Patent Application
20200062719
Benefit is claimed to European Patent Application No. EP18188930.4, filed Aug. 14, 2018, the contents of which are incorporated by referenced herein in their entirety.
The present invention relates to an in vitro/ex vivo method for producing induced pluripotent stem cells from non-pluripotent donor cells.
Pluripotent stem cells, such as embryonic stem cells, have the potential to differentiate into any of the three germ layers: endoderm, mesoderm and ectoderm, and therefore give rise to any cell type derived from these germ layers.
Nuclear reprogramming from terminally differentiated somatic cells into induced pluripotent stem cells (iPSCs) achieved by ectopic expression of a core of transcription factors, like Oct4, Sox2, Klf4, c-Myc, Nanog and Lin28 provides a promising source for autologous organ transplantation, drug discovery and disease modelling, opening a new era in the field of regenerative medicine.
Methods available for the generation of pluripotent stem cells are somatic cell nuclear transfer (SCNT) and reprogramming of human fibroblasts. Both methods have their distinct disadvantages and limitations. The reprogramming of human fibroblasts is a time-consuming (3-4 weeks) and inefficient (<0.01% of cells) process. It also can be hampered by random mutations appearing in the course of reprogramming and during maintenance. Therefore, higher reprogramming efficiency and optimized cultivation conditions for iPSC maintenance can contribute to risk reduction. Improved reprogramming efficiency for generation of individual patients own iPSCs will also allow to avoid risks associated with autologous iPSC cell line derived allografts, like immunoreaction, evidenced by allogeneic transplantation of iPSC-derived neural cells in nonhuman primates (Morizane et al. Stem Cell Reports. 2013 Sep. 26; 1(4):283-9).
In contrast to using genetic manipulation for reprogramming somatic cells, the use of small molecules shows distinct advantages in controlling the reprogramming process. Recently a number of small molecules have been disclosed that greatly contribute to the establishment of more efficient and reliable protocols for the generation and maintenance of iPSCs (Watanabe et al, Nat Biotechnol. 2007 June; 25(6):681-6; Ying et al Nature. 2008 May 22; 453(7194):519-23). Small molecule cocktails that exhibit excellent reprogramming efficiency for the generation of mouse iPSCs have been disclosed recently (Hou et al, Science. 2013 Aug. 9; 341(6146):651-4; Zhao et al, Cell. 2015 Dec. 17; 163(7):1678-91).
Herein the inventors disclose that 2-arylpyrimidazoles—including zolpidem, an approved drug for insomnia treatment, —act as novel potent pluripotency inducers for the generation and maintenance of human iPSCs.
Based on the above-mentioned state of the art, the objective of the present invention is to provide means and methods for the induction of pluripotency in mammalian donor cells and the maintenance of pluripotency in these cells. This objective is attained by the subject matter of the claims of the present specification.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
The term pluripotent stem cell in the context of the present specification relates to cells with pluripotent abilities. Pluripotency is a continuum ranging from completely pluripotent (=omnipotent) to partially pluripotent (=multipotent) cells. Omnipotent cells can differentiate into any cell type of the body. Examples for omnipotent stem cells (=completely pluripotent) are embryonic stem cells. In contrast, adult stem cells (=partially pluripotent stem cell) can usually only differentiate into the cell type of the organ they originate from. Multipotent cells have the gene activation potential to differentiate into discrete cell types. A non-limiting example of multipotent cells are neural stem cells. In addition to pluripotency, the pluripotent stem cell has the ability to go through several cycles of cell division while maintaining its undifferentiated state. The term pluripotent stem cell therefore encompasses such cells as embryonic stem cells, adult stem cells, neural stem cells and induced pluripotent stem cells.
The term C1-C3 alkyl in the context of the present specification relates to a saturated hydrocarbon having 1, 2 or 3 carbon atoms. Non-limiting examples for a C1-C3 alkyl are methyl, ethyl and n- or iso-propyl.
The term C1-C3 alkoxy moiety in the context of the present specification relates to a C1-C3 alkyl as specified above, connected to the core moiety by an oxygen. Examples of a C1-C3 alkoxy are methoxy (CH3O—), ethoxy (CH3CH2O—) and n-propoxy (CH3CH2CH2O—) or iso-propoxy ((CH3)2CHO—).
A C1-C3 carboxylic acid in the context of the present specification relates to a linear or branched hydrocarbon having 1, 2 or 3 carbon atoms and comprising a carboxyl group (—C(═O)OH). Non-limiting examples for a C1-C3 carboxylic acid are carbonic acid (OH—COOH), methanoic acid (H—COOH), acetic acid (CH3—COOH) and propionic acid (CH3CH2COOH).
The term C1-C4 alkyl in the context of the present specification relates to a saturated linear or branched hydrocarbon having 1, 2, 3 or 4 carbon atoms, wherein in certain embodiments one carbon-carbon bond may be unsaturated and one CH2 moiety may be exchanged for oxygen (ether bridge) or nitrogen (NH, or NR with R being methyl, ethyl, or propyl; amino bridge). Non-limiting examples for a C1-C4 alkyl are methyl, ethyl, propyl, prop-2-enyl, n-butyl, 2-methylpropyl, tert-butyl, but-3-enyl, prop-2-inyl and but-3-inyl. In certain embodiments, a C1-C4 alkyl is a methyl, ethyl, propyl or butyl moiety.
A C1-C6 alkyl in the context of the present specification relates to a saturated linear or branched hydrocarbon having 1, 2, 3, 4, 5 or 6 carbon atoms, wherein one carbon-carbon bond may be unsaturated and/or one CH2 moiety may be exchanged for oxygen (ether bridge) or nitrogen (NH, or NR with R being methyl, ethyl, or propyl; amino bridge). Non-limiting examples for a C1-C6 alkyl include the examples given for C1-C4 alkyl above, and additionally 3-methylbut-2-enyl, 2-methylbut-3-enyl, 3-methylbut-3-enyl, n-pentyl, 2-methylbutyl, 3-methylbutyl, 1,1-dimethylpropyl, 1,2-dimethylpropyl, 1,2-dimethylpropyl, pent-4-inyl, 3-methyl-2-pentyl, and 4-methyl-2-pentyl. In certain embodiments, a C5 alkyl is a pentyl or cyclopentyl moiety and a C6 alkyl is a hexyl or cyclohexyl moiety.
The term C4-C7 cycloalkyl in the context of the present specification relates to a saturated hydrocarbon ring having 4, 5, 6 or 7 carbon atoms, wherein in certain embodiments, one carbon-carbon bond may be unsaturated and/or one CH2 moiety may be exchanged for oxygen (ether bridge) or nitrogen (NH, or NR with R being methyl, ethyl, or propyl; amino bridge). Non-limiting examples of a C4-C7 cycloalkyl moiety include cyclobutyl (—C4H7), cyclopentenyl (C5H9), and cyclohexenyl (C6H11) moieties. In certain embodiments, a cycloalkyl is substituted by one C1 to C4 unsubstituted alkyl moiety. In certain embodiments, a cycloalkyl is substituted by more than one C1 to C4 unsubstituted alkyl moieties.
The term unsubstituted C, alkyl when used herein in the narrowest sense relates to the moiety —CnH2n— if used as a bridge between moieties of the molecule, or —CnH2n+1 if used in the context of a terminal moiety. It may still contain fewer H atoms if a cyclical structure or one or more (non-aromatic) double bonds are present.
The term Cn alkylene in the context of the present specification relates to a saturated linear or branched hydrocarbon comprising one or more double bonds. An unsubstituted alkylene consists of C and H only. A substituted alkylene may comprise substituents as defined herein for substituted alkyl.
The term Cn alkylyne in the context of the present specification relates to a saturated linear or branched hydrocarbon comprising one or more triple bonds and may also comprise one or more double bonds in addition to the triple bond(s). An unsubstituted alkylyne consists of C and H only. A substituted alkylyne may comprise substituents as defined herein for substituted alkyl.
The term “substituted” refers to the addition of a substituent group to a parent compound.
“Substituent groups” can be protected or unprotected and can be added to one available site or to many available sites in a parent compound. Substituent groups may also be further substituted with other substituent groups and may be attached directly or by a linking group such as an alkyl or hydrocarbyl group to a parent compound. “Substituent groups” useful in the context of alkyl or oxyalkyl substitution as disclosed herein include, without limitation, halogen, oxygen, nitrogen, sulphur, hydroxyl, alkyl, alkenyl, alkynyl, acyl (—C(O)Ra), carboxyl (—C(O)ORa), aliphatic groups, alicyclic groups, alkoxy, substituted oxy (—ORa), aryl, aralkyl, heterocyclic radical, heteroaryl, heteroarylalkyl, amino (—N(Rb)(Rc)), imino(=NRb), amido (—C(O)N(Rb)(Rc) or —N(Rb)C(O)Ra), hydrazine derivates (—C(NH)NRaRb), tetrazole(CN4H2), azido (—N3), nitro (—NO2), cyano (—CN), isocyano (—NC), cyanato (—OCN), isocyanato (—NCO), thiocyanato (—SCN); isothiocyanato (—NCS); carbamido (—OC(O)N(Rb)(Rc) or —N(Rb)C(O)ORa), thiol (—SRb), sulfinyl (—S(O)Rb), sulfonyl (—S(O)2Rb), sulfonamidyl (—S(O)2N(Rb)(Rc) or —N(Rb)S(O)2Rb) and fluorinated compounds —CF3, —OCF3, —SCF3, —SOCF3 or —SO2CF3, wherein each Ra, Rb and Rc is, independently from any other Ra, Rb and Rc, H or a further substituent group with a preferred list including without limitation, C1-C3 alkyl alkyl, C2-C3 alkenyl, C2-C3 alkynyl, alkoxy, C1-C3 acyl, aryl, heteroaryl, alicyclic, heterocyclic and heteroarylalkyl.
The terms unsubstituted Cn alkyl and substituted Cn alkyl include a linear alkyl comprising or being linked to a cyclical structure, for example a cyclopropane, cyclobutane, cyclopentane or cyclohexane moiety, unsubstituted or substituted depending on the annotation or the context of mention, having linear alkyl substitutions. The total number of carbon and—where appropriate—N, O or other hetero atom in the linear chain or cyclical structure adds up to n.
Where used in the context of chemical formulae, the following abbreviations may be used: Me is methyl CH3, Et is ethyl —CH2CH3, Prop is propyl —(CH2)2CH3 (n-propyl, n-pr) or —CH(CH3)2 (iso-propyl, i-pr), but is butyl —C4H9, —(CH2)3CH3, —CHCH3CH2CH3, —CH2CH(CH3)2 or —C(CH3)3.
The term substituted alkyl in its broadest sense refers to an alkyl as defined above in the broadest sense, which is covalently linked to an atom that is not carbon or hydrogen, particularly to an atom selected from N, O, F, B, Si, P, S, Cl, Br and I, which itself may be—if applicable-linked to one or several other atoms of this group, or to hydrogen, or to an unsaturated or saturated hydrocarbon (alkyl or aryl in their broadest sense). In a narrower sense, substituted alkyl refers to an alkyl as defined above in the broadest sense that is substituted in one or several carbon atoms by groups selected from amine NH2, alkylamine NHR, imide NH, alkylimide NR, amino(carboxyalkyl) NHCOR or NRCOR, hydroxyl OH, oxyalkyl OR, oxy(carboxyalkyl) OCOR, carbonyl O and its ketal or acetal (OR)2, nitril CN, isonitril NC, cyanate CNO, isocyanate NCO, thiocyanate CNS, isothiocyanate NCS, fluoride F, choride Cl, bromide Br, iodide I, phosphonate PO3H2, PO3R2, phosphate OPO3H2 and OPO3R2, sulfhydryl SH, suflalkyl SR, sulf oxide SOR, sulfonyl SO2R, sulfanylamide SO2NHR, sulfate SO3H and sulfate ester SO3R, wherein the R substituent as used in the current paragraph, different from other uses assigned to R in the body of the specification, is itself an unsubstituted or substituted C1 to C12 alkyl in its broadest sense, and in a narrower sense, R is methyl, ethyl or propyl unless otherwise specified.
The term amino substituted alkyl or hydroxyl substituted alkyl relates to an alkyl according to the above definition that is modified by one or several amine or hydroxyl groups NH2, NHR, NR2 or OH, wherein the R substituent as used in the current paragraph, different from other uses assigned to R in the body of the specification, is itself an unsubstituted or substituted C1 to C12 alkyl in its broadest sense, and in a narrower sense, R is methyl, ethyl or propyl unless otherwise specified. An alkyl having more than one carbon may comprise more than one amine or hydroxyl. Unless otherwise specified, the term “substituted alkyl” refers to alkyl in which each C is only substituted by at most one amine or hydroxyl group, in addition to bonds to the alkyl chain, terminal methyl, or hydrogen.
The term carboxyl substituted alkyl refers to an alkyl according to the above definition that is modified by one or several carboxyl groups COOH, or derivatives thereof, particularly carboxylamides CONH2, CONHR and CONH2, or carboxylic esters COOR, with R having the meaning as laid out in the preceding paragraph and different from other meanings assigned to R in the body of this specification.
Non-limiting examples of amino-substituted alkyl include —CH2NH2, —CH2NHMe, —CH2NHEt, —CH2CH2NH2, —CH2CH2NHMe, —CH2CH2NHEt, —(CH2)3NH2, —(CH2)3NHMe, —(CH2)3NHEt, —CH2CH(NH2)CH3, —CH2CH(NHMe)CH3, —CH2CH(NHEt)CH3, —(CH2)3CH2NH2, —(CH2)3CH2NHMe, —(CH2)3CH2NHEt, —CH(CH2NH2)CH2CH3, —CH(CH2NHMe)CH2CH3, —CH(CH2NHEt)CH2CH3, —CH2CH(CH2NH2)CH3, —CH2CH(CH2NHMe)CH3, —CH2CH(CH2NHEt)CH3, —CH(NH2)(CH2)2NH2, —CH(NHMe)(CH2)2NHMe, —CH(NHEt)(CH2)2NHEt, —CH2CH(NH2)CH2NH2, —CH2CH(NHMe)CH2NHMe, —CH2CH(NHEt)CH2NHEt, —CH2CH(NH2)(CH2)2NH2, —CH2CH(NHMe)(CH2)2NHMe, —CH2CH(NHEt)(CH2)2NHEt, —CH2CH(CH2NH2)2, —CH2CH(CH2NHMe)2 and —CH2CH(CH2NHEt)2 for terminal moieties and —CH2CHNH2—, —CH2CHNHMe-, —CH2CHNHEt- for an amino substituted alkyl moiety bridging two other moieties.
Non-limiting examples of hydroxy-substituted alkyl include —CH2OH, —(CH2)2OH, —(CH2)3OH, —CH2CH(OH)CH3, —(CH2)4OH, —CH(CH2OH)CH2CH3, —CH2CH(CH2OH)CH3, —CH(OH)(CH2)2OH, —CH2CH(OH)CH2OH, —CH2CH(OH)(CH2)2OH and —CH2CH(CH2OH)2 for terminal moieties and —CHOH—, —CH2CHOH—, —CH2CH(OH)CH2—, —(CH2)2CHOHCH2—, —CH(CH2OH)CH2CH2—, —CH2CH(CH2OH)CH2—, —CH(OH)(CH2CHOH—, —CH2CH(OH)CH2OH, —CH2CH(OH)(CH2)2OH and —CH2CHCH2OHCHOH— for a hydroxyl substituted alkyl moiety bridging two other moieties.
The term halogen-substituted alkyl refers to an alkyl according to the above definition that is modified by one or several halogen atoms selected (independently) from F, Cl, Br, I.
The term fluoro substituted alkyl refers to an alkyl according to the above definition that is modified by one or several fluoride groups F. Non-limiting examples of fluoro-substituted alkyl include —CH2F, —CHF2, —CF3, —(CH2)2F, —(CHF)2H, —(CHF)2F, —C2F5, —(CH2)3F, —(CHF)3H, —(CHF)3F, —C3F7, —(CH2)4F, —(CHF)4H, —(CHF)4F and —C4F9.
Non-limiting examples of hydroxyl- and fluoro-substituted alkyl include —CHFCH2OH, —CF2CH2OH, —(CHF)2CH2OH, —(CF2)2CH2OH, —(CHF)3CH2OH, —(CF2)3CH2OH, —(CH2)3OH, —CF2CH(OH)CH3, —CF2CH(OH)CF3, —CF(CH2OH)CHFCH3, and —CF(CH2OH)CHFCF3.
The term aryl in the context of the present specification relates to a cyclic aromatic C5-C10 hydrocarbon that may comprise a heteroatom (e.g. N, O, S). Examples of aryl include, without being restricted to, phenyl and naphthyl, and any heteroaryl. A heteroaryl is an aryl that comprises one or several nitrogen, oxygen and/or sulphur atoms. Examples for heteroaryl include, without being restricted to, pyrrole, thiophene, furan, imidazole, pyrazole, thiazole, oxazole, pyridine, pyrimidine, thiazin, quinoline, benzofuran and indole. An aryl or a heteroaryl in the context of the specification additionally may be substituted by one or more alkyl groups.
An aryl methylene in the context of the present specification relates to a CH2 (-methylene) group substituted by an aryl moiety. One non-limiting example of aryl methylene is a benzyl (Bn) group. If used in particular, a heteroaryl methylene in the context of the present specification signifies a CH2 (-methylene) group substituted by a heteroaryl moiety. Examples for heteroaryl include, without being restricted to, pyrrole, thiophene, furan, imidazole, pyrazole, thiazole, oxazole, pyridine, pyrimidine, thiazin, quinoline, benzofuran and indole. An aryl or a heteroaryl in the context of this specification additionally may be substituted by one or more alkyl groups.
A first aspect of the invention relates to a method of producing a pluripotent stem cell, in particular an induced pluripotent stem cell. This method comprises contacting a non-pluripotent donor cell obtained from a mammalian donor with a compound characterized by general formula (1).
Certain embodiments of the present invention do not encompass the manipulation of cells in-vivo, but is practiced in-vitro, and does not relate to the manipulation of primates, particularly humans, or to the manipulation of primate, particularly human, embryos.
The substituent RI is attached to the six-membered ring of the pyrimidazole (imidazo[1,2-A]pyridine) moiety. The point of attachment might be any of the four carbon atoms available for substitution. The index m of RIm indicates the number of substituents that are attached to the pyrimidazole moiety. The value of m is 1 or 2.
The substituent RI is selected from —H, substituted or unsubstituted C1-C3 alkyl, substituted or unsubstituted C1-C3 alkoxy, —F, —Cl, —Br, —I, —NO2, —OH, —NH2, —SO3H, —CN, substituted or unsubstituted C1-C3 carboxylic acid, —NCO, —CNO, —NCS, —SCN, —CH2F, —CHF2, or —CF3.
In certain embodiments, the substituents are selected from halogen, oxygen, nitrogen, sulphur and hydroxyl.
The substituent Rz is selected from general formula (2) or hydrogen.
In certain embodiments, the compound according to aspect 1 is zolpidem (CAS No. 82626-48-0), with m of RIm being 1, RI being CH3, Rz being general formula (2), n of Ran being 1 and Ra being CH3.
The substituent Ra is attached to the aryl moiety. The point of attachment might be any of the six carbon atoms of the aryl moiety. The index n of Ran indicates the number of substituents that are attached to the aryl moiety. The value of n is 1 or 2.
The substituent Ra, independently from each other Ra, is selected from —H, substituted or unsubstituted C1-C3 alkyl, substituted or unsubstituted C1-C3 alkoxy, —F, —Cl, —Br, —I, —NO2, —OH, —NH2, —SO3H, —CN, substituted or unsubstituted C1-C3 carboxylic acid, —NCO, —CNO, —NCS, —SCN, —CH2F, —CHF2, or —CF3. Ra may also take any of the values given for R′, as well.
In certain embodiments, two Ra bonded to two adjacent carbon atoms in the aryl moiety form a circular structure via the hydrocarbon C4H4 (the moiety attached to the imidazole ring is a naphtyl)
The carbon atom of the aryl moiety that is linked to the imidazole moiety is not substituted by Ra.
In certain embodiments, the value of m is 1.
In certain embodiments, the value of m is 2.
In certain embodiments, the value of n is 1.
In certain embodiments, the value of n is 2.
In certain embodiments, R′ is methyl.
In certain embodiments, Ra is selected from —H, —CH3, —F, —Cl, —Br, —I, —OH, —NO2, —CN or —OMe.
In certain embodiments, Ra is methyl.
In certain embodiments, the compound used in the method according to the first aspect of the invention is characterized by general formula (3).
One of R1, R2, R3 and R4 is selected from: —H, substituted or unsubstituted C1-C3 alkyl, substituted or unsubstituted C1-C3 alkoxy, —F, —Cl, —Br, —I, —NO2, —OH, —NH2, —SO3H, —CN, substituted or unsubstituted C1-C3 carboxylic acid, —NCO, —CNO, —NCS, —SCN, —CH2F, —CHF2, or —CF3. The other ones are —H. In other words, only one of the substituents R1, R2, R3 and R4 is bonded to the pyridine moiety. The meaning of the substituents is according to the definition provided above.
The substituent Rz is selected from general formula (2) or hydrogen.
One of Ro, Rm, Rp, Rm′ and Ro′ is selected from: —H, substituted or unsubstituted C1-C3 alkyl, substituted or unsubstituted C1-C3 alkoxy, —F, —Cl, —Br, —I, —NO2, —OH, —NH2, —SO3H, —CN, substituted or unsubstituted C1-C3 carboxylic acid, —NCO, —CNO, —NCS, —SCN, —CH2F, —CHF2, or —CF3. The other ones are —H. In other words, only one of the substituents Ro, Rm, Rp, Rm′ and Ro′ is bonded to the aryl moiety. The meaning of the substituents is according to the definition provided above.
In certain embodiments, any two neighbouring positions of Ro, Rm, Rp, Rm′ or Ro′ together form a circular structure via the hydrocarbon C4H4.
In certain embodiments, Rm and Rp together form a circular structure via the hydrocarbon C4H4.
In certain embodiments, each RI, Ra, R1, R2, R3, R4, Ro, Rm, Rp, Rm′ and Ro′ is selected independently from each other from —H, —CH3, —F, —Cl, —Br, —I, —OH, —NO2, —CN or —OMe.
In certain embodiments, R1 is selected from —CH3, —H.
In certain embodiments, R2 is selected from —CH3, —H.
In certain embodiments, R3 is selected from —CH3, —H, —F, —Cl, —Br.
In certain embodiments, R4 is selected from —CH3, —H.
In certain embodiments, Ro′ is selected from —NO2, —F, —H.
In certain embodiments, Ro is selected from —NO2, —F, —H.
In certain embodiments, Rp is selected from —CH3, —F, —Cl, —Br, —NO2, —OMe, —OH, —CN, —H.
In certain embodiments, Rm is selected from —C1, —H, —F, —OH, —NO2, —OMe.
In certain embodiments, Rm′ is selected from —C1, —H, —F, —OH, —NO2, —OMe.
In certain embodiments, Rz is selected from —H or formula (2).
In certain embodiments, the compound is N,N-dimethyl-2-(6-methyl-2-p-tolylimidazo[1,2-a]pyridin-3-yl)acetamid (100).
In certain embodiments, the compound is 6-methyl-2-(p-tolyl)imidazo[1,2-a]pyridine (101).
In certain embodiments, the compound is 2-(4-fluorophenyl)-6-methyl-imidazo[1,2-a]pyridine (102).
In certain embodiments, the compound is 2-(4-chlorophenyl)-6-methyl-imidazo[1,2-a]pyridine (103).
In certain embodiments, the compound is 2-(4-bromophenyl)-6-methyl-imidazo[1,2-a]pyridine (104).
In certain embodiments, the compound is 6-methyl-2-(4-nitrophenyl)imidazo[1,2-a]pyridine (105).
In certain embodiments, the compound is 2-(4-methoxyphenyl)-6-methyl-imidazo[1,2-a]pyridine (106).
In certain embodiments, the compound is 4-(6-methylimidazo[1,2-a]pyridin-2-yl)phenol (107).
In certain embodiments, the compound is 4-(6-methylimidazo[1,2-a]pyridin-2-yl)benzonitrile (108).
In certain embodiments, the compound is 6-methyl-2-phenyl-imidazo[1,2-a]pyridine (109).
In certain embodiments, the compound is 6-methyl-2-(3-nitrophenyl)imidazo[1,2-a]pyridine (110).
In certain embodiments, the compound is 6-methyl-2-(2-nitrophenyl)imidazo[1,2-a]pyridine (111).
In certain embodiments, the compound is 2-(3-fluorophenyl)-6-methyl-imidazo[1,2-a]pyridine (112).
In certain embodiments, the compound is 2-(2-fluorophenyl)-6-methyl-imidazo[1,2-a]pyridine (113).
In certain embodiments, the compound is 2-(3-chlorophenyl)-6-methyl-imidazo[1,2-a]pyridine (114).
In certain embodiments, the compound is 3-(6-methylimidazo[1,2-a]pyridin-2-yl)phenol (115).
In certain embodiments, the compound is 2-(3-methoxyphenyl)-6-methyl-imidazo[1,2-a]pyridine (116).
In certain embodiments, the compound is 7-methyl-2-(p-tolyl)imidazo[1,2-a]pyridine (117).
In certain embodiments, the compound is 8-methyl-2-(p-tolyl)imidazo[1,2-a]pyridine (118).
In certain embodiments, the compound is 5-methyl-2-(p-tolyl)imidazo[1,2-a]pyridine (119).
In certain embodiments, the compound is 6-chloro-2-(p-tolyl)imidazo[1,2-a]pyridine (120).
In certain embodiments, the compound is 6-fluoro-2-(p-tolyl)imidazo[1,2-a]pyridine (121)
In certain embodiments, the compound is 6-bromo-2-(p-tolyl)imidazo[1,2-a]pyridine (122).
In certain embodiments, the compound is 6-methyl-2-(2-naphthyl)imidazo[1,2-a]pyridine (123).
An alternative of this first aspect of the invention relates to a method of producing a pluripotent stem cell, in particular a method of producing an induced pluripotent stem cell, wherein the method comprises contacting a non-pluripotent donor cell obtained from a mammalian (particularly a human) donor with a compound characterized by general formula (4):
Therein, each RII, independently from any other RII, is selected from
p is 1, 2 or 3, particularly p is 1 or 2, and R5 is selected from
The following combinations are not encompassed in the definition of compound (4):
In certain embodiments, the compound according to formula (4) is the compound according to formula (5), (6) or (7):
In certain embodiments, each RII, independently from any other RII, is selected from methyl and ethyl. In certain particular embodiments, all RII are methyl.
In certain embodiments, R5 is selected from substituted or unsubstituted C3-C4 alkyl. In certain particular embodiments, R5 is unsubstituted t-butyl.
In certain embodiments, R5 is selected from substituted or unsubstituted aryl. In certain particular embodiments, R5 is unsubstituted phenyl or naphtyl.
In certain embodiments, the compound according to formula (4) is selected from any one of the formulae (419), (420), (421), (422) and (423). A particular embodiment of the method of the invention uses the compound according to formula (423)
In certain embodiments, the mammalian donor is a human, in other words, a cell of human origin is modified.
In certain embodiments, the method according to the first aspect of the invention further comprises introducing into the mammalian non-pluripotent donor cell at least one element selected from:
The polypeptide is selected from:
In certain embodiments, the polypeptide is OCT4.
In certain embodiments, the polypeptide is KLF4.
In certain embodiments, the polypeptide is SOX2.
In certain embodiments, the polypeptide is L-MYC.
In certain embodiments, the polypeptide is Lin28.
The non-coding nucleic acid sequence is selected from: miR-302b, miR-372, miR-302, miR-367, miR-200c and miR-369.
In certain embodiments, a multitude of nucleic acid sequences encoding a polypeptide, polypeptides or non-coding nucleic acid sequences are introduced into the mammalian non-pluripotent donor cell. In other words, one “element” can comprise several nucleic acid sequences or polypeptides within the same category of the “element”.
In certain embodiments, the compound is used in a final concentration between 0.0005 μmol/l and 100 μmol/l.
In certain embodiments, the compound is used in a final concentration between 0.001 μmol/l and 15 μmol/l.
In certain embodiments, the compound is used in a final concentration between 0.001 μmol/l and 10 μmol/l.
According to a second aspect of the invention, a method of inducing OCT4 and NANOG in a mammalian cell is provided. The method is comprising contacting a mammalian donor cell with a compound according to the first aspect of the invention.
According to a third aspect of the invention a method of increasing methylation of histone 3 lysine 4 (H3K4) in a mammalian non-pluripotent donor cell to augment a method of producing an induced pluripotent stem cell is provided. The method is comprising contacting the donor cell with a compound according to the first aspect of the invention.
It is known in the art that fibroblasts may become resistant to reprogramming approaches to induce pluripotency. One condition known to increase the capacity of a donor cell to be reprogrammed is the maintenance of an open chromatin state that allows for transcription factor binding. In this context trimethylation of histone H3 lysine 4 (H3K4Me3) is reported to provide such an open chromatin state (A. Soufi, G. Donahue and K. S. Zaret, Cell, 2012, 151, 994-1004; Koche, et al., Cell Stem Cell, 2011, 8, 96-105; Polo and Hochedlinger, Cell Stem Cell, 2010, 7, 5-6).
According to an alternative aspect of the invention, a method for augmenting a method of producing an induced pluripotent stem cell is provided. The method is comprising contacting the donor cell with a compound according to the first aspect of the invention.
In certain embodiments according to the first, second and third aspect of the invention, a compound is used in its final concentration for a duration of 12 hours to 10 days.
In certain embodiments according to the first, second and third aspect of the invention, a compound is used in its final concentration for a duration of 1 day to 8 days.
In certain embodiments according to the first, second and third aspect of the invention, a compound is used in its final concentration for a duration of 2 days to 7 days.
In certain embodiments according to the first, second and third aspect of the invention, a compound is used in its final concentration for a duration of 2 to 8 months.
According to a fourth aspect of the invention, a method of maintaining pluripotency in mammalian pluripotent stem cells is provided. The method is comprising contacting the mammalian pluripotent stem cell with a compound according to the first aspect of the invention.
In certain embodiments, the mammalian pluripotent stem cell is a multipotent neural stem cell.
In certain embodiments, according to all aspects of the invention, the method is practiced in vitro or ex vivo.
In certain embodiments, according to all aspects of the invention the compound is used in a final concentration between 0.0005 μmol/l and 100 μmol/l.
In certain embodiments, according to all aspects of the invention the compound is used in a final concentration between 0.001 μmol/l and 15 μmol/l.
In certain embodiments, according to all aspects of the invention the compound is used in a final concentration between 0.001 μmol/l and 10 μmol/l.
According to a fifth aspect of the invention, an induced pluripotent mammalian stem cell obtained or obtainable by a method according to any one of the other aspects of the invention is provided.
According to a sixth aspect of the invention, a cell culture medium comprising a compound according to the first aspect of the invention is provided.
In certain embodiments, the compound is used in a final concentration between 0.0005 μmol/l and 100 μmol/l.
In certain embodiments, the compound is used in a final concentration between 0.001 μmol/l and 15 μmol/l.
In certain embodiments, the compound is used in a final concentration between 0.001 μmol/l and 10 μmol/l.
According to a seventh aspect of the invention, a composition for promoting formation of induced pluripotent mammalian stem cells is provided. The composition is comprising a compound according to the first aspect of the invention.
The invention is further illustrated by the following examples and figures, from which further embodiments and advantages can be drawn. These examples are meant to illustrate the invention but not to limit its scope.
Drug repurposing provides a successful way to develop new therapies with known, medically approved drugs within remarkably short periods. The inventors intentionally sought for chemicals sharing backbones with approved drugs with the expectation of having advantages in pharmacodynamics and kinetics.
In an effort to find such chemical structures able to induce pluripotency, a high-throughput screening (HTS) was performed. The screen was based on cellular luciferase reporter assays under the control of the promoter activity of a pluripotency-associated transcription factor (Oct4) in HEK293 cells. About 4000 imidazopyridine derivatives with significantly differential luciferase activity were identified in this screen.
All methods and reagents used in these examples are disclosed below.
To study the activating and inhibitory effects of the identified compounds in detail, one of the lead structures, 6-methyl-2-(p-tolyl)imidazo[1,2-a]pyridine (O4I3; (101)), was selected and synthesized. This was achieved by heating ω-bromoacetophenone with an excess of 2-aminopyridine for 3 h (
The ability of the lead compound to induce Oct4 at translational level was tested in a luciferase reporter cell line in human embryonic carcinoma NCCIT cells driven by Oct4 response elements (NCCIT-Oct4). The compound lead to a nearly 10-fold induction of Oct4 at 10 nM compared to untreated cells (
It is known in the art that Nanog is a direct target of Oct4 and can be activated by other Oct4 inducing compounds. Accordingly, a similar pattern of activation was observed in O4I3-treated NCCIT-Nanog reporter cells, carrying a Nanog response element (
To address the question whether short or longer-term activation is achieved, the induction of Oct4 was monitored over several days in these experiments. A continuous and constant activation over 4 days was observed in NCCIT-Oct4 cells treated with O4I3 (
In good agreement, the inventors found the induction of those markers, T and Gata4, in hiPSCs treated with 10 μM O4I3 (
Effect on iPSC Self Renewal
Since O4I3 induced sustainable expression of Oct4 and Nanog, the inventors questioned if it supports iPSC self-renewal in single cell expansion. Therefore, the viability of iPSCs, after replating Accutase®-dissociated single iPSCs, was tested in the presence or absence of O4I3. Rocki (Y-27632) was used for the first 24 h to increase iPSCs survival. A nearly 300% higher viability in cells treated with O4I3 (1 nM) was observed. Using 50 nM of O4I3 even 400% increase was observed (
O4I3 Maintains Pluripotency of Human iPSCs
The cellular responses to O4I3 was analyzed in two stem cell lines, NCCIT and JoPaca-1 (
Moreover, inactive phosphorylation of GSK3β was observed. Without wishing to be bound by theory, the inventors believe that this is implicating activation of PI3K/Akt and Wnt, two signaling pathways that are fundamental for maintenance of human PSCs.
Inhibition of p38 and Src was also observed. Both are known in the art as constituents of chemical cocktails for conversion of human primed iPSCs to a naïve state.
In addition, zolpidem also sustained the maintenance of iPSCs, although at a much higher concentration and with lower efficacy than O4I3 (
Therefore, the inventors investigated if O4I3 can support human PSC self-renewal. The viability of previously well-characterized hiPSCs (thereafter called hPSCs) was investigated after replating Accutase®-dissociated single hPSCs in the presence/absence of O4I3, where Rocki (Y-27632) was used for the first 24 h to increase hPSCs survival. A nearly 300% higher viability was found in cells treated with O4I3 even at 1 nM, and 400% at 50 nM (
Gene expression analysis by qRT-PCR showed that O4I3 stabilized or slightly increased the expression of pluripotency-associated genes in iPSCs, including Oct4, Sox2, Nanog and Nodal, while expression of genes regulating differentiation was reduced, like Gata4, Gata6, Pax6 and Sox7 (
Functional annotation analysis of DNA microarray profiles of gene expression in O4I3-treated iPSCs showed that O4I3 inhibited cell differentiation, while maintained cellular homeostasis (
The self-renewal of multipotent neural stem cells was also tested with the compound of the current invention. Neural stem cells were cultivated in SPN medium with or without O4I3 at different final concentrations (
Analyzing the effects of O4I3 on human fibroblasts, the activation of reprogramming associated genes, including an about 10-fold induction of Oct4, Nanog and Lin28, and an about 100-fold increase of Sox2 and E-Cadherin mRNA levels was detected. In particular, expression of several essential genes for reprogramming is equal to those in pluripotent stem cells, such as Esrrb, FGF2 and Sall4 (
O4I3 was applied in commercially available episome-based reprogramming cocktail containing episomal vectors for overexpression of Oct4, Sox2, Klf4, Lin28 and L-Myc, as well as suppression of p53. In comparison to non-treated fibroblast cultures, 20 times more alkaline phosphatase (AP) positive colonies were detected in the presence of O4I3 at a concentration of 50 nM in two tested human primary fibroblasts (HF1 and HF2) (
The iPSCs exhibited pluripotent characteristics and showed typical iPSC morphology (
The inventors compared DNA microarray data and found that the resulting iPSCs show a distinct pattern of global gene expression to human fibroblasts, which are similar to hPSCs (
Pluripotency-associated genes (Pou5F1 encoding Oct4, CDH1 encoding E-Cadherin, Epcam and DNMT3B) were highly expressed in newly generated hiPSC_1 and hiPSC_2, whereas fibroblast-related genes (CDH2, Twist1, Twist2 and Snai2) were suppressed, comparable to characterized hPSCs (
To obtain a deeper insight into the mechanism of action, global gene expression in HFF, HFF treated with O4I3 (HFF_O4I3), HFF transfected with episomal OSKM (HFF_OSKM) and hiPSCs was compared. It was found that O4I3 induced expression of genes positively regulating cell cycle progression and DNA replication (e.g. CDK1, MYC and CDC25) and promoted de-differentiation by upregulation of epithelial genes (CDH1/E-Cadherin, Epcam, Crb3 and OcIn) and downregulation of mesenchymal genes (Twist2), two essential cellular responses at the early stage of reprogramming. Of note, the overlap of up- and down-regulated genes of HFF_O4I3 and HFF_OSKM or iPSCs were more than 40% (
Gene expression profiling using O4I3-treated HFF with a subset of dysregulated genes (160 microarray probes) coding for 140 proteins with protein-protein interactions involved in epigenetic modification and chromatin remodelling. The network was built with STRING using only highest confidence level interactions between the 140 proteins (and all source of information available in STRING). Expected number of interactions (edges) for random network of the same size is 242, while the observed network has 879. Average node degree 12.6 and average local clustering coefficient is 0.665.
Gene Ontology-based functional enrichment analysis of regulated genes in HFF_0413 compared to HFF was performed and found that a number of specialized terms associated with epigenetic and chromatin regulation were the top regulated terms (
Recently, Onder et al. (Nature, 2012, 483, 598-602) screened the influence of a panel of epigenetic regulators and revealed that inhibition of DOT1L promoted iPSCs generation. The inventors analyzed the expression of those genes upon O4I3 treatment in HFFs and found that 7 genes, including DOT1L, were downregulated, which were reported by Onder et al. to enhance the reprogramming, while MBD3 was significantly upregulated, whose suppression might counteract the generation of iPSCs.
The importance of active tri-methylation of histone H3 lysine 4 (H3K4Me3) in promoting transcription factors binding to an ‘open’ chromatin state and thereby initiation of reprogramming is known in the art. In good agreement, the inventors found the abundance of H3K4Me3 in O4I3-treated reprogramming-resistant fibroblasts by immunostaining (
It is known in the art that senescence or other unknown factors can confer donor fibroblasts resistance to reprogramming. Therefore, O4I3 was tested for its ability to enable reprogramming of refractory fibroblasts. Two human fibroblasts were selected. HFF-LTR7-EGFP at passage >40 carrying EGFP driven by a LTR7 promoter, which was activated during reprogramming, and HF5, isolated from a patient sample, both of which were resistant to an episome-based reprogramming approach (
hiPSC derivation is an epigenetic reprogramming process. Genome-wide analysis of histone modification and chromatin remodeling revealed the number of alternations occurring at the early stage of reprogramming, including the hypermethylation of H3K4 and the demethylation of H3K27 and H3K9. These loosen the compacted heterochromatin and promote transcription factors binding to the “open” chromatin to initiate the reprogramming.
The inventors investigated the transfection efficiency in HF1 and HF4 using the same episomal vector carrying cytomegalovirus (CMV)-driven GFP. The inventors could not observe a significant difference between two cell lines, as determined by FACS analysis. This result suggested that the resistance was unlikely associated with low transfection efficiency. To study the epigenetic effects of O4I3 and its relevance to reprogramming, the inventors focused on two histone modifications at the promoter of OCT4, namely, H3K4Me3, known to be related to gene activation, and H3K27Me3, which indicates gene repression. Chromatin immunoprecipitation-qPCR results in two reprogrammable fibroblasts (HF1 and HF2) and in two reprogramming-resistant fibroblasts (HF3 and HF4) showed that OSKM was sufficient to induce abundant occupation of H3K4Me3 at the promoter of OCT4 in HF1 and HF2 in a comparable manner to those in iPSCs, while producing 1,000- to 10,000-fold less in reprogramming-resistant cells (
HMT and HDM are two major classes of enzymes, contributing to the regulation of histone methylation. Lysine-specific demethylase 1 (LSD1) and histone lysine demethylase 5 (KDM5, also known as JARID1) majorly catalyze demethylation of H3K4. A few KDM5 chemical inhibitors have been reported to inhibit demethylation of H3K4, leading to an increase of global methylated H3K4 in various cell types. The inventors tested the inhibitory effect of O4I3 on LSD1 and KDM5. KDM4 (also known as JMJD2), the HDM of H3K9 and H3K36, was also included. The inventors found that O4I3 inhibited KDM5 with 1050 values of 0.79 nM, whereas it inhibited KDM4 with a 500-fold less potency (1050: 249 nM). In the case of LSD1, the inventors hardly detected the inhibitory effect of the molecule even at a concentration of 100 mM (
In mammalian cells, the KDM5 family consists of four members, namely, KDM5A (known as JARID1A), KDM5B (known as JARID1B or PLU1), KDM5C (JARID1C), and KDM5D (JARID1D or SMCY). Selectivity was found for KDM5A with an IC50 value of 0.19 nM, whereas 20-, 40-, and 1,000-fold less potent 1050 values were obtained in the case of KDM5D, KDM5C, and KDM5B, respectively (
JIB-04 is a potent KDM5A inhibitor (1050: 230 nM) and was found to produce a higher induction of OCT4 compared with the pan KDM5 inhibitor, CPI-445 (
In reprogramming-resistant HF4, the level of H3K4Me3 at the promoter of OCT4 was increased by OSKM, but was still nearly 1,000-fold lower than that in PSCs (
A structure-activity relationship of the lead compound was performed to identify modifications that might further enhance the activity or exhibit other beneficial properties. The modified compounds were synthesized according to the methods disclosed herein.
The methyl group on the aryl moiety was replaced with various substituents and their activity was evaluated in NCCIT-Oct4 cells (
The position of the substituents NO2 and F was varied and resulted in a declined activity in the meta (m-) or ortho (o-) position as compared to the para position of compounds (105) and (102).
The position of the substituent was varied and a declined activity of the resulting derivatives was observed regardless of position (m- or o-) or substituent (NO2 or F).
Further modifications on the aryl moiety as well as on the pyridine moiety were tested and their activity measured in NCCIT-Oct4 cells as shown in Table 1.
The inventors adopted Hantzsch thiazole synthesis (
The inventors replaced the ethyl ester with other groups, including t-Butyl, -Ph and Naph (
O4I4 Activates OCT4-Associated Signalings in Various Cells and Extends Lifespans and C. elegans Models
Consistently, in unmodified NCCIT cells O4I4 forced the expression of OCT4 (3-fold increase as compared to 0.1% DMSO treatment) and NANOG (30-fold increase) as well as other pluripotency-related genes, like E-CADHERIN, SOX2, REX1 and STAT3, 0414-mediated enrichment of OCT4 and NANOG, as well as SOX2 and E-CADHERIN, was also detected by fluorescence-activated cell sorting. Immunoblotting showed a concentration-dependent increase of OCT4 level in O4I4-treated NCCIT cells. It was reported that removal of bFGF led to the loss of pluripotency-marker expression in hPSCs, including OCT4, SOX2, E-CADHERIN and NANOG, which however was rescued in the presence of O4I4 (
In human primary fibroblasts, O4I4 promoted the expression of pluripotency-associated genes, including OCT4, SOX2, NANOG, LIN28, E-CADHERIN, REX1 and SALL4. A dose-dependent increase of OCT4 protein in human primary fibroblasts upon treatment was confirmed by immunoblotting (
Recently, it was reported that transient expression of Yamanaka factors extended the lifespan in mice, indicating anti-aging effect of partial reprogramming. C. elegans provides a leading in vivo system in aging study. The inventors observed an increased survival ratio under oxidative stress (
O4I4 can Replace OCT4 for the Generation of Human iPSCs
To examine if O4I4 can replace OCT4 to reprogram human fibroblasts into the pluripotent state, the inventors first introduced the pluripotent reporter pT2-LTR7-GFP into human primary fibroblasts, to generate a cell line called HF1-LTR7-GFP fibroblasts. Interestingly, some colonies with weak GFP signal appeared in fibroblasts treated merely with O4I4 (
The inventors made the final combination containing O4I3, O4I4 plus SOX2, KLF4, L-MYC and LIN28, named CSKML (
In CSKML-treated fibroblasts the inventors observed a few hESC-like colonies with high GFP signal (
Several chemical cocktails (e.g. A83-01, PD0325901, PS48, parnate, CHIR99021 and sodium butyrate) with ectopic expression of OCT4 have been reported to generate human pluripotent cells. In combination of O4I3 and O4I4 (0413/4) with those chemicals, however, the inventors could not establish fully reprogrammed iPSCs from human fibroblasts, suggesting that the further optimization of the chemical cocktail is required.
To probe the effects of O4I3/4 on chromatin remodeling during reprogramming, the inventors performed ATAC-seq on fibroblasts and TRA-1-60+ cells treated with either CSKML or OSKML at different time points during reprogramming. The Principal component analysis (PCA) of the genome-wide chromatin accessibility data showed that O4I3/4 dramatically promoted chromatin remodeling toward the pluripotent state similar to OSKML-mediated reprogramming (
To explore how O4I3/4 reactivates endogenous OCT4 transcription to reprogram human fibroblasts into iPSCs, the inventors performed RNA-seq on human fibroblasts treated with 0413, 0414, 0413/4, CSKML and OSKML, respectively and ranked the gene up-regulated in human fibroblasts treated with O4I3/4 and compared to those in PSCs. As shown in
Definitely, in fibroblasts, the combination of O4I3/4 activated HMGA1 expression prior to OCT4 expression (
To figure out if HMGA1 directly activates OCT4 transcription, the inventors analyzed the potential binding sites of transcription factors at the promoters of human OCT4 using Matlnspector. HMG family (indicated as SORY for SOX/SRY-sex/testis determining and related HMG box factors) is the top one in the rank list with totally matched numbers of 50. Consistent with the previous report, the occupation of HMGA1 at the promoter of OCT4 was further confirmed by ChIP-qPCR using specific HMGA1 antibody (
Finally, the inventors attempted to replace O4I4 with HMGA1 for reprogramming. The inventors overexpressed HMGA1 in human primary fibroblasts and found that transient overexpression of HMGA1 from day 2- day 9 was more efficient to reprogram human primary fibroblasts (
Taken together, the inventors' results suggest that O4I3/4 enhanced expression of HMGA1 that contribute to endogenous OCT4 reactivation during human fibroblast reprogramming into iPSCs. Importantly, the inventors identified a novel reprograming factor HMGA1 that can replace OCT4 during human somatic cell reprograming.
To explore if there are other signaling pathways involving in HMGA1 transcription regulation, the inventors compared the differently expressed genes in CSKML-treated and SKML-treated fibroblasts as well as O4I4-treated and DMSO-treated (mock) obtained from RNA-seq. PDGFRL, BMP6 and DACT1 were induced only in CSKML and are evident to be involved in the regulation of stemness-associated signaling pathways (
Solvents and reagents obtained from commercial suppliers were at least of reagent grade and were distilled or dried according to prevailing methods prior to use, if necessary. For monitoring the reactions, Alugram SIL G/UV254 sheets for TLC (Macherey & Nagel) were used. Flash column chromatography was accomplished using silica gel 60 (Macherey & Nagel, 0.040-0.063 mm). The purity of compounds was determined at least more than 96% by HPLC analysis.
A mixture of 5-methylpyridin-2-amine and 2-bromo-1-phenylethan-1-ones (2:1) in EtOH was stirred at 60° C. for 3 h. TLC was employed to control the reaction. After removal of solvent, the solid was suspended in 1N HCl and stirred for 2-3 h, filtered and washed with water to obtain the products in good yield (>90%).
1H and 13C NMR spectra were recorded on a Varian 300 MHz NMR system (1H: 300 MHz, 13C: 75 MHz). Chemical shifts are reported in ppm from tetramethylsilane with solvent as the internal standard (1H DMSO-d6: δ 2.50; 13C DMSO-d6: δ 39.5). The following abbreviations were used to explain the multiplicities in NMR spectra: s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet. High-resolution mass spectra (HRMS) were recorded on a Bruker ApexQe hybrid 9.4 T FT-ICR (ESI).
O4I3 1H NMR (300 MHz, DMSO-d6) δ 8.71-8.62 (m, 2H), 7.93-7.69 (m, 4H), 7.32 (d, J=8.0 Hz, 2H), 2.41-2.24 (m, 6H). 13C NMR (75 MHz, DMSO-d6) δ 140.6, 139.1, 136.1, 135.6, 130.3, 127.5, 126.8, 126.5, 123.9, 111.6, 110.7, 21.4, 17.9. HRMS (ESI, C15 H14 N2) [M+H]+: calculated m/z, 223, 1230; found m/z, 223, 1230. IR (cm-1): 3342, 2159, 2021, 1661, 1540, 1534, 1527, 1505, 1456, 1366, 1360, 1311, 1269, 1195, 949, 848, 839, 805, 783, 767, 761, 740, 722.
1H NMR (300 MHz, DMSO-d6) δ 8.83-8.54 (m, 2H), 8.30-7.88 (m, 2H), 7.90-7.65 (m, 2H), 7.55-7.17 (m, 2H), 2.38 (d, J=1.1 Hz, 3H). 13C NMR (75 MHz, DMSO-d6) δ 163.4 (d, J=248.5 Hz), 139.4, 136.2, 134.9, 129.1 (d, J=8.7 Hz), 127.5, 126.9, 123.6 (d, J=3.3 Hz), 116.9 (d, J=22.1 Hz), 111.7, 111.1, 17.8. HRMS (ESI, C14 H11 F N2) [M+H]+: calculated m/z, 227, 0979; found m/z, 227.0979. IR (cm-1): 3325, 3114, 2524, 2362, 2165, 2017, 1659, 1501, 1446, 1271, 1238, 1165, 849, 823, 805, 788, 742.
1H NMR (300 MHz, DMSO-d6) δ 8.76 (d, J=0.6 Hz, 1H), 8.68 (q, J=1.2 Hz, 1H), 8.07-7.99 (m, 2H), 7.89-7.73 (m, 2H), 7.65-7.56 (m, 2H), 2.39 (d, J=1.1 Hz, 3H). 13C NMR (75 MHz, DMSO-d6) δ 139.5, 136.3, 135.2, 134.8, 129.8, 128.3, 127.5, 126.9, 126.0, 111.8, 111.6, 17.9. HRMS (ESI, C14 H11 Cl N2) [M+H]+: calculated m/z, 243.0684; found m/z, 243.0684. IR (cm-1): 3303, 2528, 2362, 2162, 2020, 1660, 1527, 1488, 1474, 1455, 1416, 1273, 1094, 1010, 941, 933, 843, 803, 769, 742, 729.
1H NMR (500 MHz, DMSO-d6) δ 8.77 (d, J=0.7 Hz, 1H), 8.68 (q, J=1.3 Hz, 1H), 8.00-7.93 (m, 2H), 7.85 (d, J=9.1 Hz, 1H), 7.80-7.73 (m, 3H), 2.40 (d, J=1.2 Hz, 3H). 13C NMR (75 MHz, DMSO-d6) δ 139.6, 136.3, 135.0, 132.8, 128.6, 127.5, 126.9, 126.5, 124.0, 112.0, 111.6, 17.9. HRMS (ESI, C14 H11 Br N2) [M+H]+: calculated m/z, 287.0178; found m/z, 287.0178. IR (cm-1): 2534, 2364, 2161, 2023, 1978, 1655, 1525, 1488, 1455, 1443, 1274, 1067, 1007, 839, 804, 786, 774, 742, 712.
1H NMR (300 MHz, DMSO-d6) δ 8.79 (s, 1H), 8.58 (d, J=1.6 Hz, 1H), 8.42-8.28 (m, 2H), 8.34-8.18 (m, 2H), 7.76 (d, J=9.2 Hz, 1H), 7.59 (d, J=9.3 Hz, 1H), 2.36 (d, J=1.1 Hz, 3H). 13C NMR (75 MHz, DMSO-d6) δ 147.8, 141.6, 136.7, 136.0, 134.3, 127.3, 126.3, 126.0, 124.8, 113.7, 113.0, 17.9. HRMS (ESI, C14 H11 N3O2) [M+H]+: calculated m/z, 254.0924; found m/z, 254.0924. IR (cm-1): 2521, 2364, 2160, 2022, 1977, 1601, 1509, 1490, 1449, 1343, 1264, 1245, 1221, 1108, 854, 834, 806, 768, 752, 741, 715.
1H NMR: δ 8.67 (q, J=1.2 Hz, 1H), 8.63 (d, J=0.7 Hz, 1H), 8.03-7.97 (m, 2H), 7.86 (d, J=9.1 Hz, 1H), 7.77 (dd, J=9.2, 1.6 Hz, 1H), 7.15-7.09 (m, 2H), 3.83 (s, 2H), 2.50 (p, J=1.8 Hz, 3H), 2.41 (d, J=1.1 Hz, 2H). 13C NMR: δ 161.2, 139.1, 135.8, 135.8, 128.3, 127.4, 126.7, 119.2, 115.2, 111.6, 109.9, 55.9, 17.9. HRMS (ESI) calculated m/z, 239.1179; found C15H15N2O m/z, 239.1179 [M+H]+. IR (cm-1): 2539, 2436, 2366, 2157, 2028, 1975, 1660, 1617, 1594, 1577, 1561, 1507, 1441, 1367, 1294, 1256, 1186, 1160, 1023, 952, 840, 808, 795, 743.
1H NMR: δ 10.22 (s, 1H), 8.66 (s, 1H), 8.54 (s, 1H), 7.85 (dd, J=9.0, 2.3 Hz, 3H), 7.76 (dd, J=9.2, 1.5 Hz, 1H), 7.03-6.90 (m, 2H), 2.41 (d, J=1.2 Hz, 3H). 13C NMR δ 159.7, 139.5, 137.2, 134.9, 128.2, 126.8, 126.5, 118.3, 116.5, 112.0, 109.2, 17.9. HRMS (ESI) calculated m/z, 225.1022; found C14 H15N20 m/z, 225.1022 [M+H]+. IR (cm-1): 2489, 2158, 2027, 1975, 1617, 1591, 1506, 1459, 1397, 1375, 1292, 1275, 1246, 1219, 1179, 1112, 951, 837, 812, 766, 741.
1H NMR: δ 8.90 (s, 1H), 8.70 (q, J=1.3 Hz, 1H), 8.29-8.18 (m, 2H), 8.09-7.98 (m, 2H), 7.88 (d, J=9.2 Hz, 1H), 7.79 (dd, J=9.3, 1.5 Hz, 1H), 2.41 (d, J=1.1 Hz, 3H). 13C NMR: δ 140.1, 136.4, 134.5, 133.6, 131.9, 127.4, 127.2, 126.9, 118.8, 113.0, 112.5, 112.2, 17.9. HRMS (ESI) calculated m/z, 234.1026; found C15H12N3 m/z, 234.1026 [M+H]+. IR (cm-1): 2781, 2702, 2536, 2498, 2446, 2368, 2156, 2025, 1974, 1656, 1613, 1557, 1528, 1498, 1446, 1302, 1267, 1163, 1135, 1039, 1021, 996, 950, 8757, 848, 835, 808, 791, 746, 717.
1H NMR: δ 8.79 (t, J=2.0 Hz, 1H), 8.68 (s, 1H), 8.47 (q, J=1.4 Hz, 1H), 8.42 (dt, J=7.8, 1.3 Hz, 1H), 8.21 (dd, J=8.2, 1.0 Hz, 1H), 7.78 (t, J=8.0 Hz, 1H), 7.66 (d, J=9.2 Hz, 1H), 7.38 (dd, J=9.0, 1.7 Hz, 1H), 2.34 (s, 3H). 13C NMR: δ 150.31, 142.50, 137.70, 136.28, 133.14, 131.96, 131.58, 128.54, 127.49, 125.29, 121.80, 113.70, 113.01, 18.10. HRMS (ESI) calculated m/z, 254.0924; found C14H12N3O2 m/z, 254.0924 [M+H]+. IR (cm-1): 2947, 2930, 2541, 2456, 2363, 2158, 2028, 1974, 1656, 1619, 1554, 1517, 1486, 1456, 1348, 1266, 1215, 1163, 1114, 1071, 970, 904, 879, 837, 808, 768, 724.
1H NMR: δ 8.40-8.34 (m, 1H), 8.18 (d, J=0.7 Hz, 1H), 7.91 (dd, J=7.8, 1.4 Hz, 1H), 7.83 (dd, J=8.0, 1.2 Hz, 1H), 7.71 (td, J=7.6, 1.3 Hz, 1H), 7.56 (td, J=7.7, 1.4 Hz, 1H), 7.48 (d, J=9.1 Hz, 1H), 7.14 (dd, J=9.2, 1.7 Hz, 1H), 2.28 (d, J=1.1 Hz, 3H). 13C NMR: δ 149.2, 144.1, 140.0, 132.4, 130.9, 129.2, 129.0, 127.4, 124.9, 124.0, 122.3, 116.7, 111.1, 18.0. HRMS (ESI) calculated m/z, 254.0924; found C14H12N3O2 m/z, 254.0924 [M+H]+. IR (cm-1): 2540, 2487, 2443, 2364, 2341, 2159, 2027, 1974, 1609, 1527, 1459, 1420, 1372, 1345, 1285, 1260, 1208, 1164, 1144, 1105, 1033, 1018, 990, 949, 854, 836, 800, 776, 761, 727.
1H NMR: δ 8.83 (s, 1H), 8.71 (q, J=1.2 Hz, 1H), 7.97 (dt, J=10.2, 2.2 Hz, 1H), 7.96-7.83 (m, 2H), 7.81 (dd, J=9.2, 1.5 Hz, 1H), 7.62 (td, J=8.1, 6.0 Hz, 1H), 7.43-7.28 (m, 1H), 2.41 (d, J=1.1 Hz, 3H). 13C NMR: δ 162.9 (d, J=244.2 Hz), 139.6, 136.4, 134.7 (d, J=2.8 Hz), 132.0 (d, J=8.5 Hz), 129.4 (d, J=8.8 Hz), 127.5, 126.9, 122.8 (d, J=2.9 Hz), 117.4 (d, J=21.1 Hz), 113.5 (d, J=24.1 Hz), 112.0, 111.9, 17.8. HRMS (ESI) calculated m/z, 227.0979; found C14H11FN2 m/z, 227.0979 [M+H]+. IR (cm-1): 3058, 3023, 3012, 2929, 2536, 2448, 2366, 2157, 2102, 2024, 1975, 1664, 1604, 1585, 1529, 1491, 1452, 1362, 1311, 1271, 1196, 1159, 1088, 799, 879, 816, 795, 746.
1H NMR: δ 8.75 (q, J=1.3 Hz, 1H), 8.64 (d, J=3.0 Hz, 1H), 8.26 (td, J=7.8, 1.7 Hz, 1H), 7.91 (d, J=9.2 Hz, 1H), 7.81 (dd, J=9.2, 1.6 Hz, 1H), 7.63-7.53 (m, 1H), 7.53-7.41 (m, 2H), 2.41 (s, 3H). 13C NMR: δ 159.6 (d, J=250.8 Hz), 139.4, 136.3, 132.5 (d, J=9.0 Hz), 130.0, 128.9, 127.2, 126.8, 125.9, 117.0 (d, J=21.4 Hz), 115.5 (d, J=11.9 Hz), 113.8 (d, J=14.0 Hz), 112.0, 18.0 (d, J=3.7 Hz). HRMS (ESI) calculated m/z, 227.0979; found C15H14FN2 m/z, 227.0979 [M+H]+. IR (cm-1): 2930, 2542, 2449, 2371, 2160, 2025, 1973, 1656, 1621, 1523, 1498, 1451, 1357, 1313, 1268, 1227, 1164, 1118, 949, 861, 805, 764, 743.
1H-NMR: 1.28 (t, 3J=6.9 Hz, 3H), 4.24 (q, 3J=6.9, 2H), 6.74 (dd, 3J=6.9 Hz, 4J=2.1 Hz, 2H), 7.36 (dd, 3J=6.9 Hz, 4J=2.1 Hz, 2H), 7.63 (s, 1H), 9.12 (s, 1H), 10.00 (s, 1H). 13C-NMR: 14.2, 60.3, 115.5, 117.2, 119.8, 132.7, 142.4, 152.8, 160.9, 164.6. IR (cm−1): 3308, 3127, 1693, 1586, 1545, 1508, 1464, 1437, 1393, 1297, 1272, 1240, 1212, 1159, 1093, 1021, 959, 876, 840, 819, 793, 771, 722, 674, HRMS (ESI) Calculated m/z: 265.0641; found m/z: 265.0641 [M+H]+. Anal. Calcd for C12H12N2O3S: C, 54.53; H, 4.58; N, 10.60. Found: C, 54.91; H, 4.67; N, 10.23.
1H-NMR: 1.28 (t, 3J=7.2 Hz, 3H), 3.72 (S, 3H), 4.25 (q, 3J=7.2 Hz, 2H), 6.92 (dd, 3J=6.9 Hz, 4J=2.1 Hz, 2H), 7.52 (dd, 3J=6.9 Hz, 4J=2.4 Hz, 2H), 7.67 (s, 1H), 10.23 (s, 1H). 13C-NMR spectrum: 14.2, 55.3, 60.4, 114.3, 117.7, 119.3, 134.1, 142.0, 154.6, 160.8, 164.1. IR (cm−1): 3019, 2833, 2541, 2159, 2031, 1976, 1714, 1635, 1588, 1535, 1510, 1323, 1267, 1253, 1212, 1182, 1125, 1109, 1035, 1017, 822, 801, 767, 661, HRMS (ESI) Calculated m/z: 279.0798; found m/z: 279.0798 [M+H]+. Anal. Calcd for C13H14N2O3S: C, 56.10; H, 5.07; N, 10.07. Found: C, 56.18; H, 5.47; N, 9.82.
1H-NMR: 1.27 (t, 3J=6.9, 3H), 2.23 (s, 3H), 4.23 (q, 3J=6.9 Hz, 2H), 7.11 (d, 3J=8.1 Hz, 2H), 7.47 (d, 3J=8.7 Hz, 2H), 7.69 (s, 1H), 10.25 (s, 1H). 13C-NMR: 14.7, 20.8, 60.8, 117.7, 118.4, 129.9, 131.1, 138.8, 142.8, 161.3, 163.9. IR (cm−1): 3262, 2509, 2158, 2023, 1977, 1732, 1542, 1508, 1438, 1190, 1188, 1026, 795, 704, 675. HRMS (ESI) Calculated m/z: 263.0849; found m/z: 263.0849 [M+H]+. Anal. Calcd for C13H14N2O2S: C, 59.52; H, 5.38; N, 10.68. Found: C, 59.32; H, 5.66; N, 10.51.
1H-NMR: 1.31 (t, 3J=7.2 Hz, 3H), 4.29 (q, 3J=6.9 Hz, 2H), 7.83-7.86 (m, 2H), 7.95 (s, 1H), 8.23-8.26 (m, 2H), 11.16 (s, 1H). 13C-NMR: 14.2, 60.6, 116.3, 120.7, 125.5, 140.5, 142.4, 146.4, 160.5, 161.8. IR (cm−1): 3316, 3114, 2440, 2159, 2031, 1976, 1688, 1594, 1561, 1527, 1510, 1487, 1419, 1323, 1303, 1254, 1234, 1181, 1112, 1093, 1027, 977, 882, 859, 847, 822, 772, 749, 689, HRMS (ESI) Calculated m/z: 294.0543; found m/z: 294.0543 [M+H]+. Anal. Calcd for C12H11N3O4S: C, 49.14; H, 3.78; N, 14.33. Found: C, 49.18; H, 3.47; N, 14.42.
1H-NMR: 1.28 (t, 3J=8.1 Hz), 4.24 (q, 3J=6.9 Hz, 2H), 7.75 (d, 3J=9.0 Hz, 2H), 7.87 (s, 1H), 7.93 (d, 3J=9.0 Hz, 2H), 10.82 (s, 1H), 11.17 (s, 1H). 13C-NMR: 14.2, 60.2, 116.1, 119.7, 122.3, 130.6, 142.4, 144.7, 160.6, 162.2, 165.3. IR (cm−1): 3640, 3261, 2924, 2520, 2163, 2023, 1722, 1674, 1595, 1548, 1439, 1372, 1322, 1277, 1179, 1121, 1099, 1020, 848, 764, 715. HRMS (ESI) Calculated m/z: 315,0410; found m/z: 315,0410 [M+Na]+. Anal. Calcd for C13H12N2O4S C, 53.42; H, 4.14; N, 9.58. Found: C, 53.63; H, 4.24; N, 9.38.
1H-NMR: 1.30 (t, 3J=6.9 Hz, 3H), 4.28 (d, 3J=6.9 Hz, 2H), 7.76-7.83 (m, 4H), 7.90 (s, 1H), 10.92 (s, 1H), 13C-NMR: 14.2, 60.6, 102.7, 116.8, 120.0, 121.9, 133.5 142.4, 144.4, 160.5, 162.0. IR(cm−1): 3631, 3304, 3190, 3120, 2514, 2212, 2162, 2023, 1975, 1694, 1601, 1524, 1448, 1411, 1316, 1216, 1174, 1121, 1088, 1019, 828, 785, 720. HRMS (ESI) Calculated m/z: 296.0464; found m/z: 296.0464 [M+Na]+. Anal. Calcd for C13H11N3O2S C, 57.13; H, 4.06; N, 15.37. Found: C, 57.18; H, 4.07; N, 15.43.
1H-NMR: 1.27 (t, 3J=6.9 Hz, 3H), 3.76 (s, 3H), 3.81 (s, 3H), 4.24 (q, 3J=7.2 Hz, 2H), 6.51-6.55 (m, 1H), 6.64-6.65 (m, 1H), 7.62 (s, 1H), 7.83-7.86 (m, 1H), 9.56 (s, 1H). 3C-NMR: 14.2, 55.4, 55.7, 60.4, 99.3, 104.4, 118.0, 122.5, 122.6, 141.1, 151.5, 156.8, 160.6, 166.2. IR (cm−1): 3053, 2974, 2522, 2159, 2031, 1977, 1729, 1618, 1586, 1518, 1460, 1334, 1257, 1213, 1197, 1179, 1156, 1129, 1097, 1032, 1011, 836, 818, 768, 666. HRMS (ESI) Calculated m/z: 309.0904; found m/z: 309.0904 [M+H]+. Anal. Calcd for C14H16N2O4S C, 54.53; H, 5.23; N, 9.09. Found: C, 54.42; H, 5.47; N, 9.01.
1H-NMR: 1.29 (t, 3J=6.9 Hz, 3H), 3.72 (s, 3H), 3.80 (s, 3H), 4.25 (q, 3J=7.2 Hz, 2H), 6.49-6.53 (m, 1H), 6.91-6.94 (m, 1H), 7.75 (s, 1H), 8.25-8.26 (m, 1H), 9.79 (s, 1H). 13C-NMR: 14.2, 55.1, 56.3, 60.3, 105.1, 105.7, 111.4, 130.6, 141.8, 142.0, 142.1, 153.3, 160.8. 163.2. IR (cm−1): 3321, 3119, 2520, 2159, 2031, 1977, 1687, 1602, 1541, 1518, 1481, 1462, 1449, 1368, 1331, 1280, 1251, 1216, 1206, 1173, 1125, 1088, 1052, 1020, 977, 957, 895, 876, 860, 786, 761, 751, 711, 654. HRMS (ESI) Calculated m/z: 309.0904; found m/z: 309.0904 [M+H]+. Anal. Calcd for C14H16N2O4S: C, 54.53; H, 5.23; N, 9.09. Found: C, 54.43; H, 5.48; N, 9.11.
1H-NMR: 1.31(t, 3J=7.2 Hz, 3H), 4.27 (d, 3J=7.2 Hz, 2H), 7.61 (s, 1H), 7.93 (m, 2H), 8.38 (s, 1H), 11.10 (s, 1H), 13C-NMR: 14.4, 61.0, 113.6-114.5, 116.9 (d, J=4.3 Hz), 120.5, 123.7 (d, J=272.8 Hz), 127.0, 134.2 (q, J=32.6 Hz), 142.7 (d, J=1.7 Hz), 161.0, 162.4. IR (cm−1): 3642, 3315, 2510, 2162, 2023, 1975, 1682, 1578, 1536, 1377, 1269, 1114, 1011, 936, 874, 691, HRMS (ESI) Calculated m/z: 407.0259; found m/z: 407.0259 [M+Na]t Anal. Calcd for C14H10F6N2O2S.0.25 H2O C, 43.25; H, 2.72; N, 7.21. Found: C, 43.46; H, 2.80; N, 6.95.
1H-NMR: 1.30 (t, 3J=7.2 Hz, 3H), 3.87 (s, 3H), 4.26 (q, 3J=7.2 Hz, 2H), 6.99-7.01 (m, 2H), 7.80 (s, 1H), 8.67 (d, 3J=2.1 Hz, 1H), 9.97 (s, 1H). 13C-NMR: 14.2, 56.0, 60.4, 111.9, 117.0, 119.9, 120.9, 124.3, 131.0, 141.8, 146.4, 160.7, 162.8. IR (cm−1): 3315, 3122, 2500, 2159, 2031, 1976, 1686, 1596, 1536, 1509, 1491, 1416, 1331, 1250, 1212, 1173, 1125, 1021, 876, 798, 786, 761, 752. HRMS (ESI) Calculated m/z: 313.0408; found m/z: 313.0408 [M+H]+. Anal. Calcd for C13H13ClN2O3S.0.5H2O: C, 48.53; H, 4.39; N, 8.71. Found: C, 48.93; H, 4.35; N, 8.37.
1H-NMR: 1.28 (t, 3J=6.9 Hz, 3H), 4.25 (q, 3J=7.2 Hz, 2H), 7.11-7.14 (m, 1H), 7.23-7.36 (m, 1H), 7.78 (s, 1H), 8.36-8.40 (m, 1H), 10.13 (s, 1H). 13C-NMR: 13C-NMR: 14.6, 60.9, 106.3 (d, J=2.1 Hz), 107.9 (dd, J=24.6, 7.5 Hz), 116.2 (dd, J=21.5, 10.2 Hz), 120.8, 130.2 (m), 142.3, 147.9 (dd, J=239.1, 2.4 Hz), 158.5 (dd, J=237.3, 2.0 Hz), 161.7, 162.8. IR (cm−1): 3246, 2928, 2518, 2159, 2031, 1976, 1716, 1702, 1538, 1511, 1456, 1432, 1369, 1333, 1318, 1257, 1226, 1197, 1172, 1142, 1116, 1092, 1020, 971, 957, 848, 839, 810, 786, 768, 742, 730, 719, 670, HRMS (ESI) Calculated m/z: 285.0504; found m/z: 285.0504 [M+H]+. Anal. Calcd for C12H10F2 N2O2S.0.67H2O: C, 49.65; H, 3.70; N, 9.65. Found: C, 49.65; H, 3.46; N, 9.22.
1H-NMR: 1.30 (t, 3J=6.9 Hz, 3H), 4.27 (q, 3J=7.2 Hz, 2H), 6.78-6.84 (m, 1H), 7.25-7.33 (m, 1H), 7.86 (s, 1H), 8.46-8.53 (m, 1H), 10.45 (s, 1H). 13C-NMR: 13C-NMR: 14.6, 60.8, 104.5 (dd, J=27.1, 23.4 Hz), 111.6 (dd, J=21.7, 3.6 Hz), 120.0, 121.8 (dd, J=9.1, 2.8 Hz), 125.8 (dd, J=11.1, 3.4 Hz), 142.4, 152.4 (dd, J=247.2, 12.2 Hz), 157.3 (dd, J=241.8, 11.3 Hz), 161.1, 164.1. IR (cm−1): 3308, 3124, 2517, 2159, 2031, 1976, 1702, 1644, 1551, 1524, 1491, 1483, 1444, 1373, 1331, 1241, 1214, 1194, 1182, 1116, 1093, 1027, 967, 876, 865, 798, 780, 743, 723, HRMS (ESI) Calculated m/z: 307.0323; found m/z: 307.0323 [M+Na]+. Anal. Calcd for C12H10F2 N2O2S.0.67H2O: C, 49.65; H, 3.70; N, 9.65. Found: C, 49.44; H, 3.91; N, 9.35.
1H-NMR: 1.27 (t, 3J=6.9 Hz, 3H), 2.29 (s, 3H), 4.23 (q, 3J=7.2 Hz, 2H), 7.19-7.20 (m, 1H), 7.22-7.23 (m, 1H), 7.71 (s, 1H), 7.81-7.84 (m, 1H), 9.63 (s, 1H). 13C-NMR: 14.2, 20.0, 60.3, 115.9, 1!8.9, 124.1, 129.1, 133.2, 135.7, 136.1, 142.1, 160.8, 165.5. IR (cm−1): 3630, 3121, 2982, 2925, 2517, 2162, 2024, 1975, 1718, 1549, 1485, 1384, 1203, 1090, 1035, 800, 728, 666. HRMS (ESI) Calculated m/z: 340.9954; found m/z: 340.9954 [M+H]+. Anal. Calcd for C13H13BrN2O2S.0.5 H2O: C, 44.58; H, 4.03; N, 8.00. Found: C, 44.59; H, 3.63; N, 7.61.
1H-NMR: 1.27 (t, 3J=8.4 Hz, 3H), 2.26 (s, 3H), 4.24 (q, 3J=7.2 Hz, 2H), 7.36-7.43 (m, 2H), 7.73 (s, 1H), 7.90-7.93 (m, 1H), 9.55 (s, 1H). 13C-NMR: 14.2, 17.7, 60.4, 115.0, 118.8, 122.5, 129.2, 131.4, 132.9, 138.4, 142.1, 160.8, 164.8. IR (cm−1): 3128, 2984, 2929, 2517, 2162, 2023, 1975, 1725, 1548, 1479, 1387, 1207, 1089, 1024, 876, 792, 711. HRMS (ESI) Calculated m/z: 340.9954; found m/z: 340.9954 [M+H]+. Anal. Calcd for C13H13BrN2O2S.0.5 H2O: C, 44.58; H, 4.03; N, 8.00. Found: C, 44.80; H, 3.81; N, 7.66.
1H-NMR: 1.27 (s, 9H), 6.44 (s, 1H), 7.33 (dd, 3J=2.1 Hz, 4J=6.9 Hz, 2H), 7.65 (dd, 3J=2.1 Hz, 4J=6.9 Hz, 2H), 10.20 (s, 1H). 13C-NMR: 14.7, 20.8, 117.7, 118.4, 129.9, 138.8, 142.8, 161.3, 163.9. IR (cm−1): 3147, 2923, 2853, 2511, 2030, 1976, 1561, 1529, 1488, 1308, 1218, 1201, 1100, 1091, 1014, 954, 854, 827, 801, 713, 692. HRMS (ESI) Calculated m/z: 267.0717; found m/z: 267.0717 [M+H]+. Anal. Calcd for C13H15ClN2S: C, 58.53; H, 5.67; N, 10.50. Found: C, 58.20; H, 5.77; N, 10.45.
1H-NMR: 7.31-7.46 (m, 6H), 7.77 (d, 3J=8.7 Hz, 2H), 7.92 (d, 3J=7.2 Hz, 2H), 10.41 (s, 1H). 13C-NMR: 103.3, 118.2, 124.4, 125.7, 127.6, 128.6, 128.8, 134.4, 140.0, 150.1, 162.7. IR (cm−1): 3378, 3112, 2509, 2159, 2031, 1976, 1585, 1556, 1481, 1442, 1416, 1386, 1323, 1301, 1278, 1215, 1199, 1172, 1090, 1071, 1055, 1025, 1011, 915, 843, 831, 919, 770, 687, 671. HRMS (ESI) Calculated m/z: 287.0404; found m/z: 287.0404 [M+H]+. Anal. Calcd for C15H11ClN2S: C, 62.84; H, 3.87; N, 9.77. Found: C, 62.91; H, 3.72; N, 9.85.
1H-NMR: 7.41-7.45 (m, 2H), 7.48-7.56 (m, 3H), 7.81-7.85 (m, 2H), 7.90-8.08 (m, 4H), 8.46 (s, 1H), 10.49 (s, 1H). 13C-NMR: 104.2, 118.4, 124.0, 124.3, 124.5, 126.0, 126.4, 127.6, 128.1, 128.2, 128.9, 131.8, 132.5, 133.2, 140.1, 150.0, 162.8. IR (cm−1): 3624, 2965, 2521, 21331, 1976, 1615, 1583, 1571, 1530, 1491, 1097, 815, 806, 770, 743. HRMS (ESI) Calculated m/z: 337.0561; found m/z: 337.0561 [M+H]+. Anal. Calcd for C19H13ClN2S: C, 67.75; H, 3.89; N, 8.32. Found: C, 67.51; H, 3.99; N, 8.24.
1H-NMR: 1.26 (s, 9H), 2.23 (s, 3H), 6.35 (s, 1H), 7.09 (d, 3J=6.9 Hz, 2H), 7.47 (d, 3J=6.4 Hz, 2H), 9.91 (s, 1H). 13C-NMR: 20.3, 29.6, 34.3, 98.7, 116.8, 129.3, 129.7, 139.1, 161.5, 162.8. HRMS (ESI) Calculated m/z: 247.1263; found m/z: 247.1263 [M+H]+. Anal. Calcd for C14H18N2S: C, 68.25; H, 7.36; N, 11.37. Found: C, 68.01; H, 7.35; N, 11.30.
1H-NMR: 1.26 (s, 9H), 2.27 (s, 3H), 6.38 (s, 1H), 6.71-6.75 (m, 1H), 7.16(t, 3J=7.7 Hz, 1H), 7.39-7.43 (m, 2H), 9.95 (s, 1H). HRMS (ESI) Calculated m/z: 247.1263; found m/z: 247.1263 [M+H]+. Anal. Calcd for C14H18N2S: C, 68.25; H, 7.36; N, 11.37. Found: C, 68.07; H, 7.21; N, 11.35.
1H-NMR: 1.23 (s, 9H), 2.20 (s, 3H), 6.25 (s, 1H), 6.96 (dd, 3J=8.1 Hz, 4J=2.1 Hz, 1H), 7.00 (s, 1H), 7.23 (d, 3J=8.1 Hz, 1H), 7.63 (s, 1H), 9.03 (s, 1H). 13C-NMR: 18.1, 29.6, 34.3, 99.1, 120.5, 123.0, 126.4, 128.5, 130.5, 139.7, 161.3, 164.8. HRMS (ESI) Calculated m/z: 247.1263; found m/z: 247.1263 [M+H]+. Anal. Calcd for C14H18N2S: C, 68.25; H, 7.36; N, 11.37. Found: C, 68.13; H, 7.31; N, 11.25.
1H-NMR: 1.27 (s, 9H), 6.40 (s, 1H), 6.91 (dt, 3J=7.4 Hz, 4J=1.1 Hz, 1H), 7.26-7.32 (m, 2H), 7.59-7.63 (m, 2H), 10.04 (s, 1H). 13C-NMR: 29.6, 34.4, 99.1, 116.5, 120.8, 128.7, 141.5, 161.5, 162.5. HRMS (ESI) Calculated m/z: 233.1107; found m/z: 233.1107 [M+H]+. Anal. Calcd for C13H16N2S: C, 67.20; H, 6.94; N, 12.06. Found: C, 67.10; H, 6.92; N, 12.25.
1H-NMR: 1.23 (s, 9H), 2.20 (s, 3H), 2.23 (s, 3H), 6.25 (s, 1H), 6.96 (dd, 3J=8.1 Hz, 4J=2.1 Hz, 1H), 7.00 (s, 1H), 7.63 (d, 3J=8.1 Hz, 1H), 9.03 (s, 1H). 13C-NMR: 17.9, 20.4, 29.6, 34.3, 98.5, 121.6, 126.9, 129.5, 131.2, 132.5, 137.3, 161.5, 165.7. HRMS (ESI) Calculated m/z: 261.1420; found m/z: 261.1420 [M+H]+. Anal. Calcd for C15H20N2S: C, 69.19; H, 7.74; N, 10.76. Found: C, 68.80; H, 7.53; N, 10.48.
1H-NMR: 1.23 (s, 9H), 2.13 (s, 3H), 2.25 (s, 3H), 6.26 (s, 1H), 6.93 (d, 3J=7.4 Hz, 1H), 7.05 (t, 3J=7.8 Hz, 1H), 7.52 (d, 3J=8.0 Hz, 1H), 9.13 (s, 1H). 13C NMR: 13.8, 20.3, 29.6, 34.5, 120.1, 125.6, 125.7, 128.8, 131.2, 137.2, 139.7, 161.5, 166.1. HRMS (ESI) Calculated m/z: 261.1420; found m/z: 261.1420 [M+H]+. Anal. Calcd for C15H20N2S: C, 69.19; H, 7.74; N, 10.76. Found: C, 68.81; H, 7.63; N, 10.49.
The generation of HEK-Oct4, NCCIT-Oct4 and NCCIT-Nanog reporter cell lines, as well as HFF-LTR7-EGFP, is known in the art (Cheng et al, J Med Chem 2015, 58 (12), 4976-83; Cheng et al, J Med Chem 2015, 58 (15), 5742-50; Wang et al, Nature 2014, 516 (7531), 405-9).
Human primary fibroblasts were isolated as described elsewhere (approved by the Ethikkommission I Heidelberg S-186/2016) and cultivated in DMEM (Gibco, Germany) containing 10% FBS (Gibco) and 1% Penicillin/Streptomycin (Gibco). NCCIT was in RPM11640 (Gibco) containing 10% FBS and 1% P/S. Cells were maintained under 5% CO2 at 37° C. in a humidified atmosphere. iPSCs were in Essential®8 medium (life technologies, Germany). Colony expansion was used for iPSCs maintenance, in which iPSC-like colonies were mechanically selected and isolated in a plate coated with Geltrex® (life technologies); the medium was refreshed very day.
Luciferase reporter assay was performed using Beatle Juice Kit (PJK, Germany) according to the manufacturer's instruction. NCCIT-Oct and NCCIT-Nanog reporter cells were plated into a 24-well plate (100,000 cells/well) for 24 h. Cells were treated with compounds as indicated and harvested with luciferase lysis buffer (25 mM Tris phosphate buffer pH=7.8, 4 mM EGTA, 1% Triton X-100, 10% glycerol and 2 mM fresh DTT, filtered through 0.45 μm sterile filter) at 37° C. for 15 min. The protein concentration was determined by Bradford assay (Sigma, Germany). 100 μL reaction mixture containing luciferin and ATP was added to 20 μL cell lysis in a white plate (Gibco, Germany), incubated for 5 min and measured by a luminometer plate-reader. The activity was determined as percent luminous intensity of treated cells over control cells from at least five-independent experiments.
qRT-PCR
Quantitative reverse-transcription real-time-PCR was performed using a Light Cycler 96 (Roche, Germany) following the manufacturer's protocol. Briefly, total RNA was isolated from cells using TRIzol (Qiagen, Germany) or NucleoSpin®RNA Plus (Macherey-Nagel, Germany). The same amount of RNA was used to reverse-transcriptional synthesize cDNA by using random primers ProtoScript® First Strand cDNA Synthesis Kit (NEB, Germany). qPCR was performed using the SYBR Green PCR master mix (qPCRBIO SyGreen Mix Lo-Rox, Nippon Genetics, Germany) and the primer pairs indicated below (MWG, Eurofins, Germany). Actin was used as an endogenous control. Data were normalized to the value of untreated cells showing the mean±SD of quadruplicates and are representative of at least three independent experiments.
iPSCs were lysed using urea-lysis buffer (1 mM EDTA, 0.5% Triton X-100, 5 mM NaF, 6 M Urea, 1 mM Na3VO4, 10 μg/mL Pepstatin, 100 μM PMSF and 3 μg/mL Aprotinin in PBS). Enhanced chemiluminescence (ECL) immunoblot analysis was performed. 40 μg of total protein was resolved on 12% SDS-PAGE gels and immunoblotted with antibodies. 13-Actin antibody was used as loading control. Primary antibodies were incubated at 1:1000 dilution in TBS (pH 7.5) with 0.1% Tween-20 and 5% BSA/milk with gentle agitation overnight at 4° C. Secondary antibodies (Dianova, Germany) were incubated in TBS (pH 7.5) with 5% Milk and 0.1% Tween-20 at a 1:10,000 dilution for 1 h at room temperature.
iPSCs were seeded in a 96-well plate coated with Geltrex. Cells were fixed with 4% PFA at RT for 15 min, and blocked with blocking buffer (5% goat serum and 0.3% Triton X-100 in PBS) for 1 h. Blocking solution was aspirated and incubated with antibodies in antibody dilution buffer (1% BSA and 0.2% Triton X-100 in PBS) at 4° C. overnight. The secondary antibodies (Goat anti-rabbit Alexa Flor 488 and Goat anti-mouse Alexa Flor 594, Dianova) were added and incubated for 1 h. Hoechst 33342 (1 μg/mL in PBS) was used to visualize nuclei.
iPSCs were seeded in a 6-well plate coated with Geltrex. Cells were harvested, fixed and permeabilized (if appropriately) as known in the art (Cheng et al, Mol Oncol. 2016 June; 10(6):806-24). Fixed cells were incubated with the primary antibody for 24 h at 4° C. and with the secondary antibody for 1 h at room temperature.
NCCIT cells were treated with O4I2 (50 μM) in RPMI 1640 medium containing 2% BSA/FBS. Medium and cells were collected. Cell pellet was solved in 0.1% Triton-x. Protein precipitated by adding MeOH (pH=2) in lysate supernatant on ice for 2 h. Metabolites were extracted from the combined supernatant with ethyl acetate. After removal of organic solvent, residue was dissolved in acetonitrile, frozen immediately in liquid N2 and stored in −80° C. until further analysis.
Additional methods including experimental procedures, chemical synthesis and characterization data can be found in the supplementary information.
Purity of synthetic products was verified using HPLC analysis on a Jasco HPLC system (PU 2085-plus, Jasco GmbH, Umstadt, Germany) equipped with a porous silica column (ReproSil-Pur ODS-3, dimensions 50×2 mm, Dr. Maisch GmbH, Ammerbuch-Entringen Germany). The synthetic products (10 mM in acetonitrile) were diluted to a final concentration of 25 μM in water. Solvent A consisted of water with 0.1% trifluoroacetic acid and solvent B consisted of acetonitrile with 0.1% trifluoroacetic acid. A linear gradient was applied going from 0% solvent B to 100% solvent B in 7 minutes, followed by another minute of 100% solvent B, after which the system was immediately brought back to 100% solvent A and flushed for 2 minutes. Absorbance was monitored at wavelength of 254 nm. It appeared that O4I2-COON eluted after approximately 3.65 minutes and O4I2 after approximately 4.50 minutes (see chromatograms in SI 3).
Samples obtained after purification were diluted to contain 20% MeOH. 100 μL of the sample was transferred to an HPLC vial and placed in the autosampler of an Agilent 1200 series HPLC machine. Sample (20 μL) was injected into the system and metabolites were separated on a C18 column (Kinetex 2.6 μm, C18, 100 Å, dimensions 100×2.1 mm, Phenomenex, Aschaffenburg, Germany). Solvent A was water with 0.1% trifluoroacetic acid and solvent B was 80% acetonitrile in water with 0.1% trifluoroacetic acid. Metabolites were separated using a linear gradient from 20% solvent A to 80% solvent B in 40 minutes. Effluent of the column was sprayed directly into the source of the ESI-Q-TOF (electrospray ionization quadrupole time-of-flight) mass spectrometer (micrOTOF, Bruker Daltonics, Bremen, Germany). Scanning mass range was set to m/z 100-1000.
The episomal vectors carrying OCT44 (#41813), SOX2/KLF4 (#27078) and L-MYC/LIN28 (#27080) were purchased from Addgene (USA). To reach the maximal efficiency, episomal expression of EBNA1 (#37624) was co-transfected with OSKML. Reprogramming was performed in 24-well plate as previously reported (Okita et al. Nat Protoc 5, 418-428 (2010); Okita et al. Nat Methods 8, 409-412 (2011); Okita et al. Science 322, 949-953 (2008)). Briefly, 10 000-20 000 cells were seeded in a 24-well plate for 24 h and then treated with O4I3 (0.25 μM) for 48 h. Cells were transfected with OSKML or SKML in presence of O4I4 (5 μM for HF1 and HF2, 20 μM for HF3) for 7 days (HF1 and HF2) or for 5 days (HF3) in DMEM/F12 GlutaMAX knockout medium containing 1% N2, 2% B27 and 100 ng/mL bFGF. Lipofectamine 3000 was used as transfection reagent (Life Technologies). Essential®8 medium was used after 10 days. After 21-28 days, TRA-1-60 staining was conducted as described before (Cheng et al. J Med Chem 58, 4976-4983 (2015); Cheng et al. J Med Chem 58, 5742-5750 (2015)). TRA-1-60 positive iPSCs-like colonies were mechanically and manually isolated and transferred into a 6-well plate coated with Geltrex® or Matrigel in Essential®8 medium. Medium was refreshed daily.
Differentiation of Mono-Layer CSKML-iPSCs into Three Germ Layers
Mono layer iPSCs (density 60-80%) in Geltrex-coated 24-well plate were used for differentiation. Differentiation medium (500 mL) contains 5 mL BSA, 20 μL 1-thioglycerol, 10 μg/mL insulin, 15 μg/mL transferrin, 0.1% polyvinyl alcohol in DMEM/F12 Glutamax knockout medium.
Endoderm: Day 1) E8 medium was switched to differentiation medium (DE) additionally containing 100 ng/mL Activin, 100 ng/mL bFGF, 10 ng/mL BMP4, 10 μM Ly294002 and 2.5 μM Chir99021. Day 2) Medium was changed with DE containing 100 ng/mL Activin, 100 ng/mL bFGF, 10 ng/mL BMP4 and 10 μM Ly294002. Day 3) RPMI 1640 medium containing 100 ng/mL Activin and 100 ng/mL bFGF was used.
Mesoderm: E8 medium was switched to differentiation medium (DE) additionally containing 100 ng/mL Activin, 20 ng/mL bFGF, 10 ng/mL BMP4, 10 μM Ly294002 and 5 μM Chir99021. The medium was changed daily for 2-3 days.
Neuroectoderm: E8 medium was switched to differentiation medium (DE) additionally containing 10 μM SB431542, 1 μM LDN193189 and 10 ng/mL bFGF. The medium was changed daily for 14 days.
To spontaneously differentiate the novel human iPSCS to embryoid bodies (EBs), the differentiation was performed according to a previously published protocol (Wang et al. Nature 516, 405-409 (2014)). Briefly, the novel human iPSCs were cultured on matrigel-coated 6-well plates. Cells from one well were dissociated with collagenase IV (1 mg ml−1), and then split into small cell clumps. The small cell clumps were transferred into one 10-cm low-attachment dish, and cultured in EB medium (knockout DMEM, 20% knockout serum replacement, 1 mM L-glutamine, 1% nonessential amino acids, 0.1 mM 2-mercaptoethanol and primocin). The medium was changed every 2 days. The EBs were cultured for 8-10 days followed by collection for RNA isolation and qPCR.
The bisulfite reaction was performed using the EpiTect Bisulfite Kit (Qiagen) according to the manufacturer's instructions. 5 ul of bisulfite-treated genomic DNA was used to amplify the OCT4 a promoter region in human iPSCs and the parental fibroblast. PCR products were cloned into pGEM-T vectors (Promega) and sequenced using the M13 forward primer. Primers used to amplify the OCT4 promoter region were described in a previous publication (Grabundzija et al. Nucleic acids research 41, 1829-1847 (2013)).
Cells (50 000) were lysed in a lysis buffer (10 mM Tris HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL-CA630). TransNGS®Tn5 DNA library pre Kit for Illumina was used to prepare DNA library for sequencing.
Epi5® Episomal iPSC Reprogramming Kit (Life technologies) was used to reprogram human fibroblasts according to the manufacturer's protocol. Briefly, 5,000-50,000 cells were seeded in a 24-well plate for 24 h and then transfected with episomal vectors in N2 B27 medium. After 14 days, cells were re-suspended with 0.5 mM EDTA and re-plated in a 6-well plate in Essential®8 medium. Colonies were isolated after 3-4 weeks with the help of alkaline phosphatase (AP) live stain (Life technologies). Medium was refreshed daily.
iPSC Single Cell Expansion
iPSC single cell expansion was performed according to a well-established protocol known in the art (Watanabe et al, Nat Biotechnol, 2007, 25(6), 681-6). Briefly, iPSCs were dissociated with Accutase® as single cell suspension and re-seeded in a Geltrex-coated 96-well plate in the presence of Rock inhibitor for the first 24 h in combination with/without O4I3. Cell viability was performed in MTT assay as disclosed elsewhere (Cheng et al, Mol Oncol. 2016 June; 10(6):806-24).
Gene expression profiling of human PSCs, iPSCs and fibroblast samples was conducted on the Illumina Human Sentrix-12v4 BeadChip array by the Genomics and Proteomics Core Facility of DKFZ. Two sets of samples were profiled: (i) three hPSC samples, corresponding to treatments with two O4I3 doses (1 nM and 10 nM) and not-treated hPSCs; (ii) three fibroblast samples, corresponding to two treatments (one with O4I3 and one with OSKM) and not-treated fibroblast.
Gene expression analysis was performed in R 3.3.2 computing environment and packages from the open-source software development project Bioconductor 3.4. Clustering and functional enrichment analysis was performed with the standalone tool STEM 1.3.11, while heatmap visualization of gene expression was performed with the package pheatmap 1.0.8. The genome-wide expression profiles of iPSCs were determined using the Human-HT12-V4 Expression BeadChip. Three samples were profiled, corresponding to two O4I3 treatments (one with 1 μM and one with 10 μM) and not-treated iPSCs. Quality assessment and pre-processing of raw data was done with the package beadarray 2.24.2. Pre-processing involved default image processing (with median-based local background), default Illumina removal for outlying observations, mean summarization of bead-level observations into probe-level data, quantile normalization of probe-level data and log 2 transformation. The resulting probes were matched to genes using annotations from the package illuminaHumanv4.db 1.26.0. After filtering probes that poorly matched the annotated genes (quality status of no-match and bad) as well as low-expression probes (detection score>0.05), 14109 probes were available for clustering analysis with STEM, a tool for clustering short time series data that can differentiate between real and random temporal expression patterns. For this purpose, one probe per gene (the one with highest variance, if multiple probes matched to single gene) was selected and the data converted into fold changes with respect to the not-treated iPSCs. The data was analyzed as short time series of length three (corresponding to dose level of 0, 1, and 10 μM), by treating dose level as time factor. STEM was applied in default mode, except for the following settings: at least one measurement with absolute fold change of 0.65; significance of model profiles corrected by false discovery rate method; cellular component terms, terms with evidence code IEA and NAS or terms that had less than 10 genes in-common with the identified model profiles (or clusters of similar model profiles) were excluded from the Gene Ontology (GO) enrichment analysis; multiple testing correction of GO term significance values were determined by the randomization test, with 5000 randomly sampled gene sets per term.
Fibroblast/iPSC experiment data analysis; approximately 18 000 probes, after filtering, were available for differentially expression analysis. The latter was based on fold changes, i.e., the probes with at least two-fold expression relative to the untreated fibroblast were selected as differentially expressed; since single biological replicates per treatment were used, statistical tests were not applicable. Global gene expression comparison between pairs of samples were visualized by scatter plots, plotted with the package ggplot2 2.2.1, while the heatmaps of gene expressions were visualized with the package ComplexHeatmap 1.12.0. In addition, columns and rows in the heatmaps were reordered with hierarchical clustering based on average linkage and Euclidean distance or Pearson correlation. Functional enrichment analysis on differentially expressed probes was performed with gProfileR version r1732_e89_eg36 via the R interface in the package gProfileR version 0.6.1. More specifically, the query lists were treated as unordered human gene lists, and the set of probes retained after filtering was supplied as a background. Multiple testing correction was done by the FDR method according to Benjamini and Hochberg with 0.05 FDR cut-off, including biological processes and molecular functions from the Gene Ontology database with size of 5 up to 500 genes.
Fibroblasts were treated with O4I3 0.5 μM for 2 days in the presence/absence of reprogramming transcription factors. The expression of H3K4Me3 was visualized by using H3K4Me3 antibody as described before for immunocytochemistry. The signal intensity was analyzed using ImageJ software as single cell level randomly selected from at least three independent experiments.
Statistical and graphical analyses of the data (except DNA microarray) were performed using Microsoft Excel 2007 software. The statistical significance of compared measurements was performed by using the Student's one-tailed or two-tailed t-test, considering P=0.05 as statistically significant.
To assess the number of TRA-1-60+ colonies, 10,000 fibroblast cells/well in 96-well plates were transfected with episomal OSKM (Epi5 kit, Thermofisher Scientific) in the presence/absence of small molecules, as indicated in the text. Immunostaining was performed using TRA-1-60 antibody in living cells after 32 days. Transfection efficiency was indicated by quantifying the expression of EGFP (Addgene plasmid #27082).
iPSCs Differentiation
Cellartis iPS cell to hepatocyte differentiation system (Takara, Germany) was used for differentiation of iPSCs to endoderm. StemDiff neuron differentiation kit (08500, Stem Cell Technologies, Germany) was used for differentiation of iPSCs to neuroectoderm. To differentiate iPSCs to mesoderm, cells were seeded in Geltrex-coated plates as single cells and cultivated till the density reached to at least 80%. N2+627 medium was used to replace E8 medium. Activin (100 ng/mL), bFGF (20 ng/mL), BMP4 (10 ng/mL), Ly2 (10 μM) and Chir (5μ) were freshly added. The medium was changed every two days for 14 days.
Measurement of methylated H3K4 and the in vitro activity of LSD1, KDM4, and KDM5 Demethylases
Epiquik histone demethylase (H3K4 specific) activity/inhibition assay kit (Epigentek, Biocat, Germany) was used to measure the protective effect of O4I3 and zolpidem on the methylation of H3K4. Their inhibitory effects on LSD1, KDM5s, and KDM4 were determined using Epigenase jarid demethylase activity/inhibition assay kit, Epigenase JMJD2 demethylase activity/inhibition assay kit and EpiQuik histone demethylase LSD1 activity/inhibition assay kit (Epigentek, Biocat, Germany). The total nuclear extraction was used according to manufacturer's instructions. For measuring KDM5A, KDM5B, KDM5C, and KDM5D activity, magnetic beads were used to immunoprecipitate the respective enzymes from 108 cells according to the manufacturer's instructions (Cell Signaling Technologies).
SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technologies) was used to isolate DNA precipitated with H3K4Me3 or H3K27Me3 antibody. According to the manufacturer's protocol, 106 cells/sample were collected. Non-target Rabbit IgG and total Histone H3 antibodies (provided in the kit) were used as negative and positive controls, respectively. KDM5A-D enzymes were purified using immunoprecipitation with magnetic beads according to the manufacture's protocol. Recruited DNA was subjected to qRT-PCR using ChIP primers sets, and human RPL30 exon 3 primer pairs were used as positive control.
C. elegans Strains and Cultural Condition
Three strains N2 (wild type), TJ356 [daf-16p::daf-16a/b::GFP+rol-6(su1006)] and CF1038 [daf-16(mu86)] were offered by Caenorhabditis Genetics Center (CGC, University of Minnesota, USA). All strains were maintained on nematode growth media (NGM) agar, which content Escherichia coli OP50 as a nutrient source and incubated at 20° C.
Eggs were released by lysing gravid adults with bleaching for 10 min. Resuspended eggs in sterile M9 buffer and incubated at 20° C. for 16-18 h. After all the worms were synchronized at the same L1 larval stage, transferred them into the liquid S-media which contents E. coli OP50 (0D600=0.8-1.2). Then, synchronized worms were treated with DMSO, 50 μg/ml epigallocatechin gallate (EGCG) or O4I4 (5 μM, 10 μM, and 20 μM) for further experiments.
2′-7′-dichlorofluorescein diacetate (H2DCFDA) is a broadly known substance to quantify the ROS (reactive oxygen species) in C. elegans. After H2DCFDA (non-fluorescent) penetrates the cell membrane, it will be turned into a highly fluorescent dye 2′-7-dichlorofluorescein (DCF) via the biochemical reaction of enzymatically deacetylated and oxidization by ROS. Due to the fluorescent intensity, the ROS level in C. elegans can be estimated.
The strains N2 (wild type) and CF1038 (daf-16 mutant) were synchronized and treated as described before. 50 μM H2DCFDA was added into all samples after incubated 48 h. Samples were covered by foil paper to avoid the light and incubated another 1 h. Afterward, 10 μl worms were transferred on a glass slide and paralyzed with 10 μl of 10 mM sodium azide. BIOREVO BZ9000 fluorescence microscope was used to detect the production of DCF, and Image J 1.52a could analyze the ROS level in C. elegans via estimating the densitometrically.
After 48 h treatment, around 60 wild-type C. elegans (N2) worms in each sample were transferred into a new liquid S-media which contains 80 μM of superoxide-generating compound juglone (5-hydroxy-1,4-naphthalenedione) for 24 h. If a worm has response via a gentle touch with platinum wire, it is considered as a live worm. Conversely, a dead worm was considered by no response. The function of the survival rate is shown below.
In this experiment, transgenic worms TJ356 (Daf-16::GFP) are employed to study our target substance affects the localization of daf-1 6. After 24 h treatment, worms were transferred to a glass slide and paralyzed with 10 mM sodium azide. BZ9000 fluorescence microscope was used to observe the localization of daf-1 6. In each sample, around 50 worms were scored for three localization patterns: cytoplasmic, intermediate and nuclear.
O4I4 (0.5 μM) were continuously added in medium until all the worms die. During the experiment period, every two days or three days, worms were counted either live or die by responding to a gentle touch with a platinum wire. Dead worms were discarded, and live worms were transferred to a new NGM plate to ensure they do not go through the dauer stage.
| Number | Date | Country | Kind |
|---|---|---|---|
| 18188930.4 | Aug 2018 | EP | regional |
