WO2009051712A1 - Dnai amphoteric liposome formulation - Google Patents

Dnai amphoteric liposome formulation Download PDF

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Publication number
WO2009051712A1
WO2009051712A1 PCT/US2008/011748 US2008011748W WO2009051712A1 WO 2009051712 A1 WO2009051712 A1 WO 2009051712A1 US 2008011748 W US2008011748 W US 2008011748W WO 2009051712 A1 WO2009051712 A1 WO 2009051712A1
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Prior art keywords
mixture
dnai
mole
lipid
liposomes
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PCT/US2008/011748
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French (fr)
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Wendi Rodrigueza
Neal Clifford Goodwin
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Pronai Therapeutics, Inc.
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Publication of WO2009051712A1 publication Critical patent/WO2009051712A1/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/10—Dispersions; Emulsions
    • A61K9/127—Liposomes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/0008—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'non-active' part of the composition delivered, e.g. wherein such 'non-active' part is not delivered simultaneously with the 'active' part of the composition
    • A61K48/0025—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'non-active' part of the composition delivered, e.g. wherein such 'non-active' part is not delivered simultaneously with the 'active' part of the composition wherein the non-active part clearly interacts with the delivered nucleic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/14—Particulate form, e.g. powders, Processes for size reducing of pure drugs or the resulting products, Pure drug nanoparticles
    • A61K9/19—Particulate form, e.g. powders, Processes for size reducing of pure drugs or the resulting products, Pure drug nanoparticles lyophilised, i.e. freeze-dried, solutions or dispersions
    • 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
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1135—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against oncogenes or tumor suppressor genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3515—Lipophilic moiety, e.g. cholesterol
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/30—Special therapeutic applications
    • C12N2320/32—Special delivery means, e.g. tissue-specific

Definitions

  • the invention relates to compositions and methods of using the same to treat cancer.
  • the invention provides oligonucleotides sequestered with stable, size-selected amphoteric liposomes for the treatment of cancer.
  • Oncogenes have become the central concept in understanding cancer biology and may provide valuable targets for therapeutic drugs.
  • the oncogenes are overexpressed, and may be associated with tumorigenicity (Tsujimoto et al, Science 228:1440-1443 (1985)).
  • tumorigenicity Tujimoto et al, Science 228:1440-1443 (1985)
  • high levels of expression of the human bcl-2 gene have been found in all lymphomas with a t(14; 18) chromosomal translocations including most follicular B cell lymphomas and many large cell non-Hodgkin's lymphomas.
  • oncogenes include TGF- ⁇ , c-ki-ras, ras, Her-2 and c-myc. [003] The expression of oncogenes may be inhibited by single stranded DNAi oligonucleotides. Nucleic acid therapeutics, however, often lack therapeutic efficacy due to instability in body fluids or inefficient uptake into cells.
  • the invention provides compositions and methods for preparing and using liposomes for the delivery of DNAi oligonucleotides for the treatment of cancer.
  • the invention relates to liposomes that have an amphoteric character, e.g., the liposomes have an anionic or neutral charge at physiological pH and a cationic charge at an acidic pH of about 4.
  • the invention also relates to size selected DNAi-amphoteric liposomal mixtures that are stable over time.
  • the amphoteric liposomes of the present invention exhibit high sequestration efficiency, where the DNAi liposomes have a final DNAi oligonucleotide concentration between about 1 to 4 mg/mL (e.g., about 2 mg/mL) at a lipid concentration of about 100 mM or less; colloidal and serum stability; enhanced uptake into cells and tumors due to average liposome sizes of less than 200 ⁇ m; and low toxicity relative to liposomes formed with cationic lipids that are used in conventional transfection reagents.
  • a final DNAi oligonucleotide concentration between about 1 to 4 mg/mL (e.g., about 2 mg/mL) at a lipid concentration of about 100 mM or less
  • colloidal and serum stability e.g., about 2 mg/mL
  • enhanced uptake into cells and tumors due to average liposome sizes of less than 200 ⁇ m
  • amphoteric liposomes containing a DNAi oligonucleotide and a cryoprotectant, a lyoprotectant and/or a stabilizer may be frozen and thawed and/or lyophilized and reconstituted, and retain efficacy in treating tumors.
  • DNAi-amphoteric liposomes have a defined average diameter and a low polydispersity index, which have improved efficacy in treating tumors.
  • the invention provides amphoteric liposomes, a DNAi oligonucleotide and a cryoprotectant and/or lyoprotectant.
  • the cryoprotectant and/or lyoprotectant is a disaccharide.
  • the cryoprotectant and/or lyoprotectant is mannitol, sucrose or trehalose, or a combination thereof.
  • the cryoprotectant is a combination of two or more cryoprotectants.
  • the amphoteric liposomes have an isoelectric point of between 4 and 8. In a further embodiment, the amphoteric liposomes are negatively charged or neutral at pH 7.4 and positively charged at pH 4. [008] In yet another embodiment of the first aspect, the amphoteric liposomes include amphoteric lipids. In a further embodiment, the amphoteric lipids can be HistChol, HistDG, isoHistSucc DG, Acylcarnosine, HCChol or combinations thereof. In another embodiment, the amphoteric liposomes include a mixture of one or more cationic lipids and one or more anionic lipids.
  • the cationic lipids can be DMTAP, DPTAP, DOTAP, DC-Choi, MoChol and HisChol, or combinations thereof
  • the anionic lipids can be CHEMS, DGSucc, Cet-P, DMGSucc, DOGSucc, POGSucc, DPGSucc, DG Succ, DMPS, DPPS, DOPS, POPS, DMPG, DPPG, DOPG, POPG, DMPA, DPPA, DOPA, POPA or combinations thereof.
  • the liposomes also include neutral lipids.
  • the neutral lipids include sterols and derivatives thereof.
  • the sterols comprise cholesterol and derivatives thereof.
  • the neutral lipids may also include neutral phospholipids.
  • the phospholipids include phosphatidylcholines or phosphatidylcholines and phosphoethanolamines.
  • the phosphatidylcholines are POPC, OPPC, natural or hydrogenated soy bean PC, natural or hydrogenated egg PC, DMPC, DPPC or DOPC and derivatives thereof and the phosphatidylethanolamines are DOPE, DMPE, DPPE or derivatives and combinations thereof.
  • the phosphatidylcholine is POPC, OPPC, soy bean PC or egg PC and the phosphatidylethanolamines is DOPE.
  • the lipids of the amphoteric liposomes include DOPE, POPC, CHEMS and MoChol; POPC, Choi, CHEMS and DOTAP; POPC, Choi, Cet-P and MoChol, or POPC, DOPE, MoChol and DMGSucc.
  • the DNAi-amphoteric liposomes can be formed from a lipid phase comprising a mixture of lipid components with amphoteric properties, wherein the total amount of charged lipids in the liposome can vary from 5 mole % to 70 mole %, the total amount of neutral lipids may vary from 20 mole % to 70 mole %, a DNAi oligonucleotide and a cryoprotectant.
  • the amphoteric liposomes include 3 to 20 mole % of POPC, 10 to 60 mole % of DOPE, 10 to 60 mole % of MoChol and 10 to 60 mole % of CHEMS.
  • the liposomes include POPC, DOPE, MoChol and CHEMS in the molar ratios of POPC/DOPE/MoChol/CHEMS of about 6/24/47/23 or 15/45/20/20.
  • the liposomes include 3 to 20 mole % of POPC, 10 to 40 mole % of DOPE, 15 to 60 mole % of MoChol and 15 to 60 mole % of DMGSucc.
  • the liposomes include POPC, DOPE, DMGSucc and MoChol in the molar ratios of POPC/DOPE/DMGSucc/MoChol of about 6/24/47/23 or 6/24/23/47.
  • the liposomes include 10 to 50 mole % of POPC, 20 to 60 mole % of Choi, 10 to 40 mole % of CHEMS and 5 to 20 mole % of DOTAP.
  • the liposomes include POPC, Choi, CHEMS and DOTAP in the molar ratio of POPC/Chol/CHEMS/DOTAP of about 30/40/20/10.
  • the liposomes include 10 to 40 mole % of POPC, 20 to 50 mole % of Choi, 5 to 30 mole % of Cet-P and 10 to 40 mole % of MoChol.
  • the molar ratio of POPC/Chol/Cet-P/MoChol is about 35/35/10/20.
  • the DNAi oligonucleotide contained in the liposomal mixture comprises an oligomer that hybridizes to SEQ ID NO: 1249, the complement of SEQ ID NO: 1249 or portions thereof.
  • the oligomer can be SEQ ID NO: 1250, 1251, 1252, 1253, 1267-1447 or the complement thereof.
  • the oligomer can be SEQ ID NO: 1250 or 1251 or the complement thereof.
  • the liposomal mixture of this invention may include a second oligomer, e.g., comprising one of SEQ ED NOs: 2-281, 283-461, 463-935, 937-1080, and 1082-1248.
  • the DNAi oligonucleotide contained in the liposomal mixture comprises an oligomer that hybridizes to SEQ ID NO:936, the complement there of or portions thereof.
  • the oligomer has the sequence of SEQ ID NO:940 or
  • the DNAi oligonucleotide contained in the liposomal mixture comprises an oligomer that hybridizes to SEQ ED NO:1, SEQ ED NO:282, SEQ ED NO:462,
  • SEQ ED NO: 1081 or the complements thereof.
  • the oligonucleotides contained in the liposomal mixture are between
  • the liposome-oligonucleotide mixture includes SEQ ED NO: 1250 or
  • amphoteric liposomes comprising POPC, DOPE, MoChol and CHEMS in the molar ratio of POPC/DOPE/MoChol/CHEMS of about 6/24/47/23 and sucrose.
  • the liposome-oligonucleotide mixture includes SEQ ED NO: 1250 or 1251 and amphoteric liposomes comprising POPC, DOPE, MoChol and CHEMS in the molar ratio of POPC/DOPE/MoChol/CHEMS of about 15/45/20/20 and sucrose.
  • the DNAi-amphoteric liposome mixture has an average diameter between 70 and 150 ⁇ m. In one embodiment, the average diameter is between 90 and 130 ⁇ m. In another embodiment of the sixth aspect the DNAi-amphoteric liposomes have a polydispersity index of between 0 and 0.3, and in another embodiment, the polydispersity index is between 0 and 0.15.
  • the amphoteric liposomes have a DNAi oligonucleotide concentration of at least 2 mg/mL at a lipid concentration of 100 mM or less.
  • the invention provides a method of preparing amphoteric liposomes containing a DNAi oligonucleotide and a cryoprotectant.
  • the method comprises providing a lipid mixture in a solvent and an aqueous solution of one or more
  • DNAi oligonucleotides mixing the lipid mixture and the DNAi oligonucleotides by injecting the lipid mixture into the DNAi oligonucleotide solution, and adding a cryoprotectant.
  • the method further comprises diluting the lipid-DNAi oligonucleotide mixture with an aqueous buffer solution of about pH 8 to 10, or with an aqueous buffer solution to adjust the mixture to physiological pH.
  • the method further comprises extruding the lipid-DNAi oligonucleotide mixture through a membrane with a pore size of about 80 ⁇ m to about 300 ⁇ m.
  • the method further comprises passing the DNAi-amphoteric liposome mixture through a sterile 0.22 micron filter.
  • the method results in liposomes having an average diameter between 70 and 150 ⁇ m, having a polydispersity index between 0 and 0.3.
  • the method results in an encapsulation efficiency of at least 35%.
  • the invention provides a method of introducing the DNAi oligonucleotide-liposome mixture to cells or an animal.
  • the method includes administering the mixture to a mammal to treat cancer.
  • the administered mixtures can reduce or stop tumor growth in mammals.
  • the introduction of the mixture results in a reduction of cell proliferation.
  • the mixture is administered to a cancer cell, a non-human animal or a human.
  • the mixture is introduced to an animal at a dosage of between 1 mg to 100 mg per kg of body weight, or between 0.1 mg to 100 mg per kg of body weight, or between 0.01 mg to 100 mg per kg of body weight.
  • the mixture is introduced to the animal one or more times per day or continuously.
  • the mixture is introduced to the animal via topical, pulmonary or parenteral administration or via a medical device.
  • the mixture administered to the animal or cells further includes another known chemotherapy agent, and/or a cell targeting component.
  • Figure 1 shows an overview of the process for preparing DNAi-liposomes.
  • Figure 2 is a diagram of a crossflow process used to generate DNAi loaded liposomes.
  • Figure 3 shows graphs indicating the size and polydispersity indices of DNAi- liposomes treated with and without extrusion and filtration.
  • Figure 4 is a graph showing the size distribution of DNAi-liposomes after the steps in liposome production.
  • Figure 5 shows graphs of size distributions of liposomes after freeze-thaw cycles.
  • Figure 6 shows the effect of SEQ ID NO: 1251 sequestered in amphoteric liposomes on the size of tumors from non-Hodgkin's Lymphoma WSU-DLCL2 xenografts in SCID mice.
  • Figure 7 shows the effect of different lots of SEQ ID NO: 1251 sequestered in amphoteric liposomes on the size of tumors from non-Hodgkin's Lymphoma WSU-DLCL2 xenografts in SCID mice.
  • Figure 8 shows the tumor burden in mice carrying non-Hodgkin's Lymphoma WSU-
  • Figure 9 shows a dose response evaluation of two formulations of SEQ ID NO: 1251 sequestered in amphoteric liposomes on WSU-DLCL2 xenograft bearing mice.
  • Figure 10 shows an enlarged view of a dose response evaluation of two formulations of SEQ ID NO: 1251 sequestered in amphoteric liposomes on WSU-DLCL2 xenograft bearing mice.
  • Figure 11 shows a dose response animal body weight evaluation in WSU-DLCL2 xenograft bearing mice treated with two formulations of SEQ ID NO: 1251 sequestered in amphoteric liposomes.
  • Figure 12 shows the effect of SEQ ID NO: 1251 sequestered in amphoteric liposomes on the size of tumors from PC-3 xenografts in nude mice.
  • Figure 13 shows the effect of SEQ ID NO: 1251 sequestered in amphoteric liposomes on the growth rate of tumors from PC-3 xenografts in nude mice.
  • Figure 14 shows graphs showing the efficacy of frozen and thawed liposomes containing oligonucleotides of SEQ ID NO: 1251 in mice bearing xenografts Of WSU-DLCL 2 cells.
  • Figure 15 shows graphs showing weight response evaluation of liposomes containing oligonucleotides of SEQ ID NO: 1251 in mice bearing xenografts Of WSU-DLCL 2 cells.
  • Figure 16 shows graphs indicating the mean time to 750 mm 3 tumor endpoint values.
  • Figure 17 is a Kaplan-Meier plot showing animal survival to 2000 mm 3 tumor volume in response to treatment.
  • Figure 18A shows graphs showing the efficacy of frozen and thawed liposomes containing oligonucleotides of SEQ ID NO: 1251 at different dose regimens in mice bearing xenografts Of WSU-DLCL 2 cells.
  • Figure 18B is a Kaplan-Meier plot showing animal survival to 2000 mm 3 tumor volume in response to treatment.
  • Figure 18C shows a graph showing weight response evaluation of liposomes containing oligonucleotides of SEQ ED
  • aliphatic encompasses the terms alkyl, alkenyl, alkynyl, each of which being optionally substituted as set forth below.
  • an "alkyl” group refers to a saturated aliphatic hydrocarbon group containing 1-8 (e.g., 1-6 or 1-4) carbon atoms.
  • An alkyl group can be straight or branched. Examples of alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, n-heptyl or 2-ethylhexyl.
  • An alkyl group can be substituted (i.e., optionally substituted) with one or more substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, cycloaliphaticcarbonyl, (heterocycloaliphatic)carbonyl, nitro, cyano, amino, amido, acyl, sulfonyl, sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, cycloaliphaticoxy, heterocycloaliphaticoxy, aryloxy, heteroaryloxy, aralkyloxy, heteroarylalkoxy, or hydroxy.
  • substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl,
  • substituted alkyls include carboxyalkyl (such as HOOC-alkyl, alkoxycarbonylalkyl and alkylcarbonyloxyalkyl), cyanoalkyl, hydroxyalkyl, alkoxyalkyl, acylalkyl, hydroxyalkyl, aralkyl, (alkoxyaryl)alkyl, (sulfonylamino)alkyl (such as (alkylsulfonylamino)alkyl), aminoalkyl, amidoalkyl, (cycloaliphatic)alkyl, cyanoalkyl, or haloalkyl.
  • carboxyalkyl such as HOOC-alkyl, alkoxycarbonylalkyl and alkylcarbonyloxyalkyl
  • cyanoalkyl such as HOOC-alkyl, alkoxycarbonylalkyl and alkylcarbonyloxyalkyl
  • cyanoalkyl such as HOOC-al
  • an "alkenyl” group refers to an aliphatic carbon group that contains 2- 8 (e.g., 2-6 or 2-4) carbon atoms and at least one double bond. Like an alkyl group, an alkenyl group can be straight or branched. Examples of an alkenyl group include, but are not limited to, allyl, isoprenyl, 2-butenyl and 2-hexenyl.
  • An alkenyl group can be optionally substituted with one or more substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, (cycloaliphatic)carbonyl, (heterocycloaliphatic )carbonyl, nitro, cyano, amino, amido, acyl, sulfonyl, sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, aralkyloxy, (heteroaryl)alkoxy, or hydroxy.
  • substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, hetero
  • an "alkynyl” group refers to an aliphatic carbon group that contains 2- 8 (e.g., 2-6 or 2-4) carbon atoms and has at least one triple bond.
  • An alkynyl group can be straight or branched. Examples of an alkynyl group include, but are not limited to, propargyl and butynyl.
  • An alkynyl group can be optionally substituted with one or more substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, (cycloaliphatic)carbonyl, (heterocycloaliphatic)carbonyl, nitro, cyano, amino, amido, acyl, sulfonyl, sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, aralkyloxy, (heteroaryl)alkoxy, or hydroxy.
  • substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, hetero
  • an “amido” encompasses both “aminocarbonyl” and “carbonylamino”. These terms when used alone or in connection with another group refers to an amido group such as N(R X ) 2 -C(O)- or R Y C(O)-N(R X ) 2 - when used terminally and -C(O)- N(R X )- or -N(R X )-C(O)- when used internally, wherein R x and R ⁇ are defined below.
  • amido groups include alkylamido (such as alkylcarbonylamino and alkylcarbonylamino), (heterocycloaliphatic) amido, (heteroaralkyl) amido, (heteroaryl) amido, (heterocycloalkyl)alkylamido, arylamido, aralkylamido, (cycloalkyl)alkylamido and cycloalkylamido.
  • an "amino" group refers to -NR X R Y wherein each of R x and R ⁇ is independently hydrogen, alkyl, cycloaliphatic, (cycloaliphatic)aliphatic, aryl, araliphatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, heteroaryl, carboxy, sulfanyl, sulfinyl, sulfonyl, (aliphatic)carbonyl, (cycloaliphatic)carbonyl, ((cycloaliphatic)aliphatic)carbonyl, arylcarbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, (heteroaryl)carbonyl, or (heteroaraliphatic)carbonyl, each of which being defined herein and being optionally substituted.
  • amino groups include alkylamino, dialkylamino, and arylamino.
  • amino groups include alkylamino, dialkylamino, and arylamino.
  • an "aryl” group used alone or as part of a larger moiety as in “aralkyl”, “aralkoxy”, or “aryloxyalkyl” refers to monocyclic (e.g., phenyl); bicyclic (e.g., indenyl, naphthalenyl, tetrahydronaphthyl, tetrahydroindenyl); and tricyclic (e.g., fluorenyl tetrahydrofluorenyl, or tetrahydroanthracenyl, anthracenyl).
  • the bicyclic and tricyclic groups include benzofused 2-3 membered carbocyclic rings.
  • a benzofused group includes phenyl fused with two or more C 4-8 carbocyclic moieties.
  • An aryl is optionally substituted with one or more substituents including aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic ring of a benzofused bicyclic or tricyclic aryl); nitro; carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cyclo
  • an aryl can be unsubstituted.
  • substituted aryls include haloaryl [e.g., mono-, di ( such as p,m-dihaloaryl), and (trihalo)aryl]; (carboxy)aryl [e.g., (alkoxycarbonyl)aryl, ((aryalkyl)carbonyloxy)aryl, and (alkoxycarbonyl)aryl]; (amido)aryl [e.g., (aminocarbonyl)aryl, (((alkylamino)alkyl)aminocarbonyl)aryl, (alkylcarbonyl)aminoaryl, (arylaminocarbonyl)aryl, and (((heteroaryl)amino)carbonyl)aryl]; aminoaryl [e.g., ((alkylsulfonyl)amino)aryl and ((dialkyl)amin
  • an "araliphatic” such as an “aralkyl” group refers to an aliphatic group (e.g., a C 1-4 alkyl group) that is substituted with an aryl group.
  • "Aliphatic,” “alkyl,” and “aryl” are defined herein.
  • An example of an araliphatic such as an aralkyl group is benzyl.
  • a "bicyclic ring system” includes 8-12 (e.g., 9, 10, or 11) membered structures that form two rings, wherein the two rings have at least one atom in common (e.g., 2 atoms in common).
  • Bicyclic ring systems include bicycloaliphatics (e.g., bicycloalkyl or bicycloalkenyl), bicycloheteroaliphatics, bicyclic aryls, and bicyclic heteroaryls.
  • a "cycloaliphatic” group encompasses a "cycloalkyl” group and a “cycloalkenyl” group, each of which being optionally substituted as set forth below.
  • a "cycloalkyl” group refers to a saturated carbocyclic mono- or bicyclic (fused or bridged) ring of 3-10 (e.g., 5-10) carbon atoms.
  • Examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, norbornyl, cubyl, octahydro-indenyl, decahydro-naphthyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.3.2.]Decyl, bicyclo[2.2.2]octyl, adamantyl, azacycloalkyl or ((aminocarbonyl)cycloalkyl)cycloalkyl.
  • a "cycloalkenyl” group refers to a non-aromatic carbocyclic ring of 3-10 (e.g., 4-8) carbon atoms having one or more double bonds.
  • Examples of cycloalkenyl groups include cyclopentenyl, 1,4-cyclohexa-di-enyl, cycloheptenyl, cyclooctenyl, hexahydro-indenyl, octahydro-naphthyl, cyclohexenyl, cyclopentenyl, bicyclo[2.2.2]octenyl, and bicyclo[3.3.1]nonenyl.
  • a cycloalkyl or cycloalkenyl group can be optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (heterocycloaliphatic) aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic )oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic )carbonylamino, (cycloaliphatic)carbonylamino, ((cycloaliphatic)aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocyclo
  • sulfonyl e.g., alkylsulfonyl and arylsulfonyl
  • sulfinyl e.g., alkylsulfinyl
  • sulfanyl e.g., alkylsulfanyl
  • cyclic moiety includes cycloaliphatic, heterocycloaliphatic, aryl, or heteroaryl, each of which has been defined previously.
  • heterocycloaliphatic encompasses a heterocycloalkyl group and a heterocycloalkenyl group, each of which being optionally substituted as set forth below.
  • heterocycloalkyl refers to a 3-10 membered mono- or bicylic (fused or bridged) (e.g., 5- to 10-membered mono- or bicyclic) saturated ring structure, in which one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof).
  • heterocycloalkyl group examples include piperidyl, piperazyl, tetrahydropyranyl, tetrahydrofuryl, 1,4-dioxolanyl, 1,4-dithianyl, 1,3-dioxolanyl, oxazolidyl, isoxazolidyl, morpholinyl, thiomorpholyl, octahydro-benzofuryl, octahydro-chromenyl, octahydro-thiochromenyl, octahydro-indolyl, octahydro-pyrindinyl, decahydro-quinolinyl, octahydro-benzo[fe]thiopheneyl, 2-oxa-bicyclo[2.2.2]octyl, l-aza-bicyclo[2.2.2]octyl, 3-aza- bicyclo[3.2.1]octyl
  • a monocyclic heterocycloalkyl group can be fused with a phenyl moiety such as tetrahydroisoquinoline.
  • a "heterocycloalkenyl” group refers to a mono- or bicylic (e.g., 5- to 10- membered mono- or bicyclic) non-aromatic ring structure having one or more double bonds, and wherein one or more of the ring atoms is a heteroatom (e.g., N, O, or S).
  • Monocyclic and bicycloheteroaliphatics are numbered according to standard chemical nomenclature.
  • a heterocycloalkyl or heterocycloalkenyl group can be optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (heterocycloaliphatic) aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic)carbonylamino, (cycloaliphatic)carbonylamino, ((cycloaliphatic) aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycloaliphatic,
  • a “heteroaryl” group refers to a monocyclic, bicyclic, or tricyclic ring structure having 4 to 15 ring atoms wherein one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof) and wherein one ore more rings of the bicyclic or tricyclic ring structure is aromatic.
  • a heteroaryl group includes a benzofused ring system having 2 to 3 rings.
  • a benzofused group includes benzo fused with one or two 4 to 8 membered heterocycloaliphatic moieties (e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[£>]furyl, benzo[£]thiophenyl, quinolinyl, or isoquinolinyl).
  • heterocycloaliphatic moieties e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[£>]furyl, benzo[£]thiophenyl, quinolinyl, or isoquinolinyl.
  • heteroaryl examples include azetidinyl, pyridyl, lH-indazolyl, furyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, imidazolyl, tetrazolyl, benzofuryl, isoquinolinyl, benzthiazolyl, xanthene, thioxanthene, phenothiazine, dihydroindole, benzo[l,3]dioxole, benzo[b]furyl, benzo[b]thiophenyl, indazolyl, benzimidazolyl, benzthiazolyl, puryl, cinnolyl, quinolyl, quinazolyl,cinnolyl, phthalazyl, quinazolyl, quinoxalyl, isoquinolyl, 4H-quinolizyl, benzo- 1,2,5-thiadiazolyl,
  • monocyclic heteroaryls include furyl, thiophenyl, 2H-pyrrolyl, pyrrolyl, oxazolyl, thazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, 1,3,4-thiadiazolyl, 2H-pyranyl, 4-H-pranyl, pyridyl, pyridazyl, pyrimidyl, pyrazolyl, pyrazyl, or 1,3,5-triazyl.
  • Monocyclic heteroaryls are numbered according to standard chemical nomenclature.
  • bicyclic heteroaryls include indolizyl, indolyl, isoindolyl, 3H- indolyl, indolinyl, benzo[6]furyl, benzo[6]thiophenyl, quinolinyl, isoquinolinyl, indolizyl, isoindolyl, indolyl, benzo[&]furyl, bexo[fe] thiophenyl, indazolyl, benzimidazyl, benzthiazolyl, purinyl, 4H-quinolizyl, quinolyl, isoquinolyl, cinnolyl, phthalazyl, quinazolyl, quinoxalyl, 1,8-naphthyridyl, or pteridyl.
  • Bicyclic heteroaryls are numbered according to standard chemical nomenclature.
  • a heteroaryl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic or heterocyclic ring of a bicyclic or tricyclic heteroaryl); nitro; carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cycloaliphatic )carbonyl; ((cycloaliphatic)aliphatic)carbonyl; (ara
  • Non-limiting examples of substituted heteroaryls include (halo)heteroaryl [e.g., mono- and di-(halo)heteroaryl]; (carboxy)heteroaryl [e.g., (alkoxycarbonyl)heteroaryl]; cyanoheteroaryl; aminoheteroaryl [e.g., ((alkylsulfonyl)amino)heteroaryl and((dialkyl)amino)heteroaryl]; (amido)heteroaryl [e.g., aminocarbonylheteroaryl, ((alkylcarbonyl)amino)heteroaryl, ((((alkyl)amino)alkyl)aminocarbonyl)heteroaryl, (((heteroaryl)amino)carbonyl)heteroaryl, ((heteroaryl)amino)carbonyl)heteroaryl, (
  • heteroaralkyl group refers to an aliphatic group (e.g., a C M alkyl group) that is substituted with a heteroaryl group.
  • an "acyl” group refers to a formyl group or R -C(O)- (such as
  • alkylcarbonyl also referred to as "alkylcarbonyl" where R x and "alkyl” have been defined previously.
  • Acetyl and pivaloyl are examples of acyl groups.
  • alkoxy refers to an alkyl-O- group where “alkyl” has been defined previously.
  • a "carbamoyl” group refers to a group having the structure -O-CO-
  • R x and R ⁇ have been defined above and R z can be aliphatic, aryl, araliphatic, heterocycloaliphatic, heteroaryl, or heteroaraliphatic.
  • a "carboxy” group refers to -COOH, -COOR X , -OC(O)H,
  • haloaliphatic refers to an aliphatic group substituted with 1-
  • haloalkyl includes the group -CF 3 .
  • mercapto refers to -SH.
  • a "sulfo" group refers to -SO 3 H or -SO 3 R X when used terminally or
  • a "sulfamide” group refers to the structure -NR X -S(O) 2 -NR Y R Z when used terminally and -NR X -S(O) 2 -NR Y - when used internally, wherein R x , R ⁇ and R z have been defined above.
  • a "sulfamoyl” group refers to the structure -S(O) 2 -NR X R Y or -NR X -
  • sulfanyl refers to -S-R x when used terminally and -S- when used internally, wherein R x has been defined above.
  • sulfanyls include alkylsulfanyl.
  • sulfinyl group refers to -S(O)-R X when used terminally and -S(O)- when used internally, wherein R x has been defined above.
  • a "sulfonyl” group refers to-S(O) 2 -R x when used terminally and -
  • a "sulfoxy" group refers to -O-SO-R X or -SO-O-R X , when used terminally and -0-S(O)- or -S(O)-O- when used internally, where R x has been defined above.
  • halogen or halo group refers to fluorine, chlorine, bromine or iodine.
  • an "alkoxycarbonyl,” which is encompassed by the term carboxy, used alone or in connection with another group refers to a group such as alkyl-O-C(O)-.
  • alkoxyalkyl refers to an alkyl group such as alkyl-O-alkyl-, wherein alkyl has been defined above.
  • aminoalkyl refers to the structure (R x ) 2 N-alkyl-.
  • cyanoalkyl refers to the structure (NC)-alkyl-
  • urea refers to the structure -NR X -CO-NR Y R Z and a
  • thiourea group refers to the structure -NR X -CS-NR Y R Z when used terminally and -NR X -
  • terminal refers to the location of a group within a substituent.
  • a group is terminal when the group is present at the end of the substituent not further bonded to the rest of the chemical structure.
  • Carboxyalkyl i.e., R x O(O)C-alkyl is an example of a carboxy group used terminally.
  • a group is internal when the group is present in the middle of a substituent to at the end of the substituent bound to the to the rest of the chemical structure.
  • Alkylcarboxy e.g., alkyl-C(O)O- or alkyl-OC(O)-
  • alkyl-C(O)O-aryl- or alkyl-O(CO)-aryl- are examples of carboxy groups used internally.
  • substituted or unsubstituted compounds of the invention can optionally be substituted with one or more substituents, such as are illustrated generally above, or as exemplified by particular classes, subclasses, and species of the invention.
  • the variables contained herein encompass specific groups, such as alkyl and aryl. Unless otherwise noted, each of the specific groups for the variables contained herein can be optionally substituted with one or more substituents described herein. Each substituent of a specific group is further optionally substituted with one to three of halo, cyano, oxoalkoxy, hydroxyl, amino, nitro, aryl, haloalkyl, and alkyl.
  • an alkyl group can be substituted with alkylsulfanyl and the alkylsulfanyl can be optionally substituted with one to three of halo, cyano, oxoalkoxy, hydroxyl, amino, nitro, aryl, haloalkyl, and alkyl.
  • the cycloalkyl portion of a (cycloalkyl)carbonylamino can be optionally substituted with one to three of halo, cyano, alkoxy, hydroxyl, nitro, haloalkyl and alkyl.
  • the term "substituted,” whether preceded by the term “optionally” or not, refers to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent. Specific substituents are described above in the definitions and below in the description of compounds and examples thereof. Unless otherwise indicated, an optionally substituted group can have a substituent at each substitutable position of the group, and when more than one position in any given structure can be substituted with more than one substituent selected from a specified group, the substituent can be either the same or different at every position.
  • a ring substituent such as a heterocycloalkyl
  • substituents envisioned by this invention are those combinations that result in the formation of stable or chemically feasible compounds.
  • stable or chemically feasible refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and preferably their recovery, purification, and use for one or more of the purposes disclosed herein.
  • an effective amount is defined as the amount required to confer a therapeutic effect on the treated patient, and is typically determined based on age, surface area, weight and condition of the patient.
  • the interrelationship of dosages for animals and humans (based on milligrams per meter squared of body surface) is described by Freireich et al., Cancer Chemother. Rep., 50: 219 (1966).
  • Body surface area can be approximately determined from height and weight of the patient. See, e.g., Scientific Tables, Geigy Pharmaceuticals, Ardsley, New York, 537 (1970).
  • structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, (Z) and (E) double bond isomers, and (Z) and (E) conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention.
  • structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms.
  • compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a 1 3 C- or 14 C-enriched carbon are within the scope of this invention.
  • Such compounds are useful, for example, as analytical tools or probes in biological assays.
  • Amphoteric liposomes are a class of liposomes having anionic or neutral charge at about pH 7.5 and cationic charge at pH 4.
  • the oligonucleotide and/or other agents must be stably sequestered in the liposomes until eventual uptake in the target tissue or cells. Accordingly, the guidelines for liposomal formulations of the FDA regulate specific preclinical tests for liposomal drugs (http://www.fda. gov/cder/gui dance/2191 dft.pdf).
  • physiological pH can range from about 6.7 to about 7.7.
  • the pH of blood is generally about 7.4, but the pH at other physiological locations, such as vascular junctions or the extracellular matrix can be slightly acidic and thus lower than the pH of blood.
  • liposome refers to one or more lipids forming a complex, usually surrounded by an aqueous solution. Liposomes are generally spherical structures comprising lipids fatty acids, lipid bilayer type structures, unilamellar vesicles and amorphous lipid vesicles. Generally, liposomes are completely closed lipid bilayer membranes containing an entrapped aqueous volume. The liposomes may be unilamellar vesicles (possessing a single bilayer membrane) or multilamellar (onion-like structures characterized by multiple membrane bilayers, each separated from the next by an aqueous layer).
  • Liposomes of the present invention may also include a DNAi oligonucleotide as defined below, either bound to the liposomes or sequestered in or on the liposomes.
  • the molecules include, but are not limited to, DNAi oligonucleotides and/or other agents used to treat diseases such as cancer.
  • an "amphoteric liposome” is a liposome with an amphoteric character, as defined below.
  • sequestered, sequestering, or sequester refers to encapsulation, incorporation, or association of a drug, molecule, compound, including a DNAi oligonucleotide, with the lipids of a liposome.
  • the molecule may be associated with the lipid bilayer or present in the aqueous interior of the liposome or both.
  • “Sequestered” includes encapsulation in the aqueous core of the liposome.
  • part or all of the molecule is located in the aqueous core of the liposome and part outside of the liposome in the aqueous phase of the liposomal suspension, where part of the molecule is located in the aqueous core of the liposome and part in the lipid portion of the liposome, or part sticking out of the liposomal exterior, where molecules are partially or totally embedded in the lipid portion of the liposome, and includes molecules associated with the liposomes, with all or part of the molecule associated with the exterior of the liposome.
  • polydispersity index is a measure of the heterogeneity of the particle dispersion (heterogeneity of the diameter of liposomes in a mixture) of the liposomes.
  • a polydispersity index can range from 0.0 (homogeneous) to 1.0 (heterogeneous) for the size distribution of liposomal formulations.
  • the amphoteric liposomes include one or more amphoteric lipids or alternatively a mix of lipid components with amphoteric properties. Suitable amphoteric lipids are disclosed in PCT International Publication Number WO02/066489 as well as in PCT International Publication Number WO03/070735, the contents of both of which are incorporated herein by reference. Alternatively, the lipid phase may be formulated using pH-responsive anionic and/or cationic components, as disclosed in PCT International Publication Number WO02/066012, the contents of which are incorporated by reference herein.
  • Cationic lipids sensitive to pH are disclosed in PCT International Publication Numbers WO02/066489 and WO03/070220, in Budker, et al. 1996, Nat. Biotechnol., 14(6):760-4, and in US Patent Number 6,258,792 the contents of which are incorporated by reference herein, and can be used in combination with constitutively charged anionic lipids or with anionic lipids that are sensitive to pH.
  • the cationic charge may also be introduced from constitutively charged lipids that are known to those skilled in the art in combination with a pH sensitive anionic lipid.
  • Amphoteric liposomes of the present invention include 1) amphoteric lipids or a mixture of lipid components with amphoteric properties, (2) neutral lipids, (3) one or more DNAi oligonucleotides, (4) a cryoprotectant and/or lyoprotectant.
  • the DNAi- liposomes have a defined size distribution and polydispersity index.
  • amphoter or “amphoteric” character refers to a structure, being a single substance (e.g., a compound) or a mixture of substances (e.g., a mixture of two or more compounds) or a supramolecular complex (e.g., a liposome) comprising charged groups of both anionic and cationic character wherein
  • Amphoter I Lipid Pairs refers to lipid pairs containing a stable cation and a chargeable anion. Examples include without limitation DDAB/CHEMS, DOTAP/CHEMS and DOTAP/DOPS. In some aspects, the ratio of the percent of cationic lipids to anionic lipids is lower than 1.
  • Amphoter II Lipid Pairs refers to lipid pairs containing a chargeable cation and a chargeable anion. Examples include without limitation Mo-Chol/CHEMS, DPIM/CHEMS or DPIM/DG-Succ. In some aspects, the ratio of the percent of cationic lipids to anionic lipids is between about 5 and 0.2.
  • Amphoter III Lipid Pairs refers to lipid pairs containing a chargeable cation and stable anion. Examples include without limitation Mo-Chol/DOPG or Mo-Chol/Chol-SO 4 . In one embodiment, the ratio of the percent of cationic lipids to anionic lipids is higher than 1.
  • DMPC Dimyristoylphosphatidylcholine [0112] DPPC Dipalmitoylphosphatidylcholine [0113] DSPC Distearoylphosphatidylcholine [0114] POPC Palmitoyl-oleoylphosphatidylcholine [0115] OPPC l-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine [0116] DOPC Dioleoylphosphatidylcholine [0117] DOPE Dioleoylphosphatidylethanolamine [0118] DMPE Dimyristoylphosphatidylethanolamine [0119] DPPE Dipalmitoylphosphatidylethanolamine [0120] DOPG Dioleoylphosphatidylglycerol [0121] POPG Palmitoyl-oleoylphosphatidylglycerol [0122] DMPG Dimyristoylphosphati
  • CTAB Cetyl-trimethylammoniumbromide
  • CPyC Cetyl-pyridiniumchloride [0147] DOTAP ( 1 ,2-dioleoyloxypropyl)-N,N,N-trimethylammonium salt [0148] DMTAP ( 1 ,2-dimyristoyloxypropyl)-N,N,N-trimethylammonium salt [0149] DPTAP ( 1 ,2-dipalraitoyloxypropyl)-N,N,N-trimethylammonium salt [0150] DOTMA (1 ,2-dioleyloxypropyl)-N,N,N-trimethylammonium chloride) [0151] DOPJE (l,2-dioleyloxypropyl)-3 dime thy lhydroxy ethyl ammoniumbromide) [0152] DDAB Dimethyldioctadecylammonium bromide [0153] DPBvI
  • DGSucc 1,2 Dipalmitoyglycerol-S-hemisuccinate & Distearoyl-, dimyristoyl-
  • BGTC bisguanidinium-tren-cholesterol [0166] BGTC bisguanidinium-tren-cholesterol [0167] DOSPER ( 1.3-dioleoyloxy-2-(6-carboxy-spermyl)-propylarnide [0168] DOSC (l ⁇ -dioleoyl-S-succinyl-sn-glyceryl choline ester) [0169] DOGSDO (1 ,2-dioleoyl-sn-glycero-3-succinyl-2-hydroxyethyl disulfide ornithine)
  • DOGSucc l,2-Dioleoylglycerol-3-hemisucinate [0171] POGSucc Palimtolyl-oleoylglycerol-oleoyl-S-hemisuccinate [0172] DMGSucc l,2-Dimyristoylglycerol-3-hemisuccinate [0173] DPGSucc l,2-Dipalmitoylglycerol-3-hemisuccinate
  • lipids that are suitable for use in the compositions in accordance with the present invention.
  • the membrane anchors of the lipids are shown exemplarily and serve only to illustrate the lipids of the invention and are not intended to limit the same.
  • Amphoteric lipids are disclosed in PCT International Publication Numbers WO02/066489 and WO03/070735, the contents of both of which are incorporated herein by reference.
  • the overall molecule assumes its pH-dependent charge characteristics by the simultaneous presence of cationic and anionic groups in the "amphoteric substance" molecule portion. More specifically, an amphoteric substance is characterized by the fact that the sum of its charge components will be precisely zero at a particular pH value. This point is referred to as isoelectric point (IP). Above the IP the compound has a negative charge, and below the IP it is to be regarded as a positive cation, the IP of the amphoteric lipids according to the invention ranging between 4.5 and 8.5.
  • a compound is formed by coupling the amino group of histidine to cholesterol hemisuccinate.
  • the product has a negative charge because the carboxyl function which is present therein is in its fully dissociated form, and the imidazole function only has low charge.
  • the amphoteric lipid is selected from the group consisting of HistChol, HistDG, isoHistSuccDG, Acylcarnosine and HCChol.
  • the amphoteric lipid is HistChol.
  • Amphoteric lipids can include, without limitation, derivatives of cationic lipids which include an anionic substituent.
  • Amphoteric lipids include, without limitation, the compounds having the structure of the formula:
  • Z is a sterol or an aliphatic
  • Sterol is selected from the group consisting of cholesterol, sitosterol, campesterol, desmosterol, fucosterol, 22-ketosterol, 20-hydroxysterol, sigmasterol, 22-hydroxycholesterol, 25 hydroxycholesterol, lanosterol, 7-dehydrocholesteril, dihydrocholesterol, 19- hydroxycholesterol, 5 ⁇ cholest-7-en-3 ⁇ -ol, 7-hydroxycholesterol, epocholesterol, ergosterol dehydroergosterol, and derivatives thereof;
  • Each Wl is independently an unsubstituted aliphatic
  • Each W2 is independently an aliphatic optionally substituted with HO(O)C-aliphatic- amino or carboxy;
  • HET is an amino, an optionally substituted heterocycloaliphatic or an optionally substituted heteroaryl.
  • the HET is an optionally substituted heterocycloaliphatic including at least one nitrogen ring atom, or an optionally substituted heteroaryl including at least one nitrogen ring atom.
  • the HET is morpholinyl, piperidinyl, piperazinlyl, pyrimidinyl, or pyridinyl.
  • the cationic lipid has the structure Sterol-X- spacerl-Y-spacer2-morpholinyl or Sterol-X-spacerl-Y-spacer2-imidazolyl.
  • the sterol is cholesterol.
  • amphoteric lipids include, without limitation, the compounds having the structure of the formula:
  • Z is a structure according to the general formula R 1 -O-CH 2
  • Sterol is selected from the group consisting of cholesterol, sitosterol, campesterol, desmosterol, fucosterol, 22-ketosterol, 20-hydroxysterol, sigmasterol, 22-hydroxycholesterol, 25 hydroxycholesterol, lanosterol, 7-dehydrocholesteril, dihydrocholesterol, 19- hydroxycholesterol, 5 ⁇ cholest-7-en-3 ⁇ -ol, 7-hydroxycholesterol, epicholesterol, ergosterol dehydroergosterol, and derivatives thereof;
  • Each Wl is independently an unsubstituted aliphatic with up to 8 carbon atoms
  • Each W2 is independently an aliphatic , carboxylic acid with up to 8 carbon atoms and 0, 1, or 2 ethyleneically unsaturated bonds;
  • HET is an amino, an optionally substituted heterocycloaliphatic or an optionally substituted heteroaryl.
  • the HET is an optionally substituted heterocycloaliphatic including at least one nitrogen ring atom, or an optionally substituted heteroaryl including at least one nitrogen ring atom.
  • the HET is morpholinyl, piperidinyl, piperazinlyl, pyrimidinyl, or pyridinyl.
  • the cationic lipid has the structure Sterol-X- spacerl-Y-spacer2-morpholinyl or Sterol-X-spacerl-Y-spacer2-imidazolyl.
  • the sterol is cholesterol.
  • the lipid phase can be formulated using pH-responsive anionic and/or cationic components, as disclosed in PCT International Publication Number WO02/066012, the contents of which are incorporated by reference herein.
  • Cationic lipids sensitive to pH are disclosed in PCT International Publication Numbers WO02/066489 and WO03/070220, in Budker, et al. (1996), Nat Biotechnol. 14(6):760-4, and in US Patent Number 6,258,792, the contents of all of which are incorporated by reference herein.
  • the cationic charge may be introduced from constitutively charged lipids known to those skilled in the art in combination with a pH sensitive anionic lipid.
  • the mixture of lipid components may comprise (i) a stable cationic lipid and a chargeable anionic lipid, (ii) a chargeable cationic lipid and chargeable anionic lipid or (iii) a stable anionic lipid and a chargeable cationic lipid.
  • the charged groups can be divided into the following 4 groups.
  • Nitrogen bases with preferred pKa values are also formed by substituting nitrogen atoms one or more times with low molecular weight alkane hydroxyls, such as hydroxymethyl or hydroxyethyl groups.
  • alkane hydroxyls such as hydroxymethyl or hydroxyethyl groups.
  • aminodihydroxypropanes triethanolamines, tris- (hydroxymethyl)methylamines, bis-(hydroxymethyl)methylamines, tris- (hydroxyethyl)methylamines, bis-(hydroxyethyl)methylamines or the corresponding substituted ethylamines.
  • amphoteric liposomes contain variable amounts of such membrane-forming or membrane-based amphiphilic materials, so that they have an amphoteric character. This means that the liposomes can change the sign of the charge completely.
  • ni is the number of these groups in the liposome.
  • cationic components include DPIM, CHIM, DORIE, DDAB, DAC-Chol, TC-Chol, DOTMA, DOGS, (C18) 2 Gly + N,N-dioctadecylamido-glycine, CTAB, CPyC, DODAP DMTAP, DPTAP, DOTAP, DC-Choi, MoChol, HisChol and DOEPC.
  • cationic lipids include DMTAP, DPTAP, DOTAP, DC-Choi, MoChol and HisChol.
  • the cationic lipids can be compounds having the structure of the formula L-X-spacerl-Y-spacer2-HET wherein:
  • L is a sterol or [aliphatic(C(O)O)-] 2 -alkyl-;
  • Sterol is selected from the group consisting of cholesterol, sitosterol, campesterol, desmosterol, fucosterol, 22-ketosterol, 20-hydroxysterol, sigmasterol, 22-hydroxycholesterol, 25 hydroxycholesterol, lanosterol, 7-dehydrocholesteril, dihydrocholesterol, 19- hydroxycholesterol, 5 ⁇ cholest-7-en-3 ⁇ -ol, 7-hydroxycholesterol, epocholesterol, ergosterol dehydroergosterol, and derivatives thereof;
  • Each spacer 1 and spacer 2 is independently an unsubstituted aliphatic
  • HET is an amino, an optionally substituted heterocycloaliphatic or an optionally substituted heteroaryl.
  • the HET is an optionally substituted heterocycloaliphatic including at least one nitrogen ring atom, or an optionally substituted heteroaryl including at least one nitrogen ring atom.
  • the HET is morpholinyl, piperidinyl, piperazinlyl, pyrimidinyl or pyridinyl.
  • the cationic lipid has the structure Sterol-X- spacer l-Y-spacer2-morpholinyl or Sterol-X-spacerl-Y-space ⁇ -imidazolyl.
  • the sterol is cholesterol.
  • pH sensitive cationic lipids can be compounds having the structure of the formula
  • L is a structure according to the general formula
  • Sterol is selected from the group consisting of cholesterol, sitosterol, campesterol, desmosterol, fucosterol, 22-ketosterol, 20-hydroxy sterol, sigmasterol, 22-hydroxycholesterol, 25 hydroxycholesterol, lanosterol, 7-dehydrocholesterol, dihydrocholesterol, 19- hydroxycholesterol, 5 ⁇ cholest-7-en-3 ⁇ -ol, 7-hydroxycholesterol, epicholesterol, ergosterol dehydroergosterol, and derivatives thereof;
  • Each spacer 1 and spacer 2 is independently an unsubstituted aliphatic with 1-8 carbon atoms;
  • HET is an amino, an optionally substituted heterocycloaliphatic or an optionally substituted heteroaryl.
  • the HET is an optionally substituted heterocycloaliphatic including at least one nitrogen ring atom, or an optionally substituted heteroaryl including at least one nitrogen ring atom.
  • the HET is morpholinyl, piperidinyl, piperazinlyl, pyrimidinyl or pyridinyl.
  • the cationic lipid has the structure Sterol-X- spacerl-Y-spacer2-morpholinyl or Sterol-X-spacerl-Y-spacer2-imidazolyl.
  • the sterol is cholesterol.
  • the amphoteric mixtures further comprise anionic lipids, either constitutively or conditionally charged in response to pH, and such lipids are also known to those skilled in the art.
  • lipids for use with the invention include DOGSucc, POGSucc, DMGSucc, DPGSucc, DMPS, DPPS, DOPS, POPS, DMPG, DPPG, DOPG, POPG, DMPA, DPPA, DOPA, POPA, CHEMS and CetylP.
  • anionic lipids include DOGSucc, DMGSucc, DMPG, DPPG, DOPG, POPG, DMPA, DPPA, DOPA, POPA, CHEMS and CetylP.
  • Neutral lipids include any lipid that remains neutrally charged at a pH between about 4 and 9.
  • Neutral lipids include, without limitation, cholesterol, other sterols and derivatives thereof, phospholipids, and combinations thereof.
  • the phospholipids include any one phospholipid or combination of phospholipids capable of forming liposomes. They include phosphatidylcholines, phosphatidylethanolamines, lecithin and fractions thereof, phosphatidic acids, phosphatidylglycerols, phosphatidylinolitols, phosphatidylserines, plasmalogens and sphingomyelins.
  • the phosphatidylcholines include, without limitation, those obtained from egg, soy beans or other plant sources or those that are partially or wholly synthetic or of variable lipid chain length and unsaturation, POPC, OPPC, natural or hydrogenated soy bean PC, natural or hydrogenated egg PC, DMPC, DPPC, DSPC, DOPC and derivatives thereof.
  • phosphatidylcholines are POPC, non-hydrogenated soy bean PC and non-hydrogenated egg PC.
  • Phosphatidylethanolamines include, without limitation, DOPE, DMPE and DPPE and derivatives thereof.
  • Phosphatidylglycerols include, without limitation, DMPG, DLPG, DPPG, and DSPG.
  • Phosphatidic acids include, without limitation, DSPA, DMPA, DLPA and DPPA.
  • Sterols include cholesterol derivatives such as 3-hydroxy-5.6-cholestene and related analogs, such as 3-amino-5.6-cholestene and 5,6-cholestene, cholestane, cholestanol and related analogs, such as 3-hydroxy-cholestane; and charged cholesterol derivatives such as cholesteryl-beta-alanine and cholesterol hemisuccinate.
  • cholesterol derivatives such as 3-hydroxy-5.6-cholestene and related analogs, such as 3-amino-5.6-cholestene and 5,6-cholestene, cholestane, cholestanol and related analogs, such as 3-hydroxy-cholestane
  • charged cholesterol derivatives such as cholesteryl-beta-alanine and cholesterol hemisuccinate.
  • neutral lipids include but are not limited to DOPE, POPC, soy bean PC or egg PC and cholesterol.
  • nucleic acid molecule refers to any nucleic acid containing molecule, including, without limitation, DNA or RNA.
  • polynucleotide(s) generally refers to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.
  • polynucleotides as used herein refers to, among others, single-and double-stranded DNA, DNA that is a mixture of single- and double- stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single- stranded or double-stranded or a mixture of single- and double-stranded regions.
  • polynucleotide refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules.
  • the regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules.
  • One of the molecules of a triple-helical region often is an oligonucleotide.
  • the term "polynucleotide,” “nucleic acid molecule” or “nucleic acid sequence” includes DNAs or RNAs that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotides,” “nucleic acid molecules” or “nucleic acid sequences” as those terms are intended herein. The terms also encompass sequences that include any of the known base analogs of DNA and RNA.
  • polynucleotide as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells, among others.
  • isolated nucleic acid sequence is meant a polynucleotide that is not immediately contiguous with either of the coding sequences with which it is immediately contiguous (one on the 5' end and one on the 3' end) in the naturally occurring genome of the organism from which it is derived.
  • the term therefore includes, for example, a recombinant DNA which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA) independent of other sequences.
  • the nucleotides of the invention can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide.
  • the term includes single and double stranded forms of DNA.
  • the term "gene” refers to a nucleic acid (e.g., DNA) sequence that includes coding sequences necessary for the production of a polypeptide, precursor or RNA (e.g., rRNA, tRNA).
  • the polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragment are retained.
  • the term also encompasses the coding region of a structural gene and the sequences preceding and following the coding region, (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons).
  • Sequences located 5' of the coding region and present on the mRNA are referred to as 5' non-translated sequences or regions. Sequences located 3' or downstream of the coding region and present on the mRNA are referred to as 3' non-translated sequences or regions.
  • the term "gene” encompasses both cDNA and genomic forms of a gene.
  • a genomic form or clone of a gene contains the coding region interrupted with non-coding sequences termed "introns" or “intervening regions” or “intervening sequences.” Introns are segments of a gene that are transcribed into nuclear RNA (hnRNA); introns may contain regulatory elements such as enhancers.
  • RNA messenger RNA
  • mRNA messenger RNA
  • the mRNA functions during translation to specify the sequence or order of amino acids in a nascent polypeptide.
  • gene expression refers to the process of converting genetic information encoded in a gene into RNA (e.g., mRNA, rRNA, tRNA, or snRNA) through "transcription" of the gene (i.e., via the enzymatic action of an RNA polymerase), and for protein encoding genes, into protein through “translation” of mRNA. Gene expression can be regulated at many stages in the process.
  • Up-regulation or “activation” refers to regulation that increases the production of gene expression products (i.e., RNA or protein), while “down-regulation” or “repression” refers to regulation that decrease production.
  • Molecules e.g., transcription factors
  • activators and “repressors,” respectively.
  • genomic forms of a gene may also include sequences located on both the 5' and 3' end of the sequences that are present on the RNA transcript. These sequences are referred to as "flanking" sequences or regions (these flanking sequences are located 5' or 3' to the non-translated sequences present on the mRNA transcript).
  • the 5' flanking region (or upstream region) may contain regulatory sequences such as promoters and enhancers that control or influence the transcription of the gene.
  • the 3' flanking region may contain sequences that direct the termination of transcription, post-transcriptional cleavage and polyadenylation.
  • nucleic acid molecule encoding refers to the order or sequence of deoxyribonucleotides along a strand of deoxyribonucleic acid. The order of these deoxyribonucleotides determines the order of amino acids along the polypeptide (protein) chain. The DNA sequence thus codes for the amino acid sequence.
  • oligonucleotide as used herein is defined as a molecule with two or more deoxyribonucleotides or ribonucleotides, often more than three, and usually more than ten.
  • Oligonucleotides can be prepared by any suitable method, including, for example, cloning and restriction of appropriate sequences and direct chemical synthesis by a method such as the phosphotriester method of Narang et al., 1979, Meth.
  • DNAi oligonucleotide refers to a single stranded nucleic acid oligonucleotide or derivative thereof, whose sequence is complementary, in part, to a portion of the longest non-transcribed region of a gene in which the oligonucleotide affects indirectly or directly the expression, regulation or production of the same or different gene, wherein the longest non-transcribed region includes any portion of the gene that is not transcribed when the transcriptional start site is the site closest to the translation start site.
  • DNAi does not include RNAi and antisense oligonucleotides that base pair only with mRNAs or pre-mRNAs and interfere with RNA processing and/or message translation.
  • dC is replaced by 5-methyl-dC where appropriate.
  • the DNAi oligonucleotides may comprise, without limitation, oligonucleotide mimetic s such as those described below.
  • the oligonucleotide compounds in accordance with this invention generally comprise from about 15 to about 35 nucleobases (i.e., from about 15 to about 35 linked bases), although both longer and shorter sequences may find use with the present invention.
  • Oligonucleotides can also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions.
  • nucleobase often referred to in the art simply as “base”
  • “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
  • Modified nucleobases include other synthetic and natural nucleobases described below.
  • promoter is meant a sequence sufficient to direct transcription.
  • Promoter also includes those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue-specific, or inducible by external signals or agents; such elements may be located in the 5' or 3' regions of the gene. Both constitutive and inducible promoters, are included in the invention (see e.g., Bitter et al., Methods in Enzymology 153:516-544, 1987).
  • promoters derived from the genome of mammalian cells e.g., metallothionein promoter
  • mammalian viruses e.g., the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter
  • Promoters produced by recombinant DNA or synthetic techniques may also be used to provide for transcription of the nucleic acid sequences of the invention.
  • the "regulatory region" of a gene is any part of a gene that regulates the expression of a gene, including, without limitation, transcriptional and translational regulation.
  • the regions include without limitation the 5' and 3' regions of genes, binding sites for regulatory factors, including without limitation transcription factor binding sites.
  • the regions also include regions that are as long as 20,000 or more base pairs upstream or downstream of translational start sites, so long as the region is involved in any way in the regulation of the expression of the gene.
  • the region may be as short as 20 base pairs or as long as thousands of base pairs.
  • the terms “complementary” or “complementarity” are used in reference to polynucleotides ⁇ i.e., a sequence of nucleotides) related by the base-pairing rules. For example, for the sequence “A-G-T,” is complementary to the sequence “T-C-A.” Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
  • the term “completely complementary,” for example when used in reference to an oligonucleotide of the present invention refers to an oligonucleotide where all of the nucleotides are complementary to a target sequence ⁇ e.g., a gene).
  • the term “partially complementary,” refers to a sequence where at least one nucleotide is not complementary to the target sequence. Preferred partially complementary sequences are those that can still hybridize to the target sequence under physiological conditions.
  • the term “partially complementary” refers to sequences that have regions of one or more non-complementary nucleotides both internal to the sequence or at either end.
  • Sequences with mismatches at the ends may still hybridize to the target sequence.
  • the term "homology" refers to a degree of complementarity. There may be partial homology or complete homology (i.e., identity).
  • a partially complementary sequence is a nucleic acid molecule that at least partially inhibits a completely complementary nucleic acid molecule from hybridizing to a target nucleic acid is "substantially homologous.” The inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or northern blot, solution hybridization and the like) under conditions of low stringency.
  • a substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous nucleic acid molecule to a target under conditions of low stringency.
  • a substantially complementary sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely complementary nucleic acid molecule to a target under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction.
  • the absence of non-specific binding may be tested by the use of a second target that is substantially non-complementary (e.g., less than about 30% identity); in the absence of nonspecific binding the probe will not hybridize to the second non-complementary target.
  • substantially homologous refers to any probe that can hybridize to either or both strands of the double-stranded nucleic acid sequence under conditions of low stringency as described above.
  • substantially homologous refers to any probe that can hybridize (i.e., it is the complement of) the single-stranded nucleic acid sequence under conditions of low stringency as described above.
  • hybridization is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is impacted by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, the T m of the formed hybrid, and the G:C ratio within the nucleic acids. A single molecule that contains pairing of complementary nucleic acids within its structure is said to be “self- hybridized.”
  • T m is used in reference to the "melting temperature.”
  • the melting temperature is the temperature at which a population of double-stranded nucleic acid molecules becomes half dissociated into single strands.
  • Inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or northern blot, solution hybridization and the like) under conditions of low stringency.
  • a substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous nucleic acid molecule to a target under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction.
  • the absence of non-specific binding may be tested by the use of a second target that is substantially non-complementary (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second non-complementary target.
  • substantially homologous refers to any probe that can hybridize to either or both strands of the double-stranded nucleic acid sequence under conditions of low stringency as described above.
  • stringency is used in reference to the conditions of temperature, ionic strength and the presence of other compounds such as organic solvents, under which nucleic acid hybridizations are conducted.
  • low stringency conditions a nucleic acid sequence of interest will hybridize to its exact complement, sequences with single base mismatches, closely related sequences (e.g., sequences with 90% or greater homology), and sequences having only partial homology (e.g., sequences with 50-90% homology).
  • intermediate stringency conditions a nucleic acid sequence of interest will hybridize only to its exact complement, sequences with single base mismatches, and closely relation sequences (e.g., 90% or greater homology).
  • a nucleic acid sequence of interest will hybridize only to its exact complement, and (depending on conditions such a temperature) sequences with single base mismatches. In other words, under conditions of high stringency the temperature can be raised so as to exclude hybridization to sequences with single base mismatches.
  • physiological conditions refers to specific stringency conditions that approximate or are conditions inside an animal (e.g., a human).
  • exemplary physiological conditions for use in vitro include, but are not limited to, 37°C, 95% air, 5% CO 2 , commercial medium for culture of mammalian cells (e.g., DMEM media available from Gibco, MD), 5-10% serum (e.g., calf serum or horse serum), additional buffers, and optionally hormone (e.g., insulin and epidermal growth factor).
  • isolated means altered “by the hand of man” from its natural state; i.e., if it occurs in nature, it has been changed or removed from its original environment or both.
  • an isolated nucleotide or “isolated polynucleotide” refers to a nucleic acid sequence that is identified and separated from at least one component or contaminant with which it is ordinarily associated in its natural source. Isolated nucleic acid is such present in a form or setting that is different from that in which it is found in nature.
  • non-isolated nucleic acids are nucleic acids such as DNA and RNA found in the state they exist in nature.
  • a given DNA sequence e.g., a gene
  • RNA sequences such as a specific mRNA sequence encoding a specific protein
  • isolated nucleic acid encoding a given protein includes, by way of example, such nucleic acid in cells ordinarily expressing the given protein where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature.
  • the isolated nucleic acid, oligonucleotide or polynucleotide may be present in single-stranded or double-stranded form.
  • the oligonucleotide or polynucleotide will contain at a minimum the sense or coding strand (i.e., the oligonucleotide or polynucleotide may be single-stranded), but may contain both the sense and anti-sense strands (i.e., the oligonucleotide or polynucleotide may be double- stranded).
  • the term "purified” or “to purify” refers to the removal of components (e.g., contaminants) from a sample.
  • components e.g., contaminants
  • antibodies are purified by removing contaminating non-immunoglobulin proteins; they are also purified by the removing immunoglobulin that does not bind to the target molecule.
  • the removal of non- immunoglobulin proteins and/or the removal of immunoglobulins that do not bind to the target molecule results in an increase in the percent of target-reactive immunoglobulins in the sample.
  • recombinant polypeptides are expressed in bacterial host cells and the polypeptides are purified by the removal of host cell proteins; the percent of recombinant polypeptides is thereby increased in the sample.
  • the present invention provides antigene inhibitors of oncogenes.
  • the present invention is not limited to the inhibition of a particular oncogene. Indeed, the present invention encompasses antigene inhibitors to any number of oncogenes including, but not limited to, those disclosed herein. i. Ras
  • c-Ha-ras One gene which has captured the attention of many scientists is the human proto- oncogene, c-Ha-ras. This gene acts as a central dispatcher, relaying chemical signals into cells and controlling cell division. Ras gene alteration may cause the gene to stay in the "on" position.
  • the ras oncogene is believed to underlie up to 30% of cancer, including colon cancer, lung cancer, bladder and mammary carcinoma (Bos, Cancer Res. 49:4682-4689 [1989]). The ras oncogene has therefore become a target for therapeutic drugs.
  • Oligonucleotides complementary to the 5' flanking region of the c-Ha-ras RNA transcript have shown to inhibit tumor growth in nude mice for up to 14 days (Gray et al, Cancer Res. 53:577-580 [1993]). It was recently reported that an antisense oligonucleotide directed to a point mutation (G>C) in codon 12 of the c-Ha-ras mRNA inhibited cell proliferation as well as tumor growth in nude mice when it was injected subcutaneously (U.S. Pat. No. 5,576,208; U.S. Pat. No. 5,582,986; Schwab et al, Proc. Natl. Acad. Sci.
  • the -her-2 also known as neu oncogene or erbB-2
  • oncogene encodes a receptor-like tyrosine kinase (RTK) that has been extensively investigated because of its role in several human carcinomas (Hynes and Stern, Biochim. et Biophy. Acta 1198:165-184 [1994]; Dougall et al, Oncogene 9:2109-2123 [1994]) and in mammalian development (Lee et al., Nature 378:394-398 [1995]).
  • RTK receptor-like tyrosine kinase
  • transmembrane receptor also known as pi 85
  • tyrosine kinase activity is a member of the epidermal growth factor (EGF) family, and thus is related to the epidermal growth factor receptor (EGFR or HER-I).
  • EGF epidermal growth factor
  • HER-2 Aberrant her-2 gene expression is present in a wide variety of cancers and are most common in breast, ovarian and gastric cancers.
  • HER-2 is overexpressed in 25-30% of all human breast and ovarian cancers. Levels of HER-2 overexpression correlate well with clinical stage of breast cancer, prognosis and metastatic potential. Overexpression of HER-2 is associated with lower survival rates, increased relapse rates and increased metastatic potential. Tan et al, (Cancer Res., 57: 1199 [1997]) have shown that overexpression of the HER-2 gene increases the metastatic potential of breast cancer cells without increasing their transformation ability.
  • HER-2 Aberrant expression of HER-2 includes both increased expression of normal HER-2 and expression of mutant HER-2.
  • Activation of the her-2 proto-oncogene can occur by any of three mechanisms—point mutation, gene amplification and overexpression. Gene amplification is the most common mechanism. Unlike the other EGF family members for whom ligand activation is necessary for promoting transformation, overexpression of HER-2 alone is sufficient for transformation (Cohen, et al, J. Biol. Chem., 271:30897 [1996]).
  • Several therapeutic approaches have been used to reduce levels of the her-2 gene product.
  • the adenovirus type 5 gene product ElA has been studied as a potential therapeutic using a breast cancer model in nude mice.
  • This gene product can repress her-2/neu overexpression by repressing her-2/neu promoter activity, and suppress the tumorigenic potential of ⁇ er-2/new-overexpressing ovarian cancer cells.
  • ElA delivered either by adenovirus or liposome significantly inhibited tumor growth and prolonged mouse survival compared with the controls (Chang et al, Oncogene 14:561 [1997]).
  • HER-2 Overexpression of HER-2 has also been found to be associated with increased resistance to chemotherapy. Thus, patients with elevated levels of HER-2 respond poorly to many drugs. Methods used to inhibit HER-2 expression have been combined with commonly used chemotherapeutic agents (Ueno et al, Oncogone 15:953 [1997]). Combining the adenovirus type 5 gene product, ElA, with taxol showed a synergistic effect in human breast cancer cells.
  • Oligonucleotides have also been used to study the function of HER-2.
  • a triplex- forming oligonucleotide targeted to the her-2 promoter, 42 to 69 nucleotides upstream of the mRNA transcription start site was found to inhibit HER-2 expression in vitro (Ebbinghaus et al, J. Clin. Invest., 92:2433 [1993]).
  • Porumb et al. (Cancer Res., 56:515 [1996]) also used a triplex-forming oligonucleotide targeted to the same her-2 promoter region. Decreases in her-2 mRNA and protein levels were seen in cultured cells. Juhl et al. (J. Biol.
  • Chem., 272:29482 [1997]) used anti-her-2 ribozymes targeted to a central region of the her-2 RNA just downstream of the transmembrane region of the protein to demonstrate a reduction in her-2 mRNA and protein levels in human ovarian cancer cells. A reduction in tumor growth in nude mice was also seen.
  • Colomer et al. (Br. J. Cancer, 70:819 [1994]) showed that phosphodiester antisense oligonucleotides targeted at or immediately downstream of, the translation initiation codon inhibited proliferation of human breast cancer cells by up to 60%.
  • Wiechen et al. (Int. J. Cancer 63:604 [1995]) demonstrated that an 18-nucleotide phosphorothioate oligonucleotide targeted to the coding region, 33 nucleotides downstream of the translation initiation codon, of her-2 reduced anchorage-independent growth of ovarian cancer cells.
  • Bertram et al. Biochem. Biophys. Res.
  • the c-myc gene product is encoded by an immediate early response gene, the expression of which can be induced by various mitogens. C-myc expression is involved in signal transduction pathways leading to cell division. Studies have demonstrated that proliferating cells have higher levels of c-myc mRNA and c-myc protein than do quiescent cells. Antibodies directed against the human c-myc protein are known to inhibit DNA synthesis in nuclei isolated from human cells. Conversely, constitutive expression of c-myc produced by gene transfer inhibits induced differentiation of several cell lines. Constitutive expression of c-myc predisposes transgenic mice to the development of tumors.
  • c-myc gene product may play a proliferative role in smooth muscle cells (SMCs). Balloon de-endothelialization and injury of rat aortas is known to increase c-myc mRNA expression of vascular SMC prior to their subsequent proliferation and migration. Also, SMCs in culture proliferate when exposed to several mitogens, including PDGF, FGF, EGF, IGF-I and to serum. Each of these mitogens has been found to be capable of increasing the expression in other cell lines of either c-myc protein, c- myc mRNA, or both. Additionally, blood serum has been found to increase c-myc mRNA levels in SMCs.
  • mitogens including PDGF, FGF, EGF, IGF-I and to serum.
  • Harel-Bellan et al. demonstrated that antisense oligonucleotides complementary to c-myc mRNA effectively inhibited the translation thereof in human T cells. These T cells were prevented from entering the S phase of cell division, c- myc proto-oncogene sequences are described in Marcu et al., Ann. Rev. Biochem., 61:809- 860 [1992]; Watt et al, Nature, 303:725-728 [1983)]; Battey et al, Cell, 34:779-787 (1983); and Epstein et al, NTIS publication PB93-100576. iv.
  • Bcl-2 [0239] In many types of human tumors, including lymphomas and leukemias, the bcl-2 gene is overexpressed, and may be associated with tumorigenicity (Tsujimoto et al, Science 228:1440-1443 [1985]). High levels of expression of the bcl-2 gene have been found in all lymphomas with t (14; 18) chromosomal translocations including most follicular B cell lymphomas and many large cell non-Hodgkin's lymphomas.
  • the bcl-2 gene has two promoters designated Pl and P2.
  • Pl from which most bcl-2 • mRNA is transcribed is located approximately 1.4 kb upstream of the translation initiation site and P2 is 1.3 kb downstream of Pl.
  • Pl is GC-rich, lacks a TATA box, has many transcription start sites and includes seven consensus binding sites for the SPl transcription factor.
  • P2 includes a CCAAT box and a TATA box and has two different transcription initiation sites. There are multiple NF-ZfB recognition sites and an SV40 enhancer-like octamer motif within P2.
  • TGF- ⁇ Transforming Growth Factor Alpha
  • EGF Epidermal Growth Factor
  • EGFR Epidermal Growth Factor Receptor
  • the sequence and three dimensional structure of both EGF and TGF- ⁇ have been determined (Campbell et al, Prog. Growth Factor Res. 1:13 [1989]).
  • TGF- ⁇ is a 50 amino acid polypeptide having about 40% homology of residues with EGF. Both peptides are characterized by three well defined loops (denoted A, B and C) and have three intramolecular disulphide bonds.
  • EGF Receptor Epidermal Growth Factor Receptor
  • the EGF Receptor is a Type 1 receptor tyrosine kinase.
  • the EGF Receptor and its ligands are of interest for their roles in normal physiological processes as well as in hyperproliferative and neoplastic diseases.
  • TGF- ⁇ The in vivo precursor of TGF- ⁇ is a 160 amino acid residue membrane-bound protein (pro-TGF-.alpha.) that is cleaved to yield a soluble compound (Massague, J. Biol. Chem., 265:21393-21396 [1990]).
  • This cleavage removes an extracellular portion comprised of 50 amino acids with a molecular weight of 6 Kd and is considered to be an important regulatory event (Pandiella et al, Proc. Natl. Acad. Sci. USA, 88:1726-1730 [1990]) that can be stimulated by phorbol esters acting via protein kinase C (Pandiella et al, J. Biol. Chem., 266:5769-5773 [1991]).
  • TGF- ⁇ Cultured human prostatic tumor lines contain elevated levels of TGF- ⁇ mRNA and proliferate in response to TGF- ⁇ (Wilding et al, The Prostate, 15:1-12 [1989]). TGF- ⁇ appears to have both autocrine and paracrine function, stimulating physiologic activities such as cell division and angiogenesis. When induced in transgenic mice, TGF- ⁇ produced epithelial hyperplasia and focal dysplastic changes that resembled carcinoma in situ (Sandgren et al, Cell, 61 : 1121-1135 [1990]).
  • KRAS c-Ki-Ras
  • the transforming gene product displayed an electrophoretic mobility in SDS- polyacrylamide gels that differed from the mobility of KRAS transforming proteins in other tumors. Thus, a previously undescribed mutation was responsible for activation of KRAS in this ovarian carcinoma.
  • Rodenhuis et al. ⁇ New Eng. J. Med. 317: 929 (1987)) used an assay based on oligonucleotide hybridization following an in vitro amplification step. Genomic DNA was examined from 39 tumor specimens obtained at thoracotomy. The KRAS gene was found to be activated by point mutations in codon 12 in 5 of 10 adenocarcinomas.
  • the present invention is not limited to the oncogenes described above.
  • the methods of the present invention are suitable for use with any oncogene with a known promoter region.
  • the present invention is not limited to the targeting of oncogenes.
  • the methods and compositions of the present invention find use in the targeting of any gene that it is desirable to down regulate the expression of.
  • the genes to be targeted include, but are not limited to, an immunoglobulin or antibody gene, a clotting factor gene, a protease, a pituitary hormone, a protease inhibitor, a growth factor, a somatomedian, a gonadotrophin, a chemotactin, a chemokine, a plasma protein, a plasma protease inhibitor, an interleukin, an interferon, a cytokine, a transcription factor, or a pathogen target (e.g., a viral gene, a bacterial gene, a microbial gene, a fungal gene).
  • a pathogen target e.g., a viral gene, a bacterial gene, a microbial gene, a fungal gene.
  • genes include, but are not limited to, ADAMTS4, ADAMTS5, APOAl, APOE, APP, B2M, COX2, CRP, DDX25, DMCl, FKBP8, GHl, GHR, IAPP, IFNAl, IFNG, ILl, 1110, IL12, IL13, IL2, IL4, IL7, IL8, IPW, MAPK14, Meil, MMP13, MYD88, NDN, PACE4, PRNP, PSENl, PSEN2, RAD51, RAD51C, SAP, SNRPN, TLR4, TLR9, TTR, UBE3A, VLA-4, and PTP-IB, c-RAF, m-TOR, LDL, VLDL, ApoB-100, HDL, VEGF, rhPDGF-BB, NADs, ICAM-I, MUCl, 2-dG, CTL, PSGL-I, E2F, NF-k
  • pathogens include, but are not limited to, Human Immunodeficiency virus, Hepatitis B virus, hepatitis C virus, hepatitis A virus, respiratory syncytial virus, pathogens involved in severe acute respiratory syndrome, West Nile virus, and food borne pathogens (e.g., E. col ⁇ ). 3. DNAi Oligonucleotide Design
  • the DNAi oligonucleotides are DNA oligomers that are complementary to either the plus strand or minus strand of double stranded DNA, and can include any oligomer that hybridizes to regulatory regions of the c-ki-ras, c-Ha-ras, c-myc, her-2, TGF-a, or bcl-2 gene.
  • those regulatory regions are defined as SEQ ID NO:1 (for her-2, or c-erb-2), SEQ ID NO:282 (for c-ki-ras), SEQ ID NO:462 (for c-Ha-ras), SEQ ID NO:936 (for c-myc), SEQ ID NO: 1081 (for TGF-a) and SEQ ID NOs: 1249 and 1254 (for bcl-2).
  • the DNA oligomers that hybridize to these regions can be 100%, 99%, 98%, 95%, 90%, 85%, 80%, 75%, 70% or 60% complementary to the sequences.
  • DNAi oligonucleotides are designed based on certain design criteria.
  • DNAi oligonucleotides can then be tested for efficacy using the methods disclosed herein.
  • the DNAi oligonucleotides are methylated on at least one, two or all of the CpG islands.
  • the DNAi oligonucleotides contain no methylation.
  • the present invention is not limited to a particular mechanism. Indeed, an understanding of the mechanism is not necessary to practice the present invention. Nonetheless, it is contemplated that DNAi oligonucleotides in some embodiments are those that have at least a 50% GC content and at least two GC dinucleotides. Also, in some embodiments, the DNAi oligonucleotides do not self hybridize.
  • DNAi oligonucleotides are designed with at least 1 A or T to minimize self hybridization. In yet further embodiments, commercially available computer programs are used to survey DNAi oligonucleotides for the ability to self hybridize. In still other embodiments, DNAi oligonucleotides are at least 10, or 15 nucleotides and no more than 100 nucleotides in length. In further embodiments, DNAi oligonucleotides are 18-26 nucleotides in length. In some embodiments, DNAi oligonucleotides comprise the universal protein binding sequences CGCCC and CGCG or the complements thereof.
  • DNAi oligonucleotides hybridize to a regulatory region of a gene upstream from the TATA box of the promoter.
  • DNAi oligonucleotides are designed to hybridize to regulatory regions of oncogenes known to be bound by proteins (e.g., transcription factors).
  • DNAi oligonucleotide compounds are not completely homologous to other regions of the human genome. The homology of the DNAi oligonucleotides to other regions of the genome can be determined using available search tools (e.g., BLAST, available at the internet site of NCBI).
  • the present invention is not limited to the DNAi oligonucleotides described herein.
  • DNAi oligonucleotides may be identified (e.g., using the criteria described above or other criteria).
  • Candidate DNAi oligonucleotides may be tested for efficacy using any suitable method. For example, candidate DNAi oligonucleotides can be evaluated for their ability to prevent cell proliferation at a variety of concentrations. In some embodiments, DNAi oligonucleotides inhibit gene expression or cell proliferation at a low concentration (e.g., less that 20 ⁇ M, or 10 ⁇ M in in vitro assays.).
  • regions within the regulatory regions of the oncogenes are further defined as regions for hybridization of DNAi oligonucleotides. In some embodiments, these regions are referred to as "hot zones.”
  • hot zones are defined based on DNAi oligonucleotide compounds that are demonstrated to be effective (see above section on DNAi oligonucleotides) and those that are contemplated to be effective based on the criteria for DNAi oligonucleotides described above.
  • hot zones encompass 10 bp upstream and downstream of each compound included in each hot zone and have at least one CG or more within an increment of 40 bp further upstream or downstream of each compound.
  • hot zones encompass a maximum of 100 bp upstream and downstream of each oligonucleotide compound included in the hot zone.
  • hot zones are defined at beginning regions of each promoter. These hot zones are defined either based on effective sequence(s) or contemplated sequences and have a preferred maximum length of 200 bp. Based on the above described criteria, exemplary hot zones were designed. These hot zones are shown in Table 1.
  • the DNAi oligomers can include any oligomer that hybridizes to SEQ ID NOs: 1249 or 1254.
  • the DNAi oligomer can be any oligomer that hybridizes to nucleotides 500-2026, nucleotides 500-1525, nucleotides 800-1225, nucleotides 900-1125, nucleotides 950-1075 or nucleotides 970-1045 of SEQ ID NO: 1249 or the complement thereof.
  • the DNAi oligonucleotides can be any oligomer that hybridizes under physiological conditions to exemplary hot zones in SEQ ID NO: 1249.
  • the oligomers that hybridize to these regions include those that are 100%, 99%, 98%, 95%, 90%, 85%, 80%, 75%, 70%, or 60% complementary to the above regions.
  • Examples of DNAi oligomers include, without limitation, those oligomers listed in SEQ ID NOs 1250-1253 and 1267-1447 and the complement thereof. In an embodiment of these aspects, the DNAi oligonucleotides are from 15-35 base pairs in length.
  • the DNAi oligomer can be SEQ ID NO: 1250, 1251, 1252, 1253, 1267-1447 or the complement thereof. In yet another embodiment, the DNAi oligomer can be SEQ ID NO: 1250, 1251, 1267, 1268, 1276, 1277, 1285, 1286 or the complement thereof. In still another embodiment, the DNAi oligomer can be SEQ ID NOs 1250, 1251, 1289-1358 or the complements thereof. In an additional embodiment the DNAi oligomer can be SEQ ID NO:1250 or l251.
  • the DNAi oligomer has the sequence of the positive strand of the bcl-2 sequence, and thus, binds to the negative strand of the sequence.
  • the DNAi oligomers can include mixtures of DNAi oligonucleotides.
  • the DNAi oligomer can include multiple DNAi oligonucleotides, each of which hybridizes to different parts of SEQ ID NOs 1249 and 1254. DNAi oligomers can hybridize to overlapping regions on those sequences or the DNAi oligomers may hybridize to non- overlapping regions.
  • DNAi oligomers can be SEQ ID NOs 1250, 1251, 1252, 1253, 1267-1447 or the complement thereof, wherein the mixture of DNAi oligomers comprises DNAi oligomers of at least 2 different sequences.
  • Other oligomers include those that hybridize to SEQ ID NO:946 or the complement thereof.
  • the oligomers can also include those that hybridize to nucleotides 1-500, 1-400, 1- 300, 1-200, 60-170, 200-1100, 400-1000, 500-800, or 600-700 of SEQ ID NO:946.
  • the oligomers that hybridize to these regions include those that are 100%, 99%, 98%, 95%, 90%, 85%, 80%, 75%, 70%, or 60% complementary to SEQ ID NO:946.
  • Examples of DNAi oligomers include, without limitation, those oligomers listed in SEQ ID NOs:937-1080 or the complements thereof.
  • the oligomer can include a mixture of oligomers, each of which hybridizes to a regulatory region of different genes.
  • the oligomer can include a first oligomer that hybridizes to SEQ ID NO: 1249 or 1254 and second oligomer that hybridizes to a regulatory region of a second gene.
  • the oligomer includes an oligomer of SEQ ED NOs 1250-1254 and 1267-1447 or the complements thereof, and an oligomer that hybridizes to SEQ ID NO:1, SEQ ID NO:282, SEQ ID NO:462, SEQ ID NO:936, or SEQ ID NO: 1081 or the complement thereof.
  • the oligomer includes SEQ ID NO 1250 or 1251 or the complement thereof and an oligomer that hybridizes to SEQ ID NO:1, SEQ ID NO:282, SEQ ID NO:462, SEQ ID NO:936, or SEQ ID NO: 1081 or the complement thereof.
  • the oligomer includes SEQ ID NO: 1250 or 1251 or the complement thereof and any of SEQ ID NOs 2-281, 283-461, 463-935, 937-1080 and 1082-1248, or the complement thereof. 6. Oligonucleotide Structure a. Methylation
  • the present invention provides oligonucleotide therapeutics that are methylated at specific sites.
  • the present invention is not limited to a particular mechanism. Indeed, an understanding of the mechanism is not necessary to practice the present invention. Nonetheless, it is contemplated that one mechanism for the regulation of gene activity is methylation of cytosine residues in DNA.
  • 5-methylcytosine (5-MeC) is the only naturally occurring modified base detected in DNA (Ehrlick et al, Science 212:1350- 1357 (1981)).
  • 5-methylcytosine 5-MeC
  • hypomethylation at specific sites or in specific regions in a number of genes is correlated with active transcription (Doerfler, Ann. Rev. Biochem.
  • DNA methylation in vitro can prevent efficient transcription of genes in a cell-free system or transient expression of transfected genes. Methylation of C residues in some specific cis-regulatory regions can also block or enhance binding of transcriptional factors or repressors (Doerfler, supra; Christman, supra; Cedar, Cell 34:5503-5513 (1988); Tate et al, Curr. Opin. Genet. Dev. 3:225-231 [1993]; Christman et al, Virus Strategies, eds. Doerfler, W. & Bohm, P. (VCH, Weinheim, N.Y.) pp. 319-333 [1993]).
  • methylation inhibitors such as L-methionine or 5-azacytodine or severe deficiency of 5-adenosine methionine through feeding of a diet depleted of lipotropes has been reported to induce formation of liver tumors in rats (Wainfan et al, Cancer Res. 52:207 ls-2077s [1992]).
  • extreme lipotrope deficient diets can cause loss of methyl groups at specific sites in genes such as c-myc, ras and c-fos (Dizik et al, Carcinogenesis 12:1307-1312 [1991]).
  • Hypomethylation occurs despite the presence of elevated levels of DNA MTase activity (Wainfan et al, Cancer Res.
  • the present invention thus takes advantage of this naturally occurring phenomena, to provide compositions and methods for site specific methylation of specific gene promoters, thereby preventing transcription and hence translation of certain genes.
  • the present invention provides methods and compositions for upregulating the expression of a gene of interest (e.g., a tumor suppressor gene) by altering the gene's methylation patterns.
  • the present invention is not limited to the use of methylated oligonucleotides. Indeed, the use of non-methylated oligonucleotides for the inhibition of gene expression is specifically contemplated by the present invention.
  • Experiments conducted during the course of development of the present invention See e.g., Example 8) demonstrated that an unmethylated oligonucleotide targeted toward Bcl-2 inhibited the growth of lymphoma cells to a level that was comparable to that of a methylated oligonucleotide.
  • the oligonucleotides can be in a naturally occurring state, and can also contain modifications or substitutions in the nucleobases, the sugar moiety and/or in the internucleoside linkage.
  • Nucleobases comprise naturally occurring nucleobases as well as non-naturally occurring nucleobases.
  • Illustrative examples of such nucleobases include without limitation adenine, cytosine, 5-methylcytosine, isocytosine, pseudoisocytosine, guanine, thymine, uracil, 5-bromouracil, 5-propynyluracil, 5-propynylcytosine, 5-propyny-6-fluoroluracil, 5- methylthiazoleuracil, 6-aminopurine, 2-aminopurine, inosine, diaminopurine, 7- deazaguanine, 7-deazaadenine, 3-deazaguanine, 3-deazaadenine, 8-azaguanine, 8-azaadenine, 7-propyne-7-deazaadenine, 7-propyne-7-deazaguanine, 2-chloro-6-aminopurine, 4- acet
  • Oligonucleotides can also have sugars other than ribose and deoxy ribose, including arabinofuranose (described in International Publication number WO 99/67378, which is herein incorporated by reference), xyloarabinofuranose (described in U.S. Patent Nos 6,316,612 and 6,489465, which are herein incorporated by reference), ⁇ -threofuranose (Schoning, et al. (2000) Science, 290, 1347-51, which is herein incorporated by reference) and L-ribofuranose.
  • Sugar mimetics can replace the sugar in the nucleotides. They include cyclohexene (Wang et al.(2000) J. Am. Chem. Soc.
  • the nucleotide derivatives can include nucleotides containing one of the following at the 2' sugar position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-0-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted Ci to Cio alkyl or C 2 to Ci 0 alkenyl and alkynyl, O[(CH 2 ) n O] m CH 2 , O(CH 2 ) n OCH 3 , O(CH 2 ) n NH 2 , O(CH 2 ) n CH 3 , O(CH 2 ) n ONH 2 , and O(CH 2 ) n ON[(CH 2 ) n CH 3 )] 2 , where n and m are from 1 to about 10, Ci to Cio lower al
  • the oligonucleotides have non-natural internucleoside linkages.
  • oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone.
  • modified oligonucleotides that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.
  • Some modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphoroselenates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3'-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3'-5' linkages, 2'-5' linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'.
  • Various salts, mixed salts and free acid forms are also included.
  • modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
  • morpholino linkages formed in part from the sugar portion of a nucleoside
  • siloxane backbones sulfide, sulfoxide and sulfone backbones
  • formacetyl and thioformacetyl backbones methylene formacetyl and thioformacetyl backbones
  • alkene containing backbones sulfamate backbones
  • sulfonate and sulfonamide backbones amide backbones; and others having mixed N, O, S and CH 2 component parts.
  • both the sugar and the internucleoside linkage (i.e., the backbone) of the nucleotide units are replaced with novel groups.
  • the base units are maintained for hybridization with an appropriate nucleic acid target compound.
  • an oligomeric compound an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA).
  • PNA peptide nucleic acid
  • the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone.
  • nucleobases are retained and.are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.
  • Representative patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos.: 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al., Science 254:1497 (1991).
  • oligonucleotides of the invention are oligonucleotides with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular -CH 2 -, -NH-O-CH 2 -, -CH 2 -N(CH 3 )-O-CH 2 - [known as a methylene (methylimino) or MMI backbone], -CH 2 -O-N(CH 3 )-CH 2 -, -CH 2 -N(CH 3 )-N(CH 3 )-CH 2 -, and -0-N(CH 3 )- CH 2 -CH 2 - [wherein the native phosphodiester backbone is represented as -0-P-O-CH 2 -] of the above referenced U.S.
  • Oligonucleotides can also have a morpholino backbone structure of the above-referenced U.S. Pat. No. 5,034,506.
  • the oligonucleotides have a phosphorothioate backbone having the following general structure.
  • Another modification of the DNAi oligonucleotides of the present invention involves adding additional nucleotides to the 3' and/or 5' ends of the DNAi oligonucleotides.
  • the 3' and 5' tails can comprise any nucleotide and can be as short as one nucleotide and as long as 20 nucleotides.
  • oligonucleotides of the present invention involves chemically linking to the oligonucleotide one or more moieties or conjugates that enhance the activity, cellular distribution or cellular uptake of the oligonucleotide.
  • Such moieties include but are not limited to lipid moieties such as a cholesterol moiety, cholic acid, a thioether, (e.g., hexyl-S-tritylthiol), a thiocholesterol, an aliphatic chain, (e.g., dodecandiol or undecyl residues), a phospholipid, (e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O- hexadecyl-rac-glycero-3-H-phosphonate), a polyamine or a polyethylene glycol chain or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl- oxycholesterol moiety.
  • lipid moieties such as a cholesterol moiety, cholic acid, a thioether, (
  • oligonucleotides containing the above-described modifications are not limited to the oligonucleotides described above. Any suitable modification or substitution may be utilized.
  • the present invention also includes pharmaceutical compositions and formulations that include the antisense compounds of the present invention as described below.
  • oligonucleotide synthesis can be used to prepare the modified DNAi oligomers of the present invention.
  • dC is replaced by 5-methyl-dC where appropriate, as taught by the present invention.
  • the modified or unmodified oligonucleotides of the present invention are most conveniently prepared by using any of the commercially available automated nucleic acid synthesizers. They can also be obtained from commercial sources that synthesize custom oligonucleotides pursuant to customer specifications.
  • chemotherapeutic agents including docetaxel and others can be combined with DNAi oligomers before or while sequestering in liposomes.
  • cryoprotectant refers to an agent or compound suitable for protecting a liposome composition from freezing damage, freeze/thaw damage and/or for lyophilization.
  • examples include sugars, disaccharides and monosaccharides, glycerol and polyethylene glycol.
  • Freezing damage refers to any one of several undesirable effects that occur upon exposure of a liposome composition to a temperature sufficient to cause one of the undesirable effects.
  • a sufficient temperature that results in freezing damage is typically a temperature lower than about O 0 C, (lower than about 5 0 C or 1O 0 C).
  • Undesirable effects include, without limitation, an increase in particle size growth due to aggregation and/or fusion of vesicles and loss of an encapsulated therapeutic agent.
  • the actual temperature that can cause onset of such an effect will vary according to the liposome formulation, e.g., the type of lipids and other bilayer components, as well as the entrapped medium and therapeutic agent.
  • Freeze/thaw damage includes the undesirable effects that are associated with freezing damage (described above), and additional effects observed as a result of at least one freezing and thawing cycle, e.g., a non-homogeneous particle size distribution. Described effects may be more pronounced during a slow thawing process, i.e., at about 2-8 0 C versus a more rapid thawing process, i.e., at room temperature or exposure to a water bath.
  • Cryoprotectants comprise sugars, including mono and disaccharides. These include, without limitation, glucose, fructose, mannose, trehalose, sucrose, xylose, ribose, maltose, lactose cellobiose, and raffinose. Other cryoprotectants include 6-amino mannose, mannitol, sorbitol, glycerol, polyethylene glycols, maltotriose, dextran, and maltodextrins.
  • sugars such as, for example, aminoglycosides, including streptomycin and dihydrostreptomycin; oligosaccharides, including raffinose and stachyose and other carbohydrates, including dextrans, maltodixtrans, dextrins, cyclodextrins, maltodextrins, cellusose and methylcellulose.
  • Hyaluronic acids can also be used.
  • Amino acids can also act as cryoprotectants. These include betaines, prolines, glycine, arginine, lysine, and alanine.
  • niacinamide creatine, monosodium glutamate, sweet whey solids, albumin, polyvinylpyrrolidine, polyvinyl alcohol, polydextran, hydroxypropyl- ⁇ - cyclodextrin, and partially hydrolysed starches
  • Proteins and peptides such as albumins, collagens, gelatins, lung surfactant proteins and fragments thereof can be used as well.
  • cryoprotectants can also be used as lyoprotectants. Lyoprotectants protect liposomes from damage due to lyophilization or freeze-drying and/or reconstitution.
  • mannitol is used as a lyoprotectant because it influences the glass transition temperature during lyophilization. Mannitol also allows for a fluffy cake after lyophilization, which facilitates reconstitution.
  • trehalose is the sole lyoprotectant.
  • a water soluble salt can also be included in the liposomal suspension medium.
  • the salt is present at a concentration effective to establish an osmotic gradient across each liposome, wherein the suspension medium has a higher osmolality than the liposome interior.
  • the salt can be any water soluble salt. Examples include, without limitation, sodium salts, such as NaCl, potassium salts, such as KCl, nitrate salts, ammonium salts and sulfate salts or combinations thereof.
  • the liposome formulations of the present invention (1) exhibit low toxicity; (2) can sequester high concentrations of oligomers e.g., the efficiency of sequestering the oligonucleotides associated with the amphoteric liposomes is about 35 %; (3) are stable in the bloodstream, such as when administered systemically, such that the oligonucleotide and/or other agents are stably sequestered in the liposomes until eventual uptake in the target tissue or cells; (4) can be optimized for delivery to animals, such as by adjusting the concentration of sequestered oligonucleotide to between about 1 to 4 mg/mL (such as about 2 mg/mL) for a lipid concentration of about 100 mM or less which provides dosing at 10 mg/kg in 200 ⁇ L of injection volume; (5) can be produced with an average diameter smaller than 200 ⁇ m, such as about 100 ⁇ m, and a narrow size distribution with a polydispersity index of about 0.2 or
  • amphoteric liposomes include one or more DNAi oligonucleotides, one or more amphoteric lipids or alternatively a mixture of lipid components with amphoteric properties and one or more neutral lipids.
  • amphoteric liposomes can be formed from a lipid phase comprising an amphoteric lipid.
  • the lipid phase can comprise 5 to 30 mole % or 10 to 25 mole % of the amphoteric lipid.
  • the amphoteric liposomes can be formed from a lipid phase comprising a mixture of lipid components with amphoteric properties.
  • the total amount of charged lipids may vary from 5 to 95 mole % , from 20 to 80 mole % or from 30 to 70 mole % of the lipid mixture.
  • the ratio of the percent of cationic lipids to anionic lipids can be between about 3 and 0.5 or between about 2 to 0.5. In some embodiments, the ratio of cationic lipids to anionic lipids is about 2. In other embodiments, the ratio of cationic lipids to anionic lipids is about 1. In other embodiments, the ratio of cationic lipids to anionic lipids is about 0.5.
  • Specific pairs of cationic and anionic lipids include, without limitation, MoChol and CHEMS, DOTAP and CHEMS, MoChol and Cet-P, and MoChol and DMGSucc.
  • Examples of charged lipid pairs further include, without limitation, between about 10 to 60 mole % of MoChol and between about 10 to 30 mole % of CHEMS; between about 5 to 30 mole % of DOTAP and between about; 10 to 30 mole % of CHEMS; between about 10 to 40 mole % MoChol and between about 5 to 30 mole % Cet-P; and between about 20 to 60 mole % MoChol and between about 20 to 60 mole % DMGSucc.
  • the amphoteric liposomes also contain neutral lipids, which can be either sterols or phospholipids, and mixtures thereof.
  • the amphoteric liposomes include neutral lipids in an amount between about 20 to 80 mole % of the lipid mixture, or between 30 and 75 mole %.
  • a number of neutral lipid combinations are useful in forming the amphoteric liposomes, such as POPC and DOPE; and POPC and cholesterol. In contrast, a combination of the neutral lipids DOPE and cholesterol is not preferred.
  • the mixture of neutral lipids includes 5 to 40 mole % POPC and 20 to 50 mole % DOPE; or 10 to 50 mole % of POPC and 30 to 50 mole % of cholesterol.
  • the ratio of the percentage of charged lipids to neutral lipids can be between about 3 and 0.2. In some embodiments, the ratio of the percentage of amphoteric lipids to neutral lipids is about 2. In other embodiments, the ratio of the percentage of amphoteric lipids to neutral lipids is about 0.5.
  • Examples of specific combinations of charged and neutral lipids for sequestering an DNAi oligomer, such as PNT-100 include POPC, DOPE, MoChol and CHEMS; POPC, DOPE, DMGSucc and MoChol; POPC, DOTAP, CHEMS and cholesterol; and POPC, MoChol, Cet-P and cholesterol.
  • the amphoteric liposome for sequestering a DNAi oligomer, such as SEQ ID NO: 1251 includes 3-20 mole % of POPC, 10 to 60 mole % of DOPE, 10 to 60 mole % of MoChol and 10 to 60 mole % of CHEMS.
  • the amphoteric liposome may include POPC/DOPE/MoChol/CHEMS in molar ratios of about 6/24/47/23 and about 15/45/20/20.
  • the amphoteric liposomes include 3 to 20 mole % of POPC, 10 to 40 mole % of DOPE, 15 to 60 mole % of MoChol and 15 to 60 mole % of DMGSucc.
  • the amphoteric liposome can include POPC/DOPE/DMGSucc/MoChol in molar ratios of about 6/24/23/47 and about 6/24/47/23.
  • the amphoteric liposome includes 10 to 50 mole % of POPC, 20 to 60 mole % of Choi, 10 to 40 mole % of CHEMS and 5 to 20 mole % of DOTAP.
  • the amphoteric liposome can include POPC/Chol/CHEMS/DOTAP in a molar ratio of about 30/40/20/10.
  • the amphoteric liposome includes 10 to 40 mole % of POPC, 20 to 50 mole % of Choi, 5 to 30 mole % of Cet-P and 10 to 40 mole % of MoChol.
  • the amphoteric liposome can include POPC/Chol/Cet-P/MoChol in a molar ratio of about 35/35/10/20.
  • any Amphoter I, II, or III lipid pair of cationic and anionic lipids can be used to form liposomes provided that the resulting liposome is amphoteric, exhibits serum stability, has low toxicity, sequesters an ample quantity of DNAi oligonucleotides, e.g., at an efficiency about 35%, (about 5%, 10%, 15%, 20%, 25%, 30%, 35% or higher) and provides for an adjustment of the oligonucleotide concentration to at least 2 mg/mL for a lipid concentration of 100 mM or less.
  • cryoprotectants and/or lyoprotectants can be included as part of either the internal or external media of the liposomes. Inclusion in the internal medium is accomplished by adding the cryoprotectant(s) and/or lyoprotectant(s) to the solute in which the liposomes are to encapsulate.
  • mannitol can be added to the solute.
  • sucrose or trehalose is added to the liposomal formulation, after the liposomes have formed.
  • the amount of sugar to be used depends on the type of sugar used and the characteristics of the liposomes. Persons skilled in the art can test various sugar types and concentrations to determine which combination works best for a particular liposome preparation.
  • the mannitol is added to achieve a concentration of 0.2- 1.5% in the solute in which the liposomes encapsulate.
  • sucrose is added at a concentration of about 2-25% after the liposomes have formed.
  • a water soluble salt can be added to the formed liposomes to establish an osmotic gradient across each liposome, wherein the suspension medium has a higher osmolality than the liposome interior, as described in the European Patent No. EP 1,196,144Bl.
  • the osmotic gradient is at least about 100 mOsm. In other embodiments, the osmotic gradient is at least about 200 or 600 mOsm.
  • the salt such as NaCl, is added to achieve a concentration of 0.2-3.6% of the formed liposomal suspension.
  • DNAi-amphoteric liposomes of the invention can be prepared by standard methods for preparing and sizing liposomes known to those skilled in the art. These methods can include the following steps: (1) mixing lipids with nucleic acids; (2) processes to ensure formation of small unilamellar vesicles; (3) removal of unsequestered nucleic acids; (4) processes to ensure the liposomes have a defined size and polydispersity index; (5) sterile filtration; (6) methods for preparing liposomes for storage; and (7) methods for preparing liposomes for administration. Methods for preparing and characterizing liposomes have been described, for example, by S. Vemuri et al. (Preparation and characterization of liposomes as therapeutic delivery systems: a review. Pharm Acta HeIv. 1995, 70(2):95-l 11), which is incorporated herein by reference.
  • Mixing lipids with nucleic acids include hydration of lipid films and powders, solvent injection and reverse-phase evaporation.
  • a mixture of lipids is dissolved in a water miscible solvent, including ethanol or propanol, and mixed with an aqueous mixture of nucleic acids by cross flow injection.
  • the lipid-nucleic acid mixture is mixed with an aqueous solution whose pH is below that of the lipid-nucleic acid mixture.
  • the temperature of the lipid mixture can range from 4° C and 100° C. In one embodiment the temperature is 55 0 C.
  • a Passive Loading Procedure is a process wherein liposomes are charged with oligonucleotides and/or other molecules where the charges of the lipids are not useful for binding the oligonucleotides and/or other molecules.
  • Advanced Loading Procedure is an ion exchange process taking advantage of the positive charge of one lipid at acidic pH to bind the oligonucleotides and/or other molecules.
  • Amphoteric liposomes used with the present invention offer the distinct advantage of binding oligonucleotides at or below their isoelectric point, thereby concentrating the active agent at the liposome surface.
  • the advanced loading procedure is described in more detail in PCT International Publication Numbers WO02/066012, WO07/064857 and in German Patent Publication Number DE 102006054192, all of which are incorporated by reference in their entirety.
  • a solution of the oligonucleotide may be contacted with an excipient at a neutral pH, thereby resulting in a passive loading procedure of a certain percentage of the solution.
  • Excipients include substances that can initiate or facilitate loading of DNAi oligonucleotides. Examples of excipients include, without limitation, acid, sodium or ammonium forms of monovalent anions such as chloride, acetate, lactobionate and formate; divalent anions such as aspartate, succinate and sulfate; and trivalent ions such as citrate and phosphate.
  • a shearing force can be applied to the aqueous dispersion of the DNAi-oligonucleotide lipid mixture.
  • the shearing force can be applied by sonication, using a microfluidizing apparatus such as a homogenizer or French press, injection, freezing and thawing, dialyzing away a detergent solution from lipids, or other known methods used to prepare liposomes.
  • the size of the liposomes can be controlled using a variety of known techniques, including the duration of shearing force and extrusion through a membrane with a defined pore size.
  • Unsequestered DNAi oligomers are removed from the liposome dispersion by buffer exchange using dialysis, size exclusion chromatography (e.g., Sephadex G-50 resin), ultrafiltration (100,000-300,000 molecular weight cutoff), or centrifugation.
  • size exclusion chromatography e.g., Sephadex G-50 resin
  • ultrafiltration 100,000-300,000 molecular weight cutoff
  • DNAi oligonucleotide loaded amphoteric liposomes may be manufactured by a machine extrusion. Lipids are mixed with the oligonucleotides using a process described in US Pat No. 6843942 and US Patent Application
  • the lipids can be extruded using machine extrusion.
  • the liposomes are loaded and filtered so that the diameter of the liposome is between 50 ⁇ m and 200 ⁇ m, the encapsulation efficiency of the oligonucleotide is at least 35% and the resulting liposomes have an oligonucleotide concentration of at least 2 mg/mL at a lipid concentration of 100 mM or less.
  • a cryoprotectant and/or lyoprotectant can be added either with the DNAi oligomer during liposome formation and/or after the liposomes are formed.
  • mannitol is added to the DNAi oligomer to a final concentration of 0.9 % during liposome formation.
  • sucrose is added to a final concentration of 5-10 % to the loaded liposomes after extrusion.
  • cryoprotectants and lyoprotectants may be added in combination to facilitate lyophilization and subsequent reconstitution of the resulting powder or residue.
  • the loaded liposomes containing cryoprotectant can be frozen in a number of different ways, including, without limitation, by flash freezing in liquid nitrogen or by placing in a freezer.
  • the temperature of the freezer can be from about -20° C to about -120°
  • the frozen liposomes can be thawed in a number of ways, including, without limitation, at room temperature, in a refrigerator, or quickly thawed in a water bath.
  • Loaded liposomes with cryoprotectant(s) and/or lyoprotectants can be dehydrated using standard freeze-drying apparatus, so that they are dehydrated under reduced pressure.
  • the liposomes and their surrounding medium can be frozen a number of ways, including, without limitation, in liquid nitrogen before being dehydrated.
  • the liposomes can also be dehydrated without prior freezing, by simply being placed under reduced pressure. This can be achieved at room temperature and at a reduced pressure provided by a vacuum pump capable of producing a pressure of about 1 mm of mercury.
  • DNAi-containing liposomes Once the DNAi-containing liposomes have been dehydrated, they can be stored for extended periods of time until they are to be used.
  • an aqueous solution such as distilled water or phosphate buffered saline, is added to the DNAi-liposomes and allowing them to rehydrate.
  • the liposomes can be resuspended into the aqueous phase by gentle swirling of the solution.
  • DNAi-liposome formulations that will be administered parentarelly must be sterile.
  • Sterile filtration can be performed before or after freeze-thaw, and before or after dehydration-rehydration.
  • the DNAi-liposome mixture can be filtered through a 0.22 micron filter or sequentially through a 0.45 and 0.22 micron filtration system.
  • the DNAi-amphoteric liposomes are prepared so that they are a defined diameter range and polydispersity index.
  • the average diameter of the DNAi liposomal mixture can range from 50-200 ⁇ m (70-150 ⁇ m; 90-130 ⁇ m).
  • the polydispersity index can range from 0-0.5 (0-0.3, 0-0.2, 0-0.1, 0-0.05).
  • non-human animals refers to all non-human animals including, without limitation, vertebrates such as rodents, non-human primates, ovines, bovines, ruminants, lagomorphs, porcines, caprines, equines, canines, felines, aves, etc.
  • transformed cell or "host cell” is meant a cell (e.g., prokaryotic or eukaryotic) into which (or into an ancestor of which) has been introduced, by means of recombinant DNA techniques, a DNA molecule encoding a polypeptide of the invention (i.e., a Methuselah polypeptide), or fragment thereof.
  • a cell e.g., prokaryotic or eukaryotic
  • a DNA molecule encoding a polypeptide of the invention i.e., a Methuselah polypeptide
  • Transformation of a host cell with recombinant DNA may be carried out by conventional techniques as are well known to those skilled in the art.
  • the host is prokaryotic, such as E. coli
  • competent cells which are capable of DNA uptake can be prepared from cells harvested after exponential growth phase and subsequently treated by the CaCl 2 method by procedures well known in the art.
  • CaCl 2 or RbCl can be used. Transformation can also be performed after forming a protoplast of the host cell or by electroporation.
  • cell culture refers to any in vitro culture of cells. Included within this term are continuous cell lines (e.g., with an immortal phenotype), primary cell cultures, transformed cell lines, finite cell lines (e.g., non-transformed cells), and any other cell population maintained in vitro.
  • the term "eukaryote” refers to organisms distinguishable from “prokaryotes.” It is intended that the term encompass all organisms with cells that exhibit the usual characteristics of eukaryotes, such as the presence of a true nucleus bounded by a nuclear membrane, within which lie the chromosomes, the presence of membrane-bound organelles and other characteristics commonly observed in eukaryotic organisms. Thus, the term includes, but is not limited to such organisms as fungi, protozoa and animals (e.g., humans).
  • the term “in vitro” refers to an artificial environment and to processes or reactions that occur within an artificial environment.
  • In vitro environments can consist of, but are not limited to, test tubes and cell culture.
  • the term "in vivo" refers to the natural environment (e.g., an animal or a cell) and to processes or reaction that occur within a natural environment.
  • the term "under conditions such that expression of a gene is inhibited” refers to conditions where an oligonucleotide of the present invention hybridizes to a gene (e.g., the promoter region of the gene) and inhibits transcription of the gene by at least 10 %, at least 25 %, at least 50% or at least 90 % relative to the level of transcription in the absence of the oligonucleotide.
  • the term "under conditions such that growth of a cell is reduced” refers to conditions where an oligonucleotide of the present invention, when administered to a cell (e.g., a cancer) reduces the rate of growth of the cell by at least 10 %, at least 25 %, at least 50 % or at least 90 % relative to the rate of growth of the cell in the absence of the oligonucleotide.
  • DNAi-amphoteric liposomes are useful for administering to animals, including humans, to treat cancer, such as by inhibiting or reducing tumor growth.
  • the animal can be a non-human animal, including mice, horses, cats, dogs, or other animals or it can be a human.
  • the mixture is introduced to the animal at a dosage of between 0.01 mg to 100 mg/kg of body weight.
  • the amphoteric liposomes can be introduced to the animal one or more times per day or continuously.
  • the mixture can be administered to the animal via different routes.
  • Administration can be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral.
  • Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Administration can also be via a medical device.
  • the liposomes can be administered to cultured cells derived from various cancers, including pancreatic cancer, colon cancer, breast cancer, bladder cancer, lung cancer, leukemia, prostate cancer, lymphoma, ovarian cancer or melanoma.
  • the liposomes can be used to target DNAi oligonucleotides to selected tissues using several techniques. The procedures involve manipulating the size of the liposomes, their net surface charge as well as the route of administration. More specific manipulations include labeling the liposomes with receptor ligands, including membrane and nuclear receptor ligands or antibodies for specific tissues or cells, Antibodies or ligands can be bound to the surface of the liposomes. IV CO-THERAPIES
  • DNAi-liposomal formulations can be administered in conjunction other agents, including chemotherapy agents and radiation therapy.
  • test compound and “candidate compound” refer to any chemical entity, pharmaceutical, drug, and the like that is a candidate for use to treat or prevent a disease, illness, sickness, or disorder of bodily function (e.g., cancer).
  • Test compounds include both known and potential therapeutic compounds.
  • a test compound can be determined to be therapeutic by screening using the screening methods of the present invention.
  • test compounds include antisense compounds.
  • known chemotherapeutic agents refers to compounds known to be useful in the treatment of disease (e.g., cancer).
  • chemotherapeutic agents affective against cancer include, but are not limited to, daunorubicin, dactinomycin, doxorubicin, bleomycin, mitomycin, nitrogen mustard, chlorambucil, melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine (CA), 5-fluorouracil (5-FU), floxuridine (5-FUdR), methotrexate (MTX), colchicine, taxotere, vincristine, vinblastine, etoposide, teniposide, cisplatin and diethylstilbestrol (DES).
  • daunorubicin dactinomycin
  • doxorubicin bleomycin
  • mitomycin nitrogen mustard
  • chlorambucil chlorambucil
  • melphalan cyclophosphamide
  • 6-mercaptopurine 6-thioguanine
  • cytarabine CA
  • Chemotherapy agents of the present invention can include any suitable chemotherapy drug or combinations of chemotherapy drugs (e.g., a cocktail).
  • exemplary chemotherapy agents include, without limitation, alkylating agents, platinums, anti-metabolites, anthracyclines, taxanes, camptothecins, nitrosoureas, EGFR inhibitors, antibiotics, HER2/neu inhibitors, angiogenesis inhibitors, kinase inhibitors, proteaosome inhibitors, immunotherapies, hormone therapies, photodynamic therapies, cancer vaccines, histone deacetylase inhibitors, sphingolipid modulators, oligomers, other unclassified chemotherapy drugs and combinations thereof.
  • Alkylating agents are chemotherapy agents that are thought to attack the negatively charged sites on the DNA (e.g., the oxygen, nitrogen, phosphorous and sulfur atoms) and bind to the DNA thus altering replication, transcription and even base pairing. It is also believed that alkylation of the DNA also leads to DNA strand breaks and DNA strand cross- linking. By altering DNA in this manner, cellular activity is effectively stopped and the cancer cell will die.
  • Common alkylating agents include, without limitation, Procarbazine, Ifosphamide, Cyclophosphamide, Melphalan, Chlorambucil, Decarbazine, Busulfan, Thiotepa, and the like. Alkylating agents such as those mentioned above can be used in combination with one or more other alkylating agents and/or with one or more chemotherapy agents of a different class(es).
  • Platinum chemotherapy agents are believed to inhibit DNA synthesis, transcription and function by cross-linking DNA subunits. (The cross-linking can happen either between two strands or within one strand of DNA.) Common platinum chemotherapy agents include, without limitation, Cisplatin, Carboplatin, Oxaliplatin, Eloxatin, and the like. Platinum chemotherapy agents such as those mentioned above can be used in combination with one or more other platinums and/or with one or more chemotherapy agents of a different class(es).
  • Anti-metabolite chemotherapy agents are believed to interfere with normal metabolic pathways, including those necessary for making new DNA.
  • Common anti-metabolites include, without limitation, Methotraxate, 5-Fluorouracil (e.g., Capecitabine), Gemcitabine (2'-deoxy-2',2'-difluorocytidine monohydrochloride ( ⁇ -isomer), Eli Lilly), 6-mercaptopurine, 6-thioguanine, fludarabine, Cladribine, Cytarabine, tegafur, raltitrexed, cytosine arabinoside, and the like.
  • Gallium nitrate is another anti-metabolite that inhibits ribonucleotides reductase.
  • Anti-metabolites such as those mentioned above can be used in combination with one or more other anti-metabolites and/or with one or more chemotherapy agents of a different class(es).
  • Anthracyclines are believed to promote the formation of free oxygen radicals. These radicals result in DNA strand breaks and subsequent inhibition of DNA synthesis and function. Anthracyclines are also thought to inhibit the enzyme topoisomerase by forming a complex with the enzyme and DNA. Common anthracyclines include, without limitation, Daunorubicin, Doxorubicin, Idarubicin, Epirubicin, Mitoxantrone, adriamycin, bleomycin, mitomycin-C, dactinomycin, mithramycin and the like. Anthracyclines such as those mentioned above can be used in combination with one or more other anthracyclines and/or with one or more chemotherapy agents of a different class(es).
  • Taxanes are believed to bind with high affinity to the microtubules during the M phase of the cell cycle and inhibit their normal function.
  • Common taxanes include, without limitation, Paclitaxel, Docetaxel, Taxotere, Taxol, taxasm, 7-epipaclitaxel, t-acetyl paclitaxel, 10-desacetyl-paclitaxel, lO-desacetyl-7-epipaclitaxel, 7-xylosylpaclitaxel, 10-desacetyl-7- epipaclitaxel, 7-N-N-dimethylglycylpaclitaxel, 7-L-alanylpaclitaxel and the like. Taxanes such as those mentioned above can be used in combination with one or more other taxanes and/or with one or more chemotherapy agents of a different class(es).
  • Camptothecins are thought to complex with topoisomerase and DNA resulting in the inhibition and function of this enzyme. It is further believed that the presence of topoisomerase is required for on-going DNA synthesis.
  • Common camptothecins include, without limitation, Irinotecan, Topotecan, Etoposide, vinca alkaloids (e.g., Vincristine, Vinblastine or Vinorelbine), amsacrine, teniposide and the like. Camptothecins such as those mentioned above can be used in combination with one or more other camptothecins and/or with one or more chemotherapy agents of a different class(es).
  • Nitrosoureas are believed to inhibit changes necessary for DNA repair. Common nitrosoureas include, without limitation, Carmustine (BCNU), Lomustine (CCNU), semustine and the like. Nitrosoureas such as those mentioned above can be used in combination with one or more other nitrosoureas and/or with one or more chemotherapy agents of a different class(es).
  • EGFR (epidermal growth factor receptor) inhibitors are thought to inhibit EGFR and interfere with cellular responses including cell proliferation and differentiation.
  • EGFR inhibitors include molecules that inhibit the function or production of one or more EGFRs. They include small molecule inhibitors of EGFRs, antibodies to EGFRs, antisense oligomers, RNAi inhibitors and other oligomers that reduce the expression of EGFRs.
  • Common EGFR inhibitors include, without limitation, Gefitinib, Erlotinib (Tarceva ® ), Cetuximab (Erbitux ® ), panitumumab (VectibixTM'Amgen) lapatinib (GlaxoSmithKline), CI1033 or PD183805 or Canternib (6-acrylamide-N-(3-chloro-4-fluro ⁇ henyl)-7-(3-morpholinopropoxy)quinazolin-4- amine, Pfizer), and the like.
  • inhibitors include PKI-166 (4-[(lR)-l-phenylethylamino]- 6-(4-hydroxyphenyl)-7H-pyrrolo[2,3- ⁇ f
  • EGFR inhibitors such as those mentioned above can be used in combination with one or more other EGFR inhibitor
  • Antibiotics are thought to promote the formation of free oxygen radicals that result in DNA breaks leading to cancer cell death.
  • Common antibiotics include, without limitation, Bleomycin and rapamycin and the like.
  • the macrolide fungicide rapamycin also called RAP, Rapamune and Sirolimus
  • FKBP12 immunophilin FK506 binding protein 12
  • mTOR mammalian target of rapamycin
  • Rapamycin macrolides include naturally occurring forms of rapamycin as well as rapamycin analogs and derivatives that target and inhibit mTOR.
  • rapamycin macrolides include, without limitation, temsirolimus (CCI-779, Wyeth)), Everolimus and ABT-578.
  • Antibiotics such as those mentioned above can be used in combination with one or more other antibiotics and/or with one or more chemotherapy agents of a different class(es).
  • HER2/neu Inhibitors are believed to block the HER2 receptor and prevent the cascade of reactions necessary for tumor survival.
  • Her2 inhibitors include molecules that inhibit the function or production of Her2. They include small molecule inhibitors of Her2, antibodies to Her2, antisense oligomers, RNAi inhibitors and other oligomers that reduce the expression of tyrosine kinases. Common HER2/neu inhibitors include, without limitation, Trastuzumab (Herceptin ® , Genentech) and the like.
  • Her2/neu inhibitors include bispecific antibodies MDX-210(FC ⁇ Rl-Her2/neu) and MDX-447 (Medarex), pertuzumab (rhuMAb 2C4, Genentech), HER2/neu inhibitors such as those mentioned above can be used in combination with one or more other HER2/neu inhibitors and/or with one or more chemotherapy agents of a different class(es).
  • Angiogenesis inhibitors are believed to inhibit vascular endothelial growth factor , (VEGF), thereby inhibiting the formation of new blood vessels necessary for tumor life.
  • VEGF inhibitors include molecules that inhibit the function or production of one or more VEGFs. They include small molecule inhibitors of VEGF, antibodies to VEGF, antisense oligomers, RNAi inhibitors and other oligomers that reduce the expression of tyrosine kinases. Common angiogenesis inhibitors include, without limitation, Bevacizumab (Avastin®, Genentech).
  • angiogenesis inhibitors include, without limitation, ZD6474 (AstraZeneca), Bay-43-9006, sorafenib (Nexavar, Bayer), semaxamib (SU5416, Pharmacia), SU6668 (Pharmacia), ZD4190 (N-(4-bromo-2-fluorophenyl)-6-methoxy-7-[2-(lH-l,2,3- triazol-l-yl)ethoxy]quinazolin-4-amine, Astra Zeneca), ZactimaTM (ZD6474, N-(4-bromo-2- fluorophenyl)-6-methoxy-7-[2-(lH-l,2,3-triazol-l-yl)ethoxy]quinazolin-4-amine, Astra Zeneca), Vatalanib, (PTK787, Novartis), the monoclonal antibody IMC-ICl 1 (Imclone) and the like.
  • Angiogenesis inhibitors such
  • Aurora kinase inhibitors include, without limitation, compounds such as 4-(4-N benzoylamino)aniline)-6-methyxy-7-(3-(l-morpholino)propoxy)quinazoline (ZM447439, Ditchfield et al., J. Cell. Biol, 161:267-80 (2003)) and Hesperadin (Haaf et al., J. Cell Biol., 161: 281-94 (2003)).
  • SRC/Abl kinase inhibitors include without limitation, AZD0530 (4-(6-chloro-2,3- methylenedioxyanilino)-7-[2-(4-methylpiperazin-l-yl)ethoxy]-5-tetrahycropyran-4- yloxyquinazoline).
  • Tyrosine kinase inhibitors include molecules that inhibit the function or production of one or more tyrosine kinases.
  • CEP-701 and CEP-751 act as tyrosine kinase inhibitors.
  • Imatinib mesylate is a tyrosine kinase inhibitor that inhibits bcr-abl by binding to the ATP binding site of bcr-abl and competitively inhibiting the enzyme activity of the protein.
  • imatinib is quite selective for bcr-abl, it does also inhibit other targets such as c-kit and PDGF-R.
  • FLT-3 inhibitors include, without limitation, tandutinib (MLN518, Millenium), Sutent (SUl 1248, 5- [5-fluoro-2-oxo-l,2- dihydroindol-(3Z)-ylidenemethyl]-2, 4-dimethyl-lH-pyrrole-3-carboxylic acid [2- diethylaminoethyl] amide, Pfizer), midostaurin (4'-N-Benzoyl Staurosporine,_Novartis), lefunomide (SUlOl) and the like.
  • MEK inhibitors include, without limitation, 2-(2-Chloro-4- iodo-phenylamino)-N-cyclopropylmethoxy-3,4-difluoro-benzamide) (PD184352/CI-1044, Pfizer), PD198306 (Pfizer), PD98059 (2'-amino-3'-methoxyflavone), UO126 (Promega), Ro092210 from fermented microbial extracts (Roche), the resorcyclic acid lactone, L783277, also isolated from microbial extracts (Merck) and the like.
  • Tyrosine kinase inhibitors such as those mentioned above can be used in combination with one or more other tyrosine kinase inhibitors and/or with one or more chemotherapy agents of a different class(es). 13. Proteaosome Inhibitors
  • Proteaosome inhibitors are believed to inhibit the breakdown of some of these proteins that have been marked for destruction. This results in growth arrest or death of the cell.
  • Common proteaosome inhibitors include, without limitation, Bortezomib, ortezomib and the like. Proteaosome inhibitors such as those mentioned above can be used in combination with one or more other proteaosome inhibitors and/or with one or more chemotherapy agents of a different class(es).
  • Immunotherapies are thought to bind to and block specific targets, thereby disrupting the chain of events needed for tumor cell proliferation.
  • Common immunotherapies include, without limitation, Rituximab and other antibodies directed against CD20, Campath-1H and other antibodies directed against CD-50, epratuzmab and other antibodies directed against CD-22, galiximab and other antibodies directed atainst CD-80, apolizumab HUlDlO and other antibodies directed against HLA-DR, and the like.
  • Radioisotopes can be conjugated to the antibody, resulting in radioimmunotherapy.
  • Two such anti-CD20 products are tositumomab (Bexxar) and ibritumomab (Zevalin).
  • Immunotherapies such as those mentioned above can be used in combination with one or more other immunotherapies and/or with one or more chemotherapy agents of a different class(es).
  • Hormone therapies are thought to block cellular receptors, inhibit the in vivo production of hormones, and/or eliminate or modify hormone receptors on cells, all with the end result of slowing or stopping tumor proliferation.
  • Common hormone therapies include, without limitation, antiestrogens (e.g., tamoxifen, toremifene, fulvestrant, raloxifene, droloxifene, idoxyfene and the like), progestogens) e.g., megestrol acetate and the like) aromatase inhibitors (e.g., Anastrozole, Letrozole, Exemestane, vorazole, exemestane, fadrozole, aminoglutethimide, exemestane, l-methyl-l,4-androstadiene-3,17-dione and the like), anti-androgens (e.g., Bicalutimide, Nilutamide, Flutamide, cy
  • Photodynamic therapies expose a photosensitizing drug to specific wavelengths of light to kill cancer cells.
  • Common photodynamic therapies include, for example, porf ⁇ mer sodium (e.g., Photofrin ® ) and the like.
  • Photodynamic therapies such as those mentioned above can be used in combination with one or more other photodynamic therapies and/or with one or more chemotherapy agents of a different class(es).
  • Cancer vaccines are thought to utilize whole, inactivated tumor cells, whole proteins, peptide fragments, viral vectors and the like to generate an immune response that targets cancer cells.
  • Common cancer vaccines include, without limitation, modified tumor cells, peptide vaccine, dendritic vaccines, viral vector vaccines, heat shock protein vaccines and the like.
  • Two specific vaccines are CeaVac (Titan Pharmaceuticals, Inc., San Francisco), which mimics the carcinoembryonic antigen (CEA), and TriAb, which mimics the human milk fat globule (HMFG) antigen.
  • CEA carcinoembryonic antigen
  • HMFG human milk fat globule
  • One or both of the antigens are found in high concentrations in colorectal and other tumor types.
  • Histone deacetylase inhibitors are able to modulate transcriptional activity and consequently, can block angiogenesis and cell cycling, and promote apoptosis and differentiation.
  • Histone deacetylase inhibitors include, without limitation, SAHA (Suberoylanilide hydroxamic acid), depsipeptide (FK288) and analogs, Pivanex (Titan), CI994 (Pfizer), MS275 PXDlOl (CuraGen, TopoTarget) MGCD0103 (MethylGene), LBH589, NVP-LAQ824 (Novartis) and the like and have been used as chemotherapy agents.
  • Histone deacetylase inhibitors such as those mentioned above can be used in combination with one or more other histone deacetylase inhibitors and/or with one or more chemotherapy agents of a different class(es).
  • Ceramide has been shown to induce apoptosis, consequently, exogenous ceramide or a short chain ceramide analog such as N-acetylsphingosine (C 2 -Cer), C ⁇ -Cer or C 8 -Cer has been used.
  • Other analogs include, without limitation, Cer 1-glucuronide, poly(ethylene glycol)-derivatized ceramides and pegylated ceramides.
  • Modulators that stimulate ceramide synthesis have been used to increase ceramide levels.
  • Compounds that stimulate serine palmitoyltransferase, an enzyme involved in ceramide synthesis include, without limitation, tetrahydrocannabinol (THC) and synthetic analogs and anandamide, a naturally occurring mammalian cannabinoid.
  • THC tetrahydrocannabinol
  • Gemcitabine, retinoic acid and a derivative, fenretinide [N-(4-hycroxyphenyl)retinamide, (4-HPR)], camptothecin, homocamptothecin, etoposide, paclitaxel, daunorubicin and fludarabine have also been shown to increase ceramide levels.
  • valspodar PSC833, Novartis
  • a non-immunosuppressive non-ephrotoxic analog of cyclosporin and an inhibitor of p- glycoprotein increases ceramide levels.
  • Modulators of sphingomyelinases can increase ceramide levels. They include compounds that lower GSH levels, as GSH inhibits sphingomyelinases. For example, betathine ( ⁇ -alanyl cysteamine disulphide), oxidizes GSH, and has produced good effects in patients with myeloma, melanoma and breast cancer.
  • betathine ⁇ -alanyl cysteamine disulphide
  • COX-2 inhibitors such as celecoxib, ketoconazole, an antifungal agent, doxorubicin, mitoxantrone, D609 (tricyclodecan-9-yl- xanthogenate), dexamethasone, and Ara-C (l-/?-D-arabinofuranosylcytosine) also stimulate sphingomyelinases.
  • the enzyme, GlcCer glucosidase which is available for use in Gaucher' s disease, particularly with retinol or pentanol as glucose acceptors and/or an activator of the enzyme can be used as therapeutic agents.
  • Saposin C and analogs thereof, as well as analogs of the anti-psychotic drug, chloropromazine may also be useful.
  • Inhibitors of glucosylceramide synthesis include, without limitation, PDMP (N- [2- hydroxy-l-(4-mo ⁇ holinylmethyl)-2-phenylethyldecanamide]), PMPP (D,L-t/ ⁇ reo-(l-phenyl- 2-hexadecanoylamino-3-morpholino-l-propanol), P4 or PPPP (D-/ ⁇ reo-l-phenyl-2- palmitoylamino-3-pyrrolidino- 1 -propanol), ethylenedioxy-P4, 2-decanoylamine-3- morpholinoprophenone, tamixofen, raloxifene, mifepristone (RU486), N-butyl deoxynojirimycin and anti androgen chemotherapy (bicalutamide + leuprolide acetate).
  • PDMP N- [2- hydroxy-l-(4-mo ⁇ holinylmethyl)-2-
  • Inhibitors of ceramidase include, without limitation, N-oleoylethanolamine, a truncated form of ceramide, D-MAPP (D-eryr ⁇ ro-2-tetradecanoylamino-l -phenyl- 1-propanol) and the related inhibitor B 13 (p-nitro-D-MAPP).
  • Inhibitors of sphingosine kinase also result in increased levels of ceramide.
  • Inhibitors include, without limitation, safingol (L-tfire ⁇ -dihydrosphingosine), N,N-dimethyl sphingosine, trimethylsphingosine and analogs and derivatives of sphingosine such as dihydrosphingosine, and myriocin.
  • safingol L-tfire ⁇ -dihydrosphingosine
  • N,N-dimethyl sphingosine trimethylsphingosine
  • analogs and derivatives of sphingosine such as dihydrosphingosine, and myriocin.
  • ceramide levels include, without limitation, miltefosine (hexadecylphosphocholine).
  • Sphingolipid modulators such as those mentioned above, can be used in combination with one or more other sphingolipid modulators and/or with one or more chemotherapy agents of a different class(es).
  • oligonucleotides of the present invention include Genasense (oblimersen, G3139, from Genta), an antisense oligonucleotide that targets bcl-2 and G4460 (LR3001, from Genta) another antisense oligonucleotide that targets c-myb.
  • Genasense oblimersen, G3139, from Genta
  • an antisense oligonucleotide that targets bcl-2 and G4460 LR3001, from Genta
  • Other oligomers include, without limitation, siRNAs, decoys, RNAi oligonucleotides and the like.
  • Oligonucleotides, such as those mentioned above can be used in combination with one or more other oligonucleotide inhibitors and/or with one or more chemotherapy agents of a different class(es).
  • chemotherapeutic agents mentioned above are also apoptosis and/or oncogene inhibitors.
  • Others include gossypol, a compound isolated from the cotton plant, obatoclax (GeminX), a small molecule inhibitor of apoptosis, bcl-2 inhibitors AT-101 (Ascenta), ABT-737 (Abbott), IPI- 194 (Abbott), TR3/Nur77 analogs, including peptides, NF ⁇ B/IKK inhibitors, cck inhibitors, P52/MDM2 modulators, caspase activators and AKt/Pkb inhibitors.
  • Other inhibitors include those that inhibit enzymes necessary for some oncogenes to function, such as farnesyl transferase. Tipifarnib (ZarmestraTM, Johnson & Johnson) is one such inhibitor.
  • Chemotherapy agents can include cocktails of two or more chemotherapy drugs mentioned above.
  • a chemotherapy agent is a cocktail that includes two or more alkylating agents, platinums, anti-metabolites, anthracyclines, taxanes, camptothecins, nitrosoureas, EGFR inhibitors, antibiotics, HER2/neu inhibitors, angiogenesis inhibitors, kinase inhibitors, proteaosome inhibitors, immunotherapies, hormone therapies, photodynamic therapies, cancer vaccines, sphingolipid modulators, oligomers or combinations thereof.
  • the chemotherapy agent is a cocktail that includes an immunotherapy, an alkylating agent, an anthracycline, a camptothecin and Prednisone.
  • the chemotherapy agent is a cocktail that includes Rituximab, an alkylating agent, an anthracycline, a camptothecin and Prednisone.
  • the chemotherapy agent is a cocktail that includes Rituximab, Cyclophosphamide, an anthracycline, a camptothecin and Prednisone.
  • the chemotherapy agent is a cocktail that includes Rituximab, Cyclophosphamide, Doxorubicin, Vincristine and Prednisone (e.g., R-CHOPS).
  • the chemotherapy agent is a cocktail that includes doxorubicin, ifosfamide and Mesna.
  • the chemotherapy agent is a cocktail that includes an antimetabolite and a taxane.
  • the chemotherapy agent includes Gemcitabine and Taxotere.
  • the chemotherapy agent is a cocktail that includes dacarbazine, Mitomycin, Doxorubicin and Cisplatin.
  • the chemotherapy agent is a cocktail that includes Doxorubicin and dacarbazine.
  • the chemotherapy agent is a cocktail that includes an alkylating agent, a camptothecins, an anthracycline and dacarbazine.
  • the chemotherapy agent includes cyclophosphamide, vincristine, doxorubicin and dacarbazine.
  • the chemotherapy agent is a cocktail that includes an alkylating agent, methotrexate, an anti-metabolite and one or more anthracyclines.
  • the chemotherapy agent includes 5-fluorouracil, methotrexate, cyclophosphamide, doxorubicin and epirubicin.
  • the chemotherapy agent is a cocktail that includes a taxane and prednisone or estramustine.
  • the chemotherapy agent can include docetaxel combined with prednisone or estramustine.
  • the chemotherapy agent includes an anthracycline and prednisone.
  • the chemotherapy agent can include mitoxantrone and prednisone.
  • the chemotherapy agent includes a rapamycin macrolide and a kinase inhibitor.
  • the kinase inhibitors can be EGFR, Her2/neu, VEGF, Aurora kinase, SRC/Abl kinase, tyrosine kinase and/or MEK inhibitors.
  • the chemotherapy agent includes two or more sphingolipid modulators.
  • the chemotherapy agent includes an oligomer, such as Genasense and one or more alkylating agents, platinums, anti-metabolites, anthracyclines, taxanes, camptothecins, nitrosoureas, EGFR inhibitors, antibiotics, HER2/neu inhibitors, angiogenesis inhibitors, kinase inhibitors, proteaosome inhibitors, immunotherapies, hormone therapies, photodynamic therapies, cancer vaccines, sphingolipid modulators or combinations thereof.
  • an oligomer such as Genasense and one or more alkylating agents, platinums, anti-metabolites, anthracyclines, taxanes, camptothecins, nitrosoureas, EGFR inhibitors, antibiotics, HER2/neu inhibitors, angiogenesis inhibitors, kinase inhibitors, proteaosome inhibitors, immunotherapies, hormone therapies, photodynamic therapies, cancer vaccines, sphingolipid modulators or combinations thereof.
  • the chemotherapy agent is a cocktail that includes an anthracycline and a taxane.
  • the chemotherapy agent is a cocktail that includes doxorubicin and paclitaxel or abraxane.
  • the chemotherapy agent is a cocktail that includes an antimetabolite and a taxane.
  • the chemotherapy agent includes gemcitabine and taxotere.
  • the chemotherapy agent is a cocktail that includes an immunotherapy and a taxane.
  • the chemotherapy agent includes taxotere and trastuzumab.
  • the chemotherapy agent includes taxotere and bevacizumab.
  • the agent includes a taxane and an antimetabolite. In another embodiment the agent includes a taxane, an antimetabloite and a platinum.
  • the agent can include taxotere, gemcitibine, and capecitabine; or the agent can include taxotere, gemcitibine, capecitabine and cisplatin.
  • the agent comprises rituximab.
  • the agent comprises doxitaxel.
  • the chemotherapy drug or drugs composing the chemotherapy agent can be administered in combination therapies with other agents, or they may be administered sequentially or concurrently to the patient.
  • radiation therapy is administered in addition to the administration of an oligonucleotide compound.
  • Radiation therapy includes both external and internal radiation therapies.
  • External radiation therapies include directing high-energy rays (e.g., x-rays, gamma rays, and the like) or particles (alpha particles, beta particles, protons, neutrons and the like) at the cancer and the normal tissue surrounding it.
  • the radiation is produced outside the patient's body in a machine called a linear accelerator.
  • External radiation therapies can be combined with chemotherapies, surgery or oligonucleotide compounds.
  • Internal radiation therapies include placing the source of the high-energy rays inside the body, as close as possible to the cancer cells. Internal radiation therapies can be combined with external radiation therapies, chemotherapies or surgery. [0388] Radiation therapy can be administered with chemotherapy simultaneously, concurrently, or separately. Moreover radiation therapy can be administered with surgery simultaneously, concurrently, or separately.
  • cancerous tissue can be excised from a patient using any suitable surgical procedure including, for example, laparoscopy, scalpel, laser, scissors and the like.
  • surgery is combined with chemotherapy.
  • surgery is combined with radiation therapy.
  • surgery is combined with both chemotherapy and radiation therapy.
  • a pharmaceutical composition comprises one or more oligonucleotide compounds and a chemotherapy agent.
  • a pharmaceutical composition comprises a oligonucleotide compound having SEQ.IDNO:1250, 1251, 1252, or 1253 sequestered in a liposome and one or more of an alkylating agent, a platinum, an antimetabolite, an anthracycline, a taxane, a camptothecins, a nitrosourea, an EGFR inhibitor, an antibiotic, a HER2/neu inhibitor, an angiogenesis inhibitor, a proteaosome inhibitor, an immunotherapy, a hormone therapy, a photodynamic therapy, a cancer vaccine, other chemotherapy agents such as those illustrated in Table 1, or combinations thereof.
  • the pharmaceutical composition comprises an oligonucleotide compound and a chemotherapy agent including an immunotherapy, an alkylating agent, an anthracycline, a camptothecin and Prednisone.
  • the pharmaceutical composition comprises one or more oligonucleotide compounds comprising SEQ ID NOs 2-281, 283-461, 463-935, 937-1080, 1082-1248, 1250-1254 and 1267-1477 sequestered in a liposome, and complements thereof; and a chemotherapy agent including an immunotherapy, an alkylating agent, an anthracycline, a camptothecin, and Prednisone.
  • the pharmaceutical composition comprises an oligonucleotide compound and a chemotherapy agent that includes Rituximab, Cyclophosphamide, an anthracycline, a camptothecin and Prednisone.
  • the pharmaceutical composition comprises an oligonucleotide and a chemotherapy agent including Rituximab, Cyclophosphamide, Doxorubicin, Vincristine and Prednisone (e.g., R-CHOPS).
  • the pharmaceutical composition comprises an oligonucleotide comprising SEQ ID NO: 1251 sequestered in a liposome and doxocycline. In still another embodiment, the pharmaceutical composition comprises an oligonucleotide comprising SEQ ID NO: 1251 sequestered in a liposome and rituximab.
  • the pharmaceutical composition comprises an oligonucleotide comprising SEQ ID NO:940 or SEQ ID NO:943 or the complement thereof sequestered in a liposome and one or more of doxorubicin, paclitaxel, abraxane, gemcitabine, taxotere, trastuzumab, bevacizumab, capecitabine and cisplatin.
  • Other embodiments of the invention provide pharmaceutical compositions containing (a) one or more oligonucleotide compounds and (b) a chemotherapy agent. Examples of such chemotherapeutic agents include, without limitation, those listed above.
  • Anti-inflammatory drugs including but not limited to nonsteroidal anti-inflammatory drugs and corticosteroids, and antiviral drugs, including but not limited to ribivirin, vidarabine, acyclovir and ganciclovir, may also be combined in compositions of the invention.
  • Other non-oligonucleotide chemotherapeutic agents are also within the scope of this invention. Two or more combined compounds may be used together or sequentially. For example, in one embodiment, an oligomer sequestered in a liposome is administered once daily for five or more days and the chemotherapy agent is administered every second day for one week or more.
  • compositions of the present invention can optionally include medicaments such as anesthesia, nutritional supplements (e.g., vitamins, minerals, protein and the like), chromophores, combinations thereof, and the like.
  • medicaments such as anesthesia, nutritional supplements (e.g., vitamins, minerals, protein and the like), chromophores, combinations thereof, and the like.
  • compositions of the present invention may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, intranasally, intraoccularly, buccally, vaginally, or via an implanted reservoir.
  • parenteral as used herein includes subcutaneous, intravenous, intramuscular, intra-articular, intra-synovial, intrasternal, intrathecal, intrahepatic, intralesional and intracranial injection or infusion techniques.
  • the compositions are administered orally, intraperitoneally or intravenously.
  • Sterile injectable forms of the compositions of this invention may be aqueous or oleaginous suspension.
  • suspensions may be formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally- acceptable diluent or solvent, for example as a solution in 1,3-butanediol.
  • acceptable vehicles and solvents that may be employed are water, Ringer's solution and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil may be employed including synthetic mono- or di-glycerides.
  • Fatty acids such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions.
  • These oil solutions or suspensions may also contain a long-chain alcohol diluent or dispersant, such as carboxymethyl cellulose or similar dispersing agents that are commonly used in the formulation of pharmaceutically acceptable dosage forms including emulsions and suspensions.
  • compositions of this invention may be orally administered in any orally acceptable dosage form including, but not limited to, capsules, tablets, aqueous suspensions or solutions.
  • carriers commonly used include lactose and corn starch.
  • Lubricating agents such as magnesium stearate, are also typically added.
  • useful diluents include lactose and dried cornstarch.
  • the pharmaceutically acceptable compositions of this invention may be administered in the form of suppositories for rectal administration. These can be prepared by mixing the agent with a suitable non-irritating excipient that is solid at room temperature but liquid at rectal temperature and therefore will melt in the rectum to release the drug. Such materials include cocoa butter, beeswax and polyethylene glycols.
  • a suitable non-irritating excipient that is solid at room temperature but liquid at rectal temperature and therefore will melt in the rectum to release the drug.
  • Such materials include cocoa butter, beeswax and polyethylene glycols.
  • the pharmaceutically acceptable compositions of this invention may also be administered topically, especially when the target of treatment includes areas or organs readily accessible by topical application, including diseases of the eye, the skin or the lower intestinal tract. Suitable topical formulations are readily prepared for each of these areas or organs.
  • Topical application for the lower intestinal tract can be effected in a rectal suppository formulation (see above) or in a suitable enema formulation. Topically- transdermal patches may also be used.
  • the pharmaceutically acceptable compositions may be formulated in a suitable ointment containing the active component suspended or dissolved in one or more carriers.
  • Carriers for topical administration of the compounds of this invention include, but are not limited to, mineral oil, liquid petrolatum, white petrolatum, propylene glycol, polyoxyethylene, polyoxypropylene compound, emulsifying wax and water.
  • the pharmaceutically acceptable compositions can be formulated in a suitable lotion or cream containing the active components suspended or dissolved in one or more pharmaceutically acceptable carriers.
  • Suitable carriers include, but are not limited to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol,
  • the pharmaceutically acceptable compositions may be formulated as micronized suspensions in isotonic, pH adjusted sterile saline, or, preferably, as solutions in isotonic, pH adjusted sterile saline, either with or without a preservative such as benzylalkonium chloride.
  • the pharmaceutically acceptable compositions may be formulated in an ointment such as petrolatum.
  • compositions of this invention may also be administered by nasal aerosol or inhalation.
  • Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and may be prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other conventional solubilizing or dispersing agents.
  • compositions of this invention are formulated for oral administration.
  • compositions should be formulated so that a dosage of between 0.01-100 mg/kg body weight/day of the modulator can be administered to a patient receiving these compositions.
  • a specific dosage and treatment regimen for any particular patient will depend upon a variety of factors, including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, rate of excretion, drug combination, and the judgment of the treating physician and the severity of the particular disease being treated.
  • the amount of a compound of the present invention in the composition will also depend upon the particular compound in the composition.
  • additional therapeutic agents which are normally administered to treat or prevent that condition, may also be present in the compositions of this invention.
  • additional therapeutic agents normally administered to treat or prevent a particular disease, or condition are known as "appropriate for the disease, or condition, being treated.”
  • EXAMPLE 2 Production of Amphoteric Liposomes Charged with Oligonucleotides Using a Lipid Film-Hydration Method
  • the lipid composition of the liposomes as well as the methods of preparing them are chosen so that the encapsulation efficiency is greater than 35 % and the liposome size smaller than 200 ⁇ m, and ideally near 100 ⁇ m to maximize tumor penetration.
  • the DNAi oligonucleotide concentration should be at least 2 mg/mL at a lipid concentration of 100 mM or less. This allows dosing at 10 mg/kg in 200 uL of injection volume.
  • One method for preparing liposomes is by a modified lipid film / hydration / extrusion method. Lipids are dissolved in chloroform or chloroform/methanol and dried completely in a rotary evaporator. The lipid films are next hydrated with various amounts of the oligonucleotides SEQ ID NO: 1251 (PNTlOO) or the complement of PNT-100 (PNT-IOOR) hydrated in buffer.
  • the lipid film is hydrated with PBS containing 405 mg oligonucleotides for 1 hr at 40° C at a final lipid concentration of 100 mM. After three freeze-thaw steps, the resulting vesicles are extruded through a polycarbonate membrane stack containing different pore sizes between 100 and 800 ⁇ m. The resulting suspension is sedimented three times at 25s.
  • PBS is Phosphate Buffered Saline, which has the formula: 10.1 mM Na 2 PO 4 , 1.76 mM KH 2 PO 4 , 137 mM NaCl, 2.68 mM KCl, pH 7.5.
  • the vesicles are prepared by either the passive or advanced loading procedure and extruded using a device for producing lipid vesicles (See, for example, U.S. Patent No. 6,843,942 and U.S. Patent Application No. 2004/0032037, each of which is incorporated by reference herein in its entirety).
  • Particle properties were measured using a Zetasizer 3000 HAS (Malvern) or a Nicomp 370. Liposomes were diluted in appropriate buffer to a final lipid concentration of 0.2 - 0.6 mM. Size values are recorded as Z average and size distribution was calculated in the Multimodal mode. For Zeta potential measurement, liposomes were also diluted to 0.2 - 0.6 mM.
  • formulation B with DOTAP at 10 % could not be loaded efficiently by the advanced loading procedure, and the passive loading procedure was used.
  • a ratio of cationic lipid charge to anionic nucleotide charge at low pH (N/P) of 3.3 was found to be the best compromise to produce small particles, high encapsulation efficiency and oligonucleotide concentration to lipid concentration of at least 2.0 mg/mL of oligonucleotide at 100 mM lipid concentration.
  • Liposomes were prepared as described in U.S. Patent No. 6,843,942.
  • lipid-oligonucleotide mixture 15 mL of ethanol.
  • the ethanolic lipid solution at 55° C was injected into 40 mL of a solution of an oligonucleotide in 20 mM sodium acetate, pH 4.0 and mixed continuously.
  • the rates of mixing were 400 mL/min of the oligonucleotide mixture and 170 mL/min of the lipid mixture.
  • the lipid-oligonucleotide mixture was immediately diluted (cross-flow injection) with 160 mL of an aqueous solution of 100 mM NaCl, 136 mM Na 2 HPO 4 , pH 9.0.
  • Liposomes were prepared using increasing oligonucleotide amounts as shown below in Table
  • Liposomes were extruded using a Lipex extruder (Lipex Biomembranes, Inc.,
  • the liposomal mixture was dialyzed or ultrafiltered to remove unincorporated oligonucleotides and to remove ethanol.
  • the liposome suspension was filtered through a Pall Mini
  • Kleenpack capsule equipped with a 0.22 ⁇ m Supor membrane (Pall Corp. East Hills, NY).
  • the oligonucleotide used in the above experiments is SEQ ID NO: 1251.
  • Z is the average diameter of the liposomes
  • PDI is the polydispersity index.
  • the batches were also both extruded and filtered.
  • the amount of the oligonucleotide recovered, determined by HPLC, is shown in Table 4. The sample was first extracted with methanol-chloroform, centrifuged and the aqueous layer was analyzed by HPLC.
  • the HPLC column was a Dionex DNApac PA200, 250 x 4 mm.
  • the mobile phase was solvent A: 100 mM TRIS pH 8.0, 10 % acetonitrile and solvent B: 100 mM TRIS pH 8.0, 2 M LiCl, 10 % acetonitrile.
  • the flow rate was 1.5 mL/min.
  • the column temperature was 7O 0 C, autosampler temperature 5 0 C, injector volume 10 ⁇ L, and the detector wavelength was 260 ⁇ m. Table 4
  • the oligonucleotide used in the above experiments is SEQ ID NO: 1251.
  • the amount of oligonucleotide used for each batch is indicated in Table 3.
  • Direct + ExIOO indicates that the liposomes were extruded through a 100 ⁇ m membrane.
  • the size (Fig. 3A) and polydispersity indices (Fig. 3B) data indicate that liposomes generated by additional extrusion through 100 ⁇ m membranes are very similar to liposomes generated by 200 ⁇ m extrusion.
  • the amount of released oligonucleotide is strongly affected by the additional 100 ⁇ m step as shown in Fig. 3C.
  • Liposomes were produced as described in Example 3 to yield about 170 mL of liposome suspensions.
  • the liposomes were extruded three to five times through 0.2 ⁇ m polycarbonate membranes using a 47 mm Millipore high pressure filter holder.
  • 10 mL of liposomal suspensions were extruded using the Lipex extruder. Both extrusion devices were pressurized with nitrogen at 6 - 9 bar and the flow rate was between 40 and 70 mL per minute.
  • Three batches calculated to yield a final concentration of 3.2, 3.6 and 4.0 mg/mL of oligonucleotide were prepared. The amount of oligonucleotide to yield a final concentration of 3.2 mg/mL is 90 mg on the small scale production described in Example 3.
  • the average sizes and polydispersity indices of the different batches are shown in Table 5. Table 5
  • DNAi-liposomes used to treat tumors in mice were prepared by the above methods. Briefly, 3 volumes of ethanol, containing the lipid mixture D (POPC/DOPE/MoChol/Chems 6:24:47:23) (133 mM, heated to 55° C) and 8 volumes of 20 mM NaAc/300 mM Sucrose/pH 4, containing 2.71 mg/mL PNTlOO (SEQ ED NO:1251) or PNTlOO-R (SEQ ID NO: 1288) in case of PNT2254 or PNT2254R production, or containing 1.36 mg/mL PNTlOO in case of PNT2253 production, were continuously mixed using an injection device as disclosed in US Patent 6,843,942 and US patent application No.
  • the acidic mixture was shifted to pH 7.5 by an additional continuous mixing step with 32 volumes of 100 mM NaCl, 136 mM Phosphate, pH 9.
  • the resulting liposomal suspension was concentrated 10 fold and dialyzed against PBS, pH 7.4 to wash out non- encapsulated PNTlOO or PNTlOO-R and excess ethanol.
  • the concentration of PNT-100 in PNT2253 and PNT2254 are 2.0 mg/mL and 4.0 mg/mL, respectively.
  • Example 4 The three batches described in Example 4 were frozen at -70 ° C and stored for two days at -20 0 C to simulate a freezing procedure and to test for oligonucleotide release. After thawing at room temperature, samples were analyzed for size and size distribution. The three batches contained 5 % sucrose in the final solution. Data in Table 5 above indicate that freezing and thawing of the liposomes further improves homogeneity. In addition, liposomes were filtered in an Amicon stirring cell and the filtrate was analyzed for possible oligonucleotide release due to freezing and thawing. Released oligonucleotide was below 1
  • sucrose at a final concentration of 300 mM was added to the oligonucleotide solution before mixing with the lipid mixture.
  • sucrose was added to the loaded liposomes to a final concentration of 5 - 10 %.
  • mice Seven days after transplantation, mice were injected intravenously with 10 mg/kg of the PNT-100 (SEQ ID NO: 1251) formulations and 10 mg/kg of PNT-100R (SEQ ID NO: 1288) formulations. The injections were performed daily for 8 days in six mice. The size of the tumors was measured up to 30 days after implantation. All animals survived with no gross toxic pathology.
  • PNT-100 SEQ ID NO: 1251
  • PNT-100R SEQ ID NO: 1288
  • Results in Figure 6 show that PNT-100 slows tumor growth.
  • 340.9 and 340.8 are formulations with PNT-100 and PNT-100R, respectively.
  • the tumor burden was calculated from the size measurements of the tumors.
  • Fig. 8 shows that the tumor burden in mice treated with PNT2253 was dramatically less than the tumor burden in mice treated with PNT2253R (PNT-IOOR in formulation D) or PBS.
  • a dose response experiment was performed in WSU-DLCL2 xenograft bearing mice with PNT-100 in formulation D, with a PNT-100 concentration of 4 mg/mL (PNT2254) and 2 mg/mL (PNT2253).
  • C.B.-17 ACID mice between 6 and 8 weeks old were supplied by Taconic (Hudson, NY). When the tumors reached approximately 100 mm 3 volume, treatment with PNT2253 or PNT2254 was initiated.
  • the animals were checked at least three times weekly for tumor growth by caliper measurements, and the animals were weighed at least three times weekly. Tumor volumes of all treatment groups were analyzed using GraphPadTM statistical software.
  • a maximum tolerated dose of 20 mg/kg/day of PNT2254 and 10 mg/kg/day of PNT2253 was established. (Figs. 9 and 10) Toxicity was achieved at 30 mg/kg/day for PNT2254 and at 20 mg/kg/day for PNT2253, and dosing was stopped after two days due to animal efficacy. A steep dose response was seen with strong anti-tumor efficacy for an extended time period after one dosing cycle. The effect of the two formulations at various dosages on body weight of the mice was determined and is shown in Fig. 11. For both formulations, a dose of 10 mg/kg/day was efficacious while causing minimal weight loss. [0449] A mathematical measure of each dose was calculated that determined the drug response in delaying tumor growth rate to 750 mg size in PNT2254 and PNT2253 drugged vs. control non-drugged tumors (Tables 7 and 8).
  • T and C are the median times in days for the treatment group (T) and the control group (C) tumors to reach a predetermined weight (750 mg).
  • T-C is a measure of tumor growth delay and is the difference in the median days to 750 mg between the treated (T) and the control (C) group.
  • Log 10 kill Gross T-C value in days/3.32 X T d .
  • T d is the mean tumor doubling time (days) estimated from a log-linear growth plot of the control tumors growing in exponential phase. The higher the Logio kill Gross value, the more efficacious the drug, and a value over 2.8 is considered highly efficacious (Corbett, T.H.
  • PNT2253 treatment resulted in increased toxicity compared to PNT2254.
  • the most efficacious dose was 10 mg/kg/day for both PNT2253 and PNT2254, and the maximum tolerated dose is 20 mg/kg/day for PNT2254 and 10 mg/kg/day of PNT2253.
  • mice were generated in mice as described in Example 6. A total of 48 mice were used for the study and were divided into six days after xenograft trocar transplantation. Approximate animal tumor volumes were sized matched to standardize starting cohorts for average tumor size. Mice bearing approximately 100 mm 3 xenografts were injected intravenously with 10 mg/kg of PNT2255F or PNT22255R as shown in Table 9. Table 9
  • the dosage is 10 mg/kg of PNT-100. *One animal did not develop a palpable tumor.
  • Animals were checked three times weekly for tumor growth by caliper measurements until the end of the study. An approximate tumor volume was calculated using the formula V ⁇ (a x b 2 ), where b is the smaller of two perpendicular diameters. Animals were also weighed three times weekly for the duration of the study. Animals were sacrificed when tumors exceeded 2000 mm 3 volume.
  • TTE Tumor growth delay
  • the value for b is the (y) intercept and m is the slope of the line calculated from a linear regression of log-transformed tumor growth data for each tumor calculated from a minimum of three time points preceding 750 mm 3 and a minimum of one that surpassed the time point for 750 mm 3 .
  • Mice with tumors were administered PNT2255 and/or rituximab on days 4-8 post trocar and tumors were monitored until animals were euthanized due to tumors reaching a 2000 mm 3 endpoint or on day 81, which was the conclusion of the study. Tumors that did not reach 750 mm3 by day 81 were assigned TTE values of 81 days.
  • Treatment efficacy was determined by comparing TTE values calculated for each treatment group and by calculating TGD (T-C) for each drug treatment group where T represents the median TTE in days for each drug treatment group and C represents the median TTE in days for the control group.
  • T represents the median TTE in days for each drug treatment group
  • C represents the median TTE in days for the control group.
  • the student's t test with Mann-Whitney ranking analysis was performed for the comparison of each study group TTE value for significance. A 95 % confidence value was used and a Mann-Whitney U ⁇ 18 value was considered significant with 0 being most significant.
  • Mann-Whitney analysis is a method that analyzes each study tumor independently for statistical significance comparisons between treatment groups. There were no non-treatment related deaths (NTR), non-treatment metastatic related deaths (NTRm), and treatment related deaths (TR) in this study.
  • MTV mean tumor volume growth curves with standard error were calculated for each treatment group. The mean values excluded euthanized animals one time point after the day of euthanasia. Kaplan-Meier plots were generated with Prism 4.0 software to plot the percentage of animals that survived with tumors below 2000 mm 3 . [0460] As shown in Table 9 above, eight animals were dosed in all cohorts except for the PNT2255R cohort that had seven animals dosed because one animal did not form a palpable tumor. Tumors grew progressively in all control animals with a median TTE value of 17.7 days, and all tumors grew progressively until day 29 when tumor burden reached 2000 mm 3 in all animals.
  • TGD Tumor Growth Delay
  • C is the median TTE for control tumors.
  • TFS is the number of tumor free survivors; CR (Complete Response) indicates the number of mice whose tumors disappeared; PR (Partial Response) indicates the number of mice whose tumors reduced in size.
  • the antitumor efficacy data in Figure 14, the mouse body weight data in Figure 15, and the mean TTE statistical comparison ( Figure 16) analysis illustrate several important findings about the efficacy seen with PNT2255 and rituximab therapy.
  • PNT2255F at 10 mg/kg administered daily for five days resulted in 4/8 tumors with complete responses (CR) and 2/8 tumor free survivors through day 81. 5/8 animals had partial responses (PR) and 6/8 animals reached 2000 mm 3 tumor burden by day 57.
  • PNT2255R at 10 mg/kg administered daily for five days resulted in 1/7 tumors with complete responses (CR) and 0/7 tumor free survivors through day 81.
  • Rituximab at 20 mg/kg administered on days 2 and 5 resulted in 7/8 tumors with complete responses (CR) and 4/8 tumor free survivors through day 81.
  • PNT2255R at 10 mg/kg administered daily for five days along with rituxiamb at 20 mg/kg administered on days 2 and 5 resulted in 6/8 tumors with complete responses (CR) and 5/8 tumor free survivors through day 81.
  • PNT2255R and PNT2255F single-agent therapy demonstrated significant tumor growth delay indicated by extended TTE and TGD values compared to controls.
  • PNT2255F was more efficacious that PNT2255R with a 2 times greater TGD value (23.1 days vs. 11.4 days).
  • PNT2255F treatment resulted in 2/8 tumor free survivors and 5/8 complete responses compared to 0/7 tumor free survivors and 1/7 complete responses obtained with PNT2255R.
  • PNT 2256 is a PNT-100 liposomal preparation, prepared as in Example 4 with sucrose added before freezing and thawing. PNT2256 contains 4 mg/mL of PNT-100. Tumors from WSU-DLCL2 cells were generated in mice and animals were treated as described in Example 8. Mice were treated with frozen and thawed PNT2256 with three different administration regimens: (1) i.v. injection daily for five days; i.v. injection every other day for two weeks and i.v. injection every third day for three weeks. The results are shown in Figure 18 and Table 11. Table 11
  • PNT2256F at 10 mg/kg administered daily for five days resulted in 4/7 tumors with complete responses (CR) and 1/7 tumor free survivors through day 81. 5/7 animals had partial responses (PR).
  • the median TTE value was 47.7 days and the TGD value was 23.1 days.
  • PNT2256F at 10 mg/kg administered every other day for two weeks resulted in 0/7 tumors with complete responses (CR) and 0/7 tumor free survivors through day 81. 0/7 animals had partial responses (PR).
  • the median TTE value was 18.3 days and the TGD value was 8.4 days.
  • PNT2256F at 10 mg/kg administered every third day for three weeks resulted in 0/7 tumors with complete responses (CR) and 0/7 tumor free survivors through day 81. 0/7 animals had partial responses (PR).
  • the median TTE value was 19.6 days and the TGD value was 9.5 days.
  • PNT2256F at 10 mg/kg administered daily for five days in combination with rituximab administered at 20 mg/kg administered on days 2 and 5 resulted in 4/7 tumors with complete responses (CR) and 2/7 tumor free survivors through day 81. 4/7 animals had partial responses (PR).
  • the median TTE value was 76.1 days and the TGD value was 66.0 days.

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Abstract

The invention provides compositions comprising DNAi-oligonucleotides sequestered in stable, size-selected amphoteric liposomes for treating cancer. The invention also provides methods of preparing the compositions.

Description

DNAi AMPHOTERIC LIPOSOME FORMULATION
This application claims the benefit of the U.S. Provisional Application No. 60/979,891 filed on October 15, 2007 which is herein incorporated by reference.
BRIEF DESCRIPTION OF THE INVENTION
[001] The invention relates to compositions and methods of using the same to treat cancer. In particular, the invention provides oligonucleotides sequestered with stable, size-selected amphoteric liposomes for the treatment of cancer.
BACKGROUND
[002] Oncogenes have become the central concept in understanding cancer biology and may provide valuable targets for therapeutic drugs. In many types of human tumors, including lymphomas and leukemias, the oncogenes are overexpressed, and may be associated with tumorigenicity (Tsujimoto et al, Science 228:1440-1443 (1985)). For instance, high levels of expression of the human bcl-2 gene have been found in all lymphomas with a t(14; 18) chromosomal translocations including most follicular B cell lymphomas and many large cell non-Hodgkin's lymphomas. High levels of bcl-2 gene expression have also been found in certain leukemias that do not have a t(14; 18) chromosomal translation, including most cases of chronic lymphocytic leukemia acute, many lymphocytic leukemias of the pre-B cell type, neuroblastomas, nasophryngeal carcinomas, and many adenocarcinomas of the prostate, breast and colon. (Reed et al, Cancer Res. 51 :6529 [1991]; Yunis et al, New England J. Med. 320:1047; Campos et al, Blood 81:3091-3096 [1993]; McDonnell et al, Cancer Res. 52:6940-6944 [1992); Lu et al, Int. J Cancer 53:29-35 [1993]; Bonner et al, Lab Invest. 68:43 A [1993]. Other oncogenes include TGF-α, c-ki-ras, ras, Her-2 and c-myc. [003] The expression of oncogenes may be inhibited by single stranded DNAi oligonucleotides. Nucleic acid therapeutics, however, often lack therapeutic efficacy due to instability in body fluids or inefficient uptake into cells.
[004] There is therefore a need for a stable and efficient delivery of such DNAi oligonucleotides in body fluids and cells for the treatment of cancer.
SUMMARY OF THE INVENTION
[005] The invention provides compositions and methods for preparing and using liposomes for the delivery of DNAi oligonucleotides for the treatment of cancer. In general, the invention relates to liposomes that have an amphoteric character, e.g., the liposomes have an anionic or neutral charge at physiological pH and a cationic charge at an acidic pH of about 4. The invention also relates to size selected DNAi-amphoteric liposomal mixtures that are stable over time. Advantageously, the amphoteric liposomes of the present invention exhibit high sequestration efficiency, where the DNAi liposomes have a final DNAi oligonucleotide concentration between about 1 to 4 mg/mL (e.g., about 2 mg/mL) at a lipid concentration of about 100 mM or less; colloidal and serum stability; enhanced uptake into cells and tumors due to average liposome sizes of less than 200 ηm; and low toxicity relative to liposomes formed with cationic lipids that are used in conventional transfection reagents. Furthermore, amphoteric liposomes containing a DNAi oligonucleotide and a cryoprotectant, a lyoprotectant and/or a stabilizer may be frozen and thawed and/or lyophilized and reconstituted, and retain efficacy in treating tumors. In addition, DNAi-amphoteric liposomes have a defined average diameter and a low polydispersity index, which have improved efficacy in treating tumors.
[006] In a first aspect, the invention provides amphoteric liposomes, a DNAi oligonucleotide and a cryoprotectant and/or lyoprotectant. In an embodiment of the first aspect, the cryoprotectant and/or lyoprotectant is a disaccharide. In a further embodiment, the cryoprotectant and/or lyoprotectant is mannitol, sucrose or trehalose, or a combination thereof. In another embodiment, the cryoprotectant is a combination of two or more cryoprotectants.
[007] In another embodiment of the first aspect, the amphoteric liposomes have an isoelectric point of between 4 and 8. In a further embodiment, the amphoteric liposomes are negatively charged or neutral at pH 7.4 and positively charged at pH 4. [008] In yet another embodiment of the first aspect, the amphoteric liposomes include amphoteric lipids. In a further embodiment, the amphoteric lipids can be HistChol, HistDG, isoHistSucc DG, Acylcarnosine, HCChol or combinations thereof. In another embodiment, the amphoteric liposomes include a mixture of one or more cationic lipids and one or more anionic lipids. In yet another embodiment, the cationic lipids can be DMTAP, DPTAP, DOTAP, DC-Choi, MoChol and HisChol, or combinations thereof, and the anionic lipids can be CHEMS, DGSucc, Cet-P, DMGSucc, DOGSucc, POGSucc, DPGSucc, DG Succ, DMPS, DPPS, DOPS, POPS, DMPG, DPPG, DOPG, POPG, DMPA, DPPA, DOPA, POPA or combinations thereof.
[009] In another embodiment, the liposomes also include neutral lipids. In a further embodiment, the neutral lipids include sterols and derivatives thereof. In an even further embodiment, the sterols comprise cholesterol and derivatives thereof. The neutral lipids may also include neutral phospholipids. In one embodiment, the phospholipids include phosphatidylcholines or phosphatidylcholines and phosphoethanolamines. In another embodiment, the phosphatidylcholines are POPC, OPPC, natural or hydrogenated soy bean PC, natural or hydrogenated egg PC, DMPC, DPPC or DOPC and derivatives thereof and the phosphatidylethanolamines are DOPE, DMPE, DPPE or derivatives and combinations thereof. In a further embodiment, the phosphatidylcholine is POPC, OPPC, soy bean PC or egg PC and the phosphatidylethanolamines is DOPE.
[010] In an even further embodiment, the lipids of the amphoteric liposomes include DOPE, POPC, CHEMS and MoChol; POPC, Choi, CHEMS and DOTAP; POPC, Choi, Cet-P and MoChol, or POPC, DOPE, MoChol and DMGSucc.
[Oil] In a second aspect, the DNAi-amphoteric liposomes can be formed from a lipid phase comprising a mixture of lipid components with amphoteric properties, wherein the total amount of charged lipids in the liposome can vary from 5 mole % to 70 mole %, the total amount of neutral lipids may vary from 20 mole % to 70 mole %, a DNAi oligonucleotide and a cryoprotectant. In an embodiment of the second aspect, the amphoteric liposomes include 3 to 20 mole % of POPC, 10 to 60 mole % of DOPE, 10 to 60 mole % of MoChol and 10 to 60 mole % of CHEMS. In a further embodiment, the liposomes include POPC, DOPE, MoChol and CHEMS in the molar ratios of POPC/DOPE/MoChol/CHEMS of about 6/24/47/23 or 15/45/20/20. In yet another embodiment, the liposomes include 3 to 20 mole % of POPC, 10 to 40 mole % of DOPE, 15 to 60 mole % of MoChol and 15 to 60 mole % of DMGSucc. In a further embodiment, the liposomes include POPC, DOPE, DMGSucc and MoChol in the molar ratios of POPC/DOPE/DMGSucc/MoChol of about 6/24/47/23 or 6/24/23/47. In still another embodiment, the liposomes include 10 to 50 mole % of POPC, 20 to 60 mole % of Choi, 10 to 40 mole % of CHEMS and 5 to 20 mole % of DOTAP. In a further embodiment, the liposomes include POPC, Choi, CHEMS and DOTAP in the molar ratio of POPC/Chol/CHEMS/DOTAP of about 30/40/20/10. In yet another embodiment the liposomes include 10 to 40 mole % of POPC, 20 to 50 mole % of Choi, 5 to 30 mole % of Cet-P and 10 to 40 mole % of MoChol. In a further embodiment, the molar ratio of POPC/Chol/Cet-P/MoChol is about 35/35/10/20.
[012] In a third aspect the DNAi oligonucleotide contained in the liposomal mixture comprises an oligomer that hybridizes to SEQ ID NO: 1249, the complement of SEQ ID NO: 1249 or portions thereof. In one embodiment, the oligomer can be SEQ ID NO: 1250, 1251, 1252, 1253, 1267-1447 or the complement thereof. In yet another embodiment the oligomer can be SEQ ID NO: 1250 or 1251 or the complement thereof. [013] The liposomal mixture of this invention may include a second oligomer, e.g., comprising one of SEQ ED NOs: 2-281, 283-461, 463-935, 937-1080, and 1082-1248.
[014] In a fourth aspect, the DNAi oligonucleotide contained in the liposomal mixture comprises an oligomer that hybridizes to SEQ ID NO:936, the complement there of or portions thereof. In an embodiment, the oligomer has the sequence of SEQ ID NO:940 or
943 or the complement thereof.
[015] In a fifth aspect the DNAi oligonucleotide contained in the liposomal mixture comprises an oligomer that hybridizes to SEQ ED NO:1, SEQ ED NO:282, SEQ ED NO:462,
SEQ ED NO: 1081, or the complements thereof.
[016] In embodiments, the oligonucleotides contained in the liposomal mixture are between
15 and 35 base pairs in length.
[017] In a sixth aspect, the liposome-oligonucleotide mixture includes SEQ ED NO: 1250 or
1251 and amphoteric liposomes comprising POPC, DOPE, MoChol and CHEMS in the molar ratio of POPC/DOPE/MoChol/CHEMS of about 6/24/47/23 and sucrose.
[018] In a seventh aspect, the liposome-oligonucleotide mixture includes SEQ ED NO: 1250 or 1251 and amphoteric liposomes comprising POPC, DOPE, MoChol and CHEMS in the molar ratio of POPC/DOPE/MoChol/CHEMS of about 15/45/20/20 and sucrose.
[019] In an eighth aspect, the DNAi-amphoteric liposome mixture has an average diameter between 70 and 150 ηm. In one embodiment, the average diameter is between 90 and 130 ηm. In another embodiment of the sixth aspect the DNAi-amphoteric liposomes have a polydispersity index of between 0 and 0.3, and in another embodiment, the polydispersity index is between 0 and 0.15.
[020] In a ninth aspect, the amphoteric liposomes have a DNAi oligonucleotide concentration of at least 2 mg/mL at a lipid concentration of 100 mM or less.
[021] In a tenth aspect, the invention provides a method of preparing amphoteric liposomes containing a DNAi oligonucleotide and a cryoprotectant. In one embodiment the method comprises providing a lipid mixture in a solvent and an aqueous solution of one or more
DNAi oligonucleotides, mixing the lipid mixture and the DNAi oligonucleotides by injecting the lipid mixture into the DNAi oligonucleotide solution, and adding a cryoprotectant. In another embodiment the method further comprises diluting the lipid-DNAi oligonucleotide mixture with an aqueous buffer solution of about pH 8 to 10, or with an aqueous buffer solution to adjust the mixture to physiological pH. In yet another embodiment, the method further comprises extruding the lipid-DNAi oligonucleotide mixture through a membrane with a pore size of about 80 ηm to about 300 ηm. In still another embodiment, the method further comprises passing the DNAi-amphoteric liposome mixture through a sterile 0.22 micron filter. In further embodiments, the method results in liposomes having an average diameter between 70 and 150 ηm, having a polydispersity index between 0 and 0.3. In yet another embodiment, the method results in an encapsulation efficiency of at least 35%. [022] In an eleventh aspect, the invention provides a method of introducing the DNAi oligonucleotide-liposome mixture to cells or an animal. In one embodiment, the method includes administering the mixture to a mammal to treat cancer. The administered mixtures can reduce or stop tumor growth in mammals. In another embodiment, the introduction of the mixture results in a reduction of cell proliferation. In another embodiment, the mixture is administered to a cancer cell, a non-human animal or a human. In a further embodiment, the mixture is introduced to an animal at a dosage of between 1 mg to 100 mg per kg of body weight, or between 0.1 mg to 100 mg per kg of body weight, or between 0.01 mg to 100 mg per kg of body weight. In yet another embodiment, the mixture is introduced to the animal one or more times per day or continuously. In still another embodiment, the mixture is introduced to the animal via topical, pulmonary or parenteral administration or via a medical device. In an even further embodiment, the mixture administered to the animal or cells further includes another known chemotherapy agent, and/or a cell targeting component. [023] Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[024] Figure 1 shows an overview of the process for preparing DNAi-liposomes. [025] Figure 2 is a diagram of a crossflow process used to generate DNAi loaded liposomes. [026] Figure 3 shows graphs indicating the size and polydispersity indices of DNAi- liposomes treated with and without extrusion and filtration.
[027] Figure 4 is a graph showing the size distribution of DNAi-liposomes after the steps in liposome production.
[028] Figure 5 shows graphs of size distributions of liposomes after freeze-thaw cycles. [029] Figure 6 shows the effect of SEQ ID NO: 1251 sequestered in amphoteric liposomes on the size of tumors from non-Hodgkin's Lymphoma WSU-DLCL2 xenografts in SCID mice.
[030] Figure 7 shows the effect of different lots of SEQ ID NO: 1251 sequestered in amphoteric liposomes on the size of tumors from non-Hodgkin's Lymphoma WSU-DLCL2 xenografts in SCID mice. [031] Figure 8 shows the tumor burden in mice carrying non-Hodgkin's Lymphoma WSU-
DLCL2 xenografts treated with SEQ ID NO: 1251 sequestered in amphoteric liposomes.
[032] Figure 9 shows a dose response evaluation of two formulations of SEQ ID NO: 1251 sequestered in amphoteric liposomes on WSU-DLCL2 xenograft bearing mice.
[033] Figure 10 shows an enlarged view of a dose response evaluation of two formulations of SEQ ID NO: 1251 sequestered in amphoteric liposomes on WSU-DLCL2 xenograft bearing mice.
[034] Figure 11 shows a dose response animal body weight evaluation in WSU-DLCL2 xenograft bearing mice treated with two formulations of SEQ ID NO: 1251 sequestered in amphoteric liposomes.
[035] Figure 12 shows the effect of SEQ ID NO: 1251 sequestered in amphoteric liposomes on the size of tumors from PC-3 xenografts in nude mice.
[036] Figure 13 shows the effect of SEQ ID NO: 1251 sequestered in amphoteric liposomes on the growth rate of tumors from PC-3 xenografts in nude mice.
[037] Figure 14 shows graphs showing the efficacy of frozen and thawed liposomes containing oligonucleotides of SEQ ID NO: 1251 in mice bearing xenografts Of WSU-DLCL2 cells.
[038] Figure 15 shows graphs showing weight response evaluation of liposomes containing oligonucleotides of SEQ ID NO: 1251 in mice bearing xenografts Of WSU-DLCL2 cells.
[039] Figure 16 shows graphs indicating the mean time to 750 mm3 tumor endpoint values.
[040] Figure 17 is a Kaplan-Meier plot showing animal survival to 2000 mm3 tumor volume in response to treatment.
[041] Figure 18A shows graphs showing the efficacy of frozen and thawed liposomes containing oligonucleotides of SEQ ID NO: 1251 at different dose regimens in mice bearing xenografts Of WSU-DLCL2 cells. Figure 18B is a Kaplan-Meier plot showing animal survival to 2000 mm3 tumor volume in response to treatment. Figure 18C shows a graph showing weight response evaluation of liposomes containing oligonucleotides of SEQ ED
NO: 1251 at different dose regimens in mice bearing xenografts Of WSU-DLCL2 cells
DETAILED DESCRIPTION I. DEFINITIONS
[042] To facilitate understanding of the invention, a number of terms are defined below. [043] For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed. Additionally, general principles of organic chemistry are described in "Organic Chemistry", Thomas Sorrell, University Science Books, Sausalito: 1999, and "March's Advanced Organic Chemistry", 5th Ed., Ed.: Smith, M.B. and March, J., John Wiley & Sons, New York: 2001.
[044] As used herein the term "aliphatic' encompasses the terms alkyl, alkenyl, alkynyl, each of which being optionally substituted as set forth below.
[045] As used herein, an "alkyl" group refers to a saturated aliphatic hydrocarbon group containing 1-8 (e.g., 1-6 or 1-4) carbon atoms. An alkyl group can be straight or branched. Examples of alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, n-heptyl or 2-ethylhexyl. An alkyl group can be substituted (i.e., optionally substituted) with one or more substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, cycloaliphaticcarbonyl, (heterocycloaliphatic)carbonyl, nitro, cyano, amino, amido, acyl, sulfonyl, sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, cycloaliphaticoxy, heterocycloaliphaticoxy, aryloxy, heteroaryloxy, aralkyloxy, heteroarylalkoxy, or hydroxy. Without limitation, some examples of substituted alkyls include carboxyalkyl (such as HOOC-alkyl, alkoxycarbonylalkyl and alkylcarbonyloxyalkyl), cyanoalkyl, hydroxyalkyl, alkoxyalkyl, acylalkyl, hydroxyalkyl, aralkyl, (alkoxyaryl)alkyl, (sulfonylamino)alkyl (such as (alkylsulfonylamino)alkyl), aminoalkyl, amidoalkyl, (cycloaliphatic)alkyl, cyanoalkyl, or haloalkyl.
[046] As used herein, an "alkenyl" group refers to an aliphatic carbon group that contains 2- 8 (e.g., 2-6 or 2-4) carbon atoms and at least one double bond. Like an alkyl group, an alkenyl group can be straight or branched. Examples of an alkenyl group include, but are not limited to, allyl, isoprenyl, 2-butenyl and 2-hexenyl. An alkenyl group can be optionally substituted with one or more substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, (cycloaliphatic)carbonyl, (heterocycloaliphatic )carbonyl, nitro, cyano, amino, amido, acyl, sulfonyl, sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, aralkyloxy, (heteroaryl)alkoxy, or hydroxy.
[047] As used herein, an "alkynyl" group refers to an aliphatic carbon group that contains 2- 8 (e.g., 2-6 or 2-4) carbon atoms and has at least one triple bond. An alkynyl group can be straight or branched. Examples of an alkynyl group include, but are not limited to, propargyl and butynyl. An alkynyl group can be optionally substituted with one or more substituents such as halo, cycloaliphatic, heterocycloaliphatic, aryl, heteroaryl, alkoxy, aroyl, heteroaroyl, (cycloaliphatic)carbonyl, (heterocycloaliphatic)carbonyl, nitro, cyano, amino, amido, acyl, sulfonyl, sulfinyl, sulfanyl, sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, carboxy, carbamoyl, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, aralkyloxy, (heteroaryl)alkoxy, or hydroxy.
[048] As used herein, an "amido" encompasses both "aminocarbonyl" and "carbonylamino". These terms when used alone or in connection with another group refers to an amido group such as N(RX)2-C(O)- or RYC(O)-N(RX)2- when used terminally and -C(O)- N(RX)- or -N(RX)-C(O)- when used internally, wherein Rx and Rγ are defined below. Examples of amido groups include alkylamido (such as alkylcarbonylamino and alkylcarbonylamino), (heterocycloaliphatic) amido, (heteroaralkyl) amido, (heteroaryl) amido, (heterocycloalkyl)alkylamido, arylamido, aralkylamido, (cycloalkyl)alkylamido and cycloalkylamido.
[049] As used herein, an "amino" group refers to -NRXRY wherein each of Rx and Rγ is independently hydrogen, alkyl, cycloaliphatic, (cycloaliphatic)aliphatic, aryl, araliphatic, heterocycloaliphatic, (heterocycloaliphatic)aliphatic, heteroaryl, carboxy, sulfanyl, sulfinyl, sulfonyl, (aliphatic)carbonyl, (cycloaliphatic)carbonyl, ((cycloaliphatic)aliphatic)carbonyl, arylcarbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, (heteroaryl)carbonyl, or (heteroaraliphatic)carbonyl, each of which being defined herein and being optionally substituted. Examples of amino groups include alkylamino, dialkylamino, and arylamino. [050] When the term "amino" is not the terminal group (e.g., alkylcarbonylamino), it is represented by -NRX-. Rx has the same meaning as defined above. [051] As used herein, an "aryl" group used alone or as part of a larger moiety as in "aralkyl", "aralkoxy", or "aryloxyalkyl" refers to monocyclic (e.g., phenyl); bicyclic (e.g., indenyl, naphthalenyl, tetrahydronaphthyl, tetrahydroindenyl); and tricyclic (e.g., fluorenyl tetrahydrofluorenyl, or tetrahydroanthracenyl, anthracenyl). The bicyclic and tricyclic groups include benzofused 2-3 membered carbocyclic rings. For example, a benzofused group includes phenyl fused with two or more C4-8 carbocyclic moieties. An aryl is optionally substituted with one or more substituents including aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic ring of a benzofused bicyclic or tricyclic aryl); nitro; carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cycloaliphatic)carbonyl; ((cycloaliphatic)aliphatic)carbonyl; (araliphatic)carbonyl; (heterocycloaliphatic)carbonyl; ((heterocycloaliphatic) aliphatic)carbonyl; and (heteroaraliphatic)carbonyl]; sulfonyl [e.g., aliphaticsulfonyl and aminosulfonyl]; sulfinyl [e.g., aliphaticsulfinyl]; sulfanyl [e.g., aliphaticsulfanyl]; nitro; cyano; halo; hydroxyl; mercapto; sulfoxy; urea; thiourea; sulfamoyl; sulfamide; and carbamoyl. Alternatively, an aryl can be unsubstituted. [052] Non-limiting examples of substituted aryls include haloaryl [e.g., mono-, di ( such as p,m-dihaloaryl), and (trihalo)aryl]; (carboxy)aryl [e.g., (alkoxycarbonyl)aryl, ((aryalkyl)carbonyloxy)aryl, and (alkoxycarbonyl)aryl]; (amido)aryl [e.g., (aminocarbonyl)aryl, (((alkylamino)alkyl)aminocarbonyl)aryl, (alkylcarbonyl)aminoaryl, (arylaminocarbonyl)aryl, and (((heteroaryl)amino)carbonyl)aryl]; aminoaryl [e.g., ((alkylsulfonyl)amino)aryl and ((dialkyl)amino)aryl]; (cyanoalkyl)aryl; (alkoxy)aryl; (sulfamoyl)aryl [e.g., (aminosulfonyl)aryl]; (alkylsulfonyl)aryl; (cyano)aryl; (hydroxyalkyl)aryl; ((alkoxy)alkyl)aryl; (hydroxyl)aryl, ((carboxy)alkyl)aryl; (((dialkyl)amino)alkyl)aryl; (nitroalkyl)aryl; (((alkylsulfonyl)amino)alkyl)aryl; ((heterocycloaliphatic )carbonyl)aryl; ((alkylsulfonyl)alkyl)aryl; (cyanoalkyl)aryl; (hydroxyalkyl)aryl; (alkylcarbonyl)aryl; alkylaryl; (trihaloalkyl)aryl; p-amino-m- alkoxycarbonylaryl; p-amino-m-cyanoaryl; p-halo-m-aminoaryl; and (m- (heterocycloaliphatic)-ø-(alkyl))aryl.
[053] As used herein, an "araliphatic" such as an "aralkyl" group refers to an aliphatic group (e.g., a C1-4 alkyl group) that is substituted with an aryl group. "Aliphatic," "alkyl," and "aryl" are defined herein. An example of an araliphatic such as an aralkyl group is benzyl.
[054] As used herein, a "bicyclic ring system" includes 8-12 (e.g., 9, 10, or 11) membered structures that form two rings, wherein the two rings have at least one atom in common (e.g., 2 atoms in common). Bicyclic ring systems include bicycloaliphatics (e.g., bicycloalkyl or bicycloalkenyl), bicycloheteroaliphatics, bicyclic aryls, and bicyclic heteroaryls. [055] As used herein, a "cycloaliphatic" group encompasses a "cycloalkyl" group and a "cycloalkenyl" group, each of which being optionally substituted as set forth below. [056] As used herein, a "cycloalkyl" group refers to a saturated carbocyclic mono- or bicyclic (fused or bridged) ring of 3-10 (e.g., 5-10) carbon atoms. Examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, norbornyl, cubyl, octahydro-indenyl, decahydro-naphthyl, bicyclo[3.2.1]octyl, bicyclo[2.2.2]octyl, bicyclo[3.3.1]nonyl, bicyclo[3.3.2.]Decyl, bicyclo[2.2.2]octyl, adamantyl, azacycloalkyl or ((aminocarbonyl)cycloalkyl)cycloalkyl. A "cycloalkenyl" group, as used herein, refers to a non-aromatic carbocyclic ring of 3-10 (e.g., 4-8) carbon atoms having one or more double bonds. Examples of cycloalkenyl groups include cyclopentenyl, 1,4-cyclohexa-di-enyl, cycloheptenyl, cyclooctenyl, hexahydro-indenyl, octahydro-naphthyl, cyclohexenyl, cyclopentenyl, bicyclo[2.2.2]octenyl, and bicyclo[3.3.1]nonenyl.
[057] A cycloalkyl or cycloalkenyl group can be optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (heterocycloaliphatic) aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic )oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic )carbonylamino, (cycloaliphatic)carbonylamino, ((cycloaliphatic)aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycloaliphatic)carbonylamino, ((heterocycloaliphatic)aliphatic)carbonylamino, (heteroaryl)carbonylamino, and (heteroaraliphatic)carbonylamino], nitro, carboxy [e.g., HOOC-, alkoxycarbonyl, and alkylcarbonyloxy], acyl [e.g., (cycloaliphatic)carbonyl, ((cycloaliphatic) aliphatic )carbonyl, (araliphatic)carbonyl, (heterocycloaliphatic )carbonyl,
((heterocycloaliphatic)aliphatic)carbonyl, and (heteroaraliphatic)carbonyl], nitro, cyano, halo, hydroxy, mercapto, sulfonyl [e.g., alkylsulfonyl and arylsulfonyl], sulfinyl [e.g., alkylsulfinyl], sulfanyl [e.g., alkylsulfanyl], sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[058] As used herein, "cyclic moiety" includes cycloaliphatic, heterocycloaliphatic, aryl, or heteroaryl, each of which has been defined previously.
[059] As used herein, the term "heterocycloaliphatic" encompasses a heterocycloalkyl group and a heterocycloalkenyl group, each of which being optionally substituted as set forth below.
[060] As used herein, a "heterocycloalkyl" group refers to a 3-10 membered mono- or bicylic (fused or bridged) (e.g., 5- to 10-membered mono- or bicyclic) saturated ring structure, in which one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof). Examples of a heterocycloalkyl group include piperidyl, piperazyl, tetrahydropyranyl, tetrahydrofuryl, 1,4-dioxolanyl, 1,4-dithianyl, 1,3-dioxolanyl, oxazolidyl, isoxazolidyl, morpholinyl, thiomorpholyl, octahydro-benzofuryl, octahydro-chromenyl, octahydro-thiochromenyl, octahydro-indolyl, octahydro-pyrindinyl, decahydro-quinolinyl, octahydro-benzo[fe]thiopheneyl, 2-oxa-bicyclo[2.2.2]octyl, l-aza-bicyclo[2.2.2]octyl, 3-aza- bicyclo[3.2.1]octyl, and 2,6-dioxa-tricyclo[3.3.1.03'7]nonyl. A monocyclic heterocycloalkyl group can be fused with a phenyl moiety such as tetrahydroisoquinoline. A "heterocycloalkenyl" group, as used herein, refers to a mono- or bicylic (e.g., 5- to 10- membered mono- or bicyclic) non-aromatic ring structure having one or more double bonds, and wherein one or more of the ring atoms is a heteroatom (e.g., N, O, or S). Monocyclic and bicycloheteroaliphatics are numbered according to standard chemical nomenclature. [061] A heterocycloalkyl or heterocycloalkenyl group can be optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl], cycloaliphatic, (cycloaliphatic) aliphatic, heterocycloaliphatic, (heterocycloaliphatic) aliphatic, aryl, heteroaryl, alkoxy, (cycloaliphatic)oxy, (heterocycloaliphatic)oxy, aryloxy, heteroaryloxy, (araliphatic)oxy, (heteroaraliphatic)oxy, aroyl, heteroaroyl, amino, amido [e.g., (aliphatic)carbonylamino, (cycloaliphatic)carbonylamino, ((cycloaliphatic) aliphatic)carbonylamino, (aryl)carbonylamino, (araliphatic)carbonylamino, (heterocycloaliphatic)carbonylamino, ((heterocycloaliphatic) aliphatic)carbonylamino, (heteroaryl)carbonylamino, and (heteroaraliphatic)carbonylamino], nitro, carboxy [e.g., HOOC-, alkoxycarbonyl, and alkylcarbonyloxy], acyl [e.g., (cycloaliphatic)carbonyl, ((cycloaliphatic) aliphatic)carbonyl, (araliphatic)carbonyl, (heterocycloaliphatic)carbonyl, ((heterocycloaliphatic)aliphatic)carbonyl, and (heteroaraliphatic)carbonyl], nitro, cyano, halo, hydroxy, mercapto, sulfonyl [e.g., alkylsulfonyl and arylsulfonyl], sulfinyl [e.g., alkylsulfinyl], sulfanyl [e.g., alkylsulfanyl], sulfoxy, urea, thiourea, sulfamoyl, sulfamide, oxo, or carbamoyl.
[062] A "heteroaryl" group, as used herein, refers to a monocyclic, bicyclic, or tricyclic ring structure having 4 to 15 ring atoms wherein one or more of the ring atoms is a heteroatom (e.g., N, O, S, or combinations thereof) and wherein one ore more rings of the bicyclic or tricyclic ring structure is aromatic. A heteroaryl group includes a benzofused ring system having 2 to 3 rings. For example, a benzofused group includes benzo fused with one or two 4 to 8 membered heterocycloaliphatic moieties (e.g., indolizyl, indolyl, isoindolyl, 3H-indolyl, indolinyl, benzo[£>]furyl, benzo[£]thiophenyl, quinolinyl, or isoquinolinyl). Some examples of heteroaryl are azetidinyl, pyridyl, lH-indazolyl, furyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, imidazolyl, tetrazolyl, benzofuryl, isoquinolinyl, benzthiazolyl, xanthene, thioxanthene, phenothiazine, dihydroindole, benzo[l,3]dioxole, benzo[b]furyl, benzo[b]thiophenyl, indazolyl, benzimidazolyl, benzthiazolyl, puryl, cinnolyl, quinolyl, quinazolyl,cinnolyl, phthalazyl, quinazolyl, quinoxalyl, isoquinolyl, 4H-quinolizyl, benzo- 1,2,5-thiadiazolyl, or 1,8-naphthyridyl. [063] Without limitation, monocyclic heteroaryls include furyl, thiophenyl, 2H-pyrrolyl, pyrrolyl, oxazolyl, thazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, 1,3,4-thiadiazolyl, 2H-pyranyl, 4-H-pranyl, pyridyl, pyridazyl, pyrimidyl, pyrazolyl, pyrazyl, or 1,3,5-triazyl. Monocyclic heteroaryls are numbered according to standard chemical nomenclature. [064] Without limitation, bicyclic heteroaryls include indolizyl, indolyl, isoindolyl, 3H- indolyl, indolinyl, benzo[6]furyl, benzo[6]thiophenyl, quinolinyl, isoquinolinyl, indolizyl, isoindolyl, indolyl, benzo[&]furyl, bexo[fe] thiophenyl, indazolyl, benzimidazyl, benzthiazolyl, purinyl, 4H-quinolizyl, quinolyl, isoquinolyl, cinnolyl, phthalazyl, quinazolyl, quinoxalyl, 1,8-naphthyridyl, or pteridyl. Bicyclic heteroaryls are numbered according to standard chemical nomenclature.
[065] A heteroaryl is optionally substituted with one or more substituents such as aliphatic [e.g., alkyl, alkenyl, or alkynyl]; cycloaliphatic; (cycloaliphatic)aliphatic; heterocycloaliphatic; (heterocycloaliphatic)aliphatic; aryl; heteroaryl; alkoxy; (cycloaliphatic)oxy; (heterocycloaliphatic)oxy; aryloxy; heteroaryloxy; (araliphatic)oxy; (heteroaraliphatic)oxy; aroyl; heteroaroyl; amino; oxo (on a non-aromatic carbocyclic or heterocyclic ring of a bicyclic or tricyclic heteroaryl); nitro; carboxy; amido; acyl [ e.g., aliphaticcarbonyl; (cycloaliphatic )carbonyl; ((cycloaliphatic)aliphatic)carbonyl; (araliphatic)carbonyl; (heterocycloaliphatic)carbonyl; ((heterocycloaliphatic) aliphatic)carbonyl; and (heteroaraliphatic)carbonyl]; sulfonyl [e.g., aliphaticsulfonyl and aminosulfonyl]; sulfinyl [e.g., aliphaticsulfinyl]; sulfanyl [e.g., aliphaticsulfanyl]; nitro; cyano; halo; hydroxyl; mercapto; sulfoxy; urea; thiourea; sulfamoyl; sulfamide; or carbamoyl. Alternatively, a heteroaryl can be unsubstituted.
[066] Non-limiting examples of substituted heteroaryls include (halo)heteroaryl [e.g., mono- and di-(halo)heteroaryl]; (carboxy)heteroaryl [e.g., (alkoxycarbonyl)heteroaryl]; cyanoheteroaryl; aminoheteroaryl [e.g., ((alkylsulfonyl)amino)heteroaryl and((dialkyl)amino)heteroaryl]; (amido)heteroaryl [e.g., aminocarbonylheteroaryl, ((alkylcarbonyl)amino)heteroaryl, ((((alkyl)amino)alkyl)aminocarbonyl)heteroaryl, (((heteroaryl)amino)carbonyl)heteroaryl, ((heterocycloaliphatic )carbonyl)heteroaryl, and ((alkylcarbonyl)amino)heteroaryl] ; (cyanoalkyl)heteroaryl; (alkoxy)heteroaryl; (sulfamoyl)heteroaryl [e.g., (aminosulfonyl)heteroaryl]; (sulfonyl)heteroaryl [e.g., (alkylsulfonyl)heteroaryl] ; (hydroxyalkyl)heteroaryl; (alkoxyalkyl)heteroaryl; (hydroxyl)heteroaryl; ((carboxy)alkyl)heteroaryl; [((dialkyl)amino)alkyl]heteroaryl; (heterocycloaliphatic)heteroaryl; (cycloaliphatic)heteroaryl; (nitroalkyl)heteroaryl; (((alkylsulfonyl)amino)alkyl)heteroaryl; ((alkylsulfonyl)alkyl)heteroaryl; (cyanoalkyl)heteroaryl; (acyl)heteroaryl [e.g., (alkylcarbonyl)heteroaryl]; (alkyl)heteroaryl, and (haloalkyl)heteroaryl [e.g., trihaloalkylheteroaryl].
[067] A "heteroaraliphatic (such as a heteroaralkyl group) as used herein, refers to an aliphatic group (e.g., a CM alkyl group) that is substituted with a heteroaryl group.
"Aliphatic," "alkyl," and "heteroaryl" have been defined above.
[068] As used herein, an "acyl" group refers to a formyl group or R -C(O)- (such as
-alkyl-C(O)-, also referred to as "alkylcarbonyl") where Rx and "alkyl" have been defined previously. Acetyl and pivaloyl are examples of acyl groups.
[069] As used herein, an "alkoxy" group refers to an alkyl-O- group where "alkyl" has been defined previously.
[070] As used herein, a "carbamoyl" group refers to a group having the structure -O-CO-
NRXRY or -NRX-CO-O-RZ wherein Rx and Rγ have been defined above and Rz can be aliphatic, aryl, araliphatic, heterocycloaliphatic, heteroaryl, or heteroaraliphatic.
[071] As used herein, a "carboxy" group refers to -COOH, -COORX, -OC(O)H,
-OC(O)RX when used as a terminal group or -OC(O)- or -C(O)O-; when used as an internal group.
[072] As used herein, a "haloaliphatic" group refers to an aliphatic group substituted with 1-
3 halogen. For instance, the term haloalkyl includes the group -CF3.
[073] As used herein, a "mercapto" group refers to -SH.
[074] As used herein, a "sulfo" group refers to -SO3H or -SO3RX when used terminally or
-S(O)3- when used internally.
[075] As used herein, a "sulfamide" group refers to the structure -NRX-S(O)2-NRYRZ when used terminally and -NRX-S(O)2-NRY- when used internally, wherein Rx, Rγ and Rz have been defined above.
[076] As used herein, a "sulfamoyl" group refers to the structure -S(O)2-NRXRY or -NRX -
S(O)2-R2 when used terminally or -S(O)2-NRX- or -NRX -S(O)2- when used internally, wherein Rx, Rγ and Rz are defined above.
[077] As used herein a "sulfanyl" group refers to -S-Rx when used terminally and -S- when used internally, wherein Rx has been defined above. Examples of sulfanyls include alkylsulfanyl.
[078] As used herein a "sulfinyl" group refers to -S(O)-RX when used terminally and -S(O)- when used internally, wherein Rx has been defined above.
[079] As used herein, a "sulfonyl" group refers to-S(O)2-Rx when used terminally and -
S(O)2- when used internally, wherein Rx has been defined above. [080] As used herein, a "sulfoxy" group refers to -O-SO-RX or -SO-O-RX, when used terminally and -0-S(O)- or -S(O)-O- when used internally, where Rx has been defined above.
[081] As used herein, a "halogen" or "halo" group refers to fluorine, chlorine, bromine or iodine.
[082] As used herein, an "alkoxycarbonyl," which is encompassed by the term carboxy, used alone or in connection with another group refers to a group such as alkyl-O-C(O)-.
[083] As used herein, an "alkoxyalkyl" refers to an alkyl group such as alkyl-O-alkyl-, wherein alkyl has been defined above.
[084] As used herein, a "carbonyl" refers to -C(O)-.
[085] As used herein, an "oxo" refers to =0.
[086] As used herein, an "aminoalkyl" refers to the structure (Rx)2N-alkyl-.
[087] As used herein, a "cyanoalkyl" refers to the structure (NC)-alkyl-
[088] As used herein, a "urea" group refers to the structure -NRX-CO-NRYRZ and a
"thiourea" group refers to the structure -NRX-CS-NRYRZ when used terminally and -NRX-
CO-NRY- or -NRX-CS-NRY- when used internally, wherein Rx, Rγ, and Rz have been defined above.
[089] As used herein, a "guanidino" group refers to the structure -N=C(N (Rx RY))N(RXRY) wherein Rx and Rγ have been defined above.
[090] As used herein, the term "amidino" group refers to the structure
-C=(NRX)N(RXRY) wherein Rx and Rγ have been defined above.
[091] The terms "terminally" and "internally" refer to the location of a group within a substituent. A group is terminal when the group is present at the end of the substituent not further bonded to the rest of the chemical structure. Carboxyalkyl, i.e., RxO(O)C-alkyl is an example of a carboxy group used terminally. A group is internal when the group is present in the middle of a substituent to at the end of the substituent bound to the to the rest of the chemical structure. Alkylcarboxy (e.g., alkyl-C(O)O- or alkyl-OC(O)-) and alkylcarboxyaryl
(e.g., alkyl-C(O)O-aryl- or alkyl-O(CO)-aryl-) are examples of carboxy groups used internally.
[092] The phrase "optionally substituted" is used interchangeably with the phrase
"substituted or unsubstituted." As described herein, compounds of the invention can optionally be substituted with one or more substituents, such as are illustrated generally above, or as exemplified by particular classes, subclasses, and species of the invention. As described herein, the variables contained herein encompass specific groups, such as alkyl and aryl. Unless otherwise noted, each of the specific groups for the variables contained herein can be optionally substituted with one or more substituents described herein. Each substituent of a specific group is further optionally substituted with one to three of halo, cyano, oxoalkoxy, hydroxyl, amino, nitro, aryl, haloalkyl, and alkyl. For instance, an alkyl group can be substituted with alkylsulfanyl and the alkylsulfanyl can be optionally substituted with one to three of halo, cyano, oxoalkoxy, hydroxyl, amino, nitro, aryl, haloalkyl, and alkyl. As an additional example, the cycloalkyl portion of a (cycloalkyl)carbonylamino can be optionally substituted with one to three of halo, cyano, alkoxy, hydroxyl, nitro, haloalkyl and alkyl. When two alkoxy groups are bound to the same atom or adjacent atoms, the two alkxoy groups can form a ring together with the atom(s) to which they are bound. [093] In general, the term "substituted," whether preceded by the term "optionally" or not, refers to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent. Specific substituents are described above in the definitions and below in the description of compounds and examples thereof. Unless otherwise indicated, an optionally substituted group can have a substituent at each substitutable position of the group, and when more than one position in any given structure can be substituted with more than one substituent selected from a specified group, the substituent can be either the same or different at every position. A ring substituent, such as a heterocycloalkyl, can be bound to another ring, such as a cycloalkyl, to form a spiro-bicyclic ring system, e.g., both rings share one common atom. As one of ordinary skill in the art will recognize, combinations of substituents envisioned by this invention are those combinations that result in the formation of stable or chemically feasible compounds.
[094] The phrase "stable or chemically feasible," as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and preferably their recovery, purification, and use for one or more of the purposes disclosed herein.
[095] As used herein, an effective amount is defined as the amount required to confer a therapeutic effect on the treated patient, and is typically determined based on age, surface area, weight and condition of the patient. The interrelationship of dosages for animals and humans (based on milligrams per meter squared of body surface) is described by Freireich et al., Cancer Chemother. Rep., 50: 219 (1966). Body surface area can be approximately determined from height and weight of the patient. See, e.g., Scientific Tables, Geigy Pharmaceuticals, Ardsley, New York, 537 (1970).
[096] Unless otherwise stated, structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, (Z) and (E) double bond isomers, and (Z) and (E) conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention. Additionally, unless otherwise stated, structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a 13C- or 14C-enriched carbon are within the scope of this invention. Such compounds are useful, for example, as analytical tools or probes in biological assays.
II. AMPHOTERIC LIPOSOMAL DELIVERY SYSTEM
[097] Amphoteric liposomes are a class of liposomes having anionic or neutral charge at about pH 7.5 and cationic charge at pH 4. Using amphoteric liposomes as carriers of oligonucleotides and/or other agents to treat cancer in cells and in mammals, such as by inhibiting and/or reducing tumor growth, requires that the liposomes be stable in the bloodstream and in tissues. Particularly, after a systemic application, the oligonucleotide and/or other agents must be stably sequestered in the liposomes until eventual uptake in the target tissue or cells. Accordingly, the guidelines for liposomal formulations of the FDA regulate specific preclinical tests for liposomal drugs (http://www.fda. gov/cder/gui dance/2191 dft.pdf).
[098] After injection of liposomes into the blood stream, serum components interact with the liposomes, which can lead to permeabilization of the liposomes. However, release of a drug or molecule that is encapsulated in a liposome depends on molecular dimensions of the drug or molecule. Consequently, a plasmid of thousands of base pairs is released much more slowly than smaller oligonucleotides or other small molecules. For liposomal delivery of drugs or molecules, it is ideal that the release of the drug during circulation of the liposomes in the bloodstream be as low as possible.
[099] As used herein, "physiological pH" can range from about 6.7 to about 7.7. The pH of blood is generally about 7.4, but the pH at other physiological locations, such as vascular junctions or the extracellular matrix can be slightly acidic and thus lower than the pH of blood.
[0100] As used herein, "liposome" refers to one or more lipids forming a complex, usually surrounded by an aqueous solution. Liposomes are generally spherical structures comprising lipids fatty acids, lipid bilayer type structures, unilamellar vesicles and amorphous lipid vesicles. Generally, liposomes are completely closed lipid bilayer membranes containing an entrapped aqueous volume. The liposomes may be unilamellar vesicles (possessing a single bilayer membrane) or multilamellar (onion-like structures characterized by multiple membrane bilayers, each separated from the next by an aqueous layer). Liposomes of the present invention may also include a DNAi oligonucleotide as defined below, either bound to the liposomes or sequestered in or on the liposomes. The molecules include, but are not limited to, DNAi oligonucleotides and/or other agents used to treat diseases such as cancer. [0101] As used herein, an "amphoteric liposome" is a liposome with an amphoteric character, as defined below.
[0102] As used herein, sequestered, sequestering, or sequester refers to encapsulation, incorporation, or association of a drug, molecule, compound, including a DNAi oligonucleotide, with the lipids of a liposome. The molecule may be associated with the lipid bilayer or present in the aqueous interior of the liposome or both. "Sequestered" includes encapsulation in the aqueous core of the liposome. It also encompasses situations in which part or all of the molecule is located in the aqueous core of the liposome and part outside of the liposome in the aqueous phase of the liposomal suspension, where part of the molecule is located in the aqueous core of the liposome and part in the lipid portion of the liposome, or part sticking out of the liposomal exterior, where molecules are partially or totally embedded in the lipid portion of the liposome, and includes molecules associated with the liposomes, with all or part of the molecule associated with the exterior of the liposome. [0103] As used herein, "polydispersity index" is a measure of the heterogeneity of the particle dispersion (heterogeneity of the diameter of liposomes in a mixture) of the liposomes. A polydispersity index can range from 0.0 (homogeneous) to 1.0 (heterogeneous) for the size distribution of liposomal formulations.
[0104] The amphoteric liposomes include one or more amphoteric lipids or alternatively a mix of lipid components with amphoteric properties. Suitable amphoteric lipids are disclosed in PCT International Publication Number WO02/066489 as well as in PCT International Publication Number WO03/070735, the contents of both of which are incorporated herein by reference. Alternatively, the lipid phase may be formulated using pH-responsive anionic and/or cationic components, as disclosed in PCT International Publication Number WO02/066012, the contents of which are incorporated by reference herein. Cationic lipids sensitive to pH are disclosed in PCT International Publication Numbers WO02/066489 and WO03/070220, in Budker, et al. 1996, Nat. Biotechnol., 14(6):760-4, and in US Patent Number 6,258,792 the contents of which are incorporated by reference herein, and can be used in combination with constitutively charged anionic lipids or with anionic lipids that are sensitive to pH. Conversely, the cationic charge may also be introduced from constitutively charged lipids that are known to those skilled in the art in combination with a pH sensitive anionic lipid. (See also PCT International Publication Numbers WO05/094783, WO03/070735, WO04/00928, WO06/48329, WO06/053646, WO06/002991 and U.S. Patent publications 2003/0099697, 2005/0164963, 2004/0120997, 2006/159737, 2006/0216343, each of which is also incorporated in its entirety by reference.)
[0105] Amphoteric liposomes of the present invention include 1) amphoteric lipids or a mixture of lipid components with amphoteric properties, (2) neutral lipids, (3) one or more DNAi oligonucleotides, (4) a cryoprotectant and/or lyoprotectant. In addition, the DNAi- liposomes have a defined size distribution and polydispersity index. A. Lipids Used in Amphoteric Liposomes
1. Definitions
[0106] As used herein, "amphoter" or "amphoteric" character refers to a structure, being a single substance (e.g., a compound) or a mixture of substances (e.g., a mixture of two or more compounds) or a supramolecular complex (e.g., a liposome) comprising charged groups of both anionic and cationic character wherein
(i) at least one of the charged groups has a pK between 4 and 8,
(ii) the cationic charge prevails at pH 4 and
(iii) the anionic charge prevails at pH 8, resulting in an isoelectric point of neutral net charge between pH 4 and pH 8. Amphoteric character by that definition is different from zwitterionic character, as zwitterions do not have a pK in the range mentioned above. Consequently, zwitterions are essentially neutrally charged over a range of pH values. Phosphatidylcholine or phosphatidylethanolamines are neutral lipids with zwitterionic character.
[0107] As used herein, "Amphoter I Lipid Pairs" refers to lipid pairs containing a stable cation and a chargeable anion. Examples include without limitation DDAB/CHEMS, DOTAP/CHEMS and DOTAP/DOPS. In some aspects, the ratio of the percent of cationic lipids to anionic lipids is lower than 1.
[0108] As used herein, "Amphoter II Lipid Pairs" refers to lipid pairs containing a chargeable cation and a chargeable anion. Examples include without limitation Mo-Chol/CHEMS, DPIM/CHEMS or DPIM/DG-Succ. In some aspects, the ratio of the percent of cationic lipids to anionic lipids is between about 5 and 0.2. [0109] As used herein, "Amphoter III Lipid Pairs" refers to lipid pairs containing a chargeable cation and stable anion. Examples include without limitation Mo-Chol/DOPG or Mo-Chol/Chol-SO4. In one embodiment, the ratio of the percent of cationic lipids to anionic lipids is higher than 1.
2. Abbreviations
[0110] Abbreviations for lipids refer primarily to standard use in the literature and are included here as a helpful reference:
[0111] DMPC Dimyristoylphosphatidylcholine [0112] DPPC Dipalmitoylphosphatidylcholine [0113] DSPC Distearoylphosphatidylcholine [0114] POPC Palmitoyl-oleoylphosphatidylcholine [0115] OPPC l-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine [0116] DOPC Dioleoylphosphatidylcholine [0117] DOPE Dioleoylphosphatidylethanolamine [0118] DMPE Dimyristoylphosphatidylethanolamine [0119] DPPE Dipalmitoylphosphatidylethanolamine [0120] DOPG Dioleoylphosphatidylglycerol [0121] POPG Palmitoyl-oleoylphosphatidylglycerol [0122] DMPG Dimyristoylphosphatidylglycerol [0123] DPPG Dipalmitoylphosphatidylglycerol [0124] DLPG Dilaurylphosphatidylglycerol [0125] DSPG Distearoylphosphatidylglycerol [0126] DMPS Dimyristoylphosphatidylserine [0127] DPPS Dipalmitoylphosphatidylserine [0128] DOPS Dioleoy lphosphatidyl serine [0129] POPS Palmitoyl-oleoylphosphatidylserine [0130] DMPA Dimyristoylphosphatidic acid [0131] DPPA Dipalmitoylphosphatidic acid [0132] DSPA Distearoylphosphatidic acid [0133] DLPA Dilaurylphosphatidic acid [0134] DOPA Dioleoylphosphatidic acid [0135] POPA Palmitoyl-oleoylphosphatidic acid [0136] CHEMS Cholesterolhemi succinate [0137] DC-Choi 3-β-[N-(N',N'-dimethylethane) carbamoyl]cholesterol [0138] Cet-P Cetylphosphate [0139] DODAP ( 1 ,2)-dioleoyloxypropyl)-N,N-dimethylammonium chloride [0140] DOEPC l^-dioleoyl-sn-glycero-S-ethylphosphocholine [0141] DAC-Chol 3-β-[N-(N,N'-dimethylethane) carbamoyl]cholesterol [0142] TC-Chol 3-β-[N-(N',N', N'-trimethylaminoethane) carbamoyl] cholesterol [0143] DOTMA ( 1 ,2-dioleyloxypropyl)-N,N,N-trimethylammoniumchloride)
(Lipofectin®)
[0144] DOGS ((C 18)2GlySper3+) N.N-dioctadecylamido-glycyl-spermine
(Transfectam®)
[0145] CTAB Cetyl-trimethylammoniumbromide [0146] CPyC Cetyl-pyridiniumchloride [0147] DOTAP ( 1 ,2-dioleoyloxypropyl)-N,N,N-trimethylammonium salt [0148] DMTAP ( 1 ,2-dimyristoyloxypropyl)-N,N,N-trimethylammonium salt [0149] DPTAP ( 1 ,2-dipalraitoyloxypropyl)-N,N,N-trimethylammonium salt [0150] DOTMA (1 ,2-dioleyloxypropyl)-N,N,N-trimethylammonium chloride) [0151] DOPJE (l,2-dioleyloxypropyl)-3 dime thy lhydroxy ethyl ammoniumbromide) [0152] DDAB Dimethyldioctadecylammonium bromide [0153] DPBvI 4-(2,3-bis-palmitoyloxy-propyl)- 1 -methyl- 1 H-imidazole [0154] CHEvI Histaminyl-Cholesterolcarbamate [0155] MoChol 4-(2-Aminoethyl)-Moφholino-Cholesterolhemisuccinate [0156] HisChol Histaminyl-Cholesterolhemisuccinate [0157] HCChol Nα-Histidinyl-Cholesterolcarbamate [0158] HistChol Nα-Histidinyl-Cholesterol-hemisuccinate [0159] AC Acylcarnosine, Stearyl- & Palmitoylcarnosine [0160] HistDG 1,2 — Dipalmitoylglycerol-hemisuccinat-N_-Histidinyl-hemisuccinate, & Distearoyl- ,Dimyristoyl, Dioleoyl or palmitoyl-oleoylderivatives
[0161] IsoHistSuccDG l,2-ipalmitoylglycerol-O_-Histidinyl-Nα-hemisuccinat, &
Distearoyl-, Dimyristoyl, Dioleoyl or palmitoyl-oleoylderivatives
[0162] DGSucc 1,2 — Dipalmitoyglycerol-S-hemisuccinate & Distearoyl-, dimyristoyl-
Dioleoyl or palmitoyl-oleoylderivatives
[0163] EDTA-Chol cholesterol ester of ethylenediaminetetraacetic acid
[0164] Hist-PS Nα-histidinyl-phosphatidylserine
[0165] BGSC bisguanidinium-spermidine-cholesterol
[0166] BGTC bisguanidinium-tren-cholesterol [0167] DOSPER ( 1.3-dioleoyloxy-2-(6-carboxy-spermyl)-propylarnide [0168] DOSC (l^-dioleoyl-S-succinyl-sn-glyceryl choline ester) [0169] DOGSDO (1 ,2-dioleoyl-sn-glycero-3-succinyl-2-hydroxyethyl disulfide ornithine)
[0170] DOGSucc l,2-Dioleoylglycerol-3-hemisucinate [0171] POGSucc Palimtolyl-oleoylglycerol-oleoyl-S-hemisuccinate [0172] DMGSucc l,2-Dimyristoylglycerol-3-hemisuccinate [0173] DPGSucc l,2-Dipalmitoylglycerol-3-hemisuccinate
[0174] The following table provides non-limiting examples of lipids that are suitable for use in the compositions in accordance with the present invention. The membrane anchors of the lipids are shown exemplarily and serve only to illustrate the lipids of the invention and are not intended to limit the same.
MoChol DG-Succ
Figure imgf000022_0001
DOTAP IsohistsuccDG
Figure imgf000022_0002
HisChol HCChol
Figure imgf000022_0003
AC Hist-Chol
Figure imgf000023_0001
Hist-DG
Figure imgf000023_0002
3. Amphoteric Lipids
[0175] Amphoteric lipids are disclosed in PCT International Publication Numbers WO02/066489 and WO03/070735, the contents of both of which are incorporated herein by reference. The overall molecule assumes its pH-dependent charge characteristics by the simultaneous presence of cationic and anionic groups in the "amphoteric substance" molecule portion. More specifically, an amphoteric substance is characterized by the fact that the sum of its charge components will be precisely zero at a particular pH value. This point is referred to as isoelectric point (IP). Above the IP the compound has a negative charge, and below the IP it is to be regarded as a positive cation, the IP of the amphoteric lipids according to the invention ranging between 4.5 and 8.5.
[0176] The overall charge of the molecule at a particular pH value of the medium can be calculated as follows: z = ∑ni x ((qi-1) + (10(pK"pH)/(l+10(pK"pH))) qi: absolute charge of the ionic group below the pK thereof (e.g. carboxyl = 0, single- nitrogen base = 1, di-esterified phosphate group = -1) ni: number of such groups in the molecule.
[0177] For example, a compound is formed by coupling the amino group of histidine to cholesterol hemisuccinate. At a neutral pH value of 7, the product has a negative charge because the carboxyl function which is present therein is in its fully dissociated form, and the imidazole function only has low charge. At an acid pH value of about 4, the situation is reversed: the carboxyl function now is largely discharged, while the imidazole group is essentially fully protonated, and the overall charge of the molecule therefore is positive. [0178] In one embodiment, the amphoteric lipid is selected from the group consisting of HistChol, HistDG, isoHistSuccDG, Acylcarnosine and HCChol. In another embodiment, the amphoteric lipid is HistChol.
[0179] Amphoteric lipids can include, without limitation, derivatives of cationic lipids which include an anionic substituent. Amphoteric lipids include, without limitation, the compounds having the structure of the formula:
Z-X-W 1-Y-W2-HET wherein:
Z is a sterol or an aliphatic;
Sterol is selected from the group consisting of cholesterol, sitosterol, campesterol, desmosterol, fucosterol, 22-ketosterol, 20-hydroxysterol, sigmasterol, 22-hydroxycholesterol, 25 hydroxycholesterol, lanosterol, 7-dehydrocholesteril, dihydrocholesterol, 19- hydroxycholesterol, 5αcholest-7-en-3β-ol, 7-hydroxycholesterol, epocholesterol, ergosterol dehydroergosterol, and derivatives thereof;
Each Wl is independently an unsubstituted aliphatic;
Each W2 is independently an aliphatic optionally substituted with HO(O)C-aliphatic- amino or carboxy;
Each X and Y is independently absent, -(C=O)-O-, -(C=O)-NH-, -(C=O)-S-, -O-, -NH-, -S-, -CH=N-, -0-(O=C)-, -S-(O=C)-, -NH-(O=C)- -N=CH-, and
HET is an amino, an optionally substituted heterocycloaliphatic or an optionally substituted heteroaryl.
[0180] In some aspects, the HET is an optionally substituted heterocycloaliphatic including at least one nitrogen ring atom, or an optionally substituted heteroaryl including at least one nitrogen ring atom. In other aspects, the HET is morpholinyl, piperidinyl, piperazinlyl, pyrimidinyl, or pyridinyl. In another aspect, the cationic lipid has the structure Sterol-X- spacerl-Y-spacer2-morpholinyl or Sterol-X-spacerl-Y-spacer2-imidazolyl. In still further aspects, the sterol is cholesterol.
[0181] In other embodiments, amphoteric lipids include, without limitation, the compounds having the structure of the formula:
Z-X-W1-Y-W2-HET wherein:
Z is a structure according to the general formula R1-O-CH2
R2-O-CH
L-M-, wherein Rl and R2 are independently C8-C30 alkyl or acyl chains with O, 1 or 2 ethylenically unsaturated bonds and M is selected from the group consisting of -0-(C=O); - NH-(C=O)-; -S-(C=O)-; -O-; -NH-; -S-; -N=CH-; -(O=C)-O-; -S-(O=C)-; -NH-(O=C)-, - N=CH-, -S-S-; and
Sterol is selected from the group consisting of cholesterol, sitosterol, campesterol, desmosterol, fucosterol, 22-ketosterol, 20-hydroxysterol, sigmasterol, 22-hydroxycholesterol, 25 hydroxycholesterol, lanosterol, 7-dehydrocholesteril, dihydrocholesterol, 19- hydroxycholesterol, 5αcholest-7-en-3β-ol, 7-hydroxycholesterol, epicholesterol, ergosterol dehydroergosterol, and derivatives thereof;
Each Wl is independently an unsubstituted aliphatic with up to 8 carbon atoms;
Each W2 is independently an aliphatic , carboxylic acid with up to 8 carbon atoms and 0, 1, or 2 ethyleneically unsaturated bonds;
X is absent and Y is -(C=O)-O-; -(C=O)-NH-; -NH-(C=O)-O-; -0-; -NH-; -CH=N-; - 0-(O=C)-; -S-; -(O=C)-; -NH-(O=C)-; -0-(O=C)-NH-, -N=CH- and/or -S-S-; and
HET is an amino, an optionally substituted heterocycloaliphatic or an optionally substituted heteroaryl.
[0182] In some aspects, the HET is an optionally substituted heterocycloaliphatic including at least one nitrogen ring atom, or an optionally substituted heteroaryl including at least one nitrogen ring atom. In other aspects, the HET is morpholinyl, piperidinyl, piperazinlyl, pyrimidinyl, or pyridinyl. In another aspect, the cationic lipid has the structure Sterol-X- spacerl-Y-spacer2-morpholinyl or Sterol-X-spacerl-Y-spacer2-imidazolyl. In still further aspects, the sterol is cholesterol.
4. Mixtures of Lipid Components with Amphoteric Properties
[0183] Alternatively, the lipid phase can be formulated using pH-responsive anionic and/or cationic components, as disclosed in PCT International Publication Number WO02/066012, the contents of which are incorporated by reference herein. Cationic lipids sensitive to pH are disclosed in PCT International Publication Numbers WO02/066489 and WO03/070220, in Budker, et al. (1996), Nat Biotechnol. 14(6):760-4, and in US Patent Number 6,258,792, the contents of all of which are incorporated by reference herein. Alternatively, the cationic charge may be introduced from constitutively charged lipids known to those skilled in the art in combination with a pH sensitive anionic lipid. Combinations of constitutively (e.g., stable charge over a specific pH range such as a pH between about 4 and 9) charged anionic and canonic lipids, e.g. DOTAP and DPPG are not preferred. Thus, in some embodiments of the invention, the mixture of lipid components may comprise (i) a stable cationic lipid and a chargeable anionic lipid, (ii) a chargeable cationic lipid and chargeable anionic lipid or (iii) a stable anionic lipid and a chargeable cationic lipid. [0184] The charged groups can be divided into the following 4 groups.
(1) Strongly (e.g., constitutively charged) cationic, pKa > 9, net positive charge: on the basis of their chemical nature, these are, for example, ammonium, amidinium, guanidium or pyridinium groups or timely, secondary or tertiary amino functions.
(2) Weakly cationic, pKa < 9, net positive charge: on the basis of their chemical nature, these are, in particular, nitrogen bases such as piperazines, imidazoles and morpholines, purines or pyrimidines. Such molecular fragments, which occur in biological systems, are, for example, 4-imidazoles (histamine), 2-, 6-, or 9-purines (adenines, guanines, adenosines or guanosines), 1-, 2-or 4-pyrimidines (uracils, thymines, cytosines, uridines, thymidines, cytidines) or also pyridine-3-carboxylic acids (nicotinic esters or amides). Nitrogen bases with preferred pKa values are also formed by substituting nitrogen atoms one or more times with low molecular weight alkane hydroxyls, such as hydroxymethyl or hydroxyethyl groups. For example, aminodihydroxypropanes, triethanolamines, tris- (hydroxymethyl)methylamines, bis-(hydroxymethyl)methylamines, tris- (hydroxyethyl)methylamines, bis-(hydroxyethyl)methylamines or the corresponding substituted ethylamines.
(3) Weakly anionic, pKa > 4, net negative charge: on the basis of their chemical nature, these are, in particular, the carboxylic acids. These include the aliphatic, linear or branched mono-, di- or tricarboxylic acids with up to 12 carbon atoms and 0, 1 or 2 ethylenically unsaturated bonds. Carboxylic acids of suitable behavior are also found as substitutes of aromatic systems. Other weakly anionic groups are hydroxyls or thiols, which can dissociate and occur in ascorbic acid, N-substituted alloxane, N-substituted barbituric acid, veronal, phenol or as a thiol group.
(4) Strongly (e.g., constitutively charged) anionic, pKa < 4, net negative charge: on the basis of their chemical nature, these are functional groups such as sulfonate or phosphate esters.
[0185] The amphoteric liposomes contain variable amounts of such membrane-forming or membrane-based amphiphilic materials, so that they have an amphoteric character. This means that the liposomes can change the sign of the charge completely. The amount of charge carrier of a liposome, present at a given pH of the medium, can be calculated using the following formula: z = ∑ni((qi - 1) + 10(pK ~?H)/(l + 10(pK-pH)) in which qi is the absolute charge of the individual ionic groups below their pK (for example, carboxyl = 0, simple nitrogen base = 1, phosphate group of the second dissociation step = -1, etc.) ni is the number of these groups in the liposome.
[0186] At the isoelectric point, the net charge of the liposome is 0. Structures with a largely selectable isoelectric point can be produced by mixing anionic and cationic portions. [0187] In one embodiment, cationic components include DPIM, CHIM, DORIE, DDAB, DAC-Chol, TC-Chol, DOTMA, DOGS, (C18)2Gly+ N,N-dioctadecylamido-glycine, CTAB, CPyC, DODAP DMTAP, DPTAP, DOTAP, DC-Choi, MoChol, HisChol and DOEPC. In another embodiment, cationic lipids include DMTAP, DPTAP, DOTAP, DC-Choi, MoChol and HisChol.
[0188] The cationic lipids can be compounds having the structure of the formula L-X-spacerl-Y-spacer2-HET wherein:
L is a sterol or [aliphatic(C(O)O)-]2-alkyl-;
Sterol is selected from the group consisting of cholesterol, sitosterol, campesterol, desmosterol, fucosterol, 22-ketosterol, 20-hydroxysterol, sigmasterol, 22-hydroxycholesterol, 25 hydroxycholesterol, lanosterol, 7-dehydrocholesteril, dihydrocholesterol, 19- hydroxycholesterol, 5αcholest-7-en-3β-ol, 7-hydroxycholesterol, epocholesterol, ergosterol dehydroergosterol, and derivatives thereof;
Each spacer 1 and spacer 2 is independently an unsubstituted aliphatic;
Each X and Y is independently absent, -(C=O)-O-, -(C=O)-NH-, -(C=O)-S-, -O-, -NH-, -S-, -CH=N-, -0-(O=C)-, -S-(O=C)-, -NH-(O=C)-, -N=CH-, and
HET is an amino, an optionally substituted heterocycloaliphatic or an optionally substituted heteroaryl.
[0189] In some aspects, the HET is an optionally substituted heterocycloaliphatic including at least one nitrogen ring atom, or an optionally substituted heteroaryl including at least one nitrogen ring atom. In other aspects, the HET is morpholinyl, piperidinyl, piperazinlyl, pyrimidinyl or pyridinyl. In another aspect, the cationic lipid has the structure Sterol-X- spacer l-Y-spacer2-morpholinyl or Sterol-X-spacerl-Y-space^-imidazolyl. In still further aspects, the sterol is cholesterol.
[0190] In another embodiment, pH sensitive cationic lipids can be compounds having the structure of the formula
L-X-spacer 1 - Y-spacer2-HET wherein:
L is a structure according to the general formula
Figure imgf000028_0001
wherein Rl and R2 are independently C8-C30 alkyl or acyl chains with 0, 1 or 2 ethylenically unsaturated bonds and M is absent,-O-(C=O); -NH-(C=O)-; -S-(C=O)-; -O-; - NH-; -S-; -N=CH-; -(O=C)-O-; -S-(O=C)-; -NH-(O=C)-; -N=CH-, -S-S-; and
Sterol is selected from the group consisting of cholesterol, sitosterol, campesterol, desmosterol, fucosterol, 22-ketosterol, 20-hydroxy sterol, sigmasterol, 22-hydroxycholesterol, 25 hydroxycholesterol, lanosterol, 7-dehydrocholesterol, dihydrocholesterol, 19- hydroxycholesterol, 5αcholest-7-en-3β-ol, 7-hydroxycholesterol, epicholesterol, ergosterol dehydroergosterol, and derivatives thereof;
Each spacer 1 and spacer 2 is independently an unsubstituted aliphatic with 1-8 carbon atoms;
X is absent and Y is absent, -(C=O)-O-; -(C=O)-NH-J-NH-(C=O)-O-; -O-; -NH-; - CH=N-; -0-(O=C)-; -S-; -(O=C)-; -NH-(O=C)-; -0-(O=C)-NH-, -N=CH- and/or -S-S-; and
HET is an amino, an optionally substituted heterocycloaliphatic or an optionally substituted heteroaryl.
[0191] In some aspects, the HET is an optionally substituted heterocycloaliphatic including at least one nitrogen ring atom, or an optionally substituted heteroaryl including at least one nitrogen ring atom. In other aspects, the HET is morpholinyl, piperidinyl, piperazinlyl, pyrimidinyl or pyridinyl. In another aspect, the cationic lipid has the structure Sterol-X- spacerl-Y-spacer2-morpholinyl or Sterol-X-spacerl-Y-spacer2-imidazolyl. In still further aspects, the sterol is cholesterol.
[0192] The above compounds can be synthesized using syntheses of 1 or more steps, and can be prepared by one skilled in the art.
[0193] The amphoteric mixtures further comprise anionic lipids, either constitutively or conditionally charged in response to pH, and such lipids are also known to those skilled in the art. In one embodiment, lipids for use with the invention include DOGSucc, POGSucc, DMGSucc, DPGSucc, DMPS, DPPS, DOPS, POPS, DMPG, DPPG, DOPG, POPG, DMPA, DPPA, DOPA, POPA, CHEMS and CetylP. In another embodiment, anionic lipids include DOGSucc, DMGSucc, DMPG, DPPG, DOPG, POPG, DMPA, DPPA, DOPA, POPA, CHEMS and CetylP.
5. Neutral Lipids
[0194] Neutral lipids include any lipid that remains neutrally charged at a pH between about 4 and 9. Neutral lipids include, without limitation, cholesterol, other sterols and derivatives thereof, phospholipids, and combinations thereof. The phospholipids include any one phospholipid or combination of phospholipids capable of forming liposomes. They include phosphatidylcholines, phosphatidylethanolamines, lecithin and fractions thereof, phosphatidic acids, phosphatidylglycerols, phosphatidylinolitols, phosphatidylserines, plasmalogens and sphingomyelins. The phosphatidylcholines include, without limitation, those obtained from egg, soy beans or other plant sources or those that are partially or wholly synthetic or of variable lipid chain length and unsaturation, POPC, OPPC, natural or hydrogenated soy bean PC, natural or hydrogenated egg PC, DMPC, DPPC, DSPC, DOPC and derivatives thereof. In one embodiment, phosphatidylcholines are POPC, non-hydrogenated soy bean PC and non-hydrogenated egg PC. Phosphatidylethanolamines include, without limitation, DOPE, DMPE and DPPE and derivatives thereof. Phosphatidylglycerols include, without limitation, DMPG, DLPG, DPPG, and DSPG. Phosphatidic acids include, without limitation, DSPA, DMPA, DLPA and DPPA.
[0195] Sterols include cholesterol derivatives such as 3-hydroxy-5.6-cholestene and related analogs, such as 3-amino-5.6-cholestene and 5,6-cholestene, cholestane, cholestanol and related analogs, such as 3-hydroxy-cholestane; and charged cholesterol derivatives such as cholesteryl-beta-alanine and cholesterol hemisuccinate.
[0196] In one embodiment neutral lipids include but are not limited to DOPE, POPC, soy bean PC or egg PC and cholesterol. B. DNAi Oligonucleotides
1. Definitions
[0197] As used herein, the term "nucleic acid molecule", "nucleic acid sequence" or "polynucleotide" refers to any nucleic acid containing molecule, including, without limitation, DNA or RNA. The term polynucleotide(s) generally refers to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. Thus, for instance, polynucleotides as used herein refers to, among others, single-and double-stranded DNA, DNA that is a mixture of single- and double- stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single- stranded or double-stranded or a mixture of single- and double-stranded regions. [0198] In addition, "polynucleotide" as used herein refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules. The regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules. One of the molecules of a triple-helical region often is an oligonucleotide. [0199] The term "polynucleotide," "nucleic acid molecule" or "nucleic acid sequence" includes DNAs or RNAs that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "polynucleotides," "nucleic acid molecules" or "nucleic acid sequences" as those terms are intended herein. The terms also encompass sequences that include any of the known base analogs of DNA and RNA. [0200] It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term "polynucleotide" as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells, among others. [0201] By "isolated nucleic acid sequence" is meant a polynucleotide that is not immediately contiguous with either of the coding sequences with which it is immediately contiguous (one on the 5' end and one on the 3' end) in the naturally occurring genome of the organism from which it is derived. The term therefore includes, for example, a recombinant DNA which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA) independent of other sequences. The nucleotides of the invention can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide. The term includes single and double stranded forms of DNA.
[0202] The term "gene" refers to a nucleic acid (e.g., DNA) sequence that includes coding sequences necessary for the production of a polypeptide, precursor or RNA (e.g., rRNA, tRNA). The polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragment are retained. The term also encompasses the coding region of a structural gene and the sequences preceding and following the coding region, (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons). Sequences located 5' of the coding region and present on the mRNA are referred to as 5' non-translated sequences or regions. Sequences located 3' or downstream of the coding region and present on the mRNA are referred to as 3' non-translated sequences or regions. The term "gene" encompasses both cDNA and genomic forms of a gene. A genomic form or clone of a gene contains the coding region interrupted with non-coding sequences termed "introns" or "intervening regions" or "intervening sequences." Introns are segments of a gene that are transcribed into nuclear RNA (hnRNA); introns may contain regulatory elements such as enhancers. Introns are removed or "spliced out" from the nuclear or primary transcript; introns therefore are absent in the messenger RNA (mRNA) transcript. The mRNA functions during translation to specify the sequence or order of amino acids in a nascent polypeptide. [0203] As used herein, the term "gene expression" refers to the process of converting genetic information encoded in a gene into RNA (e.g., mRNA, rRNA, tRNA, or snRNA) through "transcription" of the gene (i.e., via the enzymatic action of an RNA polymerase), and for protein encoding genes, into protein through "translation" of mRNA. Gene expression can be regulated at many stages in the process. "Up-regulation" or "activation" refers to regulation that increases the production of gene expression products (i.e., RNA or protein), while "down-regulation" or "repression" refers to regulation that decrease production. Molecules (e.g., transcription factors) that are involved in up-regulation or down-regulation are often called "activators" and "repressors," respectively.
[0204] In addition to containing introns, genomic forms of a gene may also include sequences located on both the 5' and 3' end of the sequences that are present on the RNA transcript. These sequences are referred to as "flanking" sequences or regions (these flanking sequences are located 5' or 3' to the non-translated sequences present on the mRNA transcript). The 5' flanking region (or upstream region) may contain regulatory sequences such as promoters and enhancers that control or influence the transcription of the gene. The 3' flanking region may contain sequences that direct the termination of transcription, post-transcriptional cleavage and polyadenylation.
[0205] As used herein, the terms "nucleic acid molecule encoding," "DNA sequence encoding," and "DNA encoding" refer to the order or sequence of deoxyribonucleotides along a strand of deoxyribonucleic acid. The order of these deoxyribonucleotides determines the order of amino acids along the polypeptide (protein) chain. The DNA sequence thus codes for the amino acid sequence. [0206] The term "oligonucleotide" as used herein is defined as a molecule with two or more deoxyribonucleotides or ribonucleotides, often more than three, and usually more than ten. The exact size of an oligonucleotide will depend on many factors, including the ultimate function or use of the oligonucleotide. Oligonucleotides can be prepared by any suitable method, including, for example, cloning and restriction of appropriate sequences and direct chemical synthesis by a method such as the phosphotriester method of Narang et al., 1979, Meth. Enzymol., 68:90-99; the phosphodiester method of Brown et al., 1979, Method Enzymol., 68: 109-151, the diethylphosphoramidite method of Beaucage et al., 1981, Tetrahedron Lett., 22:1859-1862; the triester method of Matteucci et al., 1981, J. Am. Chem. Soc, 103:3185-3191, or automated synthesis methods; and the solid support method of U.S. Pat. No. 4,458,066.
[0207] As used herein, a "DNAi oligonucleotide" or "DNAi" refers to a single stranded nucleic acid oligonucleotide or derivative thereof, whose sequence is complementary, in part, to a portion of the longest non-transcribed region of a gene in which the oligonucleotide affects indirectly or directly the expression, regulation or production of the same or different gene, wherein the longest non-transcribed region includes any portion of the gene that is not transcribed when the transcriptional start site is the site closest to the translation start site. DNAi does not include RNAi and antisense oligonucleotides that base pair only with mRNAs or pre-mRNAs and interfere with RNA processing and/or message translation. [0208] In some embodiments utilizing methylated oligonucleotides the nucleotide, dC, is replaced by 5-methyl-dC where appropriate.
[0209] The DNAi oligonucleotides may comprise, without limitation, oligonucleotide mimetic s such as those described below. The oligonucleotide compounds in accordance with this invention generally comprise from about 15 to about 35 nucleobases (i.e., from about 15 to about 35 linked bases), although both longer and shorter sequences may find use with the present invention.
[0210] Oligonucleotides can also include nucleobase (often referred to in the art simply as "base") modifications or substitutions. As used herein, "unmodified" or "natural" nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases described below.
[0211] By "promoter" is meant a sequence sufficient to direct transcription. "Promoter" also includes those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue-specific, or inducible by external signals or agents; such elements may be located in the 5' or 3' regions of the gene. Both constitutive and inducible promoters, are included in the invention (see e.g., Bitter et al., Methods in Enzymology 153:516-544, 1987). For example, when cloning in mammalian cell systems, promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter) may be used. Promoters produced by recombinant DNA or synthetic techniques may also be used to provide for transcription of the nucleic acid sequences of the invention.
[0212] As used herein, the "regulatory region" of a gene is any part of a gene that regulates the expression of a gene, including, without limitation, transcriptional and translational regulation. The regions include without limitation the 5' and 3' regions of genes, binding sites for regulatory factors, including without limitation transcription factor binding sites. The regions also include regions that are as long as 20,000 or more base pairs upstream or downstream of translational start sites, so long as the region is involved in any way in the regulation of the expression of the gene. The region may be as short as 20 base pairs or as long as thousands of base pairs.
[0213] As used herein, the terms "complementary" or "complementarity" are used in reference to polynucleotides {i.e., a sequence of nucleotides) related by the base-pairing rules. For example, for the sequence "A-G-T," is complementary to the sequence "T-C-A." Complementarity may be "partial," in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be "complete" or "total" complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
[0214] As used herein, the term "completely complementary," for example when used in reference to an oligonucleotide of the present invention refers to an oligonucleotide where all of the nucleotides are complementary to a target sequence {e.g., a gene). [0215] As used herein, the term "partially complementary," refers to a sequence where at least one nucleotide is not complementary to the target sequence. Preferred partially complementary sequences are those that can still hybridize to the target sequence under physiological conditions. The term "partially complementary" refers to sequences that have regions of one or more non-complementary nucleotides both internal to the sequence or at either end. Sequences with mismatches at the ends may still hybridize to the target sequence. [0216] The term "homology" refers to a degree of complementarity. There may be partial homology or complete homology (i.e., identity). A partially complementary sequence is a nucleic acid molecule that at least partially inhibits a completely complementary nucleic acid molecule from hybridizing to a target nucleic acid is "substantially homologous." The inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or northern blot, solution hybridization and the like) under conditions of low stringency. A substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous nucleic acid molecule to a target under conditions of low stringency. Likewise, A substantially complementary sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely complementary nucleic acid molecule to a target under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction. The absence of non-specific binding may be tested by the use of a second target that is substantially non-complementary (e.g., less than about 30% identity); in the absence of nonspecific binding the probe will not hybridize to the second non-complementary target. [0217] When used in reference to a double-stranded nucleic acid sequence such as a cDNA or genomic clone, the term "substantially homologous" refers to any probe that can hybridize to either or both strands of the double-stranded nucleic acid sequence under conditions of low stringency as described above.
[0218] When used in reference to a single-stranded nucleic acid sequence, the term "substantially homologous" refers to any probe that can hybridize (i.e., it is the complement of) the single-stranded nucleic acid sequence under conditions of low stringency as described above.
[0219] As used herein, the term "hybridization" is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is impacted by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, the Tm of the formed hybrid, and the G:C ratio within the nucleic acids. A single molecule that contains pairing of complementary nucleic acids within its structure is said to be "self- hybridized."
[0220] As used herein, the term "Tm" is used in reference to the "melting temperature." The melting temperature is the temperature at which a population of double-stranded nucleic acid molecules becomes half dissociated into single strands. Methods or equations for calculating the Tm of nucleic acids is well known in the art. As indicated by standard references, a simple estimate of the Tm value may be calculated by the equation Tm = 81.5 + 0.41(% G + C), when a nucleic acid is in aqueous solution at 1 M NaCl (See e.g., Anderson and Young, Quantitative Filter Hybridization, in Nucleic Acid Hybridization (1985)). Other references include more sophisticated computations that take structural as well as sequence characteristics into account for the calculation of Tm.
[0221] Inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or northern blot, solution hybridization and the like) under conditions of low stringency. A substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous nucleic acid molecule to a target under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction. The absence of non-specific binding may be tested by the use of a second target that is substantially non-complementary (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second non-complementary target.
[0222] When used in reference to a double-stranded nucleic acid sequence such as a cDNA or genomic clone, the term "substantially homologous" refers to any probe that can hybridize to either or both strands of the double-stranded nucleic acid sequence under conditions of low stringency as described above.
[0223] As used herein the term "stringency" is used in reference to the conditions of temperature, ionic strength and the presence of other compounds such as organic solvents, under which nucleic acid hybridizations are conducted. Under "low stringency conditions" a nucleic acid sequence of interest will hybridize to its exact complement, sequences with single base mismatches, closely related sequences (e.g., sequences with 90% or greater homology), and sequences having only partial homology (e.g., sequences with 50-90% homology). Under "medium stringency conditions," a nucleic acid sequence of interest will hybridize only to its exact complement, sequences with single base mismatches, and closely relation sequences (e.g., 90% or greater homology). Under "high stringency conditions," a nucleic acid sequence of interest will hybridize only to its exact complement, and (depending on conditions such a temperature) sequences with single base mismatches. In other words, under conditions of high stringency the temperature can be raised so as to exclude hybridization to sequences with single base mismatches.
[0224] As used herein, the term "physiological conditions" refers to specific stringency conditions that approximate or are conditions inside an animal (e.g., a human). Exemplary physiological conditions for use in vitro include, but are not limited to, 37°C, 95% air, 5% CO2, commercial medium for culture of mammalian cells (e.g., DMEM media available from Gibco, MD), 5-10% serum (e.g., calf serum or horse serum), additional buffers, and optionally hormone (e.g., insulin and epidermal growth factor).
[0225] The term "isolated" means altered "by the hand of man" from its natural state; i.e., if it occurs in nature, it has been changed or removed from its original environment or both. For example, when used in relation to a nucleic acid, as in "an isolated nucleotide" or "isolated polynucleotide" refers to a nucleic acid sequence that is identified and separated from at least one component or contaminant with which it is ordinarily associated in its natural source. Isolated nucleic acid is such present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids are nucleic acids such as DNA and RNA found in the state they exist in nature. For example, a given DNA sequence (e.g., a gene) as found on the host cell chromosome in proximity to neighboring genes; RNA sequences, such as a specific mRNA sequence encoding a specific protein, are found in the cell as a mixture with numerous other mRNAs that encode a multitude of proteins. However, isolated nucleic acid encoding a given protein includes, by way of example, such nucleic acid in cells ordinarily expressing the given protein where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature. The isolated nucleic acid, oligonucleotide or polynucleotide may be present in single-stranded or double-stranded form. When an isolated nucleic acid, oligonucleotide or polynucleotide is used to express a protein, the oligonucleotide or polynucleotide will contain at a minimum the sense or coding strand (i.e., the oligonucleotide or polynucleotide may be single-stranded), but may contain both the sense and anti-sense strands (i.e., the oligonucleotide or polynucleotide may be double- stranded).
[0226] As used herein, the term "purified" or "to purify" refers to the removal of components (e.g., contaminants) from a sample. For example, antibodies are purified by removing contaminating non-immunoglobulin proteins; they are also purified by the removing immunoglobulin that does not bind to the target molecule. The removal of non- immunoglobulin proteins and/or the removal of immunoglobulins that do not bind to the target molecule results in an increase in the percent of target-reactive immunoglobulins in the sample. In another example, recombinant polypeptides are expressed in bacterial host cells and the polypeptides are purified by the removal of host cell proteins; the percent of recombinant polypeptides is thereby increased in the sample. 2. Targets a. Oncogene Targets
[0227] In some embodiments, the present invention provides antigene inhibitors of oncogenes. The present invention is not limited to the inhibition of a particular oncogene. Indeed, the present invention encompasses antigene inhibitors to any number of oncogenes including, but not limited to, those disclosed herein. i. Ras
[0228] One gene which has captured the attention of many scientists is the human proto- oncogene, c-Ha-ras. This gene acts as a central dispatcher, relaying chemical signals into cells and controlling cell division. Ras gene alteration may cause the gene to stay in the "on" position. The ras oncogene is believed to underlie up to 30% of cancer, including colon cancer, lung cancer, bladder and mammary carcinoma (Bos, Cancer Res. 49:4682-4689 [1989]). The ras oncogene has therefore become a target for therapeutic drugs. [0229] There are several reports showing that oligonucleotides complementary to various sites of ras mRNA can inhibit synthesis of ras protein (ρ21), which decreases the cell proliferation rate in cell culture (U.S. Pat. No. 5,576,208; U.S. Pat. No. 5,582,986; Daska et al, Oncogene Res. 5:267-275 [1990]; Brown et al., Oncogene Res. 4:243-252 [1989]; Saison-Behmoaras et al., EMBO J. 10:1111-1116 [1991)]. Oligonucleotides complementary to the 5' flanking region of the c-Ha-ras RNA transcript have shown to inhibit tumor growth in nude mice for up to 14 days (Gray et al, Cancer Res. 53:577-580 [1993]). It was recently reported that an antisense oligonucleotide directed to a point mutation (G>C) in codon 12 of the c-Ha-ras mRNA inhibited cell proliferation as well as tumor growth in nude mice when it was injected subcutaneously (U.S. Pat. No. 5,576,208; U.S. Pat. No. 5,582,986; Schwab et al, Proc. Natl. Acad. Sci. USA 91:10460-10464 [1994]; each of which is herein incorporated by reference). Researchers have also reported that antisense drugs shrank ovarian tumors in small clinical trials (Roush et al, Science 276: 1192-1194 [1997]). ii. Her-2
[0230] The -her-2 (also known as neu oncogene or erbB-2) oncogene encodes a receptor-like tyrosine kinase (RTK) that has been extensively investigated because of its role in several human carcinomas (Hynes and Stern, Biochim. et Biophy. Acta 1198:165-184 [1994]; Dougall et al, Oncogene 9:2109-2123 [1994]) and in mammalian development (Lee et al., Nature 378:394-398 [1995]). Her-2 is one of the most frequently altered genes in cancer. It encodes a transmembrane receptor (also known as pi 85) with tyrosine kinase activity and is a member of the epidermal growth factor (EGF) family, and thus is related to the epidermal growth factor receptor (EGFR or HER-I). Aberrant her-2 gene expression is present in a wide variety of cancers and are most common in breast, ovarian and gastric cancers. HER-2 is overexpressed in 25-30% of all human breast and ovarian cancers. Levels of HER-2 overexpression correlate well with clinical stage of breast cancer, prognosis and metastatic potential. Overexpression of HER-2 is associated with lower survival rates, increased relapse rates and increased metastatic potential. Tan et al, (Cancer Res., 57: 1199 [1997]) have shown that overexpression of the HER-2 gene increases the metastatic potential of breast cancer cells without increasing their transformation ability.
[0231] Aberrant expression of HER-2 includes both increased expression of normal HER-2 and expression of mutant HER-2. Activation of the her-2 proto-oncogene can occur by any of three mechanisms—point mutation, gene amplification and overexpression. Gene amplification is the most common mechanism. Unlike the other EGF family members for whom ligand activation is necessary for promoting transformation, overexpression of HER-2 alone is sufficient for transformation (Cohen, et al, J. Biol. Chem., 271:30897 [1996]). [0232] Several therapeutic approaches have been used to reduce levels of the her-2 gene product. The adenovirus type 5 gene product ElA has been studied as a potential therapeutic using a breast cancer model in nude mice. This gene product can repress her-2/neu overexpression by repressing her-2/neu promoter activity, and suppress the tumorigenic potential of Λer-2/new-overexpressing ovarian cancer cells. In mice bearing her-2/neu- overexpressing breast cancer xenografts, ElA delivered either by adenovirus or liposome significantly inhibited tumor growth and prolonged mouse survival compared with the controls (Chang et al, Oncogene 14:561 [1997]). Clinical trials have been conducted to evaluate a bispecific antibody which targets the extracellular domains of both the HER-2/neu protein product and Fc gamma RIII (CD 16), the Fc gamma receptor expressed by human natural killer cells, neutrophils, and differentiated mononuclear phagocytes (Weiner et al., J. Hematotherapy, 4:471 [1995]).
[0233] Overexpression of HER-2 has also been found to be associated with increased resistance to chemotherapy. Thus, patients with elevated levels of HER-2 respond poorly to many drugs. Methods used to inhibit HER-2 expression have been combined with commonly used chemotherapeutic agents (Ueno et al, Oncogone 15:953 [1997]). Combining the adenovirus type 5 gene product, ElA, with taxol showed a synergistic effect in human breast cancer cells. Zhang et al, (Oncogene, 12:571 [1996]) demonstrated that emodin, a tyrosine- specific inhibitor, sensitized non-small cell lung cancer (NSCLC) cells to a variety of chemotherapeutic drugs, including cisplatin, doxorubicin and etoposide. A HER-2 antibody was found to increase the efficacy of tamoxifen in human breast cancer cells (Witters et al, Breast Cancer Res. and Treatment, 42:1 [1997]).
[0234] Oligonucleotides have also been used to study the function of HER-2. A triplex- forming oligonucleotide targeted to the her-2 promoter, 42 to 69 nucleotides upstream of the mRNA transcription start site was found to inhibit HER-2 expression in vitro (Ebbinghaus et al, J. Clin. Invest., 92:2433 [1993]). Porumb et al. (Cancer Res., 56:515 [1996]) also used a triplex-forming oligonucleotide targeted to the same her-2 promoter region. Decreases in her-2 mRNA and protein levels were seen in cultured cells. Juhl et al. (J. Biol. Chem., 272:29482 [1997]) used anti-her-2 ribozymes targeted to a central region of the her-2 RNA just downstream of the transmembrane region of the protein to demonstrate a reduction in her-2 mRNA and protein levels in human ovarian cancer cells. A reduction in tumor growth in nude mice was also seen.
[0235] An antisense approach has been used as a potential therapeutic for HER-2 overexpressing cancers. Pegues et al. (Cancer Lett., 117:73 [1997]) cloned a 1.5 kb fragment of her-2 in an antisense orientation into an expression vector; transfecting of this construct into ovarian cancer cells resulted in a reduction of anchorage-independent growth. Casalini et al. (Int. J. Cancer 72:631 [1997]) used several human her-2 antisense vector constructs, containing her-2 fragments from 151 bp to 415 bp in length, to demonstrate reduction in HER-2 protein levels and anchorage-independent growth in lung adenocarcinoma cells. Colomer et al. (Br. J. Cancer, 70:819 [1994]) showed that phosphodiester antisense oligonucleotides targeted at or immediately downstream of, the translation initiation codon inhibited proliferation of human breast cancer cells by up to 60%. Wiechen et al. (Int. J. Cancer 63:604 [1995]) demonstrated that an 18-nucleotide phosphorothioate oligonucleotide targeted to the coding region, 33 nucleotides downstream of the translation initiation codon, of her-2 reduced anchorage-independent growth of ovarian cancer cells. Bertram et al. (Biochem. Biophys. Res. Commun., 200:661 [1994]) used antisense phosphorothioate oligonucleotides targeted to the translation initiation region and a sequence at the 3' part of the translated region of the mRNA which has high homology to a tyrosine kinase consensus sequence, and demonstrated a 75% reduction in HER-2 protein levels in human breast cancer cells. Liu et al, (Antisense and Nucleic Acid Drug Develop., 6:9 [1996]) used antisense phosphorothioate oligonucleotides targeted to the 5' cap site and coding region. The most effective oligonucleotide, targeted to the 5' cap site, reduced HER-2 protein expression by 90%. Cell proliferation was also reduced by a comparable amount. Vaughn et al. (Nuc. Acids Res., 24:4558 [1996]) used phosphorothioate, phosphorodithioate and chimeric antisense oligonucleotides targeted at or adjacent to (either side) the translation initiation region of her-2. An alternating dithioate/diester oligonucleotide targeted to the translation initiation region worked slightly better than an all phosphorothioate oligonucleotide. Brysch et al. (Cancer Gene Ther., 1: 99 [1994]) used chemically modified antisense oligonucleotides targeted to the translation initiation codon of HER-2 to reduce protein levels and cause growth arrest of human breast cancer cell line. iii. C-Myc
[0236] The c-myc gene product is encoded by an immediate early response gene, the expression of which can be induced by various mitogens. C-myc expression is involved in signal transduction pathways leading to cell division. Studies have demonstrated that proliferating cells have higher levels of c-myc mRNA and c-myc protein than do quiescent cells. Antibodies directed against the human c-myc protein are known to inhibit DNA synthesis in nuclei isolated from human cells. Conversely, constitutive expression of c-myc produced by gene transfer inhibits induced differentiation of several cell lines. Constitutive expression of c-myc predisposes transgenic mice to the development of tumors. [0237] Some studies have suggested that the c-myc gene product may play a proliferative role in smooth muscle cells (SMCs). Balloon de-endothelialization and injury of rat aortas is known to increase c-myc mRNA expression of vascular SMC prior to their subsequent proliferation and migration. Also, SMCs in culture proliferate when exposed to several mitogens, including PDGF, FGF, EGF, IGF-I and to serum. Each of these mitogens has been found to be capable of increasing the expression in other cell lines of either c-myc protein, c- myc mRNA, or both. Additionally, blood serum has been found to increase c-myc mRNA levels in SMCs.
[0238] Harel-Bellan et al. (J. Immun. 140; 2431-2435 (1988)) demonstrated that antisense oligonucleotides complementary to c-myc mRNA effectively inhibited the translation thereof in human T cells. These T cells were prevented from entering the S phase of cell division, c- myc proto-oncogene sequences are described in Marcu et al., Ann. Rev. Biochem., 61:809- 860 [1992]; Watt et al, Nature, 303:725-728 [1983)]; Battey et al, Cell, 34:779-787 (1983); and Epstein et al, NTIS publication PB93-100576. iv. Bcl-2 [0239] In many types of human tumors, including lymphomas and leukemias, the bcl-2 gene is overexpressed, and may be associated with tumorigenicity (Tsujimoto et al, Science 228:1440-1443 [1985]). High levels of expression of the bcl-2 gene have been found in all lymphomas with t (14; 18) chromosomal translocations including most follicular B cell lymphomas and many large cell non-Hodgkin's lymphomas. High levels of expression of the bcl-2 gene have also been found in certain leukemias that do not have a t(14; 18) chromosomal translation, including most cases of chronic lymphocytic leukemia acute, many lymphocytic leukemias of the pre-B cell type, neuroblastomas, nasophryngeal carcinomas, and many adenocarcinomas of the prostate, breast and colon. (Reed et al., Cancer Res. 51:6529 [1991]; Yunis et al, New England J. Med. 320:1047; Campos et al, Blood 81:3091- 3096 [1993]; McDonnell et al, Cancer Res. 52:6940-6944 [1992); Lu et al, Int. J Cancer 53:29-35 [1993]; Bonner et al, Lab Invest. 68:43A [1993]).
[0240] The bcl-2 gene has two promoters designated Pl and P2. Pl from which most bcl-2 • mRNA is transcribed is located approximately 1.4 kb upstream of the translation initiation site and P2 is 1.3 kb downstream of Pl. (See Seto, M. et al. EMBO J. 7, 123-131 (1988).) Pl is GC-rich, lacks a TATA box, has many transcription start sites and includes seven consensus binding sites for the SPl transcription factor. P2 includes a CCAAT box and a TATA box and has two different transcription initiation sites. There are multiple NF-ZfB recognition sites and an SV40 enhancer-like octamer motif within P2. (See Heckman, C.A., et al. Oncogene 21, 3898-3908 (2002).) (See SEQ ID NO: 1254). Most human follicular lymphomas contain t(14;18) chromosomal translocations that result from 3' -bcl-2 gene region breakpoints. (See Tsujimoto, Y. et al. Proc. Natl. Acad. ScL U. S. A 84, 1329-1331 (1987).) These translocations place bcl-2 expression under control of the immunoglobulin heavy chain (IgH) locus enhancer resulting in upregulation of bcl-2 expression. Alternatively, there are 5' -bcl-2 breakpoint regions that result from fusions with either the IgH locus or two different immunoglobulin light chain (IgL) loci that are found in some DLCL lymphoma patient isolates. (See Yonetani, N. et al. Jpn. J. Cancer Res. 92, 933-940 (2001).) These 5' -bcl-2 breakpoints have been mapped in separate heterogeneous patient isolates to a region spanning 378 to 2312 bp upstream of the translation initiation site. (See SEQ ID NOs:1255-1266.) Regions around the breakpoints may be sequences that can be used for bcl-2 DNAi oligonucleotide design. v. TGF-a
[0241] Transforming Growth Factor Alpha (TGF-α) is a polypeptide of 50 amino acids. It was first isolated from a retrovirus-transformed mouse cell line and subsequently was identified in human tumor cells, in early rat embryo cells and in cell cultures from the human pituitary gland. TGF-α is closely related to Epidermal Growth Factor (EGF), both structurally and functionally, and both bind to the same receptor, i.e., Epidermal Growth Factor Receptor (EGFR). The sequence and three dimensional structure of both EGF and TGF-α have been determined (Campbell et al, Prog. Growth Factor Res. 1:13 [1989]). TGF- α is a 50 amino acid polypeptide having about 40% homology of residues with EGF. Both peptides are characterized by three well defined loops (denoted A, B and C) and have three intramolecular disulphide bonds.
[0242] Several growth factors, including TGF-α and EGF, are believed to exert their biological effects via interaction with the Epidermal Growth Factor Receptor (EGF Receptor). The EGF Receptor is a Type 1 receptor tyrosine kinase. The EGF Receptor and its ligands are of interest for their roles in normal physiological processes as well as in hyperproliferative and neoplastic diseases.
[0243] The in vivo precursor of TGF-α is a 160 amino acid residue membrane-bound protein (pro-TGF-.alpha.) that is cleaved to yield a soluble compound (Massague, J. Biol. Chem., 265:21393-21396 [1990]). This cleavage removes an extracellular portion comprised of 50 amino acids with a molecular weight of 6 Kd and is considered to be an important regulatory event (Pandiella et al, Proc. Natl. Acad. Sci. USA, 88:1726-1730 [1990]) that can be stimulated by phorbol esters acting via protein kinase C (Pandiella et al, J. Biol. Chem., 266:5769-5773 [1991]).
[0244] Cultured human prostatic tumor lines contain elevated levels of TGF-α mRNA and proliferate in response to TGF-α (Wilding et al, The Prostate, 15:1-12 [1989]). TGF-α appears to have both autocrine and paracrine function, stimulating physiologic activities such as cell division and angiogenesis. When induced in transgenic mice, TGF-α produced epithelial hyperplasia and focal dysplastic changes that resembled carcinoma in situ (Sandgren et al, Cell, 61 : 1121-1135 [1990]).
Vi. c-ki-Ras
[0245] The c-Ki-Ras (KRAS) oncogene is expressed ubiquitously. KRAS, with a length of more than 30 kb, is much larger than HRAS or NRAS. Although the 3 ras genes, HRAS, KRAS, and NRAS, have different genetic structures, all code for proteins of 189 amino acid residues, generically designated p21. These genes acquire malignant properties by single point mutations that affect the incorporation of the 12th or 61st amino acid residue of their respective p21. KRAS is involved in malignancy much more often than is HRAS. In a study of 96 human tumors or tumor cell lines in the NIH 3T3 transforming system, (Pulciani et al, Nature 300: 539 (1982) found a mutated HRAS locus only in T24 bladder cancer cells, whereas transforming KRAS genes were identified in 8 different carcinomas and sarcomas. [0246] In a serous cystadenocarcinoma of the ovary, Feig et al. {Science 223: 698 (1984)) showed the presence of an activated KRAS oncogene not activated in normal cells of the same patient. The transforming gene product displayed an electrophoretic mobility in SDS- polyacrylamide gels that differed from the mobility of KRAS transforming proteins in other tumors. Thus, a previously undescribed mutation was responsible for activation of KRAS in this ovarian carcinoma. To study the role of oncogenes in lung cancer, Rodenhuis et al. {New Eng. J. Med. 317: 929 (1987)) used an assay based on oligonucleotide hybridization following an in vitro amplification step. Genomic DNA was examined from 39 tumor specimens obtained at thoracotomy. The KRAS gene was found to be activated by point mutations in codon 12 in 5 of 10 adenocarcinomas. Two of these tumors were less than 2 cm in size and had not metastasized. No HRAS, KRAS, or NRAS mutations were observed in 15 squamous cell carcinomas, 10 large cell carcinomas, 1 carcinoid, 2 metastatic adenocarcinomas from primary tumors outside the lung, and 1 small cell carcinoma. An approximately 20-fold amplification of the unmutated KRAS gene was observed in a tumor that proved to be a solitary lung metastasis of a rectal carcinoma. Yanez et al. (Oncogene 1:315 (1987)) found mutations in codon 12 of the KRAS gene in 4 of 16 colon cancers, 2 of 27 lung cancers, and 1 of 8 breast cancers; no mutations were found at position 61. Of the 6 possible amino acid replacements in codon 12, all but one were represented in the 7 mutations identified.
[0247] The upstream regions of a number of oncogenes including bcl-2, TGF-α, c-ki-ras, c- myc, c-erb-2 (Her-2), and c-Ha-ras can also be investigated to find regions to which DNAi oligonucleotides could bind based on preferred design criteria. vii. Other Oncogene Targets
[0248] The present invention is not limited to the oncogenes described above. The methods of the present invention are suitable for use with any oncogene with a known promoter region. Exemplary oncogenes included, but are not limited to, BCR/ABL, ABL1/BCR, ABL, BCLl, CD24, CDK4, EGFR/ERBB-1, HSTFl, INTlAVNTl, INT2, MDM2, MET, MYB, MYC, MYCN, MYCLl, RAFl, NRAS, REL, AKT2, APC, BCL2-ALPHA, BCL2-BETA, BCL3, BCR, BRCAl, BRCA2, CBL, CCNDl, CDKNlA, CDKNlC, CDKN2A, CDKN2B, CRK, CRK-π, CSF1R/FMS, DBL, DDOST, DCC, DPC4/SMAD4, E-CAD, E2F1/RBAP, ELKl, ELK3, EPH, EPHAl, E2F1, EPHA3, ERG, ETSl, ETS2, FER, FGR, FLI1/ERGB2, FOS, FPS/FES, FRAl, FRA2, FYN, HCK, HEK, HER3/ERBB-2, ERBB-3, HER4/ERBB-4, HST2, INK4A, INK4B, JUN, JUNB, JUND, KIP2, KIT, KRAS2A, KRAS2B, LCK, LYN, MAS, MAX, MCC, MLHl, MOS, MSH2, MYBA, MYBB, NFl, NF2, P53, PDGFB, PIMl, PTC, RBl, RET, ROSl, SKI, SRCl, TALI, TGFBR2, THRAl, THRB, TIAMl, TRK, VAV, VHL, WAFl, WNT2, WTl, YESl, ALK/NPMl, AMIl, AXL, FMS, GIP, GLI, GSP, HOXI l, HST, IL3, INT2, KS3, K-SAM, LBC, LMO-I, LMO-2, L-MYC, LYLl, LYT-IO, MDM-2, MLHl, MLL, MLM, N-MYC, OST, PAX-5, PMS-I, PMS-2, PRAD-I, RAF, RHOM-I, RHOM-2, SIS, TAL2, TANl, TIAMl, TSC2, TRK, TSCl, STKIl, PTCH, MENl, MEN2, P57/KIP2, PTEN, HPCl, ATM, XPA/XPG, BCL6, DEK, AKAP13, CDHl, BLM, EWSR1/FLI1, FES, FGF3, FGF4, FGF6, FANCA, FLI1/ERGB2, FOSLl, F0SL2, GLI, HRASl, HRX/MLLTl, HRX/MLLT2, KRAS2, MADH4, MASl, MCF2, MLLT1/MLL, MLLT2/HRX, MTG8/RUNX1, MYCLKl, MYH11/CBFB, NFKB2, NOTCHl, NPM1/ALK, NRG/REL, NTRKl, PBX1/TCF3, PML/RARA, PRCAl, RUNXl, RUNX1/CBFA2T1, SET, TCF3/PBX1, TGFBl, TLXl, P53, WNTl, WNT2, WTl, αv-β3, PKCα, TNFα, Clusterin, Surviving, TGFβ, c-fos, c-SRC, and INT-I. b. Non-Oncogene Targets
[0249] The present invention is not limited to the targeting of oncogenes. The methods and compositions of the present invention find use in the targeting of any gene that it is desirable to down regulate the expression of. For example, in some embodiments, the genes to be targeted include, but are not limited to, an immunoglobulin or antibody gene, a clotting factor gene, a protease, a pituitary hormone, a protease inhibitor, a growth factor, a somatomedian, a gonadotrophin, a chemotactin, a chemokine, a plasma protein, a plasma protease inhibitor, an interleukin, an interferon, a cytokine, a transcription factor, or a pathogen target (e.g., a viral gene, a bacterial gene, a microbial gene, a fungal gene).
[0250] Examples of specific genes include, but are not limited to, ADAMTS4, ADAMTS5, APOAl, APOE, APP, B2M, COX2, CRP, DDX25, DMCl, FKBP8, GHl, GHR, IAPP, IFNAl, IFNG, ILl, 1110, IL12, IL13, IL2, IL4, IL7, IL8, IPW, MAPK14, Meil, MMP13, MYD88, NDN, PACE4, PRNP, PSENl, PSEN2, RAD51, RAD51C, SAP, SNRPN, TLR4, TLR9, TTR, UBE3A, VLA-4, and PTP-IB, c-RAF, m-TOR, LDL, VLDL, ApoB-100, HDL, VEGF, rhPDGF-BB, NADs, ICAM-I, MUCl, 2-dG, CTL, PSGL-I, E2F, NF-kB, HIF, and GCPRs.
[0251] In other embodiments, gene from a pathogen is targeted. Exemplary pathogens include, but are not limited to, Human Immunodeficiency virus, Hepatitis B virus, hepatitis C virus, hepatitis A virus, respiratory syncytial virus, pathogens involved in severe acute respiratory syndrome, West Nile virus, and food borne pathogens (e.g., E. colϊ). 3. DNAi Oligonucleotide Design
[0252] The DNAi oligonucleotides are DNA oligomers that are complementary to either the plus strand or minus strand of double stranded DNA, and can include any oligomer that hybridizes to regulatory regions of the c-ki-ras, c-Ha-ras, c-myc, her-2, TGF-a, or bcl-2 gene. For the purposes of this invention, those regulatory regions are defined as SEQ ID NO:1 (for her-2, or c-erb-2), SEQ ID NO:282 (for c-ki-ras), SEQ ID NO:462 (for c-Ha-ras), SEQ ID NO:936 (for c-myc), SEQ ID NO: 1081 (for TGF-a) and SEQ ID NOs: 1249 and 1254 (for bcl-2). The DNA oligomers that hybridize to these regions can be 100%, 99%, 98%, 95%, 90%, 85%, 80%, 75%, 70% or 60% complementary to the sequences. [0253] In some embodiments, DNAi oligonucleotides are designed based on certain design criteria. Such DNAi oligonucleotides can then be tested for efficacy using the methods disclosed herein. For example, in some embodiments, the DNAi oligonucleotides are methylated on at least one, two or all of the CpG islands. In other embodiments, the DNAi oligonucleotides contain no methylation. The present invention is not limited to a particular mechanism. Indeed, an understanding of the mechanism is not necessary to practice the present invention. Nonetheless, it is contemplated that DNAi oligonucleotides in some embodiments are those that have at least a 50% GC content and at least two GC dinucleotides. Also, in some embodiments, the DNAi oligonucleotides do not self hybridize. In further embodiments, DNAi oligonucleotides are designed with at least 1 A or T to minimize self hybridization. In yet further embodiments, commercially available computer programs are used to survey DNAi oligonucleotides for the ability to self hybridize. In still other embodiments, DNAi oligonucleotides are at least 10, or 15 nucleotides and no more than 100 nucleotides in length. In further embodiments, DNAi oligonucleotides are 18-26 nucleotides in length. In some embodiments, DNAi oligonucleotides comprise the universal protein binding sequences CGCCC and CGCG or the complements thereof. [0254] In some embodiments, DNAi oligonucleotides hybridize to a regulatory region of a gene upstream from the TATA box of the promoter. In further embodiments, DNAi oligonucleotides are designed to hybridize to regulatory regions of oncogenes known to be bound by proteins (e.g., transcription factors). In some embodiments, DNAi oligonucleotide compounds are not completely homologous to other regions of the human genome. The homology of the DNAi oligonucleotides to other regions of the genome can be determined using available search tools (e.g., BLAST, available at the internet site of NCBI). [0255] The present invention is not limited to the DNAi oligonucleotides described herein. Other suitable DNAi oligonucleotides may be identified (e.g., using the criteria described above or other criteria). Candidate DNAi oligonucleotides may be tested for efficacy using any suitable method. For example, candidate DNAi oligonucleotides can be evaluated for their ability to prevent cell proliferation at a variety of concentrations. In some embodiments, DNAi oligonucleotides inhibit gene expression or cell proliferation at a low concentration (e.g., less that 20 μM, or 10 μM in in vitro assays.).
4. Oligonucleotide Zones
[0256] In some embodiments, regions within the regulatory regions of the oncogenes are further defined as regions for hybridization of DNAi oligonucleotides. In some embodiments, these regions are referred to as "hot zones."
[0257] In some embodiments, hot zones are defined based on DNAi oligonucleotide compounds that are demonstrated to be effective (see above section on DNAi oligonucleotides) and those that are contemplated to be effective based on the criteria for DNAi oligonucleotides described above. In further embodiments, hot zones encompass 10 bp upstream and downstream of each compound included in each hot zone and have at least one CG or more within an increment of 40 bp further upstream or downstream of each compound. In yet further embodiments, hot zones encompass a maximum of 100 bp upstream and downstream of each oligonucleotide compound included in the hot zone. In additional embodiments, hot zones are defined at beginning regions of each promoter. These hot zones are defined either based on effective sequence(s) or contemplated sequences and have a preferred maximum length of 200 bp. Based on the above described criteria, exemplary hot zones were designed. These hot zones are shown in Table 1.
Table 1 Exem lar Hot Zones
Figure imgf000046_0001
5. DNAi Oligomers
[0258] The DNAi oligomers can include any oligomer that hybridizes to SEQ ID NOs: 1249 or 1254. In another aspect, the DNAi oligomer can be any oligomer that hybridizes to nucleotides 500-2026, nucleotides 500-1525, nucleotides 800-1225, nucleotides 900-1125, nucleotides 950-1075 or nucleotides 970-1045 of SEQ ID NO: 1249 or the complement thereof. In another aspect, the DNAi oligonucleotides can be any oligomer that hybridizes under physiological conditions to exemplary hot zones in SEQ ID NO: 1249. The oligomers that hybridize to these regions include those that are 100%, 99%, 98%, 95%, 90%, 85%, 80%, 75%, 70%, or 60% complementary to the above regions. Examples of DNAi oligomers include, without limitation, those oligomers listed in SEQ ID NOs 1250-1253 and 1267-1447 and the complement thereof. In an embodiment of these aspects, the DNAi oligonucleotides are from 15-35 base pairs in length.
[0259] For the bcl-2 gene, the DNAi oligomer can be SEQ ID NO: 1250, 1251, 1252, 1253, 1267-1447 or the complement thereof. In yet another embodiment, the DNAi oligomer can be SEQ ID NO: 1250, 1251, 1267, 1268, 1276, 1277, 1285, 1286 or the complement thereof. In still another embodiment, the DNAi oligomer can be SEQ ID NOs 1250, 1251, 1289-1358 or the complements thereof. In an additional embodiment the DNAi oligomer can be SEQ ID NO:1250 or l251.
[0260] In a further embodiment of these aspects, the DNAi oligomer has the sequence of the positive strand of the bcl-2 sequence, and thus, binds to the negative strand of the sequence. [0261] In other aspects, the DNAi oligomers can include mixtures of DNAi oligonucleotides. For instance, the DNAi oligomer can include multiple DNAi oligonucleotides, each of which hybridizes to different parts of SEQ ID NOs 1249 and 1254. DNAi oligomers can hybridize to overlapping regions on those sequences or the DNAi oligomers may hybridize to non- overlapping regions. In other embodiments, DNAi oligomers can be SEQ ID NOs 1250, 1251, 1252, 1253, 1267-1447 or the complement thereof, wherein the mixture of DNAi oligomers comprises DNAi oligomers of at least 2 different sequences. [0262] Other oligomers include those that hybridize to SEQ ID NO:946 or the complement thereof. The oligomers can also include those that hybridize to nucleotides 1-500, 1-400, 1- 300, 1-200, 60-170, 200-1100, 400-1000, 500-800, or 600-700 of SEQ ID NO:946. The oligomers that hybridize to these regions include those that are 100%, 99%, 98%, 95%, 90%, 85%, 80%, 75%, 70%, or 60% complementary to SEQ ID NO:946. Examples of DNAi oligomers include, without limitation, those oligomers listed in SEQ ID NOs:937-1080 or the complements thereof.
[0263] In other embodiments, the oligomer can include a mixture of oligomers, each of which hybridizes to a regulatory region of different genes. For instance, the oligomer can include a first oligomer that hybridizes to SEQ ID NO: 1249 or 1254 and second oligomer that hybridizes to a regulatory region of a second gene. In some embodiments, the oligomer includes an oligomer of SEQ ED NOs 1250-1254 and 1267-1447 or the complements thereof, and an oligomer that hybridizes to SEQ ID NO:1, SEQ ID NO:282, SEQ ID NO:462, SEQ ID NO:936, or SEQ ID NO: 1081 or the complement thereof. In other embodiments, the oligomer includes SEQ ID NO 1250 or 1251 or the complement thereof and an oligomer that hybridizes to SEQ ID NO:1, SEQ ID NO:282, SEQ ID NO:462, SEQ ID NO:936, or SEQ ID NO: 1081 or the complement thereof. In yet other embodiments, the oligomer includes SEQ ID NO: 1250 or 1251 or the complement thereof and any of SEQ ID NOs 2-281, 283-461, 463-935, 937-1080 and 1082-1248, or the complement thereof. 6. Oligonucleotide Structure a. Methylation
[0264] In some embodiments, the present invention provides oligonucleotide therapeutics that are methylated at specific sites. The present invention is not limited to a particular mechanism. Indeed, an understanding of the mechanism is not necessary to practice the present invention. Nonetheless, it is contemplated that one mechanism for the regulation of gene activity is methylation of cytosine residues in DNA. 5-methylcytosine (5-MeC) is the only naturally occurring modified base detected in DNA (Ehrlick et al, Science 212:1350- 1357 (1981)). Although not all genes are regulated by methylation, hypomethylation at specific sites or in specific regions in a number of genes is correlated with active transcription (Doerfler, Ann. Rev. Biochem. 52:93-124 [1984]; Christman, Curr. Top. Microbiol. Immunol. 108:49-78 [1988]; Cedar, Cell 34:5503-5513 [1988]). DNA methylation in vitro can prevent efficient transcription of genes in a cell-free system or transient expression of transfected genes. Methylation of C residues in some specific cis-regulatory regions can also block or enhance binding of transcriptional factors or repressors (Doerfler, supra; Christman, supra; Cedar, Cell 34:5503-5513 (1988); Tate et al, Curr. Opin. Genet. Dev. 3:225-231 [1993]; Christman et al, Virus Strategies, eds. Doerfler, W. & Bohm, P. (VCH, Weinheim, N.Y.) pp. 319-333 [1993]).
[0265] Disruption of normal patterns of DNA methylation has been linked to the development of cancer (Christman et al, Proc. Natl. Acad. Sci. USA 92:7347-7351 [1995]). The 5-MeC content of DNA from tumors and tumor derived cell lines is generally lower than normal tissues (Jones et al, Adv. Cancer Res 40:1-30 [1983]). Hypomethylation of specific oncogenes such as c-myc, c-Ki-ras and c-Ha-ras has been detected in a variety of human and animal tumors (Nambu et al, Jpn. J. Cancer (Gann) 78:696-704 [1987]; Feinberg et al, Biochem. Biophys. Res. Commun. 111 :47-54 [1983]; Cheah et al, JNCI73:1057-1063 [1984]; Bhave et al, Carcinogenesis (Lond) 9:343-348 [1988]. In one of the best studied examples of human tumor progression, it has been shown that hypomethylation of DNA is an early event in development of colon cancer (Goetz et al, Science 228:187-290 [1985]). Interference with methylation in vivo can lead to tumor formation. Feeding of methylation inhibitors such as L-methionine or 5-azacytodine or severe deficiency of 5-adenosine methionine through feeding of a diet depleted of lipotropes has been reported to induce formation of liver tumors in rats (Wainfan et al, Cancer Res. 52:207 ls-2077s [1992]). Studies show that extreme lipotrope deficient diets can cause loss of methyl groups at specific sites in genes such as c-myc, ras and c-fos (Dizik et al, Carcinogenesis 12:1307-1312 [1991]). Hypomethylation occurs despite the presence of elevated levels of DNA MTase activity (Wainfan et al, Cancer Res. 49:4094-4097 [1989]). Genes required for sustained active proliferation become inactive as methylated during differentiation and tissue specific genes become hypomethylated and are active. Hypomethylation can then shift the balance between the two states. In some embodiments, the present invention thus takes advantage of this naturally occurring phenomena, to provide compositions and methods for site specific methylation of specific gene promoters, thereby preventing transcription and hence translation of certain genes. In other embodiments, the present invention provides methods and compositions for upregulating the expression of a gene of interest (e.g., a tumor suppressor gene) by altering the gene's methylation patterns.
[0266] The present invention is not limited to the use of methylated oligonucleotides. Indeed, the use of non-methylated oligonucleotides for the inhibition of gene expression is specifically contemplated by the present invention. Experiments conducted during the course of development of the present invention (See e.g., Example 8) demonstrated that an unmethylated oligonucleotide targeted toward Bcl-2 inhibited the growth of lymphoma cells to a level that was comparable to that of a methylated oligonucleotide. b. Bases
[0267] The oligonucleotides can be in a naturally occurring state, and can also contain modifications or substitutions in the nucleobases, the sugar moiety and/or in the internucleoside linkage.
[0268] Nucleobases comprise naturally occurring nucleobases as well as non-naturally occurring nucleobases. Illustrative examples of such nucleobases include without limitation adenine, cytosine, 5-methylcytosine, isocytosine, pseudoisocytosine, guanine, thymine, uracil, 5-bromouracil, 5-propynyluracil, 5-propynylcytosine, 5-propyny-6-fluoroluracil, 5- methylthiazoleuracil, 6-aminopurine, 2-aminopurine, inosine, diaminopurine, 7- deazaguanine, 7-deazaadenine, 3-deazaguanine, 3-deazaadenine, 8-azaguanine, 8-azaadenine, 7-propyne-7-deazaadenine, 7-propyne-7-deazaguanine, 2-chloro-6-aminopurine, 4- acetylcytosine, 5-hydroxymethylcytosine, 8-hydroxy-N6-methyladenosine, aziridinylcytosine, 5-(carboxyhydroxyl-methyl) uracil, 5-fluorouracil, 5- carboxymethylaminomethyl-2-thiouracil, 5-carboxymethylaminomethyluracil, dihydrouracil, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1- methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, N6-methyladenine, 7-methylguanine and other alkyl derivatives of adenine and guanine, 2- propyl adenine and other alkyl derivatives of adenine and guanine, 2-aminoadenine, 5- methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'-methoxycarbonylmethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine, 2-thiocytosine, 2-thiothymine, 5-halouracil, 5-halocytosine, 6-azo uracil, cytosine and thymine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, 8-halo, 8- amino, 8-thiol, 8-hydroxyl and other 8-substituted adenines and guanines, 5-trifluoromethyl uracil and cytosine, N-uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, queosine, xanthine, hypoxanthine, 2-thiocytosine, 2,6-diaminopurine, 5-substituted pyrimidines, 6- azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. c. Sugars and Sugar Substitutes
[0269] Oligonucleotides can also have sugars other than ribose and deoxy ribose, including arabinofuranose (described in International Publication number WO 99/67378, which is herein incorporated by reference), xyloarabinofuranose (described in U.S. Patent Nos 6,316,612 and 6,489465, which are herein incorporated by reference), α-threofuranose (Schoning, et al. (2000) Science, 290, 1347-51, which is herein incorporated by reference) and L-ribofuranose. Sugar mimetics can replace the sugar in the nucleotides. They include cyclohexene (Wang et al.(2000) J. Am. Chem. Soc. 122, 8595-8602; Vebeure et al. Nucl. Acids Res. (2001) 29, 4941-4947, which are herein incorporated by reference), a tricyclo group (Steffens, et al. J. Am. Chem. Soc. (1997) 119, 11548-11549, which is herein incorporated by reference), a cyclobutyl group, a hexitol group (Maurinsh, et al. (1997) J. Org. Chem, 62, 2861-71; J. Am. Chem. Soc. (1998) 120, 5381-94, which are herein incorporated by reference), an altritol group (Allart, et al., Tetrahedron (1999) 6527-46, which is herein incorporated by reference), a pyrrolidine group (Scharer, et al., J. Am. Chem. Soc, 117, 6623-24, which is herein incorporated by reference), carbocyclic groups obtained by replacing the oxygen of the furnaose ring with a methylene group (Froehler and Ricca, J. Am. Chem. Soc. 114, 8230-32, which is herein incorporated by reference) or with an S to obtain 4'-thiofuranose (Hancock, et al., Nucl. Acids Res. 21, 3485-91, which is herein incorporated by reference), and/or morpholino group (Heasman, (2002) Dev. Biol., 243, 209- 214, which is herein incorporated by reference) in place of the pentofuranosyl sugar. Morpholino oligonucleotides are commercially available from Gene Tools, LLC (Corvallis Oregon, USA).
[0270] The nucleotide derivatives can include nucleotides containing one of the following at the 2' sugar position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-0-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted Ci to Cio alkyl or C2 to Ci0 alkenyl and alkynyl, O[(CH2)nO]mCH2, O(CH2)nOCH3, O(CH2)nNH2, O(CH2)nCH3, O(CH2)nONH2, and O(CH2)nON[(CH2)nCH3)]2, where n and m are from 1 to about 10, Ci to Cio lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O- alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ON)2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, 2'-methoxyethoxy (2'-0-CH2CH2OCH3, also known as 2'-O-(2-methoxyethyl) or 2'- MOE) (Martin et al, HeIv. Chim. Acta 78:486 [1995]) i.e., an alkoxyalkoxy group, T- dimethylaminooxyethoxy (i.e., an O(CH2)2ON(CH3)2 group), also known as 2'-DMAOE, and 2'-dimethylaminoethoxyethoxy (also known in the art as 2'-O-dimethylaminoethoxyethyl or 2'-DMAEOE), i.e., 2'-O-CH2-O-CH2-N(CH2)2, 2'-methoxy (2'-0-CH3), 2'-aminopropoxy(2'- OCH2CH2CH2NH2) and 2'-fluoro (2'-F). Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked oligonucleotides and the 5' position of 5' terminal nucleotide. d. Internucleoside Linkages and Backbones
[0271] In some embodiments, the oligonucleotides have non-natural internucleoside linkages. As defined in this specification, oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. For the purposes of this specification, modified oligonucleotides that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.
[0272] Some modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphoroselenates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3'-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3'-5' linkages, 2'-5' linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'. Various salts, mixed salts and free acid forms are also included.
[0273] Other modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts.
[0274] In yet other oligonucleotide mimetics, both the sugar and the internucleoside linkage (i.e., the backbone) of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and.are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos.: 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al., Science 254:1497 (1991).
[0275] In some embodiments, oligonucleotides of the invention are oligonucleotides with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular -CH2-, -NH-O-CH2-, -CH2-N(CH3)-O-CH2- [known as a methylene (methylimino) or MMI backbone], -CH2-O-N(CH3)-CH2-, -CH2-N(CH3)-N(CH3)-CH2-, and -0-N(CH3)- CH2-CH2- [wherein the native phosphodiester backbone is represented as -0-P-O-CH2-] of the above referenced U.S. Pat. No. 5,489,677, and the amide backbones of the above referenced U.S. Pat. No. 5,602,240. Oligonucleotides can also have a morpholino backbone structure of the above-referenced U.S. Pat. No. 5,034,506.
[0276] In some embodiments the oligonucleotides have a phosphorothioate backbone having the following general structure.
Figure imgf000053_0001
e. Other Modifications
[0277] Another modification of the DNAi oligonucleotides of the present invention involves adding additional nucleotides to the 3' and/or 5' ends of the DNAi oligonucleotides. The 3' and 5' tails can comprise any nucleotide and can be as short as one nucleotide and as long as 20 nucleotides.
[0278] Yet a nother modification of the oligonucleotides of the present invention involves chemically linking to the oligonucleotide one or more moieties or conjugates that enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety, cholic acid, a thioether, (e.g., hexyl-S-tritylthiol), a thiocholesterol, an aliphatic chain, (e.g., dodecandiol or undecyl residues), a phospholipid, (e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O- hexadecyl-rac-glycero-3-H-phosphonate), a polyamine or a polyethylene glycol chain or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl- oxycholesterol moiety.
[0279] One skilled in the relevant art knows well how to generate oligonucleotides containing the above-described modifications. The present invention is not limited to the oligonucleotides described above. Any suitable modification or substitution may be utilized. [0280] It is not necessary for all positions in a given compound to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single compound or even at a single nucleoside within an oligonucleotide. The present invention also includes pharmaceutical compositions and formulations that include the antisense compounds of the present invention as described below.
7. Preparation and Formulation of DNAi Oligonucleotides [0281] Any of the known methods of oligonucleotide synthesis can be used to prepare the modified DNAi oligomers of the present invention. In some embodiments utilizing methylated oligonucleotides the nucleotide, dC is replaced by 5-methyl-dC where appropriate, as taught by the present invention. The modified or unmodified oligonucleotides of the present invention are most conveniently prepared by using any of the commercially available automated nucleic acid synthesizers. They can also be obtained from commercial sources that synthesize custom oligonucleotides pursuant to customer specifications. [0282] In additional embodiments, chemotherapeutic agents, including docetaxel and others can be combined with DNAi oligomers before or while sequestering in liposomes.
C. Cryoprotectants and Lyoprotectants
[0283] As used herein, "cryoprotectant" refers to an agent or compound suitable for protecting a liposome composition from freezing damage, freeze/thaw damage and/or for lyophilization. Examples include sugars, disaccharides and monosaccharides, glycerol and polyethylene glycol.
[0284] "Freezing damage" or "freeze damage" refers to any one of several undesirable effects that occur upon exposure of a liposome composition to a temperature sufficient to cause one of the undesirable effects. A sufficient temperature that results in freezing damage is typically a temperature lower than about O0C, (lower than about 50C or 1O0C). Undesirable effects include, without limitation, an increase in particle size growth due to aggregation and/or fusion of vesicles and loss of an encapsulated therapeutic agent. The actual temperature that can cause onset of such an effect will vary according to the liposome formulation, e.g., the type of lipids and other bilayer components, as well as the entrapped medium and therapeutic agent. Sometimes freezing damage is less at very cold temperatures, particularly if the rate of freezing and subsequent thawing is rapid. [0285] "Freeze/thaw damage", as used herein, includes the undesirable effects that are associated with freezing damage (described above), and additional effects observed as a result of at least one freezing and thawing cycle, e.g., a non-homogeneous particle size distribution. Described effects may be more pronounced during a slow thawing process, i.e., at about 2-80C versus a more rapid thawing process, i.e., at room temperature or exposure to a water bath.
[0286] Cryoprotectants comprise sugars, including mono and disaccharides. These include, without limitation, glucose, fructose, mannose, trehalose, sucrose, xylose, ribose, maltose, lactose cellobiose, and raffinose. Other cryoprotectants include 6-amino mannose, mannitol, sorbitol, glycerol, polyethylene glycols, maltotriose, dextran, and maltodextrins. Other, more complicated sugars can be used, such as, for example, aminoglycosides, including streptomycin and dihydrostreptomycin; oligosaccharides, including raffinose and stachyose and other carbohydrates, including dextrans, maltodixtrans, dextrins, cyclodextrins, maltodextrins, cellusose and methylcellulose. Hyaluronic acids can also be used. Amino acids can also act as cryoprotectants. These include betaines, prolines, glycine, arginine, lysine, and alanine. In addition, niacinamide, creatine, monosodium glutamate, sweet whey solids, albumin, polyvinylpyrrolidine, polyvinyl alcohol, polydextran, hydroxypropyl-β- cyclodextrin, and partially hydrolysed starches can be used. Proteins and peptides, such as albumins, collagens, gelatins, lung surfactant proteins and fragments thereof can be used as well.
[0287] The cryoprotectants detailed above can also be used as lyoprotectants. Lyoprotectants protect liposomes from damage due to lyophilization or freeze-drying and/or reconstitution. In one embodiment, mannitol is used as a lyoprotectant because it influences the glass transition temperature during lyophilization. Mannitol also allows for a fluffy cake after lyophilization, which facilitates reconstitution. In another embodiment, trehalose is the sole lyoprotectant.
[0288] A water soluble salt can also be included in the liposomal suspension medium. The salt is present at a concentration effective to establish an osmotic gradient across each liposome, wherein the suspension medium has a higher osmolality than the liposome interior. The salt can be any water soluble salt. Examples include, without limitation, sodium salts, such as NaCl, potassium salts, such as KCl, nitrate salts, ammonium salts and sulfate salts or combinations thereof.
D. Amphoteric Liposome Formulations
1. Description
[0289] Advantageously, the liposome formulations of the present invention (1) exhibit low toxicity; (2) can sequester high concentrations of oligomers e.g., the efficiency of sequestering the oligonucleotides associated with the amphoteric liposomes is about 35 %; (3) are stable in the bloodstream, such as when administered systemically, such that the oligonucleotide and/or other agents are stably sequestered in the liposomes until eventual uptake in the target tissue or cells; (4) can be optimized for delivery to animals, such as by adjusting the concentration of sequestered oligonucleotide to between about 1 to 4 mg/mL (such as about 2 mg/mL) for a lipid concentration of about 100 mM or less which provides dosing at 10 mg/kg in 200 μL of injection volume; (5) can be produced with an average diameter smaller than 200 ηm, such as about 100 ηm, and a narrow size distribution with a polydispersity index of about 0.2 or less, which maximizes tumor penetration; and (6) can be stabilized with a cryoprotectant. [0290] As described above, the amphoteric liposomes include one or more DNAi oligonucleotides, one or more amphoteric lipids or alternatively a mixture of lipid components with amphoteric properties and one or more neutral lipids. In some embodiments of the present invention, amphoteric liposomes can be formed from a lipid phase comprising an amphoteric lipid. The lipid phase can comprise 5 to 30 mole % or 10 to 25 mole % of the amphoteric lipid. Alternatively, the amphoteric liposomes can be formed from a lipid phase comprising a mixture of lipid components with amphoteric properties. The total amount of charged lipids may vary from 5 to 95 mole % , from 20 to 80 mole % or from 30 to 70 mole % of the lipid mixture.
[0291] The ratio of the percent of cationic lipids to anionic lipids can be between about 3 and 0.5 or between about 2 to 0.5. In some embodiments, the ratio of cationic lipids to anionic lipids is about 2. In other embodiments, the ratio of cationic lipids to anionic lipids is about 1. In other embodiments, the ratio of cationic lipids to anionic lipids is about 0.5. [0292] Specific pairs of cationic and anionic lipids include, without limitation, MoChol and CHEMS, DOTAP and CHEMS, MoChol and Cet-P, and MoChol and DMGSucc. Examples of charged lipid pairs further include, without limitation, between about 10 to 60 mole % of MoChol and between about 10 to 30 mole % of CHEMS; between about 5 to 30 mole % of DOTAP and between about; 10 to 30 mole % of CHEMS; between about 10 to 40 mole % MoChol and between about 5 to 30 mole % Cet-P; and between about 20 to 60 mole % MoChol and between about 20 to 60 mole % DMGSucc.
[0293] The amphoteric liposomes also contain neutral lipids, which can be either sterols or phospholipids, and mixtures thereof. The amphoteric liposomes include neutral lipids in an amount between about 20 to 80 mole % of the lipid mixture, or between 30 and 75 mole %. [0294] A number of neutral lipid combinations are useful in forming the amphoteric liposomes, such as POPC and DOPE; and POPC and cholesterol. In contrast, a combination of the neutral lipids DOPE and cholesterol is not preferred. In some embodiments, the mixture of neutral lipids includes 5 to 40 mole % POPC and 20 to 50 mole % DOPE; or 10 to 50 mole % of POPC and 30 to 50 mole % of cholesterol. The ratio of the percentage of charged lipids to neutral lipids can be between about 3 and 0.2. In some embodiments, the ratio of the percentage of amphoteric lipids to neutral lipids is about 2. In other embodiments, the ratio of the percentage of amphoteric lipids to neutral lipids is about 0.5. [0295] Examples of specific combinations of charged and neutral lipids for sequestering an DNAi oligomer, such as PNT-100 (SEQ ID NO:1251), include POPC, DOPE, MoChol and CHEMS; POPC, DOPE, DMGSucc and MoChol; POPC, DOTAP, CHEMS and cholesterol; and POPC, MoChol, Cet-P and cholesterol. In some embodiments, the amphoteric liposome for sequestering a DNAi oligomer, such as SEQ ID NO: 1251, includes 3-20 mole % of POPC, 10 to 60 mole % of DOPE, 10 to 60 mole % of MoChol and 10 to 60 mole % of CHEMS. The amphoteric liposome may include POPC/DOPE/MoChol/CHEMS in molar ratios of about 6/24/47/23 and about 15/45/20/20. In another embodiment, the amphoteric liposomes include 3 to 20 mole % of POPC, 10 to 40 mole % of DOPE, 15 to 60 mole % of MoChol and 15 to 60 mole % of DMGSucc. The amphoteric liposome can include POPC/DOPE/DMGSucc/MoChol in molar ratios of about 6/24/23/47 and about 6/24/47/23. In still another embodiment, the amphoteric liposome includes 10 to 50 mole % of POPC, 20 to 60 mole % of Choi, 10 to 40 mole % of CHEMS and 5 to 20 mole % of DOTAP. The amphoteric liposome can include POPC/Chol/CHEMS/DOTAP in a molar ratio of about 30/40/20/10. In still another embodiment, the amphoteric liposome includes 10 to 40 mole % of POPC, 20 to 50 mole % of Choi, 5 to 30 mole % of Cet-P and 10 to 40 mole % of MoChol. The amphoteric liposome can include POPC/Chol/Cet-P/MoChol in a molar ratio of about 35/35/10/20.
[0296] In general, any Amphoter I, II, or III lipid pair of cationic and anionic lipids can be used to form liposomes provided that the resulting liposome is amphoteric, exhibits serum stability, has low toxicity, sequesters an ample quantity of DNAi oligonucleotides, e.g., at an efficiency about 35%, (about 5%, 10%, 15%, 20%, 25%, 30%, 35% or higher) and provides for an adjustment of the oligonucleotide concentration to at least 2 mg/mL for a lipid concentration of 100 mM or less.
[0297] One or more cryoprotectants and/or lyoprotectants can be included as part of either the internal or external media of the liposomes. Inclusion in the internal medium is accomplished by adding the cryoprotectant(s) and/or lyoprotectant(s) to the solute in which the liposomes are to encapsulate. For example, mannitol can be added to the solute. In another embodiment, sucrose or trehalose is added to the liposomal formulation, after the liposomes have formed.
[0298] The amount of sugar to be used depends on the type of sugar used and the characteristics of the liposomes. Persons skilled in the art can test various sugar types and concentrations to determine which combination works best for a particular liposome preparation. In one embodiment, the mannitol is added to achieve a concentration of 0.2- 1.5% in the solute in which the liposomes encapsulate. In another embodiment, sucrose is added at a concentration of about 2-25% after the liposomes have formed. [0299] In addition to sugars or other cryoprotectants, a water soluble salt can be added to the formed liposomes to establish an osmotic gradient across each liposome, wherein the suspension medium has a higher osmolality than the liposome interior, as described in the European Patent No. EP 1,196,144Bl. In one embodiment, the osmotic gradient is at least about 100 mOsm. In other embodiments, the osmotic gradient is at least about 200 or 600 mOsm. In another embodiment, the salt, such as NaCl, is added to achieve a concentration of 0.2-3.6% of the formed liposomal suspension.
2. Preparation of DNAi-Amphoteric Liposomes
[0300] DNAi-amphoteric liposomes of the invention can be prepared by standard methods for preparing and sizing liposomes known to those skilled in the art. These methods can include the following steps: (1) mixing lipids with nucleic acids; (2) processes to ensure formation of small unilamellar vesicles; (3) removal of unsequestered nucleic acids; (4) processes to ensure the liposomes have a defined size and polydispersity index; (5) sterile filtration; (6) methods for preparing liposomes for storage; and (7) methods for preparing liposomes for administration. Methods for preparing and characterizing liposomes have been described, for example, by S. Vemuri et al. (Preparation and characterization of liposomes as therapeutic delivery systems: a review. Pharm Acta HeIv. 1995, 70(2):95-l 11), which is incorporated herein by reference.
[0301] Mixing lipids with nucleic acids include hydration of lipid films and powders, solvent injection and reverse-phase evaporation. In one embodiment, a mixture of lipids is dissolved in a water miscible solvent, including ethanol or propanol, and mixed with an aqueous mixture of nucleic acids by cross flow injection. In another embodiment, the lipid-nucleic acid mixture is mixed with an aqueous solution whose pH is below that of the lipid-nucleic acid mixture. The temperature of the lipid mixture can range from 4° C and 100° C. In one embodiment the temperature is 550C.
[0302] As used herein, a Passive Loading Procedure (PLP) is a process wherein liposomes are charged with oligonucleotides and/or other molecules where the charges of the lipids are not useful for binding the oligonucleotides and/or other molecules. Advanced Loading Procedure (ALP) is an ion exchange process taking advantage of the positive charge of one lipid at acidic pH to bind the oligonucleotides and/or other molecules. [0303] Amphoteric liposomes used with the present invention offer the distinct advantage of binding oligonucleotides at or below their isoelectric point, thereby concentrating the active agent at the liposome surface. The advanced loading procedure is described in more detail in PCT International Publication Numbers WO02/066012, WO07/064857 and in German Patent Publication Number DE 102006054192, all of which are incorporated by reference in their entirety.
[0304] A solution of the oligonucleotide may be contacted with an excipient at a neutral pH, thereby resulting in a passive loading procedure of a certain percentage of the solution. The use of high concentrations of the excipient, ranging from about 50 mM to about 150 mM, is one method to achieve substantial encapsulation of the active agent. Excipients include substances that can initiate or facilitate loading of DNAi oligonucleotides. Examples of excipients include, without limitation, acid, sodium or ammonium forms of monovalent anions such as chloride, acetate, lactobionate and formate; divalent anions such as aspartate, succinate and sulfate; and trivalent ions such as citrate and phosphate.
[0305] Often multilamellar vesicles will form spontaneously when amphiphilic lipids are hydrated, whereas the formation of small unilamellar vesicles usually requires a process involving substantial energy input, such as ultrasonication, high pressure homogenization, injection of lipid solutions in ethanol or another water miscible solvent, including propanol or isopropanol into a water phase containing the cargo to be sequestered and/or extrusion through filters or membranes of defined pore size.
[0306] To form unilammellar liposomes, a shearing force can be applied to the aqueous dispersion of the DNAi-oligonucleotide lipid mixture. The shearing force can be applied by sonication, using a microfluidizing apparatus such as a homogenizer or French press, injection, freezing and thawing, dialyzing away a detergent solution from lipids, or other known methods used to prepare liposomes.
[0307] The size of the liposomes can be controlled using a variety of known techniques, including the duration of shearing force and extrusion through a membrane with a defined pore size.
[0308] Unsequestered DNAi oligomers are removed from the liposome dispersion by buffer exchange using dialysis, size exclusion chromatography (e.g., Sephadex G-50 resin), ultrafiltration (100,000-300,000 molecular weight cutoff), or centrifugation.
[0309] In one embodiment of the invention, DNAi oligonucleotide loaded amphoteric liposomes may be manufactured by a machine extrusion. Lipids are mixed with the oligonucleotides using a process described in US Pat No. 6843942 and US Patent Application
No. 2004/0032037. The lipids can be extruded using machine extrusion. The liposomes are loaded and filtered so that the diameter of the liposome is between 50 ηm and 200 ηm, the encapsulation efficiency of the oligonucleotide is at least 35% and the resulting liposomes have an oligonucleotide concentration of at least 2 mg/mL at a lipid concentration of 100 mM or less.
[0310] A cryoprotectant and/or lyoprotectant can be added either with the DNAi oligomer during liposome formation and/or after the liposomes are formed. In one embodiment, mannitol is added to the DNAi oligomer to a final concentration of 0.9 % during liposome formation. In another embodiment, sucrose is added to a final concentration of 5-10 % to the loaded liposomes after extrusion. In yet another embodiment, cryoprotectants and lyoprotectants may be added in combination to facilitate lyophilization and subsequent reconstitution of the resulting powder or residue.
[0311] The loaded liposomes containing cryoprotectant can be frozen in a number of different ways, including, without limitation, by flash freezing in liquid nitrogen or by placing in a freezer. The temperature of the freezer can be from about -20° C to about -120°
C. The frozen liposomes can be thawed in a number of ways, including, without limitation, at room temperature, in a refrigerator, or quickly thawed in a water bath.
[0312] Loaded liposomes with cryoprotectant(s) and/or lyoprotectants can be dehydrated using standard freeze-drying apparatus, so that they are dehydrated under reduced pressure.
The liposomes and their surrounding medium can be frozen a number of ways, including, without limitation, in liquid nitrogen before being dehydrated. Alternatively, the liposomes can also be dehydrated without prior freezing, by simply being placed under reduced pressure. This can be achieved at room temperature and at a reduced pressure provided by a vacuum pump capable of producing a pressure of about 1 mm of mercury.
[0313] Once the DNAi-containing liposomes have been dehydrated, they can be stored for extended periods of time until they are to be used.
[0314] To rehydrate, an aqueous solution, such as distilled water or phosphate buffered saline, is added to the DNAi-liposomes and allowing them to rehydrate. The liposomes can be resuspended into the aqueous phase by gentle swirling of the solution.
[0315] DNAi-liposome formulations that will be administered parentarelly must be sterile.
Sterile filtration can be performed before or after freeze-thaw, and before or after dehydration-rehydration. The DNAi-liposome mixture can be filtered through a 0.22 micron filter or sequentially through a 0.45 and 0.22 micron filtration system.
[0316] For better efficacy, the DNAi-amphoteric liposomes are prepared so that they are a defined diameter range and polydispersity index. The average diameter of the DNAi liposomal mixture can range from 50-200 ηm (70-150 ηm; 90-130 ηm). The polydispersity index can range from 0-0.5 (0-0.3, 0-0.2, 0-0.1, 0-0.05). III USE OF AMPHOTERIC LIPOSOMES SEQUESTERING DNAi OLIGOMERS
[0317] As used herein, the term "non-human animals" refers to all non-human animals including, without limitation, vertebrates such as rodents, non-human primates, ovines, bovines, ruminants, lagomorphs, porcines, caprines, equines, canines, felines, aves, etc. [0318] By "transformation" or "transfection" is meant a permanent or transient genetic change induced in a cell following incorporation of new DNA (i.e., DNA exogenous to the cell). Where the cell is a mammalian cell, a permanent genetic change is generally achieved by introduction of the DNA into the genome of the cell.
[0319] By "transformed cell" or "host cell" is meant a cell (e.g., prokaryotic or eukaryotic) into which (or into an ancestor of which) has been introduced, by means of recombinant DNA techniques, a DNA molecule encoding a polypeptide of the invention (i.e., a Methuselah polypeptide), or fragment thereof.
[0320] Transformation of a host cell with recombinant DNA may be carried out by conventional techniques as are well known to those skilled in the art. Where the host is prokaryotic, such as E. coli, competent cells which are capable of DNA uptake can be prepared from cells harvested after exponential growth phase and subsequently treated by the CaCl2 method by procedures well known in the art. Alternatively, MgCl2 or RbCl can be used. Transformation can also be performed after forming a protoplast of the host cell or by electroporation.
[0321] As used herein, the term "cell culture" refers to any in vitro culture of cells. Included within this term are continuous cell lines (e.g., with an immortal phenotype), primary cell cultures, transformed cell lines, finite cell lines (e.g., non-transformed cells), and any other cell population maintained in vitro.
[0322] As used, the term "eukaryote" refers to organisms distinguishable from "prokaryotes." It is intended that the term encompass all organisms with cells that exhibit the usual characteristics of eukaryotes, such as the presence of a true nucleus bounded by a nuclear membrane, within which lie the chromosomes, the presence of membrane-bound organelles and other characteristics commonly observed in eukaryotic organisms. Thus, the term includes, but is not limited to such organisms as fungi, protozoa and animals (e.g., humans). [0323] As used herein, the term "in vitro" refers to an artificial environment and to processes or reactions that occur within an artificial environment. In vitro environments can consist of, but are not limited to, test tubes and cell culture. The term "in vivo" refers to the natural environment (e.g., an animal or a cell) and to processes or reaction that occur within a natural environment. [0324] As used herein, the term "under conditions such that expression of a gene is inhibited" refers to conditions where an oligonucleotide of the present invention hybridizes to a gene (e.g., the promoter region of the gene) and inhibits transcription of the gene by at least 10 %, at least 25 %, at least 50% or at least 90 % relative to the level of transcription in the absence of the oligonucleotide.
[0325] As used herein, the term "under conditions such that growth of a cell is reduced" refers to conditions where an oligonucleotide of the present invention, when administered to a cell (e.g., a cancer) reduces the rate of growth of the cell by at least 10 %, at least 25 %, at least 50 % or at least 90 % relative to the rate of growth of the cell in the absence of the oligonucleotide.
[0326] DNAi-amphoteric liposomes are useful for administering to animals, including humans, to treat cancer, such as by inhibiting or reducing tumor growth. The animal can be a non-human animal, including mice, horses, cats, dogs, or other animals or it can be a human. In one embodiment, the mixture is introduced to the animal at a dosage of between 0.01 mg to 100 mg/kg of body weight. In another embodiment, the amphoteric liposomes can be introduced to the animal one or more times per day or continuously. [0327] The mixture can be administered to the animal via different routes. Administration can be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Administration can also be via a medical device.
[0328] The liposomes can be administered to cultured cells derived from various cancers, including pancreatic cancer, colon cancer, breast cancer, bladder cancer, lung cancer, leukemia, prostate cancer, lymphoma, ovarian cancer or melanoma.
[0329] The liposomes can be used to target DNAi oligonucleotides to selected tissues using several techniques. The procedures involve manipulating the size of the liposomes, their net surface charge as well as the route of administration. More specific manipulations include labeling the liposomes with receptor ligands, including membrane and nuclear receptor ligands or antibodies for specific tissues or cells, Antibodies or ligands can be bound to the surface of the liposomes. IV CO-THERAPIES
[0330] The DNAi-liposomal formulations can be administered in conjunction other agents, including chemotherapy agents and radiation therapy.
[0331] The terms "test compound" and "candidate compound" refer to any chemical entity, pharmaceutical, drug, and the like that is a candidate for use to treat or prevent a disease, illness, sickness, or disorder of bodily function (e.g., cancer). Test compounds include both known and potential therapeutic compounds. A test compound can be determined to be therapeutic by screening using the screening methods of the present invention. In some embodiments of the present invention, test compounds include antisense compounds. [0332] As used herein, the term "known chemotherapeutic agents" refers to compounds known to be useful in the treatment of disease (e.g., cancer). Exemplary chemotherapeutic agents affective against cancer include, but are not limited to, daunorubicin, dactinomycin, doxorubicin, bleomycin, mitomycin, nitrogen mustard, chlorambucil, melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine (CA), 5-fluorouracil (5-FU), floxuridine (5-FUdR), methotrexate (MTX), colchicine, taxotere, vincristine, vinblastine, etoposide, teniposide, cisplatin and diethylstilbestrol (DES).
A. Chemotherapy Agents
[0333] Chemotherapy agents of the present invention can include any suitable chemotherapy drug or combinations of chemotherapy drugs (e.g., a cocktail). Exemplary chemotherapy agents include, without limitation, alkylating agents, platinums, anti-metabolites, anthracyclines, taxanes, camptothecins, nitrosoureas, EGFR inhibitors, antibiotics, HER2/neu inhibitors, angiogenesis inhibitors, kinase inhibitors, proteaosome inhibitors, immunotherapies, hormone therapies, photodynamic therapies, cancer vaccines, histone deacetylase inhibitors, sphingolipid modulators, oligomers, other unclassified chemotherapy drugs and combinations thereof.
1. Alkylating Agents
[0334] Alkylating agents are chemotherapy agents that are thought to attack the negatively charged sites on the DNA (e.g., the oxygen, nitrogen, phosphorous and sulfur atoms) and bind to the DNA thus altering replication, transcription and even base pairing. It is also believed that alkylation of the DNA also leads to DNA strand breaks and DNA strand cross- linking. By altering DNA in this manner, cellular activity is effectively stopped and the cancer cell will die. Common alkylating agents include, without limitation, Procarbazine, Ifosphamide, Cyclophosphamide, Melphalan, Chlorambucil, Decarbazine, Busulfan, Thiotepa, and the like. Alkylating agents such as those mentioned above can be used in combination with one or more other alkylating agents and/or with one or more chemotherapy agents of a different class(es).
2. Platinums
[0335] Platinum chemotherapy agents are believed to inhibit DNA synthesis, transcription and function by cross-linking DNA subunits. (The cross-linking can happen either between two strands or within one strand of DNA.) Common platinum chemotherapy agents include, without limitation, Cisplatin, Carboplatin, Oxaliplatin, Eloxatin, and the like. Platinum chemotherapy agents such as those mentioned above can be used in combination with one or more other platinums and/or with one or more chemotherapy agents of a different class(es).
3. Anti-metabolites
[0336] Anti-metabolite chemotherapy agents are believed to interfere with normal metabolic pathways, including those necessary for making new DNA. Common anti-metabolites include, without limitation, Methotraxate, 5-Fluorouracil (e.g., Capecitabine), Gemcitabine (2'-deoxy-2',2'-difluorocytidine monohydrochloride (β-isomer), Eli Lilly), 6-mercaptopurine, 6-thioguanine, fludarabine, Cladribine, Cytarabine, tegafur, raltitrexed, cytosine arabinoside, and the like. Gallium nitrate is another anti-metabolite that inhibits ribonucleotides reductase. Anti-metabolites such as those mentioned above can be used in combination with one or more other anti-metabolites and/or with one or more chemotherapy agents of a different class(es).
4. Anthracyclines
[0337] Anthracyclines are believed to promote the formation of free oxygen radicals. These radicals result in DNA strand breaks and subsequent inhibition of DNA synthesis and function. Anthracyclines are also thought to inhibit the enzyme topoisomerase by forming a complex with the enzyme and DNA. Common anthracyclines include, without limitation, Daunorubicin, Doxorubicin, Idarubicin, Epirubicin, Mitoxantrone, adriamycin, bleomycin, mitomycin-C, dactinomycin, mithramycin and the like. Anthracyclines such as those mentioned above can be used in combination with one or more other anthracyclines and/or with one or more chemotherapy agents of a different class(es).
5. Taxanes
[0338] Taxanes are believed to bind with high affinity to the microtubules during the M phase of the cell cycle and inhibit their normal function. Common taxanes include, without limitation, Paclitaxel, Docetaxel, Taxotere, Taxol, taxasm, 7-epipaclitaxel, t-acetyl paclitaxel, 10-desacetyl-paclitaxel, lO-desacetyl-7-epipaclitaxel, 7-xylosylpaclitaxel, 10-desacetyl-7- epipaclitaxel, 7-N-N-dimethylglycylpaclitaxel, 7-L-alanylpaclitaxel and the like. Taxanes such as those mentioned above can be used in combination with one or more other taxanes and/or with one or more chemotherapy agents of a different class(es).
6. Camptothecins
[0339] Camptothecins are thought to complex with topoisomerase and DNA resulting in the inhibition and function of this enzyme. It is further believed that the presence of topoisomerase is required for on-going DNA synthesis. Common camptothecins include, without limitation, Irinotecan, Topotecan, Etoposide, vinca alkaloids (e.g., Vincristine, Vinblastine or Vinorelbine), amsacrine, teniposide and the like. Camptothecins such as those mentioned above can be used in combination with one or more other camptothecins and/or with one or more chemotherapy agents of a different class(es).
7. Nitrosoureas
[0340] Nitrosoureas are believed to inhibit changes necessary for DNA repair. Common nitrosoureas include, without limitation, Carmustine (BCNU), Lomustine (CCNU), semustine and the like. Nitrosoureas such as those mentioned above can be used in combination with one or more other nitrosoureas and/or with one or more chemotherapy agents of a different class(es).
8. EGFR Inhibitors
[0341] EGFR (epidermal growth factor receptor) inhibitors are thought to inhibit EGFR and interfere with cellular responses including cell proliferation and differentiation. EGFR inhibitors include molecules that inhibit the function or production of one or more EGFRs. They include small molecule inhibitors of EGFRs, antibodies to EGFRs, antisense oligomers, RNAi inhibitors and other oligomers that reduce the expression of EGFRs. Common EGFR inhibitors include, without limitation, Gefitinib, Erlotinib (Tarceva®), Cetuximab (Erbitux®), panitumumab (Vectibix™'Amgen) lapatinib (GlaxoSmithKline), CI1033 or PD183805 or Canternib (6-acrylamide-N-(3-chloro-4-fluroφhenyl)-7-(3-morpholinopropoxy)quinazolin-4- amine, Pfizer), and the like. Other inhibitors include PKI-166 (4-[(lR)-l-phenylethylamino]- 6-(4-hydroxyphenyl)-7H-pyrrolo[2,3-<f|pyrimidine, Novartis), CL-387785 (N-[4-(3- bromoanilino)quinazolin-6-yl]but-2-ynamide), EKB-569 (4-(3-chloro-4-fluroranilino)-3- cyano-6-(4-dimethylaminobut2(E)-enamido)-7-ethozyquinoline, Wyeth), lapatinib (GW2016, GlaxoSmithKline), EKB509 (Wyeth), Panitumumab (ABX-EGF, Abgenix), matuzumab (EMD 72000, Merck), and the monoclonal antibody RH3 (New York Medical). EGFR inhibitors such as those mentioned above can be used in combination with one or more other EGFR inhibitors and/or with one or more chemotherapy agents of a different class(es). 9. Antibiotics
[0342] Antibiotics are thought to promote the formation of free oxygen radicals that result in DNA breaks leading to cancer cell death. Common antibiotics include, without limitation, Bleomycin and rapamycin and the like. The macrolide fungicide rapamycin (also called RAP, Rapamune and Sirolimus) binds intracellularly to the to the immunophilin FK506 binding protein 12 (FKBP12) and the resultant complex inhibits the serine protein kinase activity of mammalian target of rapamycin (mTOR). Rapamycin macrolides include naturally occurring forms of rapamycin as well as rapamycin analogs and derivatives that target and inhibit mTOR. Other rapamycin macrolides include, without limitation, temsirolimus (CCI-779, Wyeth)), Everolimus and ABT-578. Antibiotics such as those mentioned above can be used in combination with one or more other antibiotics and/or with one or more chemotherapy agents of a different class(es).
10. HER2/neu Inhibitors
[0343] HER2/neu Inhibitors are believed to block the HER2 receptor and prevent the cascade of reactions necessary for tumor survival. Her2 inhibitors include molecules that inhibit the function or production of Her2. They include small molecule inhibitors of Her2, antibodies to Her2, antisense oligomers, RNAi inhibitors and other oligomers that reduce the expression of tyrosine kinases. Common HER2/neu inhibitors include, without limitation, Trastuzumab (Herceptin®, Genentech) and the like. Other Her2/neu inhibitors include bispecific antibodies MDX-210(FCγRl-Her2/neu) and MDX-447 (Medarex), pertuzumab (rhuMAb 2C4, Genentech), HER2/neu inhibitors such as those mentioned above can be used in combination with one or more other HER2/neu inhibitors and/or with one or more chemotherapy agents of a different class(es).
11. Angiogenesis Inhibitors
[0344] Angiogenesis inhibitors are believed to inhibit vascular endothelial growth factor , (VEGF), thereby inhibiting the formation of new blood vessels necessary for tumor life. VEGF inhibitors include molecules that inhibit the function or production of one or more VEGFs. They include small molecule inhibitors of VEGF, antibodies to VEGF, antisense oligomers, RNAi inhibitors and other oligomers that reduce the expression of tyrosine kinases. Common angiogenesis inhibitors include, without limitation, Bevacizumab (Avastin®, Genentech). Other angiogenesis inhibitors include, without limitation, ZD6474 (AstraZeneca), Bay-43-9006, sorafenib (Nexavar, Bayer), semaxamib (SU5416, Pharmacia), SU6668 (Pharmacia), ZD4190 (N-(4-bromo-2-fluorophenyl)-6-methoxy-7-[2-(lH-l,2,3- triazol-l-yl)ethoxy]quinazolin-4-amine, Astra Zeneca), Zactima™ (ZD6474, N-(4-bromo-2- fluorophenyl)-6-methoxy-7-[2-(lH-l,2,3-triazol-l-yl)ethoxy]quinazolin-4-amine, Astra Zeneca), Vatalanib, (PTK787, Novartis), the monoclonal antibody IMC-ICl 1 (Imclone) and the like. Angiogenesis inhibitors such as those mentioned above can be used in combination with one or more other angiogenesis inhibitors and/or with one or more chemotherapy agents of a different class(es).
12. Other Kinase Inhibitors
[0345] In addition to EGFR, ΗER2 and VEGF inhibitors, other kinase inhibitors are used as chemotherapeutic agents. Aurora kinase inhibitors include, without limitation, compounds such as 4-(4-N benzoylamino)aniline)-6-methyxy-7-(3-(l-morpholino)propoxy)quinazoline (ZM447439, Ditchfield et al., J. Cell. Biol, 161:267-80 (2003)) and Hesperadin (Haaf et al., J. Cell Biol., 161: 281-94 (2003)). Other compounds suitable for use as Aurora kinase inhibitors are described in Vankayalapati H, et al., MoI. Cancer Ther. 2:283-9 (2003). SRC/Abl kinase inhibitors include without limitation, AZD0530 (4-(6-chloro-2,3- methylenedioxyanilino)-7-[2-(4-methylpiperazin-l-yl)ethoxy]-5-tetrahycropyran-4- yloxyquinazoline). Tyrosine kinase inhibitors include molecules that inhibit the function or production of one or more tyrosine kinases. They include small molecule inhibitors of tyrosine kinases, antibodies to tyrosine kinases and antisense oligomers, RNAi inhibitors and other oligomers that reduce the expression of tyrosine kinases. CEP-701 and CEP-751 (Cephalon) act as tyrosine kinase inhibitors. Imatinib mesylate is a tyrosine kinase inhibitor that inhibits bcr-abl by binding to the ATP binding site of bcr-abl and competitively inhibiting the enzyme activity of the protein. Although imatinib is quite selective for bcr-abl, it does also inhibit other targets such as c-kit and PDGF-R. FLT-3 inhibitors include, without limitation, tandutinib (MLN518, Millenium), Sutent (SUl 1248, 5- [5-fluoro-2-oxo-l,2- dihydroindol-(3Z)-ylidenemethyl]-2, 4-dimethyl-lH-pyrrole-3-carboxylic acid [2- diethylaminoethyl] amide, Pfizer), midostaurin (4'-N-Benzoyl Staurosporine,_Novartis), lefunomide (SUlOl) and the like. MEK inhibitors include, without limitation, 2-(2-Chloro-4- iodo-phenylamino)-N-cyclopropylmethoxy-3,4-difluoro-benzamide) (PD184352/CI-1044, Pfizer), PD198306 (Pfizer), PD98059 (2'-amino-3'-methoxyflavone), UO126 (Promega), Ro092210 from fermented microbial extracts (Roche), the resorcyclic acid lactone, L783277, also isolated from microbial extracts (Merck) and the like. Tyrosine kinase inhibitors such as those mentioned above can be used in combination with one or more other tyrosine kinase inhibitors and/or with one or more chemotherapy agents of a different class(es). 13. Proteaosome Inhibitors
[0346] Proteaosome inhibitors are believed to inhibit the breakdown of some of these proteins that have been marked for destruction. This results in growth arrest or death of the cell. Common proteaosome inhibitors include, without limitation, Bortezomib, ortezomib and the like. Proteaosome inhibitors such as those mentioned above can be used in combination with one or more other proteaosome inhibitors and/or with one or more chemotherapy agents of a different class(es).
14. Immunotherapies
[0347] Immunotherapies are thought to bind to and block specific targets, thereby disrupting the chain of events needed for tumor cell proliferation. Common immunotherapies include, without limitation, Rituximab and other antibodies directed against CD20, Campath-1H and other antibodies directed against CD-50, epratuzmab and other antibodies directed against CD-22, galiximab and other antibodies directed atainst CD-80, apolizumab HUlDlO and other antibodies directed against HLA-DR, and the like. Radioisotopes can be conjugated to the antibody, resulting in radioimmunotherapy. Two such anti-CD20 products are tositumomab (Bexxar) and ibritumomab (Zevalin). Immunotherapies such as those mentioned above can be used in combination with one or more other immunotherapies and/or with one or more chemotherapy agents of a different class(es).
15. Hormone Therapies
[0348] Hormone therapies are thought to block cellular receptors, inhibit the in vivo production of hormones, and/or eliminate or modify hormone receptors on cells, all with the end result of slowing or stopping tumor proliferation. Common hormone therapies include, without limitation, antiestrogens (e.g., tamoxifen, toremifene, fulvestrant, raloxifene, droloxifene, idoxyfene and the like), progestogens) e.g., megestrol acetate and the like) aromatase inhibitors (e.g., Anastrozole, Letrozole, Exemestane, vorazole, exemestane, fadrozole, aminoglutethimide, exemestane, l-methyl-l,4-androstadiene-3,17-dione and the like), anti-androgens (e.g., Bicalutimide, Nilutamide, Flutamide, cyproterone acetate, and the like), luteinizing hormone releasing hormone agonist (LHRH Agonist) (e.g., Goserelin, Leuprolide, buserelin and the like); 5-α-reductase inhibitors such as finasteride, and the like. Hormone therapies such as those mentioned above can be used in combination with one or more other hormone therapies and/or with one or more chemotherapy agents of a different class(es). 16. Photodynamic Therapies
[0349] Photodynamic therapies expose a photosensitizing drug to specific wavelengths of light to kill cancer cells. Common photodynamic therapies include, for example, porfϊmer sodium (e.g., Photofrin®) and the like. Photodynamic therapies such as those mentioned above can be used in combination with one or more other photodynamic therapies and/or with one or more chemotherapy agents of a different class(es).
17. Cancer Vaccines
[0350] Cancer vaccines are thought to utilize whole, inactivated tumor cells, whole proteins, peptide fragments, viral vectors and the like to generate an immune response that targets cancer cells. Common cancer vaccines include, without limitation, modified tumor cells, peptide vaccine, dendritic vaccines, viral vector vaccines, heat shock protein vaccines and the like. Two specific vaccines are CeaVac (Titan Pharmaceuticals, Inc., San Francisco), which mimics the carcinoembryonic antigen (CEA), and TriAb, which mimics the human milk fat globule (HMFG) antigen. One or both of the antigens are found in high concentrations in colorectal and other tumor types.
18. Histone Deacetylase Inhibitors
[0351] Histone deacetylase inhibitors are able to modulate transcriptional activity and consequently, can block angiogenesis and cell cycling, and promote apoptosis and differentiation. Histone deacetylase inhibitors include, without limitation, SAHA (Suberoylanilide hydroxamic acid), depsipeptide (FK288) and analogs, Pivanex (Titan), CI994 (Pfizer), MS275 PXDlOl (CuraGen, TopoTarget) MGCD0103 (MethylGene), LBH589, NVP-LAQ824 (Novartis) and the like and have been used as chemotherapy agents. Histone deacetylase inhibitors such as those mentioned above can be used in combination with one or more other histone deacetylase inhibitors and/or with one or more chemotherapy agents of a different class(es).
19. Sphingolipid Modulators
[0352] Modulators of Sphingolipid metabolism have been shown to induce apoptosis. For reviews see N.S. Radin, Biochem J, 371:243-56 (2003); D.E. Modrak, et al., MoI. Cancer Ther, 5:200-208 (2006), K. Desai, et al., Biochim Biophys Acta, 1585:188-92 (2002) and CP. Reynolds, et al. and Cancer Lett, 206, 169-80 (2004), all of which are incorporated herein by reference. Modulators and inhibitors of various enzymes involved in sphingolipid metabolism can be used as chemotherapeutic agents. [0353] (a) Ceramide has been shown to induce apoptosis, consequently, exogenous ceramide or a short chain ceramide analog such as N-acetylsphingosine (C2-Cer), Cβ-Cer or C8-Cer has been used. Other analogs include, without limitation, Cer 1-glucuronide, poly(ethylene glycol)-derivatized ceramides and pegylated ceramides.
[0354] (b) Modulators that stimulate ceramide synthesis have been used to increase ceramide levels. Compounds that stimulate serine palmitoyltransferase, an enzyme involved in ceramide synthesis, include, without limitation, tetrahydrocannabinol (THC) and synthetic analogs and anandamide, a naturally occurring mammalian cannabinoid. Gemcitabine, retinoic acid and a derivative, fenretinide [N-(4-hycroxyphenyl)retinamide, (4-HPR)], camptothecin, homocamptothecin, etoposide, paclitaxel, daunorubicin and fludarabine have also been shown to increase ceramide levels. In addition, valspodar (PSC833, Novartis), a non-immunosuppressive non-ephrotoxic analog of cyclosporin and an inhibitor of p- glycoprotein, increases ceramide levels.
[0355] (c) Modulators of sphingomyelinases can increase ceramide levels. They include compounds that lower GSH levels, as GSH inhibits sphingomyelinases. For example, betathine (β-alanyl cysteamine disulphide), oxidizes GSH, and has produced good effects in patients with myeloma, melanoma and breast cancer. COX-2 inhibitors, such as celecoxib, ketoconazole, an antifungal agent, doxorubicin, mitoxantrone, D609 (tricyclodecan-9-yl- xanthogenate), dexamethasone, and Ara-C (l-/?-D-arabinofuranosylcytosine) also stimulate sphingomyelinases.
[0356] (d) Molecules that stimulate the hydrolysis of glucosylceramide also raise ceramide levels. The enzyme, GlcCer glucosidase, which is available for use in Gaucher' s disease, particularly with retinol or pentanol as glucose acceptors and/or an activator of the enzyme can be used as therapeutic agents. Saposin C and analogs thereof, as well as analogs of the anti-psychotic drug, chloropromazine, may also be useful.
[0357] (e) Inhibitors of glucosylceramide synthesis include, without limitation, PDMP (N- [2- hydroxy-l-(4-moφholinylmethyl)-2-phenylethyldecanamide]), PMPP (D,L-t/ιreo-(l-phenyl- 2-hexadecanoylamino-3-morpholino-l-propanol), P4 or PPPP (D-/Λreo-l-phenyl-2- palmitoylamino-3-pyrrolidino- 1 -propanol), ethylenedioxy-P4, 2-decanoylamine-3- morpholinoprophenone, tamixofen, raloxifene, mifepristone (RU486), N-butyl deoxynojirimycin and anti androgen chemotherapy (bicalutamide + leuprolide acetate). Zavesca, (l,5-(butylimino)-l,5-dideoxy-D-glucitol) usually used to treat Gaucher's disease, is another inhibitor of glucosylceramide synthesis. [0358] (f) Inhibitors of ceramidase include, without limitation, N-oleoylethanolamine, a truncated form of ceramide, D-MAPP (D-eryrΛro-2-tetradecanoylamino-l -phenyl- 1-propanol) and the related inhibitor B 13 (p-nitro-D-MAPP).
[0359] (g) Inhibitors of sphingosine kinase also result in increased levels of ceramide.
Inhibitors include, without limitation, safingol (L-tfireø-dihydrosphingosine), N,N-dimethyl sphingosine, trimethylsphingosine and analogs and derivatives of sphingosine such as dihydrosphingosine, and myriocin.
[0360] (h) Fumonisins and fumonisin analogs, although they inhibit ceramide synthase, also increase levels of sphinganine due to the inhibition of de novo sphingolipid biosynthesis, resulting in apoptosis.
[0361] (i) Other molecules that increase ceramide levels include, without limitation, miltefosine (hexadecylphosphocholine). Sphingolipid modulators, such as those mentioned above, can be used in combination with one or more other sphingolipid modulators and/or with one or more chemotherapy agents of a different class(es).
20. Oligomers
[0362] In addition to the oligonucleotides of the present invention, other oligonucleotides have been used as cancer therapies. They include Genasense (oblimersen, G3139, from Genta), an antisense oligonucleotide that targets bcl-2 and G4460 (LR3001, from Genta) another antisense oligonucleotide that targets c-myb. Other oligomers include, without limitation, siRNAs, decoys, RNAi oligonucleotides and the like. Oligonucleotides, such as those mentioned above, can be used in combination with one or more other oligonucleotide inhibitors and/or with one or more chemotherapy agents of a different class(es).
21. Apoptosis and Oncogene Inhibitors
[0363] Many of the chemotherapeutic agents mentioned above are also apoptosis and/or oncogene inhibitors. Others include gossypol, a compound isolated from the cotton plant, obatoclax (GeminX), a small molecule inhibitor of apoptosis, bcl-2 inhibitors AT-101 (Ascenta), ABT-737 (Abbott), IPI- 194 (Abbott), TR3/Nur77 analogs, including peptides, NFκB/IKK inhibitors, cck inhibitors, P52/MDM2 modulators, caspase activators and AKt/Pkb inhibitors. Other inhibitors include those that inhibit enzymes necessary for some oncogenes to function, such as farnesyl transferase. Tipifarnib (Zarmestra™, Johnson & Johnson) is one such inhibitor.
22. Other Chemotherapy Drugs
[0364] Additional unclassified chemotherapy agents are described in Table 2 below. Table 2 Additional Unclassified Chemotherapy Agents.
Figure imgf000072_0001
Figure imgf000073_0001
Figure imgf000074_0001
Figure imgf000075_0001
Figure imgf000076_0001
Figure imgf000077_0001
22. Cocktails
[0365] Chemotherapy agents can include cocktails of two or more chemotherapy drugs mentioned above. In several embodiments, a chemotherapy agent is a cocktail that includes two or more alkylating agents, platinums, anti-metabolites, anthracyclines, taxanes, camptothecins, nitrosoureas, EGFR inhibitors, antibiotics, HER2/neu inhibitors, angiogenesis inhibitors, kinase inhibitors, proteaosome inhibitors, immunotherapies, hormone therapies, photodynamic therapies, cancer vaccines, sphingolipid modulators, oligomers or combinations thereof.
[0366] In one embodiment, the chemotherapy agent is a cocktail that includes an immunotherapy, an alkylating agent, an anthracycline, a camptothecin and Prednisone. In other embodiments, the chemotherapy agent is a cocktail that includes Rituximab, an alkylating agent, an anthracycline, a camptothecin and Prednisone. In other embodiments, the chemotherapy agent is a cocktail that includes Rituximab, Cyclophosphamide, an anthracycline, a camptothecin and Prednisone. In still other embodiments, the chemotherapy agent is a cocktail that includes Rituximab, Cyclophosphamide, Doxorubicin, Vincristine and Prednisone (e.g., R-CHOPS).
[0367] In another embodiment, the chemotherapy agent is a cocktail that includes doxorubicin, ifosfamide and Mesna.
[0368] In other embodiments, the chemotherapy agent is a cocktail that includes an antimetabolite and a taxane. For example, the chemotherapy agent includes Gemcitabine and Taxotere. [0369] In other embodiments, the chemotherapy agent is a cocktail that includes dacarbazine, Mitomycin, Doxorubicin and Cisplatin.
[0370] In other embodiments, the chemotherapy agent is a cocktail that includes Doxorubicin and Dacarbazine.
[0371] In alternative embodiments, the chemotherapy agent is a cocktail that includes an alkylating agent, a camptothecins, an anthracycline and dacarbazine. In other examples, the chemotherapy agent includes cyclophosphamide, vincristine, doxorubicin and dacarbazine. [0372] In still other embodiments, the chemotherapy agent is a cocktail that includes an alkylating agent, methotrexate, an anti-metabolite and one or more anthracyclines. For example, the chemotherapy agent includes 5-fluorouracil, methotrexate, cyclophosphamide, doxorubicin and epirubicin.
[0373] In yet other embodiments, the chemotherapy agent is a cocktail that includes a taxane and prednisone or estramustine. For example, the chemotherapy agent can include docetaxel combined with prednisone or estramustine.
[0374] In still yet another embodiment, the chemotherapy agent includes an anthracycline and prednisone. For example, the chemotherapy agent can include mitoxantrone and prednisone.
[0375] In other embodiments, the chemotherapy agent includes a rapamycin macrolide and a kinase inhibitor. The kinase inhibitors can be EGFR, Her2/neu, VEGF, Aurora kinase, SRC/Abl kinase, tyrosine kinase and/or MEK inhibitors.
[0376] In another embodiment the chemotherapy agent includes two or more sphingolipid modulators.
[0377] In still another embodiment the chemotherapy agent includes an oligomer, such as Genasense and one or more alkylating agents, platinums, anti-metabolites, anthracyclines, taxanes, camptothecins, nitrosoureas, EGFR inhibitors, antibiotics, HER2/neu inhibitors, angiogenesis inhibitors, kinase inhibitors, proteaosome inhibitors, immunotherapies, hormone therapies, photodynamic therapies, cancer vaccines, sphingolipid modulators or combinations thereof.
[0378] In yet another embodiment, the chemotherapy agent is a cocktail that includes an anthracycline and a taxane. In another embodiment, the chemotherapy agent is a cocktail that includes doxorubicin and paclitaxel or abraxane.
[0379] In other embodiments, the chemotherapy agent is a cocktail that includes an antimetabolite and a taxane. For example, the chemotherapy agent includes gemcitabine and taxotere. [0380] In other embodiments, the chemotherapy agent is a cocktail that includes an immunotherapy and a taxane. For example, the chemotherapy agent includes taxotere and trastuzumab. In another embodiment, the chemotherapy agent includes taxotere and bevacizumab.
[0381] In other embodiments, the agent includes a taxane and an antimetabolite. In another embodiment the agent includes a taxane, an antimetabloite and a platinum. For example, the agent can include taxotere, gemcitibine, and capecitabine; or the agent can include taxotere, gemcitibine, capecitabine and cisplatin.
[0382] In another embodiment, the agent comprises rituximab.
[0383] In yet another embodiment, the agent comprises doxitaxel.
[0384] Moreover, the chemotherapy drug or drugs composing the chemotherapy agent can be administered in combination therapies with other agents, or they may be administered sequentially or concurrently to the patient.
C. Radiation Therapy
[0385] In several embodiments of the present invention, radiation therapy is administered in addition to the administration of an oligonucleotide compound. Radiation therapy includes both external and internal radiation therapies.
1. External Radiation Therapy
[0386] External radiation therapies include directing high-energy rays (e.g., x-rays, gamma rays, and the like) or particles (alpha particles, beta particles, protons, neutrons and the like) at the cancer and the normal tissue surrounding it. The radiation is produced outside the patient's body in a machine called a linear accelerator. External radiation therapies can be combined with chemotherapies, surgery or oligonucleotide compounds.
2. Internal Radiation Therapy
[0387] Internal radiation therapies include placing the source of the high-energy rays inside the body, as close as possible to the cancer cells. Internal radiation therapies can be combined with external radiation therapies, chemotherapies or surgery. [0388] Radiation therapy can be administered with chemotherapy simultaneously, concurrently, or separately. Moreover radiation therapy can be administered with surgery simultaneously, concurrently, or separately.
D. Surgery
[0389] In alternative embodiments, of the present invention, surgery is used to remove cancerous tissue from a patient. Cancerous tissue can be excised from a patient using any suitable surgical procedure including, for example, laparoscopy, scalpel, laser, scissors and the like. In several embodiments, surgery is combined with chemotherapy. In other embodiments, surgery is combined with radiation therapy. In still other embodiments, surgery is combined with both chemotherapy and radiation therapy.
V. PHARMACEUTICAL COMPOSITIONS A. Combinations
[0390] In one aspect of the present invention, a pharmaceutical composition comprises one or more oligonucleotide compounds and a chemotherapy agent. For example, a pharmaceutical composition comprises a oligonucleotide compound having SEQ.IDNO:1250, 1251, 1252, or 1253 sequestered in a liposome and one or more of an alkylating agent, a platinum, an antimetabolite, an anthracycline, a taxane, a camptothecins, a nitrosourea, an EGFR inhibitor, an antibiotic, a HER2/neu inhibitor, an angiogenesis inhibitor, a proteaosome inhibitor, an immunotherapy, a hormone therapy, a photodynamic therapy, a cancer vaccine, other chemotherapy agents such as those illustrated in Table 1, or combinations thereof. [0391] In one embodiment, the pharmaceutical composition comprises an oligonucleotide compound and a chemotherapy agent including an immunotherapy, an alkylating agent, an anthracycline, a camptothecin and Prednisone. For example, the pharmaceutical composition comprises one or more oligonucleotide compounds comprising SEQ ID NOs 2-281, 283-461, 463-935, 937-1080, 1082-1248, 1250-1254 and 1267-1477 sequestered in a liposome, and complements thereof; and a chemotherapy agent including an immunotherapy, an alkylating agent, an anthracycline, a camptothecin, and Prednisone. In other embodiments, the pharmaceutical composition comprises an oligonucleotide compound and a chemotherapy agent that includes Rituximab, Cyclophosphamide, an anthracycline, a camptothecin and Prednisone. In still other embodiments, the pharmaceutical composition comprises an oligonucleotide and a chemotherapy agent including Rituximab, Cyclophosphamide, Doxorubicin, Vincristine and Prednisone (e.g., R-CHOPS).
[0392] In another embodiment, the pharmaceutical composition comprises an oligonucleotide comprising SEQ ID NO: 1251 sequestered in a liposome and doxocycline. In still another embodiment, the pharmaceutical composition comprises an oligonucleotide comprising SEQ ID NO: 1251 sequestered in a liposome and rituximab.
[0393] In yet another embodiment, the pharmaceutical composition comprises an oligonucleotide comprising SEQ ID NO:940 or SEQ ID NO:943 or the complement thereof sequestered in a liposome and one or more of doxorubicin, paclitaxel, abraxane, gemcitabine, taxotere, trastuzumab, bevacizumab, capecitabine and cisplatin. [0394] Other embodiments of the invention provide pharmaceutical compositions containing (a) one or more oligonucleotide compounds and (b) a chemotherapy agent. Examples of such chemotherapeutic agents include, without limitation, those listed above. Anti-inflammatory drugs, including but not limited to nonsteroidal anti-inflammatory drugs and corticosteroids, and antiviral drugs, including but not limited to ribivirin, vidarabine, acyclovir and ganciclovir, may also be combined in compositions of the invention. Other non-oligonucleotide chemotherapeutic agents are also within the scope of this invention. Two or more combined compounds may be used together or sequentially. For example, in one embodiment, an oligomer sequestered in a liposome is administered once daily for five or more days and the chemotherapy agent is administered every second day for one week or more.
[0395] Pharmaceutical compositions of the present invention can optionally include medicaments such as anesthesia, nutritional supplements (e.g., vitamins, minerals, protein and the like), chromophores, combinations thereof, and the like.
B. Formulations, Administration and Uses
[0396] The compositions of the present invention may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, intranasally, intraoccularly, buccally, vaginally, or via an implanted reservoir. The term "parenteral" as used herein includes subcutaneous, intravenous, intramuscular, intra-articular, intra-synovial, intrasternal, intrathecal, intrahepatic, intralesional and intracranial injection or infusion techniques. Preferably, the compositions are administered orally, intraperitoneally or intravenously. Sterile injectable forms of the compositions of this invention may be aqueous or oleaginous suspension. These suspensions may be formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally- acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium.
[0397] For this purpose, any bland fixed oil may be employed including synthetic mono- or di-glycerides. Fatty acids, such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions. These oil solutions or suspensions may also contain a long-chain alcohol diluent or dispersant, such as carboxymethyl cellulose or similar dispersing agents that are commonly used in the formulation of pharmaceutically acceptable dosage forms including emulsions and suspensions. Other commonly used surfactants, such as Tweens, Spans and other emulsifying agents or bioavailability enhancers which are commonly used in the manufacture of pharmaceutically acceptable solid, liquid, or other dosage forms may also be used for the purposes of formulation. [0398] The pharmaceutically acceptable compositions of this invention may be orally administered in any orally acceptable dosage form including, but not limited to, capsules, tablets, aqueous suspensions or solutions. In the case of tablets for oral use, carriers commonly used include lactose and corn starch. Lubricating agents, such as magnesium stearate, are also typically added. For oral administration in a capsule form, useful diluents include lactose and dried cornstarch. When aqueous suspensions are required for oral use, the active ingredient is combined with emulsifying and suspending agents. If desired, certain sweetening, flavoring or coloring agents may also be added.
[0399] Alternatively, the pharmaceutically acceptable compositions of this invention may be administered in the form of suppositories for rectal administration. These can be prepared by mixing the agent with a suitable non-irritating excipient that is solid at room temperature but liquid at rectal temperature and therefore will melt in the rectum to release the drug. Such materials include cocoa butter, beeswax and polyethylene glycols. [0400] The pharmaceutically acceptable compositions of this invention may also be administered topically, especially when the target of treatment includes areas or organs readily accessible by topical application, including diseases of the eye, the skin or the lower intestinal tract. Suitable topical formulations are readily prepared for each of these areas or organs.
[0401] Topical application for the lower intestinal tract can be effected in a rectal suppository formulation (see above) or in a suitable enema formulation. Topically- transdermal patches may also be used.
[0402] For topical applications, the pharmaceutically acceptable compositions may be formulated in a suitable ointment containing the active component suspended or dissolved in one or more carriers. Carriers for topical administration of the compounds of this invention include, but are not limited to, mineral oil, liquid petrolatum, white petrolatum, propylene glycol, polyoxyethylene, polyoxypropylene compound, emulsifying wax and water. Alternatively, the pharmaceutically acceptable compositions can be formulated in a suitable lotion or cream containing the active components suspended or dissolved in one or more pharmaceutically acceptable carriers. Suitable carriers include, but are not limited to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol,
2-octyldodecanol, benzyl alcohol and water.
[0403] For ophthalmic use, the pharmaceutically acceptable compositions may be formulated as micronized suspensions in isotonic, pH adjusted sterile saline, or, preferably, as solutions in isotonic, pH adjusted sterile saline, either with or without a preservative such as benzylalkonium chloride. Alternatively, for ophthalmic uses, the pharmaceutically acceptable compositions may be formulated in an ointment such as petrolatum.
[0404] The pharmaceutically acceptable compositions of this invention may also be administered by nasal aerosol or inhalation. Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and may be prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other conventional solubilizing or dispersing agents.
[0405] In several embodiments, the pharmaceutically acceptable compositions of this invention are formulated for oral administration.
[0406] The amount of the compounds of the present invention that may be combined with the carrier materials to produce a composition in a single dosage form will vary depending upon the host treated, the particular mode of administration. Preferably, the compositions should be formulated so that a dosage of between 0.01-100 mg/kg body weight/day of the modulator can be administered to a patient receiving these compositions.
[0407] It should also be understood that a specific dosage and treatment regimen for any particular patient will depend upon a variety of factors, including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, rate of excretion, drug combination, and the judgment of the treating physician and the severity of the particular disease being treated. The amount of a compound of the present invention in the composition will also depend upon the particular compound in the composition.
[0408] Depending upon the particular condition, or disease, to be treated or prevented, additional therapeutic agents, which are normally administered to treat or prevent that condition, may also be present in the compositions of this invention. As used herein, additional therapeutic agents normally administered to treat or prevent a particular disease, or condition, are known as "appropriate for the disease, or condition, being treated." [0409] The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.
EXAMPLES
EXAMPLE l. Materials
[0410] The synthesis of MoChol and HisChol were described in US Patent Application No. 2004/0131666 and PCT International Application No. WO 02/066490. The other lipids are available from commercial sources. For example, DOTAP and cholesterol are available from Merck, DMG-Succ is available from Chiroblock GmbH, CHEMS can be obtained from Sigma Chemical Company, DPPG, DOPE and POPC are available from Genzyme or Lipoid and Egg phosphatidylcholine is available from Lipoid.
EXAMPLE 2: Production of Amphoteric Liposomes Charged with Oligonucleotides Using a Lipid Film-Hydration Method
[0411] The lipid composition of the liposomes as well as the methods of preparing them are chosen so that the encapsulation efficiency is greater than 35 % and the liposome size smaller than 200 ηm, and ideally near 100 ηm to maximize tumor penetration. For administering to animals, the DNAi oligonucleotide concentration should be at least 2 mg/mL at a lipid concentration of 100 mM or less. This allows dosing at 10 mg/kg in 200 uL of injection volume.
[0412] One method for preparing liposomes is by a modified lipid film / hydration / extrusion method. Lipids are dissolved in chloroform or chloroform/methanol and dried completely in a rotary evaporator. The lipid films are next hydrated with various amounts of the oligonucleotides SEQ ID NO: 1251 (PNTlOO) or the complement of PNT-100 (PNT-IOOR) hydrated in buffer.
A. Advanced Loading Procedure
[0413] 2400 μmole of lipid is hydrated with 10 mM NaOAc, 150 mM NaCl (pH adjusted using citrate) containing 48.8 to 95.2 mg of oligonucleotides for 30 min at 40° C. After three freeze-thaw steps, the resulting multilamellar vesicle mixture is passed several times through a polycarbonate membrane (100 ηm pore size) using high pressure pumps. Immediately after the extrusion step, the pH of the liposome suspension is shifted to pH 7.5. The resulting suspension is sedimented at 25s using T865 (Sorvall Ultra Pro80) or TLA 100.4 rotors (Beckman Optima-MAX) to remove unsequestered oligonucleotide and to exchange the buffer with phosphate buffered saline (PBS). B. Passive Loading Procedure
[0414] The lipid film is hydrated with PBS containing 405 mg oligonucleotides for 1 hr at 40° C at a final lipid concentration of 100 mM. After three freeze-thaw steps, the resulting vesicles are extruded through a polycarbonate membrane stack containing different pore sizes between 100 and 800 ηm. The resulting suspension is sedimented three times at 25s. (PBS is Phosphate Buffered Saline, which has the formula: 10.1 mM Na2PO4, 1.76 mM KH2PO4, 137 mM NaCl, 2.68 mM KCl, pH 7.5.)
C. Machine Extrusion
[0415] The vesicles are prepared by either the passive or advanced loading procedure and extruded using a device for producing lipid vesicles (See, for example, U.S. Patent No. 6,843,942 and U.S. Patent Application No. 2004/0032037, each of which is incorporated by reference herein in its entirety).
[0416] Particle properties were measured using a Zetasizer 3000 HAS (Malvern) or a Nicomp 370. Liposomes were diluted in appropriate buffer to a final lipid concentration of 0.2 - 0.6 mM. Size values are recorded as Z average and size distribution was calculated in the Multimodal mode. For Zeta potential measurement, liposomes were also diluted to 0.2 - 0.6 mM.
Table 2 Li osome Formulations
Figure imgf000085_0001
[0417] For all formulations in Table 2, active loading using either manual or machine extrusion in general gave better results. The encapsulation efficiencies ranged from 37 - 77 %, liposome size ranged from 124 - 201 ηm and the oligonucleotide concentration at a lipid concentration of 100 mM ranged from 1.1 to 3.5 mg/mL. Machine extrusion gave similar results as manual extrusion with the possible exception that machine extrusion resulted in more uniform liposome size, ranging from 135-179 ηm. Machine extrusion is preferred for larger volumes.
[0418] The passive loading procedure resulted in lower encapsulation efficiencies, ranging from 11 - 21 %. However, liposome size ranged from 122 - 182 ηm and the oligonucleotide concentration at a lipid concentration of 100 mM ranged from 2.0 - 3.7 mg/mL. All formulations that were passively loaded were manually extruded because attempts at machine extrusion created a high back pressure.
[0419] The advanced loading procedure could not be used for all formulations because of the low loading capacity of formulations that contain less than 20 % cationic lipid.
Consequently, formulation B with DOTAP at 10 % could not be loaded efficiently by the advanced loading procedure, and the passive loading procedure was used.
[0420] A ratio of cationic lipid charge to anionic nucleotide charge at low pH (N/P) of 3.3 was found to be the best compromise to produce small particles, high encapsulation efficiency and oligonucleotide concentration to lipid concentration of at least 2.0 mg/mL of oligonucleotide at 100 mM lipid concentration.
EXAMPLE 3. Small Scale Production of DNAi-Liposomes By Injection of Lipids Into a
Nucleic Acid Solution
[0421] Liposomes were prepared as described in U.S. Patent No. 6,843,942.
[0422] Specifically, 2000 μmol of lipids of composition D in Table 2 above were dissolved in
15 mL of ethanol. The ethanolic lipid solution at 55° C was injected into 40 mL of a solution of an oligonucleotide in 20 mM sodium acetate, pH 4.0 and mixed continuously. The rates of mixing were 400 mL/min of the oligonucleotide mixture and 170 mL/min of the lipid mixture. The lipid-oligonucleotide mixture was immediately diluted (cross-flow injection) with 160 mL of an aqueous solution of 100 mM NaCl, 136 mM Na2HPO4, pH 9.0.
Liposomes were prepared using increasing oligonucleotide amounts as shown below in Table
3.
[0423] Liposomes were extruded using a Lipex extruder (Lipex Biomembranes, Inc.,
Vancouver BC, Canada) equipped with a 200 ηm polycarbonate membrane. Extrusion was also performed with a 100 ηm membrane, or first through a 200 ηm membrane and next through a 100 ηm membrane.
[0424] In some instances, the liposomal mixture was dialyzed or ultrafiltered to remove unincorporated oligonucleotides and to remove ethanol.
[0425] Alternatively, or in addition, the liposome suspension was filtered through a Pall Mini
Kleenpack capsule equipped with a 0.22 μm Supor membrane (Pall Corp. East Hills, NY).
[0426] An overview of the procedure is shown in Figure 1. The crossflow process, in which the DNAi oligonucleotide is mixed with the lipids and diluted with a buffer is shown in
Figure 2. [0427] Using the above procedure, the amount oligonucleotide was varied to determine the optimal amount to use. Table 3
Figure imgf000087_0001
[0428] The oligonucleotide used in the above experiments is SEQ ID NO: 1251. Z is the average diameter of the liposomes, and PDI is the polydispersity index. [0429] The batches were also both extruded and filtered. The amount of the oligonucleotide recovered, determined by HPLC, is shown in Table 4. The sample was first extracted with methanol-chloroform, centrifuged and the aqueous layer was analyzed by HPLC. The HPLC column was a Dionex DNApac PA200, 250 x 4 mm. The mobile phase was solvent A: 100 mM TRIS pH 8.0, 10 % acetonitrile and solvent B: 100 mM TRIS pH 8.0, 2 M LiCl, 10 % acetonitrile. The flow rate was 1.5 mL/min. A gradient starting with 98 % solution A, 2 % solution B, and ending with 100 % solution B after 30 minutes was used. The column temperature was 7O0C, autosampler temperature 50 C, injector volume 10 μL, and the detector wavelength was 260 ηm. Table 4
Figure imgf000087_0002
Figure imgf000088_0001
[0430] The oligonucleotide used in the above experiments is SEQ ID NO: 1251. The amount of oligonucleotide used for each batch is indicated in Table 3.
[0431] The above experiments indicate that extrusion does not induce the release of the sequestered oligonucleotide and sequestration of the oligonucleotide is independent of the initial oligonucleotide to lipid ratio. Loss of the oligonucleotide by extrusion and filtration is about 7 %.
[0432] Lipid losses for the 6 batches above after extrusion and filtration ranged from 6 - 9 %. [0433] Additional experiments were performed comparing extrusion trhough 200 ηm and 100 ηm membranes. Results are shown in Figure 3. Direct indicates that the liposomes were neither extruded nor filtered. Ex200 SF0,2 indicates that the liposomes were extruded through a 200 ηm membrane and subsequently filtered through a 0.22 μm filter. Ex200 SF0,2 ExIOO indicates that the liposomes were extruded through a 200 ηm membrane, filtered through a 0.22 μm filter and subsequently extruded through a 100 ηm membrane. Direct + ExIOO indicates that the liposomes were extruded through a 100 ηm membrane. The size (Fig. 3A) and polydispersity indices (Fig. 3B) data indicate that liposomes generated by additional extrusion through 100 ηm membranes are very similar to liposomes generated by 200 ηm extrusion. The amount of released oligonucleotide is strongly affected by the additional 100 ηm step as shown in Fig. 3C.
[0434] The above results taken together indicate that batches 3 and 4, with 78 and 90 mg of oligonucleotide, respectively, in the 40 mL of aqueous buffer gave the best results with respect to size, polydispersity index and amount of oligonucleotide in the liposomes.
EXAMPLE 4 Large Scale Production of DNAi-Liposomes
[0435] Liposomes were produced as described in Example 3 to yield about 170 mL of liposome suspensions. The liposomes were extruded three to five times through 0.2 μm polycarbonate membranes using a 47 mm Millipore high pressure filter holder. In parallel, 10 mL of liposomal suspensions were extruded using the Lipex extruder. Both extrusion devices were pressurized with nitrogen at 6 - 9 bar and the flow rate was between 40 and 70 mL per minute. Three batches calculated to yield a final concentration of 3.2, 3.6 and 4.0 mg/mL of oligonucleotide were prepared. The amount of oligonucleotide to yield a final concentration of 3.2 mg/mL is 90 mg on the small scale production described in Example 3. The average sizes and polydispersity indices of the different batches are shown in Table 5. Table 5
Figure imgf000089_0001
[0436] Ultrafiltration or diafiltration was performed after five extrusion cycles. Filtration through a 0.22 μm filter was subsequently performed. The freeze/thaw step was performed last. (See next example.) The above process was performed with an oligonucleotide of SEQ ID NO: 1251. Size distributions of the liposomes after each step are shown in Figure 4, which shows that the size distribution does not change significantly after extrusion. [0437] The above data indicate that five extrusion cycles are necessary to reduce the polydispersity index so that the mixture can be filtered through a 0.22 μm filter with minimal loss. Data for batch 1 show that three extrusion cycles are not sufficient. During filtration of batch 1 through a 0.22 μm filter there was an increase in pressure, with greater loss of material than for the other batches. Table 6 below shows data for losses during filtration for the different batches. Table 6
Figure imgf000090_0001
[0438] The losses were mainly due to non-specific binding.
[0439] Preparation of DNAi-liposomes used to treat tumors in mice were prepared by the above methods. Briefly, 3 volumes of ethanol, containing the lipid mixture D (POPC/DOPE/MoChol/Chems 6:24:47:23) (133 mM, heated to 55° C) and 8 volumes of 20 mM NaAc/300 mM Sucrose/pH 4, containing 2.71 mg/mL PNTlOO (SEQ ED NO:1251) or PNTlOO-R (SEQ ID NO: 1288) in case of PNT2254 or PNT2254R production, or containing 1.36 mg/mL PNTlOO in case of PNT2253 production, were continuously mixed using an injection device as disclosed in US Patent 6,843,942 and US patent application No. 2004/0032037. The acidic mixture was shifted to pH 7.5 by an additional continuous mixing step with 32 volumes of 100 mM NaCl, 136 mM Phosphate, pH 9. The resulting liposomal suspension was concentrated 10 fold and dialyzed against PBS, pH 7.4 to wash out non- encapsulated PNTlOO or PNTlOO-R and excess ethanol. The concentration of PNT-100 in PNT2253 and PNT2254 are 2.0 mg/mL and 4.0 mg/mL, respectively.
EXAMPLE 5 Effect of Freezing and Thawing on DNAi-Liposomes
[0440] The three batches described in Example 4 were frozen at -70 ° C and stored for two days at -200C to simulate a freezing procedure and to test for oligonucleotide release. After thawing at room temperature, samples were analyzed for size and size distribution. The three batches contained 5 % sucrose in the final solution. Data in Table 5 above indicate that freezing and thawing of the liposomes further improves homogeneity. In addition, liposomes were filtered in an Amicon stirring cell and the filtrate was analyzed for possible oligonucleotide release due to freezing and thawing. Released oligonucleotide was below 1
%.
[0441] The size distributions of the three batches were measured after one, two, three, four and five freeze-thaw cycles. Figure 5 shows graphs of the results, which show that repeated freeze-thaw cycles do not significantly affect the size distributions of the liposomes.
[0442] Sucrose at a final concentration of 300 mM was added to the oligonucleotide solution before mixing with the lipid mixture. Alternatively, or in addition, after or during ultrafiltration or diafiltration, sucrose was added to the loaded liposomes to a final concentration of 5 - 10 %.
EXAMPLE 6 Response of WSU-DLCL2 Tumors to PlSfT- 100 in Liposomes [0443] Liposomes containing the oligonucleotide PNT-100 (SEQ ID NO: 1251) were tested in a human lymphoma model. Lymphoma cells. WSU-DLCL2 cells (Wayne State University Diffuse Large Cell Lymphoma) were obtained from Dr. Ramzi Mohammad, Karmanos Cancer Institute, Wayne State University. Xenografts were transplanted subcutaneously into C17/SCED mice. Seven days after transplantation, mice were injected intravenously with 10 mg/kg of the PNT-100 (SEQ ID NO: 1251) formulations and 10 mg/kg of PNT-100R (SEQ ID NO: 1288) formulations. The injections were performed daily for 8 days in six mice. The size of the tumors was measured up to 30 days after implantation. All animals survived with no gross toxic pathology.
[0444] Results in Figure 6 show that PNT-100 slows tumor growth. 340.9 and 340.8 are formulations with PNT-100 and PNT-100R, respectively.
[0445] Experiments done with other lots of PNT-100-liposome formulation D (Table 2 above) gave similar results, as shown in Fig. 7. Mice were administered 10 mg/kg PNT2253 (PNT-100 in formulation D) daily for eight days, an i.v. bolus injection and tumor volume response was caliper measured (left panel). Data show 57 % tumor growth inhibition at day 28 post xenograft transplantation or 14 days post drug treatment (n = 6; p = 0.004). Mice were administered 10 mg/kg PNT2253 daily for five days via an i.v. bolus injection and tumor response was caliper measured. Data shows 46 % tumor growth inhibition at day 26 post xenograft transplantation or 19 days post drug treatment (n = 8; p = 0.007). Studies were concluded when control animal xenografts reached > 2000 mm3.
[0446] The tumor burden was calculated from the size measurements of the tumors. Fig. 8 shows that the tumor burden in mice treated with PNT2253 was dramatically less than the tumor burden in mice treated with PNT2253R (PNT-IOOR in formulation D) or PBS. [0447] A dose response experiment was performed in WSU-DLCL2 xenograft bearing mice with PNT-100 in formulation D, with a PNT-100 concentration of 4 mg/mL (PNT2254) and 2 mg/mL (PNT2253). C.B.-17 ACID mice between 6 and 8 weeks old were supplied by Taconic (Hudson, NY). When the tumors reached approximately 100 mm3 volume, treatment with PNT2253 or PNT2254 was initiated. The mice received 0, 0.3, 3, 10, or 20 mg/kg of PNT2254 daily for five days, 30 mg/kg of PNT2254 daily for 2 days, 60 mg/kg of PNT2254 once, 0.3, 3, or 10 mg/kg of PNT2253 daily for 5 days, 20 mg/kg of PNT2253 daily for 2 days, or 30 mg/kg of PNT2253 once via an iv bolus injection, [n = 7 (PNT2254) or 8 (PNT2255)]. The animals were checked at least three times weekly for tumor growth by caliper measurements, and the animals were weighed at least three times weekly. Tumor volumes of all treatment groups were analyzed using GraphPad™ statistical software. [0448] A maximum tolerated dose of 20 mg/kg/day of PNT2254 and 10 mg/kg/day of PNT2253 was established. (Figs. 9 and 10) Toxicity was achieved at 30 mg/kg/day for PNT2254 and at 20 mg/kg/day for PNT2253, and dosing was stopped after two days due to animal efficacy. A steep dose response was seen with strong anti-tumor efficacy for an extended time period after one dosing cycle. The effect of the two formulations at various dosages on body weight of the mice was determined and is shown in Fig. 11. For both formulations, a dose of 10 mg/kg/day was efficacious while causing minimal weight loss. [0449] A mathematical measure of each dose was calculated that determined the drug response in delaying tumor growth rate to 750 mg size in PNT2254 and PNT2253 drugged vs. control non-drugged tumors (Tables 7 and 8).
Table 7 Antitumor Activit of PNT2254 in WSU-DLCL2-Bearin SCID Mice
Figure imgf000092_0001
[0450] T and C are the median times in days for the treatment group (T) and the control group (C) tumors to reach a predetermined weight (750 mg). T-C is a measure of tumor growth delay and is the difference in the median days to 750 mg between the treated (T) and the control (C) group. Log10 kill Gross = T-C value in days/3.32 X Td. Td is the mean tumor doubling time (days) estimated from a log-linear growth plot of the control tumors growing in exponential phase. The higher the Logio kill Gross value, the more efficacious the drug, and a value over 2.8 is considered highly efficacious (Corbett, T.H. et al., "Transplantable Syngeneic Rodent Tumors", Tumor Models in Cancer Research. Ed. Teicher B.A. Totowa, NJ: Humana Press Inc., 2002. 41-71). Volume and weight were calculated according to the formula described by Cammisuli, S., et al., Int. J. Cancer, 65, 351- 9, 1996.
[0451] PNT2253 treatment resulted in increased toxicity compared to PNT2254. The most efficacious dose was 10 mg/kg/day for both PNT2253 and PNT2254, and the maximum tolerated dose is 20 mg/kg/day for PNT2254 and 10 mg/kg/day of PNT2253.
EXAMPLE 7 Response of PC-3 Tumors to PNT-100
[0452] The different formulations were tested in a PC-3 human prostate carcinoma model. Xenografts were generated by sub-cutaneous injection of 2 X 106 PC-3 cells (ATCC CRL 1435) into nude mice. Mice bearing 50-200 mm3 xenografts were injected intravenously with 10 mg/kg of PNT-100 (SEQ ID NO: 1251) or PNT-100R (SEQ ID NO:1288) in one of the formulations B, D or F on days 1, 2, and 5 and with 7.5 mg/kg on days 3 and 4. Results show a decrease in tumor growth with PNT-100, but not with PNT-100R (Fig. 12 and 13). N = 5. These results indicate that amphoteric liposomes loaded with PNT-100 are also efficacious in tumors generated from human prostate carcinoma cells.
EXAMPLE 8 Response of WSU-DLCL? Tumors to Frozen and Thawed DNAi-Liposomes [0453] The antitumor activity of liposomes loaded with PNT-100 with sucrose added and which were frozen and thawed was determined in WSU-DLCL2-bearing SCID mice. The liposomes loaded with PNT-100 were prepared as in Example 4, with sucrose added to the oligonucleotide-liposomes to a final concentration of 10 % before freezing and thawing. The PNT-100 liposomes, termed PNT2255F, contained 2 mg/mL of sequestered PNT-100 and were frozen and thawed once as described in example 5. PNT-100 liposomes containing 2 mg/mL of sequestered PNT-100, which were not frozen and thawed before use are termed PNT2255R.
[0454] Tumors from WSU-DLCL2 cells were generated in mice as described in Example 6. A total of 48 mice were used for the study and were divided into six days after xenograft trocar transplantation. Approximate animal tumor volumes were sized matched to standardize starting cohorts for average tumor size. Mice bearing approximately 100 mm3 xenografts were injected intravenously with 10 mg/kg of PNT2255F or PNT22255R as shown in Table 9. Table 9
Figure imgf000094_0001
[0455] The dosage is 10 mg/kg of PNT-100. *One animal did not develop a palpable tumor. [0456] Animals were checked three times weekly for tumor growth by caliper measurements until the end of the study. An approximate tumor volume was calculated using the formula Vλ(a x b2), where b is the smaller of two perpendicular diameters. Animals were also weighed three times weekly for the duration of the study. Animals were sacrificed when tumors exceeded 2000 mm3 volume.
[0457] Tumor volumes of all treatment groups were analyzed using Prism™ 4.0 (GraphPad; San Diego, CA) and Microsoft Excel statistical software. Tumor growth delay (TGD) was used to analyze drug treatment effects on time to tumor endpoint (TTE). The tumor endpoint for TTE analysis was set at 750 mm3, which is a value that was within the control tumor exponential growth phase. TTE was defined in days by the formula: TTE = [logio(750) - b]/m for this study. The value for b is the (y) intercept and m is the slope of the line calculated from a linear regression of log-transformed tumor growth data for each tumor calculated from a minimum of three time points preceding 750 mm3 and a minimum of one that surpassed the time point for 750 mm3. Mice with tumors were administered PNT2255 and/or rituximab on days 4-8 post trocar and tumors were monitored until animals were euthanized due to tumors reaching a 2000 mm3 endpoint or on day 81, which was the conclusion of the study. Tumors that did not reach 750 mm3 by day 81 were assigned TTE values of 81 days.
[0458] Treatment efficacy was determined by comparing TTE values calculated for each treatment group and by calculating TGD (T-C) for each drug treatment group where T represents the median TTE in days for each drug treatment group and C represents the median TTE in days for the control group. The student's t test with Mann-Whitney ranking analysis was performed for the comparison of each study group TTE value for significance. A 95 % confidence value was used and a Mann-Whitney U < 18 value was considered significant with 0 being most significant. Mann-Whitney analysis is a method that analyzes each study tumor independently for statistical significance comparisons between treatment groups. There were no non-treatment related deaths (NTR), non-treatment metastatic related deaths (NTRm), and treatment related deaths (TR) in this study.
[0459] Mean tumor volume (MTV) growth curves with standard error were calculated for each treatment group. The mean values excluded euthanized animals one time point after the day of euthanasia. Kaplan-Meier plots were generated with Prism 4.0 software to plot the percentage of animals that survived with tumors below 2000 mm3. [0460] As shown in Table 9 above, eight animals were dosed in all cohorts except for the PNT2255R cohort that had seven animals dosed because one animal did not form a palpable tumor. Tumors grew progressively in all control animals with a median TTE value of 17.7 days, and all tumors grew progressively until day 29 when tumor burden reached 2000 mm3 in all animals. All other cohort animals were sacrificed when individual animal tumor burden reached 2000 mm3 or when the study was concluded 81 days post tumor trocar. [0461] Complete regression (CR) was recorded as tumor shrinkage below measurable size for three consecutive time points, partial regression (PR) was recorded as a < 50% reduction from initial tumor size for three consecutive time points, and CR responses through the 81 day study endpoint were recorded as tumor free survivor (TFS). Results are shown in Table 10 and Figures 14, 15 and 16. Table 10
Figure imgf000095_0001
[0462] TTE (Time to Tumor Endpoint) = [Iogl0(750)-b]/m; b = (y) intercept; m = slope of the line calculated from a linear regression of log-transformed tumor growth data for each tumor calculated from a minimum of three time points preceding 750 mm3 and a minimum of one that surpassed the time point for 750 mm3.
[0463] TGD (Tumor Growth Delay) = T - C. T is the median TTE for drug treated tumors;
C is the median TTE for control tumors.
[0464] TFS is the number of tumor free survivors; CR (Complete Response) indicates the number of mice whose tumors disappeared; PR (Partial Response) indicates the number of mice whose tumors reduced in size. [0465] The antitumor efficacy data in Figure 14, the mouse body weight data in Figure 15, and the mean TTE statistical comparison (Figure 16) analysis illustrate several important findings about the efficacy seen with PNT2255 and rituximab therapy. [0466] PNT2255F at 10 mg/kg administered daily for five days resulted in 4/8 tumors with complete responses (CR) and 2/8 tumor free survivors through day 81. 5/8 animals had partial responses (PR) and 6/8 animals reached 2000 mm3 tumor burden by day 57. The median TTE value was 40.8 days and was highly significant compared to control tumors (p < 0.0002; Mann Whitney U = 0) giving a TGD value of 23.1 days.
[0467] PNT2255R at 10 mg/kg administered daily for five days resulted in 1/7 tumors with complete responses (CR) and 0/7 tumor free survivors through day 81. 1/7 animals had a partial response (PR) and 7/7 animals reached 2000 mm3 tumor burden by day 50. The median TTE value was 29.1 days which was highly significant compared to control tumors (p < 0.0003; Mann Whitney U = 0) giving a TGD value of 11.4 days. [0468] Rituximab at 20 mg/kg administered on days 2 and 5 resulted in 7/8 tumors with complete responses (CR) and 4/8 tumor free survivors through day 81. 8/8 animals had partial responses (PR) and 3/8 animals reached 2000 mm3 tumor burden; two animals at day 71 and one animal at day 81. 1/8 animals reached near 2000 mm3 (1862 mm ) tumor burden by the 81 day study completion date. The median TTE value was 76.1 days which was highly significant compared to the control group (p < 0.0002; Mann Whitney U = 0) giving a TGD value of 58.3 days.
[0469] PNT2255F at 10 mg/kg administered daily for five days along with rituximab at 20 mg/kg administered days 2 and 5 resulted in 7/8 tumors with complete responses (CR) and 5/8 tumor free survivors through day 81. 7/8 animals had partial responses (PR) and 1/8 animals reached 2000 mm3 tumor burden at day 67. 2/8 animals reached the 81 day study endpoint with measurable tumor burden (1568 and 1980 mm3). The median TTE value was a highly significant value of 81 days compared to controls (p < 0.0002; Mann Whitney U = 0) and the TGD value was 63.3 days. Synergy was not established due to the high response to rituximab alone.
[0470] PNT2255R at 10 mg/kg administered daily for five days along with rituxiamb at 20 mg/kg administered on days 2 and 5 resulted in 6/8 tumors with complete responses (CR) and 5/8 tumor free survivors through day 81. 8/8 animals had partial responses (PR)and 2/8 animals reached 2000 mm3 tumor burden at day 71. 1/8 animals reached the 81 day study endpoint with measurable tumor burden near 2000 mm3 (1960 mm3). The median TTE value was highly significant at 81 days and the TGD value was 63.2 days. Synergy was not established due to the high response to rituximab alone.
[0471] With respect to side effects, there were no treatment related deaths (TR) with the 5 different regimens and no significant weight loss (Figure 15A). There was no mean % weight loss greater than 2 % for any of the treatment groups during the treatment cycle (Figure 15B). [0472] Kaplan-Meir survival to 2000 mm3 tumor endpoint analysis was performed and the data is shown in Figure 17. There was a considerable survivor benefit seen with all treatments and incremental increases in survival to the 81 day study endpoint seen in response to PNT2255F (25 %), rituximab only (62.5 %), PNT2255R + rituximab (75 %), and PNT2255F + rituximab (87.5 %).
[0473] PNT2255R and PNT2255F single-agent therapy demonstrated significant tumor growth delay indicated by extended TTE and TGD values compared to controls. PNT2255F was more efficacious that PNT2255R with a 2 times greater TGD value (23.1 days vs. 11.4 days). PNT2255F treatment resulted in 2/8 tumor free survivors and 5/8 complete responses compared to 0/7 tumor free survivors and 1/7 complete responses obtained with PNT2255R. PNT2255F TTE was significantly more efficacious than PNT2255R TTE (p < 0.0281; Mann- Whitney U= 11.0). Rituximab single-agent therapy was highly efficacious with a TGD of 58.3 days compared to controls and 4/8 tumor free survivors and 7/8 complete responses. PNT2255R or PNT2255F combination treatment with rituximab increased the TGD to 63.2 and 63.3 days. However, there was no statistical significance between the TTE values obtained with rituximab only vs. rituximab in combination with either PNT2255R or PNT2255F (p > 0.05; Mann-Whitney U > 18). Consequently, rituximab-PNT2255 treatment synergy was not obtained in this experiment. Finally, this experiment definitively showed that PNT2255 efficacy can be maintained after freezing and thawing.
EXAMPLE 9 Effect of Various Dose and Administration Regimens on the Efficacy of PNT- 100 Frozen and Thawed Liposomes
[0474] PNT 2256 is a PNT-100 liposomal preparation, prepared as in Example 4 with sucrose added before freezing and thawing. PNT2256 contains 4 mg/mL of PNT-100. Tumors from WSU-DLCL2 cells were generated in mice and animals were treated as described in Example 8. Mice were treated with frozen and thawed PNT2256 with three different administration regimens: (1) i.v. injection daily for five days; i.v. injection every other day for two weeks and i.v. injection every third day for three weeks. The results are shown in Figure 18 and Table 11. Table 11
Figure imgf000098_0001
[0475] PNT2256F at 10 mg/kg administered daily for five days resulted in 4/7 tumors with complete responses (CR) and 1/7 tumor free survivors through day 81. 5/7 animals had partial responses (PR). The median TTE value was 47.7 days and the TGD value was 23.1 days.
[0476] PNT2256F at 10 mg/kg administered every other day for two weeks resulted in 0/7 tumors with complete responses (CR) and 0/7 tumor free survivors through day 81. 0/7 animals had partial responses (PR). The median TTE value was 18.3 days and the TGD value was 8.4 days.
[0477] PNT2256F at 10 mg/kg administered every third day for three weeks resulted in 0/7 tumors with complete responses (CR) and 0/7 tumor free survivors through day 81. 0/7 animals had partial responses (PR). The median TTE value was 19.6 days and the TGD value was 9.5 days.
[0478] The above results indicate that administration of PNT2256F daily for five days resulted in better efficacy than the other administration regimens. The results also indicate that PNT2255F and PNT2256F have similar efficacy.
[0479] Rituximab administered at 2 mg/kg administered on days 2 and 5 resulted in 1/7 tumors with complete responses (CR) and 0/7 tumor free survivors through day 81. 6/7 animals had partial responses (PR). The median TTE value was 43.9 days and the TGD value was 33.8 days.
[0480] PNT2256F at 10 mg/kg administered daily for five days in combination with rituximab administered at 20 mg/kg administered on days 2 and 5 resulted in 4/7 tumors with complete responses (CR) and 2/7 tumor free survivors through day 81. 4/7 animals had partial responses (PR). The median TTE value was 76.1 days and the TGD value was 66.0 days. [0481] These results indicate that PNT2256F in combination with rituximab administered twice at 2 mg/kg is more efficacious than either alone.
OTHER EMBODIMENTS
[0482] It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages and modifications are within the scope of the following claims.
[0483] All publications, patent publications and applications mentioned in this specification are herein incorporated by reference in their entireties to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
SEQUENCE LISTING SUMMARY
The following is a brief outline of the sequence listing.
SEQ ID NO: 1 c-myc upstream region
SEQ K) NOs:2-145, 375-432 c-myc DNAi oligonucleotides
446-450
SEQ ID NO: 146 bcl-2 upstream region
SEQ ID NO: 152 bcl-2 secondary promoter sequence
SEQ ID NOs: 153-163 bcl-2 upstream sequences
SEQ ID NOs: 147-151, 164-374, bcl-2 DNAi oligomers
433-445

Claims

What is claimed is:
1. A mixture comprising amphoteric liposomes, a DNAi oligonucleotide and a cryoprotectant and/or a lyoprotectant, wherein the DNAi oligonucleotide is an oligonucleotide that hybridizes under physiological conditions to nucleotides 500- 1575 of SEQ ID NO: 146 or to nucleotides 1-900 of SEQ BD NO: 1 or the complements thereof.
2. The mixture of claim 1 wherein the cryoprotectant and/or lyoprotectant is a disaccharide.
3. The mixture of claim 1 wherein the cryoprotectant and/or lyoprotectant is mannitol, sucrose or trehalose.
4. The mixture of claim 1 wherein the cryoprotectant is a combination of two or more cryoprotectants and/or lyoprotectants.
5. The mixture of any of claims 1-4, wherein the amphoteric liposomes have an isoelectric point between 4 and 8.
6. The mixture of any of claims 1-5, wherein the amphoteric liposomes are negatively charged or neutral at pH 7.4 and positively charged at pH 4.
7. The mixture of any of claims 1-6 wherein the amphoteric liposomes are formed from a lipid phase comprising an amphoteric lipid.
8. The mixture of claim 7, wherein the amphoteric lipid is selected from the group consisting of HistChol, HistDG, isoHistSuccDG, Acylcarnosine and HCChol.
9. The mixture of any of claims 1-6, wherein the amphoteric liposomes are formed from a lipid phase comprising a mixture of lipid components with amphoteric properties.
10. The mixture of claim 9, wherein the mixture of lipid components comprises anionic and/or cationic components, wherein at least one such component is pH responsive.
11. The mixture of claim 10, wherein the mixture of lipid components are selected from the group consisting of (i) a stable cationic lipid and a chargeable anionic lipid, (ii) a chargeable cationic lipid and chargeable anionic lipid or (iii) a stable anionic lipid and a chargeable cationic lipid.
12. The mixture of claim 10, wherein the lipid components comprise one or more anionic lipids selected from the group consisting of DOGSucc, POGSucc, DMGSucc, DPGSucc, DGSucc, DMPS, DPPS, DOPS, POPS, DMPG, DPPG, DOPG, POPG, DMPA, DPPA, DOPA, POPA, CHEMS and Cet-P.
13. The mixture of in any of claims 10 to 12, wherein the lipid components comprise one or more cationic lipids selected from the group consisting of DMTAP, DPTAP, DOTAP, DC-Choi, MoChol, HisChol, DPIM, CHIM, DORIE, DDAB,DAC-Chol, TC-Chol, DOTMA, DOGS, (C18)2Gly+ N,N-dioctadecylamido-glycine, CTAP, CPyC, DODAP and DOEPC.
14. The mixture of claim 10 wherein the anionic lipid is selected from CHEMS, Cet-P and DMGSucc, and the cationic lipid is selected from DOTAP and MoChol.
15. The mixture of any of claims 7 to 14, wherein said lipid phase further comprises neutral lipids.
16. The mixture of claim 15, wherein the neutral lipids comprise sterols and derivatives thereof, neutral phospholipids or combinations thereof.
17. The mixture of claim 16 wherein the neutral phospholipids comprise phosphatidylcholines, phosphatidylethanolamines or combinations thereof.
18. The mixture of claim 17 wherein the phosphatidylcholines are selected from the group consisting of POPC, OPPC, natural or hydrogenated soy bean PC, natural or hydrogenated egg PC, DMPC, DPPC or DOPC and derivatives thereof and the phosphatidylethanolamines are selected from the group consisting of DOPE, DMPE, DPPE and derivatives thereof.
19. The mixture of claim 18 wherein the phosphatidylcholine is POPC and the phosphatidylethanolamine is DOPE.
20. The mixture of claim 16 wherein the neutral lipids are POPC and cholesterol.
21. The mixture of claim 16 wherein the amphoteric liposomes comprise DOPE, POPC, CHEMS and MoChol; POPC, DOPE, MoChol and DMGSucc; POPC, Choi, CHEMS and DOTAP; or POPC, Choi, CetP and MoChol.
22. A mixture comprising amphoteric liposomes comprising
(i) a DNAi oligonucleotide that hybridizes under physiological conditions to nucleotides 500-1575 of SEQ ID NO:146 or to nucleotides 1-900 of SEQ ID NO: 1 or the complements thereof.; (ii) a mixture of lipid components with amphoteric properties comprising anionic or cationic components, wherein at least one such component is pH responsive;
(iii) neutral lipids comprising phosphatidylcholines, phosphatidylethanolamines or sterols, wherein the mixture contains 30 to 70 mole % amphoteric lipids and 30 to 60 mole % neutral lipids; and
(iv) a cryoprotectant.
23. The mixture of claim 22, wherein the cationic lipids are selected from the group consisting of DMTAP, DPTAP, DPTAP, DOTAP, DC-Choi, TC-Chol, MoChol, HisChol, DPIM, CHIM, DORIE, DDAB, DAC-Chol, TC-Chol, DOTMA, DOGS, (C18)2Gly+N,N-dioctadecylamido-glycine, CTAB, CPyC, DODAP, DOEPC and derivatives thereof, and the anionic lipids are selected from the group consisting of DOGSucc, POGSucc, DMGSucc, DPGSucc, DGSucc, DMPS, DPPS, DOPS, POPS, DMPG, DPPG, DOPG, POPG, DMPA, DPPA, DOPA, POPA, CHEMS, Cet-P and derivatives thereof, and wherein the phosphatidylcholines are selected from the group consisting of POPC, natural or hydrogenated soy bean PC, natural or hydrogenated egg PC, DMPC, DPPC or DOPC and derivatives thereof, the phosphatidylethanolamines are selected from the group consisting of DOPE, DMPE, DPPE and derivatives thereof, and the sterol is cholesterol or a derivative thereof.
24. The mixture of claim 23, wherein the mixture comprises 10 to 60 mole % of MoChol and 10 to 30 mole % of CHEMS.
25. The mixture of claim 23, wherein the mixture comprises 10 to 30 mole % of CHEMS and 5 to 40 mole % of DOTAP.
26. The mixture of claim 23, wherein the mixture comprises 10 to 60 mole % of MoChol and 5 to 30 mole % of Cet-P.
27. The mixture of claim 23, wherein the mixture comprises 20 to 60 mole % of MoChol and 20 to 60 mole % of DMGSucc.
28. The mixture of claim 23, wherein the mixture comprises 5 to 40 mole % of POPC and 20 to 50 mole % of DOPE.
29. The mixture of claim 23, wherein the mixture comprises 10 to 50 mole % of POPC and 30 to 50 mole % of Choi.
30. The mixture of claim 23, wherein the mixture comprises 3 to 20 mole % of POPC, 10 to 60 mole % of DOPE, 10 to 60 mole % of MoChol and 10 to 60 mole % of CHEMS.
31. The mixture of claim 23, wherein the molar ratio of POPC/DOPE/MoChol/CHEMS is about 6/24/47/23 or about 15/45/20/20.
32. The mixture of claim 23, wherein the mixture comprises 3 to 20 mole % of POPC, 10 to 40 mole % of DOPE, 15 to 60 mole % of DMGSucc and 15 to 60 mole % of MoChol.
33. The mixture of claim 23, wherein the molar ratio of POPC/DOPE/DMGSucc/MoChol is about 6/24/23/47 or about 6/24/47/23.
34. The mixture of claim 23, wherein the mixture comprises 10 to 50 mole % of POPC, 20 to 60 mole % of Choi, 10 to 40 mole % of CHEMS and 5 to 20 mole % of DOTAP.
35. The mixture of claim 23, wherein the molar ratio of POPC/Chol/CHEMS/DOTAP is about 30/40/20/10.
36. The mixture of claim 23, wherein the mixture comprises 10 to 40 mole % of POPC, 20 to 50 mole % of Choi, 5 to 30 mole % of Cet-P and 10 to 40 mole % of MoChol.
37. The mixture of claim 23, wherein the molar ratio of POPC/Chol/Cet-P/MoChol is about 35/35/10/20.
38. The mixture of claim 22, wherein the cryoprotectant and/or lyoprotectant is a disaccharide.
39. the mixture or claim 22, wherein the cryoprotectant and/or lyoprotectant is mannitol or trehalose.
40. The mixture of claim 22, wherein the cryoprotectant comprises two or more cryoprotectants.
41. The mixture of any one of the preceding claims wherein the average diameter of the DNAi-amphoteric liposomes is between 70 and 150 ηm.
42. The mixture of any of claims 1-40, wherein the average diameter of the DNAi- amphoteric liposomes is between 90 and 130 ηm.
43. The mixture of claim 41 or 42, wherein the polydispersity index of the DNAi- amphoteric liposomes is between 0 and 0.3.
44. The mixture of claim 41 or 42, wherein the polydispersity index of the DNAi- amphoteric liposomes is between 0 and 0.2.
45. The mixture of any of the preceding claims, wherein the DNAi oligonucleotide comprises an oligomer that hybridizes under physiological conditions to nucleotides 800-1225 of SEQ ID NO: 146 or the complement thereof.
46. The mixture of any of claims 1-44, wherein the DNAi oligonucleotide comprises an oligomer that hybridizes under physiological conditions to nucleotides 900-1125 of SEQ ID NO: 146 or the complement thereof.
47. The mixture of any of claims 1-44, wherein the DNAi oligonucleotide comprises an oligomer that hybridizes under physiological conditions to nucleotides 950-1075 of SEQ ED NO: 146 or the complement thereof.
48. The mixture of any of claims 1-44, wherein the DNAi oligonucleotide comprises an oligomer that hybridizes under physiological conditions to nucleotides 970-1045 of SEQ ID NO: 146 or the complement thereof.
49. The mixture of any of claims 1-44, wherein the DNAi oligonucleotide comprises SEQ ID NO: 147, 148 or the complement thereof.
50. The mixture of any of claims 1-44, wherein the DNAi oligonucleotide comprises an oligomer that hybridizes under physiological conditions to nucleotides 1-250 or 540- 770 of SEQ ED NO: 1.
51. The mixture of any of claims 1-44, wherein the DNAi oligonucleotide comprises SEQ ED NO: 5, 8 or 377.
52. The mixture of any of the preceding claims wherein the mixture further comprises another DNAi oligonucleotide.
53. The mixture of any of the preceding claims, wherein the amphoteric liposomes have a DNAi oligonucleotide concentration of at least 2 mg/mL at a lipid concentration of 100 mM or less.
54. A method comprising i) providing the mixture of any of the preceding claims and a proliferating cell; and ii) introducing the mixture into the cell.
55. The method of claim 54, wherein introducing the composition results in a reduction of proliferation of the cell.
56. The method of claim 54, wherein the cell is a cancer cell.
57. The method of any of claims 54-56, wherein the cell is in an animal.
58. The method of claim 57, wherein the mixture is introduced to the animal at a dosage of between 0.01 mg to 100 mg per kg of body weight.
59. The method of any of claims 54 - 56, wherein the cell is in cell culture.
60. The method of claim 54 or 57, further comprising the step of introducing a test compound to the cell.
61. The method of claim 60, wherein the test compound is a known chemotherapy agent.
62. The method of claim 56, wherein the cancer is selected from the group consisting of pancreatic cancer, colon cancer, breast cancer, bladder cancer, lung cancer, leukemia, prostate cancer, lymphoma, ovarian cancer and melanoma.
63. A method of preparing a mixture comprising amphoteric liposomes, a DNAi oligonucleotide and a cryoprotectant and/or lyoprotectant comprising: i) providing a lipid mixture in a solvent and an aqueous solution of one or more DNAi oligonucleotides; ii) mixing the lipid mixture and the DNAi oligonucleotides by injecting the lipid mixture into the DNAi oligonucleotide solution; and iii) adding a cryoprotectant and/or a lyoprotectant; wherein the DNAi oligonucleotide hybridizes under physiological conditions to nucleotides 500-1575 of SEQ ID NO: 146 or to nucleotides 1-900 of SEQ ID NO:1 or the complements thereof.
64. The method of claim 63, further comprising diluting the lipid-DNAi oligonucleotide mixture with an aqueous buffer solution having a pH of about 8 to 10.
65. The method of claim 63 or 64, further comprising the step of extruding the lipid- DNAi oligonucleotide mixture through a membrane with a pore size of about 80 ηm to about 300 ηm.
66. The method of any of claims 62 - 65, further comprising the step of filtering the DNAi-liposomes through a 0.22 micron filter.
67. The method of any of claims 63 - 68, wherein the average diameter of the DNAi- amphoteric liposomes is between 70 and 150 ηm.
68. The method of any of claims 63 - 67, wherein the polydispersity index of the DNAi- amphoteric liposomes is between 0 and 0.3.
69. The method of any of claims 63 -67, wherein the efficiency of encapsulation of the oligonucleotides is at least 35 %.
70. The method of any of claims 63 - 67, wherein the liposomes produced have an oligonucleotide concentration of at least 2 mg/mL at a lipid concentration of 100 mM or less.
71. The method of any of claims 63 - 67, wherein the average diameter of the DNAi liposomes is between 70 and 150 ηm, the polydispersity index is between 0 and 0.3, the efficiency of encapsulation of the oligonucleotides is at least 35% and the liposomes have an oligonucleotide concentration of at least 2 mg/mL at a lipid concentration of 100 mM or less.
72. A pharmaceutical composition comprising the mixture of any of claims 1 to 53.
73. A mixture comprising amphoteric liposomes and an oligonucleotide comprising SEQ ID NO: 148 or 147 wherein the liposomes comprise POPC, DOPE, MoChol and CHEMS in the molar ratio of POPC/DOPE/MoChol/CHEMS of 15/45/20/20 and 5% sucrose.
74. A mixture comprising amphoteric liposomes and an oligonucleotide comprising SEQ ID NO: 148 or 147 wherein the liposomes comprise POPC, DOPE, MoChol and CHEMS in the molar ratio of POPC/DOPE/MoChol/CHEMS of 6/24/47/23 and 5% sucrose.
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Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2010209012A (en) * 2009-03-11 2010-09-24 Ichimaru Pharcos Co Ltd Ph-responsive liposome
US8367628B2 (en) 2005-12-01 2013-02-05 Pronai Therapeutics, Inc. Amphoteric liposome formulation
US8815599B2 (en) 2004-06-01 2014-08-26 Pronai Therapeutics, Inc. Methods and compositions for the inhibition of gene expression
US9895313B2 (en) 2015-03-03 2018-02-20 Cureport, Inc. Combination liposomal pharmaceutical formulations
US10736845B2 (en) 2015-03-03 2020-08-11 Cureport Inc. Dual loaded liposomal pharmaceutical formulations
WO2024167537A1 (en) * 2023-02-08 2024-08-15 Leuvian Llc Lyoprotectant and cryoprotectant compositions and uses thereof

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007064857A2 (en) * 2005-12-01 2007-06-07 Pronai Therapeutics, Inc. Amphoteric liposome formulation
WO2008103431A2 (en) * 2007-02-23 2008-08-28 Pronai Therapeutics, Inc. Dnai - liposomes

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007064857A2 (en) * 2005-12-01 2007-06-07 Pronai Therapeutics, Inc. Amphoteric liposome formulation
WO2008103431A2 (en) * 2007-02-23 2008-08-28 Pronai Therapeutics, Inc. Dnai - liposomes

Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8815599B2 (en) 2004-06-01 2014-08-26 Pronai Therapeutics, Inc. Methods and compositions for the inhibition of gene expression
US9393258B2 (en) 2004-06-01 2016-07-19 Pronai Therapeutics, Inc. Methods and compositions for the inhibition of gene expression
US8367628B2 (en) 2005-12-01 2013-02-05 Pronai Therapeutics, Inc. Amphoteric liposome formulation
JP2010209012A (en) * 2009-03-11 2010-09-24 Ichimaru Pharcos Co Ltd Ph-responsive liposome
EP2407158A1 (en) * 2009-03-11 2012-01-18 Bionanosheeter Co., Ltd. Ph-responsive liposome
EP2407158A4 (en) * 2009-03-11 2013-09-04 Bionanosheeter Co Ltd Ph-responsive liposome
US8871252B2 (en) 2009-03-11 2014-10-28 Nanotheta Co, Ltd. pH-responsive liposome
US9895313B2 (en) 2015-03-03 2018-02-20 Cureport, Inc. Combination liposomal pharmaceutical formulations
US10561611B2 (en) 2015-03-03 2020-02-18 Cureport, Inc. Combination liposomal pharmaceutical formulations
US10736845B2 (en) 2015-03-03 2020-08-11 Cureport Inc. Dual loaded liposomal pharmaceutical formulations
WO2024167537A1 (en) * 2023-02-08 2024-08-15 Leuvian Llc Lyoprotectant and cryoprotectant compositions and uses thereof

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