WO1994022886A9 - Liaisons par oligonucleocides heteroatomiques - Google Patents

Liaisons par oligonucleocides heteroatomiques

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Publication number
WO1994022886A9
WO1994022886A9 PCT/US1994/003536 US9403536W WO9422886A9 WO 1994022886 A9 WO1994022886 A9 WO 1994022886A9 US 9403536 W US9403536 W US 9403536W WO 9422886 A9 WO9422886 A9 WO 9422886A9
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compound
group
oligonucleotide
alkyl
substituted
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PCT/US1994/003536
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English (en)
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WO1994022886A1 (fr
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Priority to US08/522,374 priority Critical patent/US6087482A/en
Publication of WO1994022886A1 publication Critical patent/WO1994022886A1/fr
Publication of WO1994022886A9 publication Critical patent/WO1994022886A9/fr

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  • This invention relates to the design, synthesis and application of nuclease resistant macromolecules that function as oligonucleotide mimics and are useful for therapeutics, diagnostics and as research reagents.
  • the macromolecules have modified linkages in place of the phosphorodiester inter-sugar linkages found in wild type nucleic acids.
  • the macromolecules are resistant to nuclease degradation and are capable of modulating the activity of DNA and RNA.
  • Methods for synthesizing the macromolecules and for modulating the production of proteins, utilizing the macromolecules of the invention are also provided. Also provided are intermediate compositions useful in the synthesis of the macromolecules. BACKGROUND OF THE INVENTION
  • Classical therapeutics generally has focused upon interactions with proteins in an effort to moderate their disease causing or disease potentiating functions. Recently, however, attempts have been made to moderate the production of proteins by interactions with the molecules (i.e., intracellular RNA) that direct their synthesis. These interactions have involved hybridization of complementary "antisense" oligonucleotides or certain analogs thereof to RNA. Hybridization is the sequence-specific hydrogen bonding of oligonucleotides or oligonucleotide analogs to RNA or to single stranded DNA. By interfering with the production of proteins, it has been hoped to effect therapeutic results with maximum effect and minimal side effects.
  • oligonucleotides and oligonucleotide analogs like other therapeutics, depends on a number of factors that influence the effective concentration of these agents at specific intracellular targets.
  • One important factor for oligonucleotides is the stability of the species in the presence of nucleases. It is unlikely that unmodified oligonucleotides will be useful therapeutic agents because they are rapidly degraded by nucleases. Modification of oligonucleotides to render them resistant to nucleases therefore is greatly desired.
  • oligonucleotides Modification of oligonucleotides to enhance nuclease resistance generally has taken place on the phosphorus atom of the sugar-phosphate backbone. Phosphorothioates, methyl phosphonates, phosphoramidites and phosphotriesters have been reported to confer various levels of nuclease resistance. Phosphate-modified oligonucleotides, however, generally have suffered from inferior hybridization properties. See, e . g. , Cohen, J.S., ed. Oligonucleotides: Antisense Inhibitors of Gene Expression, (CRC Press, Inc., Boca Raton FL, 1989).
  • Another key factor is the ability of antisense compounds to traverse the plasma membrane of specific cells involved in the disease process.
  • Cellular membranes consist of lipid-protein bilayers that are freely permeable to small, nonionic, lipophilic compounds and are inherently impermeable to most natural metabolites and therapeutic agents. See, e . g. , Wilson, Ann. .Rev. Biochem. 1978, 47, 933.
  • the biological and antiviral effects of natural and modified oligonucleotides in cultured mammalian cells have been well documented. It appears that these agents can penetrate membranes to reach their intracellular targets.
  • modified oligonucleotides and oligonucleotide analogs are internalized less readily than their natural counterparts.
  • the activity of many previously available antisense oligonucleotides has not been sufficient for practical therapeutic, research or diagnostic purposes.
  • Two other serious deficiencies of prior art compounds designed for antisense therapeutics are inferior hybridization to intracellular RNA and the lack of a defined chemical or enzyme-mediated event to terminate essential R ⁇ A functions.
  • Modifications to enhance the effectiveness of the antisense oligonucleotides and overcome these problems have taken many forms. These modifications include heterocyclic base modifications, sugar moiety modifications and sugar-phosphate backbone modifications. Prior sugar-phosphate backbone modifications, particularly on the phosphorus atom, have effected various levels of resistance to nucleases. However, while the ability of an antisense oligonucleotide to bind to specific DNA or RNA with fidelity is fundamental to antisense methodology, modified phosphorus oligonucleotides have generally suffered from inferior hybridization properties .
  • Another object of the invention is to provide oligonucleotide analogs having greater efficacy than unmodified antisense oligonucleotides.
  • the present invention provides compositions that are useful for modulating the activity of an RNA or DNA molecule and that generally comprise oligonucleotide-mimicking macromolecules.
  • the macromolecules are constructed from a plurality of linked nucleosides.
  • the phosphorodiester linkage of the sugar phosphate backbone found in wild type nucleic acids has been replaced with a 3 or 4 atom linking groups.
  • Such linking groups maintain a desired atomic spacing between the 3'-carbon of one nucleoside and the 4' -carbon (as numbered in reference to the numbering of a pentofuranosyl nucleoside) of an adjacent nucleoside.
  • the oligonucleotide-mimicking macromolecules of the invention comprise a selected linked sequence of nucleosides that are specifically hybridizable with a preselected nucleotide sequence of single stranded or double stranded DNA or RNA.
  • oligonucleotide-mimicking macromolecules of the invention are synthesized conveniently, through solid state support or solution methodology, to be complementary to or at least specifically hybridizable with a preselected nucleotide sequence of the RNA or DNA.
  • Solid state support synthesis is effected utilizing commercially available nucleic acid synthesizers. The use of such synthesizers is generally understood by persons of ordinary skill in the art as being effective in generating nearly any desired oligonucleotide or oligonucleotide mimic of reasonable length.
  • the oligonucleotide-mimicking macromolecules of the invention also can include nearly any modification known in the art to improve the properties of wild type oligonucleotides.
  • the macromolecules can incorporate modifications known to increase nuclease resistance or hybridization.
  • novel macromolecules that function as antisense oligonucleotide mimics are provided to enhance cellular uptake, nuclease resistance, and hybridization properties and to provide a defined chemical or enzymatically mediated event to terminate essential RNA functions.
  • oligonucleotide-mimicking macromolecules can be useful in therapeutics and for other objects of this invention. At least a portion of the macromolecules of the invention has structure 1:
  • L 1 -L 2 -L 3 -L 4 is CR 1a R 1b -CR 2a R 2b -CR 3a R 3b -Z 4 , CR 1a R 1b -CR 2a R 2b -Z 3 -Z 4 , CR 1a R 1b -Z 2 -CR 2a R 2b -Z 4 , Z 1 -CR 1a R 1b -CR 2a R 2b -Z 4 , CR 1a R 1b -Z 2 -Z 3 -Z 4 , Z 1 -CR 2a R 2b -Z 3 -Z 4 or Z 1 -Z 2 -CR 3a R 3b -Z 4 ;
  • X is H, OH, O-R 5 , S-R 5 , NR 4 -R E , R 5 , F, Cl, Br, CN, CF 3 , OCF 3 , OCN, SOCH 3 , SO 2 CH 3 , ONO 2 , NO 2 , N 3 , heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino or substituted silyl, an RNA cleaving group, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide;
  • J 1 is O, S, Se, or NR 4 ;
  • J 2 is OH, OR 5 , SH, SR 5 , SeH, R 5 , BH 3 or NR 4 R 5 ;
  • R 4 , R 5 and R 6 are, independently, H; C 1 to C 10 straight or branched chain lower alkyl or substituted lower alkyl; C 2 to C 10 straight or branched chain lower alkenyl or substituted lower alkenyl; C 2 to C 10 straight or branched chain lower alkynyl or substituted lower alkynyl; a 14 C containing lower alkyl, lower alkenyl or lower alkynyl; C 7 to C 14 substituted or unsubstituted alkaryl or aralkyl; a 14 C containing C 7 to C 14 alkaryl or aralkyl; C 6 to C 14 aryl; alicyclic; heterocyclic; a reporter molecule; an RNA cleaving group; a group for improving the pharmacokinetic properties of an oligonucleotide; or a
  • Q is O, CHF, CF 2 or CH 2 ;
  • n is an integer greater than 0;
  • Bx is a variable heterocyclic base moiety.
  • the remainder of the molecule is composed of chemical functional groups that do not hinder, and preferably enhance, hybridization with RNA or single stranded or double stranded DNA.
  • structure 1. at its 3' and 5' terminal ends can, independently, bear any of the following groups: H, hydroxyl, aminomethyl, hydrazinomethyl, hydroxymethyl, C- formyl, phthalimidomethyl, aryl-substituted imidazolidino, aminohydroxylmethyl, ortho -methylaminobenzenethio, methylphosphonate, methyl-alkylphosphonate, a nucleoside, a nucleotide, an oligonucleotide, an oligonucleoside, or a hydroxyl-protecped or amine-protected derivative thereof.
  • L 1 -L 2 -L 3 -L 4 is CR 1a R 1b -CR 2a R 2b -CR 3a R 3b -Z 4
  • Z 4 is O, S or NR 4
  • L 1 -L 2 -L 3 -L 4 is CR 1a R 1a -CR 2a R 2b -Z 3 -Z 4
  • Z 3 and Z 4 are, independently, O, S or NR 4 .
  • L 1 -L 2 -L 3 -L 4 is CR 1a R 1b -Z 2 -CR 3a R 3b -Z 4 , and Z 2 and Z 4 are, independently, O, S or NR 4 .
  • L 1 -L 2 -L 3 -L 4 is Z 1 -CR 2a R 2b -CR 3a R 3b -Z 4 , and Z 1 and Z 4 are, independently, O, S or NR 4 .
  • This preferred embodiments includes compounds wherein Z 1 and Z 4 are O; and R 2a , R 2b , R 3a and R 3b are H.
  • L 1 -L 2 -L 3 -L 4 is CR 1a R 1b -Z 2 -Z 3 -Z 4 , and Z 2 , Z 3 and Z 4 are, independently, O, S or NR 4 .
  • L 1 -L 2 -L 3 -L 4 is Z 1 -Z 2 -CR 3a R 3b -Z 4 , and Z 1 , Z 2 and Z 4 are, independently, O, S or NR 4 .
  • L 1 -L 2 -L 3 -L 4 is Z 1 -CR 2a R 2b -Z 3 -Z 4
  • Z 1 , Z 3 and Z 4 are, independently, O, S or NR 4 .
  • Z 1 is O or CH 2 ;
  • Z 4 is O;
  • J 1 and J 2 are O or S.
  • L 1 -L 2 -L 3 -L 4 includes at least one double bond therein.
  • L 1 -L 2 -L 3 -L 4 include at least one of an alkene, imine, hydrazone or oxime linkage within L 1 -L 2 -L 3 -L 4 .
  • Such linkage are formed by selecting R 4 and R 5 to be one of an electron pair such that one of L 1 -L 2 , or L 2 -L 3 together is an alkene moiety; or one of L 1 -L 2 or L 2 -L 3 or L 3 -L 4 together is an imine moiety; or one of L 1 -L 2 -L 3 or L 2 -L 3 -L 4 together is a oxime or hydrazone moiety.
  • L 2 , L 3 and L 4 together with at least two additional carbon or hetero atoms, form a 5 or 6 membered ring.
  • L 1 , L 2 , and L 3 are, independently, O, S, NR 4 , CH 2 or Si(R 6 ) 2 with at least one of L 1 , L 2 or L 3 being Si(R 6 ) 2 and L 4 is O, S, Se or NR 4 .
  • at least one of L 1 , L 2 , L 3 or L 4 is Se.
  • Q is O and X is H or OH.
  • R 4 is H or C 1 to C 10 straight or branched chain alkyl or substituted alkyl.
  • R 5 is C 1 to C 10 straight or branched chain lower alkyl or substituted lower alkyl; C 2 to C 10 straight or branched chain lower alkenyl or substituted lower alkenyl; C 2 to C 10 straight or branched chain lower alkynyl or substituted lower alkynyl; or C 7 to C 14 alkaryl or aralkyl.
  • R 4 and R 5 are, independently, H or C 1 to C 10 straight or branched chain lower alkyl or substituted lower alkyl.
  • Bx preferably is a naturally occurring or synthetic purine or pyrimidine heterocyclic bases, including but not limited to adenine, guanine, cytosine, thymine, uracil, 5-methylcytosine, hypoxanthine or 2-aminoadenine.
  • heterocyclic bases include 2-methylpurine, 2,6-diaminopurine, 6-mercaptopurine, 2,6-dimercaptopurine, 2-amino-6-mercaptopurine, 5-methylcytosine, 4-amino-2-mercaptopyrimidine, 2,4-dimercaptopyrimidine and 5-fluorocytosine.
  • the macromolecules preferably are included in a pharmaceutically acceptable carrier for therapeutic administration.
  • the present invention provides methods of modulating the production or activity of a protein in a cell system or an organism comprising contacting the cell system or organism with an oligonucleotide-mimicking macromolecule having structure 1 .
  • the invention also provides methods of treating an organism having a disease characterized by the undesired production of a protein comprising contacting the organism with an oligonucleotide-mimicking macromolecule having structure 1 .
  • the invention provides methods of in vi tro assaying a sequence-specific nucleic acid comprising contacting a test solution containing the nucleic acid with an oligonucleotide-mimicking macromolecule having structure 1.
  • the methods comprise the steps of contacting a first nucleoside or oliognucleoside bearing a leaving group at its 4' -position (as numbered in reference to the numbering of a pentofuranosyl nucleoside) with a second nucleoside or oligonucleoside bearing a nucleophile at its 3' -position to form a linkage having formula L 1 -L 2 -L 3 -L 4 .
  • the methods comprise the steps of contacting a first xylo nucleoside or oliognucleoside having a xylo nucleoside bearing a leaving group at its 3 '-position, with a second nucleoside or oligonucleoside bearing a nucleophile at its 4' -position (as numbered in reference to the numbering of a pentofuranosyl nucleoside) to form a linkage having formula L 1 -L 2 -L 3 -L 4 .
  • the methods comprise the steps of contacting a first nucleoside or oligonucleoside bearing at least a portion but not all of the L 1 -L 2 -L 3 -L 4 linker at its 3' position with a second nucleoside or oligonucleoside bearing the remainder of the L 1 -L 2 -L 3 -L 4 linker at its 4' position (as numbered in reference to the numbering of a pentofuranosyl nucleoside) to join said nucleosides or oligonucleosides by the L 1 -L 2 -L 3 -L 4 linker.
  • Figure 1 shows a preferred iterative synthetic scheme according to the invention.
  • Figure 2 shows a number of synthetic pathways according to the invention.
  • Figure 3 shows a representative synthesis of 3'-O-(2- hydroxyethyl) nucleosides and 5'-acetoxy nucleosides.
  • Figure 4 shows a representative coupling of 3'-O-(2-hydroxyethyl) nucleosides and 5'-acetoxy nucleosides.
  • FIGS 5 to 23 illustrate representative synthetic schemes for the preparation of compounds of the invention.
  • nucleoside refers to a unit composed of a heterocyclic base and a sugar, generally a pentose sugar.
  • the heterocyclic base typically is guanine, adenine, cytosine, thymine or uracil.
  • the sugar is normally deoxyribose, i . e . , erythro-pentofuranosyl, or ribose, i . e . , ribopentofuranosyl.
  • Synthetic sugars also are known, including arabino, xylo or, lyxo pentofuranosyl sugars and hexose sugars.
  • reference to the sugar portion of a nucleoside or other nucleic acid species shall be understood to refer to either a true sugar or to a species replacing the pentofuranosyl or 2'-deoxypentofuranosyl sugar moieties of wild type nucleic acids.
  • reference to the heterocyclic base portion of a nucleoside or other nucleic acid species shall be understood to refer to either a natural, modified or synthetic base replacing one or more of the traditional base moiety of wild type nucleic acids.
  • reference to inter-sugar linkages shall be taken to include moieties serving to join the sugar or sugar substitute moiety together in the fashion of wild type nucleic acids.
  • nucleotide refers to a nucleoside having a phosphate group esterified to one of its 2', 3' or 5' sugar hydroxyl groups.
  • the phosphate group normally is a monophosphate, a diphosphate or triphosphate.
  • oligonucleotide refers to a plurality of monophosphate nucleotide units that typically are formed in a specific sequence from naturally occurring bases and pentofuranosyl sugars joined by native phosphodiester bonds.
  • a homo-oligonucleotide is formed from nucleotide units having the same heterocyclic base, i.e. poly (A).
  • poly (A) The term oligonucleotide generally refers to both naturally occurring and synthetic species formed from naturally occurring subunits.
  • oligonucleotide analog has been used in various published patent application specifications and other literature to refer to molecular species similarly to oligonucleotides but that have non-naturally occurring portions. This term has been used to identify oligonucleotide-like molecules that have altered sugar moieties, altered base moieties or altered inter-sugar linkages.
  • oligonucleotide analog has been used to denote structures having altered inter-sugar linkages including phosphorothioate, methyl phosphonate, phosphotriester or phosphoramidate inter-nucleoside linkages used in place of phosphodiester inter-nucleoside linkages; purine and pyrimidine heterocyclic bases other than guanine, adenine, cytosine, thymine or uracil and sugars having other than the ⁇ pentofuranosyl configuration or sugars having substituent groups at their 2' position or substitutions for one or more of the hydrogen atoms.
  • modified oligonucleotide also has been used in the literature to denote such structures.
  • Oligonucleotide mimics refers to macromolecular moieties that function similarly to or “mimic” the function of oligonucleotides but have non-naturally occurring inter-sugar linkages. Oligonucleotide mimics thus can have natural or altered or non-naturally occurring sugar moieties and natural or altered or non-naturally occurring base moieties in combination with non-naturally occurring dephospho linkages. Certain dephospho linkages have been reviewed by Uhlmann, E. and Peyman, A.
  • oligonucleoside an altered inter-sugar linkage
  • oligonucleoside or oligonucleotidemimicking macromolecule thus refers to a plurality of joined nucleoside units connected by dephospho linkages.
  • oligomers is intended to encompass oligonucleotides, oligonucleotide analogs, oligonucleosides or oligonucleotide-mimicking macromolecules.
  • linkage is from the 3' carbon of one nucleoside to the 4' carbon (as numbered in reference to the numbering of a pentofuranosyl sugar as explained in greater detail below) of a second nucleoside.
  • the term “oligomer” can also include other linkages such as a 2' ⁇ 5' linkage or a 3 ' ⁇ 5' linkage (both as numbered in reference to the numbering of a pentofuranosyl sugar).
  • nucleoside compounds of the invention as identified in the specification and claims attached hereto, both as free nucleosides and as nucleosidic units of dimeric, trimeric and other higher order structures of the invention, lack a 5' methylene group of conventional pentofuranosyl nucleosides. In one sense these compounds can be considered as 4'-desmethyl pentofuranosyl nucleosides. In these compounds, a hetero atoms occupies the position normally occupied by the 5' -methylene group of a conventional pentofuranosyl nucleoside.
  • the tetrahydrofuranyl ring is number counterclockwise and the position occupied by the hetero atom (in what would be the 5' position of a conventional nucleoside) is identified as the 2 position. If the compound is a tetrahydrofuranosyl nucleoside that is not a part of a dimeric, trimer or other higher ordered structure, the heterocyclic base takes priority and the ring is numbered clockwise with the position occupied by the nucleobase being the 2 position.
  • convention pentofuranosyl nucleoside numbering has been used (except where otherwise noted) for the tetrahydrofuranyl nucleosides.
  • Alkyl groups of the invention include but are not limited to C 1 -C 12 straight and branched chained alkyls such as methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, undecyl, dodecyl, isopropyl, 2-butyl, isobutyl,
  • Alkenyl groups include but are not limited to unsaturated moieties derived from the above alkyl groups including but not limited to vinyl, allyl and crotyl.
  • Alkynyl groups include unsaturated moieties having at least one triple bond that are derived from the above alkyl groups including but are not limited to ethynyl and propargyl.
  • Aryl groups include but are not limited to phenyl, tolyl, benzyl, naphthyl, anthracyl, phenanthryl, pyrenyl, and xylyl.
  • Halogens include fluorine, chlorine and bromine.
  • Suitable heterocyclic groups include but are not limited to imidazole, tetrazole, triazole, pyrrolidine, piperidine, piperazine and morpholine.
  • Amines include amines of all of the above alkyl, alkenyl and aryl groups including primary and secondary amines and "masked amines" such as phthalimide. Amines are also meant to include polyalkylamino compounds and aminoalkylamines such as aminopropylamine and further heterocyclo-alkylamines such as imidazol-1, 2 or 4-yl-propylamine.
  • Substituent groups for the above include but are not limited to other alkyl, haloalkyl, alkenyl, alkynyl, alkoxy, thioalkoxy, haloalkoxy and aryl groups as well as halogen, hydroxyl, amino, azido, carboxy, cyano, nitro, mercapto, sulfides, sulfones, sulfoxides, keto, carboxy, nitrates, nitrites, nitroso, nitrile, trifluoromethyl, O-alkyl, S-alkyl, NH-alkyl, amino, silyl, amides, ester, ethers, carbonates, carbamates, ureas, imidazoles, intercalators, conjugates, polyamines, polyamides, polyethylene glycols, polyethers, groups that enhance the pharmacodynamic properties of oligonucleotides, and groups that enhance the pharmacokinetic properties of oli
  • substituent groups also include rhodamines, coumarins, acridones, pyrenes, stilbenes, oxazolo-pyridocarbazoles, anthraquinones, phenanthridines, phenazines, azidobenzenes, psoralens, porphyrins and cholesterols.
  • One particularly preferred group is CF 3 .
  • Typical intercalators and conjugates include cholesterols, phospholipids, biotin, phenanthroline, phenazine, phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines, coumarins, and dyes.
  • Halogens include fluorine, chlorine, bromine, and iodine.
  • Groups that enhance the pharmacodynamic properties include groups that improve oligonucleotide uptake, enhance oligonucleotide resistance to degradation, and/or strengthen sequence-specific hybridization with RNA.
  • Groups that enhance the pharmacokinetic properties include groups that improve oligonucleotide uptake, distribution, metabolism or excretion.
  • Antisense therapy is the use of oligonucleotides or other oligomers for the purpose of binding with complementary strands of RNA or DNA.
  • the oligonucleotide and the RNA or DNA strand can be considered to be “duplexed” together in a manner analogous to native, double stranded DNA.
  • the oligonucleotide strand and the RNA or DNA strand can be considered to be complementary strands in the same context as native double stranded DNA. In such complementary strands, the individual strands are positioned with respect to one another to allow Watson-Crick type hybridization of the heterocyclic bases of one strand to the heterocyclic bases of the opposing strand.
  • Antisense therapeutics can be practiced in a plethora of organisms ranging from unicellular prokaryotes and eukaryotes to multicellular eukaryotes . Any organism that utilizes DNA-RNA transcription or RNA-protein translation as a fundamental part of its hereditary, metabolic or cellular control is susceptible to antisense therapeutics and/or prophylactics. Seemingly diverse organisms such as bacteria, yeast, protozoa, algae, all plant and all higher animal forms, including warm-blooded animals, can be treated by antisense therapy.
  • each of the cells of multicellular eukaryotes includes both DNA-RNA transcription and RNA-protein translation as an integral part of their cellular activity
  • antisense therapeutics and/or diagnostics can also be practiced on such cellular populations.
  • many of the organelles, e . g. , mitochondria and chloroplasts, of eukaryotic cells include transcription and translation mechanisms.
  • single cells, cellular populations or organelles can also be included within the definition of organisms that are capable of being treated with antisense therapeutics or diagnostics.
  • therapeutics is meant to include the eradication of a disease state, killing of an organism, e . g. , bacterial, protozoan or other infection, or control of erratic or harmful cellular growth or gene expression.
  • serial number 463,358 filed January 11, 1990, entitled Compositions And Methods For Detecting And Modulating RNA Activity
  • serial number 566,836, filed August 13, 1990, entitled Novel Nucleoside Analogs
  • serial number 566,977 filed August 13, 1990, entitled Sugar Modified Oligonucleotides That Detect And Modulate Gene Expression
  • serial number 703,619 filed May 21, 1991, entitled Backbone Modified Oligonucleotide Analogs
  • serial number PCT/US91/00243 filed January 11, 1991, entitled Compositions and Methods For Detecting And Modulating
  • oligonucleotides and other oligomers have application in diagnostics, therapeutics, and as research reagents and kits.
  • oligonucleotides or other oligomers would be administered to an animal, including humans, suffering from a disease state that is desirous to treat.
  • This invention is directed to certain macromolecules that function like oligonucleotides yet exhibit other useful properties.
  • the macromolecules are constructed from nucleoside units. These nucleoside units are joined by a linkage of the invention to form dimeric units as illustrated by structure 1 wherein n is 1:
  • the dimeric units can be further extended to trimeric, tetrameric and other, higher order macromolecules by the addition of further nucleosides (structure 1 wherein n > 1).
  • the dimeric units (and/or the higher order units) also can be linked via linkages other than those of the invention, as for instance, via a normal phosphodiester linkage, a phosphorothioate linkage, a phosphoramidate linkage, a phosphotriester linkage, a methyl or other alkylphosphonate linkage, a phosphorodithioate linkage or other linkage.
  • a single linkage is used to join nucleosides to form a macromolecule of the invention.
  • m and r are 0, q is 1, n and p are greater than 1, and E is OH.
  • two or more different linkages are used.
  • m and r are 0, q is 1, and n and p are greater than 1.
  • the nucleoside are joined in groups of two, three or more nucleoside that together form a unit.
  • An activated phosphityl moiety is located at the 3' terminus of this unit and a hydroxyl moiety bearing a removable hydroxyl blocking group is located at the 5' terminus.
  • a first unit (a group of two, three or more nucleosides linked together via a first linkage of the invention) and to a second unit (a group of two, three or more nucleosides linked together via the first linkage or via a second linkage of the invention) are connected through a phosphate linkage.
  • the macromolecule is elongated by the addition of further units of nucleosides (linked together via the first, a second or additional linkages of the invention) by joining these additional units to the existing linked units via further phosphorus linkages.
  • r is 0 or 1
  • m is a positive number
  • q is greater than 1
  • n and p are positive numbers.
  • compounds having structure 1 are prepared by using a first sugar or sugar analog having a 4' nucleophilic substituent (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) to displace a leaving group from a 3' functionalized second sugar or sugar analog moiety.
  • a nucleoside having a 4' substituent (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) of structure Y-Z n -R A -Z 4 - where is group comprising a one, two, or three carbon backbone ( e . g. , - (C ⁇ 2 ) 1 .
  • Y is a selectively removable protecting group and Z n is one of Z 1 or Z 2 as defined above, is removably attached to a solid support.
  • the process further comprises removing the protecting group and reacting the deprotected nucleophilic group with a compound having
  • R B is a leaving group.
  • the group Y is acid labile and the group R B is amenable to SN-2 displacement when the 3' carbon of its sugar moiety is attacked by a 4' nucleophile (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) of a similar moiety.
  • R A can be substituted with one or more ionizable functions, especially amino, hydroxyl, and carboxylate functions.
  • Y is any convenient terminating function such as polyamine or a polyethylene glycol. It is preferred that the deprotected hydroxyl group have its nucleophilicity improved by reacting the composition with a suitable base prior to the nucleophilic displacement.
  • the group Y can include any blocking or protecting group which is selectively removable and which otherwise is consistent with the present invention. It is preferred in some embodiments that Y be acid labile under relatively mild conditions. Thus, tetrahydropyranyl, tert-butyl, bis-(p-methyoxyphenyl)phenylmethyl (DMT) groups can be used. It is preferred that tert-butyl group be employed. Where Z n is 0, for example, protecting group Y can be removed under acidic conditions and the resulting hydroxyl group treated with base to produce a nascent nucleophile.
  • a wide variety of bases can be so employed, including sodium hydride, Grignard reagents, especially methylmagnesium chloride, t-butyl magnesium chloride, lithium diisopropyl amide, methyl lithium, n-butyl lithium and DBU.
  • Anhydrous conditions are generally required.
  • a representative iterative synthetic scheme is shown in Figure 1.
  • the Y-Z n -R A -Z 4 - functionality in any given iteration can be the same or different from that selected in prior iterations; indeed, a number of variations may be employed within a single oligonucleoside.
  • further functionality can be provided at the 3' position.
  • a 3' leaving group, R B is provided.
  • the macromolecules of the invention also can be prepared through displacement of a leaving group from the 4' position (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) of a nucleoside or the 4' terminal position (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) of an oligonucleoside.
  • the 4' -functionalized moiety (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) has structure 3:
  • R c is a leaving group such as, for example, alkyl and aryl sulfonyl leaving group including p-toluenesulfonyl (tosyl) 4-dimethylaminoazobenzenesulfonyl (dabsyl), 5-dimethylaminonaphthalenesulfonyl (dansyl) , trifluoromethylsulfonyl (triflate), methylsulfonyl (mesyl); halogens; o-trichloroacetimidates; 2,4,6-trichlorophenyl; dialkyl phosphite and acyloxy leaving groups including acetoxy, benzoyloxy, p-methoxybenzoyloxy and p-methylbenzoyloxy and other known leaving groups.
  • R c is a leaving group such as, for example, alkyl and aryl sulfonyl leaving group including p-toluene
  • R D can be H, hydroxyl, aminomethyl, hydrazinomethyl, hydroxymethyl, C-formyl, phthalimidohydroxymethyl, aryl-substituted imidazolidino, aminohydroxylmethyl, ortiio-methylaminobenzenethio, methylphosphonate, methyl-alkylphosphonate, a nucleoside, a nucleotide, an oligonucleotide, an oligonucleoside, or a hydroxyl-protected or amine-protected derivative thereof.
  • B x can be a heterocyclic base selected from adenine, guanine, uracil, thymine, cytosine, 2-aminoadenosine or 5-methylcytosine, although other naturally occurring and non-naturally occurring species can be employed.
  • Representative heterocyclic bases are disclosed in U.S. Patent No. 3,687,808
  • oligonucleosides having structure 1 can be prepared by reacting structure 3 with compounds having structure 4 :
  • R F is, for example, L 1 -L 2 -L 3 -Z 4 .
  • R F is, for example, L 1 -L 2 -L 3 -Z 4 .
  • Other representative nucleosides having structure 4. are shown in Figure 2.
  • the 4' -desmethyl end (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) may be substituted with polyamines or polyethylene glycols for enhanced oligonucleoside properties as set forth in U.S. Patent No. 5,138,045, issued August 11, 1992 and incorporated by reference herein.
  • a nucleoside analog is attached to a solid support in any conventional fashion. It is customary, and preferred, to employ a linker to a solid support such as a polymeric carrier at the 3' position.
  • the nucleoside analog moiety does not have a 5' carbon, but rather is substituted in the 4' position with leaving group R c .
  • the nucleoside analog moiety is prepared with any base or base analog, B x and either a pentofuranosyl moiety, where Q is oxygen, or a cyclopentane moiety where Q is CH 2 .
  • a 2' hydroxyl functionality is present (X is OH) such that the resulting oligonucleoside will have increased hybridization properties with RNA.
  • the 2'-hydroxyl groups can be protected as necessary by means well known to persons of ordinary skill in the art. The only requirement for this group and for its protection is that the same be designed so as to not interfere with substantive reactions in accordance with this invention.
  • the 2'- hydroxyl group will replaced with other functional groups as for example 2'-alkoxy groups, 2'-alkoxy groups that are substituted with other groups including imidazole and other heterocycle groups, 2'-halogen particularly fluoro.
  • the synthetic procedures of the invention can be repeated sequentially in order to construct oligonucleosides of any reasonably desired length.
  • a number of monomeric species may be inserted into the chain to incorporate varying bases B x , varying hydroxylic substituents at 2' carbon atoms, and varying linking functions L 1 -L 2 -L 3 -L 4 .
  • the linking functions can be part of a 5 or 6 membered ring.
  • L 2 , L 3 and L 4 together with 2 or 3 additional carbon- or hetero- atoms can form a heterocycle. Accordingly, it should be appreciated that this reaction scheme is quite general and will likely be appropriate for a variety of substitution schemes.
  • each step may be performed a plurality of times in order to ensure substantial completeness of the addition of each nucleoside subunit. It will be appreciated that a number of other reaction schemes may be employed in order to provide the carbon-atom and hetero-atom backbone (the linking group) between sugars and sugar analogs of nucleic acid species in accordance with the present invention.
  • carbon or heteroatom backbone means that there is a chain of carbon and heteroatoms connecting between the 4' position (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) of one sugar or sugar analog and the 3' position of a second sugar or sugar analog.
  • this chain is a four atom chain.
  • this four carbon or heteroatom backbone there will be a total of four such atoms (the carbon plus the hetero atoms) in the backbone.
  • the L 1 -L 2 -L 3 -L 4 backbone linking the nucleosides of the macromolecules of the invention will include a phosphorous atom at one of the L 2 , L 2 or L 3 positions.
  • Z 1 , Z 2 and Z 4 O or S
  • Y 1 O or S
  • Y 1 O
  • Y 2 is OH.
  • various phosphate moieties can be formed including phosphodiesters, phosphorothioates, phosphorodithioates, phosphoroselenates, phosphorodiselenates, phosphoramidates, boranophosphates, alkyl phosphonates, phosphotriesters, phosphonates and H-phosphonates.
  • Figure 3 shows the synthesis of a 3'-O-(2-hydroxyethyl) nucleoside 10 and a 4'-acetoxy nucleoside 8 (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside).
  • a common precursor, 3, was utilized for the synthesis of both 8 and 10.
  • This precursor, nucleoside 3, having blocking groups on both the base and the sugar, is derivated from a sugar blocked thymidine, nucleoside 2, that, in turn is obtained from thymidine.
  • the 3'-O-(2-hydroxyethyl) nucleoside 10 was prepared by generating the 3'-O-ethylacetate derivative 9, which then was hydrolyzed in methanol and sodium borohydride to produce 3'-O-(2-hydroxyethyl) nucleoside 10.
  • the 4'-acetoxy nucleoside 8 (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) was prepared by treating 3'-O-benzoyl nucleoside 4 with hydrogen fluoride-pyridine to give the 5' hydroxyl derivative 5, which was oxidized by a modification of the procedure of Corey and Samuelsson, J. Org. Chem . 1984, 49 , 4735 to provide 5'-tert-butyl carboxylate derivative 6.
  • the 4'-tert-butyl carboxylate 6 was treated with CF 3 COOH to provide the free acid derivative 7, which was treated with Pb(OAc) 4 and pyridine to provide 4'- acetoxy nucleoside 8 (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside).
  • Use of the 3'-O-benzoyl group allows for acyl group participation during displacement of the 4'-acetoxy group (as numbered using the sugar ring numbering of a pentofuranosyl nucleoside) to give the desired isomer upon completion of the displacement reaction used to effect dimer formation.
  • Figure 4 illustrates a reaction scheme wherein a compound, as for instances, compound 10 having an L 1 -L 2 -L 3 -L 4 group attached there to is reacted with a compound having a leaving group in the 4' position to form a dimer.
  • An example is the coupling of compounds 8 and 10 using trimethylsilyltriflate in methylene chloride to provide glycollinked dimer 11.
  • Figure 4 further illustrates deprotection, re-protection and activation (phosphitylation) with groups suitable for solid state oligonucleoside synthesis.
  • phosphitylation phosphitylation
  • Compound 13 is the protected with a 5' DMT group and 3' phosphitylated.
  • Figures 5 through 18 illustrates synthetic schemes for the preparation of nucleoside intermediates as well as dimeric structures. Nucleoside intermediate compounds of Figures 5 through 18 are further reacted to form dimeric structures of Figure 4. In these examples, reference is made in certain instances to Figure 4 and to the L 1 , L 2 , L 3 and L 4 identifiers of Figure 4. To assist in identifying the compounds of the examples, in all instances wherein one or more of L 1 , L 2 , L 3 or
  • the silyl ether 4 (96.0 g, 136.4 mmol) in THF (600 mL) was treated with hydrogen fluoride-pyridine (70% HF in pyridine, 30 mL) at 0 °C for 4 h under a N 2 atmosphere.
  • the resultant mixture was diluted with AcOEt (600 mL) and washed with H 2 O (2 ⁇ 300 mL).
  • the organic layer was dried (MgSO 4 ) and concentrated at reduced pressure.
  • the residue was purified by silica gel column chromatography (CH 2 Cl 2 /AcOEt 10:1) to give 61.6 g (97%) of 5 as a white solid.
  • Trimethylsilyl triflate (TMSOTf, 0.25 mL, 288 mg, 1.30 mmol) was added a via syringe in one portion to a stirred solution of 8 (410 mg, 0.83 mmol) and 10 (609 mg, 0.95 mmol) in CH 2 Cl 2 (20 mL) at -23 °C. The resultant yellow solution was stirred at -23 °C for 4 h under N 2 . The reaction mixture was poured into a bilayer solution of AcOEt/H 2 O (10:1, 110 mL) containing Et 3 N (1 mL). The organic layer was dried (MgSO 4 ) and concentrated under reduced pressure.
  • (+, THF-5-C), 127.67, 128.09, 128.33 (-, aromatic-C), 128.63 (- , ribo-6-C), 129.07 (+, aromatic-C), 129.86 (-, THF-6-C), 130.20, 130.30 (+, aromatic-C), 132.44 132.85 (+, aromatic-C), 133.74, 134.00, 135.24, 135.38, 135.62 (-, aromatic-C), 138.06 (+, aromatic-C), 150.95 (+, THF-2-C), 151.42 (+, ribo-2-C), 163.24 (+, THF-4-C), 163.49 (+, ribo-4-C), 165.65 (+, benzoyl C O).
  • the dimer 22 is converted to its phosphoramidite as per the phosphitylation procedure of Example 15 to give the title compound, 23.
  • Compound 20 will be oxidized with RuO 4 as per the procedure of Varma, R.S. and Hogan, M.E., Tetrahedron Letts .
  • the dimer 35 is converted to its phosphoramidite as per the phosphitylation procedure of Example 15 to give the title compound, 36.
  • the reaction mixture was added to a bilayer of AcOEt/H 2 O (100 mL, 9:1 mixture) and Et 3 N (3 mL).
  • the organic phase was separated, dried over MgSO 4 and evaporated under reduced pressure.
  • the residue was purified by silica gel chromatography (hexanes/AcOEt, 10:1 ⁇ 2:1) to yield 0.61 g (30.3%) of the title compound as a yellow syrup.
  • the dimer 45 is converted to its phosphoramidite as per the phosphitylation procedure of Example 15 to give the title compound, 46 as a white foam.
  • R f (CHCl 3 /MeOH 10:1): 0.73; 31 P NMR (CDCl 3 ) : ⁇ 149.26 and 149.60 ppm (diastereomer).
  • Compound 55 will be treated with NaBH 4 to furnish the title compound 56.
  • the dimer 67 is converted to its phosphoramidite as per the phosphitylation procedure of Example 15 to give the title compound, 68.
  • Compound 69 will treated with benzylcarbazat and activated molecular sieves (3A) in dimethylacetamide under anhydrous conditions at 110 °C utilizing the protocol of Nucleosides & Nucleotides 1990 9, 89.
  • the solvent will be removed under vacuum and the residue purified by silica gel chromatography to give a 3'-(benzylcarbazat) ethyl intermediate.
  • the intermediate carbazat is treated with palladium on charcoal in anhydrous MeOH/HCl (2% HCl by weight) under an atmosphere of hydrogen.
  • the reaction mixture is filtered and the solvent evaporated under vacuum.
  • the dimer 73 is converted to its phosphoramidite as per the phosphitylation procedure of Example 15 to give the title compound, 74.
  • (+)-1- [1R,3S,4S)-3-azido-4-(hydroxymethyl)cyclopentyl]-5-methyl-2,4-(1H,3H)-pyrimidindione (75) is prepared as per the procedure of Bodenteich, M. and Griengl, H., Tetrahedron Letts . 1987 28 , 5311.
  • This 3-azido carbocyclic analogue of thymidine will be treated as per the procedures of Examples 1 and 2 to blocking both the base portion and the 5'-hydroxy moiety of the pseudo sugar portion to give the title compound, 76.
  • Compound 80 is de-blocked as per the procedures of
  • Compound 82 will be treated with N-(ß-chloroethyl)phthalimide (Chem Service Inc., West Chester, PA) to give the title compound, 83.
  • the dimer 87 is converted to its phosphoramidite as per the phosphitylation procedure of Example 15 to give the title compound, 88.
  • Compound 10 is converted to the chloroethyl derivative with triphenylphosphine and carbon tetrachloride in DMF via the procedure of Verheydan, J.P.H. and Moffatt, J.G. J. Org. Chem. 1972 37, 2289 to give the title compound, 89.
  • Compound 39 is converted to the chloropropyl derivative with triphenylphosphine and carbon tetrachloride in DMF via the procedure of Verheydan, J.P.H. and Moffatt, J.G. J. Org. Chem. 1972 37, 2289 to give the title compound, 90.
  • Thymidine was converted to its 5'-O-trityl derivative with trityl chloride in pyridine in the normal manner followed by blocking of the 3'-hydroxyl with a t-butyldiphenylsilyl group utilizing the protocol of Example 1. Treatment with aqueous acetic acid at 80° C gives the title compound, 95.
  • Compound 100 is treated as per the procedure of Step 1 of Example 1 of PCT published application WO 91/06629 (or via the procedure of Mattecuui, M., Tet. Letts . 1990 31 , 2385) to give the title compound, 101.
  • Compound 100 will be treated with chloromethyl-t-butyl mercaptan to form the intermediate 3'-deoxy-3'-(tert-butylthiomethylhydroxymethyl-5'-O-(tert-butyldiphenylsilyl)thymidine followed by treatment with 5% trifluoroacetic acid to give the title compound, 103.
  • this compound can be prepared as per the procedure of Divakar, et. al., J. Chem. Soc. Perkin . Trans . 1 1990, 969.
  • the compound was identified by a reduction in its R f on a TLC.
  • the compound proved to be unstable to isolation. It is therefore further used directly in situ following its preparation.
  • 5'-O-(tert-butyldiphenylsilyl) thymidine is substituted for the 5'-O-trityl thymidine starting material of the reference to prepare the title compound, 105.
  • Compound 106 is treated with tetrazole diisopropylamine salt (35 mg, 0.2 mmol) and 2-cyanoethyl-N,N,N',N'-tetra- isopropylphosphorodiamidite as per Example 15 to give the title compound, 107.
  • the P III compound 108 from Example 106 will be oxidized to the P v phosphate in the normal manner utilized for normal solid state oligonucleotide synthesis (see Oligonucleotide synthesis, a practical approach, Gait, M.J.Ed, IRL Press, Oxford Press 1984) to give the title compound, 109.
  • the P III compound 108 from Example 106 will be oxidized with the Beaucage reagent to the P v thiophosphate in the normal manner utilized for normal solid state phosphorothioate oligonucleotide synthesis (see Oligonucleotide synthesis, a practical approach, Eckstein, F. Ed, IRL Press, Oxford Press 1991) to give the title compound, 110.
  • EXAMPLE 109
  • Compound 106 will be treated 2-cyanoethyl N,N-diisopropylmonochlorophosphoramidite as per the procedure of Cosstick, R. and Vyle, J.S. Nucleic Acids Research 1990 18, 829 to yield the title compound, 120.
  • the P III compound 121 from Example 118 will be oxidized to the P v phosphate using tetrabutylammonium periodate as the oxidization agent to give the title compound, 122.
  • the P III compound 121 from Example 118 will be oxidized with sulfur to the P v thiophosphate as per the procedure of Cosstick, R. and Vyle, J.S. Nucleic Acids Research 1990 18, 829 to give the title compound 123.
  • Adenine is condensed with 1,2,3,5-tetra-O-acetyl-D-xylopentofuranoside in the presence of TiCl 4 as the condensation catalyst in a polar solvent utilizing the method of Szarek, W.A., Ritchie, R.G.S., and Vyas, D.M. (1978), Carbohydr. Res . , 62:89.
  • 8-Mercaptoadenine is alkylated with 5-deoxy-5-iodo- 1,2-O-isopropylidine-xylofuranose followed by treatment with acetic acid/acetic anhydride/sulfuric acid and then ammonia. This yields an 8-5'-anhydro intermediate nucleoside that is oxidized with aqueous N-bromosuccinimide to give the sulfoxide.
  • uracil is condensedwith 1,3,5-tri-O-acetyl-2-deoxy-2-methoxy-D-threo-pentofuranoside to yield the title compound.
  • cytosine is condensed with 1,3,5-tri-O-acetyl-2-deoxy-2-O-allyl-D-threo-pentofuranoside to yield the title compound.
  • guanine is condensed with 1,2,3,5-tetra-O-acetyl-D-xylopentofuranoside to yield the title compound.
  • 5-Amino-4,6-dichloropyrimidine is treated with ( ⁇ )-4 ⁇ -amino-2 ⁇ ,3ß-dihydroxy-1 ⁇ -cyclopentanemethanol to give a pyrimidine intermediate that is aminated and ring closed to yield the carbocyclic analog of xylofuranosyladenine as per the procedure of Vince, R. and Daluge, S. (1972), J. Med. Chem . , 15:171.
  • uracil is condensed with 1,3,5,-tri-O-acetyl-2-deoxy-2-fluoro-D-threo-pentofuranoside to yield the title compound.
  • cytosine is condensed with 1,3,5,-tri-O-acetyl-2-deoxy-2-fluoro-D-threo- pentofuranoside to yield the title compound.
  • Compound 126 will be treated with DMT-C1 in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p- toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L. (1965), J. Org. Chem. , 30:3401 to yield the 3'-tosyl protected xylo nucleoside intermediate.
  • Compound 125 will be treated with NaH to extract the hydroxyl proton and further treated with the above 3'-tosyl protected xylo nucleoside intermediate to yield the title compound.
  • Compound 127 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L. (1965), J. Org. Chem. , 30:3401 to yield the 3'-tosyl protected xylo nucleoside intermediate.
  • Compound 125 will be treated with NaH to extract the hydroxyl proton and further treated with the above 3'-tosyl protected xylo nucleoside intermediate to yield the title compound.
  • EXAMPLE 139 EXAMPLE 139
  • Compound 128 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L.
  • Compound 129 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L.
  • Compound 130 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p- toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L.
  • Compound 131 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with ptoluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L. (1965), J. Org. Chem., 30:3401 to yield the 3'-tosyl protected xylo nucleoside intermediate.
  • Compound 125 will be treated with NaH to extract the hydroxyl proton and further treated with the above 3'-tosyl protected xylo nucleoside intermediate to yield the title compound.
  • EXAMPLE 143 EXAMPLE 143
  • Compound 132 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMD protected intermediate will be treated with p- toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L. (1965), J. Org. Chem . , 30:3401 to yield the 3'-tosyl protected xylo nucleoside intermediate.
  • Compound 125 will be treated with NaH to extract the hydroxyl proton and further treated with the above 3'-tosyl protected xylo nucleoside intermediate to yield the title compound.
  • Compound 133 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5' -DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L. (1965), J. Org. Chem . , 30:3401 to yield the 3'-tosyl protected xylo nucleoside intermediate.
  • Compound 125 will be treated with NaH to extract the hydroxyl proton and further treated with the above 3'-tosyl protected xylo nucleoside intermediate to yield the title compound.
  • Compound 134 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of
  • Compound 135 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L. (1965), J. Org. Chem . , 30:3401 to yield the 3'-tosyl protected xylo nucleoside intermediate.
  • Compound 125 will be treated with NaH to extract the hydroxyl proton and further treated with the above 3'-tosyl protected xylo nucleoside intermediate to yield the title compound.
  • Compound 136 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of
  • Compound 137 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L.
  • Compound 138 will be treated with DMT-C1 in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p-toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L.
  • Compound 139 will be treated with DMT-Cl in pyridine and Et 3 N as per the procedure of Example 14.
  • the 5'-DMT protected intermediate will be treated with p- toluenesulfonylchloride in pyridine as per the procedure of Reist, E.J., Bartuska, V.J., Calkins, D.F., and Goodman, L.
  • Compound 119 is treated as per the procedure of Step 1 of Example 1 of PCT published application WO 91/06629 (or via the procedure of Mattecuui, M., Tet. Letts. 1990 31, 2385) to give the title compound, 157.
  • 3-(Aden-9-yl)-5-hydroxy-1,2-cyclopentene obtained from the coupling of cyclopentene epoxide and adenine according to the method of Trost, et. al., J. Am. Chem . Soc . 1988, 110, 621-622, is successively silylated, benzoylated, and tritylated according to standard procedures to provide 3-(N6-benzoyladenyl)- 5-triphenylmethoxyl-1,2-cyclopentene.
  • Cis-hydroxylation and selective t-butyldimethylsilylation provides the 2'- O-t-butyldimethylsilyl derivative.
  • CPG control-glass pore silica gel
  • the final product 4'-desmethyl-4'-O-t-butoxyethyl-2'-t-butyldimethylsilyl-3'-CPG-N6-benzoyl adenine
  • the CPG-bound 4'-desmethyl ribonucleosides can be converted to their 2'-deoxy forms by the successive treatment of the polymer with tetrabutyl ammonium fluoride, thiocarbonylimidazole, and tributyl tin hydride. These procedures are appropriate for the preparation of CPG bound carbocyclic 4' -desmethyl derivatives of the other natural occurring bases or nucleic acids base analogs.
  • 3-(Aden-9-yl)-5-hydroxy-1,2-cyclopentene obtained from the coupling of cyclopentene epoxide and adenine according to Trost, et al . is successively silylated, benzoylated, and tritylated according to standard procedures to provide 3 - ( N 6 -benzoyladenyl ) - 5 - triphenylmethoxy- 1 , 2 - cyclopentene .
  • Cis-hydroxylation and selective t-butyldimethylsilylation provides the 2'-O-t-butyldimethylsilyl derivative.
  • This material is treated with trichloroacetonitrile and sodium hydride in dry acetonitrile to afford the a trichloroacetimidate which is subsequently SN2 displaced by water.
  • Preparation and reactivity of trichloroacetimidates has been described.
  • the resulting ⁇ -3'-hydroxyl group is activated for SN-2 reaction by the action of trichloroacetonitrile/ sodium hydride.
  • the ⁇ -3 '-hydroxy group may also be activated for SN2 reactions by the treatment with trifluoromethanesulfonic acid anhydride and pyridine.
  • This procedure provides the triflate group in the -3' -position of the 4'-desmethyl-4'-O-t-butoxyethyl-2'-t-butyldimethylsilyl-N 6 - benzoyl adenine.
  • This procedure is of a general nature and can be applied to the synthesis of any carbocyclic 4'-desmethyl- ribonucleoside.
  • the carbocyclic nucleoside antibiotic (-)-neplanocin A obtained from fermentation or total synthesis; Johnson, et. al . , Tet . Lett . 1987, 28, 4131; base analogs of (-) -neplanocin, Biggadike, A., et al . , J. Chem . Soc , Chem . Comm . 1990, 458 as its N 6 -benzoyl derivative is reduced with a borane reagent and then protected as its isopropylidine.
  • the unprotected 5'-hydroxyl is oxidized with oxygen and platinum oxide, and subsequent, reductive decarboxylation with lead tetraacetate provides 4'-desmethyl carbocyclic adenosine.
  • This oxidation/reduction closely follows a known procedures.
  • the 4'-desmethyl carbocyclic adenosine 2,3-isopropylidine is successively treated with t-butoxyethyl bromide and pyridine, mild acid, and t-butyldimethysilyl chloride in pyridine to afford the 4'-desmethyl carbocyclic derivative with an ⁇ - 3'-hydroxyl group unprotected.
  • This intermediate was described in paragraph A. Conversion into an activated ⁇ -3 '-leaving group is described in paragraph B.
  • 4-p-Tosylate-1,2-cyclopentene is treated with appropriately protected bases to afford cyclopentenylated bases of the natural nucleoside bases or analogs of the nucleic acids bases.
  • Hindered face ( ⁇ -face) hydroxylation provides 3,4-dihydroxy cyclopentyl-protected bases which are treated with t-butoxyethyl bromide and the isomers are separated by chromatography.
  • the appropriate isomer is treated with trichloroacetonitrile and sodium hydride in acetonitrile to provide 4'-desmethyl-4'-O-t-butoxyethyl-3'-O-trichloroacetimidyl-2'-deoxy carbocyclic nucleosides.
  • CPG-bound ribo or 2'-deoxyribonucleosides are treated with oxygen saturated acetonitrile and platinum oxide to provide the 4'-desmethyl- 4'-carboxylate derivative.
  • the CPG column is treated with lead tetraacetate to reductively decarboxylate the bound nucleoside.
  • the resultant 4'-hydroxyl group is alkylated with t-butoxyethyl bromide in pyridine to provide CPG-bound 4'-desmethyl-4'-O-t-butoxyethyl-2'-deoxy (or 2'-t-butyldimethylsilyl) nucleosides.
  • 3'-O-position by standard procedures such as the 2',3'-O- isopropylidinyl or 3'-O-benzoyl were successively oxidized and reduc.tively decarboxy1ated with oxygen/platinum oxide and LTA to afford a 4'-hydroxyl group.
  • These protected nucleosides are converted to their 4'-desmethyl-4'- O-t-butoxyethyl derivatives by treatment with t-butoxyethyl bromide and pyridine.
  • the appropriately CPG-bound 4' -desmethylnucleoside (ribo or 2'-deoxyribo or carbocyclic ribo or 2'-deoxyribo) that will become the 3'-terminal base is placed in an Applied Biosystems, Inc. (ABI) column and attached to an ABI 380B automated DNA Synthesizer.
  • the automated (computer controlled) steps of a cycle that is required to couple a desmethyl nucleoside unit to the growing chain is as follows.
  • polyethylene glycols PEGs
  • terminal alkyl bromides or phthaloyl and trifluoroacetyl protected polyalkyl amines with terminal alkyl bromides are reacted with the CPG-bound oligonucleoside in the presence of base.
  • Deprotection, workup, and purification provides 4'-polyethylene glycol or 4'-polyamines nucleosides and carbocyclic nucleosides linked via ethylene glycol moieties.
  • T*T represents the dimer 14.
  • the DMT protected phosphoramidite activated dimer 16 was use in the normal manner as a standard amidite during the synthesis. Coupling efficiencies were greater than 96% for each step of the synthesis with the overall coupling efficiency greater than 91% for the oligomer. The resulting oligomer was characterized by both gel chromatography and by HPLC using standard protocols. EXAMPLE 164
  • Compound 97 is treated with (CH 3 ) 3 SiN 3 in the presence of a Lewis acid utilizing the procedure of Gyorgydeak, Z., Ling, I. and Bognar, R., Liebigs Ann. Chem. 1983 279 to give the title compound.
  • the P III compound 163 from Example 167 will be oxidized to the P v phosphate using tetrabutylammonium periodate as the oxidization agent to give the title compound, 164.
  • the P III compound 163 from Example 167 will be oxidized with sulfur to the P v thiophosphate as per the procedure of Cosstick, R. and Vyle, J.S. Nucleic Acids Research 199018, 829 to give the title compound 165.
  • Tr Tr
  • 6.85 - 6.82 m, 4 H, Tr
  • Compound 187 was further used to prepare a 5 atom phosphate linkage between adjacent nucleosides that corresponds to a normal phosphate linkage with the exception that an additional methylene group is positioned immediately adjacent the 3' carbon atom of the sugar ring of the 5'-terminus nucleoside and repositions the oxygen atom that would normally occupy that position one atom further away from that sugar 3' carbon atom.
  • Oligonucleotides incorporating this linkage were prepared utilizing standard solid state phosphoramidite synthesis procedures on a standard DNA synthesizer. Compound 187 was used in the normal manner as the phosphoramidite being added during the appropriate cycle of the synthesizer.
  • oligonucleotides containing this linkage were prepared, including the oligonucleotides of the sequence:
  • Oligonucleotide-mimicking macromolecules of the invention can be assessed for their resistance to serum nucleases by incubation of the oligonucleotide-mimicking macromolecules in media containing various concentrations of fetal calf serum or adult human serum. Labeled oligonucleotide-mimicking macromolecules are incubated for various times , treated with protease K and then analyzed by gel electrophoresis on 20% polyacrylamine-urea denaturing gels and subsequent autoradiography . Autoradiograms are quantitated by laser densitometry .
  • cytoplasmic nucleases an HL 60 cell line can be used for the cytoplasmic nucleases .
  • a post -mitochondrial supernatant is prepared by differential centrifugation and the labelled macromolecules are incubated in this supernatant for various times .
  • macromolecules are assessed for degradation as outlined above for serum nucleolytic degradation .
  • Autoradiography results are quantitated for evaluation of the macromolecules of the invention . It is expected that the macromolecules will be completely resistant to serum and cytoplasmic nucleases .
  • oligonucleotides and oligonucleotide-mimicking macromolecules of the invention can be done to determine the exact effect of the macromolecule linkage on degradation .
  • the oligonucleotide-mimicking macromolecules are incubated in defined reaction buffers specific for various selected nucleases. Following treatment of the products with protease K, urea is added and analysis on 20% polyacrylamide gels containing urea is done.
  • an animal suspected of having a disease characterized by excessive or abnormal supply of 5-lipoxygenase is treated by administering the macromolecule of the invention.
  • Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Such treatment is generally continued until either a cure is effected or a diminution in the diseased state is achieved. Long term treatment is likely for some diseases.
  • the oligonucleotide-mimicking macromolecules of this invention will also be useful as research reagents when used to cleave or otherwise modulate 5-lipoxygenase mRNA in crude cell lysates or in partially purified or wholly purified RNA preparations.
  • This application of the invention is accomplished, for example, by lysing cells by standard methods, optimally extracting the RNA and then treating it with a composition at concentrations ranging, for instance, from about 100 to about 500 ng per 10 Mg of total RNA in a buffer consisting, for example, of 50 mm phosphate, pH ranging from about 4-10 at a temperature from about 30° to about 50° C.
  • the cleaved 5-lipoxygenase RNA can be analyzed by agarose gel electrophoresis and hybridization with radiolabeled DNA probes or by other standard methods.
  • the oligonucleotide-mimicking macromolecules of the invention will also be useful in diagnostic applications, particularly for the determination of the expression of specific mRNA species in various tissues or the expression of abnormal or mutant RNA species.
  • the macromolecules target a abnormal mRNA by being designed complementary to the abnormal sequence, they would not hybridize to normal mR ⁇ A.
  • Tissue samples can be homogenized, and RNA extracted by standard methods.
  • the crude homogenate or extract can be treated for example to effect cleavage of the target R ⁇ A.
  • the product can then be hybridized to a solid support which contains a bound oligonucleotide complementary to a region on the 5' side of the cleavage site. Both the normal and abnormal 5' region of the mR ⁇ A would bind to the solid support.
  • the 3' region of the abnormal RNA, which is cleaved, would not be bound to the support and therefore would be separated from the normal mR ⁇ A.
  • Targeted mR ⁇ A species for modulation relates to 5lipoxygenase; however, persons of ordinary skill in the art will appreciate that the present invention is not so limited and it is generally applicable.
  • the inhibition or modulation of production of the enzyme 5-lipoxygenase is expected to have significant therapeutic benefits in the treatment of disease.
  • an assay or series of assays is required.
  • the cellular assays for 5-lipoxygenase preferably use the human promyelocytic leukemia cell line HL-60. These cells can be induced to differentiate into either a monocyte like cell or neutrophil like cell by various known agents. Treatment of the cells with 1.3% dimethyl sulfoxide, DMSO, is known to promote differentiation of the cells into neutrophils. It has now been found that basal HL-60 cells do not synthesize detectable levels of 5-lipoxygenase protein or secrete leukotrienes (a downstream product of 5-lipoxygenase). Differentiation of the cells with DMSO causes an appearance of 5-lipoxygenase protein and leukotriene biosynthesis 48 hours after addition of DMSO. Thus induction of 5-lipoxygenase protein synthesis can be utilized as a test system for analysis of oligonucleotide-mimicking macromolecules which interfere with 5-lipoxygenase synthesis in these cells.
  • a second test system for oligonucleotide-mimicking macromolecules makes use of the fact that 5-lipoxygenase is a "suicide" enzyme in that it inactivates itself upon reacting with substrate.
  • 5-lipoxygenase is a "suicide" enzyme in that it inactivates itself upon reacting with substrate.
  • Treatment of differentiated HL-60 or other cells expressing 5 lipoxygenase, with 10 ⁇ M A23187, a calcium ionophore promotes translocation of 5-lipoxygenase from the cytosol to the membrane with subsequent activation of the enzyme. Following activation and several rounds of catalysis, the enzyme becomes catalytically inactive.
  • treatment of the cells with calcium ionophore inactivates endogenous 5-lipoxygenase.
  • Macromolecules directed against 5-lipoxygenase can be tested for activity in two HL-60 model systems using the following quantitative assays. The assays are described from the most direct measurement of inhibition of 5-lipoxygenase protein synthesis in intact cells to more downstream events such as measurement of 5-lipoxygenase activity in intact cells.
  • a direct effect which oligonucleotide-mimicking macromolecules can exert on intact cells and which can be easily be quantitated is specific inhibition of 5-lipoxygenase protein synthesis.
  • cells can be labelled with 35 S-methionine (50 ⁇ Ci/mL) for 2 hours at 37°C to label newly synthesized protein.
  • Cells are extracted to solubilize total cellular proteins and 5-lipoxygenase is immunoprecipitated with 5-lipoxygenase antibody followed by elution from protein A Sepharose beads.
  • the immunoprecipitated proteins are resolved by SDS-polyacrylamide gel electrophoresis and exposed for autoradiography.
  • the amount of immunopre cipitated 5-lipoxygenase is quantitated by scanning densitometry.
  • a predicted result from these experiments would be as follows.
  • the amount of 5-lipoxygenase protein immunoprecipitated from control cells would be normalized to 100%.
  • Treatment of the cells with 1 ⁇ M, 10 ⁇ M, and 30 ⁇ M of the macromolecules of the invention for 48 hours would reduce immunoprecipitated 5-lipoxygenase by 5%, 25% and 75% of control, respectively.
  • Cytosolic proteins are incubated with 10 ⁇ M 14 C-arachidonic acid, 2mM ATP, 50 ⁇ M free calcium, 100 ⁇ g/ml phosphatidylcholine, and 50 mM bis-Tris buffer, pH 7.0, for 5 min at 37° C.
  • the reactions are quenched by the addition of an equal volume of acetone and the fatty acids extracted with ethyl acetate.
  • the substrate and reaction products are separated by reverse phase HPLC on a Novapak C18 column (Waters Inc., Millford, MA). Radioactive peaks are detected by a Beckman model 171 radiochromatography detector. The amount of arachidonic acid converted into diHETE's and mono-HETE's is used as a measure of 5-lipoxygenase activity.
  • a predicted result for treatment of DMSO differentiated HL-60 cells for 72 hours with effective the macromolecules of the invention at 1 ⁇ M, 10 ⁇ M, and 30 ⁇ M would be as follows. Control cells oxidize 200 pmol arachidonic acid/5 min/10 6 cells. Cells treated with 1 ⁇ M, 10 ⁇ M, and 30 ⁇ M of an effective oligonucleotide-mimicking macromolecule would oxidize 195 pmol , 140 pmol , and 60 pmol of arachidonic acid/5 min/10 6 cells respectively.
  • a quantitative competitive enzyme linked immunosorbant assay (ELISA) for the measurement of total 5-lipoxygenase protein in cells has been developed. Human 5-lipoxygenase expressed in E.
  • coli and purified by extraction, Q-Sepharose, hydroxyapatite, and reverse phase HPLC is used as a standard and as the primary antigen to coat microtiter plates. 25 ng of purified 5-lipoxygenase is bound to the microtiter plates overnight at 4° C. The wells are blocked for 90 min with 5% goat serum diluted in 20 mM Tris ⁇ HCL buffer, pH 7.4, in the presence of 150 mM NaCl (TBS).
  • Cell extracts (0.2% Triton X- 100, 12,000 ⁇ g for 30 min.) or purified 5-lipoxygenase were incubated with a 1:4000 dilution of 5-lipoxygenase polyclonal antibody in a total volume of 100 ⁇ L in the microtiter wells for 90 min.
  • the antibodies are prepared by immunizing rabbits with purified human recombinant 5-lipoxygenase.
  • the wells are washed with TBS containing 0.05% tween 20 (TBST), then incubated with 100 ⁇ L of a 1:1000 dilution of peroxidase conjugated goat anti-rabbit IgG (Cappel Laboratories, Malvern, PA) for 60 min at 25° C.
  • the wells are washed with TBST and the amount of peroxidase labelled second antibody determined by development with tetramethylbenzidine.
  • Predicted results from such an assay using a 30 mer oligonucleotide-mimicking macromolecule at 1 ⁇ M, 10 ⁇ M, and 30 ⁇ M would be 30 ng, 18 ng and 5 ng of 5-lipoxygenase per 10 6 cells, respectively with untreated cells containing about 34 ng 5-lipoxygenase.
  • a net effect of inhibition of 5-lipoxygenase biosynthesis is a diminution in the quantities of leukotrienes released from stimulated cells.
  • DMSO-differentiated HL-60 cells release leukotriene B4 upon stimulation with the calcium ionophore A23187.
  • Leukotriene B4 released into the cell medium can be quantitated by radioimmunoassay using commercially available diagnostic kits (New England Nuclear, Boston, MA).
  • Leukotriene B4 production can be detected in HL-60 cells 48 hours following addition of DMSO to differentiate the cells into a neutrophil-like cell. Cells (2 ⁇ 10 5 cells/mL) will be treated with increasing concentrations of the macromolecule for 48-72 hours in the presence of 1.3% DMSO.
  • the cells are washed and resuspended at a concentration of 2 ⁇ 10 6 cell/mL in Dulbecco's phosphate buffered saline containing 1% delipidated bovine serum albumin. Cells are stimulated with 10 ⁇ M calcium ionophore A23187 for 15 min and the quantity of LTB4 produced from 5 ⁇ 10 5 cell determined by radioimmunoassay as described by the manufacturer.
  • Inhibition of the production of 5-lipoxygenase in the mouse can be demonstrated in accordance with the following protocol.
  • Topical application of arachidonic acid results in the rapid production of leukotriene B 4 , leukotriene C 4 and prostaglandin E 2 in the skin followed by edema and cellular infiltration.
  • Certain inhibitors of 5-lipoxygenase have been known to exhibit activity in this assay.
  • 2 mg of arachidonic acid is applied to a mouse ear with the contralateral ear serving as a control.
  • the polymorphonuclear cell infiltrate is assayed by myeloperoxidase activity in homogenates taken from a biopsy 1 hour following the administration of arachidonic acid.
  • the edematous response is quantitated by measurement of ear thickness and wet weight of a punch biopsy. Measurement of leukotriene B 4 produced in biopsy specimens is performed as a direct measurement of 5-lipoxygenase activity in the tissue. Oligonucleotide-mimicking macromolecules will be applied topically to both ears 12 to 24 hours prior to administration of arachidonic acid to allow optimal activity of the compounds. Both ears are pretreated for 24 hours with either 0.1 ⁇ mol, 0.3 ⁇ mol, or 1.0 ⁇ mol of the macromolecule prior to challenge with arachidonic acid. Values are expressed as the mean for three animals per concentration.
  • Inhibition of polymorphonuclear cell infiltration for 0.1 ⁇ mol, 0.3 ⁇ mol, and 1 ⁇ mol is expected to be about 10%, 75% and 92% of control activity, respectively.
  • Inhibition of edema is expected to be about 3%, 58% and 90%, respectively while inhibition of leukotriene B 4 production would be expected to be about 15%, 79% and 99%, respectively.

Abstract

L'invention se rapporte à des macromolécules imitant les oligonucléotides, qui sont pourvues d'une plus grande résistance aux nucléases. Le remplacement des liaisons inter-sucres de phosphorodiester normales se trouvant dans les oligonucléotides naturels par quatre groupes de liaison d'atomes permettent de former des composés uniques qui sont utiles dans la régulation de l'expression d'ARN et à des fins thérapeutiques. Des procédés de synthèse et d'utilisation sont également décrits.
PCT/US1994/003536 1990-07-27 1994-03-30 Liaisons par oligonucleocides heteroatomiques WO1994022886A1 (fr)

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US7544794B1 (en) * 2005-03-11 2009-06-09 Steven Albert Benner Method for sequencing DNA and RNA by synthesis
JP5645840B2 (ja) 2008-12-02 2014-12-24 株式会社Ｗａｖｅ Ｌｉｆｅ Ｓｃｉｅｎｃｅｓ Ｊａｐａｎ リン原子修飾核酸の合成方法
WO2011005761A1 (fr) 2009-07-06 2011-01-13 Ontorii, Inc Nouveaux précurseurs d'acide nucléique et leurs méthodes d'utilisation
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US9605019B2 (en) 2011-07-19 2017-03-28 Wave Life Sciences Ltd. Methods for the synthesis of functionalized nucleic acids
EP2872485B1 (fr) 2012-07-13 2020-12-16 Wave Life Sciences Ltd. Groupe auxiliaire asymétrique
BR112016016400A2 (pt) 2014-01-16 2017-10-03 Wave Life Sciences Ltd Composições de oligonucleotídeos quiralmente controlados, seu uso, sua composição farmacêutica, e métodos

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