WO2006119619A1 - Oligonucleotides inhibiting cell proliferation - Google Patents

Oligonucleotides inhibiting cell proliferation Download PDF

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Publication number
WO2006119619A1
WO2006119619A1 PCT/CA2006/000735 CA2006000735W WO2006119619A1 WO 2006119619 A1 WO2006119619 A1 WO 2006119619A1 CA 2006000735 W CA2006000735 W CA 2006000735W WO 2006119619 A1 WO2006119619 A1 WO 2006119619A1
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Prior art keywords
oligonucleotide
formulation
cell proliferation
activity
oligonucleotide formulation
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PCT/CA2006/000735
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French (fr)
Inventor
Andrew Vaillant
Jean-Marc Juteau
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Replicor Inc.
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Publication of WO2006119619A1 publication Critical patent/WO2006119619A1/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/56—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule
    • A61K47/59—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents

Definitions

  • the invention relates to a method for inhibiting cellular proliferation with oligonucleotides (ONs) encapsulated with a delivery system and acting predominantly by a sequence independent mode of action.
  • the invention also relates to the use of ONs and encapsulated ONs as therapeutic agents, and more particularly for their use in methods of treatment and formulations for the treatment of cancer and other cell proliferation related diseases.
  • Oligonucleotides are short, typically single stranded nucleic acid fragments, designed to hybridize with a specific nucleic acid or protein target. ONs can be chemically modified in order to increase their stability and improve their pharmacokinetic behavior in vivo.
  • oligonucleotides Four mechanisms of action have been reported for sequence-specific activity of oligonucleotides: 1) complimentary ONs hybridizing according to Watson-Crick base pairing to specific mRNAs, which either block translation or induce mRNA degradation by RNAse H; 2) they can bind to genomic DNA in the nucleus and block transcription (Hoogsten-type base triplets); 3) complementary ONs can bind to splice sites in mRNA, preventing correct RNA splicing or preventing aberrant RNA splicing; 4) non-nucleic acid hybridization mechanism of action, also referred to as aptameric binding, where specific binding of an ON (aptamer) to a target protein occurs by nature of the three dimensional shape that a particular ON sequence adopts in solution, analogous to antibody-antigen recognition.
  • ONs are known to have certain non-sequence specific activities.
  • the non-sequence specific effects of ON treatment have been described in simple in vitro systems.
  • the mechanisms for these non sequence-specific effects of ONs may be related to (1) the structure of the ON itself, (2) hybridization to DNA or mRNA other than the target sequence, with subsequent RNase cleavage, (3) binding to proteins or other molecules, and/or (4) ON degradation products, which in themselves can affect cellular functions.
  • Phosphorothioate ONs (PS-ONs) having four adjacent guanosine bases have also been shown to be growth-inhibitory.
  • PS-ONs have further been shown to bind proteins such as bFGF, VEGF, PKC, DNA polymerase, telomerase, HIV reverse transcriptase, tyrosine kinase, tyrosine kinase receptors and other proteins in a sequence- independent fashion.
  • PS-ONs have also been reported to cause sequence-independent induction of tumor necrosis factor, induction of SpI binding activity, and inhibition of transferrin receptor expression.
  • Papucci et al. 2002, Antisense & Nucleic Acid Drug Development 12: 21-31 reported induction of apoptosis by transfecting cultured cells with unmodified ONs using DOTAP. Such effects of these ONs were mediated by a non-antisense mechanism that required the wild-type form of p53 and was dependent on ON concentration. Apoptosis induction appeared to be determined by the 3' and 5' free ends of ONs, which activated p53 independently from their sequence. The effective molar concentration resulting from their experiments was larger than 20 ⁇ M.
  • These delivery systems include cationic molecules such as cationic lipid based systems such as DOTAP, DOTAP/DOPE, DOTAP/cholesterol, DOTAP/DOPE/Cholesterol, Pegylated-liposomes, dendrimers such as polyamidoamine, PLGA and PLA, cyclodextrins, polyethyleneimine and cationic cardiolipins (Jaaskelainen et al, 2000, Journal of Pharmaceutical Sciences 10: 187-193; Akhtar et al , 2000, Advanced Drug Delivery Reviews 44: 3-21; Hughes et al , 2001, Drug Discovery Today 6: 303-315; Dass, 2002, Journal of Pharmacy and Pharmacology 54: 3-27; Dass, 2002, Drug Delivery 9: 169-180).
  • cationic molecules such as cationic lipid based systems such as DOTAP, DOTAP/DOPE, DOTAP/cholesterol, DOTAP/DOPE/Cholesterol, Pegylated-lip
  • the invention relates to a method for inhibiting cellular proliferation with oligonucleotides (ONs) encapsulated with a delivery system and acting predominantly by a sequence independent mode of action.
  • the invention also relates to ONs and their use as therapeutic agents, and more particularly for their use in methods of treatment and formulations for the treatment of cancer and other cell proliferation related diseases.
  • One embodiment of the present invention is to provide an anti-cell proliferation encapsulated oligonucleotide formulation comprising at least one oligonucleotide and at least one delivery system, said oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity.
  • an anti-cell proliferation encapsulated oligonucleotide formulation comprising at least one oligonucleotide and at least one linear delivery system, said oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity, said activity acting through a PEI- mediated mode of action.
  • the oligonucleotide formulation of the present invention comprises a mixture of at least two different oligonucleotides.
  • Another embodiment of the present invention is to provide an anti-cell proliferation randomer oligonucleotide formulation, comprising at least one randomer oligonucleotide and at least one delivery system, said randomer oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity.
  • An additional embodiment of the present invention is to provide an anti-cell proliferation randomer oligonucleotide formulation, comprising at least one linear randomer oligonucleotide and at least one linear delivery system, said randomer oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity, and said activity acting through a PEI-mediated mode of action.
  • the oligonucleotide formulation of the present invention comprises a mixture of at least two randomer oligonucleotides of different lengths.
  • the delivery system comprises at least one cationic molecule.
  • the cationic molecule is a cationic lipid, most preferably the cationic is a cationic dendrimer.
  • the cationic molecule is polyethyleneimine.
  • the polyethyleneimine is a mixture of linear polyethyleneimines.
  • the mixture can comprise polyethyleneimines of molecular weight higher than 2,000 Da and lower than 50,000 Da.
  • said linear polyethyleneimines can have a molecular weight higher than 20,000Da and lower than 25,000 Da.
  • said linear polyethyleneimines can have an average molecular weight in between 20,000Da and lower than 25,000 Da.
  • the oligonucleotide formulation has an IC 50 for inhibition of proliferating cells of 0.10 ⁇ M or less, of 0.05 ⁇ M or less, of 0.025 ⁇ M or less; or of 0.015 ⁇ M or less.
  • Another embodiment of the present invention is to provide an oligonucleotide formulation, wherein said oligonucleotide is at least 10, 15, 20, 30, 40 or 50 nucleotides in length.
  • the oligonucleotide formulation of comprises an oligonucleotide comprising at least one phosphodiester linkage.
  • the oligonucleotide formulation of contains an oligonucleotide comprising at least one modification to its chemical structure.
  • the oligonucleotide can comprise at least two different modifications to its chemical structure.
  • one of said at least two different modifications is a sulfur modification, a phosphorothioated linkage, a phosphorodithioated linkage, a sulfur modified nucleobase moiety or is a sulfur modified ribose moiety.
  • the oligonucleotide used in the formulation comprises at least one T modification to the ribose moiety.
  • said one T modification to the ribose moiety is a 2'-0 alkyl modified ribose moiety, a 2'-0 methyl modified ribose, a T- methoxyethyl modified ribose or a 2'-FANA modified ribose.
  • the oligonucleotide used in the formulation comprises at least one methylphosphonate linkage.
  • the oligonucleotide used in the formulation is a concatemer consisting of two or more oligonucleotide sequences joined by a linker.
  • the oligonucleotide is linked or conjugated at one or more nucleotide residues thereof to a molecule modifying the characteristics of the oligonucleotide to obtain one or more characteristics selected from the group consisting of higher stability, lower serum interaction, higher cellular uptake, an improved ability to be formulated for delivery, a detectable signal, higher anti-cell proliferation activity, better pharmacokinetic properties, specific tissue distribution and lower toxicity.
  • the oligonucleotide comprised in the oligonucleotide formulation comprises at least one base which is capable of hybridizing via non- Watson-Crick interactions.
  • the oligonucleotide comprised in the oligonucleotide formulation comprises at least one Gquartet motif portion.
  • the oligonucleotide comprised in the oligonucleotide formulation comprises at least one CpG motif portion.
  • the oligonucleotide formulation comprises an oligonucleotide comprising a portion complementary to an mRNA.
  • the oligonucleotide of the present invention comprises at least a portion of its sequence derived from a genome.
  • the oligonucleotide having a portion of its sequence derived from a genome has an anti-cell proliferation activity that is predominantly a sequence independent mode of action.
  • the oligonucleotide formulation comprises an oligonucleotide having at most 90%, preferably 80%, more preferably 75% identity with a genomic sequence; at most 60%, preferably 50%, more preferably 40% identity with a genomic sequence.
  • the oligonucleotide formulation comprises an oligonucleotide having at least a portion of its sequence involved in an aptameric interaction with a cellular component.
  • the oligonucleotide formulation comprises an oligonucleotide having at least a portion of its sequence comprising polyA, polyC, polyG, polyT, polyAC, poly AG, polyAT, polyCG, polyCT, polyGT, polyU, PoIyAU, polyCU, poly GU or poly TU.
  • the oligonucleotide formulation comprises an oligonucleotide having at least a portion of its sequence comprising two or more repeated sequences.
  • the oligonucleotide formulation comprises a mixture of at least two different oligonucleotides.
  • the mixture is at least of 10 different oligonucleotides, of 100 different oligonucleotides, of 1000 different oligonucleotides, most preferably of 10 6 different oligonucleotides.
  • Another embodiment of the present invention is to provide an oligonucleotide formulation, wherein said different oligonucleotides are at least 10, 15, 20, 30, 40 or 50 nucleotides in length.
  • an anti-cell proliferation pharmaceutical composition comprising a therapeutically effective amount of at least one pharmacologically acceptable anti-cell proliferation encapsulated oligonucleotide formulation according to the present invention; and a pharmaceutically acceptable carrier.
  • the anti-cell proliferation pharmaceutical composition is adapted for the treatment, control, or prevention of a cell proliferation disease.
  • the anti-cell proliferation pharmaceutical composition of the present invention is adapted for delivery by a mode selected from the group consisting of ocular administration, oral ingestion, enteral administration, inhalation, cutaneous injection, subcutaneous injection, intramuscular injection, intraperitoneal injection, intrathecal injection, intratrachael injection, skin topical administration, rectal administration, vaginal administration, sublingual administration and intravenous injection.
  • the anti-cell proliferation pharmaceutical composition further comprises at least one other anti-cell proliferation drug in combination.
  • the cell proliferation disease is cancer or tumor cells.
  • said subject is a human, a non-human animal or a plant.
  • oligonucleotide means oligodeoxynucleotide or oligodeoxyribonucleotide or oligoribonucleotide.
  • oligonucleotide refers to an oligomer or polymer of ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA) and/or analogs thereof. This term includes oligonucleotides composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally-occurring portions which function similarly.
  • Oligonucleotides that include backbone and/or other modifications can also be referred to as oligonucleosides. Except otherwise specified, oligonucleotide definition includes homopolymers, heteropolymers, randomers (see below), random sequence oligonucleotides, genomic-derived sequence oligonucleotides and oligonucleotides purified from natural source.
  • sequence independent activity indicates that the mechanism by which the material exhibits an anti-cell proliferation effect is not due to hybridization of complementary nucleic acid sequences, e.g., an antisense effect nor it is due to a sequence-specific aptameric activity.
  • a “sequence dependant mode of action or activity” means that the anti-cell proliferation effect of a material involves hybridization of complementary nucleic acid sequences or involves a sequence-specific aptameric interaction.
  • anti-cell proliferation means inhibiting or stopping the proliferation of dividing cells. The term also includes killing or inducing apoptosis of dividing cells.
  • An anti-cell proliferation compound can be used to treat a cell proliferation disease.
  • cell proliferation disease means a disease involving unwanted or uncontrolled proliferation of cells. Such cell proliferation diseases include, without limitation, cancer, restenosis, macular degeneration, unwanted angiogenesis, psoriasis, benign proliferative skin diseases, ichthyosis, papilloma, scleroderma, hemangioma, diabetic retinopathy, neovascular glaucoma and rheumatoid arthritis.
  • anti- cell proliferation refers to an effect of the presence of the encapsulated oligonucleotides or other material in inhibiting the proliferation of dividing cells, cancer or tumor cells, i.e., reducing the number of viable cells compared to untreated cells, in a system or organism otherwise suitable for growth of such cells.
  • the anticancer oligonucleotides will have anti-cell proliferation activity against multiple cell types.
  • anti-cell proliferation encapsulated oligonucleotide formulation refers to a preparation including at least one anti-cell proliferation encapsulated oligonucleotide that is adapted for use as an anti-cell proliferation agent.
  • the expression refers to a formulation comprising an encapsulated oligonucleotide having an anti proliferation activity on a cell.
  • the formulation includes the oligonucleotide or oligonucleotides, and can contain other materials that do not interfere with use as an anti-cell proliferation agent in vivo. Such other materials can include without restriction diluents, excipients, carrier materials, delivery systems and/or other anti-cell proliferation materials.
  • composition refers to an anti-cell proliferation oligonucleotide formulation that includes a physiologically or pharmaceutically acceptable carrier or excipient. Such compositions can also include other components that do not make the composition unsuitable for administration to a desired subject, e.g., a human.
  • the phrase "adapted for use as an anti-cell proliferation agent" indicates that the material exhibits an anti-cell proliferation effect and does not include any component or material that makes it unsuitable for use in inhibiting cell proliferation in an in vivo system, e.g., for administering to a subject such as a human subject.
  • the term "subject" refers to a living higher organism, including, for example, animals such as mammals, e.g., humans, non-human primates, non-human animals and plants, e.g., fruit trees.
  • the term "randomer” is intended to mean a single stranded nucleic acid, modified or not, having a wobble (N) at every position, such as NNNNNNNNNN.
  • Each wobbled nucleotide position actually exists as a random population of the five naturally occurring bases on the nucleotide (adenine, guanine, cytosine, thymine, uracil) at this particular position, resulting in a completely degenerate pool of ONs of the same size but having no sequence identity as a population.
  • Randomers can also include nucleobases which do not occur naturally including without restriction hypoxanthine, xanthosine, imidazole, 2-aninopurines, 5- nitroindole.
  • degenerate means that a sequence is made of a mix of nucleotides.
  • a completely degenerated sequence means that A, C, G, and T (or other nucleobases) are used at each position of the sequence and nucleotide position are identified by N.
  • Degenerate can apply to a sequence, a portion of a sequence or one nucleotide position in a sequence.
  • the term "delivery system” refers to a component or components that, when combined with an ON as described herein, facilitates transfer of ONs inside cells, increases the amount of the ON that contacts the intended location in vivo, and/or extends the duration of its presence at the target, e.g., by at least 10, 20, 50, or 100%, or even more as compared to the amount and/or duration in the absence of the delivery system.
  • the term delivery system also means encapsulation system or encapsulation reagent.
  • To encapsulate ONs means to put in contact an ON with a delivery system or an encapsulation reagent.
  • An ON in contact with a delivery system can be referred to as an "encapsulated ON".
  • terapéuticaally effective amount refers to an amount that is sufficient to effect a therapeutically or prophylactically significant reduction in cell proliferation when administered to a typical subject of the intended type.
  • oligonucleotide, formulation, or composition should be administered in a therapeutically effective amount.
  • the phrase "derived from a genome” indicates that a particular sequence has a nucleotide base sequence that has at least 70% identity to a genomic nucleotide sequence or its complement (e.g., is the same as or complementary to a genomic sequence), or is a corresponding RNA sequence.
  • the term indicates that the sequence is at least 70% identical to a genomic sequence of a particular gene involved in a disease or condition against which the oligonucleotide is directed, or to its complementary sequence.
  • the identity is at least 80, 90, 95, 98, 99, or 100%.
  • Genome can be from an animal, e.g. a human, from a microorganism, e.g. a virus, a bacteria, a parasite, or from plant.
  • Fig. 1 illustrates the in vivo efficacy of 5% dextrose (1) compared to the efficacy of PEI 23k linear encapsulated REP 2006.
  • the present invention is concerned with the identification and use of encapsulated anti- cell proliferation ONs that act by a sequence independent mechanism, and includes the discovery that for many proliferating cell types, the anti-proliferation activity is greater for larger ONs starting with 6mer ONs, and is typically optimal for ONs that are 15 nucleotides or more in length.
  • a number of antisense ONs have been tested for anti-cell proliferation and induction apoptosis activity.
  • antisense ONs are typically sequence-specific targeting mRNA, and typically are about 16-25 nucleotides in length.
  • the anti-cell proliferation effect of encapsulated randomer ONs is sequence independent. Considering the volumes and concentrations of ONs used in these tests, it is theoretically impossible that a particular sequence is present at more than 1 copy in the mixture. This means that there can be no antisense or sequence-specific aptameric effect in these ONs randomers. In all examples, should the cell proliferation inhibition effect be caused by the sequence-specificity of the ONs, such effect would thus have to be caused by only one molecule, a result that does not appear possible. For example, for an ON randomer 40 bases in length, any particular sequence in the population would theoretically represent only 1/4 40 or 1/8.27X10 "25 of the total fraction.
  • randomers may inhibit cellular proliferation by several mechanisms, including but not limited to the following: 1) mimicking DNA damage in the nucleus of the cell by presenting DNA or RNA ends and then signaling to the cell to enter into apoptosis; 2) binding to cell proteins implicated in cell division or mitosis such as, but without limitation, cytoskeletal proteins, mitochondrial proteins, polymerases, DNA repair proteins or proteins involved in the apoptotic signaling cascade.
  • naked (unencapsulated) ONs do not display any detectable anti-cell proliferation activity while encapsulated ONs display potent inhibition of cell proliferation.
  • Several different delivery agents do not give the same activity, some are very active and others totally inactive.
  • some delivery agents are only active in a selected cell lines while others have broad spectrum activity in all cell lines tested.
  • the need for a specific delivery agent may indicate that the ON has to be delivered inside the cell to specific compartments and/or freed from the delivery agent inside the cell for the anti-proliferative activity to be realized.
  • PEI polyethyleneimine
  • the present invention discloses the use of sequence independent ONs encapsulated with PEI as part of a formulation for the treatment of cellular proliferation diseases.
  • One skilled in the art applying the teaching of the present invention could also use ONs with different chemical modifications.
  • a modification of the ON such as, but not limited to, a phosphorothioate modification or other sulfur modifications, could be beneficial for anti-cell proliferation activity.
  • Such sulfur modifications may include without restriction mono and diphosphorothioation of the phosphodiester linkage, 4' or 5' thiolation of the uracil moiety, 5' thiolation of the cytidine moiety, 2' or 4' thiolation of the thymine moiety, 6' thiolation of the guanine moiety, sulfur modifications to any other nucleobase moiety and sulfur modification to the ribose moiety of any nucleotide.
  • ONs of the present invention may have more than one sulfur substitution on each nucleotide, which can potentially increase the activity.
  • any single or multiple sulfur substitution may be combined with other modifications known to improve properties of ONs.
  • ONs of this invention may also have chemical modifications including without restriction: any T ribose modification including 2'-0 methyl, 2'-fluorine, 2'-FANA, 2'-methoxyethyl, locked nucleic acids, methylphosphonates and phosphorodiamidate morpholino oligomers.
  • ONs may have a structure of or comprise a portion consisting of glycol nucleic acid (GNA) with an acyclic propylene glycol phosphodiester backbone forms stable antiparallel duplexes following the Watson-Crick base pairing rules (Zhang L, et al, 2005, J. Am. Chem. Soc. 127: 4174-4175).
  • GNA glycol nucleic acid
  • Such GNA may comprise phosphorothioate linkages.
  • the encapsulation agent or delivery system described in this invention comprises alone or in combination and without restriction cationic or polycationic molecules, cationic lipids, cationic polymers.
  • Cationic polymers include without restriction PEI, branched-PEI, linear-PEI, conjugated PEI, PEI conjugated with polyethylene glycol (PEG) and PEI conjugated with cyclodextrine.
  • the encapsulation agent or delivery system may also include without restriction dimyristoylamidoglycyl-N-isopropoxycarbonyl-arginine dihydrochloride (G.S.
  • One aspect of the present invention provides an encapsulated anti-cell proliferation ON targeting cancer cells or cells involved in proliferation diseases.
  • Such encapsulated ON comprises at least one active encapsulated ON and is adapted for use as an anti-cell proliferation agent.
  • the encapsulation agent used with the ON is PEI, more preferably in a linear form, more preferably with a molecular weight greater the 2,000Da and less than 50,000Da and more preferably with an average molecular weight of 23,000Da.
  • the encapsulated ONs of this invention may be in the form of a formulation targeting cancer cells or cells involved in proliferation diseases.
  • Such formulation comprises at least one active encapsulated ON and is adapted for use as an anti-cell proliferation agent.
  • the encapsulation agent used with the ON described in this formulation is PEI, more preferably in a linear form, more preferably with a molecular weight greater the 2,000Da and less than 50,000Da and more preferably with an average molecular weight of 23,000Da.
  • the encapsulated ONs of this invention may be in the form of a pharmaceutical composition useful for treating (or prophylaxis of) cancer and other cell proliferation diseases, which may be approved by a regulatory agency for use in humans or in non-human animals, and/or against a particular cancer.
  • Such pharmaceutical composition comprises at least one therapeutically active encapsulated ON and is adapted for use as an anti-cell proliferation agent.
  • the encapsulation agent used with the ON described in this composition is PEI, more preferably in a linear form, more preferably with a molecular weight greater the 2,000Da and less than 50,000Da and more preferably with an average molecular weight of 23,000Da.
  • This pharmaceutical composition may include physiologically and/or pharmaceutically acceptable carrier. A person skilled in the art would appreciate that the carrier would be adapted depending on the route of administration.
  • the pharmaceutical composition of the invention may also contain other active factors and/or agents and/or molecules which enhance activity.
  • the invention provides a kit that includes at least one encapsulated ON, ON mixture, ON formulation, or pharmaceutical composition that includes such ON, ON mixture, or ON formulation in a labeled package, where the label on the package indicates that the ON can be used against at least one disease or condition described herein.
  • the kit includes a pharmaceutical composition that includes at least one ON as described herein.
  • the kit contains a mixture of at least two different ONs.
  • the ON is adapted for in vivo use in an animal and/or the label indicates that the ON or composition is acceptable and/or approved for use in an animal; the animal is a mammal, such as human, or a non-human mammal such as bovine, porcine, a ruminant, ovine, or equine; the animal is a non-human animal; the animal is a bird, and the kit is approved by a regulatory agency such as the U.S. Food and Drug Administration or equivalent agency for use in an animal, e.g., a human.
  • a regulatory agency such as the U.S. Food and Drug Administration or equivalent agency for use in an animal, e.g., a human.
  • a method for the prophylaxis or treatment of cancer in a subject by administering to a subject in need of such treatment a therapeutically effective amount of at least one pharmacologically acceptable encapsulated ON as described herein, e.g., an ON at least 6 nucleotides in length, or a pharmaceutical composition or formulation or mixture containing such ON(s).
  • a pharmacologically acceptable encapsulated ON as described herein, e.g., an ON at least 6 nucleotides in length, or a pharmaceutical composition or formulation or mixture containing such ON(s).
  • Administration of the encapsulated ONs of this invention used in the pharmaceutical composition or formulation or to practice a method of treating a human or an animal can be carried out in a variety of conventional ways for example using oral ingestion, oral mucosal delivery, intranasal drops or spray, intraocular injection, subconjunctival injection, eye drops, ear drops, by inhalation, intratracheal injection or spray, intrabronchial injection or spray, intrapleural injection, intraperitoneal injection perfusion or irrigation, intrathecal injection or perfusion, intracranial injection or perfusion, intramuscular injection, intravenous injection or perfusion, intraarterial injection or perfusion, intralymphatic injection or perfusion, subcutaneous injection or perfusion, intradermal injection, topical skin application, by organ perfusion, by topical application during surgery, intratumoral injection, topical application, gastric injection perfusion or irrigation, enteral injection or perfusion, colonic injection perfusion or irrigation, rectal injection perfusion or irrigation, by rectal suppository or enema
  • the pharmaceutical composition or ON formulation of the present invention may further contain other chemotherapeutic drugs for the treatment of cancer and other cell proliferation diseases.
  • additional factors and/or agents may be included in the pharmaceutical composition, for example, to produce a combined, complementary or synergistic effect with the ONs of the invention.
  • sequence independent ON sequence portion(s) of the encapsulated ON is/are coupled with antisense sequence portion(s) to increase the activity of the final ON.
  • the non-specific portion of the ON is described in the present invention.
  • the antisense portion can be complementary to an oncogene mRNA or to other genes important for cell proliferation or for the progression of cancers.
  • sequence independent sequence portion(s) of the encapsulated ON is/are coupled with a G-rich motif ON portion(s) to improve the activity of the final ON.
  • the non-specific portion of the ON is described in the present invention.
  • the G-rich motif portion can, as non-limiting examples, include, CpG, Gquartet, and/or CG that are described in the literature as stimulators of the immune system.
  • an ON composed of one or more types of non- Watson- Crick nucleotides/nucleosides.
  • Such ONs can mimic PS-ONs and other modifications with some of the following characteristics similar to PS-ONs: a) the total charge; b) the space between the units; c) the length of the chain; d) a net dipole with accumulation of negative charge on one side; e) the ability to bind to proteins; f) the ability to be encapsulated with delivery systems; h) an acceptable therapeutic index and i) an anti-cell proliferation activity.
  • the ON can have a phosphorothioate backbone but is not limited to it.
  • the present invention involves the discovery that oligonucleotides (ONs), e.g., oligodeoxynucleotides (ODNs), including modified oligonucleotides, can have a therapeutic application through a sequence independent mode of action. It is not necessary for the oligonucleotide to be complementary to any sequence or to have a particular distribution of nucleotides in order to have activity.
  • ONs oligonucleotides
  • ODNs oligodeoxynucleotides
  • modified oligonucleotides can have a therapeutic application through a sequence independent mode of action. It is not necessary for the oligonucleotide to be complementary to any sequence or to have a particular distribution of nucleotides in order to have activity.
  • oligonucleotide agents that can have activity against diseases and conditions described herein. Such agents are particularly advantageous in view of the limited therapeutic options currently available.
  • oligonucleotides useful in the present invention can be of various lengths, e.g., at least 10, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 50, 60, 70, 80, 90, 100, 1 10, 120, 140, 160, or more nucleotides in length.
  • the oligonucleotide can be in a range, e.g., a range defined by taking any two of the preceding listed values as inclusive end points of the range, for example 10-20, 20-30, 20- 40, 30-40, 30-50, 40-50, 40-60, 40-80, 50-60, 50-70, 60-70, 70-80, 60-120, and 80-120 nucleotides.
  • a minimum length or length range is combined with any other of the oligonucleotide specifications listed herein for the present oligonucleotides.
  • the nucleotide can include various modifications, e.g., stabilizing modifications, and thus can include at least one modification in the phosphodiester linkage and/or on the sugar, and/or on the base.
  • the oligonucleotide can include one or more phosphorothioate linkages, phosphorodithioate linkages, and/or methylphosphonate linkages.
  • Different chemically compatible modified linkages can be combined, e.g., modifications where the synthesis conditions are chemically compatible.
  • the oligonucleotides can include phosphodiester linkages, e.g., include at least one phosphodiester linkage, or at least 5, 10, 20, 30% or more phosphodiester linkages.
  • Additional useful modifications include, without restriction, modifications at the T- position of the sugar, such as 2'-O-alkyl modifications such as 2'-O-methyl modifications, T- amino modifications, 2'-halo modifications such as 2'-fluoro; acyclic nucleotide analogs. Other modifications are also known in the art and can be used.
  • the oligonucleotide has modified linkages throughout, e.g., phosphorothioate; has a 3'- and/or 5'- cap; includes a terminal 3'-5' linkage; the oligonucleotide is or includes a concatemer consisting of two or more oligonucleotide sequences joined by a linker(s).
  • the present invention further provides an oligonucleotide linked or conjugated at one or more nucleotide residues, to a molecule modifying the characteristics of the oligonucleotide to obtain one or more characteristics selected from the group consisting of higher stability, lower serum interaction, higher cellular uptake, higher protein interaction, an improved ability to be formulated for delivery, a detectable signal, higher activity, better pharmacokinetic properties, specific tissue distribution, lower toxicity.
  • the oligonucleotide includes at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 95, or 100% modified linkages, e.g., phosphorothioate, phosphorodithioate, and/or methylpho sphonate .
  • modified linkages e.g., phosphorothioate, phosphorodithioate, and/or methylpho sphonate .
  • at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 95%, or all of the nucleotides are modified at the 2'-position of the ribose, e.g., 2'-0Me, 2'-F, 2 '-amino.
  • modified linkages are combined with 2 '-modifications in oligonucleotides, for example, at least 30% modified linkages and at least 30% 2 '-modifications; or respectively at least 40% and 40%, at least 50% and 50%, at least 60% and 60%, at least 70% and 70%, at least 80% and 80%, at least 90% and 90%, 100% and 100%.
  • the oligonucleotide includes at least 30, 40, 50, 60, 70, 80, 90, or 100% modified linkages and at least 30, 40, 50, 60, 70, 80, 90, or 100% 2 '-modifications where embodiments include each combination of listed modified linkage percentage and 2 '-modification percentage (e.g., at least 50% modified linkage and at least 80% 2 '-modifications, and at least 80% modified linkages and 100% 2 '-modifications).
  • the modified linkages are phosphorothioate linkages; the modified linkages are phosphorodithioate linkages; the 2 '-modifications are 2'-OMe; the 2 '-modifications are 2'-fluoro; the 2 '-modifications are a combination of 2'-OMe and 2'-fluoro; the modified linkages are phosphorothioate linkages and the 2' -modifications are 2'-OMe; the modified linkages are phosphorothioate linkages and the 2'-modifications are 2'-fluoro; the modified linkages are phosphorodithioate linkages and the 2 '-modifications are 2'-OMe; the modified linkages are phosphorodithioate linkages and the 2' -modifications are 2'-OMe; the modified linkages are phosphorodithioate linkages and the 2' -modifications are 2'-fluoro; the modified linkages are phosphorodithioate linkages and the
  • the oligonucleotide is at least 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 110, or 120 nucleotides in length, or is in a length range defined by taking any two of the specified lengths as inclusive endpoints of the range.
  • all but 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 of the internucleotidic linkages and/or 2'-positions of the ribose moiety are modified, e.g., with linkages modified with phosphorothioate, phosphorodithioate, or methylphosphonate linkages and/or 2'-0Me, 2'-F, and/or 2'-amino modifications of the ribose moiety.
  • the oligonucleotide includes at least 1 , 2, 3, or 4 ribonucleotides, or at least 10, 20, 30, 40, 50, 60, 70, 80, 90%, or even 100% ribonucleotides.
  • the oligonucleotide includes non-nucleotide groups in the chain (i.e., form part of the chain backbone) and/or as side chain moieties, e.g., 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, or even more, or up to 5, 10, 20% or more of the chain moieties and/or side chain moieties.
  • the oligonucleotide is free of self-complementary sequences longer than 5, 8, 10, 15, 20, 25, 30 nucleotides; the oligonucleotide is free of catalytic activity, e.g., cleavage activity against RNA; the oligonucleotide does not induce an RNAi mechanism.
  • the oligonucleotide binds protein involved in a disease or condition described in the present invention ; the sequence of the oligonucleotide (or a portion thereof, e.g., at least 20, 30, 40, 50, 60, 70% or more) is derived from a genome; the activity of an oligonucleotide with a sequence derived from a genome is not superior to a randomer oligonucleotide or a random oligonucleotide of the same length; the oligonucleotide includes a portion complementary to a genome sequence and a portion not complementary to a genome sequence; unless otherwise indicated, the sequence of the oligonucleotide includes A(x), C(x), G(x), T(x), U(x), I(x), AC(x), AG(x), AT(x), AU(x), CG(x), CT(x), CU(x), GT(x), GU(x), TU(
  • the oligonucleotide is at least 10, 15, 20, 25, 29, 30, 32, 34, 35, 36, 38, 40, 45, 46, 50, 60, 70, 80, 90, 100, 110, 120, 140, or 160 nucleotides in length or is in a range defined by taking any two of the listed values as inclusive endpoints, or the length of the specified repeat sequence is at least a length or in a length range just specified);
  • the oligonucleotide includes a combination of repeat sequences (e.g., repeat sequences as specified above), including, for example, each combination of the above monomer and/or dimer repeats taken 2, 3, or 4 at a time;
  • the oligonucleotide is single stranded (RNA or DNA);
  • the oligonucleotide is double stranded (RNA or DNA);
  • the oligonucleotide includes at least one Gquartet or CpG portion;
  • the oligonucleotide includes a portion complementary to a
  • Oligonucleotides can also be used in combinations, e.g., as a mixture. Such combinations or mixtures can include, for example, at least 2, 3, 4, 5, 10, 20, 50, 100, 1000, 10000, 100,000, 1,000,000, or more different oligonucleotides, e.g., any combination of oligonucleotides are described herein. Such combinations or mixtures can, for example, be different sequences and/or different lengths and/or different modifications and/or different linked or conjugated molecules. In another embodiment, in such combinations or mixtures, a plurality of oligonucleotides having a minimum length or are in a length range as specified above for oligonucleotides.
  • the sequence of the oligonucleotide is not perfectly complementary to any equal length portion of the a genome sequence, or has less than 95, 90, 80, 70, 60, or 50% complementarity to any equal length portion of the genomic sequence, the oligonucleotide sequence does not consist essentially of polyA, polyC, polyG, polyT, Gquartet, or a TG-rich sequence.
  • TG-rich indicates that the sequence of the oligonucleotide consists of at least 50 percent T and G nucleotides, or if so specified, at least 60, 70, 80, 90, or 95% T and G, or even 100%.
  • the invention provides a mixture of oligonucleotides that includes at least two different oligonucleotides as described herein, e.g., at least 2, 3, 4, 5, 7, 10, 50, 100, 1000, 10,000, 100,000, 1,000,000, or even more.
  • oligonucleotide includes at least 20 linked nucleotides.
  • the oligonucleotide may also include additional, non-nucleotide moieties, which may form part of the backbone of the oligonucleotide chain. Unless otherwise indicated, when non-nucleotide moieties are present in the backbone, at least 10 of the linked nucleotides are contiguous.
  • sequence independent mode of action indicates that the particular biological activity is not dependent on a particular oligonucleotide sequence in the oligonucleotide.
  • the activity does not depend on sequence dependent hybridization such as with antisense activity, or a particular sequence resulting in a sequence dependent aptameric interaction.
  • non- sequence complementary mode of action indicates that the mechanism by which the material exhibits an effect is not due to hybridization of complementary nucleic acid sequences, e.g., an antisense effect.
  • sequence complementary mode of action means that the effect of a material involves hybridization of complementary nucleic acid sequences or sequence specific aptameric interaction.
  • sequence complementary mode of action means that the activity of the oligonucleotide satisfies at least one of the 3 tests provided herein.
  • the oligonucleotide satisfies test 1, test 2 or test 3; the oligonucleotide satisfies a combination of two of the tests, i.e , tests 1 & 2; tests 1 & 3 or tests 2 & 3; the oligonucleotide satisfies all of tests 1, 2, 3, and 4.
  • a related aspect concerns an oligonucleotide randomer or randomer formulation that contains at least one randomer, where the activity of the randomer occurs principally by a sequence independent, e.g., non-sequence complementary mode of action.
  • a randomer formulation can, for example, include a mixture of randomers of different lengths, e.g., at least 2, 3, 5, 10, or more different lengths, or other mixtures as described herein.
  • Example 1 PS-ON randomers inhibit the proliferation of human cancer cell lines.
  • this PS-ON randomer has the same anti-proliferative effects in several different human cancer cell lines suggests that it is working by interfering with a cellular mechanism common to all cells. Since this PS-ON randomer has no sequence identity (it is completely degenerate), its anti-proliferative activity probably results from some physio- chemical, sequence-independent property of ONs which interferes with mechanisms important in cell division. Alternatively, these small linear pieces of DNA could be recognized in the nucleus of the cell as DNA damage, resulting in the induction of apoptotic mechanisms in these cells. Furthermore, the fact that this effect was only highly potent with specific encapsulation reagents suggests that the intracellular DNA delivery with different encapsulation reagents is not the same and that ONs need to be delivered into an appropriate cellular compartment for it to be active.
  • ONs except where noted otherwise are synthesized at the University of Calgary Core DNA Services lab. ONs are prepared on a 1 or 15 ⁇ mol synthesis scale, deprotected and desalted on a 50cm SephadexTM G-25 column. For randomer oligo synthesis, adenine, guanosine, cytosine and thymidine amidites are mixed together in equivalent concentrations. This is done to maximize the randomness of incorporation at each position of the ONs during synthesis.
  • Jet PEITM 23k linear polyethyleneimine, M w approx. 23100, determined by size exclusion chromatography/multiple angle laser light scattering, SEC/MALLS, from PolyPlus, France
  • DOTAP l,2-Dioleoyl-3-Trimethylammonium-Pro ⁇ ane, Avanti Polar Lipids, U.S.A.
  • DOPE l ⁇ -Dilinoleoyl-sn-Glycero-S-Phosphoethanolamine, Avanti Polar Lipids
  • cholesterol SIGMA
  • TFX-IO DOPE + N,N,N',N'-tetramethyl-N,N'-bis(2-hydroxyethyl)-2,3- di(oleoyloxy)-l,4-butanediammonium iodide, Promega, U.S.A.
  • Fugene® 6 Fugene® 6 (Roche, USA)
  • Oligofectamine Invit
  • lipids were resuspended from dry powder in chloroform to 10mg/ml. These chloroform solutions were then mixed to give the desired proportions of agents. The chloroform was then evaporated under nitrogen and the dried lipid film was resuspended in aqueous buffer to 1 Omg/ml and diluted for use in encapsulation.
  • chloroform lipid-based encapsulation agents
  • the optimal ratio of DNA to encapsulation of an agent was defined as the amount of reagent which completely protects PS-ON randomers from serum interaction, determined as follows: a PS-ON randomer labeled at the 3' end with FITC using an inflexible linker (3 '-(6- Fluorescein) CPG) is used as the bait. This bait is diluted to 2nM in assay buffer (1 OmM Tris, pH7.2, 8OmM NaCl, 1OmM EDTA, 10OmM ⁇ -mercaptoethanol and 1% tween 20). The bait is then mixed with an appropriate amount of non-heat inactivated FBS to obtain saturated (complete) binding of the bait.
  • bait-serum complexes are challenged with unlabelled PS- ON randomer which competes away the bound (labeled) PS-ON randomer from the FBS.
  • the amount of encapsulation reagent which completely prevents this competition is the amount of reagent required to completely encapsulate the PS-ON randomer.
  • the bait-FBS interaction was monitored by fluorescence polarization using a TECAN Ultra plate reader.
  • Cells were plated from 2000-3000 cells per well in 96 well plates (depending on the cell line used) and allowed to proliferate in ⁇ -MEM supplemented with 10% FBS, penicillin and streptomycin. Encapsulated randomer ONs were added to cells 24 hours after plating and the cells were allowed to proliferate for 3 additional days. 3 days after dosing, cell number was determined by commassie blue quantification. Briefly, cells were fixed with 4% paraformaldehyde and 0.5% glutaraldehyde.
  • Example 3 Potency of various sizes of randomers with different encapsulations.
  • PS-ON randomers Since the anti-proliferative activity of PS-ON randomers is size dependent, this size dependence was consequently tested with a much finer size resolution using PS-ON randomers sized between 10 and 40 bases in length. These PS-ON randomers were complexed with PEI- 23 K and administered to different cell lines (Table 6). It was observed a marked drop in IC50 with PS-ON randomers greater than 10 bases, which began to plateau with randomers 15 bases or larger in all cell lines tested.
  • PEIs polyethelyene imines
  • results demonstrate that there was an optimum PEI size (for the sizes tested) for anti-proliferative activity, with linear PEIs in the 22-23kDa range having the most potent effect.
  • the size bracket for anti-proliferative activity of PEI with ONs is between 2,000 Da (exclusively) and 50,000 Da (exclusively) if linear or 25,000 Da if branched.
  • Example 6 Uptake into cells versus anti-proliferative effect of PS-ON randomers.
  • REP 2004 PS-ON (SEQ ID NO: 4) was tagged at the 5' end with FITC and subjected to encapsulation as described above. These complexes were incubated with various cell lines for either 6 or 24 hours, after which cells were washed 2X with phosphate buffered saline and then lysed. The concentration of REP 2004 in pmol/cell was determined in cell lysates using fluorometry with a standard curve of FITC-labelled REP 2004 (SEQ ID NO: 4) (Table 8).
  • DOTAP:DOPE (90/10) 1 20E-03 1 20E-03 567E-04 9 93 E-04 8 51 E-04 1 02E 03 3 66E-04 4 67E-04 8 49E-04 1 04E-03 2 44E-04 3 36E 04
  • DOTAP PEG-PE (99/1) 1 23E-03 1 65E-03 4 93E-04 8 50E-04 9 59 E-04 1 06E-03 2 65E-04 3 83E-04 8 34E-04 1 17E-03 2 36E-04 1 83E-04
  • FITC-labelled REP 2004 (SEQ ID NO: 4) was encapsulated and incubated with different cells as previously indicated. Cells were then fixed with 4% paraformaldehyde and the localization of FITC-labelled REP2004 (SEQ ID NO: 4) was visualized by epifluorescence microscopy (Tables 9-13). It was noted that those reagents which gave a diffuse nuclear staining were those which displayed the most potent anti-proliferative activity when complexed with PS- ON randomers.
  • results show that two effective reagents, PEI-23K and PEI-22K, gave a diffuse nuclear staining. All other reagents gave either a punctuate cytoplasmic, perinuclear staining or a non-diffuse nuclear staining or a nucleolar staining.
  • the non-diffuse staining could be characterized either as non-nucleolar or as a staining pattern similar to that seen with euchromatin staining by Hoechst.
  • Example 8 Encapsulated REP 2006 (SEQ ID NO: 6) has potent in vivo anti-cancer activity.
  • mice were treated with PEI-23K encapsulated REP 2006 on days 0-4, 7-11 , 13-17, and so on until the endpoint (morbidity) was reached.
  • the treatment of mice with 10mg/kg of PEI-23K encapsulated REP 2006 (SEQ ID NO: 6) resulted in a significant extension of the survival in mice with B16 tumours compared to untreated controls. (Fig. 1).
  • Example 9 Encapsulated defibrotide has antiproliferative activity.
  • defibrotide which is linear single stranded DNA harvested from an animal source and processed to have an average size of 50 bases.
  • Defibrotide was encapsulated by PEI-23K and when so encapsulated, displayed potent anti-proliferative activity in HeLa cells with an IC50 of 0.77 ⁇ g/ml.
  • Non-encapsulated defibrotide had no anti-proliferative activity. This example suggests that any appropriately encapsulated linear DNA can have anti-proliferative activity.
  • Example 10 Encapsulated ONs induce apoptosis of HeIa cells
  • Example 11 Tests for the determination of encapsulated ONs have sequence-independent activity.
  • encapsulated ONs are sequence-independent
  • any one skilled in the art could prepare encapsulated sequence- specific ONs, for example an antisense ON targeting a specific mRNA, using the encapsulation reagents described herein.
  • an ON would have benefited from the encapsulation of sequence-independent ONs, has described herein.
  • An encapsulated ON shall be considered to have a reasonable part of its function due to sequence-independent activity if it meets the criteria of any one of the 2 tests outlined below
  • An encapsulated ON having a reasonable part of its function due to sequence-independent activity shall be considered to benefit from the inventions described herein.
  • the encapsulated ONs used in the following tests must be prepared following the general methodology described in example 13 for the synthesis of PS-ONs and in example 1 for the cellular proliferation assay.
  • This test serves to measure the anti-cell proliferation activity of an encapsulated, sequence-specific candidate ON when part of its sequence is made degenerate. If the degenerate version of the encapsulated candidate ON having the same chemistry retains its activity as described below, is it deemed to have sequence-independent activity.
  • Candidate encapsulated ONs will be made degenerate according to the following rule:
  • X the number of bases on each end of the ON to be made degenerate (but having the same chemistry as the candidate encapsulated ON)
  • X must be equal to or greater than 4
  • the IC50 generation will be performed using the assays described herein in example 1.
  • a control where only the transfection reagent is added to the cells (in equivalent concentration as would be present with an encapsulated ON) must be performed. This control must not demonstrate a toxic or antiproliferative effect greater than 15% of the untreated control in the range where the encapsulated ON is maximally effective.
  • IC50 values shall be generated using a minimum of seven concentrations of candidate ON (where the encapsulation reagent:DNA ratio is kept constant), with three or more points in the linear range of the dose response curve.
  • the IC50 of the encapsulated candidate ON shall be compared to its degenerate counterpart. If the IC50 of the partially degenerate encapsulated ON is less than 5 -fold greater than the original candidate encapsulated ON (based on minimum triplicate measurements, standard deviation not to exceed 15% of mean) then the ON shall be deemed to have sequence independent activity.
  • This test serves to compare the anti-cell proliferation activity of an encapsulated candidate ON with the anti-cell proliferation activity of an encapsulated randomer ON of equivalent size and chemistry.
  • the IC50 generation will be performed using the assays described herein in example 1.
  • a control where only the transfection reagent is added to the cells (in equivalent concentration as would be present with an encapsulated ON) must be performed. This control must not demonstrate a toxic or anti -proliferative effect greater than 15% of the untreated control in the range where the encapsulated ON is maximally effective.
  • IC50 values shall be generated using a minimum of seven concentrations of the candidate ON (where the encapsulation reagent:DNA ratio is kept constant), with three or more points in the linear range of the dose response curve.
  • the IC50 of the encapsulated candidate ON shall be compared to that of an encapsulated ON randomer of equivalent size and chemistry. If the IC50 of the encapsulated ON randomer is less than 5-fold greater than the candidate encapsulated ON (based on minimum triplicate measurements, standard deviation not to exceed 15% of mean) then the candidate encapsulated ON shall be deemed to have sequence independent activity.
  • a test to determinate if a candidate ON has a PEI-mediated antiproliferative activity has a PEI-mediated antiproliferative activity.
  • any one skilled in the art could prepare encapsulated sequence-specific ONs, for example an antisense ON targeting a specific mRNA, using the encapsulation reagents described herein.
  • an ON would have benefited from the present invention, i.e. of the requirement of specific reagents having the novel property of efficiently delivering DNA inside the nucleus (e.g. PEI) which is unrelated to their efficiency in delivering ONs inside cells (transfection).
  • An encapsulated ON shall be considered to utilize the novel properties of specific encapsulation reagents described herein (e.g. PEI) if it meets the criteria of any one of the test outlined below.
  • An encapsulated ON requiring the use of specific encapsulation reagents described herein shall be considered to benefit from the inventions described herein.
  • the encapsulated ONs used in the following tests must be prepared following the general methodology described in this example for the synthesis of PS-ONs and cell proliferation assay.
  • transfection reagents Commercially available which are used routinely to assess the antisense activity of sequence-specific ONs in transformed human cell lines (e.g. HeLa cells). These reagents include LipofectamineTM, Lipofectin®, Effectene TM, OligofectamineTM, FugeneTM and Polyfect®. It was established that on the basis of its ability to deliver DNA to the cell, PEI is only marginally efficient in delivery antisense ON and it has been well established by others in the field that any of these other reagents described above are efficient in delivering DNA to the cell and are sufficient for demonstrating antisense activity. Thus, if a candidate ON specifically requires the use of PEI for its anti-proliferative activity, such an encapsulated candidate ON shall be deemed to act through a PEI-mediated mode of action and thus to be benefiting from the inventions described herein.
  • the IC50 generation will be performed using the assays described herein in example 1.
  • a control where only the transfection reagent is added to the cells (in equivalent concentration as would be present with an encapsulated ON) must be performed. This control must not demonstrate a toxic or anti-proliferative effect greater than 15% of the untreated control in the range where the encapsulated ON is maximally effective.
  • IC50 values shall be generated using a minimum of seven concentrations of the candidate ON (where the encapsulation reagent: DNA ratio is kept constant), with three or more points in the linear range of the dose response curve.
  • the IC50 of the encapsulated candidate ON using at least three different encapsulation reagents including PEI shall be compared. If the IC50 of the PEI-encapsulated candidate ON is 2-fold smaller or less than the encapsulated candidate ONs using any other encapsulation reagent (based on minimum triplicate measurements, standard deviation not to exceed 15% of mean) then the candidate encapsulated ON shall be deemed to act through a PEI mediated mode of action. Thresholds used in tests
  • the thresholds described in tests 1, 2 and 3 above are the default thresholds. If specifically indicated, other thresholds can be used in the comparison tests described above. Thus for example, if specifically indicated, the threshold for determining whether an encapsulated ON is acting with sequence-independent activity or requires PEI for its activity can be any of 10-fold, 8-fold, 6-fold, 5-fold, 4-fold, 3-fold, 2-fold, 1.5-fold, or equal.
  • the encapsulated ON can be required to satisfy any two (e.g., tests 1 & 2, 1 & 3, 2 & 3,), or all 3 tests at a default threshold, or if specifically indicated, at another threshold(s) as indicated above.
  • the present oligonucleotides can by synthesized using methods known in the art. For example, unsubstituted and substituted phosphodiester (P-O) oligonucleotides can be synthesized on an automated DNA synthesizer (e.g., Applied Biosystems model 380B or Akta Oligopilot 100) using standard phosphoramidite chemistry with oxidation by iodine.
  • P-O phosphodiester
  • the thioation wait step can be increased to 68 sec, followed by the capping step.
  • the oligonucleotides can be purified by precipitating twice with 2.5 volumes of ethanol from a 0.5 M NaCl solution.

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Abstract

The present invention is concerned with the identification and use of encapsulated anti-cell proliferation oligonucleotides, with a delivery system, that act by a sequence independent mechanism. The present invention also disclosed the use of the oligonocleotides for the treatment of cancer and other cell proliferation related disease.

Description

Oligonucleotides inhibiting cell proliferation
TECHNICAL FIELD
[0001] The invention relates to a method for inhibiting cellular proliferation with oligonucleotides (ONs) encapsulated with a delivery system and acting predominantly by a sequence independent mode of action. The invention also relates to the use of ONs and encapsulated ONs as therapeutic agents, and more particularly for their use in methods of treatment and formulations for the treatment of cancer and other cell proliferation related diseases.
BACKGROUND OF INVENTION
[0002] Oligonucleotides (ONs) are short, typically single stranded nucleic acid fragments, designed to hybridize with a specific nucleic acid or protein target. ONs can be chemically modified in order to increase their stability and improve their pharmacokinetic behavior in vivo. Four mechanisms of action have been reported for sequence-specific activity of oligonucleotides: 1) complimentary ONs hybridizing according to Watson-Crick base pairing to specific mRNAs, which either block translation or induce mRNA degradation by RNAse H; 2) they can bind to genomic DNA in the nucleus and block transcription (Hoogsten-type base triplets); 3) complementary ONs can bind to splice sites in mRNA, preventing correct RNA splicing or preventing aberrant RNA splicing; 4) non-nucleic acid hybridization mechanism of action, also referred to as aptameric binding, where specific binding of an ON (aptamer) to a target protein occurs by nature of the three dimensional shape that a particular ON sequence adopts in solution, analogous to antibody-antigen recognition.
[0003] ONs are known to have certain non-sequence specific activities. The non-sequence specific effects of ON treatment have been described in simple in vitro systems. The mechanisms for these non sequence-specific effects of ONs may be related to (1) the structure of the ON itself, (2) hybridization to DNA or mRNA other than the target sequence, with subsequent RNase cleavage, (3) binding to proteins or other molecules, and/or (4) ON degradation products, which in themselves can affect cellular functions. Phosphorothioate ONs (PS-ONs) having four adjacent guanosine bases have also been shown to be growth-inhibitory. ONs have further been shown to bind proteins such as bFGF, VEGF, PKC, DNA polymerase, telomerase, HIV reverse transcriptase, tyrosine kinase, tyrosine kinase receptors and other proteins in a sequence- independent fashion. PS-ONs have also been reported to cause sequence-independent induction of tumor necrosis factor, induction of SpI binding activity, and inhibition of transferrin receptor expression.
[0004] The use of PS-ONs can create problems when interpreting data derived from in vitro and in vivo experiments. These problems are mainly due to the above mentioned non-sequence specific effects (Stein and Narayanan, 1994, Curr Opin Oncol. 6: 587-594). The requirements for antisense activity of ONs in vivo are: a) nuclease stability, b) entry into target cells, c) retention by target cells, d) ability to interact with their cellular targets, mRNA, pre-mRNA and genomic DNA and e) minimal non-sequence-specific interactions with other macromolecules (Stein and Cheng, 1993, Science 261: 1004-1012). Maximizing sequence specificity and minimizing sequence nonspecificity is a key element in designing therapeutically effective antisense ONs (Stein, 2001, J. Clin. Invest. 108: 641-644).
[0005] Many studies have described the use of ONs to inhibit cell proliferation or induce apoptosis by a sequence-dependent activity. In these studies, the negative control, being a sense ON, a mismatch ON or a scrambled ON, showed little or no activity.
[0006] In US patent No 5,286,717, it was shown that the c-myc antisense PS-ON provided a significant inhibition of HL60 cell proliferation as measured by cell count. This patent claims a compound for inhibiting the expression of an oncogene in a host, the compound comprising a mixed linkage PS-ON having a complementary base sequence with a portion of the c-myc oncogene. [0007] A study demonstrated that antisense PS-ONs targeting the mRNA of genes Ha-Ras, cHA-Ras and cKi-Ras substantially inhibited cell proliferation. However these inhibitions were specific to cell lines not necessarily to the reduction of the gene expression (Chen et al , 1996, J. Biol. Chem. 271 : 28259-28265).
[0008] Cioffi et al. (1997, MoI Pharmacol. 51 : 383-389) demonstrated that treatment of rat AlO cells with PS-ONs directed against A-Raf or C-Raf mRNA resulted in a potent and specific degradation of mRNA and inhibition of protein expression. In addition, ablation of these Raf isozymes by antisense ONs significantly reduced serum-induced proliferation.
[0009] Sequence-specific abrogation of c-Raf expression by PS-ONs showed the occurrence of classical apoptotic markers which was followed by cell death, affecting most of the cell population of lung, cervical, prostate and colon carcinoma cell lines (Lau et al , 1998, Oncogene 16: 1899-1902).
[0010] Down-regulation of HΕR2/neu expression using PS-ONs resulted in the activation of apoptotic cell death pathways in cells that overexpress HER2/neu in a sequence-specific fashion (Roh et al, 2000, Cancer Research 60: 560-565).
[001 1] A study reported that BcI- 2 antisense PS-ONs complexed with cationic cholesterol derivative liposomes were introduced into human cervix epithelial carcinoma cell lines, and mouse fibroblast NIH3T3 cells and showed induction of apoptosis (including necrosis in some cases). However, nonsense ONs corresponding to a scrambled-sequence control hardly induced apoptosis (Noguchi et al. , 2003, Journal of Controlled Release 88: 313-320).
[0012] Perez et al. (1994, Proc. Natl. Acad. Sci. USA 91 : 5957-5961) showed in diverse cell types that PS-ONs, independent of their base sequence, mediated the induction of a SpI transcription factor. This was dependant on the NF-kB activity, since inhibition of NF-kB activity abolished the PS-ON-induced SpI activity. [0013] Antisense PS-ON against the Bcr-Abl fusion gene showed significant inhibition of chronic myeloid leukemia cell lines compared to sense PS-ONs but the effect was independent of the type of breakpoint expressed in each cell line (O'brien et al, 1994, Leukemia 8: 2156-2162). Another group also suggested non-antisense mechanism of action using Bcr-Abl antisense phosphodiester-tailed methylphosphonate ONs (Toon et al, 1997, British Journal of haematology 96: 377-381).
[0014] Wang et al. (1996, J Clin Invest. 98: 443-450) examined the effects C28 PS-ON, a 28- mer PS cytidine homopolymer, on smooth muscle cell (SMC) proliferation induced by several SMC mitogens. C28 PS-ON significantly inhibited SMC proliferation induced by 10% FBS as well as the mitogens PDGF, bFGF, and EGF without cytotoxicity, without transfection agents or delivery systems and at concentration ranging from 2 to 20 uM giving a maximum of 76% reduction of proliferation in some cases.
[0015] Morassutti et al (1999, Biochimie 81 : 115-1 122) examined the ability of modified GTn ONs with different degrees of phosphorothioate modifications to bind specifically to the same nuclear proteins recognized by the GTn phosphodiester analogues and their cytotoxic effect on the human T-lymphoblastic CCRF-CEM cell line. They showed that the fully phosphorothioated GTn ON was neither able to specifically recognize those nuclear proteins, nor cytotoxic. In contrast, the 3'-phosphorothioate-protected GTn ONs were able to elicit a dose-dependent growth inhibition effect, but this activity was moderated by additional thioation of the backbone in these sequences.
[0016] It was reported by Xu et al. (2001, The Journal of Biological Chemistry 276: 43221- 43230) that G-rich ONs comprising a phosphodiester backbone and 3'-C3 aminoalkyl modifications could inhibit cell proliferation by inhibiting DNA replication in non-antisense manner.
[0017] Papucci et al. (2002, Antisense & Nucleic Acid Drug Development 12: 21-31) reported induction of apoptosis by transfecting cultured cells with unmodified ONs using DOTAP. Such effects of these ONs were mediated by a non-antisense mechanism that required the wild-type form of p53 and was dependent on ON concentration. Apoptosis induction appeared to be determined by the 3' and 5' free ends of ONs, which activated p53 independently from their sequence. The effective molar concentration resulting from their experiments was larger than 20μM.
[0018] In cultured cells, the internalization of naked ONs is generally inefficient but there are several examples in the literature where antisense effects have been achieved in vivo without a delivery system (Hughes et al, 2001, Drug Discovery Today 6: 303-315). Several groups described use of delivery systems for ONs mainly in cultured cell applications. These delivery systems include cationic molecules such as cationic lipid based systems such as DOTAP, DOTAP/DOPE, DOTAP/cholesterol, DOTAP/DOPE/Cholesterol, Pegylated-liposomes, dendrimers such as polyamidoamine, PLGA and PLA, cyclodextrins, polyethyleneimine and cationic cardiolipins (Jaaskelainen et al, 2000, Journal of Pharmaceutical Sciences 10: 187-193; Akhtar et al , 2000, Advanced Drug Delivery Reviews 44: 3-21; Hughes et al , 2001, Drug Discovery Today 6: 303-315; Dass, 2002, Journal of Pharmacy and Pharmacology 54: 3-27; Dass, 2002, Drug Delivery 9: 169-180).
[0019] Boussif and collaborators (Boussif et al, 1995, Proc. Natl. Acad. Sci. USA 92: 7297- 7301; US patent No 6,013,240) described the use of polyethyleneimine (PEI) as a transfection agent for ONs. They showed the delivery of an unmodified antisense ON against the start region of the chicken α-thyroid hormone receptor in cultured cells using PEI of molecular weight 80OkDa or 5OkDa. Later, Dheur et al. (1999, Antisense & Nucleic Acid Drug Development 9: 515-525) reported that PEI, which forms a very stable complex with a 20-mer PS-ON, did not enhance its antisense activity like it did with an unmodified ON. Jaaskelainen et al. (2000 Journal of Pharmaceutical Sciences 10: 187-193) also reported PEI 25kDa and PEI 80OkDa had no detectable effect as antisense PS-ON carriers. [0020] There are several methods for treating or preventing cellular proliferation-related diseases including cancer. However, a wide variety of diseases implicating cellular proliferation still cannot be cured or adequately controlled or prevented. In addition, the therapies currently available often result in serious side effects and toxicities.
[0021] There is a need for novel compounds, methods of treatment, and formulations to control cellular proliferation, such as cancer, and even more desirably in a wide spectrum of cancer subtypes.
SUMMARY OF THE INVENTION
[0022] The invention relates to a method for inhibiting cellular proliferation with oligonucleotides (ONs) encapsulated with a delivery system and acting predominantly by a sequence independent mode of action. The invention also relates to ONs and their use as therapeutic agents, and more particularly for their use in methods of treatment and formulations for the treatment of cancer and other cell proliferation related diseases.
[0023] One embodiment of the present invention is to provide an anti-cell proliferation encapsulated oligonucleotide formulation comprising at least one oligonucleotide and at least one delivery system, said oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity.
[0024] In another embodiment of the present invention, there is provided an anti-cell proliferation encapsulated oligonucleotide formulation comprising at least one oligonucleotide and at least one linear delivery system, said oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity, said activity acting through a PEI- mediated mode of action.
[0025] According to the present invention, the oligonucleotide formulation of the present invention comprises a mixture of at least two different oligonucleotides. [0026] Another embodiment of the present invention is to provide an anti-cell proliferation randomer oligonucleotide formulation, comprising at least one randomer oligonucleotide and at least one delivery system, said randomer oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity.
[0027] An additional embodiment of the present invention is to provide an anti-cell proliferation randomer oligonucleotide formulation, comprising at least one linear randomer oligonucleotide and at least one linear delivery system, said randomer oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity, and said activity acting through a PEI-mediated mode of action.
[0028] In one embodiment of the present invention, the oligonucleotide formulation of the present invention comprises a mixture of at least two randomer oligonucleotides of different lengths.
[0029] In one embodiment of the present invention, the delivery system comprises at least one cationic molecule. Preferably, the cationic molecule is a cationic lipid, most preferably the cationic is a cationic dendrimer. In addition, the cationic molecule is polyethyleneimine.
[0030] In accordance with the present invention, the polyethyleneimine is a mixture of linear polyethyleneimines. The mixture can comprise polyethyleneimines of molecular weight higher than 2,000 Da and lower than 50,000 Da. Further, said linear polyethyleneimines can have a molecular weight higher than 20,000Da and lower than 25,000 Da. In addition, said linear polyethyleneimines can have an average molecular weight in between 20,000Da and lower than 25,000 Da.
[0031] In a further embodiment of the present invention, the oligonucleotide formulation has an IC50 for inhibition of proliferating cells of 0.10 μM or less, of 0.05 μM or less, of 0.025 μM or less; or of 0.015 μM or less. [0032] Another embodiment of the present invention is to provide an oligonucleotide formulation, wherein said oligonucleotide is at least 10, 15, 20, 30, 40 or 50 nucleotides in length.
[0033] In another embodiment, the oligonucleotide formulation of comprises an oligonucleotide comprising at least one phosphodiester linkage.
[0034] In one embodiment of the present invention, the oligonucleotide formulation of contains an oligonucleotide comprising at least one modification to its chemical structure. In addition, the oligonucleotide can comprise at least two different modifications to its chemical structure. In another embodiment, one of said at least two different modifications is a sulfur modification, a phosphorothioated linkage, a phosphorodithioated linkage, a sulfur modified nucleobase moiety or is a sulfur modified ribose moiety.
[0035] In accordance with the present invention, the oligonucleotide used in the formulation comprises at least one T modification to the ribose moiety. In addition, said one T modification to the ribose moiety is a 2'-0 alkyl modified ribose moiety, a 2'-0 methyl modified ribose, a T- methoxyethyl modified ribose or a 2'-FANA modified ribose.
[0036] In accordance with the present invention, the oligonucleotide used in the formulation comprises at least one methylphosphonate linkage.
[0037] In accordance with the present invention, the oligonucleotide used in the formulation is a concatemer consisting of two or more oligonucleotide sequences joined by a linker.
[0038] In a further embodiment, the oligonucleotide is linked or conjugated at one or more nucleotide residues thereof to a molecule modifying the characteristics of the oligonucleotide to obtain one or more characteristics selected from the group consisting of higher stability, lower serum interaction, higher cellular uptake, an improved ability to be formulated for delivery, a detectable signal, higher anti-cell proliferation activity, better pharmacokinetic properties, specific tissue distribution and lower toxicity.
[0039] Preferably, the oligonucleotide comprised in the oligonucleotide formulation comprises at least one base which is capable of hybridizing via non- Watson-Crick interactions.
[0040] Preferably, the oligonucleotide comprised in the oligonucleotide formulation comprises at least one Gquartet motif portion.
[0041] In addition, the oligonucleotide comprised in the oligonucleotide formulation comprises at least one CpG motif portion.
[0042] In another embodiment of the present invention, the oligonucleotide formulation comprises an oligonucleotide comprising a portion complementary to an mRNA.
[0043] In a further embodiment, the oligonucleotide of the present invention comprises at least a portion of its sequence derived from a genome. The oligonucleotide having a portion of its sequence derived from a genome has an anti-cell proliferation activity that is predominantly a sequence independent mode of action. Further, The oligonucleotide formulation comprises an oligonucleotide having at most 90%, preferably 80%, more preferably 75% identity with a genomic sequence; at most 60%, preferably 50%, more preferably 40% identity with a genomic sequence.
[0044] In another embodiment of the present invention, the oligonucleotide formulation comprises an oligonucleotide having at least a portion of its sequence involved in an aptameric interaction with a cellular component.
[0045] In another embodiment of the present invention, the oligonucleotide formulation comprises an oligonucleotide having at least a portion of its sequence comprising polyA, polyC, polyG, polyT, polyAC, poly AG, polyAT, polyCG, polyCT, polyGT, polyU, PoIyAU, polyCU, poly GU or poly TU. [0046] According to the present invention, the oligonucleotide formulation comprises an oligonucleotide having at least a portion of its sequence comprising two or more repeated sequences.
[0047] In a further embodiment, the oligonucleotide formulation comprises a mixture of at least two different oligonucleotides. Preferably, the mixture is at least of 10 different oligonucleotides, of 100 different oligonucleotides, of 1000 different oligonucleotides, most preferably of 106 different oligonucleotides.
[0048] Another embodiment of the present invention is to provide an oligonucleotide formulation, wherein said different oligonucleotides are at least 10, 15, 20, 30, 40 or 50 nucleotides in length.
[0049] In accordance to the present invention, there is also provided an anti-cell proliferation pharmaceutical composition comprising a therapeutically effective amount of at least one pharmacologically acceptable anti-cell proliferation encapsulated oligonucleotide formulation according to the present invention; and a pharmaceutically acceptable carrier.
[0050] Preferably, the anti-cell proliferation pharmaceutical composition is adapted for the treatment, control, or prevention of a cell proliferation disease.
[0051] In a further embodiment, the anti-cell proliferation pharmaceutical composition of the present invention is adapted for delivery by a mode selected from the group consisting of ocular administration, oral ingestion, enteral administration, inhalation, cutaneous injection, subcutaneous injection, intramuscular injection, intraperitoneal injection, intrathecal injection, intratrachael injection, skin topical administration, rectal administration, vaginal administration, sublingual administration and intravenous injection.
[0052] In a further embodiment, the anti-cell proliferation pharmaceutical composition further comprises at least one other anti-cell proliferation drug in combination. [0053] In another embodiment, it is provided a use of a therapeutically effective amount of at least one pharmacologically acceptable anti-cell proliferation encapsulated oligonucleotide formulation according to the present invention for the prophylaxis or treatment of a cell proliferation disease in a subject. Preferably, the cell proliferation disease is cancer or tumor cells. Preferably, said subject is a human, a non-human animal or a plant.
[0054] In the context of the present invention, unless specifically limited the term "oligonucleotide (ON)" means oligodeoxynucleotide or oligodeoxyribonucleotide or oligoribonucleotide. Thus, "oligonucleotide" refers to an oligomer or polymer of ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA) and/or analogs thereof. This term includes oligonucleotides composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally-occurring portions which function similarly. Examples of modifications that can be used are described herein. Oligonucleotides that include backbone and/or other modifications can also be referred to as oligonucleosides. Except otherwise specified, oligonucleotide definition includes homopolymers, heteropolymers, randomers (see below), random sequence oligonucleotides, genomic-derived sequence oligonucleotides and oligonucleotides purified from natural source.
[0055] As used herein in connection with anti-cell proliferation action of a material, the phrase "sequence independent activity" or "sequence independent mode of action" indicates that the mechanism by which the material exhibits an anti-cell proliferation effect is not due to hybridization of complementary nucleic acid sequences, e.g., an antisense effect nor it is due to a sequence-specific aptameric activity. Conversely, a "sequence dependant mode of action or activity" means that the anti-cell proliferation effect of a material involves hybridization of complementary nucleic acid sequences or involves a sequence-specific aptameric interaction.
[0056] As used herein the term "anti-cell proliferation" means inhibiting or stopping the proliferation of dividing cells. The term also includes killing or inducing apoptosis of dividing cells. An anti-cell proliferation compound can be used to treat a cell proliferation disease. [0057] As used herein the term "cell proliferation disease" means a disease involving unwanted or uncontrolled proliferation of cells. Such cell proliferation diseases include, without limitation, cancer, restenosis, macular degeneration, unwanted angiogenesis, psoriasis, benign proliferative skin diseases, ichthyosis, papilloma, scleroderma, hemangioma, diabetic retinopathy, neovascular glaucoma and rheumatoid arthritis.
[0058] As used herein in connection with oligonucleotides or other materials, the term "anti- cell proliferation" refers to an effect of the presence of the encapsulated oligonucleotides or other material in inhibiting the proliferation of dividing cells, cancer or tumor cells, i.e., reducing the number of viable cells compared to untreated cells, in a system or organism otherwise suitable for growth of such cells. In certain embodiments of the present invention, the anticancer oligonucleotides will have anti-cell proliferation activity against multiple cell types.
[0059] The term "anti-cell proliferation encapsulated oligonucleotide formulation" refers to a preparation including at least one anti-cell proliferation encapsulated oligonucleotide that is adapted for use as an anti-cell proliferation agent. Briefly, the expression refers to a formulation comprising an encapsulated oligonucleotide having an anti proliferation activity on a cell. The formulation includes the oligonucleotide or oligonucleotides, and can contain other materials that do not interfere with use as an anti-cell proliferation agent in vivo. Such other materials can include without restriction diluents, excipients, carrier materials, delivery systems and/or other anti-cell proliferation materials.
[0060] As used herein, the term "pharmaceutical composition" refers to an anti-cell proliferation oligonucleotide formulation that includes a physiologically or pharmaceutically acceptable carrier or excipient. Such compositions can also include other components that do not make the composition unsuitable for administration to a desired subject, e.g., a human.
[0061] As used in connection with an anti-cell proliferation formulation, pharmaceutical composition, or other material, the phrase "adapted for use as an anti-cell proliferation agent" indicates that the material exhibits an anti-cell proliferation effect and does not include any component or material that makes it unsuitable for use in inhibiting cell proliferation in an in vivo system, e.g., for administering to a subject such as a human subject.
[0062] As used herein in connection with administration of an anti-cell proliferation material, the term "subject" refers to a living higher organism, including, for example, animals such as mammals, e.g., humans, non-human primates, non-human animals and plants, e.g., fruit trees.
[0063] In the present invention, the term "randomer" is intended to mean a single stranded nucleic acid, modified or not, having a wobble (N) at every position, such as NNNNNNNNNN. Each wobbled nucleotide position actually exists as a random population of the five naturally occurring bases on the nucleotide (adenine, guanine, cytosine, thymine, uracil) at this particular position, resulting in a completely degenerate pool of ONs of the same size but having no sequence identity as a population. Randomers can also include nucleobases which do not occur naturally including without restriction hypoxanthine, xanthosine, imidazole, 2-aninopurines, 5- nitroindole.
[0064] In the present invention, the term degenerate means that a sequence is made of a mix of nucleotides. A completely degenerated sequence means that A, C, G, and T (or other nucleobases) are used at each position of the sequence and nucleotide position are identified by N. Degenerate can apply to a sequence, a portion of a sequence or one nucleotide position in a sequence.
[0065] As used herein, the term "delivery system" refers to a component or components that, when combined with an ON as described herein, facilitates transfer of ONs inside cells, increases the amount of the ON that contacts the intended location in vivo, and/or extends the duration of its presence at the target, e.g., by at least 10, 20, 50, or 100%, or even more as compared to the amount and/or duration in the absence of the delivery system. The term delivery system also means encapsulation system or encapsulation reagent. To encapsulate ONs means to put in contact an ON with a delivery system or an encapsulation reagent. An ON in contact with a delivery system can be referred to as an "encapsulated ON". [0066] The term "therapeutically effective amount" refers to an amount that is sufficient to effect a therapeutically or prophylactically significant reduction in cell proliferation when administered to a typical subject of the intended type. In aspects involving administration of an anti-cell proliferation oligonucleotide to a subject, typically the oligonucleotide, formulation, or composition should be administered in a therapeutically effective amount.
[0067] The phrase "derived from a genome" indicates that a particular sequence has a nucleotide base sequence that has at least 70% identity to a genomic nucleotide sequence or its complement (e.g., is the same as or complementary to a genomic sequence), or is a corresponding RNA sequence. In particular embodiments of the present invention, the term indicates that the sequence is at least 70% identical to a genomic sequence of a particular gene involved in a disease or condition against which the oligonucleotide is directed, or to its complementary sequence. In particular embodiments, the identity is at least 80, 90, 95, 98, 99, or 100%. Genome can be from an animal, e.g. a human, from a microorganism, e.g. a virus, a bacteria, a parasite, or from plant.
BRIEF DESCRIPTION OF THE DRAWINGS
[0068] Fig. 1 illustrates the in vivo efficacy of 5% dextrose (1) compared to the efficacy of PEI 23k linear encapsulated REP 2006.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
[0069] The present invention is concerned with the identification and use of encapsulated anti- cell proliferation ONs that act by a sequence independent mechanism, and includes the discovery that for many proliferating cell types, the anti-proliferation activity is greater for larger ONs starting with 6mer ONs, and is typically optimal for ONs that are 15 nucleotides or more in length. [0070] As described hereinabove, a number of antisense ONs have been tested for anti-cell proliferation and induction apoptosis activity. However, such antisense ONs are typically sequence-specific targeting mRNA, and typically are about 16-25 nucleotides in length.
[0071] As demonstrated by the results in the examples submitted herewith, the anti-cell proliferation effect of encapsulated randomer ONs is sequence independent. Considering the volumes and concentrations of ONs used in these tests, it is theoretically impossible that a particular sequence is present at more than 1 copy in the mixture. This means that there can be no antisense or sequence-specific aptameric effect in these ONs randomers. In all examples, should the cell proliferation inhibition effect be caused by the sequence-specificity of the ONs, such effect would thus have to be caused by only one molecule, a result that does not appear possible. For example, for an ON randomer 40 bases in length, any particular sequence in the population would theoretically represent only 1/440 or 1/8.27X10"25 of the total fraction. Given that 1 mole = 6.022X1023 molecules, and the fact that our largest synthesis is currently done at the 15 micromole scale, all possible sequences will not be present and also, each sequence is present most probably as only one copy. Of course, one skilled in the art applying the teaching of the present invention could also use sequence specific ONs, but utilize the sequence independent activity discovered in the present invention.
[0072] In the present invention, randomers (or other random ONs) may inhibit cellular proliferation by several mechanisms, including but not limited to the following: 1) mimicking DNA damage in the nucleus of the cell by presenting DNA or RNA ends and then signaling to the cell to enter into apoptosis; 2) binding to cell proteins implicated in cell division or mitosis such as, but without limitation, cytoskeletal proteins, mitochondrial proteins, polymerases, DNA repair proteins or proteins involved in the apoptotic signaling cascade.
[0073] According to the discussion above and the data reported herein, it appears that encapsulated random ONs and ON randomers have broad-spectrum activity against many types of tumor cells and or cell lines. Therefore to test this hypothesis, several ON randomers of different sizes were selected to be tested in various cell lines.
[0074] As described in examples, naked (unencapsulated) ONs do not display any detectable anti-cell proliferation activity while encapsulated ONs display potent inhibition of cell proliferation. This demonstrates the requirement of a delivery system for the anti-proliferative activity of ONs. Several different delivery agents do not give the same activity, some are very active and others totally inactive. Moreover, some delivery agents are only active in a selected cell lines while others have broad spectrum activity in all cell lines tested. The need for a specific delivery agent may indicate that the ON has to be delivered inside the cell to specific compartments and/or freed from the delivery agent inside the cell for the anti-proliferative activity to be realized.
[0075] Since encapsulated ON randomers are sufficient for inhibition of cell proliferation, it is interesting to see if this activity can be maintained in the absence of the PS modification or in presence of other modifications. In examples, it is demonstrated that other modifications to ON randomers also result in anti-cell proliferation activity when these ONs are encapsulated. The observation that encapsulated single stranded DNA from a natural source has anti proliferation activity suggests that any appropriately encapsulated linear DNA have anti-proliferative activity.
[0076] Contrary to the use of polyethyleneimine (PEI) to deliver nucleic acid as described by Boussif et al. (1995, Proc. Natl. Acad. Sci. USA 92: 7297-7301) and in US patent No 6,013,240, the present invention describes the delivery of a sequence independent PEI-encapsulated ON compared to these two references describing the delivery of plasmid and antisense ONs which are sequence specific. A person skilled in the art would not predict the usefulness of using PEI to deliver non-sequence specific pieces of nucleic acids. This effect of PEI-encapsulated ONs on cell proliferation is unexpected from the previous art. Also, the present invention discloses the use of sequence independent ONs encapsulated with PEI as part of a formulation for the treatment of cellular proliferation diseases. [0077] One skilled in the art applying the teaching of the present invention could also use ONs with different chemical modifications. A modification of the ON, such as, but not limited to, a phosphorothioate modification or other sulfur modifications, could be beneficial for anti-cell proliferation activity. Such sulfur modifications may include without restriction mono and diphosphorothioation of the phosphodiester linkage, 4' or 5' thiolation of the uracil moiety, 5' thiolation of the cytidine moiety, 2' or 4' thiolation of the thymine moiety, 6' thiolation of the guanine moiety, sulfur modifications to any other nucleobase moiety and sulfur modification to the ribose moiety of any nucleotide. Moreover, ONs of the present invention may have more than one sulfur substitution on each nucleotide, which can potentially increase the activity. Finally, any single or multiple sulfur substitution may be combined with other modifications known to improve properties of ONs. ONs of this invention may also have chemical modifications including without restriction: any T ribose modification including 2'-0 methyl, 2'-fluorine, 2'-FANA, 2'-methoxyethyl, locked nucleic acids, methylphosphonates and phosphorodiamidate morpholino oligomers. Moreover ONs may have a structure of or comprise a portion consisting of glycol nucleic acid (GNA) with an acyclic propylene glycol phosphodiester backbone forms stable antiparallel duplexes following the Watson-Crick base pairing rules (Zhang L, et al, 2005, J. Am. Chem. Soc. 127: 4174-4175). Such GNA may comprise phosphorothioate linkages.
[0078] The encapsulation agent or delivery system described in this invention comprises alone or in combination and without restriction cationic or polycationic molecules, cationic lipids, cationic polymers. Cationic polymers include without restriction PEI, branched-PEI, linear-PEI, conjugated PEI, PEI conjugated with polyethylene glycol (PEG) and PEI conjugated with cyclodextrine. The encapsulation agent or delivery system may also include without restriction dimyristoylamidoglycyl-N-isopropoxycarbonyl-arginine dihydrochloride (G.S. 3815), (such as in Cytofectin™); 2,3-dioleyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-l- propanaminium trifluoroacetate (DOSPA) + DOPE (3:1), (such as in Lipofectamine 2000™); DOPE + CDAN (cholestrol derivative) (1 : 1), (such as in Trogene ™); and polyamidoamine dendrimers (such as in Polyfect™).
[0079] One aspect of the present invention provides an encapsulated anti-cell proliferation ON targeting cancer cells or cells involved in proliferation diseases. Such encapsulated ON comprises at least one active encapsulated ON and is adapted for use as an anti-cell proliferation agent. Preferably, the encapsulation agent used with the ON is PEI, more preferably in a linear form, more preferably with a molecular weight greater the 2,000Da and less than 50,000Da and more preferably with an average molecular weight of 23,000Da.
[0080] In another embodiment of the present invention, the encapsulated ONs of this invention may be in the form of a formulation targeting cancer cells or cells involved in proliferation diseases. Such formulation comprises at least one active encapsulated ON and is adapted for use as an anti-cell proliferation agent. Preferably, the encapsulation agent used with the ON described in this formulation is PEI, more preferably in a linear form, more preferably with a molecular weight greater the 2,000Da and less than 50,000Da and more preferably with an average molecular weight of 23,000Da.
[0081] In another aspect of the present invention, the encapsulated ONs of this invention may be in the form of a pharmaceutical composition useful for treating (or prophylaxis of) cancer and other cell proliferation diseases, which may be approved by a regulatory agency for use in humans or in non-human animals, and/or against a particular cancer. Such pharmaceutical composition comprises at least one therapeutically active encapsulated ON and is adapted for use as an anti-cell proliferation agent. Preferably, the encapsulation agent used with the ON described in this composition is PEI, more preferably in a linear form, more preferably with a molecular weight greater the 2,000Da and less than 50,000Da and more preferably with an average molecular weight of 23,000Da. This pharmaceutical composition may include physiologically and/or pharmaceutically acceptable carrier. A person skilled in the art would appreciate that the carrier would be adapted depending on the route of administration. The pharmaceutical composition of the invention may also contain other active factors and/or agents and/or molecules which enhance activity.
[0082] In another aspect, the invention provides a kit that includes at least one encapsulated ON, ON mixture, ON formulation, or pharmaceutical composition that includes such ON, ON mixture, or ON formulation in a labeled package, where the label on the package indicates that the ON can be used against at least one disease or condition described herein.
[0083] In particular embodiments the kit includes a pharmaceutical composition that includes at least one ON as described herein. In one embodiment, the kit contains a mixture of at least two different ONs. In a further embodiment, the ON is adapted for in vivo use in an animal and/or the label indicates that the ON or composition is acceptable and/or approved for use in an animal; the animal is a mammal, such as human, or a non-human mammal such as bovine, porcine, a ruminant, ovine, or equine; the animal is a non-human animal; the animal is a bird, and the kit is approved by a regulatory agency such as the U.S. Food and Drug Administration or equivalent agency for use in an animal, e.g., a human.
[0084] In yet another embodiment of the present invention, it is provided a method for the prophylaxis or treatment of cancer in a subject by administering to a subject in need of such treatment a therapeutically effective amount of at least one pharmacologically acceptable encapsulated ON as described herein, e.g., an ON at least 6 nucleotides in length, or a pharmaceutical composition or formulation or mixture containing such ON(s).
[0085] Administration of the encapsulated ONs of this invention used in the pharmaceutical composition or formulation or to practice a method of treating a human or an animal can be carried out in a variety of conventional ways for example using oral ingestion, oral mucosal delivery, intranasal drops or spray, intraocular injection, subconjunctival injection, eye drops, ear drops, by inhalation, intratracheal injection or spray, intrabronchial injection or spray, intrapleural injection, intraperitoneal injection perfusion or irrigation, intrathecal injection or perfusion, intracranial injection or perfusion, intramuscular injection, intravenous injection or perfusion, intraarterial injection or perfusion, intralymphatic injection or perfusion, subcutaneous injection or perfusion, intradermal injection, topical skin application, by organ perfusion, by topical application during surgery, intratumoral injection, topical application, gastric injection perfusion or irrigation, enteral injection or perfusion, colonic injection perfusion or irrigation, rectal injection perfusion or irrigation, by rectal suppository or enema, by urethral suppository or injection, intravesical injection perfusion or irrigation, or intraarticular injection.
[0086] The pharmaceutical composition or ON formulation of the present invention may further contain other chemotherapeutic drugs for the treatment of cancer and other cell proliferation diseases. Such additional factors and/or agents may be included in the pharmaceutical composition, for example, to produce a combined, complementary or synergistic effect with the ONs of the invention.
[0087] In another approach, sequence independent ON sequence portion(s) of the encapsulated ON is/are coupled with antisense sequence portion(s) to increase the activity of the final ON. The non-specific portion of the ON is described in the present invention. The antisense portion can be complementary to an oncogene mRNA or to other genes important for cell proliferation or for the progression of cancers.
[0088] In another approach, sequence independent sequence portion(s) of the encapsulated ON is/are coupled with a G-rich motif ON portion(s) to improve the activity of the final ON. The non-specific portion of the ON is described in the present invention. The G-rich motif portion can, as non-limiting examples, include, CpG, Gquartet, and/or CG that are described in the literature as stimulators of the immune system.
[0089] Another approach is to use an ON composed of one or more types of non- Watson- Crick nucleotides/nucleosides. Such ONs can mimic PS-ONs and other modifications with some of the following characteristics similar to PS-ONs: a) the total charge; b) the space between the units; c) the length of the chain; d) a net dipole with accumulation of negative charge on one side; e) the ability to bind to proteins; f) the ability to be encapsulated with delivery systems; h) an acceptable therapeutic index and i) an anti-cell proliferation activity. The ON can have a phosphorothioate backbone but is not limited to it. Examples of non-Watson-Crick nucleotides/nucleosides are described in Kool (2002, Ace. Chem. Res. 35: 936-943) and Takeshita et al. (1987, J. Biol. Chem. 262:10171-10179), where ONs containing synthetic abasic sites are described.
Oligonucleotides used in this invention
[0090] The present invention involves the discovery that oligonucleotides (ONs), e.g., oligodeoxynucleotides (ODNs), including modified oligonucleotides, can have a therapeutic application through a sequence independent mode of action. It is not necessary for the oligonucleotide to be complementary to any sequence or to have a particular distribution of nucleotides in order to have activity.
[0091] In addition, it is disclosed in the present invention that different length oligonucleotides have varying effect. For example, present results indicate that the length of oligonucleotide that produces maximal effect when modified with sulfur linkages is typically in the range of 30-120 nucleotides but not restricted to these length. In view of the present discoveries concerning properties of oligonucleotides, this invention provides oligonucleotide agents that can have activity against diseases and conditions described herein. Such agents are particularly advantageous in view of the limited therapeutic options currently available.
[0092] In one embodiment, oligonucleotides useful in the present invention can be of various lengths, e.g., at least 10, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 50, 60, 70, 80, 90, 100, 1 10, 120, 140, 160, or more nucleotides in length. Likewise, the oligonucleotide can be in a range, e.g., a range defined by taking any two of the preceding listed values as inclusive end points of the range, for example 10-20, 20-30, 20- 40, 30-40, 30-50, 40-50, 40-60, 40-80, 50-60, 50-70, 60-70, 70-80, 60-120, and 80-120 nucleotides. In particular embodiments, a minimum length or length range is combined with any other of the oligonucleotide specifications listed herein for the present oligonucleotides. [0093] In another embodiment of the present invention, the nucleotide can include various modifications, e.g., stabilizing modifications, and thus can include at least one modification in the phosphodiester linkage and/or on the sugar, and/or on the base. For example, the oligonucleotide can include one or more phosphorothioate linkages, phosphorodithioate linkages, and/or methylphosphonate linkages. Different chemically compatible modified linkages can be combined, e.g., modifications where the synthesis conditions are chemically compatible. While modified linkages are useful, the oligonucleotides can include phosphodiester linkages, e.g., include at least one phosphodiester linkage, or at least 5, 10, 20, 30% or more phosphodiester linkages. Additional useful modifications include, without restriction, modifications at the T- position of the sugar, such as 2'-O-alkyl modifications such as 2'-O-methyl modifications, T- amino modifications, 2'-halo modifications such as 2'-fluoro; acyclic nucleotide analogs. Other modifications are also known in the art and can be used. In particular embodiments, the oligonucleotide has modified linkages throughout, e.g., phosphorothioate; has a 3'- and/or 5'- cap; includes a terminal 3'-5' linkage; the oligonucleotide is or includes a concatemer consisting of two or more oligonucleotide sequences joined by a linker(s).
[0094] The present invention further provides an oligonucleotide linked or conjugated at one or more nucleotide residues, to a molecule modifying the characteristics of the oligonucleotide to obtain one or more characteristics selected from the group consisting of higher stability, lower serum interaction, higher cellular uptake, higher protein interaction, an improved ability to be formulated for delivery, a detectable signal, higher activity, better pharmacokinetic properties, specific tissue distribution, lower toxicity.
[0095] In one embodiment, the oligonucleotide includes at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 95, or 100% modified linkages, e.g., phosphorothioate, phosphorodithioate, and/or methylpho sphonate . [0096] In another embodiment of the present invention, at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 95%, or all of the nucleotides are modified at the 2'-position of the ribose, e.g., 2'-0Me, 2'-F, 2 '-amino.
[0097] In a further embodiment, modified linkages are combined with 2 '-modifications in oligonucleotides, for example, at least 30% modified linkages and at least 30% 2 '-modifications; or respectively at least 40% and 40%, at least 50% and 50%, at least 60% and 60%, at least 70% and 70%, at least 80% and 80%, at least 90% and 90%, 100% and 100%. In a further embodiment, the oligonucleotide includes at least 30, 40, 50, 60, 70, 80, 90, or 100% modified linkages and at least 30, 40, 50, 60, 70, 80, 90, or 100% 2 '-modifications where embodiments include each combination of listed modified linkage percentage and 2 '-modification percentage (e.g., at least 50% modified linkage and at least 80% 2 '-modifications, and at least 80% modified linkages and 100% 2 '-modifications). In a particular embodiment of each of the combinations percentages described, the modified linkages are phosphorothioate linkages; the modified linkages are phosphorodithioate linkages; the 2 '-modifications are 2'-OMe; the 2 '-modifications are 2'-fluoro; the 2 '-modifications are a combination of 2'-OMe and 2'-fluoro; the modified linkages are phosphorothioate linkages and the 2' -modifications are 2'-OMe; the modified linkages are phosphorothioate linkages and the 2'-modifications are 2'-fluoro; the modified linkages are phosphorodithioate linkages and the 2 '-modifications are 2'-OMe; the modified linkages are phosphorodithioate linkages and the 2' -modifications are 2'-fluoro; the modified linkages are phosphorodithioate linkages and the 2 '-modifications are a combination of 2'-OMe and 2'-fluoro. In a certain embodiment of oligonucleotides as described herein that combine a particular percentage of modified linkages and a particular percentage of 2 '-modifications, the oligonucleotide is at least 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 110, or 120 nucleotides in length, or is in a length range defined by taking any two of the specified lengths as inclusive endpoints of the range.
[0098] In another embodiment, all but 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 of the internucleotidic linkages and/or 2'-positions of the ribose moiety are modified, e.g., with linkages modified with phosphorothioate, phosphorodithioate, or methylphosphonate linkages and/or 2'-0Me, 2'-F, and/or 2'-amino modifications of the ribose moiety.
[0099] In one embodiment of the present invention, the oligonucleotide includes at least 1 , 2, 3, or 4 ribonucleotides, or at least 10, 20, 30, 40, 50, 60, 70, 80, 90%, or even 100% ribonucleotides.
[0100] In a particular embodiment, the oligonucleotide includes non-nucleotide groups in the chain (i.e., form part of the chain backbone) and/or as side chain moieties, e.g., 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, or even more, or up to 5, 10, 20% or more of the chain moieties and/or side chain moieties.
[0101] In a further embodiment, the oligonucleotide is free of self-complementary sequences longer than 5, 8, 10, 15, 20, 25, 30 nucleotides; the oligonucleotide is free of catalytic activity, e.g., cleavage activity against RNA; the oligonucleotide does not induce an RNAi mechanism.
[0102] According to the present invention, the oligonucleotide binds protein involved in a disease or condition described in the present invention ; the sequence of the oligonucleotide (or a portion thereof, e.g., at least 20, 30, 40, 50, 60, 70% or more) is derived from a genome; the activity of an oligonucleotide with a sequence derived from a genome is not superior to a randomer oligonucleotide or a random oligonucleotide of the same length; the oligonucleotide includes a portion complementary to a genome sequence and a portion not complementary to a genome sequence; unless otherwise indicated, the sequence of the oligonucleotide includes A(x), C(x), G(x), T(x), U(x), I(x), AC(x), AG(x), AT(x), AU(x), CG(x), CT(x), CU(x), GT(x), GU(x), TU(x), AI(x), IC(x), IG(x), IT(x) IU(x) where x is 2, 3, 4, 5, 6, ... 60 ... 120 (in particular embodiments the oligonucleotide is at least 10, 15, 20, 25, 29, 30, 32, 34, 35, 36, 38, 40, 45, 46, 50, 60, 70, 80, 90, 100, 110, 120, 140, or 160 nucleotides in length or is in a range defined by taking any two of the listed values as inclusive endpoints, or the length of the specified repeat sequence is at least a length or in a length range just specified); the oligonucleotide includes a combination of repeat sequences (e.g., repeat sequences as specified above), including, for example, each combination of the above monomer and/or dimer repeats taken 2, 3, or 4 at a time; the oligonucleotide is single stranded (RNA or DNA); the oligonucleotide is double stranded (RNA or DNA); the oligonucleotide includes at least one Gquartet or CpG portion; the oligonucleotide includes a portion complementary to a mRNA and is at least 29, 37, or 38 nucleotides in length (or other length as specified above); the oligonucleotide includes at least one non- Watson-Crick oligonucleotide and/or at least one nucleotide that participates in non- Watson-Crick binding with another nucleotide and/or at least one nucleotide that cannot form base pairs with other nucleotides; the oligonucleotide is a random oligonucleotide, the oligonucleotide is a randomer or includes a randomer portion, e.g., a randomer portion that has a length of at least 5, 10, 15, 20, 25, 30, 35, 40 or more contiguous oligonucleotides or a length as specified above for oligonucleotide length or at least 10, 20, 30, 40, 50, 60, 70, 80, 90% or all the nucleotides are randomer; the oligonucleotide is linked or conjugated at one or more nucleotide residues to a molecule that modifies the characteristics of the oligonucleotide, e.g. to provide higher stability (such as stability in serum or stability in a particular solution), lower serum interaction, higher cellular uptake, higher protein interaction, improved ability to be formulated for delivery, a detectable signal, improved pharmacokinetic properties, specific tissue distribution, and/or lower toxicity.
[0103] Oligonucleotides can also be used in combinations, e.g., as a mixture. Such combinations or mixtures can include, for example, at least 2, 3, 4, 5, 10, 20, 50, 100, 1000, 10000, 100,000, 1,000,000, or more different oligonucleotides, e.g., any combination of oligonucleotides are described herein. Such combinations or mixtures can, for example, be different sequences and/or different lengths and/or different modifications and/or different linked or conjugated molecules. In another embodiment, in such combinations or mixtures, a plurality of oligonucleotides having a minimum length or are in a length range as specified above for oligonucleotides. In a further embodiment of such combinations or mixtures, at least one, a plurality, or each of the oligonucleotides can have any of the other properties specified herein for individual oligonucleotides (which can also be in any consistent combination). [0104] According to the present invention, the sequence of the oligonucleotide is not perfectly complementary to any equal length portion of the a genome sequence, or has less than 95, 90, 80, 70, 60, or 50% complementarity to any equal length portion of the genomic sequence, the oligonucleotide sequence does not consist essentially of polyA, polyC, polyG, polyT, Gquartet, or a TG-rich sequence.
[0105] As used in connection with the present oligos, the term "TG-rich" indicates that the sequence of the oligonucleotide consists of at least 50 percent T and G nucleotides, or if so specified, at least 60, 70, 80, 90, or 95% T and G, or even 100%.
[0106] In a related aspect, the invention provides a mixture of oligonucleotides that includes at least two different oligonucleotides as described herein, e.g., at least 2, 3, 4, 5, 7, 10, 50, 100, 1000, 10,000, 100,000, 1,000,000, or even more.
[0107] Specification of particular lengths for oligonucleotides, e.g., at least 20 nucleotides in length, means that the oligonucleotide includes at least 20 linked nucleotides. Unless clearly indicated to the contrary, the oligonucleotide may also include additional, non-nucleotide moieties, which may form part of the backbone of the oligonucleotide chain. Unless otherwise indicated, when non-nucleotide moieties are present in the backbone, at least 10 of the linked nucleotides are contiguous.
[0108] As used herein in connection with the action of an oligonucleotide, "sequence independent mode of action" indicates that the particular biological activity is not dependent on a particular oligonucleotide sequence in the oligonucleotide. For example, the activity does not depend on sequence dependent hybridization such as with antisense activity, or a particular sequence resulting in a sequence dependent aptameric interaction. Similarly, the phrase "non- sequence complementary mode of action" indicates that the mechanism by which the material exhibits an effect is not due to hybridization of complementary nucleic acid sequences, e.g., an antisense effect. Conversely, a "sequence complementary mode of action" means that the effect of a material involves hybridization of complementary nucleic acid sequences or sequence specific aptameric interaction. Thus, indicating that the activity of a material is due to a sequence independent mode of action" or that the activity is "not primarily due to a sequence complementary mode of action" means that the activity of the oligonucleotide satisfies at least one of the 3 tests provided herein. In a particular embodiment, the oligonucleotide satisfies test 1, test 2 or test 3; the oligonucleotide satisfies a combination of two of the tests, i.e , tests 1 & 2; tests 1 & 3 or tests 2 & 3; the oligonucleotide satisfies all of tests 1, 2, 3, and 4.
[0109] A related aspect concerns an oligonucleotide randomer or randomer formulation that contains at least one randomer, where the activity of the randomer occurs principally by a sequence independent, e.g., non-sequence complementary mode of action. Such a randomer formulation can, for example, include a mixture of randomers of different lengths, e.g., at least 2, 3, 5, 10, or more different lengths, or other mixtures as described herein.
[0110] The present invention would be readily understood by referring to the following examples which are given to illustrate the invention rather than to limits its scope.
[011 1] ON that can be used, for example, without limitation, in the present invention are listed in the following.
Figure imgf000028_0001
Figure imgf000029_0001
Figure imgf000030_0001
Figure imgf000031_0001
Figure imgf000032_0001
Figure imgf000033_0001
Figure imgf000033_0002
Figure imgf000034_0001
Example 1 PS-ON randomers inhibit the proliferation of human cancer cell lines.
[0112] It is disclosed that a 21 base phosphorothioate ON (PS-ON) DB-CTL (SEQ ID NO: 124) randomer is able to inhibit the proliferation of several different human cancer cell lines (Table 1). This was also confirmed for REP 2004 (SEQ ID NO: 4) (Table 2) however this PS- ON randomer only displayed this anti-proliferative activity in all cell lines when encapsulated by reagents Lipofectamine™ 2000, Cytofectin™, DMRIE-C, Trogene™ or PEI-23K (linear polyethyleneimine. When encapsulated with several other reagents, all known to deliver DNA into the cell and routinely used for DNA transfection, little or no anti-proliferative effect is observed. Some cell lines reported herein have specific anti -proliferation activity with the 21 base PS-ON randomer with Polyfect™ (in G361 cells) and with Trogene™ (in MCF-7 and A549 cells).
Table 1
Antiproliferative activity of encapsulated 21 base randomer DB-CTL (SEQ ID NO 124)
(2 54ug/ml)
Figure imgf000036_0001
[0113] This experiment shows that delivery system such as but not limited to Polyfect™, Lipofectm™, Cytofectin™, DMRIE-C, Trogene™ or PEI-23K can be used with an ON of the present invention to inhibit the proliferation of cells with a sequence independent mode of action
Table 2 Antiproliferative activity of encapsulated REP 2004 (2ug/ml)
Figure imgf000037_0001
[01 14] This experiment shows that delivery system such as but not limited to Lipofectamine™ 2000, Cytofectin™, DMRIE-C, Trogene™, PEI-23K, DOTAP in combination, Lipofectin®, Superfect®, Effectene®, PEI-25kBr, PEI-22k linear, A-FECT, Metafectene, Transfect-AM- DOPE, Oligofectamine™, Captisol® and Polyfect™ can be used with an ON of the present invention to inhibit 20% and more the proliferation of cells with a sequence independent mode of action.
[01 15] The fact that this PS-ON randomer has the same anti-proliferative effects in several different human cancer cell lines suggests that it is working by interfering with a cellular mechanism common to all cells. Since this PS-ON randomer has no sequence identity (it is completely degenerate), its anti-proliferative activity probably results from some physio- chemical, sequence-independent property of ONs which interferes with mechanisms important in cell division. Alternatively, these small linear pieces of DNA could be recognized in the nucleus of the cell as DNA damage, resulting in the induction of apoptotic mechanisms in these cells. Furthermore, the fact that this effect was only highly potent with specific encapsulation reagents suggests that the intracellular DNA delivery with different encapsulation reagents is not the same and that ONs need to be delivered into an appropriate cellular compartment for it to be active.
Oligonucleotide synthesis
[01 16] All ONs (except where noted otherwise) are synthesized at the University of Calgary Core DNA Services lab. ONs are prepared on a 1 or 15 μmol synthesis scale, deprotected and desalted on a 50cm Sephadex™ G-25 column. For randomer oligo synthesis, adenine, guanosine, cytosine and thymidine amidites are mixed together in equivalent concentrations. This is done to maximize the randomness of incorporation at each position of the ONs during synthesis.
Oligonucleotide encapsulation
[0117] The following encapsulation agents, either alone or in combination, were used: Jet PEI™ (23k linear polyethyleneimine, Mw approx. 23100, determined by size exclusion chromatography/multiple angle laser light scattering, SEC/MALLS, from PolyPlus, France), DOTAP (l,2-Dioleoyl-3-Trimethylammonium-Proρane, Avanti Polar Lipids, U.S.A.), DOPE (l^-Dilinoleoyl-sn-Glycero-S-Phosphoethanolamine, Avanti Polar Lipids), cholesterol (SIGMA), TFX-IO (DOPE + N,N,N',N'-tetramethyl-N,N'-bis(2-hydroxyethyl)-2,3- di(oleoyloxy)-l,4-butanediammonium iodide, Promega, U.S.A.), Fugene® 6 (Roche, USA), Oligofectamine (Invitrogen, U.S.A.), Captisol® (heptasulfobutyl ether-b-cyclodextrin, from Cydex, U.S.A.), HCD (2-hydroxypropyl-β-cyclodextrin, from Sigma, U.S.A), PEI-25KBr (branched poly ethyleneimine, Mw=25000, Mn=IOOOO, from Sigma- Aldrich, U.S.A.), PEI-800K (linear polyethyleneimine, Mr=600000- 1000000, from Fluka, Germany), PEI-800, PEI- 1320, PEI-2000, PEI-50k (all linear, from Sigma. U.S.A.), Polyfect (dendrimers) from Qiagen, U.S.A., DMRIE-C (l,2-dimyristyloxypropyl-3-dimethyl-hydroxy ethyl ammonium bromide + cholesterol (1 : 1), from Invitrogen, U.S.A.), Cytofectin™ (dimyristoylamidoglycyl-N- isopropoxycarbonyl-arginine dihydrochloride [G. S. 3815), from Gene Therapy Systems Inc., U.S.A.), Lipofectamine 2000™ (2,3-dioleyloxy-N-[2(sperminecarboxamido)ethyl]-N,N- dimethyl-1-propanaminium trifluoroacetate (DOSPA) + DOPE (3:1), from Invitrogen, U.S.A.), Lipofectin™ (N-[I -(2,3- dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA) + DOPE (1 :1), from Invitrogen, U.S.A.), TROGENE™ (DOPE + CDAN (cholestrol derivative) (1 : 1), from Avanti Polar Lipids. U.S.A.), Superfect® (Qiagen, U.S.A.), Effectene® (Qiagen, U.S.A.), PEI-CAT (polyethelyeneimine catmer, from Sigma, U.S.A.), PEI-750KBr (branched polyethyleneimine Mw=750000, Mn=60000, from Sigma, U.S.A.), PEI-22K (linear polyethylene imine Mw=22000, from Fermentas, France), mPEG2000PE (l,2-Dioleoyl-sn-Glycero-3- Phosphoethanolamine-N-[Methoxy(Polyethylene glycol)-2000], from Avanti Polar Lipids, U.S.A.), mPEG2000 ceramide (N-Palmitoyl-Sphingosine-l-[Succinyl(MethoxyPolyethylene Glycol)2000], from Avanti Polar Lipids, U.S.A.), A-FECT (tetraether bilipid, from Berina, Germany).
[0118] To combine two or more lipid-based encapsulation agents (for example DOTAP and DOPE), lipids were resuspended from dry powder in chloroform to 10mg/ml. These chloroform solutions were then mixed to give the desired proportions of agents. The chloroform was then evaporated under nitrogen and the dried lipid film was resuspended in aqueous buffer to 1 Omg/ml and diluted for use in encapsulation.
[0119] For all reagents, DNA and the encapsulation reagent (both in aqueous buffer) were mixed and the encapsulation reaction was allowed to proceed for 20 min. These complexes were then added directly to cells (30ul / well of a 96 well plate). Lipofectin was preincubated in aqueous buffer for 30 minutes prior to mixing with the DNA.
Determining ratio of DNA: reagent required for optimal encapsulation
[0120] The optimal ratio of DNA to encapsulation of an agent was defined as the amount of reagent which completely protects PS-ON randomers from serum interaction, determined as follows: a PS-ON randomer labeled at the 3' end with FITC using an inflexible linker (3 '-(6- Fluorescein) CPG) is used as the bait. This bait is diluted to 2nM in assay buffer (1 OmM Tris, pH7.2, 8OmM NaCl, 1OmM EDTA, 10OmM β-mercaptoethanol and 1% tween 20). The bait is then mixed with an appropriate amount of non-heat inactivated FBS to obtain saturated (complete) binding of the bait. These bait-serum complexes are challenged with unlabelled PS- ON randomer which competes away the bound (labeled) PS-ON randomer from the FBS. The amount of encapsulation reagent which completely prevents this competition (i.e. no free unlabelled PS-ON randomer being present) is the amount of reagent required to completely encapsulate the PS-ON randomer. The bait-FBS interaction was monitored by fluorescence polarization using a TECAN Ultra plate reader.
Measuring cellular proliferation
[0121] Cells were plated from 2000-3000 cells per well in 96 well plates (depending on the cell line used) and allowed to proliferate in α-MEM supplemented with 10% FBS, penicillin and streptomycin. Encapsulated randomer ONs were added to cells 24 hours after plating and the cells were allowed to proliferate for 3 additional days. 3 days after dosing, cell number was determined by commassie blue quantification. Briefly, cells were fixed with 4% paraformaldehyde and 0.5% glutaraldehyde. After fixation, cells were stained with commassie blue (0.5% Coomassie Brilliant Blue R-250, 40% MeOH, 10% acetic acid in H2O) for 15 minutes followed by 2 X 10 minute washed in destain (30% MeOH, 10% acetic acid in H2O). After washing, bound coomassie dye was released from the cells with a solubilization solution (ImI HCl in 49ml isopropanol). The amount of dye released was quantified by absorbance spectroscopy at 570nm. This technique has been shown to be a direct quantative measure of cell number.
Measuring cellular viability
[0122] The metabolic activity of cells cultured and treated as described above was monitored 3 days after treatment by Alamar Blue conversion. The conversion of Alamar blue to its fluorescent form (a measure of mitochondrial activity) was measured at 545nm using a TECAN Ultra plate reader.
Measuring induction of apoptosis
[0123] The induction of apoptosis at 1, 2 or 3 days after treatment was monitored by measuring the activation of Caspases 3 and 7 using a commercially available assay kit (Promega).
Example 2 Effect of randomer modification on anti-proliferative activity.
[0124] To determine if the chemical modification of ON randomers was involved in their antiproliferative activity, 40 base ON randomers which contained different chemical modifications: unmodified (REP2015, SEQ ID NO: 15), phosphorothiate-modified (REP 2006, SEQ ID NO: 6), phosphorothiate/2-OMe gapmer modified (REP 2024, SEQ ID NO: 24) and phosphorothiate/2- OMe modified (2107, SEQ ID NO: 103) were encapsulated with either DOTAP or PEI-23K. These complexes were then tested for their anti-proliferative activity in several human cancers cell lines (Table 3). As predicted, it was observed little or no antiproliferative activity in any cell line with the DOTAP-randomer complexes. However, linear PEI-23K-randomer complexes displayed significant anti-proliferative activity in all cell lines tested. To verify that the activity of different ON randomers was dependent on their presence inside the cell, their antiproliferative activity was tested in the absence of any encapsulation in HeLa cells (Table 4) In all cases the cells were unperturbed by exposure to unencapsulated randomers.
Table 3
Effect of encapsulation reagent and randomer modification on anti-proliferative activity (2.54 ug/ml).
Figure imgf000042_0001
Table 4 Anti-proliferative activity of unencapsulated randomers (7.69 ug/ml)
Figure imgf000043_0001
Example 3 Potency of various sizes of randomers with different encapsulations.
[0125] In order to define the effect of various encapsulation reagents and randomer modifications on the anti-proliferative activity of encapsulated randomer complexes, dose response curves were generated in HeLa cells with a variety of encapsulation reagents, randomer modifications and randomer sizes (Table 5) which allowed to generate IC50 values for each complex (IC50 = the concentration of encapsulated ONs with has a 50% inhibition of cellular proliferation compared to untreated cells).
Table 5 Effect of randomer encapsulations and modifications on anti-proliferative activity in HeLa cells
Figure imgf000044_0001
[0126] In this experiment, it was clear that the activity was dependent on randomer size; with larger randomers being more active than smaller ones. The activity is not restricted to any type of chemical modification tested here. Results showed that PEI-23K linear encapsulated randomers were more potent compared to other encapsulation reagents.
Example 4 Effect of PS-ON randomer size on anti-proliferative activity.
[0127] Since the anti-proliferative activity of PS-ON randomers is size dependent, this size dependence was consequently tested with a much finer size resolution using PS-ON randomers sized between 10 and 40 bases in length. These PS-ON randomers were complexed with PEI- 23 K and administered to different cell lines (Table 6). It was observed a marked drop in IC50 with PS-ON randomers greater than 10 bases, which began to plateau with randomers 15 bases or larger in all cell lines tested.
[0128] To determine the potency of PS-ON randomers in different cancer cell lines, dose response curves for the anti-proliferative activity of the 40 base PS-ON randomer (REP 2006, SEQ ID NO: 6) encapsulated with PEI-23K were generated (Table 6).
Table 6
Effect of PEI-23K encapsulated randomers of different sizes on antiproliferative activity in different cell lines
Figure imgf000046_0001
[0129] In all the cell lines tested, these complexes were similarly active This demonstrated the anti-cancer potential of this complex in several different cancers Even if the antiproliferative activity is good with all sizes of ON, it is clear that most potent activity is reached at 15-16 base pair and more In the present application, an oligonucleotide having an IC50 below 3μM is considered to have good anti-prohferative activity and thus have utility Example 5 Effect of PEI size on anti-proliferative activity of PS-ON randomers
[0130] Since polyethelyene imines (PEIs) are available in a variety of different sizes, the optimum size PEI to maximize the anti-proliferative effect of encapsulated ONs was determined (Table 7).
Table 7 Effect of PEI size on anti-proliferative effect of PEI-encapsulated REP 2006 (SEQ ID NO: 6).
Figure imgf000047_0001
[0131] In this experiment, results demonstrate that there was an optimum PEI size (for the sizes tested) for anti-proliferative activity, with linear PEIs in the 22-23kDa range having the most potent effect. The size bracket for anti-proliferative activity of PEI with ONs is between 2,000 Da (exclusively) and 50,000 Da (exclusively) if linear or 25,000 Da if branched. Example 6 Uptake into cells versus anti-proliferative effect of PS-ON randomers.
[0132] Since so many encapsulation agents were not effective, it was decided to look at the relative delivery (uptake) into cells of REP 2004 (SEQ ID NO: 4) PS-ON in the presence of different encapsulation reagents.
[0133] REP 2004 PS-ON (SEQ ID NO: 4) was tagged at the 5' end with FITC and subjected to encapsulation as described above. These complexes were incubated with various cell lines for either 6 or 24 hours, after which cells were washed 2X with phosphate buffered saline and then lysed. The concentration of REP 2004 in pmol/cell was determined in cell lysates using fluorometry with a standard curve of FITC-labelled REP 2004 (SEQ ID NO: 4) (Table 8).
Table 8
OO
Figure imgf000049_0001
4-.
Figure imgf000050_0001
Table 8 Continued - delivery agents
Delivery agents 293A PC3 Du 145
10% serum 80% serum 10% serum 80% serum 10% serum 80% serum
6h 24h 6h I 24h 6h I 24h 6h 24h 6h 24h 6h I 24h
Rep2004-FL 1 30E-04 1 41 E-04 4 83E-05 4 44E-05 1 43E-04 9 40E-05 6 99E-05 4 46E-05 1 32E-04 7 43E-05 5 29E-05 3 43E-05
DOTAP 1 34E-04 1 59E-04 573E-04 1 13E-03 8 54E-04 1 1 1 E-03 2 97E-04 4 59E-04 8 57E-04 1 14E-03 2 35E-04 2 38 E-04
DOTAP:DOPE (50/50) 4 06E-04 3 95E-04 198E-04 2 46E-04 3 74E-04 3 23E-04 1 61 E-04 1 90E-04 3 48E-04 3 04E-04 1 53E-04 9 93E-05
DOTAP:DOPE (90/10) 1 20E-03 1 20E-03 567E-04 9 93 E-04 8 51 E-04 1 02E 03 3 66E-04 4 67E-04 8 49E-04 1 04E-03 2 44E-04 3 36E 04
DOTAP:cholesterol (50/50) 1 03E-03 1 15E-03 4 25E-04 5 56E-04 8 01 E-04 9 02 E-04 2 66E-04 2 68E-04 8 32E-04 5 82E-04 2 41 E-04 1 71 E-04
DOTAP:cholesterol (83/17) 1 17E-03 1 06E-03 5 82E-04 6 43E-04 8 20 E-04 7 90E-04 4 36E-04 3 53E-04 8 30E-04 4 84E-04 3 84E-04 2 39 E-04
DOTAP: PEG-PE (99/1) 1 23E-03 1 65E-03 4 93E-04 8 50E-04 9 59 E-04 1 06E-03 2 65E-04 3 83E-04 8 34E-04 1 17E-03 2 36E-04 1 83E-04
DOTAP:PEG-PE (90/10) 1 24E-03 1 54E-03 4 19E-04 5 28E-04 1 03E-03 9 70E-04 2 37E-04 2 67E-04 1 03E-03 1 05E-03 1 66E-04 1 86E-04
DOTAP:DOPE:PEG-PE (49.5/49 5/1 ) 6 15E-04 6 97E-04 1 58E-04 2 36E-04 5 78 E-04 5 46E-04 1 68 E-04 1 59E-04 5 53E-04 6 31 E-04 1 40E-04 9 17E-05
O
Figure imgf000051_0001
Figure imgf000052_0001
Figure imgf000053_0001
[0134] This data suggests that the localization of the delivered PS-ON is more important than the amount of PS-ON delivered.
Example 7 Effect of different encapsulation reagents on cellular localization of REP 2004 (SEQ ID
NO: 4).
[0135] FITC-labelled REP 2004 (SEQ ID NO: 4) was encapsulated and incubated with different cells as previously indicated. Cells were then fixed with 4% paraformaldehyde and the localization of FITC-labelled REP2004 (SEQ ID NO: 4) was visualized by epifluorescence microscopy (Tables 9-13). It was noted that those reagents which gave a diffuse nuclear staining were those which displayed the most potent anti-proliferative activity when complexed with PS- ON randomers.
Table 9 Localization of REP 2004 (SEQ ID NO- 4) in HeLa cells with different encapsulation reagents
Figure imgf000054_0001
Table 10 Localization of REP 2004 (SEQ ID NO: 4) in G361 cells with different encapsulation reagents.
Figure imgf000055_0001
Table 11 Localization of REP 2004 (SEQ ID NO: 4) in MCF-7 cells with different encapsulation reagents.
Figure imgf000056_0001
Table 12 Localization of REP 2004 in DU- 145 cells with different encapsulation reagents
Figure imgf000057_0001
Table 13 Localization of REP 2004 (SEQ ID NO: 4) in 293A cells with different encapsulation reagents.
Figure imgf000058_0001
[0136] In this experiment, results show that two effective reagents, PEI-23K and PEI-22K, gave a diffuse nuclear staining. All other reagents gave either a punctuate cytoplasmic, perinuclear staining or a non-diffuse nuclear staining or a nucleolar staining. The non-diffuse staining could be characterized either as non-nucleolar or as a staining pattern similar to that seen with euchromatin staining by Hoechst. These data suggest that the mode of action for ON encapsulated with PEI may be different than ON encapsulated with other encapsulating agents.
Example 8 Encapsulated REP 2006 (SEQ ID NO: 6) has potent in vivo anti-cancer activity.
[0137] The anti-cancer activity of encapsulated REP 2006 in vivo using an intraperitoneal model of cancer progression. B 16-Fl melanoma cells were cultured in vitro in tissue culture flasks using standard procedures. On Day 0, approximately 75 x 106 cells were collected and washed three times by low speed centrifugation in sterile Phosphate Buffer Saline (PBS). A cell suspension was then prepared at 5 x 106 cells/ml in PBS. Mice were inoculated intraperitoneally at day O with 106 B16-F1 cells (in 200 ul). Mice were treated with PEI-23K encapsulated REP 2006 on days 0-4, 7-11 , 13-17, and so on until the endpoint (morbidity) was reached. The treatment of mice with 10mg/kg of PEI-23K encapsulated REP 2006 (SEQ ID NO: 6) resulted in a significant extension of the survival in mice with B16 tumours compared to untreated controls. (Fig. 1).
Example 9 Encapsulated defibrotide has antiproliferative activity.
[0138] Since it is disclosed that encapsulated unmodified ONs can have anti-proliferative activity, it is hypothesized that any linear DNA would also have anti-proliferative effects. This hypothesis was tested using defibrotide, which is linear single stranded DNA harvested from an animal source and processed to have an average size of 50 bases. Defibrotide was encapsulated by PEI-23K and when so encapsulated, displayed potent anti-proliferative activity in HeLa cells with an IC50 of 0.77 μg/ml. Non-encapsulated defibrotide had no anti-proliferative activity. This example suggests that any appropriately encapsulated linear DNA can have anti-proliferative activity.
Example 10 Encapsulated ONs induce apoptosis of HeIa cells
[0139] To more clearly establish the pro-apoptotic action of PEI-encapsulated ONs, the induction of caspase activity in HeLa cells treated with PEI-23K encapsulated ONs was observed. For these experiments, a commercial caspase activity assay (Promega Capsase-GLO 3/7) was used (Table 14). Table 14 PEI-23K-encapsulated REP 2006 (SEQ ID NO 6) induces apoptosis in HeLa cells
Figure imgf000060_0001
[0140] A dose dependent increase in caspase activity measured 24h after treatment which was concomitant with increasing antiproliferative activity with PEI-23K encapsulated REP 2006 (SEQ ID NO 6). No caspase activation was seen with either REP 2006 (SEQ ID NO: 6) or PEI- 23K alone
Example 11 Tests for the determination of encapsulated ONs have sequence-independent activity.
[0141] It is shown herein that the anti-cell proliferation activity of encapsulated ONs is sequence-independent Of course any one skilled in the art could prepare encapsulated sequence- specific ONs, for example an antisense ON targeting a specific mRNA, using the encapsulation reagents described herein. However such an ON would have benefited from the encapsulation of sequence-independent ONs, has described herein. An encapsulated ON shall be considered to have a reasonable part of its function due to sequence-independent activity if it meets the criteria of any one of the 2 tests outlined below An encapsulated ON having a reasonable part of its function due to sequence-independent activity shall be considered to benefit from the inventions described herein. The encapsulated ONs used in the following tests must be prepared following the general methodology described in example 13 for the synthesis of PS-ONs and in example 1 for the cellular proliferation assay.
[0142] In each test the encapsulating agent and the ratio of encapsulating agent to DNA (massrmass) is the same for all encapsulated ONs that are compared.
TEST #1
Effect of partial degeneracy of an encapsulated, sequence-specific candidate ON on its anti-cell proliferation activity.
[0143] This test serves to measure the anti-cell proliferation activity of an encapsulated, sequence-specific candidate ON when part of its sequence is made degenerate. If the degenerate version of the encapsulated candidate ON having the same chemistry retains its activity as described below, is it deemed to have sequence-independent activity. Candidate encapsulated ONs will be made degenerate according to the following rule:
L = the number of bases in the candidate encapsulated ON
X = the number of bases on each end of the ON to be made degenerate (but having the same chemistry as the candidate encapsulated ON)
If L is even, then X=integer (L/4)
If L is odd, then X=integer ((L+l)/4)
X must be equal to or greater than 4
[0144] If the candidate encapsulated ON is claimed to have an anti-cell proliferation activity, the IC50 generation will be performed using the assays described herein in example 1. For the assay to be valid, a control where only the transfection reagent is added to the cells (in equivalent concentration as would be present with an encapsulated ON) must be performed. This control must not demonstrate a toxic or antiproliferative effect greater than 15% of the untreated control in the range where the encapsulated ON is maximally effective. IC50 values shall be generated using a minimum of seven concentrations of candidate ON (where the encapsulation reagent:DNA ratio is kept constant), with three or more points in the linear range of the dose response curve. Using these tests, the IC50 of the encapsulated candidate ON shall be compared to its degenerate counterpart. If the IC50 of the partially degenerate encapsulated ON is less than 5 -fold greater than the original candidate encapsulated ON (based on minimum triplicate measurements, standard deviation not to exceed 15% of mean) then the ON shall be deemed to have sequence independent activity.
TEST #2
Comparison of anti-cell proliferation activity of an encapsulated candidate ON with an encapsulated ON randomer.
[0145] This test serves to compare the anti-cell proliferation activity of an encapsulated candidate ON with the anti-cell proliferation activity of an encapsulated randomer ON of equivalent size and chemistry.
[0146] If the candidate encapsulated ON is claimed to have an anti-cell proliferation activity, the IC50 generation will be performed using the assays described herein in example 1. For the assay to be valid, a control where only the transfection reagent is added to the cells (in equivalent concentration as would be present with an encapsulated ON) must be performed. This control must not demonstrate a toxic or anti -proliferative effect greater than 15% of the untreated control in the range where the encapsulated ON is maximally effective. IC50 values shall be generated using a minimum of seven concentrations of the candidate ON (where the encapsulation reagent:DNA ratio is kept constant), with three or more points in the linear range of the dose response curve. Using this test, the IC50 of the encapsulated candidate ON shall be compared to that of an encapsulated ON randomer of equivalent size and chemistry. If the IC50 of the encapsulated ON randomer is less than 5-fold greater than the candidate encapsulated ON (based on minimum triplicate measurements, standard deviation not to exceed 15% of mean) then the candidate encapsulated ON shall be deemed to have sequence independent activity.
A test to determinate if a candidate ON has a PEI-mediated antiproliferative activity.
[0147] It is shown herein that the efficient induction of apoptosis and inhibition of cellular proliferation require specific delivery into appropriate cellular compartments using appropriate encapsulation reagents. Moreover, it is demonstrated that many encapsulation reagents normally used for the encapsulation and delivery of ONs inside cells (transfection reagents) do not result in anti-proliferative activity when used to encapsulate sequence-independent ONs, even though they efficiently deliver ONs inside the cell and have been shown to be sufficient for demonstrating antisense activity of sequence-specific ONs in cell culture. Of course any one skilled in the art could prepare encapsulated sequence-specific ONs, for example an antisense ON targeting a specific mRNA, using the encapsulation reagents described herein. However such an ON would have benefited from the present invention, i.e. of the requirement of specific reagents having the novel property of efficiently delivering DNA inside the nucleus (e.g. PEI) which is unrelated to their efficiency in delivering ONs inside cells (transfection). An encapsulated ON shall be considered to utilize the novel properties of specific encapsulation reagents described herein (e.g. PEI) if it meets the criteria of any one of the test outlined below. An encapsulated ON requiring the use of specific encapsulation reagents described herein (e.g PEI) shall be considered to benefit from the inventions described herein. The encapsulated ONs used in the following tests must be prepared following the general methodology described in this example for the synthesis of PS-ONs and cell proliferation assay.
[0148] In each test the encapsulating agent and the ratio of encapsulating agent to DNA (mass:mass) is the same for all encapsulated ONs that are compared. Test #3 Requirement of PEI for the anti-cell proliferation activity of an encapsulated candidate ON.
[0149] There are several transfection reagents commercially available which are used routinely to assess the antisense activity of sequence-specific ONs in transformed human cell lines (e.g. HeLa cells). These reagents include Lipofectamine™, Lipofectin®, Effectene ™, Oligofectamine™, Fugene™ and Polyfect®. It was established that on the basis of its ability to deliver DNA to the cell, PEI is only marginally efficient in delivery antisense ON and it has been well established by others in the field that any of these other reagents described above are efficient in delivering DNA to the cell and are sufficient for demonstrating antisense activity. Thus, if a candidate ON specifically requires the use of PEI for its anti-proliferative activity, such an encapsulated candidate ON shall be deemed to act through a PEI-mediated mode of action and thus to be benefiting from the inventions described herein.
[0150] If the candidate encapsulated ON is claimed to have an anti-cell proliferation activity, the IC50 generation will be performed using the assays described herein in example 1. For the assay to be valid, a control where only the transfection reagent is added to the cells (in equivalent concentration as would be present with an encapsulated ON) must be performed. This control must not demonstrate a toxic or anti-proliferative effect greater than 15% of the untreated control in the range where the encapsulated ON is maximally effective. IC50 values shall be generated using a minimum of seven concentrations of the candidate ON (where the encapsulation reagent: DNA ratio is kept constant), with three or more points in the linear range of the dose response curve. Using this test, the IC50 of the encapsulated candidate ON using at least three different encapsulation reagents including PEI, shall be compared. If the IC50 of the PEI-encapsulated candidate ON is 2-fold smaller or less than the encapsulated candidate ONs using any other encapsulation reagent (based on minimum triplicate measurements, standard deviation not to exceed 15% of mean) then the candidate encapsulated ON shall be deemed to act through a PEI mediated mode of action. Thresholds used in tests
[0151] The purpose of these tests are to determine by a reasonable analysis, if encapsulated ONs benefit from or utilize the sequence-independent anti-cell proliferation properties of PEI- encapsulated ONs which we have described herein or are acting with sequence-dependent activity.
[0152] The thresholds described in tests 1, 2 and 3 above are the default thresholds. If specifically indicated, other thresholds can be used in the comparison tests described above. Thus for example, if specifically indicated, the threshold for determining whether an encapsulated ON is acting with sequence-independent activity or requires PEI for its activity can be any of 10-fold, 8-fold, 6-fold, 5-fold, 4-fold, 3-fold, 2-fold, 1.5-fold, or equal.
[0153] Similarly, though the default is that satisfying any one of the above 3 tests is sufficient, if specifically indicated, the encapsulated ON can be required to satisfy any two (e.g., tests 1 & 2, 1 & 3, 2 & 3,), or all 3 tests at a default threshold, or if specifically indicated, at another threshold(s) as indicated above.
Example 12 Methodologies
[0154] The following methods are provided for application in the tests described in example 11.
Oligonucleotide Synthesis
[0155] The present oligonucleotides can by synthesized using methods known in the art. For example, unsubstituted and substituted phosphodiester (P-O) oligonucleotides can be synthesized on an automated DNA synthesizer (e.g., Applied Biosystems model 380B or Akta Oligopilot 100) using standard phosphoramidite chemistry with oxidation by iodine. Phosphorothioates (P=S) can be synthesized as for the phosphodiester oligonucleotides except the standard oxidation bottle can be replaced by 0.2 M solution of 311-l,2-benzodithiole-3-one 1,1 -dioxide in acetonitrile for the step-wise thioation of the phosphite linkages. The thioation wait step can be increased to 68 sec, followed by the capping step. After cleavage from the support column and deblocking in concentrated ammonium hydroxide at 550C. (18 h), the oligonucleotides can be purified by precipitating twice with 2.5 volumes of ethanol from a 0.5 M NaCl solution.
[0156] While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth, and as follows in the scope of the appended claims.

Claims

WHAT IS CLAIMED IS:
1. An anti-cell proliferation encapsulated oligonucleotide formulation comprising at least one oligonucleotide and at least one delivery system, said oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity.
2. An anti-cell proliferation encapsulated oligonucleotide formulation comprising at least one oligonucleotide and at least one linear delivery system, said oligonucleotide having an anti- cell proliferation activity, said activity being a sequence independent activity, said activity acting through a PEI-mediated mode of action,
3. The oligonucleotide formulation of claim 1 or 2, wherein said oligonucleotide formulation comprises a mixture of at least two different oligonucleotides.
4. An anti-cell proliferation randomer oligonucleotide formulation, comprising at least one randomer oligonucleotide and at least one delivery system, said randomer oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity.
5. An anti-cell proliferation randomer oligonucleotide formulation, comprising at least one linear randomer oligonucleotide and at least one linear delivery system, said randomer oligonucleotide having an anti-cell proliferation activity, said activity being a sequence independent activity, said activity acting through a PEI-mediated mode of action.
6. The oligonucleotide formulation of claim 4 or 5 comprising a mixture of at least two randomer oligonucleotides of different lengths.
7. The oligonucleotide formulation of any one of claims 1 to 6 wherein said delivery system comprises at least one cationic molecule.
8. The oligonucleotide formulation of claim 7 wherein said cationic molecule is a cationic lipid.
9. The oligonucleotide formulation of claim 7 wherein said cationic is a cationic dendrimer.
10. The oligonucleotide formulation of claim 7 wherein said cationic molecule is polyethyleneimine.
11. The oligonucleotide formulation of claim 10 wherein said polyethyleneimine is a mixture of linear polyethyleneimines
12. The oligonucleotide formulation of claim 11 wherein said mixture comprises polyethyleneimines of molecular weight higher than 2,000 Da and lower than 50,000 Da.
13. The oligonucleotide formulation of any one of claims 11-12 wherein said polyethyleneimines have a molecular weight higher than 20,000Da and lower than 25,000 Da.
14. The oligonucleotide formulation of any one of claims 11-13 wherein said polyethyleneimines have an average molecular weight in between 20,000Da and lower than 25,000 Da.
15. The oligonucleotide formulation of any one of claims 1-14, wherein said formulation has an IC50 for inhibition of proliferating cells of 0.10 μM or less.
16. The oligonucleotide formulation of any one of claims 1-15, wherein said formulation has an IC50 for inhibition of proliferating cells of 0.05 μM or less.
17. The oligonucleotide formulation of any one of claims 1-16, wherein said formulation has an IC50 for inhibition of proliferating cells of 0.025 μM or less.
18. The oligonucleotide formulation of any one of claims 1-17, wherein said formulation has an IC50 for inhibition of proliferating cells of 0.015 μM or less.
19. The oligonucleotide formulation of any one of claims 1 to 18, wherein said oligonucleotide is at least 10 nucleotides in length.
20. The oligonucleotide formulation of any one of claims 1 to 19, wherein said oligonucleotide is at least 15 nucleotides in length.
21. The oligonucleotide formulation of any one of claims 1 to 20, wherein said oligonucleotide is at least 20 nucleotides in length.
22. The oligonucleotide formulation of any one of claims 1 to 21, wherein said oligonucleotide is at least 30 nucleotides in length.
23. The oligonucleotide formulation of any one of claims 1 to 22, wherein said oligonucleotide is at least 40 nucleotides in length.
24. The oligonucleotide formulation of any one of claims 1 to 23, wherein said oligonucleotide is at least 50 nucleotides in length.
25. The oligonucleotide formulation of any one of claims 1-24, wherein said oligonucleotide comprises at least one phosphodiester linkage.
26. The oligonucleotide formulation of any one of claims 1-25, wherein said oligonucleotide comprises at least one modification to its chemical structure.
27. The oligonucleotide formulation of any one of claims 1-26, wherein said oligonucleotide comprises at least two different modifications to its chemical structure.
28. The oligonucleotide formulation of claim 27, wherein one of said at least two different modifications is a sulfur modification.
29. The oligonucleotide formulation of any one of claims 27-28, wherein one of said at least two different modifications is a phosphorothioated linkage.
30. The oligonucleotide formulation of any one of claims 27-29, wherein one of said at least two different modifications is a phosphorodithioated linkage.
31. The oligonucleotide formulation of any one of claims 27-30, wherein one of said at least two different modifications is a sulfur modified nucleobase moiety.
32. The oligonucleotide formulation of any one of claims 27-31, wherein one of said at least two different modifications is a sulfur modified ribose moiety.
33. The oligonucleotide formulation of any one of claims 1-32, wherein said oligonucleotide comprises at least one 2' modification to the ribose moiety.
34. The oligonucleotide formulation of claim 33, wherein said one 2' modification to the ribose moiety is a 2'-0 alkyl modified ribose moiety.
35. The oligonucleotide formulation of any one of claims 33-34, wherein said one 2' modification to the ribose moiety is a 2'-0 methyl modified ribose.
36. The oligonucleotide formulation of any one of claims 33-35, wherein said one 2' modification to the ribose moiety is a 2'-methoxyethyl modified ribose.
37. The oligonucleotide formulation of any one of claims 33-36, wherein said one 2' modification to the ribose moiety is a 2'-FANA modified ribose.
38. The oligonucleotide formulation of any one of claims 1-37, wherein said oligonucleotide comprises at least one methylphosphonate linkage.
39. The oligonucleotide formulation of any one of claims 1-38, wherein said oligonucleotide is a concatemer consisting of two or more oligonucleotide sequences joined by a linker.
40. The oligonucleotide formulation of any one of claims 1-39, wherein said oligonucleotide is linked or conjugated at one or more nucleotide residues thereof to a molecule modifying the characteristics of the oligonucleotide to obtain one or more characteristics selected from the group consisting of higher stability, lower serum interaction, higher cellular uptake, an improved ability to be formulated for delivery, a detectable signal, higher anti-cell proliferation activity, better pharmacokinetic properties, specific tissue distribution and lower toxicity.
41. The oligonucleotide formulation of any one of claims 1-40, wherein said oligonucleotide comprises at least one base which is capable of hybridizing via non- Watson-Crick interactions.
42. The oligonucleotide formulation of any one of claims 1-3, 7-41, wherein said oligonucleotide comprises at least one Gquartet motif portion.
43. The oligonucleotide formulation of any one of claims 1-3, 7-42, wherein said oligonucleotide comprises at least one CpG motif portion.
44. The oligonucleotide formulation of any one of claims 1-3, 7-43, wherein said oligonucleotide comprises a portion complementary to an mRNA.
45. The oligonucleotide formulation of any one of claims 1-3, 7-44, wherein at least a portion of the sequence of said oligonucleotide is derived from a genome.
46. The oligonucleotide formulation of any one of claims 1-3, 7-45, wherein at least a portion of the sequence of said oligonucleotide is derived from a genome and has an anti-cell proliferation activity that is predominantly a sequence independent mode of action.
47. The oligonucleotide formulation of any one of claims 1-3, 7-46, wherein said oligonucleotide has at most 90%, preferably 80%, more preferably 75% identity with a genomic sequence.
48. The oligonucleotide formulation of any one of claims 1-3, 7-47, wherein said oligonucleotide has at most 60%, preferably 50%, more preferably 40% identity with a genomic sequence.
49. The oligonucleotide formulation of any one of claims 1-3, 7-48, wherein at least a portion of the sequence of said oligonucleotide is involved in an aptameric interaction with a cellular component.
50. The oligonucleotide formulation of any one of claims 1-3, 7-49, wherein at least a portion of the sequence of said oligonucleotide comprises polyA, polyC, polyG, polyT, polyAC, polyAG, polyAT, polyCG, polyCT, polyGT, polyU, PoIyAU, polyCU, polyGU or polyTU.
51. The oligonucleotide formulation of any one of claims 1 to 50, wherein at least a portion of the sequence of said oligonucleotide comprises two or more repeated sequences.
52. The oligonucleotide formulation of any one of claims 1 to 51, comprising a mixture of at least two different oligonucleotides.
53. The oligonucleotide formulation of any one of claims 1-52, comprising a mixture of at least 10 different oligonucleotides.
54. The oligonucleotide formulation of any one of claims 1-53, comprising a mixture of at least 100 different oligonucleotides.
55. The oligonucleotide formulation of any one of claims 1-54, comprising a mixture of at least 1000 different oligonucleotides.
56. The oligonucleotide formulation of any one of claims 1-55, comprising a mixture of at least 106 different oligonucleotides.
57. The oligonucleotide formulation of any one claims 52-56, wherein said different oligonucleotides are at least 10 nucleotides in length.
58. The oligonucleotide formulation of any one claims 52-57, wherein said different oligonucleotides are at least 15 nucleotides in length.
59. The oligonucleotide formulation of any one claims 52-58, wherein said different oligonucleotides are at least 20 nucleotides in length.
60. The oligonucleotide formulation of any one of claims 52-59, wherein said different oligonucleotides are at least 30 nucleotides in length.
61. The oligonucleotide formulation of any one of claims 52-60, wherein a plurality of said different oligonucleotides are at least 40 nucleotides in length.
62. The oligonucleotide formulation of any one of claims 52-61, wherein a plurality of said different oligonucleotides are at least 50 nucleotides in length.
63. An anti-cell proliferation pharmaceutical composition comprising a therapeutically effective amount of at least one pharmacologically acceptable anti-cell proliferation encapsulated oligonucleotide formulation according to any of claims 1 to 62; and a pharmaceutically acceptable carrier.
64. The anti-cell proliferation pharmaceutical composition of claim 63, adapted for the treatment, control, or prevention of a cell proliferation disease.
65. The anti-cell proliferation pharmaceutical composition of any one of claims 63-64, adapted for delivery by a mode selected from the group consisting of ocular administration, oral ingestion, enteral administration, inhalation, cutaneous injection, subcutaneous injection, intramuscular injection, intraperitoneal injection, intrathecal injection, intratrachael injection, skin topical administration, rectal administration, vaginal administration, sublingual administration and intravenous injection.
66. The anti-cell proliferation pharmaceutical composition of any one of claims 63-65, wherein said composition further comprises at least one other anti-cell proliferation drug in combination.
67. Use of a therapeutically effective amount of at least one pharmacologically acceptable anti- cell proliferation encapsulated oligonucleotide formulation according to any of claims 1 to 62 for the prophylaxis or treatment of a cell proliferation disease in a subject.
68. The use of claim 67, wherein said cell proliferation disease is cancer or tumor cells.
69. The use of claim 64, wherein said subject is a human.
70. The use of claim 64, wherein said subject is a non-human animal.
71. The use of claim 64, wherein said subject is a plant.
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