs.” 5-Methylcytosine, like cytosine, pairs with guanine Highly methylated DNA tends to be less transcriptionally active. Histone acetylation, methylation, ubiquitylation, and phosphorylation modifications typically occur at the N-termini of histones.
  • HATs histone acetyltransferase enzymes
  • EPCs endothelial progenitor cells
  • MSCs mesenchymal stem cells
  • EPCs endothelial progenitor cells
  • epigenetic modulators can rescue gene expression of these progenitor and stem cells and thus restore their tissue repairing and angiogenic capacities.
  • the candidate diseases that are applied by this new cell therapy include peripheral vascular disease, myocardial ischemia, heart failure, diabetic wounds, diabetic neuropathy, and stroke.
  • D-BMCs diabetic bone marrow-derived cells
  • composition comprising compounds or combinations of: DNA methyltransferase inhibitors (e.g., 5-Aza-2′-Deoxycytidine, 5-Aza or RG1 08), histone deacetylase (HDAC) inhibitors (e.g., valproic acid, VPA), and histone methyltransferase (HMT) inhibitors (e.g., compounds of formula I for G9a and GLP HMTs).
  • DNA methyltransferase inhibitors e.g., 5-Aza-2′-Deoxycytidine, 5-Aza or RG1 08
  • HDAC histone deacetylase
  • VPA valproic acid
  • HMT histone methyltransferase
  • the disclosure contemplates the use of quinazoline compounds disclosed herein to generate epigenetically altered cells. Although it is not intended that certain embodiments of the disclosure be limited by any particular mechanism, it is believed that the compounds typically have the ability to inhibit the function of methyltransferases such as G9a methyltransferase.
  • contemplated quinazoline compounds have Formula I:
  • R 1 , R 2 , R 3 , R 4 , R 5 , and R 6 are each the same or different hydrogen, alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein each R 1 , R 2 , R 3 , R 4 , R 5 , and R 6 are optionally substituted with one or more, the same or different, R 7 ;
  • R 7 is alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein R 7 is optionally substituted with one or more, the same or different, R 8 ; and
  • R 8 is halogen, nitro, cyano, hydroxy, trifluoromethoxy, trifluoromethyl, amino, formyl, carboxy, carbamoyl, mercapto, sulfamoyl, methyl, ethyl, methoxy, ethoxy, acetyl, acetoxy, methylamino, ethylamino, dimethylamino, diethylamino, N-methyl-N-ethylamino, acetylamino, N-methylcarbamoyl, N-ethylcarbamoyl, N,N-dimethylcarbamoyl, N,N-diethylcarbamoyl, N-methyl-N-ethylcarbamoyl, methylthio, ethylthio, methylsulfinyl, ethylsulfinyl, mesyl, ethylsulfony
  • R 4 is alkoxy optionally substituted with one or more, the same or different, R 7 .
  • R 2 is alkylamino optionally substituted with one or more, the same or different, R 7 .
  • R 2 is a heterocyclyl optionally substituted with one or more, the same or different, R 7 .
  • R 1 is alkyl or benzyl optionally substituted with one or more, the same or different, R 7 .
  • contemplated quinazoline compounds have Formula IA:
  • R 1 , R 3 , R 4 , R 5 , and R 6 are each the same or different hydrogen, alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein each R 1 , R 3 , R 4 , R 5 , and R 6 are optionally substituted with one or more, the same or different, R 7 ;
  • R 7 is alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein R 7 is optionally substituted with one or more, the same or different, R 8 ;
  • R 8 is halogen, nitro, cyano, hydroxy, trifluoromethoxy, trifluoromethyl, amino, formyl, carboxy, carbamoyl, mercapto, sulfamoyl, methyl, ethyl, methoxy, ethoxy, acetyl, acetoxy, methylamino, ethylamino, dimethylamino, diethylamino, N-methyl-N-ethylamino, acetylamino, N-methylcarbamoyl, N-ethylcarbamoyl, N,N-dimethylcarbamoyl, N,N-diethylcarbamoyl, N-methyl-N-ethylcarbamoyl, methylthio, ethylthio, methylsulfinyl, ethylsulfinyl, mesyl, ethylsulfony
  • R 9 and R 10 are each the same or different hydrogen, alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein each R 9 and R 10 are optionally substituted with one or more, the same or different, R 11 ;
  • R 9 and R 10 come together to form a heterocyclyl optionally substituted with one or more, the same or different, R 11 ;
  • R 11 is alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein R 11 is optionally substituted with one or more, the same or different, R 12 ; and
  • R 12 is halogen, nitro, cyano, hydroxy, trifluoromethoxy, trifluoromethyl, amino, formyl, carboxy, carbamoyl, mercapto, sulfamoyl, methyl, ethyl, methoxy, ethoxy, acetyl, acetoxy, methylamino, ethylamino, dimethylamino, diethylamino, N-methyl-N-ethylamino, acetylamino, N-methylcarbamoyl, N-ethylcarbamoyl, N,N-dimethylcarbamoyl, N,N-diethylcarbamoyl, N-methyl-N-ethylcarbamoyl, methylthio, ethylthio, methylsulfinyl, ethylsulfinyl, mesyl, ethylsulfony
  • contemplated quinazoline compounds are selected from:
  • contemplated quinazoline compounds have Formula II:
  • R 2 , R 3 , R 4 , R 5 , and R 6 are each the same or different hydrogen, alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein each R 2 , R 3 , R 4 , R 5 , and R 6 are optionally substituted with one or more, the same or different, R 7 ;
  • R 7 is alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein R 7 is optionally substituted with one or more, the same or different, R 8 ;
  • R 8 is halogen, nitro, cyano, hydroxy, trifluoromethoxy, trifluoromethyl, amino, formyl, carboxy, carbamoyl, mercapto, sulfamoyl, methyl, ethyl, methoxy, ethoxy, acetyl, acetoxy, methylamino, ethylamino, dimethylamino, diethylamino, N-methyl-N-ethylamino, acetylamino, N-methylcarbamoyl, N-ethylcarbamoyl, N,N-dimethylcarbamoyl, N,N-diethylcarbamoyl, N-methyl-N-ethylcarbamoyl, methylthio, ethylthio, methylsulfinyl, ethylsulfinyl, mesyl, ethylsulfony
  • R 13 and R 14 are each the same or different hydrogen, alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein each R 13 and R 14 are optionally substituted with one or more, the same or different, R 15 ;
  • R 15 is alkyl, halogen, nitro, cyano, hydroxy, amino, mercapto, formyl, carboxy, alkanoyl, carbamoyl, alkoxy, alkylthio, alkylamino, (alkyl) 2 amino, alkylsulfinyl, alkylsulfonyl, arylsulfonyl, carbocyclyl, aryl, or heterocyclyl, wherein R 15 is optionally substituted with one or more, the same or different, R 16 ; and
  • R 16 is halogen, nitro, cyano, hydroxy, trifluoromethoxy, trifluoromethyl, amino, formyl, carboxy, carbamoyl, mercapto, sulfamoyl, methyl, ethyl, methoxy, ethoxy, acetyl, acetoxy, methylamino, ethylamino, dimethylamino, diethylamino, N-methyl-N-ethylamino, acetylamino, N-methylcarbamoyl, N-ethylcarbamoyl, N,N-dimethylcarbamoyl, N,N-diethylcarbamoyl, N-methyl-N-ethylcarbamoyl, methylthio, ethylthio, methylsulfinyl, ethylsulfinyl, mesyl, ethylsulfony
  • R 13 and R 14 are hydrogen or alkyl optionally substituted with one or more, the same or different, R 15 .
  • R 4 is alkoxy optionally substituted with one or more, the same or different, R 7 .
  • R 2 is alkylamino optionally substituted with one or more, the same or different, R 7 .
  • R 2 is a alkyl or heterocyclyl optionally substituted with one or more, the same or different, R 7 .
  • contemplated quinazoline compounds are selected from:
  • HDAC inhibitor Vorinostat or suberoylanilide hydroxamic acid (SAHA); DNA methyltransferase inhibitor: Decitabine (trade name Dacogen), or 5-aza-2′-deoxycytidine (5-aza); multiple histone 3 lysine 9 (H3K9) methyltransferases G9a and GLP inhibitor: BIX-01294; and GSK3 ⁇ inhibitor: CHIR99021 for 7 more days.
  • HDAC inhibitor Vorinostat or suberoylanilide hydroxamic acid (SAHA)
  • DNA methyltransferase inhibitor Decitabine (trade name Dacogen), or 5-aza-2′-deoxycytidine (5-aza)
  • H3K9 multiple histone 3 lysine 9
  • G9a and GLP inhibitor BIX-01294
  • GSK3 ⁇ inhibitor CHIR99021 for 7 more days.
  • N-MSCs and D-MSCs were cultured by a standard MSC culture method. The cultured MSCs are typically resee
  • RNAs from N-, D-, or epigenetic compound treated reprogrammed D-MSCs were significantly higher than D-MSCs up to N-MSCs or more ( FIG. 1 ) although different type of inhibitors showed different pattern of gene expression.
  • HDAC inhibitor showed significant increased pattern in most of genes, therefore, HDAC inhibitor, SAHA, was selected for following experiments.
  • Ki67 an effective marker for mitosis.
  • the percentage of Ki67-positive cells was 53% lower in D-MSCs compared to N-MSCs ( FIG. 2 ).
  • a colony forming unit assay was performed, which determines actively proliferating cell portions.
  • the number of colony forming units (colonies/100 cells) was 45% smaller in D-MSCs compared to N-MSCs, while RD-MSCs restored the number of colony forming up to 80% of N-MSCs ( FIG. 3 ), suggesting that the proportion of actively proliferating cells is smaller in D-MSCs than N-MSCs which could be restored by the treatment of compounds.
  • TUNEL assay was conducted to determine the effects of diabetes on the cell survival of MSCs. Compared to the N-MSCs, D-MSCs showed significantly higher number of TUNEL positive cells. However, the percent of TUNEL positive cells in RD-MSCs was reduced to normal level ( FIG. 4 ). These results suggest that apoptosis of MSCs observed in diabetes can also rescued by epigenetic compound treatment.
  • the adhesion capability of MSCs was compared because cell-adhesion mechanisms play a fundamental role during angiogenesis. Most of the adherent cells from normal bone marrow were spindle- or flatten-shaped, whereas the adherent cells from diabetes were rounded up showing that they are losing the adhesion capability. But the shape of adherent reprogrammed cells were similar to normal cells, and the number of adherent cells in these reprogrammed cells was also increased ( FIG. 5 ). Also, wound healing assay to was performed verify the migration activity of different MSCs as the cellular function for angiogenesis.
  • N-, D-, or RD-MSCs were injected into ischemic hindlimbs and monitored blood flow using LDPI.
  • PBS injection served as a control.
  • the N- and RD-MSC implanted group showed significantly improved blood flow ( FIG. 8 ), suggesting that the impaired regenerative capacity for limb ischemia of D-MSCs was restored by epigenetic compounds in experimental animal model.
  • capillary density in the ischemic muscle was quantified after the cell implantation.
  • RNA-seq next-generation RNA-sequencing
  • Down-regulated genes in D-MSCs compared to N-MSCs were enriched with functional annotation clusters associated with MAPK signaling pathway, mTOR signaling pathway, chemokine/cytokine signaling pathway, pathways in cancer, Jak-STAT signaling pathway, axon guidance as well as gene clusters involved in cellular carbohydrates metabolism including insulin signaling pathway.
  • angiogenesis related gene groups such as gene clusters in VEGF signaling pathway, chemokine signaling pathway, and cell adhesion molecules; and immune response related gene clusters including leukocyte transendothelial migration, hematopoietic cell lineage, TB cell receptor signaling pathway, Fc epsilon RI signaling pathway, Toll-like receptor signaling pathway, NK cell mediated cytotoxicity, and complement/coagulation cascades were also repressed in diabetic cells.
  • MSCs Mesenchymal Stem Cells
  • MSCs from diabetic rats were treated with various combinations of chemicals: 6 ⁇ M of SAHA, 1 ⁇ M of BIX01294, 2 ⁇ M of 5-aza (Dacogen), and 6 ⁇ M of CHIR99021 for 7 days.
  • the primers and probes were designed using Primer Express 3.0 (Applied Biosystems).
  • MSCs were plated at 200 cells/cm 2 and the number of resultant cells was determined.
  • immunocytochemistry with anti-Ki-67 antibody (Millipore) was performed.
  • colony forming unit assay one hundred MSCs were plated onto 100 mm dishes and cultured for 14 days. The cells were stained with crystal violet and the number of colonies were counted.
  • TdT terminal deoxynucleotidyltransferase
  • TUNEL dUTP-biotin nick end labeling
  • MSCs were plated in confluence in 24-well plates (1.5 ⁇ 10 5 cells/300 ⁇ l/well) and starved for 24 h in serum-free DMEM media. After 24 h the medium was discarded and the monolayer was scratched with a sterile plastic pipette tip. The cells were washed three times with DMEM, and 300 ⁇ l of DMEM medium with serum were added. At 0 and 24 h, images were taken (Nikon Eclipse Ti). The area of each dish was measured using Image J.
  • Unilateral hindlimb ischemia was created in normal F344 rats by ligation of the femoral artery and removing all arterial branches.
  • Three hundred thousand DiI-labeled MSCs in 500 ⁇ l of PBS were intramuscularly injected into the ischemic hindlimbs. Blood flow in the hindlimb was measured using a Laser Doppler perfusion imager (LDPI, Moor instrument, UK). Mean values of perfusion was calculated from the stored digital color-coded images.
  • the level of blood flow of the ischemic (left) limb was normalized to that of non-ischemic (right) limb to avoid data variations caused by ambient light and temperature.
  • the hindlimb muscles were harvested, fixed with 4% paraformaldehyde at 4° C. overnight, and frozen-sectioned. To visualize capillaries, the sections were stained using BS lectin-I and the capillary density was determined under conventional epifluorescence microscopy.
  • the converted cDNAs from isolated RNAs, immunoprecipitated/captured DNA, input, and negative control (in the absence of biotin) were used to generate DNA libraries following the Illumina protocol. 38-cycle single end sequencing was performed. Image processing and sequence extraction were done using the standard Illumina Pipeline. Two independent libraries and runs (one lane per library) for each biological replicate were generated. FASTQ sequence files were aligned to reference genome using Bowtie. The best alignment and reporting option were used for all conditions, corresponding to no more than 2 bp mismatches across each 38 bp read. Mapped reads were assembled into RNA transcripts using the Cufflinks software (version 1.3.0).
  • Cufflinks was run using the annotation file of known genes and the mapped reads produced by Tophat. Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) value (a normalized gene expression value that are comparable between different samples and genes) together with confidence intervals were estimated for each replicate. R/bioconductor packages were used to generate the heatmap and box plot of the different expressed genes comparing N-MSC, D-MSC, and RD-MSC. Database for Annotation, Visualization and Integrated Discovery (DAVID) tool was used to generate the functional annotation charts for impaired (N-MSC vs. D-MSC) and restored (D-MSC vs. RD-MSC) gene expressions.
  • DAVID Annotation, Visualization and Integrated Discovery
  • the cells were grown on the 10-cm plates to 85% confluence. Formaldehyde was added to a final concentration of 1%, and the plates were incubated for 10 min at 37° C. The cross-linking reaction was stopped by the addition of 100 mM glycine containing protease inhibitors (Complete; RocheApplied Science).
  • Cells were washed in dilution buffer (0.01% SDS, 1% Triton X-100, 1.2 mM EDTA, 16.7 mMTris-HCl, 150 mMNaCl, pH 8.0 plus protease inhibitors), resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mMTris-HCl, pH 8.0 plus protease inhibitors) and sonicated to shear the DNA into 0.3 ⁇ 3-kb fragments.
  • dilution buffer 0.01% SDS, 1% Triton X-100, 1.2 mM EDTA, 16.7 mMTris-HCl, 150 mMNaCl, pH 8.0 plus protease inhibitors
  • lysis buffer 1% SDS, 10 mM EDTA, 50 mMTris-HCl, pH 8.0 plus protease inhibitors
  • chromatin was incubated with anti-H3K9/14 antibodies, that can detect the changes of histone acetylation as activation mark, or anti-rabbit IgG antibody (negative control) overnight at 4° C. Then, protein G beads were added and the chromatin was incubated for 2 hours in rotation. An aliquot of chromatin that was not incubated with an antibody was used as the input control sample. Antibody-bound protein/DNA complexes were eluted and subjected to PCR analysis.
  • Reagents and conditions (a) Benzyl bromide, K 2 CO 3 , dry DMF, rt; (b) HNO 3 69.5%, (Ac) 2 O, 0° C. then rt; (c) iron dust, NH 4 Cl, i-PrOH-H 2 O (5:3), reflux; (d) i) methyl chloroformate, DIPEA, DMF-DCM (2:1), 0° C.
  • EPCs Endothelial Progenitor Cells
  • EPCs diabetic endothelial progenitor cells
  • STZ streptozotocin
  • N-EPCs normal EPCs
  • MNCs bone marrow-derived mononuclear cells isolated from the tibia and femur were plated on cell culture dishes coated with rat vitronectin and cultured in EBM-2 medium containing 5% FBS and cytokine cocktail, singleQuots® for 7 days.
  • FIG. 12 The left panel shows a set of representative mRNA expression profiles comparing N-EPCs and D-EPCs.
  • the microarray profiles illustrate some of the increased (>5 fold) angiogenic factors (the black spots) in N-EPCs v.s., D-EPCs. Gene expression is significantly suppressed in D-EPCs.
  • EPCs Endothelial Progenitor Cells
  • EPCs diabetic endothelial progenitor cells
  • STZ streptozotocin
  • N-EPCs normal EPCs
  • MNCs bone marrow-derived mononuclear cells isolated from the tibia and femur were plated on cell culture dishes coated with rat vitronectin and cultured in EBM-2 medium containing 5% FBS and cytokine cocktail, singleQuots® for 7 days.
  • FIG. 12 The left panel shows a set of representative mRNA expression profiles comparing N-EPCs and D-EPCs.
  • the microarray profiles illustrate some of the increased (>5 fold) angiogenic factors (the black spots) in N-EPCs v.s., D-EPCs. Gene expression is significantly suppressed in D-EPCs.
  • RNAs were collected at the 10 day of culture for extraction of genomic DNAs and RNAs for epigenetic profiling by modified methylation-sensitive restriction enzyme (MSRE)-PCR assay (EpiMarkTM, NEB) and qRT-PCR, respectively.
  • MSRE modified methylation-sensitive restriction enzyme
  • MSRE-PCR assay purified genomic DNAs were treated with methylation sensitive restriction enzyme, followed by the treatment of T4-BGT and UDP-Glucose (UDP-Glc) for adding a glucose moiety to 5-hydroxymethylcytosine (5-hmC).
  • T4-BGT and UDP-Glucose UDP-Glucose
  • UDP-Glc UDP-Glucose
  • D-EPCs have significantly high DNA methylation in the promoters of angiogenic genes such as Akt1, Hgf, Mapk14, Sphk1, Vegfc, Nudt6, Kdr, Vegfa, and Pten which were identified by the above microarray studies, and treatments with compounds reduced DNA methylation at these promoters and enhance gene expression ( FIG. 13 ).
  • reduced cell biologic function such as cell adhesion, migration and tube formation were all increased.
  • Human BM-derived EPCs were cultured similarly. Two approaches were used for reprogramming diabetic EPCs. Initially we used an unselected approach employing combinations of compounds. For the combinatorial approach, combinations of the three classes of compounds were used and the gene and epigenetic changes were determined. In the next targeted approach, selective reagents were chose accordingly to the methylation and histone modification status of key factors identified.
  • EPC function may be attributed to VEGF, SDF-1, CXCR4, HIF1 ⁇ , IGF-1, or Akt12.
  • EPCs from diabetic subjects were cultured.
  • the cultured EPCs are typically reseeded at day 4 and cultured for another 3-7 days.
  • HDAC inhibitors SAHA, sodium butyrate, and VPA, two DNA methylation inhibitor 5-Aza and RG108, and multiple histone 3 lysine 9 (H3K9) methyltransferases G9a and GLP inhibitors of formula I were used.
  • Compounds were tested to find candidates which induce the highest cell functionality with minimum toxicity.
  • the following assays was conducted comparing N-EPCs, D-EPCs, and rescued diabetic EPCs (RD-EPCs) to determine rescued diabetic (RD)-EPCs with respect to their biological potency.
  • RD-EPCs were identified that possess the highest angiogenic and neurotrophic capacity.
  • a short duration of compound treatment should be sufficient to reverse the epigenetic modifications incurred by diabetes, and culture conditions will then guide their fate back to more na ⁇ ve EPCs.
  • This new reprogramming technology can be applied and expanded to diabetic bone marrow-derived stem or progenitor cells including MSCs, EPCs, and even to unfractionated bone marrow-derived mononuclear cells (BM-MNCs).

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