Patent Grant
8183361
The present invention relates to compositions containing oligonucleotides, and particularly to oligonucleotide-containing compositions suitable for administration to humans and other mammals.
Oligonucleotides, oligonucleotide analogs and other sequence-specific binding polymers designed to block translation of selected messenger RNA (the sense strand) are commonly called antisense oligonucleotides. Development of such oligonucleotides, for therapeutic applications entails selecting a target genetic sequence unique and critical to the pathogen or pathogenic state one wishes to treat. One then assembles an oligomer of genetic bases (adenine, cytosine, guanine, and thymine or uracil) complementary to that selected sequence. When such an antisense oligonucleotide binds to its targeted disease-causing sequence, it can inactivate that target and thereby alleviate the disease.
Antisense oligonucleotides offer the prospect of safe and effective therapeutics for a broad range of intractable diseases. Nonetheless, developing therapeutics that function by a true antisense mechanism presents a number of forbidding challenges. The oligonucleotides should achieve adequate efficacy at a concentration attainable within the cells of the patient. They should inhibit their selected target sequences without concomitant attack on any other sequences in the patient's pool of approximately 200 million bases of unique-sequence RNA. They should be stable in extracellular compartments and within cells. They must be deliverable into the cellular compartments containing their targeted sequences. They should be adequately soluble in aqueous solution. Finally, they should exhibit little or no toxicity at therapeutic concentrations.
First-generation antisense oligonucleotides comprised natural genetic material (Belikova et al. (1967) Tetrahedron Lett. 37, 3557-3562; Zamecnik et al. (1978) Proc. Natl. Acad. Sci. USA 75, 280-284; Summerton (1979) J. Theor. Biol. 78, 77-99) and often contained crosslinking agents for binding their targets irreversibly (Summerton et al. (1978) J. Mol. Biol. 122, 145-162). As the design challenges became more fully appreciated, a number of non-natural antisense structural types were developed in an effort to improve efficacy, stability and delivery. Of particular note are the early non-ionic DNA analogs including phosphotriester-linked DNA and methylphosphonate-linked DNA (Cohen (1989) Oligodeoxynucleotides: Antisense Inhibitors of Gene Expression, CRC Press, pp. 82-92). Other nucleic acid analogs of note include carbamate-linked DNA (Cohen (1989) Oligodeoxynucleotides Antisense Inhibitors of Gene Expression, CRC Press, pp. 97-117), phosphoroamidate-linked DNA (Froehler et al. (1988) Nucleic Acids Res. 16, 4831-4839) and 2′-O-methyl RNA (Shibahara et al. (1989) Nucleic Acids Res. 17, 239-252). These second generation oligonucleotides include oligonucleotides containing acyclic backbone moieties, including nylon (Weller et al. (1991) J. Org. Chem. 56, 6000-6006; Huang et al. (1991) J. Org. Chem. 56, 6007-6018), the exceptionally high-affinity peptide nucleic acids (PNA) (Egholm et al. (1992) J. Am. Chem. Soc. 114, 1895-1897) and related types (U.S. Pat. No. 5,217,866).
One approach to improving the potency of antisense oligonucleotides is to enhance the affinity or the efficiency with which the antisense oligonucleotides interact with their targets and induce RNase degradation of their target gene transcripts. The doses at which effects have been observed generally range from 10 to 30 mg/kg i.v. (Miragha et al. (2000) Antisense Nuc. Acid Drug Devel. 10, 453-461). Some clinical studies, however, have not demonstrated antisense activity at doses up to 30 mg/kg i.v. (Rudin et al. (2001) Clin. Cancer Res. 7, 1214-1220; Kushner et al. (2000) Curr. Oncol. Reports 2, 23-30), indicating that results vary based on the structure of the oligonucleotide administered. Typical dose-response curves for antisense oligonucleotides both in vivo and in vitro, often reveal that less than a factor of ten often separates the concentration producing antisense activity from the concentration producing no activity (Branch (1998) Trends Biochem. Sci. 23, 45-50). Since the ratio of antisense to non-antisense effects drops sharply outside a restricted concentration range, it remains challenging to identify common structural features for any antisense oligonucleotide that will enhance affinity and efficiency of the oligonucleotide for its target. Furthermore, no studies to date have identified common structural features of antisense oligonucleotides that would make them suitable for oral administration, thus necessitating intravenous administration (Chen et al. (2000) Antisense Nuc. Acid. Drug Develop. 10, 415-422). Identification of common structural modifications of antisense oligonucleotides that facilitate oral or topical administration would therefore also be advantageous.
Although each of these newer structural types provides one or more significant advantages over the first-generation oligonucleotides, none yet appear to provide the full combination of properties needed in antisense therapeutics for successful therapeutic applications.
The invention encompasses a composition suitable for administration in a mammal comprising a modified oligonucleotide of about seven to seventy-five nucleotides containing seven or more contiguous ribose groups linked by achiral 5′ to 3′ internucleoside phosphate linkages, wherein the modified oligonucleotide is complementary to a region of a gene associated with a pathological disorder. In some embodiments, the mammal is a human and the oligonucleotide is a ribonucleotide or deoxyribonucleotide. The modified oligonucleotide can be complementary to a region of the gene selected from the group consisting of the 5′ UTR region, translational start site, the 3′ UTR, and translational termination site.
In some embodiments, the gene is a gene selected from Table 1 and the pathological disorder is selected from the group consisting of abnormal appetite, hypertension, hypercholesteroremia, hyperlipidemia, erectile dysfunction, eczema, depression, anxiety, stress, inflammatory bowel syndrome, ulcerative colitis, Crohn's disease, renal stones, gall stones, constipation, migraine headache, seizure, multiple sclerosis, polymyositis, fibromyalgia, Parkinson's disease, ALS, chronic pain, pre-menstrual syndrome, sinusitis, colds, trauma, carpal tunnel syndrome, chronic fatigue syndrome, rosacea, arthritis, psoriasis, prostatitis, inflammation, heartburn, infection, poison ivy, colon cancer, malignant melanoma and malignant nasal polyps. In preferred embodiments, the modified oligonucleotide is selected from the group consisting of SEQ ID NO: 1-81
In some embodiments, the modified oligonucleotide is present in the composition at a concentration effective to reduce the expression of the gene when administered. When the composition is administered, the modified oligonucleotide is administered at a dose of less than 100 μg/kg, preferably less than 50 μg/kg, more preferably less than 5.0 μg/kg, even more preferably less than 0.50 μg/kg, yet even more preferably less than 0.050 μg/kg, and most preferably less than 0.0050 μg/kg. Furthermore, the modified oligonucleotide present in the composition may be suitable for oral administration.
The modified oligonucleotides present in the compositions of the invention preferably have a Tm of about 75-115° C. at a concentration of 1 mM and a length of 10 to 26 bases, or a Tm of 40° C. to 85° C. at a concentration of 1 pM and a length of 10 to 26 bases. In one embodiment, the ribose group has a modified 2′ substituent selected from the group consisting of hydrogen, methoxy, propoxy, methoxy-ethoxy, flourine, chlorine, bromine and iodine. In another embodiment, the modified oligonucleotide is 3′ or 5′ end-blocked.
The compositions of the invention may be formulated as pharmaceutical compositions, nutritional or dietary supplement compositions, or as cosmetic compositions. In some embodiments, the compositions of the invention comprise two or more different modified oligonucleotides, while in other embodiments, three or more different modified oligonucleotides.
The invention also encompasses a method of treating a patient with a pathological disorder comprising administering one or more of the aforementioned modified oligonucleotides of the invention, wherein the modified oligonucleotides are about seven to seventy-five nucleotides, contain seven or more contiguous ribose groups linked by achiral 5′ to 3′ internucleoside phosphate linkages. Preferably, the modified oligonucleotide is complementary to a region of a gene associated with the pathological disorder. More preferably, the gene is selected from Table 1 and the aforementioned pathological disorders are selected from the group consisting of abnormal appetite, hypertension, hypercholesteroremia, hyperlipidemia, erectile dysfunction, eczema, depression, anxiety, stress, inflammatory bowel syndrome, ulcerative colitis, Crohn's disease, renal stones, gall stones, constipation, migraine headache, seizure, multiple sclerosis, polymyositis, fibromyalgia, Parkinson's disease, ALS, chronic pain, pre-menstrual syndrome, sinusitis, colds, trauma, carpal tunnel syndrome, chronic fatigue syndrome, rosacea, arthritis, psoriasis, prostatitis, inflammation, heart burn, infection, poison ivy, colon cancer, malignant melanoma and malignant nasal polyps.
As mentioned above, the invention includes a nutritional supplement comprising a modified oligonucleotide of about seven to seventy-file nucleotides containing seven or more contiguous ribose groups linked by achiral 5′ to 3′ internucleoside phosphate linkages. The invention also includes a method of supplementing the diet of an individual comprising administering this nutritional supplement, wherein administration of the nutritional supplement improves the health of the individual.
The invention further includes a cosmetic composition comprising a modified oligonucleotide of about seven to seventy-file nucleotides containing seven or more contiguous ribose groups linked by achiral 5′ to 3′ internucleoside phosphate linkages, wherein the modified oligonucleotide is complementary to a region of a gene associated with a skin disorder. The invention also includes a method of improving the appearance of the skin in an individual with a skin disorder comprising administering this cosmetic composition.
The present invention relates to compositions that comprise oligonucleotide molecules, and the use of such compositions to treat the symptoms of diseases/conditions such as acroparaesthsia, allergic (psoric) conditions, allergic reactions, alopecia, amnesia, anaphrodisia, angina, arthritis, asthenopia, biliary sycosis, burns, cancerous conditions, such as colon cancer, malignant melanoma and malignant nasal polyps, carpal tunnel syndrome, colds, conjunctivitis, Crohn's disease, depression, depressive psychosis, dysthyroidism, epilepsy, erectile dysfunction, excessive appetite (i.e., appetite control and suppression, promotion of healthy weight loss while naturally satisfying the appetite), gingivitis, heart burn (i.e., relief of occasional heartburn or occasional acid indigestion), hemorrhage, hypertension (i.e. helps maintain cardiovascular function, and a healthy heart and circulatory system), high cholesterol (i.e., helps to maintain cholesterol levels that are already within the normal range), hyperthyroidism, infections, inflammatory disease, lack of willpower, laryngitis, leukopenia, liver disorders, mental disorders (i.e., reduces stress, frustration, muscle tension, anxiety, and occasional simple nervous tension; enhances resistance to stress), myopia, neurosis, neurological disorders such as multiple sclerosis and ALS, obesity, pain (i.e., relief of minor or temporary aches and pains), pancreatic disorders, poison ivy, premature senescence, pre-menstrual syndrome (i.e., treatment of common symptoms associated with the menstrual cycle such as edema, breast tenderness, headaches, skin problems, cramps and mild mood changes), prostatitis, psoriasis, rosacea, seborrhea, sinusitis, and trauma.
The Oligonucleotide
Generally
A double-stranded DNA molecule encoding a gene has both a sense and an antisense strand. The transcription of RNA uses the antisense strand to make an exact sequence copy of the sense strand (with the minor changes of employing uridine for thymidine, and an RNA backbone in lieu of a DNA backbone). Thus, the RNA formed in transcription has the same nucleotide sequence as the sense strand of the gene. The RNA transcript is processed in the cell to become mRNA, which may subsequently be used as a template to make protein.
The term “oligonucleotides” as used herein, refers to a molecule comprised of nucleotides (i.e., ribonucleotides, deoxyribonucleotides, or both). The term includes monomers and polymers of ribonucleotides and deoxyribonucleotides, or mixtures thereof, with the nucleotides being connected together via, for example 5′ to 3′ linkages, 5′ to 2′ linkages, etc. The nucleotides used in the oligonucleotides may be naturally occurring or may be synthetically produced analogues that are capable of forming base-pair relationships with naturally occurring base pairs. Examples of non-naturally occurring bases that are capable of forming base-pairing relationships include, but are not limited to, aza and deaza pyrimidine analogues, aza and deaza purine analogues, and other heterocyclic base analogues, wherein one or more of the carbon and nitrogen atoms of the purine and pyrimidine rings have been substituted by heteroatoms, e.g., oxygen, sulfur, selenium, phosphorus, etc.
The oligonucleotides of the present invention are at least five contiguous nucleotides in length. For example, the oligonucleotide can be five to seventy-five nucleotides in length. The oligonucleotide can also be at least ten sequential nucleotides and alternatively, at least fifteen sequential nucleotides in length. In one embodiment, the oligonucleotide is twelve to twenty-six nucleotides in length. The oligonucleotide sequence can be derived from any of the genes listed in Table 1 (SEQ ID NO: 82-132). Examples of suitable antisense oligonucleotide sequences for the compositions of the present invention are described in Table 1 below.
In one embodiment, the oligonucleotide composition of the present invention comprises at least about two oligonucleotides of differing sequence. In another embodiment, the oligonucleotide composition of the present invention comprises at least about three, four, five, six, seven, eight, nine, or ten oligonucleotides of differing sequences. Although Table 1 depicts the sequences as oligonucleotides containing only deoxyribonucleotide residues, it is to be understood that the present invention also includes the embodiments wherein the oligonucleotides are composed of ribonucleotide residues (e.g., by substituting uridine for thymidine, and ribosyl substituents for deoxyribosyl substituents). Moreover, it is to be understood that the present invention also includes the embodiments in which the oligonucleotides are composed of only deoxyribonucleotide residues, of only ribonucleotide residues, or of mixtures of deoxyribonucleotide and ribonucleotide residues.
The oligonucleotides in the present invention display greater than or equal to 80 percent sequence identity to a nucleotide sequence selected from the group of SEQ ID NO: 1-81 (see Table 1). Also preferred, the oligonucleotides display greater than or equal to 85 percent sequence identity to a nucleotide sequence selected from the group of SEQ ID NO: 1-81. Still preferred, the oligonucleotides display 90 percent sequence identity and still more preferred, the oligonucleotides display 95 percent sequence identity. Most preferably, the oligonucleotides of the present invention are selected such that their nucleotide sequence is complementary to the sense strand of a gene.
The degree of similarity between two sequences can be determined using methods well known to the art (e.g., computer programs including Fasta (Oxford Molecular Group Inc.) and BLAST (www.ncbi.nlm.nih.gov) (Altschul et al. (1997) Nucleic Acid Res. 25, 3389-3402). These methods can be employed to take into account gaps in the sequences due to deletions or insertions. Homology or sequence identity at the nucleotide or amino acid sequence level determined by BLAST (Basic Local Alignment Search Tool) analysis uses the algorithm employed by the programs blastp, blastn, blastx, tblastn and tblastx (Altschul et al. (1997) Nucleic Acids Res. 25, 3389-3402 and Karlin et al. (1990) Proc. Natl. Acad. Sci. USA 87, 2264-2268, both fully incorporated by reference) which are tailored for sequence similarity searching. The approach used by the BLAST program is to first consider similar segments, with gaps (non-contiguous) and without gaps (contiguous), between a query sequence and a database sequence, then to evaluate the statistical significance of all matches that are identified and finally to summarize only those matches which satisfy a preselected threshold of significance.
For a discussion of basic issues in similarity searching of sequence databases, see Altschul et al. (1994) Nature Genetics 6, 119-129 which is fully incorporated by reference. The search parameters for histogram, descriptions, alignments, expect (i.e., the statistical significance threshold for reporting matches against database sequences), cutoff, matrix and filter (low complexity) are at the default settings. The default scoring matrix used by blastp, blastx, tblastn, and tblastx is the BLOSUM62 matrix (Henikoff et al. (1992) Proc. Natl. Acad. Sci. USA 89, 10915-10919, fully incorporated by reference), recommended for query sequences over 85 nucleotides or amino acids in length.
For blastn, the scoring matrix is set by the ratios of M (i.e., the reward score for a pair of matching residues) to N (i.e., the penalty score for mismatching residues), wherein the default values for M and N are +5 and −4, respectively. Four blastn parameters were adjusted as follows: Q=10 (gap creation penalty); R=10 (gap extension penalty); wink=1 (generates word hits at every winkth position along the query); and gapw=16 (sets the window width within which gapped alignments are generated). The equivalent Blastp parameter settings were Q=9; R=2; wink=1; and gapw=32. A Bestfit comparison between sequences, available in the GCG package version 10.0, uses DNA parameters GAP=50 (gap creation penalty) and LEN=3 (gap extension penalty) and the equivalent settings in protein comparisons are GAP=8 and LEN=2.
In a related vein, the oligonucleotides described herein have a Guanine:Cytosine (GC content) greater than 35 percent. The GC content is preferably greater than 40 percent and most preferably, greater than 45 percent.
The Modified Oligonucleotide
The oligonucleotides that may be employed in accordance with the present invention may be modified. An oligonucleotide that comprises at least one modification has one or more chemical modifications at the molecular level of the natural molecular structures of all or any of the nucleic acid bases, sugar moieties, internucleoside phosphate linkages, as well as molecules having added substituents, such as diamines, cholesteryl or other lipophilic groups, or a combination of modifications at these sites. For example, oligonucleotides can be end-blocked, protonated, exhibit substantial acid resistance, substantial nuclease resistance, and contain achiral internucleoside phosphate linkages and modified ribose or deoxyribose substituents.
The term “end-blocked” as used herein refers to a nucleic acid with a chemical modification at the molecular level that prevents the degradation of selected nucleotides, e.g., by exonuclease action. This chemical modification is positioned such that it protects the integral portion of the nucleic acid, for example the portion of an RNA or DNA that is chemically similar to the gene involved in the physiological condition. An end block may be a 3′ end block, a 5′ end block, or both. For example, a 3′ end block may be at the 3′-most position of the molecule, or it may be internal to the 3′ ends, provided it is 3′ of the integral sequences of the nucleic acid.
The term “protonated compound” refers to a molecule of the invention that, when dissolved in water having a pH of 7 causes the pH of the solution to fall. Generally, compounds are protonated by adding protons to the reactive sites on the molecule, although other modifications of the molecule are possible, and are intended to be encompassed by this term. Such protonation can be accomplished, for example by incubating the compound in the presence of a strong acid, most preferably one with a volatile conjugate base. The term “protonation” and “acidification” as used interchangeably herein refers to the process by which protons (or positively charged hydrogen ions) are added to proton acceptor sites on a compound of the invention. The proton acceptor sites include the substituted or unsubstituted phosphates of the central group, as well as any additional proton acceptor sites on either the central group or the end blocking groups. As the pH of the solution is decreased, the number of these acceptor sites which are protonated increases, resulting in a more highly protonated compound.
Many nucleic acid backbones are not stable at low pH (e.g., pH 1-3) and experience depurination, although a number of backbones are relatively stable at pH 4-5. One aspect of the present invention reflects the recognition that certain modifications, including 2′-halide, 2′-O-alkyl, 3′-O-alkyl, and 2′-O-alkyl-n(O-alkyl) nucleic acid molecules are stable at the desired pH of 2 to 1. These modifications enhance the ability of the oligonucleotides of the pharmacological compositions of the present invention to affect a condition in vivo. Thus, the composition of the present invention may include nucleic acid molecules that are substantially acid resistant. The compositions of the present invention may also include nucleic acid molecules that are nuclease resistant. This includes nucleic acid molecules completely derivatized by 2′-O-methylphosphodiesters, 2′-O-alkyl, 2′-O-alkyl-n(O-alkyl), 2′-fluoro, 2′-deoxy-erythropentofuranosyl, chimeric linkages, and any other backbone modifications, as well as other modifications, which render the nucleic acid molecules substantially resistant to endogenous nuclease activity. Additional suitable methods of rendering nucleic acid molecules nuclease resistant include, but are not limited to, covalently modifying the purine or pyrimidine bases that comprise the nucleic acid. For example, bases may be methylated, hydroxymethylated, or otherwise substituted (e.g., glycosylated) such that the nucleic acid molecules comprising the modified bases are rendered substantially nuclease resistant. Nuclease resistance also aids the oligonucleotides of the compositions of the present invention in retaining their effect in vivo.
Preferably, the oligonucleotides of the of the present invention remain relatively unchanged chemically upon administration to a subject and retain their activity in acidic conditions (pH less than 6.0) or in the presence of an endonuclease or exonuclease (e.g., in an in vivo setting).
The term “substantially acid resistant” as used herein refers to nucleic acid molecules that are resistant to acid degradation as compared to unmodified nucleic acid molecules. Typically, the relative acid resistance of a nucleic acid will be measured by comparing the percent degradation of a resistant nucleic acid with the percent degradation of its unmodified counterpart (i.e., a corresponding nucleic acid of the same length and sequence having a “normal” backbone and bases). A nucleic acid that is acid resistant is preferably at least one and a half times more resistant to acid degradation, more preferably at least two times more resistant, even more preferably at least five times more resistant, and most preferably at least ten times more resistant than their unmodified counterpart.
Although certain acid resistant nucleic acid molecules exhibit marked acid stability and endonuclease resistance, they are sensitive to 3′ exonucleases. In order to enhance the exonuclease resistance of 2′-O-alkyl substituted nucleic acid molecules, the 3′ or 5′ and 3′ ends of the nucleic acid are preferably attached to a chemical moiety that provides an exonuclease blocking function. For example, one or more phosphorothioate nucleotides can be placed at either end of the RNA or DNA. Additionally, one or more inverted bases can be placed on either end of the RNA or DNA, or one or more alkyl or alcohol (e.g., butanol-substituted) nucleotides or chemical groups can be placed on one or both ends. Accordingly, a preferred embodiment of the present invention is a nucleic acid comprising a nucleic acid having the following structure: A-B-C, wherein “B” is a 2′-O-alkyl or 2′-O-alkyl-n(O-alkyl) substituted RNA between about 1 and about 98 bases in length, and “A” and “C” are respective 5′ and 3′ end blocking groups (e.g., one or more phosphorothioate nucleotides (but typically fewer than six), inverted base linkages, or alkyl, alkenyl, alkynyl, O-alkyl, and O-alkyl-n(O-alkyl) groups or substituted nucleotides). A partial list of blocking groups includes inverted bases, dideoxynucleotides, methylphosphates, alkyl groups, aryl groups, cordycepin, cytosine arabanoside, 2′-methoxy, ethoxy nucleotides, phosphoramidates, a peptide linkage, dinitrophenyl group, 2′- or 3′-O-methyl bases with phosphorothioate linkages, 3′-O-methyl bases, fluorescein, cholesterol, biotin, acridine, rhodamine, psoralen, glyceryl, methyl phosphonates, butanol, butyl, hexanol, and 3′-O-alkyls. An enzyme-resistant butanol preferably has the structure OH—CH2CH2CH2CH2 (4-hydroxybutyl), which is also referred to as a C4 spacer.
The term “substantially nuclease resistant” refers to nucleic acid molecules that are resistant to nuclease degradation, as compared to naturally occurring or unmodified nucleic acid molecules. Modified oligonucleotides of the invention are at least 1.25 times more resistant to nuclease degradation than an unmodified nucleic acid having the same sequence and number of nucleotides, more preferably at least 2 times more resistant, even more preferably at least 5 times more resistant, and most preferably at least 10 times more resistant than their unmodified counterpart. Such substantially nuclease resistant nucleic acid molecules include, but are not limited to, nucleic acid molecules with modified backbones such as ethylphosphotriesters, 2′-O-methylphosphorothioates, 2′-O-methyl-p-ethoxy ribonucleotides, 2′-O-alkyls, 2′-O-alkyl-n(O-alkyl), 2′-fluoros, 2′-deoxy-erythropentofuranosyls, 2′-O-methyl ribonucleosides, 3′-O-methylribonucleotides, inverted bases (e.g., inverted T's), or chimeric versions of these backbones.
The modified oligonucleotide includes RNA or DNA comprising modifications to the sugar moieties such as 2′-substituted or 3′-substituted ribonucleotides, or deoxyribonucleotide monomers, any of which are connected together via internucleoside linkages. Modified RNA or DNA may also be comprised of PNA or morpholino modified backbones where specificity of the sequence is maintained.
The ribose groups and the internucleoside linkages link the bases in a nucleic acid and are referred to as the nucleic acid backbone. A modified backbone includes modifications to the chemical linkage between nucleotides, as well as other modifications that may be used to enhance stability and affinity, such as modifications to the sugar structure. For example, an L-anomer of deoxyribose may be used, where the base is inverted with respect to the natural D-anomer. In one embodiment, the 2′-OH of the sugar group may be altered to 2′-halogen, 2′-O-alkyl or 2′-O-alkyl-n(O-alkyl), which provides resistance to degradation without compromising affinity. Other suitable modified backbones include the following types of internucleotide linkages: 2′-O-methyl-phosphodiesters, 2′-O-alkyl, 2′-O-ethyl, 2′-O-propyl, 2′-O-butyl, 2′-O-alkyl-n(O-alkyl), 2′-methoxyethoxy, 2′-fluoro, 2′-deoxy-erythropentofuranosyl, 3′-O-methyl, p-isopropyl oligonucleotides, 2′-O(CH2CH2O)xCH3, and/or butyne linkages. An oligonucleotide may have combinations of such modified backbones, may be completely modified, or may comprise all or some linkages being phosphodiester linkages.
Preferred internucleoside linkages on the modified oligonucleotide are achiral. The term “achiral” as used herein, refers to a molecule that is superimposable with its mirror image, whereas the term “chiral” refers to a molecule that is not superimposable with its mirror image. Oligonucleotides containing achiral 5′ to 3′ internucleoside phosphate linkages have internucleotide linkages which are achiral (i.e., no stereochemistry). The achiral oligonucleotides preferably contain at least about three to eight contiguous achiral internucleoside linkages, more preferably, nine to ten contiguous achiral internucleoside linkages, even more preferably, eleven to twelve contiguous achiral internucleoside linkages, and most preferably, is completely comprised of achiral internucleoside linkages through the entire contiguous sequence. In another embodiment, the achiral internucleoside linkages are interspersed with chiral internucleoside linkages (e.g., two contiguous achiral linkages followed by one chiral linkage followed by two contiguous achiral linkages; three contiguous achiral linkages followed by one chiral linkage; four contiguous achiral linkages followed by two achiral linkages, etc.). Examples of achiral internucleoside linkages include, but are not limited to, phosphodiester and diphosphorothioate linkages. Achiral RNA and DNA linkages in the backbone are routinely generated during automated synthesis of oligonucleotides if the final structure is a symmetrical molecule (i.e., a phosphate with the same atom attached to both sides).
The internucleoside phosphate linkages can be phosphodiester, or 3′ to 3′, 5′ to 2′ or 5′ to 5′ linkages, and combinations of such similar linkages (to produce mixed backbone modified RNA or DNA). The modifications can be internal (single or repeated) or at the end(s) of the RNA or DNA molecule. These modifications can include additions to the nucleic acid molecule, such as cholesteryl, diamine compounds with varying numbers of carbon residues between amino groups and terminal ribose, and deoxyribose or phosphate modifications which cleave or cross-link to the opposite chains or to associated enzymes or other proteins. Electrophilic groups such as ribose-dialdehyde could covalently link with an epsilon amino group of the lysyl-residue of such a protein. A nucleophilic group such as n-ethylmaleimide tethered to an RNA or DNA could covalently attach to the 5′ end of an mRNA or to another electrophilic site.
Suitable oligonucleotides for the present invention can be determined by evaluating the Delta G or Gibbs Free energy of oligonucleotide binding to the complementary RNA strand at 37° C. and the Tm. The Gibbs Free energy and Tm are measured from the part of the target gene that corresponds to the RNA oligonucleotide that is added. These values can be calculated using the program found on ftp://rna.chem.rochester.edu and are described in Matthews et al. (1999) J. Mol. Biol. 288, 911-940 and Matthews et al. (1999) RNA 5, 1458-1469.
Accordingly, a composition comprising an oligonucleotide, (i) wherein said oligonucleotide is at least 10 nucleotides in length, (ii) the Gibbs Free energy of the binding of said oligonucleotide/RNA target duplex at 37° C. is −15 kCal, (iii) said oligonucleotide is complementary to a region within the target gene selected from the group consisting of 5′ UTR, translational start site and translational termination site and (iv) wherein said target gene is a gene as listed in Table 1. The Gibbs free energy is measured between that part of the target gene that corresponds to the oligonucleotide, that part typically being the 5′UTR, translational start site or the translational termination site.
In a preferred embodiment, the Gibbs Free energy of the binding of said oligonucleotide/RNA target duplex at 37° C. is ≦−20 kCal. Also preferred, the Gibbs Free energy is ≦−25 kCal. For 12-14 mer oligonucleotides, the Gibbs Free energy is preferably ≦−15 kCal, for 15-17 mer oligonucleotides, the Gibbs Free energy is preferably ≦−20 kCal, for 18-20 mer oligonucleotides, the Gibbs Free energy is preferably ≦−25 kCal, for 21-23 mer oligonucleotides, the Gibbs Free energy is ≦−30 kCal, and for 24-26 mer oligonucleotides, the Gibbs Free energy is ≦35 kCal.
Further described in the present invention is a composition comprising an oligonucleotide, (i) wherein said oligonucleotide is at least 10 nucleotides in length, (ii) the Tm of said oligonucleotide to a target gene is about 65-90° C., (iii) said oligonucleotide is complementary to a region within the target gene selected from the group consisting of 5′ UTR, translational start site an termination site, and (iv) wherein said target gene is selected from a gene as listed in Table 1. Preferably, the oligonucleotide has a Tm of about 75-90° C. Still preferred, the oligonucleotide has a Tm of about 85-90° C. Still preferred, the Tm of said oligonucleotide to a target gene at 1M monovalent cation concentration is about 65-90° C. The Gibbs free energy is measured between that part of the target gene that corresponds to the oligonucleotide, that part typically being the 5′ UTR, translational start site or the translational termination site.
Nutritional Supplements
As used herein, the term “nutritional supplement” refers to a composition that is intended to supplement the diet. A nutritional supplement includes any dietary substance used in mammals to supplement the diet by increasing total dietary intake; or a concentrate, metabolite, constituent, extract, etc. Nutritional supplement includes any product that is intended for ingestion in tablet, capsule, powder, soft-gel, gel-cap, or liquid form. As used herein, the term “nutritional supplement” is used synomously with the term “dietary supplement” and “nutraceutical” throughout the specification.
The present invention provides a composition which is useful as a nutritional supplement to maintain or improve the an individual's health. Preferred indications for dietary supplements include, hut are not limited to, maintenance of cardiovascular function and a healthy circulatory system, maintenance of cholesterol levels that are already within the normal range, reduction of stress and frustration, relief of occasional simple nervous tension, relief of nervousness due to common everyday overwork and fatigue, alleviation of restlessness, reduction in nervous irritability, relief from anxiety, relief of muscle tension, enhancement of resistance to stress, promotion of emotional balance and a positive outlook, relief of sour stomach or upset stomach, relief of occasional heartburn or occasional acid indigestion, appetite suppression, promotion of healthy weight loss while naturally satisfying the appetite, appetite control, relief of minor or temporary aches and pains, treatment of common symptoms associated with the menstrual cycle, treatment of mild mood changes, cramps, and edema associated with the menstrual cycle, maintenance of a normal, healthy attitude during premenstrual syndrome, diminish the normal symptoms of pre-menstrual syndrome and maintenance of hormonal balance and alleviation of minor pre-menstrual syndrome symptoms such as cramping, breast tenderness, minor mood changes, headaches, bloating and skin problems.
The nutritional supplement composition of the present invention include compositions with a single oligonucleotide and/or a combination of about two or more oligonucleotides. The use of the nutritional supplement compositions of the present invention can be used to treat any of the aforementioned indications. These agents may be combined in an oral dosage with other well known nutritional supplements and/or non-flavonoid antioxidants (e.g., selenium, vitamin E (tocopherol, particularly alpha-tocopherol), vitamin C (ascorbic acid) and coenzyme Q10). Dietary fiber supplements may also be used in the composition.
Other additives may be incorporated in the nutritional supplement of the present invention. Such additives include minerals, (e.g., boron, etc. and trace metals such as zinc, magnesium, manganese, chromium, molybdenum, copper, iron, calcium, and potassium; and other micronutrients such as thiamine, riboflavin, niacin, pantothenic acid, pyridoxine, choline, biotin, inositol, para-aminobenzoic acid, vitamin D, vitamin K, vitamin A). In another embodiment of the invention a dietary fiber supplement such as oat bran or other natural fiber source may also be added to the composition.
Typically the nutritional supplement will further include a pharmaceutically acceptable carrier such as lactose, glucose, sucrose, corn starch, potato starch, cellulose acetate, ethyl cellulose, etc. Diluents and other additives such as one or more pharmaceutically acceptable binding agents, fillers, supports, thickening agents, taste-improving agents, coloring agents, preservatives, stabilizers, regulators, emulsifiers or mixtures thereof may be used depending on the form of the composition employed.
In addition to providing the aforementioned compositions, the invention also includes a method for orally administering the nutritional supplement composition in dosages effective to aid in the maintenance and improvement of an individual's health. The supplement is preferably administered orally. Suitable forms for the nutritional supplement composition for oral administration include tablets, capsules, lozenges, syrups, granules, solutions and suspensions which contain unit doses of the supplement for administration once or several times a day. The nutritional supplement composition of the invention will typically be administered orally as a liquid, tablet or a capsule. Tablets, gel tabs, capsules, liquid and sustained release formulations can be formulated and prepared according to manufacturing techniques well known in the pharmaceutical industry and in a variety of dosage forms.
In one embodiment, the nutritional supplement is a sports drink comprising one or more modified antisense oligonucleotides capable of hybridizing to one or more of the genes listed in Table 1. In a preferred embodiment, the sport drink comprises the modified oligonucleotides Asm (SEQ ID NO: 1), Pde5 (SEQ ID NO: 16), FAAH (SEQ ID NO: 23), CX2 (SEQ ID NO: 6), CRP (SEQ ID NO: 24), LO5 (SEQ ID NO: 12), P65 (SEQ ID NO: 10), CD18 (SEQ ID NO: 5).
Therapeutic Oligonucleotide Compositions
In a related vein, the present invention includes a pharmaceutical composition comprising at least about one oligonucleotide, wherein said oligonucleotide comprises (i) at least about ten contiguous nucleotides in length, (ii) at least about three to eight contiguous achiral internucleoside linkages, (iii) further comprising a pharmaceutically suitable excipient. In alternative embodiments, other oligonucleotides, described herein, are used in the inventive compositions. In some embodiments, the therapeutic composition can be a pharmaceutical or homeopathic composition.
As used herein, the term “pharmaceutical composition” refers to a therapeutic composition that is used to treat a particular disease or pathological disorder that is suitable for parenteral, oral or topical administration in humans.
The compositions containing the modified oligonucleotides of the invention in an admixture with a pharmaceutically acceptable carrier can be prepared according to known techniques. The carrier may take a wide variety of forms depending on the form of preparation desired for administration, e.g., intravenous, oral, topical, aerosol (for topical or inhalation therapy), suppository, parenteral, or spinal injection. The excipient may contain any number of carriers. In the case of homeopathic pharmaceuticals the carriers would preferably be homeopathic carriers, e.g. homeopathic agents that may increase the efficacy of the homeopathic composition or help to alleviate symptoms associated with a physiological condition. In addition, the composition may contain stabilizers, preservatives, and other ingredients, preferably in amounts from about 0.5 to 2.0 percent by weight, provided they do not adversely affect the ability of the pharmacological composition to treat the physiological condition. It is well within the skill of one in the art to determine an appropriate mode of administration and to select an appropriate delivery system.
Administration of the composition will introduce the modified oligonucleotides to the individual in a diluted amount. Exemplary ranges of dosage for oral or topical administration are between about 0.001 mg and 10 mg per day, and preferably between about 0.010 mg and 1.0 mg per day of oligonucleotide in the composition. When orally administered, it is preferred that one dosage unit be administered one to four times per day until relief is achieved or until the symptoms disappear or are satisfactorily attenuated. Normally, a patient is instructed to orally take two to three dosage units per day. The dosage unit may be placed under the tongue of the patient or simply swallowed for such oral administration.
The pharmaceutical compositions of the present invention may be formulated for administration to humans and animals in liquid form, or in tablets, pills, granules, powders, or in ointments, creams, injectables, or suppositories. Ointments and creams are impregnated with a low liquid potency or, sometimes, mother tinctures and are generally prescribed as specific remedies. Liquid compositions may be supplied in amber glass dropper bottles to protect them from light.
In preparing the compositions in oral dosage form, any of the usual pharmaceutical media may be employed, such as, for example, water, glycols, oils, alcohols, flavoring agents, preservatives, coloring agents and the like in the case of oral liquid preparations (such as, for example, suspensions, elixirs, and solutions); or carriers such as starches, sugars, diluents, granulating agents, lubricants, binders, disintegrating agents and the like in the case of oral solid preparations (such as, for example, powders, capsules and tablets). For homeopathic preparations for example, RNA can be dissolved in a liquid 1 part by weight to produce a ten volumes of liquid attenuation labeled 1×. To produce lower dilutions 1 ml of the 1× attenuation is used (mixed thoroughly) with 9 ml of diluent to produce 2×. This process is repeated until the desired attenuation is achieved.
For administration by injection, preparations may comprise an aqueous solution of a water soluble, or solubilized, and pharmacologically acceptable form of the nucleic acid in an appropriate liquid, e.g., water or saline solution. Injectable suspensions may also be prepared using appropriate liquid carriers, suspending agents, agents for adjusting the isotonicity, preserving agents, and the like. Actual methods for preparing administrable pharmacological compositions and adjustments necessary for administration to subjects will be known or apparent to those skilled in the art.
For topical administration, the carrier may take a wide variety of forms depending on the preparation, which may be a cream, dressing, gel, lotion, ointment, or liquid. A surfactant can be included in the composition to provide deeper penetration of the ingredients. Although natural surfactants are preferred, others such as isopropyl myristate can be used. In one embodiment, the composition is a cosmetic composition for topical administration to the skin. As used herein, the term “cosmetic composition” refers to a composition that is applied topically to the skin to improve the appearance of the skin.
Aerosols are prepared by dissolving or suspending the nucleic acid in a propellant such as ethyl alcohol or in propellant and solvent phases. The pharmaceutical compositions for topical or aerosol form will generally contain from about 0.001 percent by weight (of the nucleic acid) to about 40 percent by weight, preferably about 0.02 percent to about 10 percent by weight, and more preferably about 0.05 percent to about 5 percent by weight depending on the particular form employed. Suppositories are prepared by mixing the nucleic acid with a lipid vehicle such as theobroma oil, cacao butter, glycerin, gelatin, or polyoxyethylene glycols.
The compositions of the invention may also include plant or herbal extracts. For example, topical compositions may include Paraguay tea, Kola and Guarana which provide a source of methylxanthines, saponius, tannins and glycosides which have been shown to reduce swelling and redness. The extract of Paraguay tea is known as “Mate extract” and is described in the International Cosmetic Ingredient Dictionary, 5th Edition. Mate extract is commercially available in combination with extracts of Kola and Guarana that is sold by Cosmetic Ingredient Resources (Stamford, Conn.) under the “QUENCHT” trademark. Suitable herbs which can be used also include Symphytum officinale, Moschus moscheferous, Pripalia geniculata, Plantago asiatica, Causticum, Helianthemum canadense, Ornithogalum umbellatum, Clematis crispa, Impatiens pallida, Prunus cerasus, arnica, etc.
The nucleic acid molecule(s) may be combined with a lipid, cationic lipid, or anionic lipid and the active agent delivered via a nucleic acid/lipid emulsion, or a liposomal suspension. The use of cationic, anionic, and/or neutral lipid compositions or liposomes is generally described in International Publications WO90/14074, WO91/16024, WO91/17424, and U.S. Pat. No. 4,897,355, all herein incorporated by reference. By assembling nucleic acid molecules into lipid-associated structures, the nucleic acid molecules may exhibit an increased half-life in vivo. Examples of suitable anionic lipids for use with RNA or DNA include, but are not limited to, cardiolipin, dimyristoyl, dipalmitoyl, or dioleoyl phosphatidyl choline or phosphatidyl glycerol, palmitoyloleoyl phosphatidyl choline or phosphatidyl glycerol, phosphatidic acid, lysophosphatidic acid, phosphatidyl serine, phosphatidyl inositol, and anionic forms of cholesterol.
Making an Oligonucleotide Composition
The invention includes a method for making an oligonucleotide composition comprising (i) selecting an oligonucleotide that is adjacent to or overlaps a target region of a gene, (ii) determining the Gibbs Free energy value associated with said oligonucleotide in reference to said target gene, (iii) assessing Tm in reference to said target gene, and (iv) performing a sequence database search to determine if said oligonucleotide overlaps the 5′ UTR, the translational start sequence, or the translational termination site of an mRNA of a gene different from the target gene.
The oligonucleotide of the present invention can be directed to a translational start site, a 5′ UTR or a termination site. Preferably, the oligonucleotide is adjacent to or overlaps the translational start site of the gene by at least about one base. Still preferred, the oligonucleotide overlaps the translational start site by at least about two bases. Still more preferred, the oligonucleotide overlaps the translational start site by at least about three bases.
It is generally preferable to design an RNA or DNA that has the same or similar base sequence as the portion of the complement of a gene that encodes the 5′ end of an RNA. However, a nucleic acid may also have, for example, a same or similar base sequence as other regions of the gene, such as the region encoding a translation start site or the 3′ untranslated region. In another example, a nucleic acid may be designed to reflect the region around a splice donor or splice acceptor site, either with or without the intervening intron. Of particular interest are nucleic acid molecules whose sequences comprise all or a fragment of the sequence of the complement of a gene that is over-expressed in individuals exhibiting the disease or condition. The identification of overexpression of a gene can be through molecular means, e.g., detection of expression in affected tissue using conventional molecular techniques (e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press). Overexpression of a gene may also be detected using array technology, or inferred from the results of protein assays, such as ELISA.
Making a Homeopathic Oligonucleotide Composition
A method of making a homeopathic composition comprising (i) triturating solid RNA in a 1/9 ratio with lactose to produce a 1× solid and (ii) repeating the process until the desired attenuation is achieved, is described in the present invention. In a related vein, a method of making a homeopathic composition comprising (i) dissolving 1 part RNA by weight in liquid to produce ten volumes of liquid attenuation labeled 1× and optionally (ii) mixing 1 ml of the 1× attenuation with 9 ml of diluent to produce a lower concentration, is also addressed.
In another embodiment, the invention includes homeopathic compositions containing modified oligonucleotides. In one embodiment, tablets for homeopathic use are preferably produced as placebo tablets that are then medicated by dripping or spraying liquid potencies onto the tablets in such a manner as to ensure a coefficient of impregnation of almost 100 percent. The placebo tablets are preferably formed by compression. Pills or granules are preferably spherical in shape, of about 4 millimeters diameter and 3 to 5 centigrams in weight. They are preferably prepared (form pure lactose) and medicated in the same manner as tablets. For example, solid RNA can be triturated (i.e., ground up) in a 1/9 ratio with lactose (1 gram of RNA+9 grams of lactose) to produce a 1× solid. The process is repeated (1 gram of that material plus 9 grams of lactose) until the desired attenuation is achieved.
For homeopathic compositions, the excipient may contain any number of carriers, and preferably homeopathic carriers, e.g., homeopathic agents that may increase the efficacy of the homeopathic composition or help to alleviate symptoms associated with a physiological condition. For example, RNA can be dissolved in a liquid 1 part by weight to produce a ten volumes of liquid attenuation labeled 1×. To produce lower dilutions 1 ml of the 1× attenuation is used (mixed thoroughly) with 9 ml of diluent to produce 2×. This process is repeated until the desired attenuation is achieved. A homeopathic carrier solution such as that described in U.S. Pat. No. 5,603,915 may be used for increasing the efficacy of the homeopathic agent. This carrier solution is sequentially subjected to an alternating current electrical treatment and a direct current electrical treatment, after which additional ingredients such as seawater, brain hormones, and biologically active enzymes are added. The electrical treatment of the carrier, along with the addition of homeopathically active substances, can be used to increase the efficacy of the homeopathic composition. Alternatively, an electromagnetic carrier, such as described in U.S. Pat. No. 5,830,140 may be employed.
Methods of Treatment
The invention includes a method of treating a disorder comprising administering an oligonucleotide to a patient in a therapeutically effective amount. As used herein, the term “therapeutically effective” amount is meant to refer to an amount of a pharmacological composition that is non-toxic and is the lowest amount necessary to provide a desired physiological effect. Preferably, the oligonucletide compositions of the present invention are administered at concentrations at or below 100 μg per kg of body weight. Also preferred, the concentration is at or below 10 μg per kg of body weight, still preferred, the concentration is at or below 1 μg per kg of body weight, and still more preferred, the concentration is at or below 0.1 μg per kg of body weight. Furthermore, for homeopathic use, the oligonucleotide compositions of the present invention can be combined with any homeopathic drug and still elicit a therapeutic effect.
Preferably, the oligonucleotide comprises at least one modification according to the present invention. A preferred modification is the incorporation of at least about three to eight contiguous achiral internucleoside phosphate linkages into the oligonucleotide backbone. More preferably the oligonucleotide incorporates at least nine to ten continuous achiral internucleoside phosphate linkages, even more preferably, eleven to fifteen achiral internucleoside phosphate linkages, and most preferably, the entire oligonucleotide contains achiral internucleoside phosphate linkages. Also preferred, the oligonucleotide is 3′ end-blocked, comprises at least 10 contiguous nucleotides greater than or equal to 80 percent identical to a nucleotide sequence selected from SEQ ID NO: 1-81. Also preferred, the oligonucleotide is at least 85 percent identical to a nucleotide sequence selected from the group of SEQ ID NO: 1-81. Still preferred, the oligonucleotide is at least 90 percent identical and more preferred, at least 95 percent identical. Most preferably, the oligonucleotide comprises a sequence from SEQ ID NO: 1-81.
The methods of the present invention can be used to treat disorders including, but not limited to, acroparaesthsia, allergic (psoric) conditions, allergic reactions, alopecia, amnesia, anaphrodisia, angina, arthritis, asthenopia, biliary sycosis, burns, cancerous conditions, such as colon cancer, malignant melanoma and malignant nasal polyps, carpal tunnel syndrome, colds, conjunctivitis, Crohn's disease, depression, depressive psychosis, dysthyroidism, epilepsy, erectile dysfunction, excessive appetite (i.e., appetite control and suppression, promotion of healthy weight loss while naturally satisfying the appetite), gingivitis, heart burn (i.e., relief of occasional heartburn or occasional acid indigestion), hemorrhage, hypertension (i.e., helps maintain cardiovascular function, and a healthy heart and circulatory system), high cholesterol (i.e., helps to maintain cholesterol levels that are already within the normal range), hyperthyroidism, infections, inflammatory disease, lack of willpower, laryngitis, leukopenia, liver disorders, mental disorders (i.e., reduces stress, frustration, muscle tension, anxiety, and occasional simple nervous tension; enhances resistance to stress), myopia, neurosis, neurological disorders such as multiple sclerosis and ALS, obesity, pain (i.e., relief of minor or temporary aches and pains), pancreatic disorders, poison ivy, premature senescence, pre-menstrual syndrome (i.e., treatment of common symptoms associated with the menstrual cycle such as edema, breast tenderness, headaches, skin problems, cramps and mild mood changes), prostatitis, psoriasis, rosacea, seborrhea, sinusitis, and trauma.
Table 2 lists the oligonucleotides, or combinations of oligonucleotides that are preferably employed in remedies for the treatment of various symptoms and conditions. In Table 2, the use of a combination of oligonucleotides is denoted by a “/” (for example, “A/B/C” denotes the combined use of oligonucleotides A, B and C); where two or more different combinations are preferred, each such combination is presented on a separate line. The oligonucleotides are usually used in a 1:1:1 ratio, but this can vary. For example, a combination of 4×, 5×, and 6× solutions may be used, which deviates from 1:1:1.
The compositions of the present invention are formulated to contain a “nutritionally effective” or “allopathically effective” or “homeopathically effective” amount of one or more nucleic acid molecules. As used herein, the term “nutritionally effective” amount is meant to refer to an amount of a oligonucleotide composition that is non-toxic and greater than the minimum amount necessary to maintain a desired physiological effect. As used herein, the term “allopathically effective” amount is meant to refer to an amount of a oligonucleotide composition that is non-toxic and greater than the minimum amount necessary to produce a desired physiological effect.
As used herein, the term “homeopathically effective” amount is meant to refer to an amount of a oligonucleotide composition that is non-toxic and is the lowest amount necessary to provide a desired physiological effect. A homeopathic effect, in accordance with the present invention, is achieved by a dose of modified nucleic acid that will be effective in treating (i.e., relieving, ameliorating, or preventing) symptoms of a particular condition or disease. Such treatment may be prophylactic in nature (i.e., completely or partially preventing the future occurrence of a symptom) and/or it may be therapeutic in nature (i.e., providing a partial or complete cessation or amelioration of a symptom). The method of treating of the present invention covers any treatment of symptoms of a disorder in a mammal, particularly a human, and includes:
(a) preventing symptoms of a disorder from occurring in a subject that may be predisposed to a condition but has not yet been diagnosed as having it;
(b) inhibiting symptoms of a disorder (i.e., arresting its development); or
(c) relieving symptoms of a disorder (i.e., ameliorating and/or causing regression of the condition); and/or
(d) maintaining homeostasis (i.e., the normal balance of RNA or DNA in a subject).
One of ordinary skill will appreciate that, from a medical practitioner's or patient's perspective, virtually any alleviation or prevention of an undesirable symptom would be desirable. Homeopathic compositions typically employ substantially less nucleic acid than is employed in allopathic compositions. Exemplary dosages to be employed in accordance with the present invention, are described in Table 3 below.
When used in the therapeutic treatment of disease, an appropriate dosage of one or more therapeutic compositions of the invention may be determined by any of several well-established methodologies. Additionally, dosages may also be altered depending upon factors such as the severity of infection, and the size or species of the host.
Preferably, animals are treated using compositions of the present invention having agents with compositions containing nucleic acid molecules having a sequence appropriate for the particular animal. Targeted species include, but are not limited to birds, fish, and mammals (especially pigs, goats, sheep, cows, dogs, horses, cats, and most preferably, humans).
Having now generally described the invention, the same will be more readily understood through reference to the following examples, which are provided by way of illustration, and are not intended to be limiting of the present invention, unless specified. The effectiveness of the RNA oligonucleotide compositions according to the preferred embodiments of the present invention is demonstrated in the Examples below.
Individuals with cancers were typically administered a composition containing oligonucleotides complementary to cyclo-oxygenase 2 and NFκB p65 at concentrations of 3 to 30 A260/RNA/ml (1.0-10 μg/kg). Some individuals were additionally administered oligonucleotides complementary to lipoxygenase 5. After approximately one to two months of therapy, the effect of the composition was then evaluated on individuals who completed the study (see Table 4). Treatment efficacy was evaluated by each patient and confirmed by the treating physician. A scaled score of 1 to 10 was used to evaluate treatment efficacy over a period of one to two months where a score=10 represented no improvement and a score=1 represented total alleviation of symptoms.
Individuals with excessive appetite were orally administered an oligonucleotide composition containing RNA oligonucleotides complementary to the tripeptidyl gene. RNA oligonucleotide concentrations were typically 0.3 to 3.0 A260/RNA/ml and given in dosages (0.1-1.0 μg/kg of 0.5 ml twice daily). The effect of the composition was then evaluated after approximately one to two months of therapy (see Table 5). Treatment efficacy was evaluated by each patient and confirmed by the treating physician. A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a voracious appetite and a score=1 represented the absence of hunger and the ability to lose weight.
Individuals diagnosed with arthritis were orally administered oligonucleotide compositions with RNA oligonucleotides complementary to phosphodiesterase 4 and NFκB p65. Some people were additionally given compositions further containing RNA oligonucleotides complementary to other genes. RNA oligonucleotide concentrations were typically between the range of 0.3 to 300 A260/RNA/ml and given in dosages (0.1-100 μg/kg) of 0.5 ml twice daily. The effect of the composition was then evaluated after approximately one to two months of therapy (see Table 6). Treatment efficacy was evaluated by each patient and confirmed by the treating physician. A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented severe arthritis characterized by inability to freely move affected joints, restricted movement, pain and inflammation and a score=1 represented reduced inflammation, restoration of movement and the absence of pain.
Individuals with elevated blood pressure were orally administered oligonucleotide compositions with RNA oligonucleotides complementary to CE and/or neutral endopeptidase genes. Some individuals were additionally given compositions with RNA oligonucleotides complementary to other genes. Concentrations were typically 3.0 to 30 A260/RNA/ml and given in dosages (1.0-10 μg/kg) of 0.5 ml twice daily. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 7). Treatment efficacy was determined by measuring changes in blood pressure where a decrease in blood pressure below 160/89 was assessed as a successful treatment because blood pressure above this level has been associated with stroke, heart disease and kidney failure.
Individuals with elevated cholesterol were orally administered oligonucleotide compositions containing RNA oligonucleotides complementary to the 3-hydroxy-3-methylglutaryl-coenzyme A reductase gene. Some individuals were also given oligonucleotide compositions further containing RNA oligonucleotides complementary to other genes such as phosphodiesterase 4 and phosphodiesterase 5. RNA oligonucleotide concentrations were typically 3.0 to 30 A260/RNA/ml and given in dosages (1.0-10 μg/kg) of 0.5 ml twice daily. The effect of the composition on serum cholesterol was evaluated after approximately one to two months of therapy (see Table 8). Treatment efficacy was determined by measuring changes in serum cholesterol where a one-point drop corresponded to a two percent reduction in the probability of heart disease and a twenty-five-point drop corresponded to a fifty percent reduction in the probability of heart disease.
In addition, the effect of compositions containing RNA oligonucleotide with eight or more contiguous achiral internucleoside phosphate linkages on cholesterol levels was also assessed. In a representative individual, oligonucleotide compositions containing achiral RNA oligonucleotides complementary to 3-hydroxy-3-methylglutaryl-coenzyme A reductase, phosphodiesterase 4 and phosphodiesterase 5 were given orally in combination at a concentration of 3.0 A260/RNA/ml at dosages of 0.5 ml, twice daily. The achiral RNA oligonucleotides produced a decrease of 46 mg/mL in serum cholesterol. The achiral 2′methoxy-RNA supplements resulted in a 31 mg/mL decrease in serum cholesterol levels. Chiral RNA or DNA did not effect cholesterol levels.
Individuals with emotional distress were orally administered an oligonucleotide composition containing RNA oligonucleotides complementary to the phosphodiesterase 4 and phosphodiesterase 5 genes. RNA oligonucleotide concentrations were typically 0.3 to 3.0 A260/RNA/ml and were given in dosages (0.1-1.0 μg/kg) of 0.5 ml two to six times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 9). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a severely depressed patient with suicidal tendencies and a score=1 represented a emotionally stable patient.
Individuals with various gastrointestinal disorders were orally administered oligonucleotide compositions with RNA oligonucleotides complementary to the phosphodiesterase 4 and/or cyclooxygenase 2 genes. Some individuals were given compositions additionally containing RNA oligonucleotides complementary to other genes such as phosphodiesterase 5 and NFκB p65. Oligonucleotide concentrations were typically 0.3 to 3.0 A260/RNA/ml and given in 0.5 ml dosages (0.1-1.0 μg/kg) twice per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 10). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with above normal bowel movement frequency and the presence of blood in the feces and a score=1 represented a patient with normal frequency of bowel movements and the absence of blood in the feces.
Individuals with various types of inflammation were orally or topically (as indicated) administered oligonucleotide compositions containing oligonucleotides complementary to the phosphodiesterase 4 or interleukin 5 genes. Some individuals were given compositions additionally containing RNA oligonucleotides complementary to other genes such as cyclooxygenase 2 and NFκB p65. RNA oligonucleotide concentrations were typically 0.03 to 300 A260/RNA/ml given in doses (0.01-100 μg/kg) of 0.5 ml twice per day. The effect of the composition was then evaluated (see Table 11). A scaled score of 1 to 10 was used to evaluate treatment efficacy after approximately one to two months of therapy, where a score=10 represented presence of debilitating inflammation with severe pain and a score=1 represented the absence of inflammation and pain.
Individuals suffering from migraine headaches were orally administered oligonucleotide compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4, phosphodiesterase 5 cyclooxygenase 2 and 3-hydroxy-3-methylglutaryl-coenzyme A reductase genes. Oligonucleotide concentrations were typically 3.0 to 30 A260/RNA/ml taken in dosages (1.0-10 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 12). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented severe debilitating headache pain including facial pain accompanied by nausea and sensitivity to light and a score=1 represented the absence of these conditions.
Individuals with various neurological disorders were orally administered oligonucleotide compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4, cyclooxygenase 2 and p65 genes. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as lipoxygenase 5. Oligonucleotide concentrations were typically 3.0 to 30 A260/RNA/ml taken in dosages (1-10 μg/kg) of 0.5 ml two to four times per day. The effect of the compositions was evaluated after approximately one to two months of therapy (see Table 13). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with a debilitating form of the indicated neurological disorder (i.e., amyotrophic lateral sclerosis, multiple sclerosis, alzheimer's disease, parkinson's disease) and a score=1 represented a patient with no symptoms or mild symptoms associated with the indicated neurological disorder.
Individuals suffering from various types of pain were orally administered oligonucleotide compositions containing RNA oligonucleotides complementary to phosphodiesterase 4 and/or cyclooxygenase 2. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as phosphodiesterase 5 and p65. Oligonucleotide concentrations were typically 0.3 to 3.0 A260/RNA/ml and taken in dosages (0.1-10 μg/kg) of 0.5 ml two to four times a day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 14). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with severe pain requiring treatment with a subscription analgesic and a score=1 represented a patient with the absence of pain.
Female individuals diagnosed with pre-menstrual syndrome were orally administered oligonucleotide compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4 gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as phosphodiesterase 5 and cyclooxygenase 2. RNA oligonucleotide concentrations were typically 0.03 to 3.0 A260/RNA/ml taken in doses (0.01-1.0 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 15). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with cramps, bloating, irritability, nausea and vomiting and a score=1 represented a patient with the absence of these conditions.
Male individuals diagnosed with prostatitis were orally administered oligonucleotide compositions containing RNA oligonucleotides complementary to the steroid 5-alpha-reductase-2 gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as phosphodiesterase 4 and p65 (Super 8+composition=Asm, X2, D5, P65, cd-18, IL-5, LO5 and ICAM). Oligonucleotide concentrations were typically 3.0 A260/RNA/ml taken in doses (1.0 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 16). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with urgent need to urinate three to five times per night and a score=1 represented a patient who slept through the night without urinating.
Individuals suffering from cold and sinusitis symptoms were administered (intranasal) oligonucleotide compositions containing RNA oligonucleotides complementary to phosphodiesterase 4 and a DNA monomer, Nu 3. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other gene targets such as cyclooxygenase 2 and NFκB p65. RNA and DNA concentrations were typically 0.3 to 30 A260/RNA/ml (0.1-10 μg/kg). Treatment efficacy was evaluated after approximately one to two months of therapy (see Table 17). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with sneezing, stuffy nose and watery eyes and a score=1 represented a patient with the absence of these conditions.
Individuals with various types of trauma were orally or topically (as indicated) administered oligonucleotide compositions containing RNA oligonucleotides complementary to phosphodiesterase 4. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as cyclooxygenase 2 and NFκB p65. Oligonucleotide concentrations ranged from 0.3 to 3.0 A260/RNA/ml and taken in 0.5 ml doses (0.1-1.0 μg/kg) two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 18). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with severe inflammation and pain associated with the indicated trauma and a score=1 represented a patient with no inflammation or pain.
Individuals diagnosed with carpal tunnel syndrome were orally administered oligonucleotide compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4 gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as cyclooxygenase 2, NFκB p65 and other gene targets. Oligonucleotide concentrations were typically 0.03 to 300 A260/RNA/ml taken in doses (0.01-100 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 19). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with pain, tingling and numbness in the wrist area necessitating the use of a wrist brace and a score=1 represented a patient with the absence of these conditions and who did not require the assistance of a wrist brace.
Individuals diagnosed with chronic fatigue syndrome or fibromyalgia were orally administered oligonucleotide compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4 gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as cyclooxygenase 2 and p65. Oligonucleotide concentrations were typically 3.0 to 30 A260/RNA/ml taken in doses (1.0-10 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 20). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient who complained of being chronically exhaustion accompanied by minor aches and pain and a score=1 represented a patient who did not complain of any such symptom.
Individuals suffering from eczema and atopic dermatitis were orally or topically (as indicated) administered oligonucleotide compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4 gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as cyclooxygenase 2 and p65 and other gene targets. Oligonucleotide concentrations were typically 0.3 to 3.0 A260/RNA/ml taken in doses (0.1-1.0 g/kg) of 0.5 m two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 21). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented patient with itching, inflamed skin and minor bleeding, and a score=1 represented a patient with normal skin.
Male individuals suffering from erectile dysfunction were orally administered compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4 gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as phosphodiesterase-5. Oligonucleotide concentrations were typically 3.0 to 3.0 A260/RNA/ml taken in doses (1.0-10 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 22). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient who could not obtain or maintain an erection and a score=1 represented a patient who was able to obtain and maintain an erection.
Individuals suffering from acid reflux were orally administered compositions containing RNA oligonucleotides complementary to the ATP4A gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as ATP4B. Oligonucleotide concentrations were typically 3.0 to 30 A260/RNA/ml taken in doses (1.0-10 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 23). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with heartburn requiring treatment with excessive amounts of antacid medication and a score=1 represented a patient with no heartburn.
Individuals suffering from poison ivy were orally or topically (as indicated) administered compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4 gene. Oligonucleotide concentrations were typically 0.3 to 300 A260/RNA/ml taken in doses 0.1-100 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 24). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with poison ivy covering up to ninety-five percent of the entire body with dermal discharge and secondary inflammation restricting eye openings and a score=1 represented a patient without these symptoms.
Individuals with psoriasis were orally or topically administered compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4 gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as phosphodiesterase-5 and p65. Oligonucleotide concentrations were typically 0.3 to 300 A260/RNA/ml taken in doses of 0.5 ml (0.1-100 μg/kg) two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 25). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with thick silvery-colored scaly patches of skin with dermal discharge and bleeding and a score=1 represented a patient with normal skin.
Ten individuals with rosacea were orally or topically administered compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4 gene. Some individuals were given compositions containing additional RNA oligonucleotides complementary to other genes such as cyclooxygenase 2 and p65. Oligonucleotide concentrations were typically 0.3 to 300 A260/RNA/ml taken in doses (0.1-100 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was evaluated after approximately one to two months of therapy (see Table 26). A scaled score of 1 to 10 was used to evaluate treatment efficacy where a score=10 represented a patient with red, inflamed facial skin with pimples (e.g., acne) and a score represented a patient normal skin.
For animal studies, animals with different indications were provided with oligonucleotide compositions containing RNA oligonucleotides complementary to the phosphodiesterase 4, phosphodiesterase 5 genes or as indicated in FIG. 24. Some animals were additionally given compositions containing additional RNA oligonucleotides complementary to other genes such as cyclooxygenase 2 and p65. Oligonucleotide concentrations were typically 0.3 to 300 A260/RNA/ml taken in doses (0.1-100 μg/kg) of 0.5 ml two to four times per day. The effect of the composition was then evaluated (see Table 27). Treatment efficacy was evaluated by an attending veterinarian.
The following is the method for selecting nucleic acid sequences from a known gene sequence for the design of oligonucleotides. Preferred choices are sequences that either are adjacent to, or overlap the start site, followed by sequences that are in the 5′ un-translated region, followed by sequences immediately adjacent to or overlapping the termination signal. This method is very effective and when combined with, achiral RNA, it produces oligonucleotides that display therapeutic efficacy consistently.
For example, achiral RNA oligonucleotides (10-30 bases in length), or achiral 2′-methoxy oligonucleotides (10-30 bases in length), or achiral 2′-methoxy oligonucleotides (10-30 bases in length) with
(a) 3′ or 3′ & 5′ acid stable end-blocks located in the 5′ UTR, or
(b) immediately adjacent to or more preferably overlapping at least one of the three bases of the start site and extending either 5′ or 3′ of the start site, or
(c) immediately adjacent to or overlapping one of the three bases of the termination signal and extending 3′ or 5′ of the termination site that are ten to thirty contiguous bases in length and complementary to a RNA or DNA and that have the following binding characteristics:
(d) ΔG of the oligonucleotide binding the complementary RNA strand at 37° C.
(i) (G37°)≦−15 KCal or less (more negative=more stable) for 10 to 14 mer,
(ii) (G37°)≦−20 KCal or less (more negative=more stable) for 15 to 17 mer,
(iii) (G37°)≦−25 KCal or less (more negative=more stable) for 18 to 20 mer,
(iv) (G37°)≦−30 KCal or less (more negative=more stable) for 21 to 23 mer,
(v) (G37°)≦−35 KCal or less (more negative=more stable) for 24 to 30 mer,
(e) the ΔG of any hairpin structure the oligonucleotide could assume is ≧−3.0,
(f) the Tm any hairpin that could form is at least 10° C. lower than the Tm of the oligonucleotide binding to the target RNA or DNA,
(g) a melting temperature for the oligonucleotide binding to the target RNA is 45° C. by the percent GC method at 1.0 M salt
For composition parameters, the percent G+C of the oligonucleotide to be used is >35 percent and are administered so that each specific RNA is at a concentration (1.0 g/100 ml), or lower in doses not to exceed 100 μg/kg per RNA, or more preferably 10 μg/kg, or more preferably 1 μg/kg, or still more preferably <1 μg/kg. Sequences are then screened to be sure they do not overlap the same regions in other known genes by conducting BLAST searches against the entire GenBank list of human sequences.
Factors contributing to the selective inhibition of gene expression in vivo by the modified oligonucleotides of the invention include the influence of chirality on melting temperature. 2′-O-methyl modified RNA oligonucleotides with achiral linkages resemble backbone linkages that very closely resemble normal unmodified nucleic acids. Typically, oligonucleotides synthesized using phosphoramidite based synthesis of phosphorothioates produces mixed isomers present at each modified phosphorothioate linkage. A measurable result of the presence of these mixed isomers is a decrease in melting temperature of the phosphorothioate oligonucleotide in a primer target duplex as compared to an unmodified oligonucleotide in the same duplex. The melting temperature of a 2′-O-methyl RNA oligonucleotide, however, is not substantially lowered relative to an unmodified oligonucleotide. Thus, the melting temperatures for 2′-O-methyl RNA oligonucleotides closely resemble those for unmodified RNA because the presence of the 2′-O-methyl group does not result in the generation of isomers.
While the invention has been described and illustrated herein by references to various specific materials, procedures and examples, it is understood that the invention is not restricted to the particular combinations of material and procedures selected for that purpose. Numerous variations of such details can be implied as will be appreciated by those skilled in the art. It is intended that the specification and examples be considered as exemplary, only, with the true scope and spirit of the invention being indicated by the following claims. All references, patents and patent applications referred to in this application are herein incorporated by reference in their entirety.
This application is a Continuation of U.S. patent application Ser. No. 10/191,997, “Oligonucleotide-Containing Pharmacological Compositions and Their Use”, Roderic M. K. Dale, first author, filed Jul. 10, 2002 (abandoned), and claims the benefit of U.S. Provisional Application No. 60/303,820, filed on Jul. 10, 2001.
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