# Patent

## Title
Modulation of immunostimulatory properties of oligonucleotide-based compounds by utilizing modified immunostimulatory dinucleotides

## Abstract

The invention relates to the therapeutic use of oligonucleotides as immunostimulatory agents in immunotherapy applications. More particularly, the invention provides immunomers and an immunostimulatory oligonucleotides for use in methods for generating an immune response or for treating a patient in need of immunostimulation. The immunomers and an immunostimulatory oligonucleotides of the invention preferably comprise novel purines. The immunomers according to the invention further comprise at least two oligonucleotides linked at their 3′ ends, internucleoside linkages or functionalized nucleobase or sugar to a non-nucleotidic linker, at least one of the oligonucleotides being an immunomodulatory oligonucleotide and having an accessible 5′ end.

## Background
RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application Ser. No. 60/440,587, filed on Jan. 16, 2003, the entire contents of which are incorporated herein by reference.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The invention relates to immunology and immunotherapy applications using oligonucleotides as immunostimulatory agents.
2. Summary of the Related Art
Oligonucleotides have become indispensable tools in modern molecular biology, being used in a wide variety of techniques, ranging from diagnostic probing methods to PCR to antisense inhibition of gene expression and immunotherapy applications. This widespread use of oligonucleotides has led to an increasing demand for rapid, inexpensive and efficient methods for synthesizing oligonucleotides.
The synthesis of oligonucleotides for antisense and diagnostic applications can now be routinely accomplished. See, e.g., Methods in Molecular Biology, Vol. 20: Protocols for Oligonucleotides and Analogs pp. 165-189 (S. Agrawal, ed., Humana Press, 1993); Oligonucleotides and Analogues, A Practical Approach, pp. 87-108 (F. Eckstein, ed., 1991); and Uhlmann and Peyman, supra; Agrawal and Iyer, Curr. Op. in Biotech. 6:12 (1995); and Antisense Research and Applications (Crooke and Lebleu, eds., CRC Press, Boca Raton, 1993). Early synthetic approaches included phosphodiester and phosphotriester chemistries. For example, Khorana et al., J. Molec. Biol. 72:209 (1972) discloses phosphodiester chemistry for oligonucleotide synthesis. Reese, Tetrahedron Lett. 34:3143-3179 (1978), discloses phosphotriester chemistry for synthesis of oligonucleotides and polynucleotides. These early approaches have largely given way to the more efficient phosphoramidite and H-phosphonate approaches to synthesis. For example, Beaucage and Caruthers, Tetrahedron Lett. 22:1859-1862 (1981), discloses the use of deoxyribonucleoside phosphoramidites in polynucleotide synthesis. Agrawal and Zamecnik, U.S. Pat. No. 5,149,798 (1992), discloses optimized synthesis of oligonucleotides by the H-phosphonate approach. Both of these modern approaches have been used to synthesize oligonucleotides having a variety of modified internucleotide linkages. Agrawal and Goodchild, Tetrahedron Lett. 28:3539-3542 (1987), teaches synthesis of oligonucleotide methylphosphonates using phosphoramidite chemistry. Connolly et al., Biochem. 23:3443 (1984), discloses synthesis of oligonucleotide phosphorothioates using phosphoramidite chemistry. Jager et al., Biochem. 27:7237 (1988), discloses synthesis of oligonucleotide phosphoramidates using phosphoramidite chemistry. Agrawal et al., Proc. Natl. Acad. Sci. (USA) 85:7079-7083 (1988), discloses synthesis of oligonucleotide phosphoramidates and phosphorothioates using H-phosphonate chemistry.
More recently, several researchers have demonstrated the validity of the use of oligonucleotides as immunostimulatory agents in immunotherapy applications. The observation that phosphodiester and phosphorothioate oligonucleotides can induce immune stimulation has created interest in developing this side effect as a therapeutic tool. These efforts have focused on phosphorothioate oligonucleotides containing the dinucleotide natural CpG. Kuramoto et al., Jpn. J. Cancer Res. 83:1128-1131 (1992) teaches that phosphodiester oligonucleotides containing a palindrome that includes a CpG dinucleotide can induce interferon-alpha and gamma synthesis and enhance natural killer activity. Krieg et al., Nature 371:546-549 (1995) discloses that phosphorothioate CpG-containing oligonucleotides are immunostimulatory. Liang et al., J. Clin. Invest. 98:1119-1129 (1996) discloses that such oligonucleotides activate human B cells. Moldoveanu et al., Vaccine 16:1216-124 (1998) teaches that CpG-containing phosphorothioate oligonucleotides enhance immune response against influenza virus. McCluskie and Davis, J. Immunol. 161:4463-4466 (1998) teaches that CpG-containing oligonucleotides act as potent adjuvants, enhancing immune response against hepatitis B surface antigen. Hartman et al., J. Immunol 164: 1617-1624 (2000) teaches that the immunostimulatory sequence is species specific, and different between mice and primates.
Other modifications of CpG-containing phosphorothioate oligonucleotides can also affect their ability to act as modulators of immune response. See, e.g., Zhao et al., Biochem. Pharmacol. (1996) 51:173-182; Zhao et al., Biochem Pharmacol. (1996) 52:1537-1544; Zhao et al., Antisense Nucleic Acid Drug Dev. (1997) 7:495-502; Zhao et al., Bioorg. Med. Chem. Lett. (1999) 9:3453-3458; Zhao et al., Bioorg. Med. Chem. Lett. (2000) 10:1051-1054; Yu et al., Bioorg. Med. Chem. Lett. (2000) 10:2585-2588; Yu et al., Bioorg. Med. Chem. Lett. (2001) 11:2263-2267; and Kandimalla et al., Bioorg. Med. Chem. (2001) 9:807-813.
These reports make clear that there remains a need to be able to modulate the immune response caused by immunostimulatory oligonucleotides and to overcome species specificity of the immunostimulatory sequences.
BRIEF SUMMARY OF THE INVENTION
The invention provides methods for modulating the immune response caused by oligonucleotide compounds. The methods according to the invention enable modifying the cytokine profile produced by immunostimulatory oligonucleotides for immunotherapy applications. The present inventors have surprisingly discovered that modification of immunostimulatory dinucleotides allows flexibility in the nature of the immune response produced and that certain modifications overcome the species specificities observed to date of the immunostimulatory sequences. In cetain preferred embodiments, the modified dinucleotide is in the context of an “immunomer”, as further described below.
In a first aspect, therefore, the invention provides immunostimulatory oligonucleotides or immunomers comprising at least one immunostimulatory dinucleotide comprising at least one modified purine or pyrimidine.
In one embodiment, the immunomodulatory oligonucleotide or immunomer comprises an immunostimulatory dinucleotide of formula 5′-Pyr-Pur-3′, wherein Pyr is a natural or non-natural pyrimidine nucleoside and Pur is a natural or non-natural purine nucleoside. In another preferred embodiment, the immunomodulatory oligonucleotide or immunomer comprises an immunostimulatory dinucleotide of formula 5′-Pur*-Pur-3′, wherein Pur* is a non-natural purine nucleoside and Pur is a natural or non-natural purine nucleoside. A particularly preferred synthetic purine is 2-oxo-7-deaza-8-methyl-purine. When this synthetic purine is in the Pur* position of the dinucleotide, species-specificity (sequence dependence) of the immunostimulatory effect is overcome and cytokine profile is improved.
In another embodiment, the immunomodulatory oligonucleotide or immunomer comprises an immunostimulatory dinucleotide selected from the group consisting of CpG, C*pG, CpG*, and C*pG*, wherein the base of C is cytosine, the base of C* is thymine, 5-hydroxycytosine, N4-alkyl-cytosine, 4-thiouracil or other non-natural pyrimidine nucleoside or 2-oxo-7-deaza-8-methyl-purine, wherein when the base is 2-oxo-7-deaza-8-methyl-purine, it is preferably covalently bound to the 1′-position of a pentose via the 1 position of the base; the base of G is guanine, the base of G* is 2-amino-6-oxo-7-deazapurine, 2-amino-6-thiopurine, 6-oxopurine, or other non-natural purine nucleoside, and p is an internucleoside linkage selected from the group consisting of phosphodiester, phosphorothioate, and phosphorodithioate. In certain preferred embodiments, the immunostimulatory dinucleotide is not CpG.
In yet another embodiment, the immunomodulatory oligonucleotide comprises an immunostimulatory domain of formula (III):

5′-Nn-N1-Y—Z—N1-Nn-3′  (III)

    
    
        wherein:
        the base of Y is cytosine, thymine, 5-hydroxycytosine, N4-alkyl-cytosine, 4-thiouracil, or 2-oxo-7-deaza-8-methyl-purine, wherein when the base is 2-oxo-7-deaza-8-methyl-purine, it is preferably covalently bound to the 1′-position of a pentose via the 1 position of the base;
        the base of Z is guanine, 2-amino-6-oxo-7-deazapurine, 2-amino-6-thiopurine, or 6-oxopurine.
    
    


N1 and Nn independently at each occurrence, is preferably a naturally occurring or a synthetic nucleoside or an immunostimulatory moiety selected from the group consisting of a basic nucleosides, arabinonucleosides, 2′-deoxyuridine, α-deoxyribonucleosides, β-L-deoxyribonucleosides, and nucleosides linked by a phosphodiester or modified internucleoside linkage to the adjacent nucleoside on the 3′ side, the modified internucleotide linkage being selected from, without limitation, a linker having a length of from about 2 angstroms to about 200 angstroms, C2-C18 alkyl linker, poly(ethylene glycol) linker, 2-aminobutyl-1,3-propanediol linker, glyceryl linker, 2′-5′ internucleoside linkage, and phosphorothioate, phosphorodithioate, or methylphosphonate internucleoside linkage;

    
    
        provided that at least one N1 or Nn is optionally an immunostimulatory moiety;
        wherein n is a number from 0-30;
        wherein the 3′end, an internucleotide linkage, or a functionalized nucleobase or sugar may or may not be linked directly or via a non-nucleotidic linker to another oligonucleotide, which may or may not be immunostimulatory. When the immunomodulatory oligonucleotide is linked to another oligonucleotide, it is referred to as an “immunomer”.
    
    


In a second aspect, the invention provides immunomer conjugates, comprising an immunomer, as described above, and an antigen conjugated to the immunomer at a position other than the accessible 5′ end. Similarly, if the oligonucleotide is not linked to another oligonucleotide, but is linked to an antigen at any position other than its accessible 5′ end it is referred to as an “immunomodulatory oligonucleotide conjugate.”
In a third aspect, the invention provides pharmaceutical formulations comprising an immunostimulatory oligonucleotide, an immunomodulatory oligonucleotide conjugate, an immunomer or an immunomer conjugate according to the invention or combinations of two or more thereof and a physiologically acceptable carrier.
In a fourth aspect, the invention provides methods for generating an immune response in a vertebrate, such methods comprising administering to the vertebrate an immunostimulatory oligonucleotide, an immunomodulatory oligonucleotide conjugate, an immunomer or an immunomer conjugate according to the invention, or combinations of two or more thereof. In some embodiments, the vertebrate is a mammal.
In a fifth aspect, the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient an immunostimulatory oligonucleotide, an immunomodulatory oligonucleotide conjugate, an immunomer or immunomer conjugate according to the invention, or combinations of two or more thereof. In various embodiments, the disease or disorder to be treated is cancer, an autoimmune disorder, airway inflammation, asthma, allergy, or a disease caused by a pathogen.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic representation of representative immunomers of the invention.
FIG. 2 depicts several representative immunomers of the invention (All sequences are shown in SEQ ID NO: 4).
FIG. 3 depicts a group of representative small molecule linkers suitable for linear synthesis of immumomers of the invention.
FIG. 4 depicts a group of representative small molecule linkers suitable for parallel synthesis of immunomers of the invention.
FIG. 5 is a synthetic scheme for the linear synthesis of immunomers of the invention. DMTr=4,4′-dimethoxytrityl; CE=cyanoethyl.
FIG. 6 is a synthetic scheme for the parallel synthesis of immunomers of the invention. DMTr=4,4′-dimethoxytrityl; CE=cyanoethyl.
FIG. 7A is a graphic representation of the induction of IL-12 by immunomers 1-3 in BALB/c mouse spleen cell cultures. These data suggest that Immunomer 2, which has accessible 5′-ends, is a stronger inducer of IL-12 than monomeric Oligo 1, and that Immunomer 3, which does not have accessible 5′-ends, has equal or weaker ability to produce immune stimulation compared with oligo 1.
FIG. 7B is a graphic representation of the induction of IL-6 (top to bottom, respectively) by Immunomers 1-3 in BALB/c mouse spleen cells cultures. These data suggest that Immunomer 2, which has accessible 5′-ends, is a stronger inducer of IL-6 than monomeric Oligo 1, and that Immunomer 3, which does not have accessible 5′-ends, has equal or weaker ability to induce immune stimulation compared with Oligo 1.
FIG. 7C is a graphic representation of the induction of IL-10 by Immunomers 1-3 (top to bottom, respectively) in BALB/c mouse spleen cell cultures.
FIG. 8A is a graphic representation of the induction of BALB/c mouse spleen cell proliferation in cell cultures by different concentrations of Immunomers 5 and 6, which have inaccessible and accessible 5′-ends, respectively.
FIG. 8B is a graphic representation of BALB/c mouse spleen enlargement by Immunomers 4-6, which have an immunogenic chemical modification in the 5′-flanking sequence of the CpG motif. Again, the immunomer, which has accessible 5′-ends (6), has a greater ability to increase spleen enlargement compared with Immunomer 5, which does not have accessible 5′-end and with monomeric Oligo 4.
FIG. 9A is a graphic representation of induction of IL-12 by different concentrations of Oligo 4 and Immunomers 7 and 8 in BALB/c mouse spleen cell cultures.
FIG. 9B is a graphic representation of induction of IL-6 by different concentrations of Oligo 4 and Immunomers 7 and 8 in BALB/c mouse spleen cell cultures.
FIG. 9C is a graphic representation of induction of IL-10 by different concentrations of Oligo 4 and Immunomers 7 and 8 in BALB/c mouse spleen cell cultures.
FIG. 10A is a graphic representation of the induction of cell proliferation by Immunomers 14, 15, and 16 in BALB/c mouse spleen cell cultures.
FIG. 10B is a graphic representation of the induction of cell proliferation by IL-12 by different concentrations of Immunomers 14 and 16 in BALB/c mouse spleen cell cultures.
FIG. 10C is a graphic representation of the induction of cell proliferation by IL-6 by different concentrations of Immunomers 14 and 16 in BALB/c mouse spleen cell cultures.
FIG. 11A is a graphic representation of the induction of cell proliferation by Oligo 4 and 17 and Immunomers 19 and 20 in BALB/c mouse spleen cell cultures.
FIG. 11B is a graphic representation of the induction of IL-12 production by different concentrations of Oligo 4 and 17 and Immunomers 19 and 20 in BALB/c mouse spleen cell cultures.
FIG. 11C is a graphic representation of the induction of IL-6 production by different concentrations of Oligo 4 and 17 and Immunomers 19 and 20 in BALB/c mouse spleen cell cultures.
FIG. 12 is a graphic representation of BALB/c mouse spleen enlargement using oligonucleotides 4 and immunomers 14, 23, and 24.
FIG. 13 is a schematic representation of the 3′-terminal nucleoside of an oligonucleotide, showing that a non-nucleotidic linkage can be attached to the nucleoside at the nucleobase, at the 3′ position, or at the 2′ position.
FIG. 14 shows the chemical substitutions used in Example 13.
FIG. 15 shows cytokine profiles obtained using the modified oligonucleotides of Example 13.
FIG. 16 shows relative cytokine induction for glycerol linkers compared with amino linkers.
FIG. 17 shows relative cytokine induction for various linkers and linker combinations.
FIGS. 18A-E shows relative nuclease resistance for various PS and PO immunomers and oligonucleotides.
FIG. 19 shows relative cytokine induction for PO immunomers compared with PS immunomers in BALB/c mouse spleen cell cultures.
FIG. 20 shows relative cytokine induction for PO immunomers compared with PS immunomers in C3H/Hej mouse spleen cell cultures.
FIG. 21 shows relative cytokine induction for PO immunomers compared with PS immunomers in C3H/Hej mouse spleen cell cultures at high concentrations of immunomers.
FIG. 22 shows some pyrimidine and purine structures.
FIG. 23 shows some immunostimulatory oligonucleotides or immunomers used in the present study (SEQ ID NOS 4, 189, 10, 25 and 190-192, respectively in order of appearance).
FIG. 24 shows a comparison of a natural CpG motif and an immonostimulatory motif having a synthetic purine-pG dinucleotide.
FIG. 25 shows the IL-12 and IL-6 profiles of various immunostimulatory oligonucleotides used in the present study.
FIG. 26 shows the IL-12 and IL-6 profiles of additional immunostimulatory oligonucleotides used in the present study.
FIG. 27 shows the IL-12 and IL-6 profiles of immunostimulatory oligonucleotides and immunomers used in the present study.
FIG. 28 compares IL-12 and IL-6 profiles provided by mouse and human motifs in immunostimulatory oligonucleotides and immunomers.
FIG. 29 shows activation of NF-κB and degradation of Iκ-Bα in J774 cells treated with various immunostimulatory oligonucleotides and immunomers.
FIG. 30 shows immunostimulatory activity of an immunomer in human PBMC culture.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
The invention relates to the therapeutic use of oligonucleotides as immunostimulatory agents for immunotherapy applications. The issued patents, patent applications, and references that are cited herein are hereby incorporated by reference to the same extent as if each was specifically and individually indicated to be incorporated by reference. In the event of inconsistencies between any teaching of any reference cited herein and the present specification, the latter shall prevail for purposes of the invention.
The invention provides methods for enhancing the immune response caused by immunostimulatory compounds used for immunotherapy applications such as, but not limited to, treatment of cancer, autoimmune disorders, asthma, respiratory allergies, food allergies, and bacteria, parasitic, and viral infections in adult and pediatric human and veterinary applications. Thus, the invention further provides compounds having optimal levels of immunostimulatory effect for immunotherapy and methods for making and using such compounds. In addition, compounds of the invention are useful as adjuvants in combination with DNA vaccines, antibodies, and allergens; and in combination with chemotherapeutic agents and/or antisense oligonucleotides.
The present inventors have surprisingly discovered that modification of an immunomodulatory oligonucleotide to optimally present its 5′ ends dramatically affects its immunostimulatory capabilities. In addition, the present inventors have discovered that the cytokine profile and species specificity of an immune response can be modulated by using novel purine or pyrimidine structures as part of an immunomodulatory oligonucleotide or an immunomer.
In a first aspect, the invention provides immunostimulatory oligonucleotides or “immunomers”, the latter comprising at least two oligonucleotides linked at their 3′ ends, or an internucleoside linkage or a functionalized nucleobase or sugar to a non-nucleotidic linker, at least one of the oligonucleotides being an immunomodulatory oligonucleotide and having an accessible 5′ end. As used herein, the term “accessible 5′end” means that the 5′ end of the oligonucleotide is sufficiently available such that the factors that recognize and bind to immunomers and stimulate the immune system have access to it. In oligonucleotides having an accessible 5′ end, the 5′ OH position of the terminal sugar is not covalently linked to more than two nucleoside residues or any other moiety that interferes with interaction with the 5′ end. Optionally, the 5′ OH can be linked to a phosphate, phosphorothioate, or phosphorodithioate moiety, an aromatic or aliphatic linker, cholesterol, or another entity which does not interfere with accessibility. The immunostimulatory oligonucleotides or immunomers according to the invention preferably further comprise an immunostimulatory dinucleotide comprising a novel purine or pyrimidine.
In some embodiments, immunostimulatory oligonucleotides according to the invention may have oligonucleotide sequences connected 5′ to 3′ by linkers, such as those shown in FIG. 14.
In some embodiments, the immunomer comprises two or more immunostimulatory oligonucleotides, (in the context of the immunomer) which may be the same or different. Preferably, each such immunomodulatory oligonucleotide has at least one accessible 5′ end.
In certain embodiments, in addition to the immunostimulatory oligonucleotide(s), the immunomer also comprises at least one oligonucleotide that is complementary to a gene or its RNA product. As used herein, the term “complementary to” means that the oligonucleotide hybridizes under physiological conditions to a region of the gene. In some embodiments, the oligonucleotide downregulates expression of a gene. Such downregulatory oligonucleotides preferably are selected from the group consisting of antisense oligonucleotides, ribozyme oligonucleotides, small inhibitory RNAs and decoy oligonucleotides. As used herein, the term “downregulate a gene” means to inhibit the transcription of a gene or translation of a gene product. Thus, the immunomers according to these embodiments of the invention can be used to target one or more specific disease targets, while also stimulating the immune system.
In certain embodiments, the immunomer includes a ribozyme or a decoy oligonucleotide. As used herein, the term “ribozyme” refers to an oligonucleotide that possesses catalytic activity. Preferably, the ribozyme binds to a specific nucleic acid target and cleaves the target. As used herein, the term “decoy oligonucleotide” refers to an oligonucleotide that binds to a transcription factor in a sequence-specific manner and arrests transcription activity. Preferably, the ribozyme or decoy oligonucleotide exhibits secondary structure, including, without limitation, stem-loop or hairpin structures. In certain embodiments, at least one oligonucleotide comprises poly(I)-poly(C). In certain embodiments, at least one set of Nn includes a string of 3 to 10 dGs and/or Gs or 2′-substituted ribo or arabino Gs.
For purposes of the invention, the term “oligonucleotide” refers to a polynucleoside formed from a plurality of linked nucleoside units. Such oligonucleotides can be obtained from existing nucleic acid sources, including genomic or cDNA, but are preferably produced by synthetic methods. In preferred embodiments each nucleoside unit includes a heterocyclic base and a pentofuranosyl, trehalose, arabinose, 2′-deoxy-2′-substituted arabinose, 2′-O-substituted arabinose or hexose sugar group. The nucleoside residues can be coupled to each other by any of the numerous known internucleoside linkages. Such internucleoside linkages include, without limitation, phosphodiester, phosphorothioate, phosphorodithioate, alkylphosphonate, alkylphosphonothioate, phosphotriester, phosphoramidate, siloxane, carbonate, carboalkoxy, acetamidate, carbamate, morpholino, borano, thioether, bridged phosphoramidate, bridged methylene phosphonate, bridged phosphorothioate, and sulfone internucleoside linkages. The term “oligonucleotide” also encompasses polynucleosides having one or more stereospecific internucleoside linkage (e.g., (RP)- or (SP)-phosphorothioate, alkylphosphonate, or phosphotriester linkages). As used herein, the terms “oligonucleotide” and “dinucleotide” are expressly intended to include polynucleosides and dinucleosides having any such internucleoside linkage, whether or not the linkage comprises a phosphate group. In certain preferred embodiments, these internucleoside linkages may be phosphodiester, phosphorothioate, or phosphorodithioate linkages, or combinations thereof.
In some embodiments, the oligonucleotides each have from about 3 to about 35 nucleoside residues, preferably from about 4 to about 30 nucleoside residues, more preferably from about 4 to about 20 nucleoside residues. In some embodiments, the immunomers comprise oligonucleotides have from about 5 to about 18, or from about 5 to about 14, nucleoside residues. As used herein, the term “about” implies that the exact number is not critical. Thus, the number of nucleoside residues in the oligonucleotides is not critical, and oligonucleotides having one or two fewer nucleoside residues, or from one to several additional nucleoside residues are contemplated as equivalents of each of the embodiments described above. In some embodiments, one or more of the oligonucleotides have 11 nucleotides. In the context of immunostimulatory oligonucleotides, preferred embodiments have from about 13 to about 35 nucleotides, more preferably from about 13 to about 26 nucleotides.
The term “oligonucleotide” also encompasses polynucleosides having additional substituents including, without limitation, protein groups, lipophilic groups, intercalating agents, diamines, folic acid, cholesterol and adamantane. The term “oligonucleotide” also encompasses any other nucleobase containing polymer, including, without limitation, peptide nucleic acids (PNA), peptide nucleic acids with phosphate groups (PHONA), locked nucleic acids (LNA), morpholino-backbone oligonucleotides, and oligonucleotides having backbone sections with alkyl linkers or amino linkers.
The oligonucleotides of the invention can include naturally occurring nucleosides, modified nucleosides, or mixtures thereof. As used herein, the term “modified nucleoside” is a nucleoside that includes a modified heterocyclic base, a modified sugar moiety, or a combination thereof. In some embodiments, the modified nucleoside is a non-natural pyrimidine or purine nucleoside, as herein described. In some embodiments, the modified nucleoside is a 2′-substituted ribonucleoside an arabinonucleoside or a 2′-deoxy-2′-substituted-arabinoside.
For purposes of the invention, the term “2′-substituted ribonucleoside” or “2′-substituted arabinoside” includes ribonucleosides or arabinonucleoside in which the hydroxyl group at the 2′ position of the pentose moiety is substituted to produce a 2′-substituted or 2′-O-substituted ribonucleoside. Preferably, such substitution is with a lower alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an aryl group having 6-10 carbon atoms, wherein such alkyl, or aryl group may be unsubstituted or may be substituted, e.g., with halo, hydroxy, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl, carboalkoxy, or amino groups. Examples of 2′-O-substituted ribonucleosides or 2′-O-substituted-arabinosides include, without limitation 2′-O-methylribonucleosides or 2′-O-methylarabinosides and 2′-O-methoxyethylribonucleosides or 2′-O-methoxyethylarabinosides.
The term “2′-substituted ribonucleoside” or “2′-substituted arabinoside” also includes ribonucleosides or arabinonucleosides in which the 2′-hydroxyl group is replaced with a lower alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an amino or halo group. Examples of such 2′-substituted ribonucleosides or 2′-substituted arabinosides include, without limitation, 2′-amino, 2′-fluoro, 2′-allyl, and 2′-propargyl ribonucleosides or arabinosides.
The term “oligonucleotide” includes hybrid and chimeric oligonucleotides. A “chimeric oligonucleotide” is an oligonucleotide having more than one type of internucleoside linkage. One preferred example of such a chimeric oligonucleotide is a chimeric oligonucleotide comprising a phosphorothioate, phosphodiester or phosphorodithioate region and non-ionic linkages such as alkylphosphonate or alkylphosphonothioate linkages (see e.g., Pederson et al. U.S. Pat. Nos. 5,635,377 and 5,366,878).
A “hybrid oligonucleotide” is an oligonucleotide having more than one type of nucleoside. One preferred example of such a hybrid oligonucleotide comprises a ribonucleotide or 2′-substituted ribonucleotide region, and a deoxyribonucleotide region (see, e.g., Metelev and Agrawal, U.S. Pat. Nos. 5,652,355, 6,346,614 and 6,143,881).
For purposes of the invention, the term “immunostimulatory oligonucleotide” refers to an oligonucleotide as described above that induces an immune response when administered to a vertebrate, such as a fish, fowl, or mammal. As used herein, the term “mammal” includes, without limitation rats, mice, cats, dogs, horses, cattle, cows, pigs, rabbits, non-human primates, and humans. Useful immunostimulatory oligonucleotides can be found described in Agrawal et al., WO 98/49288, published Nov. 5, 1998; WO 01/12804, published Feb. 22, 2001; WO 01/55370, published Aug. 2, 2001; PCT/US01/13682, filed Apr. 30, 2001; and PCT/US01/30137, filed Sep. 26, 2001. Preferably, the immunomodulatory oligonucleotide comprises at least one phosphodiester, phosphorothioate, or phosphorodithioate internucleoside linkage.
In some embodiments, the immunomodulatory oligonucleotide comprises an immunostimulatory dinucleotide of formula 5′-Pyr-Pur-3′, wherein Pyr is a natural or synthetic pyrimidine nucleoside and Pur is a natural or synthetic purine nucleoside. In some preferred embodiments, the immunomodulatory oligonucleotide comprises an immunostimulatory dinucleotide of formula 5′-Pur*-Pur-3′, wherein Pur* is a synthetic purine nucleoside and Pur is a natural or synthetic purine nucleoside. In various places the dinucleotide is expressed as RpG, C*pG or YZ, in which case respectively, R, C*, or Y represents a synthetic purine. A particularly preferred synthetic purine is 2-oxo-7-deaza-8-methyl-purine. When this synthetic purine is in the Pur* position of the dinucleotide, species-specificity (sequence dependence) of the immunostimulatory effect is overcome and cytokine profile is improved. As used herein, the term “pyrimidine nucleoside” refers to a nucleoside wherein the base component of the nucleoside is a monocyclic nucleobase. Similarly, the term “purine nucleoside” refers to a nucleoside wherein the base component of the nucleoside is a bicyclic nucleobase. For purposes of the invention, a “synthetic” pyrimidine or purine nucleoside includes a non-naturally occurring pyrimidine or purine base, a non-naturally occurring sugar moiety, or a combination thereof.
Preferred pyrimidine nucleosides according to the invention have the structure (I):




wherein:

    
    
        D is a hydrogen bond donor;
        D′ is selected from the group consisting of hydrogen, hydrogen bond donor, hydrogen bond acceptor, hydrophilic group, hydrophobic group, electron withdrawing group and electron donating group;
        A is a hydrogen bond acceptor or a hydrophilic group;
        A′ is selected from the group consisting of hydrogen bond acceptor, hydrophilic group, hydrophobic group, electron withdrawing group and electron donating group;
        X is carbon or nitrogen; and
    
    


S′ is a pentose or hexose sugar ring, or a non-naturally occurring sugar.
Preferably, the sugar ring is derivatized with a phosphate moiety, modified phosphate moiety, or other linker moiety suitable for linking the pyrimidine nucleoside to another nucleoside or nucleoside analog.
Preferred hydrogen bond donors include, without limitation, —NH—, —NH2, —SH and —OH. Preferred hydrogen bond acceptors include, without limitation, C═O, C═S, and the ring nitrogen atoms of an aromatic heterocycle, e.g., N3 of cytosine.
In some embodiments, the base moiety in (I) is a non-naturally occurring pyrimidine base. Examples of preferred non-naturally occurring pyrimidine bases include, without limitation, 5-hydroxycytosine, 5-hydroxymethylcytosine, N4-alkylcytosine, preferably N4-ethylcytosine, and 4-thiouracil. However, in some embodiments 5-bromocytosine is specifically excluded.
In some embodiments, the sugar moiety S′ in (I) is a non-naturally occurring sugar moiety. For purposes of the present invention, a “naturally occurring sugar moiety” is a sugar moiety that occurs naturally as part of nucleic acid, e.g., ribose and 2′-deoxyribose, and a “non-naturally occurring sugar moiety” is any sugar that does not occur naturally as part of a nucleic acid, but which can be used in the backbone for an oligonucleotide, e.g, hexose. Arabinose and arabinose derivatives are examples of preferred sugar moieties.
Preferred purine nucleoside analogs according to the invention have the structure (II):




wherein:

    
    
        D is a hydrogen bond donor;
        D′ is selected from the group consisting of hydrogen, hydrogen bond donor, and hydrophilic group;
        A is a hydrogen bond acceptor or a hydrophilic group;
        X is carbon or nitrogen;
        each L is independently an atom selected from the group consisting of C, O, N and S; and
    
    


S′ is a pentose or hexose sugar ring, or a non-naturally occurring sugar.
Preferably, the sugar ring is derivatized with a phosphate moiety, modified phosphate moiety, or other linker moiety suitable for linking the pyrimidine nucleoside to another nucleoside or nucleoside analog.
Preferred hydrogen bond donors include, without limitation, —NH—, —NH2, —SH and —OH. Preferred hydrogen bond acceptors include, without limitation, C═O, C═S, —NO2 and the ring nitrogen atoms of an aromatic heterocycle, e.g., N1 of guanine.
In some embodiments, the base moiety in (II) is a non-naturally occurring purine base. Examples of preferred non-naturally occurring purine bases include, without limitation, 2-amino-6-thiopurine and 2-amino-6-oxo-7-deazapurine. In some embodiments, the sugar moiety S′ in (II) is a naturally occurring sugar moiety, as described above for structure (I).
In preferred embodiments, the immunostimulatory dinucleotide is selected from the group consisting of CpG, C*pG, CpG*, and C*pG*, wherein the base of C is cytosine, the base of C* is 2′-thymine, 5-hydroxycytosine, N4-alkyl-cytosine, 4-thiouracil or other non-natural pyrimidine, or 2-oxo-7-deaza-8-methylpurine, wherein when the base is 2-oxo-7-deaza-8-methyl-purine, it is preferably covalently bound to the 1′-position of a pentose via the 1 position of the base; the base of G is guanosine, the base of G* is 2-amino-6-oxo-7-deazapurine, 2-oxo-7-deaza-8-methylpurine, 6-thioguanine, 6-oxopurine, or other non-natural purine nucleoside, and p is an internucleoside linkage selected from the group consisting of phosphodiester, phosphorothioate, and phosphorodithioate. In certain preferred embodiments, the immunostimulatory dinucleotide is not CpG.
The immunostimulatory oligonucleotides may include immunostimulatory moieties on one or both sides of the immunostimulatory dinucleotide. Thus, in some embodiments, the immunomodulatory oligonucleotide comprises an immunostimulatory domain of structure (III):

5′-Nn-N1-Y—Z—N1-Nn-3′  (III)

wherein:

    
    
        the base of Y is cytosine, thymine, 5-hydroxycytosine, N4-alkyl-cytosine, 4-thiouracil or other non-natural pyrimidine nucleoside, or 2-oxo-7-deaza-8 methyl purine, wherein when the base is 2-oxo-7-deaza-8-methyl-purine, it is preferably covalently bound to the 1′-position of a pentose via the 1 position of the base;
        the base of Z is guanine, 2-amino-6-oxo-7-deazapurine, 2-oxo-7deaza-8-methylpurine, 2-amino-6-thio-purine, 6-oxopurine or other non-natural purine nucleoside;
        N1 and Nn, independent at each occurrence, is preferably a naturally occurring or a synthetic nucleoside or an immunostimulatory moiety selected from the group consisting of a basic nucleosides, arabinonucleosides, 2′-deoxyuridine, α-deoxyribonucleosides, β-L-deoxyribonucleosides, and nucleosides linked by a phosphodiester or modified internucleoside linkage to the adjacent nucleoside on the 3′ side, the modified internucleotide linkage being selected from, without limitation, a linker having a length of from about 2 angstroms to about 200 angstroms, C2-C18 alkyl linker, poly(ethylene glycol) linker, 2-aminobutyl-1,3-propanediol linker, glyceryl linker, 2′-5′ internucleoside linkage, and phosphorothioate, phosphorodithioate, or methylphosphonate internucleoside linkage;
        provided that at least one N1 or Nn is optionally an immunostimulatory moiety;
        wherein n is a number from 0 to 30; and
        wherein the 3′end, an internucleoside linker, or a derivatized nucleobase or sugar is linked directly or via a non-nucleotidic linker to another oligonucleotide, which may or may not be immunostimulatory.
    
    


In some preferred embodiments, YZ is arabinocytidine or 2′-deoxy-2′-substituted arabinocytidine and arabinoguanosine or 2′ deoxy-2′-substituted arabinoguanosine. Preferred immunostimulatory moieties include natural phosphodiester backbones and modifications in the phosphate backbones, including, without limitation, methylphosphonates, methylphosphonothioates, phosphotriesters, phosphothiotriesters, phosphorothioates, phosphorodithioates, triester prodrugs, sulfones, sulfonamides, sulfamates, formacetal, N-methylhydroxylamine, carbonate, carbamate, morpholino, boranophosphonate, phosphoramidates, especially primary amino-phosphoramidates, N3 phosphoramidates and N5 phosphoramidates, and stereospecific linkages (e.g., (RP)- or (SP)-phosphorothioate, alkylphosphonate, or phosphotriester linkages).
Preferred immunostimulatory moieties according to the invention further include nucleosides having sugar modifications, including, without limitation, 2′-substituted pentose sugars including, without limitation, 2′-O-methylribose, 2′-O-methoxyethyl-ribose, 2′-O-propargylribose, and 2′-deoxy-2′-fluororibose; 3′-substituted pentose sugars, including, without limitation, 3′-O-methylribose; 1′,2′-dideoxyribose; arabinose; substituted arabinose sugars, including, without limitation, 1′-methylarabinose, 3′-hydroxymethylarabinose, 4′-hydroxymethylarabinose, 3′-hydroxyarabinose and 2′-substituted arabinose sugars; hexose sugars, including, without limitation, 1,5-anhydrohexitol; and alpha-anomers. In embodiments in which the modified sugar is a 3′-deoxyribonucleoside or a 3′-O-substituted ribonucleoside, the immunostimulatory moiety is attached to the adjacent nucleoside by way of a 2′-5′ internucleoside linkage.
Preferred immunostimulatory moieties according to the invention further include oligonucleotides having other carbohydrate backbone modifications and replacements, including peptide nucleic acids (PNA), peptide nucleic acids with phosphate groups (PHONA), locked nucleic acids (LNA), morpholino backbone oligonucleotides, and oligonucleotides having backbone linker sections having a length of from about 2 angstroms to about 200 angstroms, including without limitation, alkyl linkers or amino linkers. The alkyl linker may be branched or unbranched, substituted or unsubstituted, and chirally pure or a racemic mixture. Most preferably, such alkyl linkers have from about 2 to about 18 carbon atoms. In some preferred embodiments such alkyl linkers have from about 3 to about 9 carbon atoms. Some alkyl linkers include one or more functional groups selected from the group consisting of hydroxy, amino, thiol, thioether, ether, amide, thioamide, ester, urea, and thioether. Some such functionalized alkyl linkers are poly(ethylene glycol) linkers of formula —O—(CH2—CH2—O—)n (n=1-9). Some other functionalized alkyl linkers are peptides or amino acids.
Preferred immunostimulatory moieties according to the invention further include DNA isoforms, including, without limitation, β-L-deoxyribonucleosides and α-deoxyribonucleosides. Preferred immunostimulatory moieties according to the invention incorporate 3′ modifications, and further include nucleosides having unnatural internucleoside linkage positions, including, without limitation, 2′-5′,2′-2′,3′-3′ and 5′-5′ linkages.
Preferred immunostimulatory moieties according to the invention further include nucleosides having modified heterocyclic bases, including, without limitation, 5-hydroxycytosine, 5-hydroxymethylcytosine, N4-alkylcytosine, preferably N4-ethylcytosine, 4-thiouracil, 6-thioguanine, 7-deazaguanine, inosine, nitropyrrole, C5-propynylpyrimidine, and diaminopurines, including, without limitation, 2,6-diaminopurine.
By way of specific illustration and not by way of limitation, for example, in the immunostimulatory domain of structure (III), a methylphosphonate internucleoside linkage at position N1 or Nn is an immunostimulatory moiety, a linker having a length of from about 2 angstroms to about 200 angstroms, C2-C18 alkyl linker at position X1 is an immunostimulatory moiety, and a β-L-deoxyribonucleoside at position X1 is an immunostimulatory moiety. See Table 1 below for representative positions and structures of immunostimulatory moieties. It is to be understood that reference to a linker as the immunostimulatory moiety at a specified position means that the nucleoside residue at that position is substituted at its 3′-hydroxyl with the indicated linker, thereby creating a modified internucleoside linkage between that nucleoside residue and the adjacent nucleoside on the 3′ side. Similarly, reference to a modified internucleoside linkage as the immunostimulatory moiety at a specified position means that the nucleoside residue at that position is linked to the adjacent nucleoside on the 3′ side by way of the recited linkage.








TABLE 1





Position
TYPICAL IMMUNOSTIMULATORY MOIETIES







N1
Naturally-occurring nucleosides, abasic nucleoside,



arabinonucleoside, 2′-deoxyuridine, β-L-deoxyribonucleoside



C2-C18 alkyl linker, poly(ethylene glycol) linkage,



2-aminobutyl-1,3-propanediol linker (amino linker),



2′-5′ internucleoside linkage, methylphosphonate



internucleoside linkage


Nn
Naturally-occurring nucleosides, abasic nucleoside,



arabinonucleosides, 2′-deoxyuridine, 2′-O-substituted



ribonucleoside; 2′-5′ internucleoside linkage,



methylphosphonate internucleoside linkage, provided that N1



and N2 cannot both be abasic linkages









Table 2 shows representative positions and structures of immunostimulatory moieties within an immunomodulatory oligonucleotide having an upstream potentiation domain. As used herein, the term “Spacer 9” refers to a poly(ethylene glycol) linker of formula —O—(CH2CH2—O)n—, wherein n is 3. The term “Spacer 18” refers to a poly(ethylene glycol) linker of formula —O—(CH2CH2—O)n—, wherein n is 6. As used herein, the term “C2-C18 alkyl linker refers to a linker of formula —O—(CH2)q—O—, where q is an integer from 2 to 18. Accordingly, the terms “C3-linker” and “C3-alkyl linker” refer to a linker of formula —O—(CH2)3—O—. For each of Spacer 9, Spacer 18, and C2-C18 alkyl linker, the linker is connected to the adjacent nucleosides by way of phosphodiester, phosphorothioate, or phosphorodithioate linkages.








TABLE 2





Position
TYPICAL IMMUNOSTIMULATORY MOIETY







5′ N2
Naturally-occurring nucleosides, 2-aminobutyl-1,3-propanediol linker


5′ N1
Naturally-occurring nucleosides, β-L-deoxyribonucleoside, C2-C18



alkyl linker, poly(ethylene glycol), abasic linker,



2-aminobutyl-1,3-propanediol linker


3′ N1
Naturally-occurring nucleosides, 1′,2′-dideoxyribose, 2′-O-methyl-



ribonucleoside, C2-C18 alkyl linker, Spacer 9, Spacer 18


3′ N2
Naturally-occurring nucleosides, 1′,2′-dideoxyribose, 3′-



deoxyribonucleoside, β-L-deoxyribonucleoside, 2′-O-propargyl-



ribonucleoside, C2-C18 alkyl linker, Spacer 9, Spacer 18,



methylphosphonate internucleoside linkage


3′ N3
Naturally-occurring nucleosides, 1′,2′-dideoxyribose, C2-C18 alkyl



linker, Spacer 9, Spacer 18, methylphosphonate internucleoside linkage,



2′-5′ internucleoside linkage, d(G)n, polyI-polyC


3′ N2 + 3′ N3
1′,2′-dideoxyribose, β-L-deoxyribonucleoside, C2-C18 alkyl linker,



d(G)n, polyI-polyC


3′ N3 + 3′ N4
2′-O-methoxyethyl-ribonucleoside, methylphosphonate internucleoside



linkage, d(G)n, polyI-polyC


3′ N5 + 3′ N6
1′,2′-dideoxyribose, C2-C18 alkyl linker, d(G)n, polyI-polyC


5′ N1 + 3′ N3
1′,2′-dideoxyribose, d(G)n, polyI-polyC









Table 3 shows representative positions and structures of immunostimulatory moieties within an immunomodulatory oligonucleotide having a downstream potentiation domain.









TABLE 3





Position
TYPICAL IMMUNOSTIMULATORY MOIETY







5′ N2
methylphasphonate internucleoside linkage


5′ N1
methylphasphonate internucleoside linkage


3′ N1
1′,2′-dideoxyribose, methylphosphonate internucleoside linkage,



2′-O-methyl


3′ N2
1′,2′-dideoxyribose, β-L-deoxyribonucleoside, C2-C18 alkyl linker,



Spacer 9, Spacer 18, 2-aminobutyl-1,3-propanediol linker,



methylphosphonate internucleoside linkage, 2′-O-methyl


3′ N3
3′-deoxyribonucleoside, 3′-O-substituted ribonucleoside,



2′-O-propargyl-ribonucleoside


3′ N2 + 3′ N3
1′,2′-dideoxyribose, β-L-deoxyribonucleoside









The immunomers according to the invention comprise at least two oligonucleotides linked at their 3′ ends or internucleoside linkage or a functionalized nucleobase or sugar via a non-nucleotidic linker. For purposes of the invention, a “non-nucleotidic linker” is any moiety that can be linked to the oligonucleotides by way of covalent or non-covalent linkages. Preferably such linker is from about 2 angstroms to about 200 angstroms in length. Several examples of preferred linkers are set forth below. Non-covalent linkages include, but are not limited to, electrostatic interaction, hydrophobic interactions, π-stacking interactions, and hydrogen bonding. The term “non-nucleotidic linker” is not meant to refer to an internucleoside linkage, as described above, e.g., a phosphodiester, phosphorothioate, or phosphorodithioate functional group, that directly connects the 3′-hydroxyl groups of two nucleosides. For purposes of this invention, such a direct 3′-3′ linkage (no linker involved) is considered to be a “nucleotidic linkage.”
In some embodiments, the non-nucleotidic linker is a metal, including, without limitation, gold particles. In some other embodiments, the non-nucleotidic linker is a soluble or insoluble biodegradable polymer bead.
In yet other embodiments, the non-nucleotidic linker is an organic moiety having functional groups that permit attachment to the oligonucleotide. Such attachment preferably is by any stable covalent linkage. As a non-limiting example, the linker may be attached to any suitable position on the nucleoside, as illustrated in FIG. 13. In some preferred embodiments, the linker is attached to the 3′-hydroxyl. In such embodiments, the linker preferably comprises a hydroxyl functional group, which preferably is attached to the 3′-hydroxyl by means of a phosphodiester, phosphorothioate, phosphorodithioate or non-phosphate-based linkages.
In some embodiments, the non-nucleotidic linker is a biomolecule, including, without limitation, polypeptides, antibodies, lipids, antigens, allergens, and oligosaccharides. In some other embodiments, the non-nucleotidic linker is a small molecule. For purposes of the invention, a small molecule is an organic moiety having a molecular weight of less than 1,000 Da. In some embodiments, the small molecule has a molecular weight of less than 750 Da.
In some embodiments, the small molecule is an aliphatic or aromatic hydrocarbon, either of which optionally can include, either in the linear chain connecting the oligonucleotides or appended to it, one or more functional groups selected from the group consisting of hydroxy, amino, thiol, thioether, ether, amide, thioamide, ester, urea, and thiourea. The small molecule can be cyclic or acyclic. Examples of small molecule linkers include, but are not limited to, amino acids, carbohydrates, cyclodextrins, adamantane, cholesterol, haptens and antibiotics. However, for purposes of describing the non-nucleotidic linker, the term “small molecule” is not intended to include a nucleoside.
In some embodiments, the small molecule linker is glycerol or a glycerol homolog of the formula HO—(CH2)o, —CH(OH)—(CH2)p—OH, wherein o and p independently are integers from 1 to about 6, from 1 to about 4, or from 1 to about 3. In some other embodiments, the small molecule linker is a derivative of 1,3-diamino-2-hydroxypropane. Some such derivatives have the formula HO—(CH2)m—C(O)NH—CH2—CH(OH)—CH2—NHC(O)—(CH2)m—OH, wherein m is an integer from 0 to about 10, from 0 to about 6, from 2 to about 6, or from 2 to about 4.
Some non-nucleotidic linkers according to the invention permit attachment of more than two oligonucleotides, as schematically depicted in FIG. 1. For example, the small molecule linker glycerol has three hydroxyl groups to which oligonucleotides may be covalently attached. Some immunomers according to the invention, therefore, comprise more than two oligonucleotides linked at their 3′ ends to a non-nucleotidic linker. Some such immunomers comprise at least two immunostimulatory oligonucleotides, each having an accessible 5′ end.
The immunomers of the invention may conveniently be synthesized using an automated synthesizer and phosphoramidite approach as schematically depicted in FIGS. 5 and 6, and further described in the Examples. In some embodiments, the immunomers are synthesized by a linear synthesis approach (see FIG. 5). As used herein, the term “linear synthesis” refers to a synthesis that starts at one end of the immunomer and progresses linearly to the other end Linear synthesis permits incorporation of either identical or un-identical (in terms of length, base composition and/or chemical modifications incorporated) monomeric units into the immunomers.
An alternative mode of synthesis is “parallel synthesis”, in which synthesis proceeds outward from a central linker moiety (see FIG. 6). A solid support attached linker can be used for parallel synthesis, as is described in U.S. Pat. No. 5,912,332. Alternatively, a universal solid support (such as phosphate attached controlled pore glass) support can be used.
Parallel synthesis of immunomers has several advantages over linear synthesis: (1) parallel synthesis permits the incorporation of identical monomeric units; (2) unlike in linear synthesis, both (or all) the monomeric units are synthesized at the same time, thereby the number of synthetic steps and the time required for the synthesis is the same as that of a monomeric unit; and (3) the reduction in synthetic steps improves purity and yield of the final immunomer product.
At the end of the synthesis by either linear synthesis or parallel synthesis protocols, the immunomers may conveniently be deprotected with concentrated ammonia solution or as recommended by the phosphoramidite supplier, if a modified nucleoside is incorporated. The product immunomer is preferably purified by reversed phase HPLC, detritylated, desalted and dialyzed.
Table 4A and Table 4B show representative immunomers according to the invention. Additional immunomers are found described in the Examples.







TABLE 4A







Examples of Immunomer Sequences








SEQ ID



NO.
Sequences and Modification (5′-3′)











1
5′-GAGAACGCTCGACCTT-3′


2
5′-GAGAACGCTCGACCTT-3′-3′-TTCCAGCTCGCAAGAG-5′


3
3′-TTCCAGCTCGCAAGAG-5′-5′-GAGAACGCTCGACCTT-3′


4
5′-CTATCTGACGTTCTCTGT-3′


 


5






 


6






 


7






 


8






 


9






 


10






 


11






 


12






 


13
54 -CTGACGTTCTCTGT-3′


 


14






 


15






 


16






 


17
5′-XXTGACGTTCTCTGT-3′


 


18






 


19






 


20






 


21
5′-TCTGACGTTCT-3′


 


22






 


23






 


24


























L = C3-alkyl linker; X = 1′,2′-dideoxyriboside; Y = 5OHdC;


R = 7-deaza-dG













TABLE 4B







Examples of Immunomer Sequences










SEQ ID





NO.


No.
Sequences (5′–3′)
Modifications












26
5′-TCTGTCGTTCT-X-TCTTGCTGTCT-5′
G = 2′-deoxy-7-deazaguanosine; X = glycerol




linker


 


173
5′-TCTGTCGTTCT-X-TCTTGCTGTCT-5′
G = arabinoguanosine; X = glycerol linker


 


170
5′-TCTGTCGTTCT-X-TCTTGCTGTCT-5′
C = 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-




deaza-8-methylpurine; X = glycerol linker


 


174
5′-TCTGTCGTTCT-X-TCTTGCTGTCT-5′
C = arabinocytidine; X = glycerol linker


 


175
5′-TCTGTCGTTCT-X-TCTTGCTGTCT-5′
C = 2′-deoxy-5-hydroxycytidine; X = glycerol




linker


 


176
5′-CTGTCGTTCTC-X-CTCTTGCTGTC-5′
G = 2′-deoxy-7-deazaguanosine; X = glycerol




linker


 


171
5′-CTGTCGTTCTC-X-CTCTTGCTGTC-5′
G = arabinoguanosine; X = glycerol linker


 


177
5′-CTGTCGTTCTC-X-CTCTTGCTGTC-5′
C = 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-




deaza-8-methylpurine; X = glycerol linker


 


178
5′-CTGTCGTTCTC-X-CTCTTGCTGTC-5′
C = arabinocytidine; X = glycerol linker


 


179
5′-CTGTCGTTCTC-X-CTCTTGCTGTC-5′
C = 2′-deoxy-5-hydroxycytidine; X = glycerol




linker


 


172
5′-TCGTCGTTCTG-X-GTCTTGCTGCT-5′
G = 2′-deoxy-7-deazaguanosine; X = glycerol




linker


 


180
5′-TCGTCGTTCTG-X-GTCTTGCTGCT-5′
G = arabinoguanosine; X = glycerol linker


 


181
5′-TCGTCGTTCTG-X-GTCTTGCTGCT-5′
C = 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-




deaza-8-methylpurine; X = glycerol linker


 


182
5′-TCGTCGTTCTG-X-GTCTTGCTGCT-5′
C = arabinocytidine; X = glycerol linker


 


183
5′-TCGTCGTTCTG-X-GTCTTGCTGCT-5′
C = 2′-deoxy-5-hydroxycytidine; X = glycerol




linker


 


184
5′-TC1G1TC2G2TTCTG-X-GTCTTG3C3TG4C4T-5′
C1, C2, C3, and C4 are independently 2′-




deoxycytidine, 1-(2′-deoxy-β-D-ribofuranosyl)-2-




oxo-7-deaza-8-methylpurine, arabinocytidine, or 2′-




deoxy-5-hydroxycytidine.




G1, G2, G3, and G4 are independently 2′-




deoxyguanosine, 2′-deoxy-7-deazaguanosine, or




arabinoguanosine









In a second aspect, the invention provides immunomodulatory oligonucleotide conjugates and immunomer conjugates, comprising an immunomodulatory oligonucleotide or an immunomer, as described above, and an antigen conjugated to the immunomer at a position other than the accessible 5′ end. In some embodiments, the non-nucleotidic linker comprises an antigen, which is conjugated to the oligonucleotide. In some other embodiments, the antigen is conjugated to the oligonucleotide at a position other than its 3′ end. In some embodiments, the antigen produces a vaccine effect.
The antigen is preferably selected from the group consisting of antigens associated with a pathogen, antigens associated with a cancer, antigens associated with an auto-immune disorder, and antigens associated with other diseases such as, but not limited to, veterinary or pediatric diseases. For purposes of the invention, the term “associated with” means that the antigen is present when the pathogen, cancer, auto-immune disorder, food allergy, respiratory allergy, asthma or other disease is present, but either is not present, or is present in reduced amounts, when the pathogen, cancer, auto-immune disorder, food allergy, respiratory allergy, or disease is absent.
The immunomodulatory oligonucleotide or immunomer is covalently linked to the antigen, or it is otherwise operatively associated with the antigen. As used herein, the term “operatively associated with” refers to any association that maintains the activity of both immunomer and antigen. Nonlimiting examples of such operative associations include being part of the same liposome or other such delivery vehicle or reagent. In embodiments wherein the immunomer is covalently linked to the antigen, such covalent linkage preferably is at any position on the immunomer other than an accessible 5′ end of an immunostimulatory oligonucleotide. For example, the antigen may be attached at an internucleoside linkage or may be attached to the non-nucleotidic linker. Alternatively, the antigen may itself be the non-nucleotidic linker.
In a third aspect, the invention provides pharmaceutical formulations comprising an immunomodulatory oligonucleotide, immunomodulatory oligonucleotide conjugate, immunomer or immunomer conjugate according to the invention and a physiologically acceptable carrier. As used herein, the term “physiologically acceptable” refers to a material that does not interfere with the effectiveness of the immunomer and is compatible with a biological system such as a cell, cell culture, tissue, or organism. Preferably, the biological system is a living organism, such as a vertebrate.
As used herein, the term “carrier” encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, lipid, or other material well known in the art for use in pharmaceutical formulations. It will be understood that the characteristics of the carrier, excipient, or diluent will depend on the route of administration for a particular application. The preparation of pharmaceutically acceptable formulations containing these materials is described in, e.g., Remington's Pharmaceutical Sciences, 18th Edition, ed. A. Gennaro, Mack Publishing Co., Easton, Pa., 1990.
In a fourth aspect, the invention provides methods for generating an immune response in a vertebrate, such methods comprising administering to the vertebrate an immunomodulatory oligonucleotide, immunomodulatory oligonucleotide conjugate, immunomer or immunomer conjugate according to the invention. In some embodiments, the vertebrate is a mammal. For purposes of this invention, the term “mammal” is expressly intended to include humans. In preferred embodiments, the immunomer or immunomer conjugate is administered to a vertebrate in need of immunostimulation.
In the methods according to this aspect of the invention, administration of immunomodulatory oligonucleotide, immunomodulatory oligonucleotide conjugate, immunomer or immunomer conjugate can be by any suitable route, including, without limitation, parenteral, oral, sublingual, transdermal, topical, intranasal, aerosol, intraocular, intratracheal, intrarectal, vaginal, by gene gun, dermal patch or in eye drop or mouthwash form. Administration of the therapeutic compositions of immunomers can be carried out using known procedures at dosages and for periods of time effective to reduce symptoms or surrogate markers of the disease. When administered systemically, the therapeutic composition is preferably administered at a sufficient dosage to attain a blood level of immunomer from about 0.0001 micromolar to about 10 micromolar. For localized administration, much lower concentrations than this may be effective, and much higher concentrations may be tolerated. Preferably, a total dosage of immunomer ranges from about 0.001 mg per patient per day to about 200 mg per kg body weight per day. It may be desirable to administer simultaneously, or sequentially a therapeutically effective amount of one or more of the therapeutic compositions of the invention to an individual as a single treatment episode.
In certain preferred embodiments, immunomodulatory oligonucleotide, immunomodulatory oligonucleotide conjugate, immunomer or immunomer conjugate according to the invention are administered in combination with vaccines, antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, peptides, proteins, gene therapy vectors, DNA vaccines and/or adjuvants to enhance the specificity or magnitude of the immune response. In these embodiments, the immunomers of the invention can variously act as adjuvants and/or produce direct immunostimulatory effects.
Either the immunomodulatory oligonucleotide; immunomodulatory oligonucleotide conjugate, immunomer, immunomer conjugate or the vaccine, or both, may optionally be linked to an immunogenic protein, such as keyhole limpet hemocyanin (KLH), cholera toxin B subunit, or any other immunogenic carrier protein. Any of the plethora of adjuvants may be used including, without limitation, Freund's complete adjuvant, KLH, monophosphoryl lipid A (MPL), alum, and saponins, including QS-21, imiquimod, R848, or combinations thereof.
For purposes of this aspect of the invention, the term “in combination with” means in the course of treating the same disease in the same patient, and includes administering the immunomer and/or the vaccine and/or the adjuvant in any order, including simultaneous administration, as well as temporally spaced order of up to several days apart. Such combination treatment may also include more than a single administration of the immunomer, and/or independently the vaccine, and/or independently the adjuvant. The administration of the immunomer and/or vaccine and/or adjuvant may be by the same or different routes.
The methods according to this aspect of the invention are useful for model studies of the immune system. The methods are also useful for the prophylactic or therapeutic treatment of human or animal disease. For example, the methods are useful for pediatric and veterinary vaccine applications.
In a fifth aspect, the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient an immunomodulatory oligonucleotide, immunomodulatory oligonucleotide conjugate, immunomer or immunomer conjugate according to the invention. In various embodiments, the disease or disorder to be treated is cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, allergy, asthma or a disease caused by a pathogen. Pathogens include bacteria, parasites, fungi, viruses, viroids and prions. Administration is carried out as described for the fourth aspect of the invention.
For purposes of the invention, the term “allergy” includes, without limitation, food allergies and respiratory allergies. The term “airway inflammation” includes, without limitation, asthma. As used herein, the term “autoimmune disorder” refers to disorders in which “self” proteins undergo attack by the immune system. Such term includes autoimmune asthma.
In any of the methods according to this aspect of the invention, the immunomodulatory oligonucleotide, immunomodulatory oligonucleotide conjugate, immunomer or immunomer conjugate can be administered in combination with any other agent useful for treating the disease or condition that does not diminish the immunostimulatory effect of the immunomer. For example, in the treatment of cancer, it is contemplated that the immunomodulatory oligonucleotide, immunomodulatory oligonucleotide conjugate, immunomer or immunomer conjugate may be administered in combination with a chemotherapeutic compound.
The examples below are intended to further illustrate certain preferred embodiments of the invention, and are not intended to limit the scope of the invention.
EXAMPLES
Example 1
Synthesis of Oligonucleotides Containing Immunomodulatory Moieties
Oligonucleotides were synthesized on a 1 μmol scale using an automated DNA synthesizer (Expedite 8909; PerSeptive Biosystems, Framingham, Mass.), following the linear synthesis or parallel synthesis procedures outlined in FIGS. 5 and 6.
Deoxyribonucleoside phosphoramidites were obtained from Applied Biosystems (Foster City, Calif.). 1′,2′-dideoxyribose phosphoramidite, propyl-1-phosphoramidite, 2-deoxyuridine phosphoramidite, 1,3-bis-[5-(4,4′-dimethoxytrityl)pentylamidyl]-2-propanol phosphoramidite and methyl phosponamidite were obtained from Glen Research (Sterling, Va.). β-L-2′-deoxyribonucleoside phosphoramidite, α-2′-deoxy-ribonucleoside phosphoramidite, mono-DMT-glycerol phosphoramidite and di-DMT-glycerol phosphoramidite were obtained from ChemGenes (Ashland, Mass.). (4-Aminobutyl)-1,3-propanediol phosphoramidite was obtained from Clontech (Palo Alto, Calif.). Arabinocytidine phosphoramidite, arabinoguanosine, arabinothymidine and arabinouridine were obtained from Reliable Pharmaceutical (St. Louis, Mo.). Arabinoguanosine phosphoramidite, arabinothymidine phosphoramidite and arabinouridine phosphoramidite were synthesized at Hybridon, Inc. (Cambridge, Mass.) (Noronha et al. (2000) Biochem., 39:7050-7062).
All nucleoside phosphoramidites were characterized by 31P and 1H NMR spectra. Modified nucleosides were incorporated at specific sites using normal coupling cycles. After synthesis, oligonucleotides were deprotected using concentrated ammonium hydroxide and purified by reverse phase HPLC, followed by dialysis. Purified oligonucleotides as sodium salt form were lyophilized prior to use. Purity was tested by CGE and MALDI-TOF MS.
Example 2
Analysis of Spleen Cell Proliferation
In vitro analysis of splenocyte proliferation was carried out using standard procedures as described previously (see, e.g., Zhao et al., Biochem Pharma 51:173-182 (1996)). The results are shown in FIG. 8A. These results demonstrate that at the higher concentrations, Immunomer 6, having two accessible 5′ ends results in greater splenocyte proliferation than does Immunomer 5, having no accessible 5′ end or Oligonucleotide 4, with a single accessible 5′ end. Immunomer 6 also causes greater splenocyte proliferation than the LPS positive control.
Example 3
In Vivo Splenomegaly Assays
To test the applicability of the in vitro results to an in vivo model, selected oligonucleotides were administered to mice and the degree of splenomegaly was measured as an indicator of the level of immunostimulatory activity. A single dose of 5 mg/kg was administered to BALB/c mice (female, 4-6 weeks old, Harlan Sprague Dawley Inc, Baltic, Conn.) intraperitoneally. The mice were sacrificed 72 hours after oligonucleotide administration, and spleens were harvested and weighed. The results are shown in FIG. 8B. These results demonstrate that Immunomer 6, having two accessible 5′ ends, has a far greater immunostimulatory effect than do Oligonucleotide 4 or Immunomer 5.
Example 4
Cytokine Analysis
The secretion of IL-12 and IL-6 in vertebrate cells, preferably BALB/c mouse spleen cells or human PBMC, was measured by sandwich ELISA. The required reagents including cytokine antibodies and cytokine standards were purchased form PharMingen, San Diego, Calif. ELISA plates (Costar) were incubated with appropriate antibodies at 5 μg/mL in PBSN buffer (PBS/0.05% sodium azide, pH 9.6) overnight at 4° C. and then blocked with PBS/1% BSA at 37° C. for 30 minutes. Cell culture supernatants and cytokine standards were appropriately diluted with PBS/10% FBS, added to the plates in triplicate, and incubated at 25° C. for 2 hours. Plates were overlaid with 1 μg/mL appropriate biotinylated antibody and incubated at 25° C. for 1.5 hours. The plates were then washed extensively with PBS-T Buffer (PBS/0.05% Tween 20) and further incubated at 25° C. for 1.5 hours after adding streptavidin conjugated peroxidase (Sigma, St. Louis, Mo.). The plates were developed with Sure BlueTM (Kirkegaard and Perry) chromogenic reagent and the reaction was terminated by adding Stop Solution (Kirkegaard and Perry). The color change was measured on a Ceres 900 HDI Spectrophotometer (Bio-Tek Instruments). The results are shown in Table 5A below.
Human peripheral blood mononuclear cells (PBMCs) were isolated from peripheral blood of healthy volunteers by Ficoll-Paque density gradient centrifugation (Histopaque-1077, Sigma, St. Louis, Mo.). Briefly, heparinized blood was layered onto the Histopaque-1077 (equal volume) in a conical centrifuge and centrifuged at 400×g for 30 minutes at room temperature. The buffy coat, containing the mononuclear cells, was removed carefully and washed twice with isotonic phosphate buffered saline (PBS) by centrifugation at 250×g for 10 minutes. The resulting cell pellet was then resuspended in RPMI 1640 medium containing L-glutamine (MediaTech, Inc., Herndon, Va.) and supplemented with 10% heat inactivated FCS and penicillin-streptomycin (100 U/ml). Cells were cultured in 24 well plates for different time periods at 1×106 cells/ml/well in the presence or absence of oligonucleotides. At the end of the incubation period, supernatants were harvested and stored frozen at −70° C. until assayed for various cytokines including IL-6 (BD Pharmingen, San Diego, Calif.), IL-10 (BD Pharmingen), IL-12 (BioSource International, Camarillo, Calif.), IFN-α. (BioSource International) and -γ (BD Pharmingen) and TNF-α (BD Pharmingen) by sandwich ELISA. The results are shown in Table 5 below.
In all instances, the levels of IL-12 and IL-6 in the cell culture supernatants were calculated from the standard curve constructed under the same experimental conditions for IL-12 and IL-6, respectively. The levels of IL-10, IFN-gamma and TNF-α in the cell culture supernatants were calculated from the standard curve constructed under the same experimental conditions for IL-10, IFN-gamma and TNF-α, respectively.







TABLE 5





Immunomer Structure and Immunostimulatory Activity in Human PBMC Cultures






















IL-12






(pg/mL)
IL-6 (pg/mL)













SEQ ID








NO.
Sequences and Modification (5′-3′)
Oligo Length/or Each Chain
D1
D2
D1
D2





25
5′-CTATCTGTCGTTCTCTGT-3′
18mer (PS)
184
332
3077
5369


 


26




11mer (PS)
237
352
3724
4892





 














IL-10
IFN-γ


SEQ 


(pg/mL)
(pg/mL)













ID NO.
Sequences and Modification (5′-3′)
Oligo Length/or Each Chain
D1
D2
D1
D2





25
5′-CTATCTGTCGTTCTCTGT-3′
18mer (PS)
 37
 88
 125
 84


26




11mer (PS)
 48
139
 251
 40

















TNF-α






(pg/mL)











SEQ ID






NO.
Sequences and Modification (5′-3′)
Oligo Length/or Each Chain
D1
D2





25
5′-CTATCTGTCGTTCTCTGT-3′
18mer (PS)
537
nt


 


26




11mer (PS)
681
nt









D1 and D2 are donors 1 and 2.







TABLE 5A







Immunomer Structure and Immunostimulatory Activity in BALB/c Mouse


Spleen Cell Cultures













Oligo






Length/or
IL-12
IL-6


SEQ 


ID
Sequences
Each
(pg/mL)
(pg/mL)


NO.
and Modification (5′-3′)
Chain
3 μg/mL
10 μg/mL














26




11mer (PS)
870
10670


 


27




11mer (PS)
1441
7664


 


28




11mer (PS)
1208
1021


 


29




11mer (PS)
162
1013


 


30




14mer (PO)
264
251


 


31




14mer (PO)
149
119


 


32




11mer (PS)
2520
9699


 


33




11mer (PS)
2214
16881


 


34




11mer (PS)
3945
10766


 


35




11mer (PS)
2573
19411


 


36




14mer (PO)
2699
408


 


37




14mer (PO)
839
85


 


38




14mer (PO)
143
160









Normal phase represents a phosphorothioate linkage; Italic phase represents a phosphodiester linkage.




In addition, the results shown in FIGS. 7A-C demonstrate that Oligonucleotide 2, with two accessible 5′ ends elevates IL-12 and IL-6, but not IL-10 at lower concentrations than Oligonucleotides 1 or 3, with one or zero accessible 5′ ends, respectively.
Example 5
Effect of Chain Length on Immunostimulatory Activity of Immunomers
In order to study the effect of length of the oligonucleotide chains, immunomers containing 18, 14, 11, and 8 nucleotides in each chain were synthesized and tested for immunostimulatory activity, as measured by their ability to induce secretion of the cytokines IL-12 and IL-6 in BALB/c mouse spleen cell cultures (Tables 6-8). In this, and all subsequent examples, cytokine assays were carried out in BALB/c spleen cell cultures as described in Example 4.







TABLE 6







Immunomer Structure and Immunostimulatory Activity











SEQ






ID

Oligo Length/
IL-12 (pg/mL)
IL-6 (pg/mL)


NO.
Sequences and Modification (5′-3′)
or Each Chain
@ 0.3 μg/mL
@ 0.3 μg/mL














4
5′-CTATCTGACGTTCTCTGT-3′
18mer
1802
176


 


39




18mer
1221
148


 


40




14mer
2107
548


 


41




11mer
3838
1191


 


42




8mer
567
52
















TABLE 7







Immunomer Structure and Immunostimulatory Activity











SEQ






ID

Oligo Length/
IL-12 (pg/mL)
IL-6 (pg/mL)


NO.
Sequences and Modification (5′-3′)
or Each Chain
1 μg/mL
1 μg/mL














25
5′-CTATCTGTCGTTCTCTGT-3′
18mer
291
65


 


43




18mer
430
39


 


44




14mer
813
59


 


45




12mer
1533
123


 


46




11mer
2933
505


 


47




8mer
1086
26


 


48




7mer
585
34


 


49




6mer
764
76


 


50




5mer
28
29
















TABLE 8







Immunomer Structure and Immunostimulatory Activity











SEQ






ID

Oligo Length/
IL-12 (pg/mL)
IL-6 (pg/mL)


NO.
Sequences and Modification (5′-3′)
or Each Chain
1 μg/mL
1 μg/mL














51
5′-CTCACTTTCGTTCTCTGT-3′
18mer
91
73


 


52




18mer
502
99


 


53




14mer
683
119


 


54




12mer
633
102


 


55




8mer
687
243


 


56




7mer
592
1252









The results suggest that the immunostimulatory activity of immunomers increased as the length of the oligonucleotide chains is decreased from 18-mers to 7-mers. Immunomers having oligonucleotide chain lengths as short as 6-mers or 5-mers showed immunostimulatory activity comparable to that of the 18-mer oligonucleotide with a single 5′ end. However, immunomers having oligonucleotide chain lengths as short as 6-mers or 5-mers have increased immunostimulatory activity when the linker is in the length of from about 2 angstroms to about 200 angstroms.
Example 6
Immunostimulatory Activity of Immunomers Containing a Non-Natural Pyrimidine or Non-Natural Purine Nucleoside
As shown in Tables 9-11, immunostimulatory activity was maintained for immunomers of various lengths having a non-natural pyrimidine nucleoside or non-natural purine nucleoside in the immunostimulatory dinucleotide motif.







TABLE 9







Immunomer Structure and Immunostimulatory Activity













Oligo






Length/
IL-12
IL-6


SEQ

or
(pg/mL)
(pg/mL)


ID

Each
@ 3
@ 3


NO.
Sequences and Modification (5′-3′)
Chain
μg/mL
μg/mL














51
5′-CTCACTTTCGTTCTCTGT-3′
18mer
404
348


 


57




11mer
591
365


 


58




11mer
303
283


 


59




8mer
55
66


 


60




8mer
242
143













 






















TABLE 10







Immunomer Structure and Immunostimulatory Activity











SEQ






ID

Oligo Length/
IL-12 (pg/mL)
IL-6 (pg/mL)


NO.
Sequences and Modification (5′-3′)
or Each Chain
3 μg/mL
3 μg/mL














25
5′-CTATCTGTCGTTCTCTGT-3′
18mer
379
339


 


61




11mer
1127
470


 


62




11mer
787
296


 


63




8mer
64
126


 


64




8mer
246
113













 






















TABLE 11







Immunomer Structure and Immunostimulatory Activity











SEQ






ID

Oligo Length/
IL-12 (pg/mL)
IL-6 (pg/mL)


NO.
Sequences and Modification (5′-3′)
or Each Chain
3 μg/mL
3 μg/mL














4
5′-CTATCTGACGTTCTCTGT-3′
18mer
1176
1892


 


65




18mer
443
192


 


66




18mer
627
464


 


67




14mer
548
152


 


68




14mer
1052
1020


 


69




11mer
2050
2724


 


70




11mer
1780
1741


 


71




8mer
189
55


 


72




8mer
397
212













 















Example 7
Effect of the Linker on Immunostimulatory Activity
In order to examine the effect of the length of the linker connecting the two oligonucleotides, immunomers that contained the same oligonucleotides, but different linkers were synthesized and tested for immunostimulatory activity. The results shown in Table 12 suggest that linker length plays a role in the immunostimulatory activity of immunomers. The best immunostimulatory effect was achieved with C3- to C6-alkyl linkers or a basic linkers having interspersed phosphate charges.







TABLE 12







Immunomer Structure and Immunostimulatory Activity











SEQ






ID

Oligo Length/
IL-12 (pg/mL)
IL-6 (pg/mL)


NO.
Sequences and Modification (5′-3′)
or Each Chain
0.3 μg/mL
1 μg/mL














4
5′-CTATCTGACGTTCTCTGT-3′
18mer
257
635


 


73




10mer
697
1454


 


74




10mer
1162
669


 


75




10mer
1074
1375


 


76




10mer
563
705


 


77




10mer
264
543


 


78




10mer
1750
2258


 


79




10mer
2255
2034


 


80




10mer
1493
1197


 


81




10mer
3625
2642


 


82




10mer
4248
2988


 


83




10mer
1241
1964





















 














 





















Example 8
Effect of Oligonucleotide Backbone on Immunostimulatory Activity
In general, immunostimulatory oligonucleotides that contain natural phosphodiester backbones are less immunostimulatory than are the same length oligonucleotides with a phosphorothioate backbones. This lower degree of immunostimulatory activity could be due in part to the rapid degradation of phosphodiester oligonucleotides under experimental conditions. Degradation of oligonucleotides is primarily the result of 3′-exonucleases, which digest the oligonucleotides from the 3′ end. The immunomers of this example do not contain a free 3′ end. Thus, immunomers with phosphodiester backbones should have a longer half life under experimental conditions than the corresponding monomeric oligonucleotides, and should therefore exhibit improved immunostimulatory activity. The results presented in Table 13 demonstrate this effect, with Immunomers 84 and 85 exhibiting immunostimulatory activity as determined by cytokine induction in BALB/c mouse spleen cell cultures.







TABLE 13







Immunomer Structure and Immunostimulatory Activity











SEQ






ID

Oligo Length/
IL-12 (pg/mL)
IL-6 (pg/mL)


NO.
Sequences and Modification (5′-3′)
or Each Chain
0.3 μg/mL
1 μg/mL














4
5′-CTATCTGACGTTCTCTGT-3′
18mer
225
1462


 


84




14mer
1551
159


 


85




14mer
466
467





L = C3-Linker






Example 9
Synthesis of Immunomers 73-92
Oligonucleotides were synthesized on 1 μmol scale using an automated DNA synthesizer (Expedite 8909 PerSeptive Biosystems). Deoxynucleoside phosphoramidites were obtained from Applied Biosystems (Foster City, Calif.). 7-Deaza-2′-deoxyguanosine phosphoramidite was obtained from Glen Research (Sterling Va.). 1,3-Bis-DMT-glycerol-CPG was obtained from ChemGenes (Ashland, Mass.). Modified nucleosides were incorporated into the oligonucleotides at specific site using normal coupling cycles. After the synthesis, oligonucleotides were deprotected using concentrated ammonium hydroxide and purified by reversed-phase HPLC, followed by dialysis. Purified oligonucleotides as sodium salt form were lyophilized prior to use. Purity of oligonucleotides was checked by CGE and MALDI-TOF MS (Bruker Proflex III MALDI-TOF Mass spectrometer).
Example 11
Immunomer Stability
Oligonucleotides were incubated in PBS containing 10% bovine serum at 37° C. for 4, 24 or 48 hours. Intact oligonucleotide was determined by capillary gel electrophoresis. The results are shown in Table 14.








TABLE 14







Digestion of Oligonucleotides in 10%



Bovine Serum PBS Solution










CE analysis of oligos (% intact











SEQ





ID
Sequences and Modification
oligo remained after digestion)












NO.
(5′–3′)
after 4 h
After 24 h
after 48 h















4
5-CTATCTGACGTTCTCTGT-
90.9
71.8
54.7




3′/PS


 


26
(5′-TCTGTCGTTCT)2S/PS
97.1
91.0
88.1



(G = dGdeaza)


 


86
(5′-CTGTCGTTCTCTGT)2S/PO

37.8
22.5


 


87
(5′-XXCTGTCGTTCTCTGT)2S/PO
73.1
56.8
36.8


 


88
(5′-UCTGTCGTTCTCTGT)2S/PO

48.4
36.7





X = C3-Linker, U, C = 2′-OMe-ribonucleoside






Example 12
Effect of Accessible 5′ Ends on Immunostimulatory Activity
BALB/c mouse (4-8 weeks) spleen cells were cultured in RPMI complete medium. Murine macrophage-like cells, J774 (American Type Culture Collection, 10801 University Boulevard, Manassas, Va. 20110-2209) were cultured in Dulbecco's modified Eagle's medium supplemented with 10% (v/v) FCS and antibiotics (100 IU/mL of penicillin G/streptomycin). All other culture reagents were purchased from Mediatech (Gaithersburg, Md.).
ELISAs for IL-12 and IL-6. BALB/c mouse spleen or J774 cells were plated in 24-well dishes at a density of 5×106 or 1×106 cells/mL, respectively. The CpG DNA dissolved in TE buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA) was added to a final concentration of 0.03, 0.1, 0.3, 1.0, 3.0, or 10.0 μg/mL to mouse spleen cell cultures and 1.0, 3.0, or 10.0 μg/mL to J774 cell cultures. The cells were then incubated at 37° C. for 24 hr and the supernatants were collected for ELISA assays. The experiments were performed two or three times for each CpG DNA in triplicate for each concentration.
The secretion of IL-12 and IL-6 was measured by sandwich ELISA. The required reagents, including cytokine antibodies and standards were purchased from PharMingen. ELISA plates (Costar) were incubated with appropriate antibodies at 5 μg/mL in PBSN buffer (PBS/0.05% sodium azide, pH 9.6) overnight at 4° C. and then blocked with PBS/1% BSA at 37° C. for 30 min. Cell culture supernatants and cytokine standards were appropriately diluted with PBS/1% BSA, added to the plates in triplicate, and incubated at 25° C. for 2 hr. Plates were washed and incubated with 1 μg/mL of appropriate biotinylated antibody and incubated at 25° C. for 1.5 hr. The plates were washed extensively with PBS/0.05% Tween 20 and then further incubated at 25° C. for 1.5 hr after the addition of streptavidine-conjugated peroxidase (Sigma). The plates were developed with Sure BlueTM (Kirkegaard and Perry) chromogenic reagent and the reaction was terminated by adding Stop Solution (Kirkegaard and Perry). The color change was measured on a Ceres 900 HDI Spectrophotometer (Bio-Tek Instruments) at 450 nm. The levels of IL-12 and IL-6 in the cell culture supernatants were calculated from the standard curve constructed under the same experimental conditions for IL-12 and IL-6, respectively.
The results are shown in Table 15.







TABLE 15







Phosphorothioate CpG DNA sequences and modifications used in the studya











(CpG DNA #)






SEQ ID NO.
Sequence
Length
5′-end
3′-end














89
5′-TCCATGACGTTCCTGATGC-3′
19-mer
1
1


90
5′-TCCATGACGTTCCTGATGC-3′-b
19-mer
1
blocked


91
5′-TCCATGACGTTCCTGATGC-3′-3′-g-5′
20-mer
2
blocked


92
5′-TCCATGACGTTCCTGATGC-3′-3′-h-5′
23-mer
2
blocked


93
5′-TCCATGACGTTCCTGATGC-3′-3′-i-5′
27-mer
2
blocked


94
5′-TCCATGACGTTCCTGATGC-3′-3′-j-5′
38-mer
2
blocked


95
b-5′-TCCATGACGTTCCTGATGC-3′
19-mer
blocked
1


96
3′-c-5′-5′-TCCATGACGTTCCTGATGC-3′
20-mer
blocked
2


97
3′-d-5′-5′-TCCATGACGTTCCTGATGC-3′
23-mer
blocked
2


98
3′-e-5′-5′-TCCATGACGTTCCTGATGC-3′
27-mer
blocked
2


99
3′-f-5′-5′-TCCATGACGTTCCTGATGC-3′
38-mer
blocked
2


100
5′-TCCATGACGTTCCTGATGC-3′-k
19-mer
1
blocked


101
l-5′-TCCATGACGTTCCTGATGC-3′
19-mer
blocked
1



















aSee Chart I for chemical structures b–l; 5′-CG-3′-dinucleotide is shown underlined.













TABLE 16







Induction of IL-12 and IL-6 secretion by CpG DNA-conjugates in


BALB/c mice spleen cell cultures










CpG




DNA
IL-12 (pg/mL) ±SD














#a
0.1 μg/mL
0.3 μg/mL
1.0 μg/mL
3.0 μg/mL
10.0 μg/mL







89
991 ± 121
1820 ± 224 
2391 ± 175 
3507 ± 127 
2615 ± 279 



90
526 ± 32 
2100 ± 175 
1499 ± 191 
3019 ± 35 
3489 ± 162 



91
1030 ± 11 
1348 ± 102 
2060 ± 130 
3330 ± 130 
3582 ± 259 



92
1119 ± 159 
1726 ± 207 
2434 ± 100 
2966 ± 204 
3215 ± 464 



93
1175 ± 68 
2246 ± 124 
1812 ± 75 
2388 ± 320 
2545 ± 202 



94
1087 ± 121 
1705 ± 163 
1797 ± 141 
2522 ± 195 
3054 ± 103 



95
1173 ± 107 
2170 ± 155 
2132 ± 58 
2812 ± 203 
3689 ± 94 



96
866 ± 51 
1564 ± 63 
1525 ± 63 
2666 ± 97 
4030 ± 165 



97
227 ± 3 
495 ± 96 
1007 ± 68 
897 ± 15 
1355 ± 97 



98
139 ± 18 
211 ± 12 
452 ± 22 
458 ± 29 
1178 ± 237 



99
181 ± 85 
282 ± 105
846 ± 165
2082 ± 185 
3185 ± 63 



Medium
86 ± 6 












CpG



DNA
IL-6 (pg/mL) ±SD












#a
0.1 μg/mL
0.3 μg/mL
1.0 μg/mL
3.0 μg/mL
10.0 μg/mL





89
652 ± 48 
2858 ± 180 
13320 ± 960 
18625 ± 1504 
17229 ± 1750 


90
1387 ± 152 
1426 ± 124 
5420 ± 370 
19096 ± 484 
19381 ± 2313 


91
923 ± 22 
2542 ± 81 
9054 ± 120 
14114 ± 179 
13693 ± 264 


92
870 ± 146
1905 ± 56 
7841 ± 350 
17146 ± 1246 
15713 ± 693 


93
1152 ± 238 
3499 ± 116 
7142 ± 467 
14064 ± 167 
13566 ± 477 


94
1039 ± 105 
2043 ± 157 
4848 ± 288 
15527 ± 224 
21021 ± 1427 


95
807 ± 0.5
927 ± 0.5
3344 ± 0.5 
10233 ± 0.5 
9213 ± 0.5 


96
750 ± 63 
1643 ± 30 
5559 ± 415 
11549 ± 251 
11060 ± 651 


97
302 ± 18 
374 ± 22 
1000 ± 68 
9106 ± 271 
13077 ± 381 


98
220 ± 23 
235 ± 18 
383 ± 35 
1706 ± 33 
11530 ± 254 


99
467 ± 122
437 ± 85 
1697 ± 283 
9781 ± 13 
11213 ± 294 


Medium
60 ± 12





aSee Table 1 for sequences.






Taken together, the current results suggest that an accessible 5′-end of CpG DNA is required for its optimal immunostimulatory activity and smaller groups such as a phosphorothioate, a mononucleotide, or a dinucleotide do not effectively block the accessibility of the 5′-end of CpG DNA to receptors or factors involved in the immunostimulatory pathway. However, the conjugation of molecules as large as fluorescein or larger at the 5′-end of CpG DNA could abrogate immunostimulatory activity. These results have a direct impact on the studies of immunostimulatory activity of CpG DNA-antigen/vaccine/monoclonal antibody (mAb) conjugates. The conjugation of large molecules such as vaccines or mAbs at the 5′-end of a CpG DNA could lead to suboptimal immunostimulatory activity of CpG DNA. The conjugation of functional ligands at the 3′-end of CpG DNA not only contributes to increased nuclease stability but also increased immunostimulatory potency of CpG DNA in vivo.
Example 13
Effect of Linkers on Cytokine Secretion
The following oligonucleotides were synthesized for this study. Each of these modified oligonucleotides can be incorporated into an immunomer.








TABLE 17







Sequences of CpG DNA showing the



position of substitution.











SEQ ID





NO.
Sequence (5′--->3′)a















102
CCTACTAGCGTTCTCATC




 



103
CCTACTAGC2TTCTCATC



 



104
CCTACT2GCGTTCTCATC



 



105
CCTA2TAGCGTTCTCATC



 



106
CCT22TAGCGTTCTCATC



 



107
22TACTAGCGTTCTCATC



 



108
CCTACTAGCGT2CTCATC



 



109
CCTACTAGCGTTC2CATC



 



110
CCTACTAGCGTTC22ATC



 



111
CCT6CTAGCGTTCTCATC



 



112
CCTACTAGCGTTC6CATC



 



113
CCT7CTAGCGTTCTCATC



 



114
CCTACTAGCGTTC7CATC



 



4
CTATCTGACGTTCTCTGT



 



115
CTAT1TGACGTTCTCTGT



 



116
CTA1CTGACGTTCTCTGT



 



117
CTATCTG2CGTTCTCTGT



 



118
CTATC2GACGTTCTCTGT



 



119
CTA2CTGACGTTCTCTGT



 



120
22222TGACGTTCTCTGT



 



121
 2222TGACGTTCTCTGT



 



122
  222TGACGTTCTCTGT



 



123
   22TGACGTTCTCTGT



 



124
    2TGACGTTCTCTGT



 



125
CTAT3TGACGTTCTCTGT



 



126
CTA3CTGACGTTCTCTGT



 



127
CTA33TGACGTTCTCTGT



 



128
   33TGACGTTCTCTGT



 



129
CTAT4TGACGTTCTCTGT



 



130
CTA4CTGACGTTCTCTGT



 



131
CTA44TGACGTTCTCTGT



 



132
   44TGACGTTCTCTGT



 



133
CTAT5TGACGTTCTCTGT



 



134
CTA5CTGACGTTCTCTGT



 



135
CTA55TGACGTTCTCTGT



 



136
   55TGACGTTCTCTGT



 



137
CTA6CTGACGTTCTCTGT



 



138
CTATCTGACGTTC6CTGT



 



139
CTA7CTGACGTTCTCTGT



 



140
CTATCTGACGTTC7CTGT



 



141
CTATCTG8CGTTCTCTGT



 



142
CTATCT8ACGTTCTCTGT



 



143
CTATC8GACGTTCTCTGT



 



144
CTAT8TGACGTTCTCTGT



 



145
CTA8CTGACGTTCTCTGT



 



146
CTATCTGACG8TCTCTGT



 



147
CTATCTGACGT8CTCTGT



 



148
CTATCTGACGTT8TCTGT



 



149
CTATCTGACGTTC8CTGT



 



150
CTATCTG9CGTTCTCTGT



 



151
CTATCT9ACGTTCTCTGT



 



152
CTA9CTGACGTTCTCTGT



 



153
CTATCTGACGT9CTCTGT



 



154
CTATCTGACGTTC9CTGT







aSee FIG. 14 for the chemical structures of substitutions 1–9. All CpG DNAs are phosphorothioate backbone modified.






To evaluate the optimal linker size for potentiation of immunostimulatory activity, we measured IL-12 and IL-6 secretion induced by modified CpG DNAs in BALB/c mouse spleen cell cultures. All CpG DNAs induced concentration-dependent IL-12 and IL-6 secretion. FIG. 15 shows data obtained at 1 μg/mL concentration of selected CpG DNAs, 116, 119, 126, 130, and 134, which had a linker at the fifth nucleotide position in the 5′-flanking sequence to the CpG dinucleotide compared with the parent CpG DNA. The CpG DNAs, which contained C2-(1), C3-(2), and C4-linkers (3), induced secretion of IL-12 production similar to that of the parent CpG DNA 4. The CpG DNA that contained C6 and C9-linkers (4 and 5) at the fifth nucleotide position from CpG dinucleotide in the 5′-flanking sequence induced lower levels of IL-12 secretion than did the parent CpG DNA (FIG. 15), suggesting that substitution of linkers longer than a C4-linker results in the induction of lower levels of IL-12. All five CpG DNAs, which had linkers, induced two to three times higher IL-6 secretion than did the parent CpG DNA. The presence of a linker in these CpG DNAs showed a significant effect on the induction of IL-6 compared with CpG DNAs that did not have a linker. However, we did not observe length-dependent linker effect-on IL-6 secretion.
To examine the effect on immunostimulatory activity of CpG DNA containing ethylenegylcol-linkers, we synthesized CpG DNAs 137 and 138, in which a triethyleneglycol-linker (6) is incorporated at the fifth nucleotide position in the 5′- and at the fourth nucleotide position in the 3′-flanking sequences to the CpG dinucleotide, respectively. Similarly, CpG DNAs 139 and 140 contained a hexaethyleneglycol-linker (7) in the 5′- or the 3′-flanking sequence to the CpG dinucleotide, respectively. All four modified CpG DNAs (137-140) were tested in BALB/c mouse spleen cell cultures for cytokine induction (IL-12, IL-6, and IL-10) in comparison with parent CpG DNA 4. All CpG DNAs induced concentration-dependent cytokine production over the concentration range tested (0.03-10.0 μg/mL) (data not shown). The levels of cytokines induced at 0.3 μg/mL concentration of CpG DNAs 137-140 are shown in Table 18. CpG DNAs 137 and 139, which had an ethyleneglycol-linker in the 5′-flanking sequence induced higher levels of IL-12 (2106±143 and 2066±153 pg/mL) and IL-6 (2362±166 and 2507±66 pg/mL) secretion than did parent CpG DNA 4 (Table 18). At the same concentration, 137 and 139 induced slightly lower levels of IL-10 secretion than did the parent CpG DNA (Table 18). CpG DNA 138, which had a shorter ethyleneglycol-linker (6) in the 3′-flanking sequence induced IL-12 secretion similar to that of the parent CpG DNA, but significantly lower levels of IL-6 and IL-10 (Table 18). CpG DNA 140, which had a longer ethyleneglycol-linker (7) induced significantly lower levels of all three cytokines tested compared with the parent CpG DNA (Table 18).
Though triethyleneglycol-linker (6) had a chain length similar to that of C9-linker (5), the CpG DNA containing triethyleneglycol-linker had better immunostimulatory activity than did CpG DNA containing C9-linker, as determined by induction of cytokine secretion in spleen cell cultures. These results suggest that the lower immunostimulatory activity observed with CpG DNA containing longer alkyl-linkers (4 and 5) may not be related to their increased length but to their hydrophobic characteristics. This observation prompted us to examine substitution of branched alkyl-linkers containing hydrophilic functional groups on immunostimulatory activity.







TABLE 18







Cytokine secretion induced by CpG DNAs containing an


ethyleneglycol-linker in BALB/c mice spleen cell cultures.










(CpG




DNA




Number)




SEQ ID
Cytokine, pg/mL












NO
IL-12
IL-6
IL-10







 4
1887 ± 233 
2130 ± 221 
86 ± 14



137
2106 ± 143 
2362 ± 166 
78 ± 21



138
1888 ± 259 
1082 ± 25 
47 ± 14



139
2066 ± 153 
2507 ± 66 
73 ± 17



140
1318 ± 162 
476 ± 13 
25 ± 5 



Medium
84 ± 13
33 ± 6 
2 ± 1










To test the effect on immunostimulatory activity of CpG DNA containing branched alkyl-linkers, two branched alkyl-linkers containing a hydroxyl (8) or an amine (9) functional group were incorporated in parent CpG DNA 4 and the effects on immunostimulatory activity of the resulting modified CpG DNAs (150-154-Table 19) were examined. The data obtained with CpG DNAs 150-154, containing amino-linker 9 at different nucleotide positions, in BALB/c mouse spleen cell cultures (proliferation) and in vivo (splenomegaly) are shown in Table 19.







TABLE 19







Spleen cell proliferation induced by CpG DNA containing


an aminobutyryl propanediol-linker in BALB/c mice spleen


cell cultures and splenomegaly in BALB/c mice.








(CpG



DNA










Numbera)
Spleen cell
Spleen


SEQ ID
proliferation
weight


NO.
(PI)b
(mg)c





 4
3.7 ± 0.8
121 ± 16 


159
2.5 ± 0.6
107 ± 11 


151
9.2 ± 0.7
169 ± 16 


152
8.8 ± 0.4
220 ± 8 


153
7.6 ± 0.7
127 ± 24 


154
 7.8 ± 0.04
177 ± 12 


M/V
1.2 ± 0.3
102 ± 8 


LPS
2.8 ± 0.5
ND









Parent CpG DNA 4 showed a proliferation index of 3.7±0.8 at a concentration of 0.1 μg/mL. At the same concentration, modified CpG DNAs 151-154 containing amino-linker 9 at different positions caused higher spleen cell proliferation than did the parent CpG DNA (Table 19). As observed with other linkers, when the substitution was placed adjacent to CpG dinucleotide (150), a lower proliferation index was noted compared with parent CpG DNA (Table 19), further confirming that the placement of a linker substitution adjacent to CpG dinucleotide has a detrimental effect on immunostimulatory activity. In general, substitution of an amino-linker for 2′-deoxyribonucleoside in the 5′-flanking sequence (151 and 152) resulted in higher spleen cell proliferation than found with the substitution in the 3′-flanking sequence (153 and 154). Similar results were observed in the splenomegaly assay (Table 19), confirming the results observed in spleen cell cultures. Modified CpG DNAs containing glycerol-linker (8) showed immunostimulatory activity similar to or slightly higher that that observed with modified CpG DNA containing amino-linker (9) (data not shown).
In order to compare the immunostimulatory effects of CpG DNA containing linkers 8 and 9, we selected CpG DNAs 145 and 152, which had substitution in the 5′-flanking sequence and assayed their ability to induce cytokines IL-12 and IL-6 secretion in BALB/c mouse spleen cell cultures. Both CpG DNAs 145 and 152 induced concentration-dependent cytokine secretion. FIG. 4 shows the levels of IL-12 and IL-6 induced by 145 and 152 in mouse spleen cell cultures at 0.3 μg/mL concentration compared with parent CpG DNA 4. Both CpG DNAs induced higher levels of IL-12 and IL-6 than did parent CpG DNA 4. CpG DNA containing glycerol-linker (8) induced slightly higher levels of cytokines (especially IL-12) than did CpG DNA containing amino-linker (9) (FIG. 16). These results further confirm that the linkers containing hydrophilic groups are more favorable for immunostimulatory activity of CpG DNA.
We examined two different aspects of multiple linker substitutions in CpG DNA. In one set of experiments, we kept the length of nucleotide sequence to 13-mer and incorporated one to five C3-linker (2) substitutions at the 5′-end (120-124). These modified CpG DNAs permitted us to study the effect of an increase in the length of linkers without causing solubility problems. In the second set of experiments, we incorporated two of the same linker substitutions (3, 4, or 5) in adjacent positions in the 5′-flanking sequence to the CpG dinucleotide to study if there would be any additive effect on immunostimulatory activity.
Modified CpG DNAs were studied for their ability to induce cytokine production in BALB/c mouse spleen cell cultures in comparison with parent CpG DNA 4. All CpG DNAs induced concentration-dependent cytokine production. The data obtained at 1.0 μg/mL concentration of CpG DNAs is shown in Table 20. In this assay, parent CpG DNA 4 induced 967±28 pg/mL of IL-12, 1593±94 pg/mL of IL-6, and 14±6 pg/mL of IL-10 secretion at 1 μg/mL of concentration. The data presented in Table 20 suggest that as the number of linker substitutions decreased IL-12 induction decreased. However, the induction of lower levels of IL-12 secretion by CpG DNAs 123 and 124 could be the result of the shorter length of CpG DNAs. Our studies with unmodified CpG DNA shorter than 15-nucleotides showed insignificant immunostimulatory activity (data not shown). Neither length nor the number of linker substitutions have a lesser effect on IL-6 secretion. Though IL-10 secretion increased with linker substitutions, the overall IL-10 secretion by these CpG DNAs was minimal.
CpG DNAs containing two linker substitutions (linker 3-127; linker-4-131; linker-5-135) at the fourth and fifth positions in the 5′-flanking sequences to the CpG dinucleotide and the corresponding 5′-truncated versions 128, 132, and 136, respectively, were tested for their ability to induce cytokine secretion in BALB/c mouse spleen cell cultures. The levels of IL-12 and IL-6 secreted at 1.0 μg/mL concentration are shown in FIG. 17. The results presented in FIG. 17 suggest that the immunostimulatory activity is dependent on the nature of the linker incorporated. The substitution of the fourth and fifth nucleosides with C4-linker 3 (CpG DNA 127) had an insignificant effect on cytokine secretion compared with parent CpG DNA 4, suggesting that the nucleobase and sugar ring at these positions are not required for receptor recognition and/or binding. The deletion of the nucleotides beyond the linker substitutions (CpG DNA 128) caused higher IL-12 and IL-6 secretion than that found with CpG DNAs 4 and 127. As expected, the substitution of two C6-linkers (4) resulted in IL-12 secretion lower than and IL-6 secretion similar to that induced by parent CpG DNA 4. The 5′-truncated CpG DNA 132 induced higher cytokine secretion than did CpG DNA 131. The CpG DNAs 135 and 136, which had two C9-linkers (5), induced insignificant cytokine secretion, confirming the results obtained with mono-substituted CpG DNA containing the same linker as described above.
Example 14
Effect of Phosphodiester Linkages on Cytokine Induction
To test the effect of phosphodiester linkages on immunomer-induced cytokine induction, the following molecules were synthesized.







TABLE 21







PO-Immunomer sequences and analytical data











SEQ 












ID


Molecular Weight











NO
Sequencea
Backboneb
Calculated
Found














4




PS
5702
5704


 


155




PO
5432
5428


 


156




PO
8656
8649


 


157




PO
9208
9214













 











aArrows indicate 5′-3′ directionality of CpG dinucleotide in each DNA molecule and structures of X and Y are shown in boxes.


bPS and PO stand for phosphorothioate and phosphodiester backbones, respectively.


cAs determined by MALDI-TOF mass spectrometry.






PS-CpG DNA 4(Table 21) was found to induce an immune response in mice data not shown) with PO-CpG DNA 155 serving as a control. PO-immunomers 156 and 157 each contain two identical, truncated copies of the parent CpG DNA 155 joined through their 3′-ends via a glyceryl linker, X (Table 21). While 156 and 157 each contain the same oligonucleotide segments of 14 bases, the 5′-ends of 157 were modified by the addition of two C3-linkers, Y (Table 21). All oligonucleotides 4, 155-157 contain a ‘GACGTT’ hexameric motif known to activate the mouse immune system.
The stability of PO-immunomers against nucleases was assessed by incubating CpG DNAs 4, 155-157 in cell culture medium containing 10% fetal bovine serum (FBS) (non-heat-inactivated) at 37° C. for 4, 24, and 48 hr. Intact CpG DNA remaining in the reaction mixtures were then determined by CGE. FIGS. 18A-D shows the nuclease digestion profiles of CpG DNAs 4, 155-157 incubated in 10% FBS for 24 hr. The amount of full-length CpG DNA remaining at each time point is shown in FIG. 18E. As expected, the parent PS-CpG DNA 4 is the most resistant to serum nucleases. About 55% of 18-mer 4 remained undegraded after 48 hr incubation. In contrast, only about 5% of full-length PO-immunomer 155 remained after 4 hr under the same experimental conditions confirming that DNA containing phosphodiester linkages undergoes rapid degradation. As expected, both PO-immunomers 156 and 157 were more resistant than 155 to serum nucleases. After 4 hr, about 62% and 73% of 156 and 157 respectively were intact compared with about 5% of 155 (FIG. 18E). Even after 48 hr, about 23% and 37% of 156 and 157, respectively, remained undegraded. As well as showing that 3′-3′-linked PO-immunomers are more stable against serum nucleases, these studies indicate that chemical modifications at the 5′-end can further increase nuclease stability.
The immunostimulatory activity of CpG DNAs was studied in BALB/c and C3H/HeJ mice spleen cell cultures by measuring levels of cytokines IL-12 and IL-6 secreted. All CpG DNAs induced a concentration-dependent cytokine secretion in BALB/c mouse spleen cell cultures (FIG. 19). At 3 μg/mL, PS-CpG DNA 4 induced 2656±256 and 12234±1180 pg/mL of IL-12 and IL-6 respectively. The parent PO-CpG DNA 155 did not raise cytokine levels above background except at a concentration of 10 μg/mL. This observation is consistent with the nuclease stability assay results. In contrast, PO-immunomers 156 and 157 induced both IL-12 and IL-6 secretion in BALB/c mouse spleen cell cultures.
The results presented in FIG. 19 show a clear distinction in cytokine induction profiles of PS- and PO-CpG DNAs. PO-immunomers 156 and 157 induced higher levels of IL-12 than did PS-CpG DNA 4 in BALB/c mouse spleen cell cultures (FIG. 19A). In contrast, at concentrations up to 3 μg/mL, they produced negligible amounts of IL-6 (FIG. 19B). Even at the highest concentration (10 μg/mL), PO-immunomer 156 induced significantly less IL-6 than did PS-CpG DNA 4. The presence of C3 linkers at the 5′-terminus of PO-immunomer 157 resulted in slightly higher levels of IL-6 secretion compared with 156. However, importantly, the levels of IL-6 produced by PO-immunomer 157 are much lower than those induced by PS CpG DNA 4. The inset of FIG. 19A shows the ratio of IL-12 to IL-6 secreted at 3 μg/mL concentration. In addition to increasing IL-12 secretion, PO-immunomers 156 and 157 induced higher levels of IFN-γ than did PS-CpG DNA 4 in BALB/c mouse spleen cell cultures (data not shown).
The different cytokine profiles induced by PO- and PS-CpG DNAs in BALB/c mouse spleen cell cultures prompted us to study the pattern of cytokine induction of CpG DNAs in C3H/HeJ mouse spleen cell cultures (an LPS lower-responsive strain). All three CpG DNAs tested in this assay induced concentration-dependent cytokine secretion (FIGS. 20A and B). Since PO-CpG DNA 155 failed to induce cytokine secretion in BALB/c mouse spleen cell cultures, it was not further tested in C3H/HeJ spleen cell cultures. Both PO-immunomers 156 and 157 induced higher IL-12 production than did PS-CpG DNA 4 (FIG. 21A). However, at concentrations up to 3 μg/mL, neither induced IL-6 production. At the highest concentration tested (10 μg/mL), both induced significantly less IL-6 than did PS-CpG DNA 4 (FIG. 21B). The ratio of IL-12 to IL-6 secreted is calculated to distinguish cytokine secretion profiles of PS and PO CpG DNAs (FIG. 21A inset). In addition, the C3H/HeJ spleen cell culture results suggest that the responses observed with CpG DNAs are not due to LPS contamination.
PS-CpG DNAs have been shown to induce potent antitumor activity in vivo. Since PO-CpG DNAs exhibited greater nuclease stability and induced higher levels of IL-12 and IFN-γ secretion in in vitro assays, we were interested to see if these desirable properties of PO-immunomers improve the antitumor activity in vivo. We administered PO-immunomer 157 subcutaneously at a dose of 0.5 mg/kg every other day to nude mice bearing tumor xenografts of MCF-7 breast cancer cells that express wild-type p53, or DU-145 prostate cancer cells that express mutated p53. PO-immunomer 157 gave 57% growth inhibition of MCF-7 tumors on day 15 compared with the saline control (FIG. 22A). It also produced 52% growth inhibition of DU-145 tumors on day 34 (FIG. 22B). These antitumor studies suggest that PO-immunomers of the proposed design exhibit potent antitumor activity in vivo.
Example 15
Short Immunomers
To test the effects of short immunomers on cytokine induction, the following immunomers were used. These results show that immunomers as short as 5 nucleotides per segment are effective in inducing cytokine production.







TABLE 22







Immunomer Structure and Immunostimulatory Activity in BABL/C Mouse Spleen Cell Cultures











SEQ

Oligo Length/
IL-12 (pg/mL)
IL-6 (pg/mL)


ID NO.
Sequences and Modification (5′-3′)
or Each Chain
10 μg/mL
10 μg/mL














4
5′-CTATCTGACGTTCTCTGT-3′
18mer
2731
4547


25
5′-CTATCTGTCGTTCTCTGT-3′
18mer
795
789


 


158




11mer
3490
5319


 


159




11mer
3265
4625


 


160




6mer
2085
2961


 


161




6mer
3169
5194


 


162




6mer
1015
705


 


163




5mer
2623
3619


 


164




6mer
564
845


 


165




6mer
196
0


 


166




6mer
219
0


 


167




6mer
1441
5056


 


168




6mer
198
0


 


169




6mer
2410
4857









Normal phase represents a phosphorothioate linkage.





Example 16
Effect of Incorporation of 2-oxo-7-deaza-8-methyl-purine into Mouse-Specific and Human-Specific Immunostimulatory Motifs
Mouse spleenocyte cultures were prepared and treated as described in Example 4. Cultures were treated with medium or with oligonucleotides 170, 171, or 172. (See FIG. 15). All oligonucleotides contained mouse-specific immunostimulatory motifs (GACGTT), but oligonucleotide 171 contained an RpG substitution and oligonucleotide 172 contained a CpR substitution, wherein R is 2-oxo-7-deaza-8-methyl-purine. The results are shown in FIG. 17. The RpG substitution was recognized by the mouse spleen cultures resulting in cytokine production, whereas the CpR substitution was not. Treatment of the cultures with oligonucleotides 173 or 174, containing a human-specific immunostimulatory motif GTCGTT or with an RpG substitution, respectively, showed better recognition by the mouse spleenocytes with the RpG substitution than with the native human sequence (FIG. 18). Treatment with parent oligonucleotides 170 (mouse-specific) or 173 (human-specific), compared with their respective immunomers 175 or 176 (each containing the RpG substitution) showed better results for the immunomers, suggesting that incorporation of the RpG substitution into the immunomers may overcome species-dependent selectivity (FIG. 19). Treatment of human macrophage-like cell cultures with oligonucleotides 170 or 173, compared with immunomers 175 or 176 further suggests that incorporation of the RpG substitution into immunomers overcomes species-selective activity (FIG. 20). Similar results are shown for activation of NF-κB and degradation of Iκ-Bα in J774 cells (FIG. 21). Immunomer 176 also showed immunostimulatory activity in cultures of human peripheral blood mononuclear cells (FIG. 22).
Example 17
Isolation of Human B Cells and Plasmacytoid Dendritic Cells (DDCs)
PBMCs from freshly drawn healthy volunteer blood (CBR Laboratories, Boston, Mass.) were isolated by Ficoll density gradient centrifugation method (Histopaque-1077, Sigma) and B cells were isolated from PBMCs by positive selection using the CD19 cell isolation kit (Miltenyi Biotec) according to the manufacturer's instructions.
Example 18
B Cell Assay
B-Cells were plated in 96-well plates using 1×106 cells/mL, 200 μL/well). The Immunomers were added to a final concentration of 0.3, 1.0, 3.0, or 10.0 μg/mL to the cell cultures and incubated at 37° C. for 24 hr. Supernatants were then harvested and assayed for IL-6 and IL-10 using ELISA kit (provided by PBL). Tables 23A-23D show an average±SD for Donors 1-4 with Immunomers at a final concentration of 10.0 μg/mL.








TABLE 23A







Immunomer Structure and Immunostimulatory Activity in



Human B-Cell Assay for Donor 1 (48 hs).











SEQ ID

IL-6 (pg/ml)
IL-10 (pg/ml)



NO.
Sequences and Modification (5′–3′)
10 μg/ml DN1
10 μg/ml DN1





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
2718 ± 35.5
132.7 ± 5.5



 


173
5′-TCTGTCG2TTCT-X-TCTTG2CTGTCT-5′
2737 ± 19
  144 ± 3.1


 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
2210 ± 8.5
122.5 ± 5.1


 


175
5′-TCTGTC3GTTCT-X-TCTTGC3TGTCT-5′
2175 ± 28.7
 60.2 ± 1.2


 


171
5′-CTGTCG2TTCTC-X-CTCTTG2CTGTC-5′
2714 ± 2.7
132.1 ± 1


 


178
5′-CTGTC2GTTCTC-X-CTCTTGC2TGTC-5′
2166 ± 29.6
 30.9 ± 0.2


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
2956 ± 75
158.8 ± 7.8


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
3057 ± 37.2
132.7 ± 2.7


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
2171 ± 18.6
 50.9 ± 1.6


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
3067 ± 21
 53.6 ± 0.2


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
1760 ± 2.4
 37.7 ± 1.3


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
2138 ± 41.3
 25.7 ± 0.2


 


media

1674 ± 22
  2.8 ± 0.1

















TABLE 23B







Immunomer Structure and Immunostimulatory Activity in



Human B-Cell Assay for Donor 2 (48 hs).











SEQ ID

IL-6 (pg/ml)
IL-10 (pg/ml)



NO.
Sequences and Modification (5′–3′)
10 μg/ml DN2
10 μg/ml DN2





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
 521 ± 2.6
   0 ± 0



 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
1157 ± 0.9
30.9 ± 0


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
2198 ± 2.6
 158 ± 9.7


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
2464 ± 34.5
 289 ± 23.6


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
 686 ± 1.7
18.6 ± 1


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
 867 ± 17
31.3 ± 1.5


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
 355 ± 6.1
   0 ± 0


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
 132 ± 0
   0 ± 0


 


media

65.6 ± 2.8
   0 ± 0

















TABLE 23C







Immunomer Structure and Immunostimulatory Activity in



Human B-Cell Assay for Donor 3 (48 hs).











SEQ ID

IL-6 (pg/ml)
IL-10 (pg/ml)



NO.
Sequences and Modification (5′–3′)
10 μg/ml DN3
10 μg/ml DN3





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
  495 ± 2.9
14.8 ± 0.3



 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
 1043 ± 0
28.4 ± 1.4


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
 1521 ± 24.9
27.2 ± 1.4


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
 1018 ± 13.4
33.5 ± 0.7


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
  423 ± 3.9
 9.5 ± 0.2


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
  524 ± 36.2
 9.0 ± 0.1


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
  184 ± 3.3
 5.8 ± 0.3


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
139.4 ± 0
 7.1 ± 0.3


 


media

 40.9 ± 2.6
 6.1 ± 2.4

















TABLE 23D 







Immunomer Structure and Immunostimulatory Activity in



Human B-Cell Assay for Donor 4 (48 hs).











Oligo No.






SEQ ID

IL-6 (pg/ml)
IL-10 (pg/ml)


NO.
Sequences and Modification (5′–3′)
10 μg/ml DN4
10 μg/ml DN4





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
1027 ± 0
 360 ± 59.8



 


173
5′-TCTGTCG2TTCT-X-TCTTG2CTGTCT-5′
1470 ± 46.9
 559 ± 0


 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
1272 ± 23
 470 ± 1.1


 


175
5′-TCTGTC3GTTCT-X-TCTTGC3TGTCT-5′
 848 ± 6.8
 133 ± 4.5


 


171
5′-CTGTCG2TTCTC-X-CTCTTG2CTGTC-5′
1424 ± 22
 634 ± 2.7


 


178
5′-CTGTC2GTTCTC-X-CTCTTGC2TGTC-5′
 407 ± 3.1
61.8 ± 0.1


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
2837 ± 72.2
 738 ± 5.5


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
1986 ± 34.8
 765 ± 7.9


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
1126 ± 23.1
 165 ± 1.6


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
1372 ± 14.3
 150 ± 0.9


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
 618 ± 4.9
  73 ± 3.1


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
 891 ± 13.6
37.8 ± 0.5


 


media

88.6 ± 0
 3.8 ± 0.4









Example 19
Human pDC Cultures
pDCs were isolated from human PBMCs using a BDCA-4 cell isolation kit (Miltenyi Biotec) according to the manufacturer's instructions. pDC were plated in 96-well plates using 1×106 cells/mL, 200 μL/well). The Immunomers were added to a final concentration of 0.3, 1.0, 3.0, or 10.0 μg/mL to the cell cultures and incubated at 37° C. for 24 hr. Supernatants were then harvested and assayed for IFN-α, IL-6 and TNF-α using ELISA kit (provided by PBL). Tables 24A-24D show an average±SD of IFN-α, IL-6 and TNF-α for Donors 14 with Immunomers at a concentrations of 10.0 μg/mL.








TABLE 24A







Immunomer Structure and Immunostimulatoiy Activity in



Human Dendritic Cell Assay for Donor 1 (24 hs)














IFN-α
IL-6
TNF-α



SEQ

(pg/ml)
(pg/ml)
(pg/ml)


ID

10 μg/ml
10 μg/ml
10μg/ml


NO.
Sequences and Modification (5′–3′)
DN1
DN1
DN1





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
 2524 ± 99
6089 ± 127
2643 ± 22



 


173
5′-TCTGTCG2TTCT-X-TCTTG2CTGTCT-5′
21219 ± 1253
4581 ± 54
7939 ± 0


 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
6692 ± 195
4787 ± 105
6021 ± 0


 


175
5′-TCTGTC3GTTCT-X-TCTTGC3TGTCT-5′
 4503 ± 515
2379 ± 188
3842 ± 0


 


171
5′-CTGTCG2TTCTC-X-CTCTTG2CTGTC-5′
21903 ± 64
5632 ± 190
6790 ± 0


 


178
5′-CTGTC2GTTCTC-X-CTCTTGC2TGTC-5′
  284 ± 2
2271 ± 22
2086 ± 0


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
27183 ± 88
6859 ± 38
7543 ± 39


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
  774 ± 32
4632 ± 35
5335 ± 27


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
25260 ± 2311
3678 ± 32
3010 ± 60


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
28228 ± 2202
3993 ± 42
2793 ± 15


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
19735 ± 423
3905 ± 5
2510 ± 3


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
  302 ± 2
1394 ± 123
1426 ± 23


 


media

  321 ± 2
 891 ± 0
1595 ± 0

















TABLE 24B







Immunomer Structure and Immunostimulatory Activity in



Human Dendritic Cell Assay for Donor 2 (24 hs)














IFN-α
TNF-α
IL-6



SEQ

(pg/ml)
(pg/ml)
(pg/ml)


ID

10 μg/ml
10 μg/ml
10 μg/ml


NO.
Sequences and Modification (5′–3′)
DN2
DN2
DN2





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
 1372 ± 126
1942 ± 11
 804 ± 15



 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
 4097 ± 292
2671 ± 13
 835 ± 14


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
10952 ± 208
 828 ± 14
1094 ± 18


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
 5669 ± 367
2868 ± 133
 4734 ± 19


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
 3860 ± 180
1760 ± 14
 845 ± 12


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
 3093 ± 127
2006 ± 70
 582 ± 2


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
    0 ± 0
1406 ± 18
 466 ± 0


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
    0 ± 0
 803 ± 17
 436 ± 3


 


media

    0 ± 0
   0 ± 0
   0 ± 0

















TABLE 24C







Immunomer Structure and Immunostimulatory Activity in



Human Dendritic Cell Assay For Donor 3 (24 hs)














IFN-α
TNF-α
IL-6



SEQ

(pg/ml)
(pg/ml)
(pg/ml)


ID

10 μg/ml
10 μg/ml
10 μg/ml


NO.
Sequences and Modification (5′–3′)
DN3
DN3
DN3





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
   0 ± 0
2101 ± 26
 804 ± 15



 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
2151 ± 28
3810 ± 5
 835 ± 14


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
4977 ± 2
 678 ± 13
1094 ± 18


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
2951 ± 39
2085 ± 60
4734 ± 19


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
5075 ± 154
1787 ± 14
 845 ± 12


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
3203 ± 5
2069 ± 15
 582 ± 2


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
   0 ± 0
1936 ± 13
 466 ± 0


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
   0 ± 0
 846 ± 12
 605 ± 8


 


media

   0 ± 0
   0 ± 0
   0 ± 0

















TABLE 24D







Immunomer Structure and Immunostimulatory Activity in



Human Dendritic Cell Assay for Donor 4 (24 hs)













IL-6
TNF-α



SEQ

(pg/ml)
(pg/ml)


ID

10 μg/ml
10 μg/ml


NO.
Sequences and Modification (5′–3′)
DN4
DN4





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
1144 ± 182
 411 ± 93



 


173
5′-TCTGTCG2TTCT-X-TCTTG2CTGTCT-5′
3386 ± 28
2936 ± 5


 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
4267 ± 18
1832 ± 68


 


175
5′-TCTGTC3GTTCT-X-TCTTGC3TGTCT-5′
2254 ± 41
1173 ± 23


 


171
5′-CTGTCG2TTCTC-X-CTCTTG2CTGTC-5′
5532 ± 3
3494 ± 142


 


178
5′-CTGTC2GTTCTC-X-CTCTTGC2TGTC-5′
1430 ± 17
1127 ± 55


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
6564 ± 77
2932 ± 52


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
5360 ± 147
1584 ± 24


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
3507 ± 118
2326 ± 60


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
2273 ± 92
1297 ± 36


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
2352 ± 78
1237 ± 28


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
1396 ± 20
1000 ± 0


 


media

 695 ± 19
 651 ± 3









Example 20
Human peripheral blood mononuclear cells (PBMCs) were isolated from peripheral blood of healthy volunteers and prepared as discussed above in Example 4.). Tables 25A-25D show an average±SD of IL-6 and IL-10 for Donors 1-4 with Immunomers at a concentrations of 10.0 μg/mL.








TABLE 25A







Immunomer Structure and Immunostimulatory Activity in



Human PBMC Assay for Donor 1 (48 hs)













IL-6
IL-10



SEQ

(pg/ml)
(pg/ml)


ID

10 μg/ml
10 μg/ml


NO.
Sequences and Modification (5′–3′)
DN1
DN1





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
483 ± 2.6
49.9 ± 1.3



 


173
5′-TCTGTCG2TTCT-X-TCTTG2CTGTCT-5′
722 ± 9.1
50.3 ± 1.6


 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
502 ± 14.2
46.9 ± 1.9


 


175
5′-TCTGTC3GTTCT-X-TCTTGC3TGTCT-5′
400 ± 2.8
39.4 ± 0.5


 


171
5′-CTGTCG2TTCTC-X-CTCTTG2CTGTC-5′
466 ± 17.8
47.6 ± 0.4


 


178
5′-CTGTC2GTTCTC-X-CTCTTGC2TGTC-5′
194 ± 3.5
13.6 ± 0.1


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
994 ± 12.2
57.5 ± 0.1


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
652 ± 5
57.1 ± 7.9


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
370 ± 1.9
37.6 ± 6.1


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
416 ± 2.7
28.9 ± 0.7


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
323 ± 5.9
29.7 ± 0.3


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
281 ± 3.1
30.2 ± 0.3


 


media

345 ± 7.9
 8.7 ± 0.3

















TABLE 25B







Immunomer Structure and Immunostimulatory Activity in



Human PBMC Assay for Donor 2 (48 hs)














IFN-γ
IL-6
IL-10



SEQ

(pg/ml)
(pg/ml)
(pg/ml)


ID

10 μg/ml
10 μg/ml
10 μg/ml


NO.
Sequences and Modification (5′–3′)
DN2
DN2
DN2





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
 7.8 ± 0.6
 742 ± 0.8
 175 ± 3.7



 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
26.6 ± 1.1
 939 ± 34.1
 147 ± 5.8


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
29.1 ± 0.2
1508 ± 12.3
 179 ± 5.3


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
22.3 ± 0.3
1294 ± 51.2
 397 ± 11


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
 3.8 ± 0.5
 276 ± 2.6
  58 ± 0.6


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
 3.6 ± 0.1
 590 ± 3.4
  73 ± 4.1


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
 1.1 ± 0.2
 233 ± 5.2
62.1 ± 1.4


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
 3.6 ± 0.5
 203 ± 12.3
34.8 ± 2.7


 


media

   0 ± 0
97.4 ± 2.7
 3.6 ± 1.1

















TABLE 25C







Immunomer Structure and Immunostimulatory Activity in



Human PBMC Assay for Donor 3 (48 hs)














IFN-γ
IL-6
IL-10



SEQ

(pg/ml)
(pg/ml)
(pg/ml)


ID

10 μg/ml
10 μg/ml
10 μg/ml


NO.
Sequences and Modification (5′–3′)
DN3
DN3
DN3





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
63.8 ± 6.3
 642 ± 12.6
75.2 ± 5.2



 


170
5′-TCTGTC1GTTCT-X-TCTTGC1TGTCT-5′
30.7 ± 1.1
 569 ± 6.3
53.9 ± 2.2


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
63.9 ± 2.7
 783 ± 0.9
44.5 ± 0.3


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
32.9 ± 2.4
 570 ± 3.6
  74 ± 1.1


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
32.7 ± 4.3
 283 ± 4.9
37.5 ± 0.4


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
33.7 ± 1.6
 376 ± 10.4
48.7 ± 0.6


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
  23 ± 1.4
 355 ± 5.7
41.6 ± 0.2


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
12.3 ± 1.2
57.3 ± 1.2
39.4 ± 1.3


 


media

   0 ± 0
25.3 ± 2.9
11.2 ± 0.2

















TABLE 25D







Immunomer Structure and Immunostimulatory Activity in



Human PBMC Assay for Donor 4 (48 hs)











SEQ






ID

IL-6 (pg/ml)
IL-10 (pg/ml)


NO.
Sequences and Modification (5′–3′)
10 μg/ml DN4
10 μg/ml DN4





26
5′-TCTGTCG1TTCT-X-TCTTG1CTGTCT-5′
 316 ± 20.4
 175 ± 0



 


173
5′-TCTGTCG2TTCT-X-TCTTG2CTGTCT-5′
 758 ± 61.6
 174 ± 13.2


 


175
5′-TCTGTC3GTTCT-X-TCTTGC3TGTCT-5′
 228 ± 21.2
  95 ± 3.4


 


171
5′-CTGTCG2TTCTC-X-CTCTTG2CTGTC-5′
 498 ± 5.9
 197 ± 3


 


178
5′-CTGTC2GTTCTC-X-CTCTTGC2TGTC-5′
  63 ± 0
  39 ± 1.1


 


172
5′-TCG1TCG1TTCTG-X-GTCTTG1CTG1CT-5′
1318 ± 32.8
 215 ± 0.9


 


180
5′-TCG2TCG2TTCTG-X-GTCTTG2CTG2CT-5′
 976 ± 24.9
251 ± 9.3


 


181
5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′
 449 ± 0.9
  96 ± 1.4


 


182
5′-TC2GTC2GTTCTG-X-GTCTTGC2TGC2T-5′
 210 ± 4.2
  62 ± 6.3


 


183
5′-TC3GTC3GTTCTG-X-GTCTTGC3TGC3T-5′
 237 ± 2.1
  80 ± 3.9


 


185
5′-TG1CTG1CTTG-X-GTTCG1TCG1T-5′
 636 ± 15.5
 107 ± 8.7


 


media

76.5 ± 2.4
12.6 ± 0.2





Solely for the purposes of Tables 23A–23D, 24A–24D, and 25A..25D: Normal phase represents a phosphorothioate linkage; G1 = 2′-deoxy-7-deazaguanosine, G2 = Arabinoguanosine, C1 = 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methylpurine, C2 = Arabinocytidine, C3 = 2′-deoxy-5-hydroxycytidine, X = Glycerol linker






EQUIVALENTS
While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be appreciated by one skilled in the art from a reading of this disclosure that various changes in form and detail can be made without departing from the true scope of the invention and appended claims.

## Claims

1. An immunomer compound, comprising at least two oligonucleotides linked at their 3′ ends, internucleoside linkages, functionalized nucleobase or sugar to a non-nucleotidic linker, wherein at least one of the oligonucleotides is an oligonucleotide having an accessible 5′ end and comprising an immunostimulatory dinucleotide having the structure RpG, wherein R is a nucleotide having 2-oxo-7-deaza-8-methyl-purine as a base and G is a nucleotide having a base selected from the group consisting of guanine, 2-amino-6-oxo-7-deazapurine, 2-amino-6-thiopurine, 6-oxo-purine or other non-natural purine.

2. The immunomer according to claim 1 wherein at least one of the oligonucleotides has structure


5′-Nn-N1-Y—Z—N1-Nn-3′  (III)

wherein:
Y is 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methylpurine;
Z is guanosine, 2′-deoxyguanosine, 2′-deoxy-7-deazaguanosine, 2′-deoxy-6-thioguanosine, arabinoguanosine, 2′-deoxy-2′-substituted-arabinoguanosine, 2′-O-substituted-arabino guanosine or other non-natural purine nucleotide,
N1 and Nn at each occurrence, is independently a naturally occurring or a synthetic nucleoside or an immunostimulatory moiety selected from the group consisting of abasic nucleotides, arabinonucleotides, 2′-deoxyuridine, α-deoxyribonucleotides, β-L-deoxyribonucleotides, nucleotides linked by a modified internucleotide linkage to the adjacent nucleotide on the 3′ side, nucleotides having 2′-substituted pentose sugar modifications; nucleotides having 3′-substituted pentose sugar modifications; 1′,2′-dideoxyribose; arabinose; substituted arabinose sugars, hexose sugars, and alpha-anomers, peptide nucleic acids (PNA), peptide nucleic acids with phosphate groups (PHONA), locked nucleic acids (LNA), morpholinonucleic acids, oligonucleotides having backbone linker sections having a length of from about 2 angstroms to about 200 angstroms, alkyl linkers or amino linkers, DNA isoforms, β-L-deoxyribonucleotides, α-deoxyribonucleotides, nucleotides having unnatural internucleotide linkage positions, and nucleotides having modified heterocyclic bases;
wherein the recited oligonucleotide is directly or indirectly linked to another oligonucleotide, and wherein n is a number from 0-30.

3. The immunomer according to claim 2 wherein the immunostimulatory moiety at each occurrence, is independently selected from the group consisting of abasic nucleotides, arabinonucleotides, 2′-deoxyuridine, α-deoxyribonucleotides, β-L-deoxyribonucleotides, and nucleotides linked by a phosphodiester or modified internucleotide linkage to the adjacent nucleotide on the 3′ side, oligonucleotides having backbone linker sections having a length of from about 2 angstroms to about 200 angstroms.

4. The immunomer according to claim 2 wherein the 2′-substituted pentose sugar is selected from the group consisting of 2′-O-methylribose, 2′-O-methoxyethyl-ribose, 2′-O-propargylribose, and 2′-deoxy-2′-fluororibose.

5. The immunomer according to claim 2 wherein the 3′-substituted pentose sugar is selected from the group consisting of 3′-O-methylribose.

6. The immunomer according to claim 2 wherein the modified internucleotide linkage is selected from the group consisting of C2-C18 alkyl linker, poly(ethylene glycol) linkage, 2-aminobutyl-1,3-propanediol linker, 2′-5′ internucleotide linkage, methylphosphonate internucleotide linkage; methylphosphonothioates, phosphotriesters, phosphothiotriesters, phosphorothioates, phosphorodithioates, triester prodrugs, sulfones, sulfonamides, sulfamates, formacetal, N-methylhydroxylamine, carbonate, carbamate, morpholino, boranophosphonate, phosphoramidates, and stereospecific linkages.

7. The immunomer according to claim 6 wherein the phosphoramidate is selected from the group consisting of primary amino-phosphoramidate, N3 phosphoramidate and N5 phosphoramidate.

8. The immunomer according to claim 1 wherein the G base in the immunostimulatory dinucleotide has the structure (II):



wherein:
D is a hydrogen bond donor;
D′ is selected from the group consisting of hydrogen, hydrogen bond donor, and hydrophilic group;
A is a hydrogen bond acceptor or a hydrophilic group;
X is carbon or nitrogen;
each L is independently an atom selected from the group consisting of C, O, N and S; and
S′ is a pentose or hexose sugar ring, or a non-naturally occurring sugar.

9. The immunomer according to claim 8 wherein the sugar ring is derivatized with a phosphate moiety, modified phosphate moiety, or other linker moiety suitable for linking the purine nucleoside to another nucleoside or nucleoside analog.

10. The immunomer according to claim 8 wherein the hydrogen bond donors are selected from the group consisting of —NH—, —NH2, —SH and —OH.

11. The immunomer according to claim 8 wherein the hydrogen bond acceptors are selected from the group consisting of C═O, C═S, —N═ and the ring nitrogen atoms of an aromatic heterocycle.

12. The immunomer according to claim 8 wherein the non-naturally occurring purine is 2-amino-6-thiopurine, 6-oxopurine or 2-amino-6-oxo-7-deazapurine.

13. The immunomer according to claim 1, wherein the non-nucleotidic linker is selected from the group consisting of a linker from about 2 angstroms to about 200 angstroms in length, a metal, a soluble or insoluble biodegradable polymer bead, an organic moiety having functional groups that permit attachment to the 3′-terminal nucleoside of the oligonucleotide, a biomolecule, a cyclic or acyclic small molecule, an aliphatic or aromatic hydrocarbon, either of which optionally can include, either in the linear chain connecting the oligonucleotides or appended to it, one or more functional groups selected from the group consisting of hydroxy, amino, thiol, thioether, ether, amide, thioamide, ester, urea, and thiourea; amino acids, carbohydrates, cyclodextrins, adamantane, cholesterol, haptens antibiotics, glycerol or a glycerol homolog of the formula HO—(CH2)o—CH(OH)—(CH2)p—OH, wherein o and p independently are integers from 1 to about 6, and a derivative of 1,3-diamino-2-hydroxypropane.

14. The immunomer according to claim 1, wherein G is arabinoguanosine or 2′-deoxy-2′-substituted arabinguanosine, 2′-deoxy-7-deazaguanosine or 2′-deoxy-6-thioguanosine, or 2′-deoxyinosine.

15. The immunomer according to claim 1 having the structure 5′-CTGTC1GTTCTC-X-CTCTTGC1TGTC-5′ (5′-SEQ ID NO 177-X-SEQ ID NO 177-5′); wherein X is a glycerol linker and C1 is 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methylpurine.

16. The immunomer according to claim 1 having the structure 5′-TC1GTC1GTTCTG-X-GTCTTGC1TGC1T-5′ (SEQ ID NO 181-X-SEQ ID NO 181-5′); wherein X is a glycerol linker and C1 is 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methylpurine.

17. The immunomer according to claim 1, wherein the internucleoside linkages comprise phosphorothioate linkages.

18. A composition comprising an immunomer according to claim 1 and a physiologically acceptable carrier.

19. A method for generating an immune response in a vertebrate, the method comprising administering to the vertebrate an immunomer according to claim 1.

20. The method of claim 19 further comprising administering a vaccine.

21. The method of claim 20 further comprising administering an adjuvant.

22. The method of claim 19 further comprising administering an adjuvant.