AU2002365141C1 - Modulation of immunostimulatory properties of oligonucleotide-based compounds by optimal presentation of 5' ends - Google Patents

Description

WO 03/057822 PCT/US02/34247 1 MODULATION OF IMMUNOSTIMULATORY PROPERTIIES OF OLIGONUCLEOTIDE-BASED COMPOUNDS BY OPTIMAL PRESENTATION OF 5' ENDS (Attorney Docket No. HYB-007US2) BACKGROUND OF THE INVENTION Field of the Invention The invention relates to immunology and immunotherapy applications using oligonucleotides as immunostimulatory agents.

Summary of the Related Art Oligonucleotides have become indispensable tools in moder 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 ofoligonucleotides for antisense and diagnostic applications can now be routinely accomplished. See, Methods in Molecular Biology, Vol. Protocols for Oligonucleotides and Analogs pp. 165-189 Agrawal, ed., Humana Press, 1993); Oligonucleotides and Analogues, A Practical Approach, pp. 87-108 Eckstein, ed., 1991); and Uhlmann and Peyman, supra; Agrawal and lyer, 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 Hphosphonate approaches to synthesis. For example, Beaucage and Caruthers, WO 03/057822 PCT/US02/34247 2 Tetrahedron Left. 22:1859-1862 (1981), discloses the use of deoxyribonucleoside phosphoramidites in polynucleotide synthesis. Agrawal and Zamecnik, U.S. Patent No. 5,149,798 (1992), discloses optimized synthesis of oligonucleotides by the Hphosphonate approach. Both of these modem 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 CpGcontaining 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.

WO 031057822 PCT/US02/34247 3 Other modifications of CpG-containing phosphorothioate oligonucleotides can also affect their ability to act as modulators of immune response. See, Zhao et al., Biochem. Pharmacol. (1996) 51:173-182; Zhao et al., Biochum 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 Chemn. Leu. (2000) 10:2585-2588; Yu et al., Bioorg. Med Chem. Leu. (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 enhance the immune response caused by immunostimulatory oligonucleotides.

WO 03/057822 PCT/US02/34247 BRIEF SUMMARY OF THE INVENTION The invention provides methods for enhancing the immune response caused by oligonucleotide compounds. The methods according to the invention enable increasing the immunostimulatory effect of immunostimulatory oligonucleotides for immunotherapy applications. The present inventors have surprisingly discovered that modification of an immunostimulatory oligonucleotide to optimally present its 5' end dramatically enhances its immunostimulatory capability. Such an oligonucleotide is referred to herein as an "immunomer." In a first aspect, therefore, the invention provides immunomers comprising at least two oligonucleotides linked at their 3' ends, an internuceotide linkage, or a functionalized nucleobase or sugar via a non-nucleotidic linker, at least one of the oligonucleotides being an immunostimulatory oligonucleotide and having an accessible 5' end.

In one embodiment, the 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 embodiment, the immunomer comprises an immunostimulatory dinucleotide selected from the group consisting of CpG, C*pG, CpG*, and C*pG*, wherein C is cytidine or 2'-deoxycytidine, C* is 2'-deoxythymidine. arabinocytidine, 2 '-deoxy-2'-substitutedarabinocytidine, 2'-O-substitutedarabinocytidine, hydroxycytidine, 2'-deoxy-N4-alkyl-cytidine, 2'-deoxy-4-thiouridine or other nonnatural pyrimidine nucleoside, G is guanosine or 2'-deoxyguanosine, G* is 2' deoxy- 7-deazaguanosine, 2'-deoxy-6-thioguanosine, arabinoguanosine, 2'-deoxy- 2 'substituted-arabinoguanosine, 2'-O-substituted-arabinoguanosine, or other nonnatural purine nucleoside, and p is an internucleoside linkage selected from the group consisting of phosphodiester, phosphomothioate, and phosphorodithioate. In certain preferred embodiments, the immunostimulatory dinucleotide is not CpG.

WO 031057822 WO 03157822PCT/US02/34247 In yet another embodiment, the irumunostimulatory oligonucleotide comprises an immunostimulatory domain of formula (III): '-Nn-N I -Y-Z-N I -Nn-3'(I) wherein: Y is cytidine, 2'-deoxythymidine, 2' deoxycytidine, arabinocytidine, 2'deoxythymidine, 2'-deoxy-2 '-substitutedarabinocytidine, 2 substitutedarabinocytidine, 2'-deoxy-5-hydroxycytidine, 2'-deoxy-N4-alkyl-cytidine, 2'-deoxy-4-thiouridine or other non-natural pyrimidine nucleoside; Z is guanosine or 2'-deoxyguanosine, G* is 2' deoxy-7-deazaguanosine. 2'deoxy-6-thioguanosine, arabinoguanosine. 2'-deoxy-2'substituted-arabinoguanosine, 2'-O-substituted-arabinoguanosine, deoxyinosine, or other non-natural purine nucleoside N 1, at each occurrence, is preferably a naturally occurring or a synthetic nucleoside or an immunostimulatory moiety selected from the group consisting of abasic nucleosides, arabinonucleosides, 2'-deoxyuridine, (x-deoxyribonucleosides, P-L-deoxyribonucleosidcs, and nucleosides linked by a phosphodiester or modified intemucleoside linkage to the adjacent nucleoside on the 3' side, the modified intemucleotide linkage being selected from, without limitation, a linker having a length of from about 2 angstroms to about 200 angstroms, C2-C 18 alkyl linker, poly(ethylene glycol) linker, 2-aminobutyl-I ,3-propanediol linker, glyceryl linker, 2'linkage, and phosphorothioate, phosphorodithioate, or methylphosphonate intemnucleoside linkage; Nn, at each occurrence, is a naturally occurring nucleosidc or an immunostimulatory moiety, preferably selected from the group consisting of abasic nucleosides, arabinonucleosides, 2'-deoxyuridine, ct-deoxyribonucleosides, substituted ribonucleosides, and nucleosides linked by a modified internucleoside WO 03/057822 PCT/US02/34247 6 linkage to the adjacent nucleoside on the 3' side, the modified internucleotide linkage being selected from the group consisting of amino linker, internucleoside linkage, and methylphosphonate intemucleoside linkage; provided that at least one N I or Nn is an immunostimulatory moiety; wherein n is a number from 0-30; wherein the 3'end an internucleotide linkage, or a functionalized nucleobase or sugar is linked directly or via a non-nucleotidic linker to another oligonucleotide, which may or may not be immunostimulatory.

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.

In a third aspect, the invention provides pharmaceutical formulation comprising an immunomer or an immunomer conjugate according to the invention 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 immunomer or immunomer conjugate according to the invention. 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 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, asthma, allergy, or a disease caused by a pathogen.

WO 03/057822 PCT/US02/34247 7 BRIEF DESCRIPTION OF THE DRAWINGS Figure I is a schematic representation of representative immunomers of the invention.

Figure 2 depicts several representative immunomers of the invention.

Figure 3 depicts a group of representative small molecule linkers suitable for linear synthesis of immumomers of the invention.

Figure 4 depicts a group of representative small molecule linkers suitable for parallel synthesis of immunomers of the invention.

Figure 5 is a synthetic scheme for the linear synthesis of immunomers of the invention. DMTr 4,4'-dimethoxytrityl; CE cyanoethyl.

Figure 6 is a synthetic scheme for the parallel synthesis of immunomers of the invention. DMTr 4,4'-dimethoxytrityl; CE cyanoethyl.

Figure 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 Immunomer2, which has accessible 5'-ends, is a stronger inducer of IL-12 than monomeric Oligo I, and that Immunomer 3, which does not have accessible has equal or weaker ability to produce immune stimulation compared with oligo I.

Figure 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 I, and that Immunomer 3, which does not have accessible ends, has equal or weaker ability to induce immune stimulation compared with Oligo

I.

Figure 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.

WO 03/057822 PCT/US02/34247 8 Figure 8A is a graphic representation of the induction of BALB/c mouse spleen cell proliferation in cell cultures by different concentrations of Immunomers and 6, which have inaccessible and accessible 5'-ends, respectively.

Figure 8B is a graphic representation of BALB/c mouse spleen enlargement by Immunomers 4-6, which have an immunogenic chemical modification in the flanking sequence of the CpG motif. Again, the immunomer, which has accessible has a greater ability to increase spleen enlargement compared with Immunomer 5, which does not have accessible 5'-end and with monomeric Oligo 4.

Figure 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.

Figure 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.

Figure 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.

Figure IOA is a graphic representation of the induction of cell proliferation by Immunomers 14, 15, and 16 in BALB/c mouse spleen cell cultures.

Figure 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.

Figure 10C is a graphic representation of the induction of cell proliferation by I L-6 by different concentrations of Immunomers 14 and 16 in BALB/c mouse spleen cell cultures.

WO 03/057822 PCT/US02/34247 9 Figure 1 IA 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.

Figure I B is a graphic representation of the induction of cell proliferation IL- 12 by different concentrations of Oligo 4 and 17 and Immunomers 19 and 20 in BALB/c mouse spleen cell cultures.

Figure 1 IC is a graphic representation of the induction of cell proliferation IL- 6 by different concentrations of Oligo 4 and 17 and Immunomers 19 and 20 in BALB/c mouse spleen cell cultures.

Figure 12 is a graphic representation of BALB/c mouse spleen enlargement using oligonucleotides 4 and immunomers 14, 23, and 24.

Figure 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.

Figure 14 shows the chemical substitutions used in Example 13.

Figure 15 shows cytokine profiles obtained using the modified oligonucleotides of Example 13.

Figure 16 shows relative cytokine induction for glycerol linkers compared with amino linkers.

Figure 17 shows relative cytokine induction for various linkers and linker combinations.

Figures 18 A-E shows relative nuclease resistance for various PS and PO immunomers and oligonucleotides.

Figure 19 shows relative cytokine induction for PO immunomers compared with PS immunomers in BALB/c mouse spleen cell cultures.

WO 013/057822 PCT/USO2/34247 Figure 20 shows relative cytokine induction for PO immunomers compared with PS irnmunomers in C31-IHej mouse spleen cell cultures.

Figure 21 shows relative cytokine induction for P0 immunomners compared with PS immunomers in C3H/Hej mouse spleen cell cultures at high concentrations of immunomers.

WO 03/057822 PCT/US02/34247 11 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, immunomers of the invention are useful as adjuvants in combination with DNA vaccines, antibodies, allergens, chemotherapeutic agents, and antisense oligonucleotides.

The present inventors have surprisingly discovered that modification of an immunostimulatory oligonucleotide to optimally present its 5' ends dramatically affects its immunostimulatory capabilities. Such an oligonucleotide is referred to herein as an "immunomer." In a first aspect, the invention provides immunomers comprising at least two oligonucleotides linked at their 3' ends, or an intemucleoside linkage or a functionalized nucleobase or sugar to a non-nucleotidic linker, at least one of the oligonucleotides being an immunostimulatory 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 WO 03/057822 PCT/US02/34247 12 oligonucleotides having an accessible 5' end, the 5' OH position of the terminal sugar is not covalently linked to more than two nucleoside residues. 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.

For purposes of the invention, the term "immunomer" refers to any compound comprising at least two oligonucleotides linked at their 3' ends or internucleoside linkages, or functionalized nucleobase or sugar directly or via a non-nucleotidic linker, at least one of the oligonucleotides (in the context of the immunomer) being an immunostimulatory oligonucleotide and having an accessible 5' end, wherein the compound induces an immune response when administered to a vertebrate. In some embodiments, the vertebrate is a mammal, including a human.

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 immunostimulatory 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. 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.

WO 03/057822 PCT/US02/34247 13 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 comprising poly(I)poly(dC). In certain embodiments, at least one set of Nn includes a string of 3 to 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'-substitutedarabinose, 2'-O-substitutedarabinose 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 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 WO 03/057822 PCT/US02/34247 14 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 nuclcoside residues, preferably from about 4 to about 30 nucleoside residues, more preferably from about 4 to about 20 nucleoside residues. In some embodiments, the 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.

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'-fluoroarabinoside.

WO 03/057822 PCT/US02/34247 For purposes of the invention, the term "2'-substituted ribonucleoside" includes ribonucleosides in which the hydroxyl group at the 2' position of the pentose moiety is substituted to produce a 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, with halo, hydroxy, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl, carboalkoxy, or amino groups. Examples of such 2'-O-substituted ribonucleosides include, without limitation 2'-O-methylribonucleosides and 2'-O-methoxyethylribonucleosides.

The term "2'-substituted ribonucleoside" also includes ribonucleosides 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 include, without limitation, 2'-amino, 2'-fluoro, 2'-allyl, and 2'-propargyl ribonucleosides.

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 Pederson et al. U.S. Patent 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, Metelev and Agrawal, U.S. Patent No. 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 WO 03/057822 PCT/US02/34247 16 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 November 5, 1998; WO 01/12804, published February 22, 2001; WO 01/55370, published August 2, 2001; PCT/USO 1/13682, filed April 30, 2001; and PCT/USOI/30137, filed September 26, 2001. Preferably, the immunostimulatory oligonucleotide comprises at least one phosphodiester, phosphorothioate, or phosphordithioate interucleoside linkage.

In some embodiments, the immunostimulatory 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.

As used herein, the term "pyrimidine nucleoside" refers to a nucleoside wherein the base component of the nucleoside is a pyrimidine base. Similarly, the term "purine nucleoside" refers to a nucleoside wherein the base component of the nucleoside is a purine base. For purposes of the invention, a "synthetic" pyrimidine or purine nucleoside includes a non-naturally occurring pyrimidine or purine base, a nonnaturally occurring sugar moiety, or a combination thereof.

Preferred pyrimidine nucleosides according to the invention have the structure

D

D'

A

X A'

S'

WO 03/057822 PCT/US02/34247 17 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 2

-SH

and -OH. Preferred hydrogen bond acceptors include, without limitation, C=O, C=S, and the ring nitrogen atoms of an aromatic heterocycle, N3 of cytosine.

In some embodiments, the base moiety in is a non-naturally occurring pyrimidine base. Examples of preferred non-naturally occurring pyrimidine bases include, without limitation, 5-hydroxycytosine, 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 is a non-naturally occurring sugar moiety. For purposes of the present invention, a "naturally occurring sugar WO 03/057822 PCT/US02/34247 18 moiety" is a sugar moiety that occurs naturally as part of nucleic acid, 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 a 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 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.

WO 03/057822 PCT/US02/34247 19 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 2

-SI-

and -OH. Preferred hydrogen bond acceptors include, without limitation, C=O, C=S,

-NO

2 and the ring nitrogen atoms of an aromatic heterocycle, N I of guanine.

In some embodiments, the base moiety in (11) is a non-naturally occurring purine base. Examples of preferred non-naturally occurring purine bases include, without limitation, 6-thioguanine and 7-deazaguanine. In some embodiments, the sugar moiety S' in (HI) is a naturally occurring sugar moiety, as described above for structure In preferred embodiments, the immunostimulatory dinucleotide is selected from the group consisting of CpG, C*pG, CpG*, and C*pG*, wherein C is cytidine or 2'-deoxycytidine, C* is 2'-deoxythymidine, arabinocytidine, 2'-deoxythymidine, 2'deoxy-2T-substitutedarabinocytidine, 2'-O-substitutedarabinocytidine, hydroxycytidine, 2'-deoxy-N4-alkyl-cytidine, 2'-deoxy-4-thiouridine or other nonnatural pyrimidine nucleoside, G is guanosine or 2'-deoxyguanosine, G* is 2' deoxy- 7-deazaguanosine, 2'-deoxy-6-thioguanosine, arabinoguanosine, 2 '-deoxy- 2'substituted-arabinoguanosine, 2'-O-substituted-arabinoguanosine, 2'-deoxyinosine, 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 dinucleotidc. Thus, in some embodiments, the immunostimulatory oligonucleotide comprises in immunostimulatory domain of structure (III): WO 03/057822 PCT/US02/34247 I -Y-Z-N I -Nn-3' VIII) wherein: Y is cytidine, 2'deoxythymidine, 2' deoxycytidine arabinocytidine, 2'-deoxy- 2 '-substitutedarabinocytidine, 2'-deoxythymidine, 2'-O-substitutedarabinocytidine, 2'-deoxy-5-hydroxycytidine, 2'-deoxy-N4-alkyl-cytidine, 2'-deoxy-4-thiouridime or other non-natural pyrimidine nucleoside; Z is guanosine or 2'-deoxyguanosine, G* is 2' deoxy-7-deazaguanosine, 2'deoxy-6-thioguanosine, arabinoguanosine, 2'-deoxy-2' substituted-arabinoguanosine, 2'-O-substituted-arabinoguanosine, 2'deoxyinosine, or other non-natural purine nucleoside; NI1, at each occurrence, is preferably a naturally occurring or a synthetic nucleoside or an immunostimulatory moiety selected from the group consisting of abasic nucleosides, arabinonucleosides. 2'-deoxyuridine, ot-deoxyri bon ucleosides, P-L-deoxyribonucleosides, and nucleosides linked by a phosphodiester or modified internucleoside linkage to the adjacent rnucleoside on the 3' side, the modified intemnucleotide linkage being selected from, without limitation, a linker having a length of from about 2 angstroms to about 200 angstroms, C2-C 18 alkyl linker, poly(ethylene glycol) linker, 2-aminobutyl-1,3-propanediol linker, glyceryl linker, 2'intemnucleoside linkage, and phosphorothioate, phosphorodithioate, or methylphosphonate intemucleoside linkage; Nn, at each occurrence, is preferably a naturally occurring nucleoside or an immunostimulatory moiety selected from the group consisting of abasic nucleosides, arabinonucleosides, 2'-deoxyuridine, a-deoxyribonucleosides, 2'-O-substituted ribonucleosides, and nucleosides linked by a modified internucleoside linkage to the adjacent nucleoside on the 3' side, the modified intemucleotide linkage preferably being selected from the group consisting of amino linker, intemnucleoside linkage, and methylphosphonate intemnucleoside linkage; WO 03/057822 PCT/US02/34247 21 provided that at least one N I or Nn is an immunostimulatory moiety; wherein n is a number from 0 to 30; and wherein the 3'end, an intemucleoside 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 modifications in the phosphate backbones, including, without limitation, methylphosphonates, methylphosphonothioates, phosphotriesters, phosphothiotriesters, phosphorothioates, phosphorodithioates, triester prodrugs, sulfones, sulfionamides, sulfamates, formacetal, N-methylhydroxylamine, carbonate, carbamate, morpholino, boranophosphonate, phosphoramidates, especially primary amino-phosphoramidates, N3 phosphoramidates and N5 phosphoramidates, and stereospecific linkages 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-methoxyethylribose, 2'-0-propargylribose, and 2'-deoxy-2'-fluororibose; 3'-substituted pentose sugars, including, without limitation, 3'-O-methyfribose; I ',2'-dideoxyribose; arabiriose; substituted arabinose sugars, including, without limitation, I '-methylarabinose, 3'-hydroxymethylarabi nose, 4'-hydroxymethylarabinose, 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'-deoxyribonuclcoside or a 3-0-substituted ribonucleoside, the immunostimulatory moiety is attached to the adjacent nucleoside by way of a internucleoside linkage.

WO 03/057822 PCT/US02/34247 22 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-(CH 2

-CH

2 (n Some other functionalized alkyl linkers are peptides or amino acids.

Preferred immunostimulatory moieties according to the invention further include DNA isoforms, including, without limitation, P-L-deoxyribonucleosides and a-deoxyribonucleosides. Preferred immunostimulatory moieties according to the invention incorporate 3' modifications, and further include nucleosides having unnatural interucleoside linkage positions, including, without limitation, and linkages.

Preferred immunostimulatory moieties according to the invention further include nucleosides having modified heterocyclic bases, including, without limitation, 5-hydroxymethylcytosine, N4-alkylcytosine, preferably N4-ethylcytosine, 4-thiouracil, 6-thioguanine, 7-deazaguanine, inosine, nitropyrrole, and diaminopurines, including, without limitation, 2,6-diaminopurine.

WO 03/057822 PCT/US02/34247 23 By way of specific illustration and not by way of limitation, for example, in the immunostimulatory domain of structure (III), a methylphosphonate intemucleoside linkage at position N I or Nn is an immunostimulatory moiety, a linker having a length of from about 2 angstroms to about 200 angstroms, C2-C 18 alkyl linker at position X I is an immunostimulatory moiety, and a p-L-deoxyribonucleoside at position XI is an immunostimulatory moiety. See Table I 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 intemucleoside 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 NI Naturally-occurring nucleosides, abasic nucleoside, arabinonucleoside, 2'-deoxyuridine, p-L-deoxyribonucleoside C2-C 18 alkyl linker, poly(ethylene glycol) linkage, 2-aminobutyl-1,3-propanediol linker (amino linker), intemucleoside linkage, methylphosphonate intemucleoside linkage Nn Naturally-occurring nucleosides, abasic nucleoside, arabinonucleosides, 2'-deoxyuridine, 2'-O-substituted ribonucleoside, interucleoside linkage, methylphosphonate interucleoside linkage, provided that NI and N2 cannot both be abasic linkages Table 2 shows representative positions and structures of immunostimulatory moieties within an immunostimulatory oligonucleotide having an upstream potentiation domain. As used herein, the term "Spacer 9" refers to a poly(ethylene glycol) linker of formula -O-(CH 2

CH

2 wherein n is 3. The term "Spacer 18" refers to a poly(ethylene glycol) linker of formula -O-(CH 2

CH

2 wherein n is 6.

WO 03/057822 PCT[US02/34247 24S As used herein, the term "C2-C 18 alkyl linker refers to a linker of formula -04CH2)q0O, 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-(CH 2 3 For each of Spacer 9, Spacer 18, and C2-C 18 alkyl linker, the linker is connected to the adjacent nucleosides by way of phosphodiester, phosphorothioate, or phosphorodithioate linkages.

Table 2 Position TYPICAL IMMUNOSTIMULATORY MOIETY N2 Naturally-occurring nucleosides, 2-aminobutyl-1 ,3-propanediol linker N I Naturally-occurr ing nucleosides, P-L-deoxyribonucleoside, C2-C 18 alkyl l inker, poly(ethylene glycol), abasic l inker, 2-am inobutyl-l1,3-propanediol linker 3' Ni Naturally-occurring nucleosides, I ',2'-dideoxyribose, 2'-O-methylribonucleoside, C2-C 18 alkyl l inker, Spacer 9, Spacer 18 3' N2 Naturally-occurring nucleosides, I ',2'-dideoxyribose, 3'deoxyribonucleoside, P-L-deoxyribonucleoside, 2'-O-propargylribonucleoside, C2-C 18 alkyl l inker, Spacer 9, Spacer 18, ___________methylphosphonate intemnucleoside linkage 3'N 3 Naturally-occurring nucleosides, I ',2'-dideoxyribose, C2-C 18 alkyl linker, Spacer 9, Spacer 18, methylphosphonate intemnucleoside linkage, intemnucleoside linkage, d(G)n, polyl-polydC 3'N 2+ 3'N 3 1 ',2'-dideoxyribose, P-L-deoxyribonucleoside, C2-C 18 alkyl l inker, polyl-polydC 3'N3+ 3'N 4 2'-O-methoxyethyl-ribonucleoside, methylphosphonate internucleoside d( polyi-polydC 31N5+ 3' N 6 1 ',2'-dideoxyribose, C2-CI18 alkyl linker, d(G)n, polyl-polydC 3' N 3 1',2'-dideoxyribose, d(G)n, polyl-polydC Table 3 shows representative positions and structures of immunostimulatory moieties within an immunostimulatory oligonucleotide having a downstream potentiation domain.

WO 031057822 WO 03157822PCT/US02Y3424t7 Table 3 Position TYPICAL IMMUNOSTIMULATORY

MOIETY

N2 wethylpbosphottate intcrnuclicoside linkage NI telliylphosplofate intereucleoside linkage 3 NI 1',2-dideoxyribose. methylphosplionate intertiucleesidc linkage. V-O-iiielhyl 3' N2 1%Y-didenxyribose. fl.L-deoxytibonuclcosideCZ-'2CIS alkyl linker, Spaccr Spacer 19, 2aminobutyl-1I.3-propancdiol linker, mcthylplhvsphonate ititernueleosido linkage. 2'.O-niethyl 3' N3 31'dvonyribunuclcosidc. 3'-0-substituted tibonucinoside, 2'.0propergy -i bon uclecc ide 3'2+ 3 13 l',didcoxyribose. P- L-deoxy ribofluclecaside The immunomers according to the invention comprise at least two oligonucleotides linked at their 3'ends or intemnucleoside 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, 71-stacking interactions, and hydrogen bonding. The term "non-nucleotidic linker" is not meant to refer to an internucleoside linkage, as described above, 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 3Y-3' linkage 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, WO 03/057822 PCT/US02/34247 26 the linker may be attached to any suitable position on the nucleoside, as illustrated in Figure 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-(CH 2 )o-CH(OH)-(CH 2 )p-OH, wherein o and p independently are integers from I to about 6, from I to about 4, or from I 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-(CH

2 ),-C(O)NH-CH2-CH(OH)-CH 2

-NHC(O)-(CH

2 )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.

WO 03/057822 PCT/US02/34247 27 Some non-nucleotidic linkers according to the invention permit attachment of more than two oligonucleotides, as schematically depicted in Figure 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 Figures 5 and 6, and further described in the Examples. In some embodiments, the immunomers are synthesized by a linear synthesis approach (see Figure 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 Figure A solid support attached linker can be used for parallel synthesis, as is described in U.S. Patent 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: parallel synthesis permits the incorporation of identical monomeric units; 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 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 WO 03fO57822 PCTIUS02/34247 28 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 4 shows representative immunomers according to the invention.

Additional immunomers are found described in the Examples.

Table 4. Examples of Immunomer Sequences Oligo or Sequences and Modification Immunomer No.

1 5'-GAGMACGCTCGACCTT-3' 2 51-GAGMACGCTCGACCTT-3-3-TTCCAGCTCGCAAGAG-5' 3 -3'-TTCCAGCTCGCMAGAG-5-5-GAGAACGCTCGACCTT-3 4 5'-CTATCTGACGTTCTCTGT-3' HNCO-C4HO-5CTATLTGACGTTCTCTGT-3 6 5-CTATLTGACGTTCTCTGT-3'-C 4

H

8 -CONH F-CTATLTGACGTTCTCTGT-3-C 4

H

8 -CONH -C- 7 5'-CTATCTGACGTTCTCTGT-3'-0 4

H

8 -CONH 6-CTATCTGACGTTCTCTGT-3'-C- 4

H-CONH-

7 V5'.CTATCTGACG1TCTCTGT-3'j

V_,

5'-CTATCTGACcTrCrCTGr-3- 9 5'-CTATCTGAYG1-rCTCTGT-3' 5'-CTATCTGAYGTTCTCTGT-3- I 5'.CTATCTGACRTTCTCTGT-3' I I I 3'ACGYGTTTT3 5..CTATCTGAGTTCTCTGT-3 12 5'..CTALCTGACRTTCTCTGT3' 12 5'.TALCTGACRTTCTCTGT-3 13 5*-CGACGI-CCTCT53 5'.CCTGACRTTCTCTGT-3- 1 5-CTGACGTTCTCTGT-3' 14 5t-CTGACGTTCTCTGT3- 5-CTGACGTTCTCTGT-3' 5'-CTGAYGTTCTCTGT-3' 185CTGACRTTCTCTGT3'

N--

WO 03/057822 PCT/US02/34247 29 17 5'-XXTGACGTTCTCTGT-3' 18 5'-XXXTGACGTTCTCTGT-3'- 5'-XXXTGACGTTCTCTGT-3' 19 5'-XXXTGAYGTTCTCTGT-3' 5'-XXXTGACRTTCTCTGT-3'- 5'-XXXTGACRTTCTCTGT-3' -J 21 5'-TCTGACGTTCT-3' 22 5'-XXXTCTGACGTTCT-3'- 5'-XXXTCTGACGTTCT-3'-' 23 5'-XXXTCTGAYGTTCT-3'- 5'-XXXTCTGAYGTTCT-3' 24 5'-XXXTCTGACRTTCT-3'- 5'-XXXTCTGACRTTCT-3'-J NHCOC4HB- -jNHCOC4H- Symmetric longer branches; Symmetric glycerol (short) branches L C3-alkyl linker; X 1',2'-dideoxyriboside; Y 5 0 H dC; R 7-deaza-dG 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. 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.

WO 03/057822 PCT/US02/34247 The 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 nonnucleotidic linker. Alternatively, the antigen may itself be the non-nucleotidic linker.

In a third aspect, the invention provides pharmaceutical formulations comprising an 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, 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 immunomer or immunomer conjugate according to the invention. In some embodiments, the vertebrate is a mammal. For purposes of this invention, the term WO 03/057822 PCT/US02/34247 31 "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 immunomers 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, immunomers 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 immunomer 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, WO 03/057822 PCT/US02/34247 32 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 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.

WO 03/057822 PCT/US02/34247 33 In any of the methods according to this aspect of the invention, the 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 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 I: Synthesis of Oligonucleotides Containing lInmunoniodulatory Moieties Oligonucleotides were synthesized on a I iimol scale using an automated DNA synthesizer (Expedite 8909; PerSeptive Biosystems, Framingham, MA), following the linear synthesis or parallel synthesis procedures outlined in Figures and 6.

Deoxyribonucleoside phosphoraniidites were obtained from Applied Biosystems (Foster City, CA). I ',2'-dideoxyribose phosphoramidite, propyl-lphosphoramidite, 2-deoxyuridine phosphoramidite, I dimethoxytrityl)pentylam idyll-2-propanal phosphoramidite and methyl phosponamidite were obtained from Glen Research (Sterling, VA). j3-L-2'deoxyribonucleoside phosphoramidite, c-2'-deoxyribonucleoside phosphoram id ite, mono-DMT-glycerol phosphoramidite and di-DMT-glycerol phosphoramidite were obtained from ChemGenes (Ashland, MA). (4-Aminobutyl)-l1.3-propanediol phosphoramidite was obtained from Clontech (Palo Alto, CA). Arabinocytidine phosphoramidite, arabinoguanosine, arabinothymidine and arabinouridine were obtained from Reliable Pharmaceutical (St. Louis, MO). Arabinoguanosine phosphoram idite, arabinothym idine phosphoramidite and arabinouridime WO 03/057822 PCT/US02/34247 34 phosphoramidite were synthesized at Hybridon, Inc. (Cambridge, MA) (Noronha et al. (2000) Biochem., 39:7050-7062).

All nucleoside phosphoramidites were characterized by 1 P and 'H 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, Zhao et al., Biochem Pharma 51:173- 182 (1996)). The results are shown in Figure 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 mg/kg was administered to BALB/c mice (female, 4-6 weeks old, Harlan Sprague Dawley Inc, Baltic, CT) intraperitoneally. The mice were sacrificed 72 hours after oligonucleotide administration, and spleens were harvested and weighed. The results are shown in Figure 8B. These results demonstrate that Immunomer 6, having two accessible 5' ends, has a far greater immunostimulatory effect than do Oligonucleotide 4 or Immunomer WO 03/057822 PCT/US02/34247 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, CA. ELISA plates (Costar) were incubated with appropriate antibodies at 5 pg/mL in PBSN buffer (PBS/0.05% sodium azide, pH 9.6) overnight at 4 0 C and then blocked with PBS/1% BSA at 37 "C for 30 minutes. Cell culture superatants 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 I pg/mL appropriate biotinylated antibody and incubated at 25 °C for hours. The plates were then washed extensively with PBS-T Buffer (PBS/0.05% Tween 20) and further incubated at 25 OC 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 x 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 x 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 (100U/ml). Cells were cultured in 24 well plates for different time periods at I X 106 cells/ml/well in the presence or absence of oligonucleotides. At the end of the incubation period, supernatants were harvested and WO 03/057822 PCT/US02/34247 36 stored frozen at -70 *C until assayed for various cytokines including I L-6 (BD Pharmingen, San Diego, CA), IL- IO (BD Pharmingen), IL-12 (BioSource International, Camarillo, CA), IFN-a (BioSource International) and -y (BD Pharmingen) and TNF-ax (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-aE in the cell culture supematants were calculated from the standard curve constructed under the same experimental conditions for IL- 10, IFN-gamma and TNFa, respectively.

Table 5. Immunomer Structure and Immunostimulatory Activity in Human PBMC Cultures Oligc No.

dIigI SNo.

0 Sequences and Modification 5'-CTATCTGTCGTTCTCTGT-3' Oligo Length/ or Each Chain l8mer (PS) j 5'-TCTGTCRITTCT-3'- X 11 mer (PS) [5-TCTGTCRITTCT-3 P IL-12 (PglmL) IL-6 (pg/ML) Dl D2 D1 D2 184 332 3077 5369 237 352 3724 4892 IL-10 (pg/mL) IFN-y (pg/mL) D D Dl D2 137 88 15 84 0 Sequences and Modification 01190 Length/ or Each Chain 5'-CTATCTGTCGTTCTCTGT-3' l8mer (PS) iimer ~o1 ~W 5'-TCTGTCRITTCT-3- 5'-TCTGTCRITTCT-3- x, 11 mer (PS) 48 lim ZO-1 4V Oligo Sequences and Modification No.

5'-CTATCTGTCGTTCTCTGT-3' 26- -51-TCTGTCR 1 TTCT-3'- 1 5'-TCTGTCR 1 TTCT-3'/x 01 and D2 are donors 1 and 2.

Oligo Length/ or Each Chain l8mer (PS) TNF-ci(pg/mL) Dl D-2- 537 nt 681 nt 11lmer (PS) WO 03JO57822 PCT/US02/34247 37 Table 5A. Immunomer Structure and Immunostimulatory Activity in BALB/c Mouse Spleen Cell Cultures Oligo No.

Sequences and Modification Oligo Lenigth/ or Each Chain I Imer (PS) L:iL(pgijm L) -I L -6(pglrn) -4A-I/mL 870 5'-TCTGTCRiTrCT-3- 1 TTGT-3'

/X

1 2 TTCT-3 N 2 TrCT-3' /x 2

R

2 TTCT-3- 2

R

2 TTCT-3-

/I

5'-XXTCTGTCR,TTCT-3- 5'-XXTCTGTCRiTTCT-3-

XI

IlImer (PS) '1441 IlImer (PS) 1208 1limer (PS) IT62 i 5'-CTGTCR2TrCTCTGT-3'N -er(0 33 2

R

2 TTCTCTGT-3',\ 5'-CTGTY2R 2 TTCTCTGT-3'" Xi 5'-TCTGACRi1TCT-3\ 5'-TCTGACRI1TCT-3 ,x 5'-XXTCTGACRTTCT-3, 5'-XXTCTGACRITTCT-3-,x l4mer (PO) 10670 121 251 119 9' 699 16881 10766 19411 408 86 IlImer (PS) i 520 IlImer (PS) 2214 2 TTCT-3 1 1mer PS) 5'TCTGAY 2

R

2 TTCT-3 11 mer (PS) p273 2 TTCT3 1 Xi 5 -CTGA Y 2 G TTCTCTGT-3NX TGA Y 2 G TTCTCTGT-3 1

TGACR

2 TTCTCTGT-3' N 2 TTCTCTGT-3-

X

TGA Y 2

R

2 TCTCTGT-3'\

V

2

R

2 TTCTCG-3 I X 4mer (PO) l4mer (PO) l4mer (P0) 2899 WO 03/057822 PCT/US02/34247 38 Normal phase represents a phosphorothioate linkage; Italic phase represents a phosphodiester linkage.

dG 7-deaza0 RN N/ rNH 2 0 0 S0 so AraG 0 N ANH R2 0 NH N NH- 2 0 P S "0 AraC NH- 2 Y2

OH

0'0 oP. 0 In addition, the results shown in Figures 7A-C demonstrate that Oligonucleotide 2. with two accessible 5' ends elevates IL-12 and IL-6, but not at lower concentrations than Oligonucleotides I or 3. with one or zero accessible ends, respectively.

WO 03/057822 PCT/US02/34247 39 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 I L-6 in BALB/c mouse spleen cell cultures (Tables In this, and all subsequent examples, cytokine assays were carried out in BALB/c spleen cell cultures as described in Example 4.

Table 6. lInmunomer Structure and Immunostimulatory Activity No. Sequences and Modification Oligo Length/ IL-12 (pgirnL) IL-6 (pglmL) or Each Chain C 0.3 jpg/mL 0.3 Vg/mL 4 5'-CTATCTGACGTTCTCTGT-3' I mer 1802 176 39 5lCACGCTCCG-33 'T5 8mer 1221 148 5'-CTGACGTTCTCTGT-3' 3'T5 4mer 2107 548 CTGT-3'- 4-1 5'-TCTGACGTTCT-3 YT 11lier 3838 1191 5'-TCTGACGTTCT-3- 42 6-GCGTTCT-3] -T5 8mer 567 52 5-GACGTTCT-3 T h 3-- WO 03/057822 PCT/US02/34247 Table 7. Immunomer Structure and Immunostimulatory Activity Sequences and Modification Oligo Length/ or Each Chain IL-12 (pg/mL) 1 tg/ml- IL-6 (pglmL) 1 p.g/mL -4 5'-CTATCTGTCGTTCTCTGT-3' lamer 1 Bmer 5T-CTATCTGTCGTTCTCTGT-3' 5'.CTATCTGTCGTTCTCTGT-3 3-T-6 i 1 44 6-CTGTCGTTCTCTGT 3' 5'-CTGTCGTrCTCTGT-3IF- 5'-CTGTCGTTCTCT-3-, GTTCT3-.

GTC GTTCT-3'- l4mer 12mer 11 mer 291 43 1533 43 39 123 505 3- 1 5'-GTCGTTC-3' 3-T5 5'-GTCGTrC-3' 5'-GTCG1T-3' 5'-GTCG1T-3 3-T-51 I[8mer [TOb8W 7mer 1 6mer 34 TCGTT-3'- I 5--TCGTT-Y]3'-T- 5

T-

mer WO 03/057822 PCT/US02/34247 41l Table 8. Imniunomer Structure and Immuoostimulatery Activity Sequences and Modification Oligo Length/ or Each Chain IL-12 (pg/mL) I gig/mL IL-6 (pglmL) 1 pig/mL -4 53 5'-CTCACTTTCGTTCTCTGT-3' 18mer 5'-CTCACTrTCGTTCTCTGT-3-, 5'-CTCACTTTCGTTCTCTGT-3j 5-C TrrCGTTCTCTGT-3 TTUCG1TCTCTGT- 3 -5' 6-CTTTCGTCTCT3 45 5'-TTCGTTCT-3'L 5'-TTCGTTCT-3

II

l8mer 14mer IUmer 99 12 1252 I8mer7 5-TCGTTCT3V3-T5 TCT-3'- liner The results suggest that the immunostimulatory activity of immunomers increased as the length of the oligonucleotide chains is decreased from I 8-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 I 8-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: Iminunostimulatory Activity of Immunomners Containing A Non- Natural Pyriniidine or Non-Natural Purine Nucleoside As shown in Tables 9-11, immunostimulatory activity wits maintained for immunomers; of various lengths having a non-natural pyrimidine nucleoside or nonnatural purine nucleoside in the immunostimulatory dinucleotide motif WO 03/057822 PCT/US02/34247 42 Table 9. Inimunomer Structure and Immunostimulatory Activity Sequences and Modification Oligo Length/ IL-12 (pg~mL) IL-6 (pg/mL) or Each Chain 3 Ag/mL 3 Rig/mL 5'-CTCACTTCGTTCTCTGT-3' i8mer ilmer 57 58 5!-TCTWTGTTCT-Y

-T-

5J-CTTTYGTTCT3'1h -T5 5..TCTTTCRTTCT.3} 6-TTYGTTCT-3'- 5'-TTYGTTCT-3 11mer 348 365 283 66 8mer 5TTCRTTCT-3 f- 3'-T-5' i 8mer OH2 MOHO

N

I C NH R= V N NH 2 WO 03/057822 WO 03/57822PCT[US02/31247 Table 10. Immunomer Structure and Iminunostimulatory Activity Sequences and Modification Oligo Length/ IL-12 (pg/mL) fIL-6 (pglmL) or Each Chain f3 j~glmL 1 3 gg/mL 62 63 64

I

5'-CTATCTGTCGTTCTCTGT-3' 54'-CTGTYGTTCT-3' 5-TCTGTYGTTCT-3} 5'-TCTGTCRTTCT-3' 54-CTGTCRTTCT-3' 5--GTVGTTcT-3-J- 5'-GTCRTrCT-3'- TT5 5'-GTCRTTCT-3'- 1 3l8mer 11 mer ilmer 8mer 8mer 379 1127 787 64 339 296 126 113 I C NH 00 WO 031057822 PCT/tJS02/34247 44 Table 11. Immunonier Structure and Immunostimulatory Activity Sequences and Modification Oligo Length/ or Each Chain IL-12_(pg/mL) IL-6 (pg/mL) 3 pg/mL 3 pglmL 4 4.

5'-CTATCTGACGTTCTCTGT-3' 5'-CTATCTGAYGTTCTCTGT-3' U-CTATCTGAYG1TCTCTGT-31 3-T6_ 6-CTATCTGACRTTCTCTGT-3' 6-CTATCTGACRTTCTCTGT-3 f i8mer i8mer i8mer 1176 1892 627 1464 5-CTGAYGTTCTCTGT-3' 5'-CTGAYGTTCTCTGT-3' 3'-T-5' 5'-CTGACRTTCTCTGT-3-] '-T5 5'-CTGACRTTCTCTGT-3' 'T5 l4mer 548 1052 I 5'-TCTGAYGTTCT-3- limer 2050 152 1020 2724 1741 212 i i 5'-TCTGACRTTCT-3'1 5'-GAYGTTCT-3' 5'-GAYGTTCT-3' f3-T5 ilmer Smer 1780 397 i 5'-GACRTTCT-3' T-3-1~3'T5 8mer

I

HO

HN

00 k

NH

R= UV Z N NH 2 O"0 Is~~ 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 WO 03/057822 PCT/US02/342S7 shown in Table 12 suggest that linker length plays a role in the immunostimulatory activity of immunomers. The best immunostimulatory effect was achieved with C3to C6-alkyl linkers or abasic linkers having interspersed phosphate charges.

WO 03/057822 WO 03157822PCTIJS02I342-t7 Table 12. Immunomer Structure and Immuriostimulatory Activity Sequences and Modification 5'-CTATCTGACGTTCTCTGT-3' 5'-CTGACGTTCT-3"1 x Oligo Length/ or Each Chain 18mer 10mer IL-12_(pg/mL) 0.3 ptg/mL 5'-CTGACGTTCT-3 5'-CTGACGTTCT-3 I- 10mer 1'162 5'-CTGACGTTCT-3 5'-CTGACGTTCT-3! 5'-CTGACGTTCT-3' X4 5'-CTGACGTTCT-3 -'x jiomer__ 1074 IL-6 (pglmL) 1 p~g/mL 635 1454 1375 2258 11i97- 77 5-CTGAkCGTTCT-3! .5 1mer 284 5S-CTG$CGTTCT3-a~x 78 5'-CTGACGTTCT-3'% IOmer f1750 5!-CTGACGTTCT-3 6 50-CTGACGTTCT-3 I,(3S3 5'-CTGACGTrcT-3! -~pX 3 5-CTGACGTTCT-3 3SXPX 6-CTG4ACG1TcT-3 XpXpX IlOmer I Omer 2256 811 5'-CTGACGTTCT3-, 5'-CTGACGTTCT-3 -(XOpsXG) I Omer 3625 V-ITGACGTCT3 %I, 5-CTGACGTTCT-3 (XO54psXps I Omer 4248 -12 -41 2642 2988- 5!-CTGACG1TCT-3', P03- 5'-CTGACGTTCT-3 Il 6mer X4o-(CH j2) WO 03/057822 PCT/US02134247 47 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 immunomners 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 exhibiting immunostimulatory activity as determined by cytokine induction in BALB/c mouse spleen cell cultures.

Table 13. Immunomer Structure and Immunostimulatory Activity No. Sequences and Modification Oligo Length/ IL-12 (pglmL) IL-6 (pglrnL) or Each Chain 0.pg~rnL 1 gg/mL 4 5'-CTATCTGACGTTCTCTGT-3' I Smer 225 1462 8-4 .5-CTGACGTT-CTCTGT -3 14mer 15511 159 -T-51 (P0) 6TGACGTTCTCTGT-3'-____ 5'-LCTGACGTTCTCTGT-3' -14mer 466 467 5'-LLCTGACGTTCTCTGT-3! L C3-Linker Example 9: Synthesis of Immunomers 73-92 Oligonucleotides were synthesized on I iimol scale using an automated DNA synthesizer (Expedite 8909 PerSeptive Biosystems). Deoxynucleoside phosphoramidites were obtained from Applied Biosystems (Foster City, CA). 7- WO 03/057822 PCT/US02/34247 48 Deaza-2'-deoxyguanosine phosphoramidite was obtained from Glen Research (Sterling Virginia). I ,3-Bis-DMT-glycerol-CPGi was obtained from ChemGenes (Ashland, MA). 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 H PLC, followed by dialysis. Purified oligonucleotides as sodium salt form were lyophilized prior to use. Purity of oligonuclcotides was checked by CGE and MALDI- TOF MS (Bruker Proflex Ill MALDI-TOF Mass spectrometer).

Example I1I Immunomer Stability Oligonucleotides were incubated in PBS containing 10% bovine serum at 37' C f'or 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 Olig o Sequences and Modification CE analysis of oligos intact No. oligo remained after diaestion) 4h After 24h after 48h 4 5-CTATCTGACGTTCTCTGT- 90.9 71.8 54.7 3'/PS 26 (5'-TCTGTCGTTCT) 2 S/PS 97.1 91.0 88.1 (G=dG deaza) 86 (5'-CTGTCGTTCTCTGT) 2 S/PO 37.8 22.5 87 73.1 56.8 36.8

XXCTGTCGTTCTCTGT)

2

S/PO

88 (5'-UCTGTCGTTCTCTGT) 2 S/PO 48.4 36.7 X C3-Linker, U, C 2'-OMe-ribonucleoside WO 03/057822 PCT/US02/34247 49 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, Rockville, MD) were cultured in Dulbecco's modified Eagle's medium supplemented with 10% FCS and antibiotics (100 IU/mL of penicillin G/streptomycin). All other culture reagents were purchased from Mediatech (Gaithersburg, MD).

ELISAsfor IL-12 and IL-6. BALB/c mouse spleen or J774 cells were plated in 24-well dishes at a density of 5x10 6 or Ixl0 6 cells/mL, respectively. The CpG DNA dissolved in TE buffer (10 mM Tris-HCI, 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 gg/mL to mouse spleen cell cultures and 1.0, 3.0, or 10.0 l.g/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 p.g/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 OC 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 I gg/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 OC for 1.5 hr after the addition ofstreptavidine-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 WO 03/057822 PCT/US02/34247 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 1 Table 15: Phosphorothioate CpG DNA sequences and modifications used in the study~' CPG Sequence Length 5'-end 3'-end DNA It 89 5'-TCCATGACGTTCCTGATGC-3' 19-mer 1I 5'-TCCATGACGTUFCCTGATGC-3'-b 19-mer I blocked 91 5'-TCCATGACGTTCCTGATGC-3'-3'-g-5' 20-mer 2 blocked 92 5'-TCCATGACG11'CCTGATGC-3'-3'-h-5' 23-mer 2 blocked 93 5'-TCCATGACGTTCCTGATGC-3'-3 27-mer 2 blocked 94 5'-TCCATGACG1TCCTGATGC-3'-3 38-mer 2 blocked b-S '-TCCATGACGTTCCTGATGC-3' I 9-mer blocked 1 96 3'-c-5'-5'-TCCATGACGITCCTGATGC-3' 20-mer blocked 2 97 3'-d-5 -5'-TCCATGA CGTTCCTGATGC-3' 23-mer blocked 2 98 3'-e-5'-5'-TCCATGACG1TTCCTGATGC-3' 27-mer blocked 2 99 3'-f-5'-5'-TCCATGACGTlCCTGATGC-3' 38-mer blocked 2 100 5'-TCCATGACGTTCCTGATGC-3'-k 19-mer I blocked 101 1-5 '-TCCATGACGTTCCTGATGC-3' 1 9-mer blocked I a See Chart I for chemical structures 5'-CG-3' dinucleotide is shown underlined.- WO 03/057822 WO 03/57822PCT/TS02/34247 Chart 1 R-O-

T

0 O=P-O- CCATGACGTCCGTGAT--Oo t- :PR,R' 0 3' O=P-S (K) 03' O=P-S- (h)

-I-I

(a) 0 OHPs 03'0

H

0

H

CCTAC3 5'-TCCATGjACUTU-CCGAIG-0 0 c 1 -CCTGAG-0-g 0 I~ 0 T o 3' 03 CCA-3' s- 1 5, -0

T

0 0 M

I

UUA I (jAuLjTTCCTGATGC-3' HO 0 OH 0 0 y X CH 2

OH;

x 0 XH.

-53- Table 16. Induction of IL- 12 and IL-6 secretion by CpG DNA-conjugates in BALB/c mice spleen cell cultures CpG IL-12 (pg/mL)±,SD IL-6 (pg/mL)±+SD DNA 4a 0. 1j g/mL 0.3p~glmL 1.0j.L/mL 3.Optg/m]L I 0.Opg/mL 0. 1 g/mL 0.3jtg/mL I.O~gfmL 3.0 Ag/mL I O.Og~g/m L 89 991±121 1820±224 23911175 3507±127 2615±279 652±48 2858±180 13320±960 18625±1504 17229±1750 526±32 2100±175 1499±191 3019±35 3489±162 1387±152 1426±124 5420±370 19096±484 19381±2313 91 1030±11 1348+102 2060±130 3330-+130 3582±259 923+22 2542±+81 9054±1I20 14114±1I79 13693±264 92 1119±159 1726±207 2434±100 2966±204 3215±464 870±146 1905±56 7841±350 17146±1246 15713±693 93 1175±68 2246±124 1812-+75 2388±320 2545±202 1152±238 3499±116 7142±467 14064±167 13566±477 94 1087±1-121 1705±i163 17971141 2522-±195 3054±1I03 1039-±105 2043± 15 7 4848±288 15527±224 2102111427 1173±107 2170±155 2132±58 2812±203 3689±94 807±0.5 927±0.5 3344±0.5 10233±0.5 9213±0.5 96 866±51 1564±63 1525+63 2666±+97 4030-4165 750±i63 1643±30 5559±415 11549±251 11060±651 97 227±3 495±96 1007±68 897±1I5 1355±97 302±18 374±22 1000±68 9106±271 13077±381 98 139±18 211±12 452±22 458±29 1178±237 220±23 235±18 383±35 1706±33 11530±254 99 181±85 282±105 846±+165 2082±+185 3185±63 467±122 437±85 1697±283 9781±13 11213±294 Medium 86±6 60±12 aSee Table I 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/vaccinefmonoclonal 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.

WO 03/057822 PCT/US02/34247 53 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 immunomner.

Table 17. Sequences of CpG DNA showing the position of substitution.

CpG DNA Sequence N urnber 102 CCTACTAGCG11TCTCATC 103 CCTACTAGC2TTCTCATC 104 CCTACT2GCGTFCTCATC 105 CCTA2TAGCGTTCTCATC 106 CCT22TAGCGTTCTCATC 107 22TACTAGCGTTCTCATC 108 CCTACTAGCGT2CTCATC 109 CCTACTAGCG117C2CATC 110 CCTACTAGCGTTC22ATC II1 CCT6CTAGCGTTCTCATC 112 CCTACTAGCGTTC6CATC 113 CCTICTAGCGTUCTCATC 114 CCTACTAGCGTTC7CATC 4 CTATCTGACGTrCTCTGT 115 CTATITGACGTTCTCTGT 116 CTAICTGACG1TCTCTGT 117 CTATCTG2CGTTCTCTGT 118 CTATC2GACG1TCTCTGT 119 CTA2CTGACG1TCTCTGT 120 22222TGACGTTCTCTGT 121 2222Tc3ACGTI'TCTGT 122 222TGACGTTCTCTGT 123 22TGACGTT1CTCTGT 124 2TGACG'TCTCTGT 125 CTAT3TGACGTTCTCTGT 126 CTA3CTGACGTTCTCTGT 127 CTA33TGACGTTCTCTGT 128 33TGACGTTCTCTGT 129 CTAT4TGACGTTCTCTGT 130 CTA4CTGACG1TCTCTGT 131 CTA44TGACGTTCTCTGT 132 44TGACGTTCTCTGT 133 CTATSTGACGTUCTCTGT 134 CTASCTGACGTTCTCTGT 135 WO 03/057822 PCT/US02/34247 54 136 55TGACGTT7CTCTGT 137 CTA6CTGACGTTCTCTGT 138 CTATCTGACGTTC6CTGT 139 CTA7CTGACGYFCTCTGT 140 CTATCTGACGTTC7CTGT 141 CTATCTG8CGTrCTCTGT 142 CTATCT8ACGT7CTCTGT 143 CTATC8GACGTTCTCTGT 144 CTAT8TGACGITCTCTGT 145 CTA8CTGACGTTCTCTGT 146 CTATCTGACG8TCTCTGT 147 CTATCTGACGT8CTCTGT 148 CTATCTGACGTT8TCTGT 149 CTATCTGACGTTC8CTGT 150 CTATCTG9CGTfrCTCTGT 151 CTATCT9ACG11'CTCTGT 152 CTA9CTGACG1TCTCTGT 153 CTATCTGACGT9CTCTGT 154 CTATCTGACG1TC9CTGT ~See Figure 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 BA LB/c mouse spleen cell cultures. All CpG DNAs induced concentrationdependent IL-1 2 and IL-6 secretion. Figure 15 shows data obtained at I gg/mL concentration of selected CpG DNIAs, 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- C3and C4-linkers 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-1 2 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 WO 03/057822 PCT/US02/34247 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 ofCpG DNA containing ethylenegylcol-linkers, we synthesized CpG DNAs 137 and 138, in which a triethyleneglycol-linker is incorporated at the fifth nucleotide position in the 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 in the 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 concentrationdependent cytokine production over the concentration range tested (0.03-10.0 lg/mL) (data not shown). The levels ofcytokines induced at 0.3 pg/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 in the 3'-flanking sequence induced IL-12 secretion similar to that of the parent CpG DNA, but significantly lower levels oflL-6 and IL-10 (Table 18). CpG DNA 140, which had a longer ethyleneglycol-linker induced significantly lower levels of all three cytokines tested compared with the parent CpG DNA (Table 18).

Though triethyleneglycol-linker had a chain length similar to that ofC9linker 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 WO 03/057822 PCT/US02/34247 56 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 ethyleneglycollinker in BALB/c mice spleen cell cultures.

CpG Cytokine, pg/mL

DNA

Number IL-12 IL-6 4 1887±233 21301221 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 or an amine 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 aminolinker 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.

WO 03/057822 PCT/US02/34247 57 Parent CpG DNA 4 showed a CpG Spleen cell Spleen NCpG Spleen cell Spleen proliferation index of 3.7±0.8 at a DNA proliferation weight Numbera (PI)b (mg)c concentration of 0.1 g/mL. At the same 4 3.7±0.8 121±16 concentration, modified CpG DNAs 151-154 150 2.5+0.6 107±11 15 0 2 5 0 6 1 0 7 l 1 i5 containing amino-linker 9 at different 151 9.2±0.7 169±16 151 8.±0.4 2± positions caused higher spleen cell 152 8.8d-0.4 220±8 153 7.6±0.7 127±24 proliferation than did the parent CpG DNA 154 7.8±0.04 177±12 (Table 19). As observed with other linkers, M/V 1.210.3 102±8 when the substitution was placed adjacent to LPS 2.8±0.5 ND 10 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 showed immunostimulatory activity similar to or slightly higher that that observed with modified CpG DNA containing amino-linker (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 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. Figure 4 shows the levels of IL- 12 and IL-6 induced by 145 and 152 in mouse spleen cell cultures at 0.3 lig/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 glycerollinker induced slightly higher levels of cytokines (especially IL-12) than did CpG WO 03/057822 PCT/US02/34247 58 DNA containing amino-linker (Figure 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 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 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 pg/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 pg/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; 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, WO 03/057822 PCT/US02/34247 59 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 4.g/mL concentration are shown in Figure 17. The results presented in Figure 17 suggest that the immunostimulatory activity is dependent on the nature of the linker incorporated.

The substitution of the fourth and fifth nucleosides with C4-1linker 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 C9linkers 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 CPO Sequence' Backbone Molecular Weight i~'X DNA Calculated Found' 0 4 5'-CTATCTGACGYTTCtTGT-3V PS 5702 5704 O H I 155 5'-CTATCTGACc 1 TTCTrCTGT-Y PO 5432 5428 Y 156 5.-CTGACGrTCT'CTGT.X-TGjTCTCTTGCAGTC-S' PO 8656 8649 l O '.0 157 5.-Yy(CfACCfTCTCTJT-X-TCT*CTC1TGCAGTCYY-5' PO 9208 9214 120 'Arrows indicate Y.3'directionality of CpG dinucicotide in each DNA molecule and structures of X andY arc showii in boxes.

bPS and P0 stand for phosphorothioate and phosphodiester backbones, respectively.

'As determined by MALDI-TOF mass spectrometry.

WO 03/057822 PCT/US02/34247 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 hexamcric 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. Figure 18 A-D shows the nuclease digestion profiles of CpG DNAs 4, 155-157 incubated in FBS for 24 hr. The amount of full-length CpG DNA remaining at each time point is shown in Figure 18 E. 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 POimmunomers 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 of 155 (Fig. 18 Even after 48 hr, about 23% and 37% of 156 and 157, respectively, remained undegraded. As well as showing that 3'-3'-linked POimmunomers 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 ugg/mL, PS-CpG DNA 4 induced WO 03/057822 PCT/US02/34247 61 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 pg/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 Figure 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 tg/mL, they produced negligible amounts of IL-6 (Fig. 19B). Even at the highest concentration (10 pg/mL), POimmunomer 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 Figure 19A shows the ratio of IL-12 to IL-6 secreted at 3 lg/mL concentration. In addition to increasing IL-12 secretion, PO-immunomers 156 and 157 induced higher levels of IFN-y 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 (Fig. 20A and 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. 20A). However, at concentrations up to 3 Lg/mL, neither induced IL-6 production. At the highest concentration tested itg/mL), both induced significantly less IL-6 than did PS-CpG DNA 4 (Fig. WO 03/057822 PCT/US02/34247 62 The ratio of IL-12 to IL-6 secreted is calculated to distinguish cytokine secretion profiles of PS and PO CpG DNAs (Fig. 20A 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-y 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. POimmunomer 157 gave 57% growth inhibition of MCF-7 tumors on day 15 compared with the saline control (Fig. 21A). It also produced 52% growth inhibition of DU-145 tumors on day 34 (Fig. 21B). These antitumor studies suggest that PO-immunomers of the proposed design exhibit potent antitumor activity in vivo.

Example 22: 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 nucleotides per segment are effective in inducing cvtokine production.

Table 22. Immunomer Structure and Immunostimulatory Activity in BABL/C Mouse Spleen Cell Cultures Oligo No. Sequences and Modification Oligo Length/ LL-12Jp/m_Lr IL-6(pgmL or Each Chain 10 g/mL_ 4 5'-CTATCTGACGTTCTCTGT-3' 18mer 2731 4547 5'-CTATCTGTCGTTCTCTGT-3' 18mer 795 789 158 5'-TCTGACGTTCT-3' 1imer 3490 5319 5'-TCTGACGTTCT-3'

X.

159 5'-TCTGTCGTTCT-3'\ 1 mer 3265 4625 5'-TCTGTCGTTCT-3'/

X

WO 03/057822 WO 03/57822PCTIUS02/34247 5'-TCG1TG-3'\ 5'-TCGTTG-3'/X 6mer 2085 2961 5'-TCGTTG-3'XX\ 5'-TCGTTG-3'XX

/X

6mer 162 5'-TCGTTG-3X\ 5'-TCGTTG-3'X/'1 6mer -TCGTh3'X 5'-TCGTT-3'X 5'-ACG1TG-3'X 5'-ACGTTG-3'X

/IX

6mer 1015 26-23 564 705 845 4 l 5'-GCG1TG-3'X\~ 5'-GCG1TG-3X/ 1 5'-CCG1TG-3'X 5'-CCGTTG-3'X-'1 6mer 6mer 196 219 1441 198 0 5056- 0 -GTCGTTh3'X- 5'-GTCGTT-3'X

XI

5-TGTCGT-3'X 5'-TGTCGT-3'X

/X

6mer 6mer 169 I- 6mer 2410 -X3-GTTGCT-1 Normal phase represents a phosphorotbioate linkage.

S0 0 0 0 0 D /OH 0"1 004972866 64

EOUIVALENTS

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.

As used herein, the term "comprise" and variations of the term, such as "comprising", "comprises" and "comprised", are not intended to exclude other additives, components, integers or steps.

Reference to any prior art in the specification is not, and should not be taken as, an acknowledgment, or any form of suggestion, that this prior art forms part of the common general knowledge in Australia or any other jurisdiction or that this prior art could reasonably be expected to be ascertained, understood and regarded as relevant by a person skilled in the art.

Claims (49)

1. An immunomer, comprising at least two oligonucleotides linked at their 3' ends or intemnucleoside linkages or a functionalized nucleobase or sugar to a non-nucleotidic linker, wherein at least one of the oligonucleotides is an imimunostimulatory oligonucleotide having an accessible 5' end and comprising an immunostimulatory dinucleotide selected from the group consisting of C*pG, CpG* and C*pG*. ID

2. The immunomer according to claim 1 wherein C is cytidine or 2'-deoxycytidine, C* is 2'deoxythymidine, arabinocytidine, 2'-deoxy-2'-substitutedarabinocytidine, 2'-O- substitutedarabinocytidine, 2'-deoxy-5-hydroxycytidine, 2'-deoxy-N4-alkyl-cytidine, 2'- deoxy-4-thiouridine or other non-natural pyrimidine nucleoside, G is guanosine or 2'- deoxyguanosine, G* is 2'deoxy-7-deazaguanosine, deoxy-6-thioguanosine, arabinoguanosine, 2'-deoxy-2'substituted- arabinoguanosine, 2'-O-substituted- arabinoguanosine, or other non-natural purine nucleoside, and p is an intemnucleoside linkage selected from the group consisting of phosphodiester, phosphorothioate, and phosphorodithioate.

3. The immunomer according to claim 1 wherein at least one of the oligonucleotides has the structure 1 -Y-Z-N I -Nn-3' VI) wherein: Y is cytidine, 2'-deoxycytidine arabinocytidine, 2'-deoxythymidine, 2'-deoxy-2'- substituted-arabinocytidine, 2'-O-substituted-arabinocytidine, hydroxycytidine, 2'-deoxy-N4-alkyl-cytidine, 2'-deoxy-4-thiouridine or other non-natural pyrimidine nucleoside; Z is guanosine, 2'-deoxyguanosine, 2'deoxy-7-deazaguanosine, 2'-deoxy-6-thioguanosine, arabinoguanosine, 2'-deoxy-2'substituted-arabinoguanosine, 2'-O-substituted- arabinoguanosine, 2'deoxyinosine or other non-natural purine nucleoside, 004972866 66 N1, at each occurrence, is preferably a naturally occurring or a synthetic nucleoside or an immunostimulatory moiety selected from the group consisting of abasic nucleosides, arabinonucleosides, 2'-deoxyuridine, c-deoxyribonucleosides, 3-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-l,3- propanediol linker, glyceryl linker, 2'-5'intemucleoside linkage, and phosphorothioate, phosphorodithioate, or methylphosphonate interucleoside linkage; wherein Nn, at each occurrence, is a naturally occurring nucleoside or an immunostimulatory moiety, selected from the group consisting of abasic nucleosides, arabinonucleosides, 2'-deoxyuridine, o-deoxyribonucleosides, 2'-O-substituted or 2'- substituted ribonucleosides, and nucleosides linked by a modified intemucleoside linkage to the adjacent nucleoside on the 3' side, the modified internucleotide linkage being selected from the group consisting of amino linker, internucleoside linkage, and methylphosphonate internucleoside linkage; wherein n is a number from 0-30.

4. The immunomer according to claim 1, wherein the internucleotide linkages between adjacent nucleotides comprises phosphorothioate linkages.

5. The immunomer according to claim 1, wherein G* is 2'-deoxy-7-deazaguanosine.

6. The immunomer according to claim 2 having the structure 065083572v3.doc 00 oo O O (N q \O C-) 5'-TCTGTCRTTCT-3' x 5*-TCTGTCRTTCT-3' X= 0 OH 0 dG 7 -deaza H 00 N 2 0 N "NH 2 R= 0

7. The immunomer of claim 1 wherein the immunomer comprises at least one oligonucleotide that is complementary to a gene.

8. The immunomer of claim 1 wherein the immunomer comprises at least one ribozyme or a decoy oligonucleotide.

9. The immunomer of claim 1 wherein the immunomer comprises at least one Nn portion includes a G4 tetranucleotide.

The immunomer of claim 2 wherein the non-naturally occurring pyrimidine has the structure wherein D is a hydrogen bond donor; 005083572v3.doc 0 0 D' is selected from the group consisting of hydrogen, hydrogen bond donor, hydrogen Sbond acceptor, hydrophilic group, hydrophobic group, electron withdrawing group and electron donating group, excluding bromine; 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; ID0 X is carbon or nitrogen; and 0 S' is a pentose or hexose sugar ring or a non-naturally occurring sugar.

11. The immunomer according to claim 10 wherein the sugar ring is derivatized with a phosphate moiety, modified phosphate moiety, or other non-nucleotidic linker moiety suitable for linking the pyrimidine nucleoside to another nucleoside or nucleoside analog.

12. The immunomer according to claim 10 wherein the hydrogen bond donors are selected from the group consisting of-NH-, -NH 2 -SH and -OH.

13. The immunomer according to claim 10 wherein the hydrogen bond acceptors are selected from the group consisting of C=O, C=S, and the ring nitrogen atoms of an aromatic heterocycle.

14. The immunomer according to claim 10 wherein the non-naturally occurring pyrimidine base is selected from the group consisting of 5-hydroxycytosine, hydroxymethylcytosine, N4-alkylcytosine, N4-ethylcytosine, and 4-thiouracil.

15. The immunomer according to claim 10 wherein the non-naturally occurring sugar is selected from arabinose and arabinose analogs.

16. The immunomer according to claim 2 wherein the purine nucleoside has the structure (II): 004972866 69 A XN D' II I) S. 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 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.

17. The immunomer according to claim 16 wherein 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.

18. The immunomer according to claim 16 wherein the hydrogen bond donors are selected from the group consisting of-NH-, -NH 2 -SH and -OH.

19. The immunomer according to claim 16 wherein the hydrogen bond acceptors are selected from the group consisting of C=O, C=S, and the ring nitrogen atoms of an aromatic heterocycle. The immunomer according to claim 16 wherein the non-naturally occurring purine is 6- thioguanine or 7-deazaguanine.

O65800572v .doc 00

21. The immunomer according to claim 1, wherein the non-nucleotidic linker is selected from Sthe 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 [T 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 Sfrom the group consisting of hydroxy, amino, thiol, thioether, ether, amide, thioamide, IND ester, urea, and thiourea; amino acids, carbohydrates, cyclodextrins, adamantane, cholesterol, haptens antibiotics, glycerol or a glycerol homolog of the formula HO- S(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.

22. The immunomer according to claim 1, wherein the internucleoside linkages consist essentially of phosphodiester linkages..

23. The immunomer according to claim 1, wherein C* is arabinocytosine or 2'-deoxy-2- substituted arabincytosine and G* is arabinoguanosine or 2'-deoxy-2'-substituted arabinguanosine, 2'-deoxy-7-deazaguanosine or 2'-deoxy-6-thioguanosine, or 2'- deoxyinosine.

24. An immunomer conjugate, comprising an immunomer, according to claim 1 and an antigen conjugated to the immunomer at a position other than the accessible 5' end.

A pharmaceutical formulation comprising an immunomer according to any one of claims 1 to 23 and a physiologically acceptable carrier.

26. A method for generating an immune response in a vertebrate, the method comprising administering to the vertebrate an immunomer according to any one of claims 1 to 23.

27. A method for generating an immune response in a vertebrate, the method comprising administering to the vertebrate an immunomer conjugate according to claim 23. 004972866 71

28. A method for therapeutically treating a patient having a disease or disorder, such method comprising administering to the patient an immunomer according to any one of claims 1 to 23.

29. The method according to claim 28 wherein the disease or disorder to be treated is cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, skin disorders, allergy, asthma or a disease caused by a pathogen.

A method for therapeutically treating a patient having a disease or disorder, such method comprising administering to the patient an immunomer conjugate according to claim 24.

31. A method for therapeutically treating a patient having a disease or disorder, such method comprising administering to the patient an immunomer according to claim 6.

32. The method according to claim 30 wherein the disease or disorder to be treated is cancer, an autoimmune disorder, airway inflammation, allergy, asthma or a disease caused by a pathogen.

33. The method according to claim 31 wherein the disease or disorder to be treated is cancer, an autoimmune disorder, airway inflammation, allergy, asthma or a disease caused by a pathogen.

34. The method of claim 28 further comprising administering a vaccine.

The method of claim 34, wherein the immunomer or the vaccine, or both, are linked to an immunogenic protein.

36. The method of claim 28 further comprising administering an adjuvant.

37. The immunomer according to any one of claims 1 to 23, wherein the internucleoside linkages consist essentially of phosphorothioate linkages.

38. The pharmaceutical composition according to claim 25 further comprising a vaccine. 005083572v3.doc 0 0

39. A pharmaceutical formulation comprising an immunomer according to claim 6 and a Sphysiologically acceptable carrier. S

40. A pharmaceutical formulation comprising an immunomer conjugate according to claim 24 and a physiologically acceptable carrier.

41. A method for generating an immune response in a vertebrate, the method comprising administering to the vertebrate an immunomer according to claim 6. IND S

42. A method for generating an immune response in a vertebrate, the method comprising 0administering to the vertebrate a composition according to any one of claims 25, 38, 39 or

43. A method for therapeutically treating a patient having a disease or disorder, such method comprising administering to the patient a composition or formulation according to any one of claims 25, 38, 39 or

44. The method according to claim 43 wherein the disease or disorder to be treated is cancer, an autoimmune disorder, airway inflammation, allergy, asthma or a disease caused by a pathogen.

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

46. Use of an immunomer according to any one of claims 1 to 23, or an immunomer conjugate according to claim 24 for the manufacture of a medicament for therapeutically treating a patient having a disease or a disorder.

47. Use of an immunomer according to any one of claims 1 to 23, or an immunomer conjugate according to claim 24 for generating an immune response in a vertebrate.

48. An immunomer or immunomer conjugate substantially as hereinbefore described with reference to the examples. 004972866 73

49. A method according to any one of claims 26, 28, 30, 31 or 41 to 43, substantially as hereinbefore described with reference to the examples. Dated 11 May 2007 Freehills Patent Trade Mark Attorneys Patent Attorneys for the Applicant: Idera Pharmaceuticals, Inc.