WO2003091231A1 - Pna monomer and precursor - Google Patents

Pna monomer and precursor Download PDF

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Publication number
WO2003091231A1
WO2003091231A1 PCT/IB2003/001595 IB0301595W WO03091231A1 WO 2003091231 A1 WO2003091231 A1 WO 2003091231A1 IB 0301595 W IB0301595 W IB 0301595W WO 03091231 A1 WO03091231 A1 WO 03091231A1
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compound
alkyl
phenyl
halogenated
benzothiazole
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PCT/IB2003/001595
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English (en)
French (fr)
Inventor
Sung Kee Kim
Hyunil Lee
Jong Chan Lim
Hoon Choi
Jae Hoon Jeon
Sang Youl Ahn
Sung Hee Lee
Won Jun Yoon
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Panagene, Inc.
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Priority to DK03718981.8T priority Critical patent/DK1501812T3/da
Priority to EP03718981A priority patent/EP1501812B1/en
Priority to JP2003587791A priority patent/JP4417728B2/ja
Priority to AU2003223014A priority patent/AU2003223014A1/en
Priority to DE60330766T priority patent/DE60330766D1/de
Priority to AT03718981T priority patent/ATE453631T1/de
Publication of WO2003091231A1 publication Critical patent/WO2003091231A1/en

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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
    • C07D417/04—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 directly linked by a ring-member-to-ring-member bond
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D277/00—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings
    • C07D277/60—Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings condensed with carbocyclic rings or ring systems
    • C07D277/62—Benzothiazoles
    • C07D277/68—Benzothiazoles with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached in position 2
    • C07D277/70—Sulfur atoms
    • C07D277/76—Sulfur atoms attached to a second hetero atom
    • C07D277/80—Sulfur atoms attached to a second hetero atom to a nitrogen atom
    • 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
    • C07D417/12—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 chain containing hetero atoms as chain links
    • 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
    • C07D417/14—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 three or more hetero rings
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07B—GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR
    • C07B2200/00—Indexing scheme relating to specific properties of organic compounds
    • C07B2200/11—Compounds covalently bound to a solid support
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
    • Y02P20/00—Technologies relating to chemical industry
    • Y02P20/50—Improvements relating to the production of bulk chemicals
    • Y02P20/55—Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Definitions

  • the present invention relates to monomers suitable for the preparation of PNA oligomers.
  • the present invention also relates to precursors to the monomers and methods of making the PNA monomers from the precursors. Further, the invention relates to methods of making PNA oligomers using the PNA monomers. [0003] 2. General Background and State of the Art:
  • PNA DNA analogue in which an N-(2-aminoethyl)glycine polyamide replaces the phosphate-ribose ring backbone, and methylene-carbonyl linker connects natural as well as unnatural nucleo- bases to central amine of N-(2-aminoethyl)glycine.
  • P ⁇ A is capable of sequence specific binding to D ⁇ A as well as R ⁇ A obeying the Watson-Crick base pairing rule.
  • P ⁇ As bind with higher affinity to complementary nucleic acids than their natural counterparts, partly due to the lack of negative charge on backbone, a consequently reduced charge-charge repulsion, and favorable geometrical factors (S. K. Kim et al., J. Am. Chem. Soc, 1993, 115, 6477-6481 ; B. Hyrup et al., J. Am. Chem. Soc, 1994, 116, 7964-7970; M. Egholm et al., Nature, 1993, 365, 566-568; K. L.
  • P ⁇ As can bind in either parallel or antiparallel fashion, with antiparallel mode being preferred (E. Uhlman et al., Angew. Chem. Int. Ed. Engl, 1996, 35, 2632-2635.).
  • a mismatch in a PNA/DNA duplex is much more destabilizing than a mismatch in a DNA/DNA duplex.
  • a single base mismatch results in 15 °C and 1 1 °C lowering of the Tm of PNA/DNA and DNA/DNA, respectively.
  • Homopyrimidine PNA oligomers and PNA oligomers with a high pyrimidine/purine ratio can bind to complementary DNA forming unusually stable PNA2/DNA triple helices (P. E. Nielsen et al., Science, 1991, 254, 1497- 1500; L. Betts et al., Science, 1995, 270, 1838-1841; H.
  • PNAs have amide bonds and nucleobases
  • PNAs show great resistance to both nuclease and protease.
  • DNA which depurinates on treatment with strong acids and hydrolyses in alkali hydroxides, PNAs are completely acid stable and sufficiently stable to weak bases.
  • PNA oligomers are synthesized using the well established solid phase peptide synthesis protocol. New strategies for monomers have been developed independently by several groups to optimize PNA oligomer synthesis.
  • the preparation of PNA monomers can be divided into the synthesis of a suitably protected N- aminoethylglycine and a suitably protected nucleobase acetic acid derivatives, which is followed by coupling both.
  • the first synthetic strategy reported for P ⁇ A oligomer synthesis was Merrifield solid phase synthesis using t-Boc/benzyloxycarbonyl protecting group strategy wherein the backbone amino group protected with the t-Boc and the exocyclic amino groups of the nucleobases are protected with the benzyloxycarbonyl (P. E. Nielsen et al., Science, 1991, 254, 1497-1500; M. Egholm et al., J. Am. Chem. Soc, 1992, 114, 9677-9678; M. Egholm et al., J. Am. Chem. Soc, 1992, 114, 1895-1897; M. Egholm et al., J.
  • t-Boc/benzyloxycarbonyl protection strategy is differential strategy which is defined as a system of protecting groups wherein the protecting groups are removed by the same type of reagent or condition, but rely on the different relative rates of reaction to remove one group over the other.
  • both protecting groups are acid labile, but benzyloxycarbonyl group requires a stronger acid for efficient removal.
  • acid is used to completely remove the more acid labile t-Boc group, there is a potential that a percentage of benzyloxycarbonyl group will also be removed contemporaneously.
  • the t-Boc group must be removed from amino group of backbone during each synthetic cycle for the synthesis of oligomer.
  • TFA is strong enough to prematurely deprotect a percentage of the side chain benzyloxycarbonyl group, thereby introducing the possibility of oligomer branching and reducing the overall yield of desired product.
  • Fmoc/benzhydryloxycarbonyl strategy has several drawbacks such as side reaction during the Fmoc deprotection process and instability of monomer in solution.
  • the most critical side reaction is the migration of the nucleobase acetyl group from the secondary amino function to the free N-terminal amino function of aminoethylglycine backbone under Fmoc deprotection condition (L.Christensen et al., J. Pept. Sci. 1995, 7,175-183 ).
  • the N-acetyl transfer reactions in every cycles during oligomer synthesis result in accumulation of side products which are hard to separate due to similar polarity and same molecular weight.
  • the Fmoc protecting group is very unstable in the presence of trace amine.
  • the present invention provides novel monomers for increased efficiency, high yield, and convenience during synthesis of PNA oligomers. Another object is to provide PNA monomers that can be conveniently applied to instrumentation such as automated synthesizer for synthesis of PNA oligomers.
  • the novel monomers according to the present invention are compounds having general formula I: [0014]
  • E may be nitrogen or C-R',
  • J may be sulfur or oxygen
  • R', Rl, R2, R3, R4 may be independently H, halogen such as F, CI, Br or I, CF 3 , alkyl, preferably C ⁇ -C alkyl, nitro, nitrile, alkoxy, preferably C ⁇ -C alkoxy, halogenated
  • F, CI, Br and I) alkoxy preferably halogenated C ⁇ -C 4 alkoxy, phenyl, or halogenated (such as F, CI, Br and I) phenyl,
  • R5 may be H or protected or unprotected side chain of natural or unnatural ⁇ - amino acid
  • B may be a natural or unnatural nucleobase, wherein when said nucleobase has an exocyclic amino function, said function is protected by protecting group which is labile to acids but stable to weak to medium bases in the presence of thiol.
  • B may be thymine (T), cytosine (C), adenine (A), or guanine (G).
  • the protecting group for the exocyclic amino function of B has a general formula:
  • R7 may have a general formula:
  • the residue represented by Y 1 -Y 10 is independently selected from hydrogen, halogen, such as F, CI, Br, alkyl, preferably methyl, ethyl, t-butyl, and alkoxy, such as methoxy, ethoxy, and t-butyloxy.
  • R7 may have a general formula
  • the residue represented by Z 1 -Z 5 is independently selected from hydrogen, halogen, such as F, CI, Br, alkyl, preferably methyl, ethyl, t-butyl, and alkoxy, such as methoxy, ethoxy, and t-butyloxy, and methylene dioxy of adjacent two residues.
  • R7 may have a general formula;
  • the residue represented by R8 may be alkyl or phenyl.
  • the protecting group of B may be benzyloxycarbonyl, benzhydryloxycarbonyl, 4-methoxybenzyloxycarbonyl, 3,4-dimethoxybenzyloxycarbonyl, piperonyloxycarbonyl, or 2-methylthioethoxycarbonyl.
  • nucleobase B which may be protected by piperonyloxycarbonyl derivatives.
  • the invention is directed to a cytosine moiety that is protected by piperonyloxycarbonyl derivatives having a general formula:
  • the residue represented by Q 1 -Q 5 may be independently selected from hydrogen, halogen, such as F, CI, Br, and I, nitro, alkyl, such as methyl, ethyl, and t-butyl, and alkoxy, such as methoxy, ethoxy, and t-butyloxy.
  • the invention is also directed to an adenine moiety that is protected by piperonyloxycarbonyl derivatives having a general formula:
  • Qi, Q 2 , Q3, Q4 and Q 5 are as defined above.
  • the invention is also directed to a guanine moiety that is protected by piperonyloxycarbonyl derivatives having a general formula:
  • Qi, Q 2j Q , Q and Q 5 are as defined above.
  • the present invention further provides for methods of preparing compounds of general formula I from compounds of general formula V.
  • the protecting group of B when said nucleobase of B has an exocyclic amino function is also as described above, and
  • R6 may be H, alkyl, preferably (C 1 -C 4 ) alkyl (such as methyl, ethyl, and t-butyl), or aryl.
  • the invention provides for compounds of general formula V and their preparation methods from compounds of general formula II.
  • E, J, Rl, R2, R3, R4, R5, and R6 are as defined above 10060] Also, the present invention provides compounds of formula II and their preparation methods.
  • the invention is directed to a method of making the compound of formula V, comprising coupling reaction of a compound of formula II with a nucleobase acetic acid moiety in the presence of non-nucleophilic organic base and a coupling reagent that is customarily used in peptide synthesis.
  • the present invention further provides methods of preparing compounds of formula I from compounds of general formula IV.
  • E, J, Rl , R2, R3, R4, and R5 are as defined above, and
  • HX is organic or inorganic acid.
  • the present invention also provides compounds of general formula IV and their free acid form, and their preparation methods.
  • the present invention further provides methods of preparing compounds of general formula IV from compounds of general formula II.
  • the invention is also directed to a method of making the compound of formula I, comprising coupling reaction of a compound of formula IV with a nucleobase acetic acid moiety in the presence of non-nucleophilic organic base and a coupling reagent that is customarily used in peptide synthesis.
  • the invention is also directed to a method of making the compound of formula I, comprising cyclizing a compound of formula VI in the presence of a coupling reagent that is customarily used in peptide synthesis or mixed anhydride.
  • the protecting group of B when said nucleobase of B has an exocyclic amino function is also as set forth above.
  • the invention is directed to a compound of formula II, for which its residues are defined as above.
  • the R5 residue may be H or protected or unprotected side chain of natural ⁇ -amino acid.
  • the compound of formula II may have the following configuration: Rl, R2, R3, and R4 may be H, E is nitrogen, and J is sulfur.
  • Rl, R3, and R4 may be H, R2 may be CI, E is nitrogen, and J is sulfur.
  • R3 and R4 may be H, Rl may be CI, R2 may be methoxy, E is nitrogen, and J is sulfur.
  • the invention is also directed to a method of making the compound of formula
  • the invention is further directed to a compound having formula IV and its free acid form.
  • R5 residue may be H or protected or unprotected side chain of natural ⁇ -amino acid.
  • the compound of formula IV may have the following configuration: Rl, R2, R3, and R4 may be
  • Rl is nitrogen and J is sulfur.
  • Rl, R3, and R4 may be H, R2 may be CI, E is nitrogen, and J is sulfur.
  • R3 and R4 may be H, Rl may be
  • CI, R2 may be methoxy, E is nitrogen, and J is sulfur.
  • the invention is further directed to a method of making the compound of formula IV, comprising cyclizing a compound of formula III in the presence of a coupling reagent that is customarily used in peptide synthesis or mixed anhydride, followed by deprotection of a protection group such as t-Boc in acid.
  • the entities represented by E, J, Rl, R2, R3, R4, and R5 are as defined above.
  • the invention is also directed to a method of making PNA oligomer, comprising linking together the compound of formula I.
  • FIGURE 1 shows a chart of the chemical structures of naturally and non- naturally occurring nucleobases useful for DNA recognition.
  • FIGURE 2 shows another chart of the chemical structures of naturally and non- naturally occurring nucleobases useful for DNA recognition. '
  • FIGURE 3 shows a schematic representation of the synthesis of protected backbone.
  • FIGURE 4 shows a schematic representation of the synthesis of protected piperazinone as a precursor for monomer.
  • FIGURE 5 shows a schematic representation of the synthesis of PNA monomer.
  • FIGURE 6 shows a schematic representation of the alternative synthesis of PNA monomer.
  • FIGURE 7 shows schemes of preparation of nucleobases protected with piperonyloxycarbonyl.
  • FIGURE 8 shows a schematic representation of the synthesis of PNA thymine monomer.
  • FIGURE 9 shows a schematic representation of the alternative synthesis of PNA thymine monomer.
  • FIGURE 10 shows a schematic representation of the synthesis of PNA cytosine monomer
  • FIGURE 1 1 shows a schematic representation of the alternative synthesis of
  • FIGURE 12 shows a schematic representation of the synthesis of PNA adenine monomer.
  • FIGURE 13 shows a schematic representation of the alternative synthesis of
  • FIGURE 14 shows a schematic representation of the synthesis of PNA guanine monomer.
  • FIGURE 15 shows a schematic representation of the alternative synthesis of
  • FIGURE 16 shows a schematic representation of the PNA oligomer synthesis from PNA monomers.
  • FIGURE 17 shows HPLC and MALDI-TOF results for synthesized oligomer
  • FIGURE 18 shows HPLC and MALDI-TOF results for synthesized oligomer
  • FIGURE 19 shows HPLC and MALDI-TOF results for synthesized oligomer
  • FIGURE 20 shows HPLC and MALDI-TOF results for synthesized oligomer
  • FIGURE 21 shows HPLC and MALDI-TOF results for synthesized oligomer
  • FIGURE 22 shows HPLC and MALDI-TOF results for synthesized oligomer
  • FIGURE 23 shows HPLC and MALDI-TOF results for synthesized oligomer
  • FIGURE 24 shows HPLC and MALDI-TOF results for synthesized oligomer SEQ ID NO: 8
  • FIGURE 25 shows HPLC and MALDI-TOF results for synthesized oligomer SEQ ID NO: 9
  • benzothiazole-2-sulfonyl, benzo[b]thiophene-2- sulfonyl, benzoxazole-2-sulfonyl, or benzofuran-2-sulfonyl group of compounds having general formula I play an important role not only as protecting groups of amine of backbone but also as activating groups for coupling reaction.
  • the monomers having described characteristics are useful for the synthesis of PNA oligomers by manual or automated synthesizer and the preparation of PNA oligomer library by combinatorial chemistry.
  • Nucleobase B in the general formula I is naturally attached at the position found in nature, i.e., position 1 for thymine or cytosine, and position 9 for adenine or guanine, as well as for non-naturally occurring nucleobase (nucleobase analog), or nucleobase binding moiety.
  • nucleobase analog nucleobase analog
  • nucleobase binding moiety Some nucleobases and illustrative synthetic nucleobases are shown in FIG. 1 and FIG. 2.
  • the first step for the preparation of novel monomers having general formula I is synthesis of N-[2-(benzothiazole, benzoxazole, benzo[b]thiophene, or benzofuran-2- sulfonylamino)-ethyl]-glycine derivatives having the formula II: [00111]
  • E is nitrogen and J is sulfur for N-[2-(benzothiazole-2-sulfonylamino)- ethylj-glycine derivatives; E is nitrogen and J is oxygen for N-[2-(benzoxazole-2- sulfonylamino)-ethyl]-glycine derivatives; E is C-R' and J is sulfur for N-[2- (benzo[b]thiophene-2-sulfonylamino)-ethyl]-glycine derivatives; E is C-R' and J is oxygen for N-[2-(benzofuran-2-sulfonylamnio)-ethyl]-glycine derivatives; and R', Rl, R2, R3, R4, R5, and R6 are as defined above.
  • Derivatives having formula II are generally synthesized by selective reaction of primary amine of 2-aminoglycine derivatives with sulfonyl chloride compounds having
  • E is nitrogen and J is sulfur for benzothiazole-2-sulfonyl chloride derivatives; E is nitrogen and J is oxigen for benzoxazole-2-sulfonyl chloride derivatives; E is C-R' and J is sulfur for benzo[b]thiophene-2-sulfonyl chloride derivatives; E is CH and J is oxygen for benzofuran-2-sulfonyl chloride derivatives; and [00117] R', Rl, R2, R3, and R4 are as defined above.
  • N-[2-(Benzothiazole- 2-sulfonylamino)-ethyl]-glycine derivatives are synthesized by selective reaction of primary amine of 2-aminoglycine derivatives prepared by known methods (for instance, where Rl is H, see S. A. Thomson et al., Tetrahedron, 1995, 6179-6194; where R5 is a side chain of a protected or unprotected natural or unnatural amino acid, see A. Puschl et al., Tetrahedron Lett., 1998, 39, 4707-4710).
  • Benzothiazole-2-sulfonyl chloride derivatives are prepared by known methods (E.
  • solvents of above reaction include without limitation water, toluene, benzene, ethylacetate, tetrahydrofuran, diisopropylether, diethylether, dichloromethane, chloroform, carbon tetrachloride, and acetonitrile.
  • Preferred solvent is dichloromethane.
  • non-nucleophilic organic bases include, but are not limited to, triethylamine, tripropylamine N,N-diisopropylethylamine, N-methylmorpholine, and N- ethylmorpholine.
  • Preferred non-nucleophilic organic base is triethylamine.
  • N-[2-(benzothiazole, benzoxazole, benzo[b]thiophene, or benzofuran-2- sulfonylamino)-ethyl]-glycine derivatives having the formula II are converted to corresponding acids by adding excess hydroxide ion source.
  • Preferred R6 in the formula II is methyl or ethyl.
  • hydroxide ion sources include, but are not limited to, lithium hydroxide, sodium hydroxide, and potassium hydroxide.
  • Preferred hydroxide ion source is lithium hydroxide.
  • the reaction mixture without work-up is then treated with a protecting group such as di-t-butyl dicarbonate to protect secondary amine to obtain a compound having the general formula:
  • Preferred hydrolysis reaction is carried out by adding an aqueous solution of lithium hydroxide (2 equivalent) to a solution of N-[2-(benzothiazole, benzoxazole, benzo[b]thiophene, or benzofuran-2-sulfonylamino)-ethyl]-glycine ester derivative at ambient temperature. After completion of the reaction by TLC analysis, an aqueous solution of lithium hydroxide (additional 1 equivalent) is added to the reaction mixture. The reaction mixture is stirred for sufficient time.
  • aqueous tetrahydrofuran aqueous dioxane
  • aqueous 1,2- dimethoxyethane aqueous 1,2- dimethoxyethane.
  • Preferred solvent is aqueous tetrahydrofuran.
  • the cyclization reaction of carboxylic acids having general formula III and followed by deprotection of t-Boc produces piperazinone derivatives having general formula IV .
  • the cyclization reaction occurs simultaneously during activation of carboxylic acid.
  • the activation of carboxylic acid can be conducted by general coupling reagent for peptide synthesis at ambient temperature.
  • Examples of coupling reagents include, but are not limited to, HATU, HOAt, HODhbt (L. A. Carpino et al., J. Am. Chem. Soc, 1993, 115, 4397-4398), HAPyU, TAPipU (A.
  • the solvents may be selected from tetrahydrofuran, dichloromethane, chloroform, DMF, and N-methylpyrrolidone. Preferred solvent is DMF.
  • the activation of carboxylic acid can be conducted by formation of mixed anhydride using alkyl chloroformate or alkanoyl chloride with non-nucleophilic organic base.
  • alkyl haloformates or alkanoyl chlorides include, but are not limited to, methyl chloroformate, ethyl chloroformate, propyl chloroformate, butyl chloroformate, isobutyl chloroformate, pivaloyl chloride, and adamantine carboxyl chloride.
  • the most preferred acid chloride is isobutyl chloroformate.
  • the cyclization reaction using isobutyl chloroformate is carried out by slowly adding isobutyl chlorofonnate to a reaction solution of carboxylic acid having general formula III and non-nucleophilic organic base in an anliydrous appropriate solvent at the temperature between -30 °C and 10 °C.
  • non-nucleophilic organic bases include, but are not limited to, triethylamine, tripropylamine, NN-diisopropylethylamine, N-methylmorpholine, and /V-ethylmorpholine.
  • Preferred non-nucleophilic organic base is N-methylmorpholine.
  • anhydrous appropriate solvents include, but are not limited to, acetonitrile, chloroform, dichloromethane, 1,2-dimethoxy ethane, diethyl ether, diisoproyl ether, and tetrahydrofuran.
  • Preferred solvents are dichloromethane and tetrahydrofuran.
  • the most preferred reaction temperature is in which the reaction mixture is allowed to slowly warm to 0 °C after completing addition of isobutyl chloroformate at -20 °C.
  • the t-Boc group is deprotected in the presence of acid.
  • acids include, but are not limited to, HCI, HBr, HF, HI, nitric acid, sulfuric acid, methanesulfonic acid, TFA, and trifluoromethanesulfonic acid.
  • Preferred acid is TFA.
  • the solvents used in the deprotection reaction may include without limitation dichloromethane, chloroform, carbon tetrachloride, ethyl acetate, toluene, and benzene. Preferred is dichloromethane.
  • P ⁇ A monomers having general formula I may be synthesized by at least two methods.
  • the first approach to P ⁇ A monomer syntheses is a method that introduces protected or unprotected nucleobase acetic acid moieties to protected linear backbone prior to cyclization reaction.
  • P ⁇ A monomers may be synthesized by beginning with cyclization of protected linear backbone, followed by coupling of protected or unprotected nucleobase acetic acid moieties to create desired products.
  • Method 1 [00135] The linear moieties having general formula V are prepared from protected linear backbone having general formula II by acylation of nucleobase acetic acid moieties using coupling reagents as shown in FIG. 5.
  • the coupling reaction was conducted by addition of coupling reagent to the mixture of protected linear backbone having general formula II, nucleobase acetic acid moieties, and non-nucleophilic organic base in anhydrous appropriate solvent.
  • Examples of coupling reagents include, but are not limited to, HATU, HOAt, HODhbt, HAPyU, TAPipU, HBTU, TBTU, TPTU, TSTU, TNTU, TOTU, BOP, PyBOP, BroP, PyBroP, BOI, MSNT, TDO, DCC, EDCI, CDI, HOBt, HOSu, NEPIS, BBC, BDMP, BOMI, AOP, BDP, PyAOP, TDBTU, BOP-C1, CIP, DEPBT, Dpp-Cl, EEDQ, FDPP, HOTT, TOTT, PyCloP.
  • Preferred coupling reagent is PyBOP.
  • non- nucleophilic organic bases include, but are not limited to, triethylamine, tripropylamine, NN-diisopropylethylamine, N-methylmorpholine, and N-ethylmorpholine.
  • Preferred non- nucleophilic organic base is NN-diisopropylethylamine.
  • anhydrous appropriate solvents include, but are not limited to, chloroform, dichloromethane, 1,2- dimethoxyethane, tetrahydrofuran, DMF, and N-methylpyrrolidone. Preferred solvent is DMF.
  • Compounds having the general formula V are converted to corresponding acids such as formula VI by adding an excess of hydroxide ion source.
  • R6 may be a methyl, ethyl or t-butyl.
  • hydroxide ion sources include, but are not limited to, lithium hydroxide, sodium hydroxide, and potassium hydroxide. Preferred hydroxide ion source is lithium hydroxide.
  • Examples of coupling reagents include, but are not limited to, HATU, HOAt, HODhbt, HAPyU, TAPipU, HBTU, TBTU, TPTU, TSTU, TNTU, TOTU, BOP, PyBOP, BroP, PyBroP, BOI, MSNT, TDO, DCC, EDCI, CDI, HOBt, HOSu, NEPIS, BBC, BDMP, BOMI, AOP, BDP, PyAOP, TDBTU, BOP-C1, CIP, DEPBT, Dpp-Cl, EEDQ, FDPP, HOTT, TOTT, PyCloP.
  • Preferred coupling reagent is PyBOP.
  • non-nucleophilic organic bases include, but are not limited to, triethylamine, tripropylamine, NN-diisopropylethylamine, N- methylmorpholine, and N-ethylmorpholine.
  • Preferred non-nucleophilic organic base is NN- diisopropylethylamine.
  • the solvents may be without limitation selected from tetrahydrofuran, dichloromethane, chloroform, DMF, or N-methylpyrrolidone. Preferred solvent is DMF.
  • the activation of carboxylic acid can be conducted by formation of mixed anhydride using alkyl chloroformate or alkanoyl chloride with non-nucleophilic organic base.
  • alkyl haloformates or alkanoyl chlorides include, but are not limited to, methyl chloroformate, ethyl chloroformate, propyl chloroformate, butyl chloroformate, isobutyl chloroformate, pivaloyl chloride, and adamantine carboxyl chloride.
  • the most preferred acid chloride is isobutyl chloroformate.
  • the cyclization reaction using isobutyl chloroformate is carried out by slowly adding isobutyl chloroformate to a reaction solution of carboxylic acid and non-nucleophilic organic base in an anhydrous appropriate solvent at a temperature between -30 °C and 10 °C.
  • non-nucleophilic organic bases include, but are not limited to, triethylamine, tripropylamine, NN- diisopropylethylamine, N-methylmorpholine, and N-ethylmorpholine.
  • Preferred non- nucleophilic organic base is N-methylmorpholine.
  • anhydrous appropriate solvents include, but .
  • Preferred solvents are dichloromethane and tetrahydrofuran.
  • Preferred reaction temperature is in which the reaction mixture is allowed to slowly warm to about 0 °C after completing addition of isobutyl chloroformate at -20 °C.
  • PNA monomers according to this invention may be prepared by coupling of protected or unprotected nucleobase acetic acid moieties to cyclic precursor having the general formula IV:
  • Examples of coupling reagents include, but are not limited to, HATU, HOAt, HODhbt, HAPyU, TAPipU, HBTU, TBTU, TPTU, TSTU, TNTU, TOTU, BOP, PyBOP, BroP, PyBroP, BOI, MSNT, TDO, DCC, EDCI, CDI, HOBt, HOSu, NEPIS, BBC, BDMP, BOMI, AOP, BDP, PyAOP, TDBTU, BOP-C1, CIP, DEPBT, Dpp-Cl, EEDQ, FDPP, HOTT, TOTT, PyCloP.
  • Preferred coupling reagent is PyBOP.
  • non- nucleophilic organic bases include, but are not limited to, triethylamine, tripropylamine, NN-diisopropylethylamine, N-methylmorpholine, and N-ethylmorpholine.
  • Preferred non- nucleophilic organic base is NN-diisopropylethylamine.
  • the solvent may be without limitation tetrahydrofuran, dichloromethane, chloroform, DMF, or N-methylpyrrolidone. Preferred solvent is DMF.
  • nucleobases of this invention include, but are not limited to, adenine, cytosine, guanine, thymine, uridine, 2,6-diaminopurine, and naturally or non- naturally occurring nucleobases as depicted in FIG. 1 and FIG. 2.
  • Preferred nucleobases are adenine, cytosine, guanine, and thymine.
  • Nucleobases may be protected by protecting group for the syntheses of PNA oligomers. Protecting groups may be, but are not limited to, Boc, adamantyloxycarbonyl, benzyloxycarbonyl (P. E. Nielsen et al. Science, 1991, 254, 1497- 1500; M.
  • T-monomer is a compound having general formula I-t: [00157]
  • E is nitrogen
  • J is sulfur
  • the compounds of general formula V-t are prepared by coupling reaction of (thymin-l-yl)-acetic acid with benzothiazole-2-sulfonyl, benzoxazole-
  • E is nitrogen
  • J is sulfur
  • Preferred R6 is methyl, ethyl or t-butyl.
  • PNA T-monomers having general formula I-t by simultaneous reaction during activation of carboxylic acid.
  • the activation of carboxylic acid may be conducted by general coupling reagent for peptide synthesis or mixed anhydride.
  • the reaction conditions and reagents are the same as described above.
  • PNA T-monomers can be prepared by coupling
  • C- monomer is a compound having general formula I-c:
  • E is nitrogen
  • J is sulfur
  • the precursors for PNA C-monomers are prepared by the method according to the scheme as depicted in FIG. 7 and known methods such as described in U. S. Patent No. 6,133,444; U. S. Patent No. 6,063,569; Dueholm, et al, J. Org. Chem., 1994, 59, 5767-5773; and WO 92/20702, which are incorporated by reference herein in their entirety, or modifications thereof.
  • R7 may be methyl, ethyl, benzyl, benzhydryl, 4-methoxybenzyl, 3,4- dimethoxybenzyl, piperonyl derivatives, or 2-methylthioethyl group.
  • PNA C-monomer is prepared by coupling reaction of suitably protected (cytosin-l-yl)-acetic acids with a benzothiazole-2-sulfonyl, benzoxazole-
  • E is nitrogen
  • J is sulfur
  • E is nitrogen
  • J is sulfur
  • PNA monomers having the general formula I-c by simultaneous reaction during activation of carboxylic acid.
  • the activation of carboxylic acid may be conducted by general coupling reagent for peptide synthesis or mixed anhydride.
  • the reaction conditions and reagents are the same as described above.
  • PNA C-monomer can be prepared by coupling suitably protected (cytosin-l-yl)-acetic acids to piperazinone derivatives having general formula IV.
  • the reaction conditions and reagents are the same as described above.
  • A-monomer is a compound having general formula I-a:
  • E is nitrogen
  • J is sulfur
  • the precursors for PNA A-monomers are prepared by the method according to the scheme as depicted in FIG. 7 and known methods such as described in U. S. Patent No. 6,133,444; and S. A. Thomson et al. Tetrahedron, 1995, 6179-6194, which are inco ⁇ orated by reference herein in their entirety, or modifications thereof.
  • R7 is selected from methyl, ethyl, benzyl, benzhydryl, 4-methoxybenzyl, 3,4- dimethoxybenzyl, piperonyl derivatives, and 2-methylthioethyl group.
  • PNA C-monomer is prepared by coupling reaction of suitably protected (adenin-9-yl)-acetic acids with a benzothiazole-2-sulfonyl, benzoxazole- 2-sulfonyl, benzo[b]thiophene-2-sulfonyl or benzofuran-2-sulfonyl group protected backbone ester having general formula II in the presence of coupling reagent to obtain the compound having general formula V-a:
  • E is nitrogen
  • J is sulfur
  • E is nitrogen
  • J is sulfur
  • the cyclization reaction of carboxylic acids produces PNA monomers having the general formula I-a by simultaneous reaction during activation of carboxylic acid.
  • the activation of carboxylic acid can be conducted by general coupling reagent for peptide synthesis or mixed anhydride.
  • the reaction conditions and reagents are the same as described above.
  • PNA A-monomer can be prepared by coupling suitably protected (adenin-9-yl)-acetic acids to piperazinone derivatives having general formula IV.
  • the reaction conditions and reagents are the same as described above.
  • G- monomer is a compound having general formula I-g:
  • E is nitrogen
  • J is sulfur
  • PNA G-monomers suitably protected (guanin-9-yl)-acetic acids (shown below), are prepared by the method according to the scheme depicted in FIG. 7 and known methods such as described in U. S. Patent No. 6,172,226, or modifications thereof.
  • R7 may be methyl, ethyl, benzyl, benzhydryl, 4-methoxybenzyl, 3,4- dimethoxybenzyl, piperonyl derivatives, or 2-methylthioethyl group.
  • PNA G-monomer is prepared by coupling reaction of suitably protected (guanin-9-yl)-acetic acids with a benzothiazole-2-sulfonyl, benzoxazole- 2-sulfonyl, benzo[b]thiophene-2-sulfonyl or benzofuran-2-sulfonyl group protected backbone ester having general formula II in the presence of coupling reagent to afford the compound having general formula V-g:
  • E is nitrogen
  • J is sulfur
  • E is nitrogen
  • J is sulfur
  • the cyclization reaction of carboxylic acids produces PNA monomers having the general formula I-g by simultaneous reaction during activation of carboxylic acid.
  • the activation of carboxylic acid can be conducted by general coupling reagent for peptide synthesis or mixed anhydride.
  • the reaction conditions and reagents are the same as described above.
  • PNA G-monomer can be prepared by coupling suitably protected (guanin-9-yl)-acetic acids to piperazinone derivatives having general formula IV.
  • the reaction conditions and reagents are the same as described above.
  • PNA oligomers are constructed by solid phase synthesis on a suitable support material such as, but not limited to, polystyrene, polyoxyethylene-modified polystyrene, such as , for example Tentagel ® or Controlled Pore Glass, which is provided with anchoring group which latently contains cleavable amine functional group.
  • a suitable support material such as, but not limited to, polystyrene, polyoxyethylene-modified polystyrene, such as , for example Tentagel ® or Controlled Pore Glass, which is provided with anchoring group which latently contains cleavable amine functional group.
  • PNA monomer of this invention is inco ⁇ orated by coupling reaction to solid support.
  • the next step is systematic elaboration of desired PNA oligomer sequence. This elaboration includes repeated deprotection/coupling/capping cycles.
  • the backbone protecting group on the last coupled monomer, benzothiazole-2-sulfonyl, benzoxazole-2-sulfonyl, benzo[b]thiophene-2-sulfonyl or benzofuran-2-sulfonyl group is quantitatively removed by treatment with suitable thiol in the presence of organic base to liberate terminal free amine.
  • the oligomers are cleaved from the solid support and nucleobase protecting groups are simultaneously removed by incubation for 1-2 h. at about room temperature in TFA containing cresol as a cation scavenger.
  • the acylating reaction can be accelerated by using a catalyst such as but not limited to mercury acetate, tetramethylammonium fluoride, tetraethylammonium fluoride, tetrabutylammonium fluoride, benzyltrimethylammonium fluoride, cesium fluoride, tributylphosphine, triphenylphosphine.
  • a catalyst such as but not limited to mercury acetate, tetramethylammonium fluoride, tetraethylammonium fluoride, tetrabutylammonium fluoride, benzyltrimethylammonium fluoride, cesium fluoride, tributylphosphine, triphenylphosphine.
  • Preferred catalyst is tetrabutylammonium fluoride.
  • the reaction rate depends on the solvent used and reaction temperature.
  • solvents include, but are not limited to, DMF, N-methylpyrrolidone, dimethoxyethane, dichloromethane, 1,2-dichloroethane, DMSO, tetrahydrofuran, hexamethylphophoramide, tetramethylene sulfone, isopropyl alcohol, ethyl alcohol, and mixture of selected sovents.
  • Preferred solvent is DMF.
  • the N-terminal amino protecting group is cleaved by using thiol with organic base in solvent.
  • thiols include, but are not limited to, C 2 ⁇ C 2 o alkanethiol, 4-methoxytoluenethiol, 4-methylbenzenethiol, 3,6-dioxa-l,8-octanethiol, 4- chlorotoluenethiol, benzylmercaptane, N-acetylcysteine, N-(t-Boc)cysteine methyl ester, methyl 3-mercaptopropionate, 4-methoxybenzene thiol.
  • organic bases include, but are not limited to, triethylamine, NN-diisopropyethylamine, piperidine, N- methylmo ⁇ holine, and l,8-diazabicyclo[5,4,0]undec-7-one.
  • Preferred organic base is NN- diisopropyethylamine.
  • EXAMPLE 1 N-[2-(Benzothiazole-2-sulfonylamino)-ethyl]-glycine ethyl ester
  • N-(2-aminoethyl)-glycine ethyl ester 2HC1 (1.10 g, 5.0 mmol)
  • dichloromethane 50 mL
  • triethylamine 2.02 g, 20 mmol
  • N-(2-Aminoethyl)-alanine ethylester 2HC1 prepared as described by Puschl (A.
  • the aqueous layer was acidified to pH 3 by adding 2 ⁇ HCI and extracted with dichloromethane(100 mL). The organic layer was dried over MgSO and filtered. The filtrate was concentrated in vacuo to afford the desired product (7.88 g, 95 %).
  • EXAMPLE 18 [6-N-(Piperonyloxycarbonyl)-adenin-9-yl]-acetic acid [00321] The title compound (3.67 g, 99 %) was synthesized from [6-N- (piperonyloxycarbonyl)-adenin-9-yl]-acetic acid ethyl ester (4.00 g, 10 mmol) as per the procedure of Example 17.
  • Example 20 ⁇ ⁇ MR (500 MHz; DMSO-d 6 ) ⁇ 1 1.00 (s, IH), 8.86 (brs, IH), 8.27 (d, IH),
  • Example 20 ⁇ ⁇ MR (500 MHz; DMSO-d 6 ) ⁇ 10.65 (s, IH), 8.80 (brs, 0.6H), 8.68 (brs,
  • Example 20 ⁇ ⁇ MR (500 MHz; DMSO-d 6 ) ⁇ 10.93 (s, IH), 9.00 (s, 0.6H), 8.60 (s, 0.4H),
  • EXAMPLE 33 N-[2-(Benzothiazole-2-sulfonylamino)-ethyl]-/V- ⁇ [2-N-(3,4- dimethoxybenzyloxycarbonyl)-guanin-9-yl]-acetyl ⁇ -glycine ethyl ester
  • the title compound (2.48 g, 68 %) was synthesized by the reaction of N-[2- (benzothiazole-2-sulfonylamino)-ethyl]-glycine ethyl ester (1.72g, 5 mmol) and [2-N-(3,4- dimethoxybenzyloxycarbonyl)-guanin-9-yl]-acetic acid (2.02 g, 5 mmol) as per the procedure of Example 20.
  • Example 20 ⁇ ⁇ MR (500 MHz; DMSO-d 6 ) ⁇ 8.27 (d, IH), 8.15 (dd, IH), 7.80 (s, 0.6H),
  • EXAMPLE 38 N-[2-(Benzothiazole-2-sulfonylamino)-ethyl]-N- ⁇ [4-N-(4- methoxybenzyloxycarbonyl)-cytosin- 1 -yl]-acetyl ⁇ -glycine
  • EXAMPLE 39 N-[2-(Benzothiazole-2-sulfonylamino)-ethyl]-N- ⁇ [4-N-(3,4- dimethoxybenzyloxycarbonyl)-cytosin-l-yl]-acetyl ⁇ -glycine
  • Example 36 ⁇ ⁇ MR (500 MHz; DMSO-d 6 ) ⁇ 11.60 (brs, IH), 8.56 (s, 0.5H), 8.53 (s,
  • EXAMPLE 46 N-[2-(Benzothiazole-2-sulfonylamino)-ethyl]-N- ⁇ [6-N-(2- methylthioethoxycarbonyl)-adenin-9-yl]-acetyl ⁇ -glycine
  • EXAMPLE 48 N-[2-(Benzothiazole-2-sulfonylamino)-ethyl]-N- ⁇ [2-/V-(4- methoxybenzyloxycarbonyl)-guanin-9-yl]-acetyl ⁇ -glycine
  • EXAMPLE 49 N-[2-(Benzothiazole-2-sulfonylamino)-ethyl]-N- ⁇ [2-N-(3,4- dimethoxybenzyloxycarbonyl)-guanin-9-yl]-acetyl ⁇ -glycine
  • EXAMPLE 80 - l-(Benzothiazole-2-sulfonyl)-4- ⁇ [4-N-(2- methylthioethoxycarbonyl)-cytosin-l-yl]acetyl ⁇ -piperazin-2-one [00449]
  • the title compound was synthesized from N-[2-(benzothiazole-2- sulfonylamino)-ethyl]-N- ⁇ [4-N-(2-methylthioethoxycarbonyl)]-cytosin-l-yl ⁇ -acetyl ⁇ - glycine as per the procedures of method A or B of Example 75. Yield: method A (90 %), method B (93 %).
  • ⁇ ⁇ MR (500 MHz; DMSO-d 6 ) data are the same as Example 59.
  • PNA oligomer synthesis was conducted manually on a Nova Syn TG amino resin (Nova biochem, 0.26 mmol/g loading) which is a PEG-grafted polystyrene resin with amine functionality.
  • the resin was coupled with PAL linker (5-[4-(9- fluorenylmethoxycarbonyl)amino-3,5-dimethoxyphenoxy]pentanoic acid (Advanced
  • FIGS. 17A-B show (A) HPLC and (B) MALDI-TOF profiles.
  • FIGS. 18A-B show (A) HPLC and (B) MALDI-TOF profiles.
  • FIGS. 19A-B show (A) HPLC and (B) MALDI-TOF profiles.
  • FIGS. 20A-B show (A) HPLC and (B) MALDI-TOF profiles.
  • FIGS. 21 A-B show (A) HPLC and (B) MALDI-TOF profiles.
  • FIGS. 22A-B show (A) HPLC and (B) MALDI-TOF profiles.
  • FIGS. 23A-B show (A) HPLC and (B) MALDI-TOF profiles.
  • FIGS. 24A-B show (A) HPLC and (B) MALDI-TOF profiles.
  • EXAMPLE 100 Synthesis of PNA oligomer sequence H 2 N-ACCCTACTGT-H
  • FIGS. 25A-B show (A) HPLC and (B) MALDI-TOF profiles.

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US6969766B2 (en) 2005-11-29
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