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US20080293784A1 - Epothilones c, d, e and f, preparation and compositions - Google Patents

Epothilones c, d, e and f, preparation and compositions Download PDF

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US20080293784A1
US20080293784A1 US12/110,781 US11078108A US2008293784A1 US 20080293784 A1 US20080293784 A1 US 20080293784A1 US 11078108 A US11078108 A US 11078108A US 2008293784 A1 US2008293784 A1 US 2008293784A1
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epothilone
methanol
epothilones
culture
compound
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Gerhard Hoefle
Heinrich Steinmetz
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Helmholtz Zentrum fuer Infektionsforschung HZI GmbH
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Helmholtz Zentrum fuer Infektionsforschung HZI GmbH
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
    • C07D417/06—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings linked by a carbon chain containing only aliphatic carbon atoms
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N43/00—Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds
    • A01N43/72—Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds having rings with nitrogen atoms and oxygen or sulfur atoms as ring hetero atoms
    • A01N43/74—Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds having rings with nitrogen atoms and oxygen or sulfur atoms as ring hetero atoms five-membered rings with one nitrogen atom and either one oxygen atom or one sulfur atom in positions 1,3
    • A01N43/78—1,3-Thiazoles; Hydrogenated 1,3-thiazoles
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N43/00—Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds
    • A01N43/90—Biocides, pest repellants or attractants, or plant growth regulators containing heterocyclic compounds having two or more relevant hetero rings, condensed among themselves or with a common carbocyclic ring system
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N63/00—Biocides, pest repellants or attractants, or plant growth regulators containing microorganisms, viruses, microbial fungi, animals or substances produced by, or obtained from, microorganisms, viruses, microbial fungi or animals, e.g. enzymes or fermentates
    • A01N63/20—Bacteria; Substances produced thereby or obtained therefrom
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/04—Antineoplastic agents specific for metastasis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D493/00—Heterocyclic compounds containing oxygen atoms as the only ring hetero atoms in the condensed system
    • C07D493/02—Heterocyclic compounds containing oxygen atoms as the only ring hetero atoms in the condensed system in which the condensed system contains two hetero rings
    • C07D493/04—Ortho-condensed systems
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P17/00—Preparation of heterocyclic carbon compounds with only O, N, S, Se or Te as ring hetero atoms
    • C12P17/16—Preparation of heterocyclic carbon compounds with only O, N, S, Se or Te as ring hetero atoms containing two or more hetero rings
    • C12P17/167—Heterorings having sulfur atoms as ring heteroatoms, e.g. vitamin B1, thiamine nucleus and open chain analogs
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P17/00—Preparation of heterocyclic carbon compounds with only O, N, S, Se or Te as ring hetero atoms
    • C12P17/18—Preparation of heterocyclic carbon compounds with only O, N, S, Se or Te as ring hetero atoms containing at least two hetero rings condensed among themselves or condensed with a common carbocyclic ring system, e.g. rifamycin
    • C12P17/181—Heterocyclic compounds containing oxygen atoms as the only ring heteroatoms in the condensed system, e.g. Salinomycin, Septamycin

Definitions

  • the present invention relates to epothilones C, D, E and F, their preparation and their use for the production of therapeutic compositions and compositions for plant protection.
  • the invention relates to epothilones [C and D] which are obtainable in that
  • the invention further relates to an epothilone [C] of the empirical formula C 26 H 39 NO 5 S, characterized by the 1 H- and 13 C-NMR spectrum as in Table 1.
  • the invention furthermore relates to epothilone C of the formula:
  • the invention furthermore relates to epothilone [D] of the empirical formula C 27 H 41 NO 5 S, characterized by the 1 H- and 13 C-NMR spectrum as in Table 1.
  • the invention furthermore relates to epothilone D of the formula:
  • Epothilones C and D can be used for the preparation of the compounds of the following formula 1, where for their derivatization reference can be made to the derivatization methods described in WO-A-97/19 086.
  • the invention relates to a biotransformant of epothilone A, which is obtainable in that
  • Sorangium cellulosum DSM 6773 is cultured in a manner known per se in the presence of an adsorber resin, removed from the adsorber resin and, if appropriate, the total amount or a part of the separated culture is treated with a methanolic solution of epothilone A,
  • the invention furthermore relates to a biotransformant of epothilone A of this type, which is obtainable in that in stage (a) a culture is separated off which is three or four or more days old.
  • the invention furthermore relates to a biotransformant of epothilone A of this type, which is obtainable in that in stage (b) incubation is carried out for one or two or more days.
  • the invention furthermore relates to a compound (epothilone E) of the formula:
  • the invention relates to a biotransformant of epothilone B, which is obtainable in that
  • Sorangium cellulosum DSM 6773 is cultured in a manner known per se in the presence of an adsorber resin, separated from the adsorber resin and, if appropriate, the total amount or a part of the separated culture is treated with a methanolic solution of epothilone B,
  • the invention furthermore relates to a biotransformant of epothilone B of this type, which is obtainable in that in stage (a) a culture is separated off which is three or four or more days old.
  • the invention furthermore relates to a biotransformant of epothilone B of this type, which is obtainable in that in stage (b) incubation is carried out for one or two or more days.
  • the invention furthermore relates to a compound (epothilone F) of the formula:
  • FIG. 1 shows a HPLC analysis of an XAD eluate at the end of a fermentation.
  • FIG. 2 shows an enrichment of epothilone E and F in a fermentation broth after feeding of a mixture of epothilone A and B, analysed after incubation for 48 hours.
  • FIG. 3 shows kinetics of the biotransformation of epothilone A to epothilone E by Sorangium cellulosum So ce90.
  • FIG. 4 shows biotransformation of epothilone A to epothilone E.
  • FIG. 5 shows biotransformation of epothilone B to epothilone F.
  • the compounds or epothilones according to the invention are obtainable by the abovementioned measures.
  • the invention furthermore relates to compositions for plant protection in agriculture, forestry and/or horticulture, consisting of one or more of the abovementioned epothilones C, D, E and F or consisting of one or more of the abovementioned epothilones in addition to one or more customary carrier(s) and/or diluent(s).
  • the invention finally relates to therapeutic compositions, consisting of one or more of the abovementioned compounds or one or more of the above-mentioned compounds in addition to one or more customary carrier(s) and/or diluent(s).
  • these compositions can show cytotoxic activities and/or bring about immunosuppression and/or be employed for the control of malignant tumours, it being particularly preferably possible for them to be used as cytostatics.
  • the fermentation lasts 7-10 days at 30 C, aeration with 2 m 3 /hr. By controlling the speed of rotation, the PO 2 is kept at 30%.
  • the adsorber resin is separated from the culture using a 0.7 m 2 , 100 mesh process filter and freed from polar concomitants by washing with 3 bed volumes of water/methanol 2:1. By elution with 4 bed volumes of methanol, a crude extract is obtained which is evaporated in vacuo until the water phase appears. This is extracted three times with the same volume of ethyl acetate. Evaporation of the organic phase affords 240 g of crude extract, which is partitioned between methanol and heptane in order to separate off lipophilic concomitants.
  • epothilone A 50 mg are dissolved in 1.5 ml of acetone and treated with 1.5 ml of a 0.07 molar solution of dimethyldioxirane in acetone. After standing at room temperature for 6 hours, the mixture is evaporated in vacuo and the residue is separated by preparative HPLC on silica gel (eluent: methyl tert-butyl ether/petroleum ether/methanol 33:66:1).
  • Epothilone E and F Novel Biotransformation Products of Epothilones A and B Production Strain:
  • a typical fermentation proceeds in the following manner: A 100 l bioreactor is filled with 60 l of medium (0.8% starch; 0.2% glucose; 0.2% soya flour; 0.2% yeast extract; 0.1% CaCl 2 ⁇ 2H 2 O; 0.1% MgSO 4 ⁇ 7H 2 O; 8 mg/l of Fe-EDTA; pH 7.4). 2% of adsorber resin (XAD-16, Rohm & Haas) are additionally added. The medium is sterilized by autoclaving (2 hours, 120° C.). Inoculation is carried out with 10 l of a preculture grown in the same medium (additionally 50 mM HEPES buffer pH 7.4) in a shaker flask (160 rpm, 30° C.).
  • Fermentation is carried out at 32° C. with a stirrer speed of 500 rpm and an introduction of 0.2 Ni per m 3 per hour of air, the pH is kept at 7.4 by addition of KOH.
  • the fermentation lasts 7 to 10 days.
  • the epothilones formed are continuously bound to the adsorber resin during the fermentation.
  • the resin is washed with 3 bed volumes of water and eluted with 4 bed volumes of methanol.
  • the eluate is concentrated to dryness and taken up in 700 ml of methanol.
  • the eluate is concentrated 100:1.
  • the analysis is carried out using a 1090 HPLC unit from Hewlett Packard.
  • a microbore column 125/2 Nucleosil 120-5 C 18 ) from Machery-Nagel (Düren) is used.
  • Elution is carried out using a gradient of water/acetonitrile from initially 75:25 up to 50:50 after 5.5 minutes. This ratio is maintained up to the 7th minute, in order to then increase it up to the 10th minute to 100% acetonitrile.
  • Measurement is carried out at a wavelength of 250 nm and a bandwidth of 4 nm.
  • the diode array spectra are measured in the wavelength range from 200 to 400 nm.
  • two novel substances with R t 5.29 and R t 5.91 stand out, whose adsorption spectra are identical with those of epothilones A and B (FIG. 1 ; E corresponds to A, F corresponds to B). These substances are only formed in traces under the given fermentation conditions.
  • the concentration was determined which reduces the growth by 50% (IC 50 ) and compared with the values for epothilone A.
  • a culture of Sorangium cellulosum So ce90 is used which has been shaken for four days in the presence of 2% XAD 16 adsorber resin (Rohm and Haas, Frankfurt/M.) at 30° C. and 160 rpm.
  • the culture medium has the following composition in g/litre of distilled water: potato starch (Maizena), 8; glucose (Maizena), 8; defatted soya flour, 2; yeast extract (Marcor), 2; ethylenediaminetetraacetic acid, iron(III) sodium salt, 0.008; MgSO 4 ⁇ 7H 2 O, 1; CaCl 2 ⁇ 2H 2 O, 1; HEPES 11.5.
  • the pH is adjusted to 7.4 before autoclaving with KOH.
  • the XAD is separated from the culture by sieving through a stainless steel sieve (200 ⁇ m mesh width).
  • the bacteria are sedimented by centrifugation for 10 min at 10,000 rpm and the pellet is resuspended in 1 ⁇ 5 of the culture supernatant.
  • Epothilone A or epothilone B in methanolic solution is then added to the concentrated bacterial suspension in a concentration of 0.5 ⁇ l litre.
  • the culture is cultured further as described above.
  • To analyse the biotransformation a 1 ml sample is taken at the desired times, 0.1 ml of XAD is added and the sample is shaken at 30° C. for 30 min.
  • the XAD is eluted with methanol.
  • the eluate is concentrated to dryness and taken up again in 0.2 ml of methanol. This sample is analysed by means of HPLC.
  • FIG. 4 Kinetics of the biotransformation of epothilone A to epothilone E
  • FIG. 5 Kinetics of the biotransformation of epothilone B to epothilone F.
  • strain Sorangium cellulosum So ce90 is grown for four days in 8.5 l of the above medium (but without XAD addition) in a 10 litre bioreactor at 30° C., a speed of rotation of 150 rpm and an introduction of 1 l/min of air.
  • the culture is then concentrated to 3 l by crossflow filtration.
  • 0.6 m 2 of a membrane having a pore size of 0.3 ⁇ m are used.
  • the concentrated culture is transferred to a 4 litre bioreactor and a methanolic solution of 1 g of epothilone A in 10 ml of methanol is added.
  • the culture is then cultured further for a period of time of 21.5 h.
  • the temperature is 32° C.
  • the stirrer speed is 455 rpm and the introduction of air takes place at 6 l/min.
  • 100 ml of XAD is added and the mixture is incubated further for 1 h.
  • the XAD is separated from the cells by screening and exhaustively eluted with methanol.
  • the concentrated eluate is analysed by means of HPLC.
  • Epothilone E formed after 21.5 h: 661.4 mg 66.1%
  • Epothilone A completely decomposed: 28.5%
  • Epothilone tests with cell cultures Epothilone B C A 507 477 D E F 493 IC-50 [ng/ml] 491 509 523 Mouse fibroblasts L 929 4 1 100 20 20 1.5 human tumor cell lines: HL-60 (leukaemia) 0.2 0.2 10 3 1 0.3 K-562 (leukaemia) 0.3 0.3 20 10 2 0.5 U-937 (lymphoma) 0.2 0.2 10 3 1 0.2 KB-3.1 (carcinoma of the 1 0.6 20 12 5 0.5 cervix) KB-V1 (carcinoma of the 0.3 0.3 15 3 5 0.6 cervix multires A-498 (carcinoma of the — 1.5 150 20 20 3 kidney) A-549 (carcinoma of the 0.7 0.1 30 10 3 0.1 lung)
  • the polymerization test is an in vitro test using purified tubulin from pigs' brain. Evaluation is carried out photometrically. Polymerization-promoting substances such as the epothilones reduce the time up to which half-maximal polymerization has taken place, i.e. the shorter the time, the more active the compound. w, x, y and z are four independent experiments, the relative activity is expressed in the last column in % of the control; again the lowest values indicate the best activity. The ranking list corresponds reasonably accurately to that found in cell cultures.

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Abstract

The present invention relates to epothilones C, D, E and F, their preparation and their use for the production of therapeutic compositions and compositions for plant protection.

Description

  • This application is a continuation of application Ser. No. 11/412,536 filed Apr. 27, 2006, which is a division of application Ser. No. 10/988,328 filed on Nov. 12, 2004 (now U.S. Pat. No. 7,067,544), which is a division of application Ser. No. 09/313,524, filed on May 17, 1999, which is a continuation of Application No. PCT/EP97/06442 filed on Nov. 18, 1997, which claims priority to DE 197 07 506.1 filed Feb. 25, 1997 and DE 196 47 580.5 filed Nov. 18, 1996.
    • BACKGROUND OF THE INVENTION
  • The present invention relates to epothilones C, D, E and F, their preparation and their use for the production of therapeutic compositions and compositions for plant protection.
    • Epothilones C and D
  • According to one embodiment, the invention relates to epothilones [C and D] which are obtainable in that
  • (a) Sorangium cellulosum DSM 6773 is cultured in a manner known per se in the presence of an adsorber resin,
  • (b) the adsorber resin is removed from the culture and washed with a water/methanol mixture,
  • (c) the washed adsorber resin is eluted with methanol and the eluate is concentrated to give a crude extract,
  • (d) the concentrate obtained is extracted with ethyl acetate, the extract is concentrated and partitioned between methanol and hexane,
  • (e) the methanolic phase is concentrated to give a raffinate and the concentrate is fractionated on a Sephadex column,
  • (f) a fraction containing metabolic products of the microorganism employed is obtained,
  • (g) the fraction obtained is chromatographed on a C18 reverse phase to a methanol/water mixture and, sequentially
      • after a first fraction containing epothilone A and
      • a second fraction containing epothilone B
      • a third fraction containing a first further epothilone and
      • a fourth fraction containing a second further epothilone are obtained and
  • (h1) and the epothilone of the first further fraction and/or
  • (h2) the epothilone of the second further fraction are isolated.
  • The invention further relates to an epothilone [C] of the empirical formula C26H39NO5S, characterized by the 1H- and 13C-NMR spectrum as in Table 1.
  • The invention furthermore relates to epothilone C of the formula:
  • Figure US20080293784A1-20081127-C00001
  • The invention furthermore relates to epothilone [D] of the empirical formula C27H41NO5S, characterized by the 1H- and 13C-NMR spectrum as in Table 1.
  • The invention furthermore relates to epothilone D of the formula:
  • Figure US20080293784A1-20081127-C00002
  • Epothilones C and D can be used for the preparation of the compounds of the following formula 1, where for their derivatization reference can be made to the derivatization methods described in WO-A-97/19 086.
  • Figure US20080293784A1-20081127-C00003
  • In the above formula 1:
    R═H, C1-4-alkyl;
    R1, R2, R3, R4, R═H, C1-6-alkyl,
      • C1-6-acylbenzoyl,
      • C1-4-trialkylsilyl,
      • benzyl,
      • phenyl,
      • C1-6-alkoxy-,
      • C6-alkyl-, hydroxy- and halogen-substituted benzyl or phenyl;
        where two of the radicals R1 to R5 can also combine to form the group —(CH2)n— with n=1 to 6 and the alkyl or acyl groups contained in the radicals are straight-chain or branched radicals;
        Y and Z are either identical or different and are each hydrogen, halogen, such as F, Cl, Br or I, pseudohalogen, such as —NCO, —NCS or —N3, OH, O—(C1-6)-acyl, O—(C1-6)-alkyl, O-benzoyl. Y and Z can also be the O atom of an epoxide, epothilone A and B not being claimed, or form one of the C—C bonds of a C═C double bond.
  • Thus the 12,13-double bond can be selectively
      • hydrogenated, for example catalytically or with diimine, a compound of the formula I being obtained with Y=Z=H; or
      • epoxidized, for example with dimethyldioxirane or a peracid, a compound of the formula I being obtained with Y and Z=-O—; or
      • converted into the dihalides, dipseudohalides or diazides, a compound of the formula I being obtained with Y and Z=Hal, pseudo-hal or N3.
    Epothilones E and F
  • According to a further embodiment the invention relates to a biotransformant of epothilone A, which is obtainable in that
  • (a) Sorangium cellulosum DSM 6773 is cultured in a manner known per se in the presence of an adsorber resin, removed from the adsorber resin and, if appropriate, the total amount or a part of the separated culture is treated with a methanolic solution of epothilone A,
  • (b) the culture treated with epothilone A is incubated and then treated with adsorber resin,
  • (c) the adsorber resin is separated from the culture, eluted with methanol and the eluate is concentrated to give a crude extract,
  • (d) the crude extract is partitioned between ethyl acetate and water, the ethyl acetate phase is separated off and concentrated to give an oil,
  • (e) the oil is chromatographed on a reverse phase under the following conditions:
  •
    column material: Nucleosil 100 C-18 7 μm
    column dimensions: 250 × 16 mm
    eluent: methanol/water = 60:40
    flow rate: 10 ml/min

    and fractions having a content of biotransformant and which can be detected by UV extinction at 254 nm and have an Rt value of 20 min are separated off and the biotransformants are isolated.
  • The invention furthermore relates to a biotransformant of epothilone A of this type, which is obtainable in that in stage (a) a culture is separated off which is three or four or more days old.
  • The invention furthermore relates to a biotransformant of epothilone A of this type, which is obtainable in that in stage (b) incubation is carried out for one or two or more days.
  • The invention furthermore relates to a compound of the empirical formula C26H39NO7S, characterized by the following 1H-NMR spectrum (300 MHz, CDCl3): delta=2.38 (2-Ha), 2.51 (2-Hb), 4.17 (3-H), 3.19 (6-H), 3.74 (7-H), 1.30-1.70 (8-H, 9-H2, 10-H2, 11-H2), 2.89 (12-H), 3.00 (13-H), 1.88 (14-Ha), 2.07 (14-Hb), 5.40 (15-H), 6.57 (17-H), 7.08 (19-H), 4.85 (21-H2), 1.05 (22-H3), 1.32 (23-H3), 1.17 (24-H3), 0.97 (25-H3), 2.04 (27-H3)
  • The invention furthermore relates to a compound (epothilone E) of the formula:
  • Figure US20080293784A1-20081127-C00004
  • According to a further embodiment, the invention relates to a biotransformant of epothilone B, which is obtainable in that
  • (a) Sorangium cellulosum DSM 6773 is cultured in a manner known per se in the presence of an adsorber resin, separated from the adsorber resin and, if appropriate, the total amount or a part of the separated culture is treated with a methanolic solution of epothilone B,
  • (b) the culture treated with epothilone B is incubated and then treated with adsorber resin,
  • (c) the adsorber resin is separated from the culture, eluted with methanol and the eluate is concentrated to give a crude extract,
  • (d) the crude extract is partitioned between ethyl acetate and water, the ethyl acetate phase is separated off and concentrated to give an oil,
  • (e) the oil is chromatographed on a reverse phase under the following conditions:
  •
    column material: Nucleosil 100 C-18 7 μm
    column dimensions: 250 × 16 mm
    eluent: methanol/water = 60:40
    flow rate: 10 ml/min

    and fractions having a content of biotransformant and which can be detected by UV extinction at 254 nm and have an Rt value of 24.5 min are separated off and the biotransformants are isolated.
  • The invention furthermore relates to a biotransformant of epothilone B of this type, which is obtainable in that in stage (a) a culture is separated off which is three or four or more days old.
  • The invention furthermore relates to a biotransformant of epothilone B of this type, which is obtainable in that in stage (b) incubation is carried out for one or two or more days.
  • The invention furthermore relates to a compound of the empirical formula C27H41NO7S, characterized by the following 1H-NMR spectrum (300 MHz, CDCl3): delta=2.37 (2-Ha), 2.52 (2-Hb), 4.20 (3-H), 3.27 (6-H), 3.74 (7-H), 1.30-1.70 (8-H, 9-H2, 10-H2, 11-H2), 2.78 (13-H), 1.91 (14-H), 2.06 (14-Hb), 5.42 (15-H), 6.58 (17-H), 7.10 (19-H), 4.89 (21-H2), 1.05 (22-H3), 1.26 (23-H3), 1.14 (24-H3), 0.98 (25-H3), 1.35 (26-H3), 2.06 (27-H3).
  • The invention furthermore relates to a compound (epothilone F) of the formula:
  • Figure US20080293784A1-20081127-C00005
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIG. 1 shows a HPLC analysis of an XAD eluate at the end of a fermentation.
  • FIG. 2 shows an enrichment of epothilone E and F in a fermentation broth after feeding of a mixture of epothilone A and B, analysed after incubation for 48 hours.
  • FIG. 3 shows kinetics of the biotransformation of epothilone A to epothilone E by Sorangium cellulosum So ce90.
  • FIG. 4 shows biotransformation of epothilone A to epothilone E.
  • FIG. 5 shows biotransformation of epothilone B to epothilone F.
    •  PREPARATION AND COMPOSITIONS
  • The compounds or epothilones according to the invention are obtainable by the abovementioned measures.
  • The invention furthermore relates to compositions for plant protection in agriculture, forestry and/or horticulture, consisting of one or more of the abovementioned epothilones C, D, E and F or consisting of one or more of the abovementioned epothilones in addition to one or more customary carrier(s) and/or diluent(s).
  • The invention finally relates to therapeutic compositions, consisting of one or more of the abovementioned compounds or one or more of the above-mentioned compounds in addition to one or more customary carrier(s) and/or diluent(s). In particular, these compositions can show cytotoxic activities and/or bring about immunosuppression and/or be employed for the control of malignant tumours, it being particularly preferably possible for them to be used as cytostatics.
  • In the following, the invention is illustrated and described in greater detail by the description of some selected working examples.
    • EXAMPLES Example 1 Epothilones C and D A. Production Strain and Culture Conditions According to the Epothilone Basic Patent DE-B-41 38 042.
  • B. Production with DSM 6773
  • 75 l of culture are grown as described in the basic patent and used for the inoculation of a production fermenter with 700 l of production medium consisting of 0.8% starch, 0.2% glucose, 0.2% soya flour, 0.2% yeast extract, 0.1% CaCl2×2H2O, 0.1% MgSO4×7H2O, 8 mg/l of Fe-EDTA, pH=7.4 and optionally 15 l of Amberlite XAD-16 adsorber resin. The fermentation lasts 7-10 days at 30 C, aeration with 2 m3/hr. By controlling the speed of rotation, the PO2 is kept at 30%.
    • C. Isolation
  • The adsorber resin is separated from the culture using a 0.7 m2, 100 mesh process filter and freed from polar concomitants by washing with 3 bed volumes of water/methanol 2:1. By elution with 4 bed volumes of methanol, a crude extract is obtained which is evaporated in vacuo until the water phase appears. This is extracted three times with the same volume of ethyl acetate. Evaporation of the organic phase affords 240 g of crude extract, which is partitioned between methanol and heptane in order to separate off lipophilic concomitants. By evaporation in vacuo, 180 g of raffinate are obtained from the methanol phase and are fractionated into three portions on Sephadex LH-20 (column 20×100 cm, 20 ml/min of methanol). The epothilones are contained in the fraction of a total of 72 g eluted with a 240-300 min retention time. To separate the epothilones, the fraction is chromatographed in three portions on Lichrosorb RP-18 (15 μm, column 10×40 cm, eluent 180 ml/min methanol/water 65:35). After epothilone A and B, epothilone C, with Rt=90-95 min, and epothilone D, 100-110 min, are eluted and after evaporation in vacuo obtained in a yield of 0.3 g each as colourless oils.
    • D. Physical Properties
  • Figure US20080293784A1-20081127-C00006
  • Epothilone C R═H
  • Epothilone D R═CH3
  • Epothilone C
  • C26H39NO5S [477]
  • ESI-MS: (positive ions): 478.5 for [M+H]+
  • 1H and 13C see NMR table
  • TLC: Rf=0.82
  • TLC aluminum foil 60 F 254 Merck, eluent: dichloromethane/methanol=9:1
  • Detection: UV extinction at 254 nm. Spraying with vanillin-sulphuric acid reagent, blue-grey coloration on heating to 120° C.
  • HPLC: Rt=11.5 min
  • Column: Nucleosil 100 C-18 7 μm, 125×4 mm
  • Eluent: methanol/water=65:35
  • Flow rate: 1 ml/min
  • Detection: diode array
  • Epothilone D
  • C27H41NO5S [491]
  • ESI-MS: (positive ions): 492.5 for [M+H]+
  • 1H and 13C see NMR table
  • TLC: Rt=0.82
  • TLC aluminum foil 60 F 254 Merck, eluent: dichloromethane/methanol=9:1
  • Detection: UV extinction at 254 nm. Spraying with vanillin-sulphuric acid reagent, blue-grey coloration on heating to 120° C.
  • HPLC: Rt=15.3 min
  • Column: Nucleosil 100 C-18 7 μm, 125×4 mm
  • Eluent: methanol/water=65:35
  • Flow rate: 1 ml/min
  • Detection: diode array
  • TABLE 1
    1H- and 13C-NMR data of epothilone C and epothilone
    D in [D6] DMSO at 300 MHz
    Epothilone C Epothilone D
    δ δ δ δ
    H atom (ppm) C atom (ppm) (ppm) C atom (ppm)
    1 170.3 1 170.1
     2-Ha 2.38 2 38.4 2.35 2 39.0
     2-Hb 2.50 3 71.2 2.38 3 70.8
     3-H 3.97 4 53.1 4.10 4 53.2
     3-OH 5.12 5 217.1 5.08 5 217.4
     6-H 3.07 6 45.4 3.11 6 44.4
     7-H 3.49 7 75.9 3.48 7 75.5
     7-OH 4.46 8 35.4 4.46 8 36.3
     8-H 1.34 9 27.6 1.29 9 29.9
     9-Ha 1.15 10 30.0 1.14 10 25.9
     9-Hb 1.40 11 27.6 1.38 11 31.8*
    10-Ha 1.15* 12 124.6 1.14* 12 138.3
    10-Hb 1.35* 13 133.1 1.35* 13 120.3
    11-Ha 1.90 14 31.1 1.75 14 31.6*
    11-Hb 2.18 15 76.3 2.10 15 76.6
    12-H 5.38** 16 137.3 16 137.2
    13-H 5.44** 17 119.1 5.08 17 119.2
    14-Ha 2.35 18 152.1 2.30 18 152.1
    14-Hb 2.70 19 117.7 2.65 19 117.7
    15-H 5.27 20 164.2 5.29 20 164.3
    17-H 6.50 21 18.8 6.51 21 18.9
    19-H 7.35 22 20.8 7.35 22 19.7
    21-H3 2.65 23 22.6 2.65 23 22.5
    22-H3 0.94 24 16.7 0.90 24 16.4
    23-H3 1.21 25 18.4 1.19 25 18.4
    24-H3 1.06 27 14.2 1.07 26 22.9
    25-H3 0.90 0.91 27 14.1
    26-H3 1.63
    27-H3 2.10 2.11
    *, **assignment interchangeable
    • Example 2
  • Epothilone A and 12,13-bisepi-epothilone A from Epothilone C
  • 50 mg of epothilone A are dissolved in 1.5 ml of acetone and treated with 1.5 ml of a 0.07 molar solution of dimethyldioxirane in acetone. After standing at room temperature for 6 hours, the mixture is evaporated in vacuo and the residue is separated by preparative HPLC on silica gel (eluent: methyl tert-butyl ether/petroleum ether/methanol 33:66:1).
    • Yield:
    • 25 mg of epothilone A, Rt=3.5 min (analyt. HPLC, 7 μm, column 4×250 mm, eluent see above, flow rate 1.5 ml/min)
      and
    • 20 mg of 12,13-bisepi-epothilone A, Rt=3.7 min, ESI-MS (pos. ions) m/e=494 [M+H]+
  • 1H-NMR in [D4] methanol, selected signals:
  • delta=4.32 (3-H), 3.79 (7-H), 3.06 (12-H), 3.16 (13-H), 5.54 (15-H), 6.69 (17-H), 1.20 (22-H), 1.45 (23-H)
  • Figure US20080293784A1-20081127-C00007
  • 12,13-bisepi-epothilone A R═H
    • Example 3 Epothilone E and F, Novel Biotransformation Products of Epothilones A and B Production Strain:
  • The production strain Sorangium cellulosum So ce90 was isolated in July 1985 in GBF from a soil sample from the banks of the Zambesi and deposited on 28.10.91 in the German Collection for Microorganisms under No. DSM 6773.
  • The characterization of the producer and the culture conditions are described in: Höfle, G.; N. Bedorf, K. Gerth & H. Reichenbach: Epothilones, processes for their preparation and compositions containing them. DE 41 38 042 A1, laid open on 27 May 1993.
    • Formation of Epothilones E and F During Fermentation:
  • A typical fermentation proceeds in the following manner: A 100 l bioreactor is filled with 60 l of medium (0.8% starch; 0.2% glucose; 0.2% soya flour; 0.2% yeast extract; 0.1% CaCl2×2H2O; 0.1% MgSO4×7H2O; 8 mg/l of Fe-EDTA; pH 7.4). 2% of adsorber resin (XAD-16, Rohm & Haas) are additionally added. The medium is sterilized by autoclaving (2 hours, 120° C.). Inoculation is carried out with 10 l of a preculture grown in the same medium (additionally 50 mM HEPES buffer pH 7.4) in a shaker flask (160 rpm, 30° C.). Fermentation is carried out at 32° C. with a stirrer speed of 500 rpm and an introduction of 0.2 Ni per m3 per hour of air, the pH is kept at 7.4 by addition of KOH. The fermentation lasts 7 to 10 days. The epothilones formed are continuously bound to the adsorber resin during the fermentation. After separating off the culture broth (e.g. by screening in a process filter), the resin is washed with 3 bed volumes of water and eluted with 4 bed volumes of methanol. The eluate is concentrated to dryness and taken up in 700 ml of methanol.
    • HPLC Analysis of the XAD Eluate:
  • In relation to the starting volume of the reactor (70 l), the eluate is concentrated 100:1. The analysis is carried out using a 1090 HPLC unit from Hewlett Packard. To separate the constituents, a microbore column (125/2 Nucleosil 120-5 C18) from Machery-Nagel (Düren) is used. Elution is carried out using a gradient of water/acetonitrile from initially 75:25 up to 50:50 after 5.5 minutes. This ratio is maintained up to the 7th minute, in order to then increase it up to the 10th minute to 100% acetonitrile.
  • Measurement is carried out at a wavelength of 250 nm and a bandwidth of 4 nm. The diode array spectra are measured in the wavelength range from 200 to 400 nm. In the XAD eluate, two novel substances with Rt 5.29 and Rt 5.91 stand out, whose adsorption spectra are identical with those of epothilones A and B (FIG. 1; E corresponds to A, F corresponds to B). These substances are only formed in traces under the given fermentation conditions.
    • Biotransformation of Epothilone A and B to Epothilone E and F:
  • A 500 ml culture of So ce90, 4 days old and maintained with adsorber resin, is used for the specific biotransformation. 250 ml of this are transferred to a sterile 111 Erlenmeyer flask leaving behind the XAD. A methanolic solution of a mixture of a total of 36 mg of epothilone A+14 mg of B is then added and the flask is incubated on a shaking rack for two days at 30° C. and 200 rpm. The formation of the epothilones E and F is analysed directly from 10 μl of the centrifuged culture supernatant (FIG. 2). The conversion takes place only in the presence of the cells and is dependent on the cell densities employed and the time. Kinetics of the conversion are shown for epothilone A in FIG. 3.
  • Isolation of Epothilone E and F
  • To isolate epothilone E and F, three shaker flask batches from the biotransformation (see above) are combined and shaken with 20 ml of XAD-16 for 1 h. The XAD is obtained by screening and eluted with 200 ml of methanol. The eluate is evaporated in vacuo to give 1.7 g of crude extract. This is partitioned between 30 ml of ethyl acetate and 100 ml of water. On evaporation in vacuo, 330 mg of an oily residue are obtained from the ethyl acetate phase, which are chromatographed in five runs on a 250×20 mm RP=18 column (eluent: methanol/water 58:42, detection 254 nm).
  •
    Yield: epothilone E 50 mg
    F 10 mg
    • Biological Action of Epothilone E:
  • In cell cultures, the concentration was determined which reduces the growth by 50% (IC50) and compared with the values for epothilone A.
  • IC50 (ng/ml)
    Cell line Epothilone E Epothilone A
    HeLa.KB-3.1 (human) 5 1
    Mouse fibroblasts, L929 20 4
  • Epothilone E
  • C26H39HO7S [509]
  • ESI-MS: (positive ions): 510.3 for [M+H]+
  • TLC: Rf=0.58
  • TLC aluminum foil 60 F 254 Merck, eluent: dichloromethane/methanol=9:1
  • Detection: UV extinction at 254 nm. Spraying with vanillin-sulphuric acid reagent, blue-grey colouration on heating to 120° C.
  • HPLC: Rt=5.0 min
  • Column: Nucleosil 100 C-18 7 μm, 250×4 mm
  • Eluent: methanol/water=60:40
  • Flow rate: 1.2 ml/min
  • Detection: diode array
  • 1H-NMR (300 MHz, CDCl3): delta=2.38 (2-Ha), 2.51 (2-Hb), 4.17 (3-H), 3.19 (6-H), 3.74 (7-H), 1.30-1.70 (8-H, 9-H2, 10-H2, 11-H2), 2.89 (12-H), 3.00 (13-H), 1.88 (14-Ha), 2.07 (14-Hb), 5.40 (15-H), 6.57 (17-H), 7.08 (19-H), 4.85 (21-H2), 1.05 (22-H3), 1.32 (23-H3), 1.17 (24-H3), 0.97 (25-H3), 2.04 (27-H3)
  • Epothilone F
  • C27H41NO7S [523]
  • ESI-MS: (positive ions): 524.5 for [M+H]+
  • TLC: Rf=0.58
  • TLC aluminum foil 60 F 254 Merck, eluent: dichloromethane/methanol=9:1
  • Detection: UV extinction at 254 nm. Spraying with vanillin-sulphuric acid reagent, blue-grey colouration on heating to 120° C.
  • HPLC: Rt=5.4 min
  • Column: Nucleosil 100 C-18 7 μm, 250×4 mm
  • Eluent: methanol/water=60:40
  • Flow rate: 1.2 ml/min
  • Detection: diode array
  • 1H-NMR (300 MHz, CDCl3): delta=2.37 (2-Ha), 2.52 (2-Hb), 4.20 (3-H), 3.27 (6-H), 3.74 (7-H), 1.30-1.70 (8-H, 9-H2, 10-H2, 11-H2), 2.78 (13-H), 1.91 (14-H), 2.06 (14-Hb), 5.42 (15-H), 6.58 (17-H), 7.10 (19-H), 4.89 (21-H2), 1.05 (22-H3), 1.26 (23-H3), 1.14 (24-H3), 0.98 (25-H3), 1.35 (26-H3), 2.06 (27-H3).
    • Example 4 Preparation of Epothilone E and F by Biotransformation with Sorangium Cellulosum So ce90 1) Carrying out the Biotransformation:
  • For the biotransformation, a culture of Sorangium cellulosum So ce90 is used which has been shaken for four days in the presence of 2% XAD 16 adsorber resin (Rohm and Haas, Frankfurt/M.) at 30° C. and 160 rpm. The culture medium has the following composition in g/litre of distilled water: potato starch (Maizena), 8; glucose (Maizena), 8; defatted soya flour, 2; yeast extract (Marcor), 2; ethylenediaminetetraacetic acid, iron(III) sodium salt, 0.008; MgSO4×7H2O, 1; CaCl2×2H2O, 1; HEPES 11.5. The pH is adjusted to 7.4 before autoclaving with KOH. The XAD is separated from the culture by sieving through a stainless steel sieve (200 μm mesh width). The bacteria are sedimented by centrifugation for 10 min at 10,000 rpm and the pellet is resuspended in ⅕ of the culture supernatant. Epothilone A or epothilone B in methanolic solution is then added to the concentrated bacterial suspension in a concentration of 0.5 μl litre. The culture is cultured further as described above. To analyse the biotransformation, a 1 ml sample is taken at the desired times, 0.1 ml of XAD is added and the sample is shaken at 30° C. for 30 min. The XAD is eluted with methanol. The eluate is concentrated to dryness and taken up again in 0.2 ml of methanol. This sample is analysed by means of HPLC.
  • FIG. 4) Kinetics of the biotransformation of epothilone A to epothilone E
    FIG. 5) Kinetics of the biotransformation of epothilone B to epothilone F.
    • 2) Preparation of Epothilone E by Biotransformation of 1 g of Epothilone A.
  • The strain Sorangium cellulosum So ce90 is grown for four days in 8.5 l of the above medium (but without XAD addition) in a 10 litre bioreactor at 30° C., a speed of rotation of 150 rpm and an introduction of 1 l/min of air.
  • The culture is then concentrated to 3 l by crossflow filtration. For this purpose, 0.6 m2 of a membrane having a pore size of 0.3 μm are used.
  • The concentrated culture is transferred to a 4 litre bioreactor and a methanolic solution of 1 g of epothilone A in 10 ml of methanol is added. The culture is then cultured further for a period of time of 21.5 h. The temperature is 32° C., the stirrer speed is 455 rpm and the introduction of air takes place at 6 l/min. At the time of harvesting, 100 ml of XAD is added and the mixture is incubated further for 1 h. The XAD is separated from the cells by screening and exhaustively eluted with methanol. The concentrated eluate is analysed by means of HPLC.
  • Balancing of the Biotransformation:
  • Epothilone A employed: 1000 mg=100%
  • Epothilone A recovered after 21.5 h: 53.7 mg=5.4%
  • Epothilone E formed after 21.5 h: 661.4 mg=66.1%
  • Epothilone A completely decomposed:=28.5%
    • Experiment 5
  • The epothilones according to the invention were tested with cell cultures (Table 2) and for promotion of polymerization (Table 3).
  • TABLE 2
    Epothilone tests with cell cultures
    Epothilone
    B C
    A 507 477 D E F
    493 IC-50 [ng/ml] 491 509 523
    Mouse fibroblasts L 929 4 1 100 20 20 1.5
    human tumor cell lines:
    HL-60 (leukaemia) 0.2 0.2 10 3 1 0.3
    K-562 (leukaemia) 0.3 0.3 20 10 2 0.5
    U-937 (lymphoma) 0.2 0.2 10 3 1 0.2
    KB-3.1 (carcinoma of the 1 0.6 20 12 5 0.5
    cervix)
    KB-V1 (carcinoma of the 0.3 0.3 15 3 5 0.6
    cervix multires
    A-498 (carcinoma of the — 1.5 150 20 20 3
    kidney)
    A-549 (carcinoma of the 0.7 0.1 30 10 3 0.1
    lung)
  • TABLE 3
    Polymerization test with epothilones
    Parameter: Time up to the half-maximal polymerization of the control
    Measurement: Agent Agent
    w x y z [s] [%]
    Control 200 170 180 210 190 100
    Epothilone A 95 60 70 70 74 39
    Epothilone B 23 25 30 26 14
    Epothilone C 125 76 95 80 94 49
    Epothilone D 125 73 120 106 56
    Epothilone E 80 60 50 45 59 31
    Epothilone F 80 40 30 50 50 26

    Standard Test with 0.9 mg of Tubulin/ml and 1 μM Sample Concentration
  • The polymerization test is an in vitro test using purified tubulin from pigs' brain. Evaluation is carried out photometrically. Polymerization-promoting substances such as the epothilones reduce the time up to which half-maximal polymerization has taken place, i.e. the shorter the time, the more active the compound. w, x, y and z are four independent experiments, the relative activity is expressed in the last column in % of the control; again the lowest values indicate the best activity. The ranking list corresponds reasonably accurately to that found in cell cultures.

Claims (4)

1-16. (canceled)
17. A compound of the formula:
Figure US20080293784A1-20081127-C00008
said compound having a state of purity such as to be substantially free of other major metabolic products produced by Sorangium cellulosum.
18. A composition comprising at least one compound according to claim 17, and at least one carrier or diluent.
19. A method of treating tumor comprising administering to a recipient in need thereof a therapeutic amount of a compound of the formula:
Figure US20080293784A1-20081127-C00009
wherein said tumor is selected from the group consisting of leukemia, lymphoma, carcinoma of the cervix, carcinoma of the kidney and carcinoma of the lung.
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