WO1995024222A1

WO1995024222A1 - Cyclic polycationic polymer-oligonucleotide conjugates and methods for preparing same

Info

Publication number: WO1995024222A1
Application number: PCT/US1995/002894
Authority: WO
Inventors: Stanley Stein; Ziping Wei; Tianmin Zhu; Ching-Hsuan Tung
Original assignee: University Of Medicine & Dentistry Of New Jersey
Priority date: 1994-03-07
Filing date: 1995-03-07
Publication date: 1995-09-14
Also published as: AU2116995A

Abstract

The present invention pertains to cyclic polycationic polymer-oligonucleotide conjugates comprising a polycationic polymer covalently bonded at each end to the 3'- and 5'- terminal nucleotides of a polyanionic oligonucleotide via a cross-linking agent, wherein the polycationic polymer may be represented by the formulae: (I), or (II), or (III), or (IV) R2-[[NH(CH2)b]c[NH(CH2)d]e]f[NH(CH2)g]h-NHR2, or (V), or (VI), or (VII), or (VIII), wherein R1 through R7, X, and a through i, are defined within.

Description

CYCLIC POLYCATIONIC POLYMER-OLIGONUCLEOTIDE

CONJUGATES AND METHODS FOR PREPARING SAME

BACKGROUND OF THE INVENTION

Field of the Invention

This invention pertains to cyclic polycationic polymeroligonucleotide conjugates. The cyclic conjugates comprise a polycationic polymer covalently bonded at each end to the 3'- and 5'- terminal nucleotides of a polyanionic oligonucleotide via cross-linking reagents. The polycationic polymer linked in a cyclic fashion to the polyanionic oligonucleotide helps the oligonucleotide bind to complementary strands through interactions with the oligonucleotide. The cyclic conjugates have important applications in antisense and antigene fields.

Description of the Background

The disclosures referred to herein to illustrate the background of the invention and to provide additional detail with respect to its practice are incorporated herein by reference and, for convenience, are numerically referenced in the following text and respectively grouped in the appended bibliography. Synthetic oligonucleotides provide a new approach for controlling cellular or viral gene expression at the transcription or translation level (1, 2, 3). Oligonucleotides, however, are highly sensitive to cellular nucleases and do not effectivly pass through cellular membranes. Hence, oligonucleotides have been chemically modified in order to meet the requirements for therapeutic applications (4, 5).

One of the major ways to modify oligonucleotides is to append non- nucleic acid moieties to the oligonucleotides. Oligonucleotide-intercalator conjugates have been prepared and found to have different properties depending on the attached intercalators. Oligonucleotide-acridine conjugates have been shown to increase the binding affinity of the oligonucleotide to its complementary single- stranded target or double-stranded target (6, 7). An oligonucleotide-phenanthroline conjugate has been shown to cleave double strand DNA in the presence of cupric ion and a reducing agent (8). Cationic polylysine conjugated to oligonucleotides has been shown to improve cellular uptake, nuclease stability, and binding affinity (9).

While a number of cationic polymers have been conjugated to oligonucleotides to improve the stability and cellular uptake of the oligonucleotides, none of these conjugated oligonucleotides have been entirely satisfactory. Conjugated cationic polymers have not been designed to substantially neutralize the oligonucleotide. The present invention provides such oligonucleotide conjugates having improved therapeutic properties. The cyclic oligonucleotide conjugates can be synthetically modified to vary the reactivity, the specificity, and the general utility of the oligonucleotide to greatly facilitate gene regulation. The cyclic conjugates of the present invention may be employed with pharmaceutically acceptable carriers to provide a wide variety of pharmaceutical products.

SUMMARY OF THE INVENTION

The present invention pertains to cyclic polycationic polymer- oligonucleotide conjugates comprising a polycationic polymer covalently bonded at each end to the 3 '- and 5'- terminal nucleotides of a polyanionic oligonucleotide via a cross-linking agent, wherein the polycationic polymer may be represented by the formulae: R₂-[XRιCHCO]_a-R₃ (I)

NH₂ or the formula:

or the formula:

R5-R4 R₇ or the formula:

R2-[tNH(CH2)b]c[NH(CH₂)_d]e]f[NH(CH₂)_g]_h-NHR2 (IV) or the formula:

R₂-[XCHCO]_i-R₃ (V)

R4-R5 or the formula:

_R2-_[ o_Xc„co_ro_la-_R3

R₇ R4R5 R₇ or the formula:

K.-CX HCOXK.COXCHCO^ R5R4 R₇ R5R4 or the formula:

_R2-_[XCHCOXCHCOX_R6C_OXK₆C0_la-_R3 R5R4 R5R4 R₇ R₇

wherein X is selected from the group consisting of -NH-, -O-, and -S-; R_j is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 4 carbon atoms in the chain; R2 and R3 are cross-linking agents covalently linking the polycationic polymer to the oligonucleotide; R4 is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 5 carbon atoms in the chain; R5 is selected from the group consisting of primary amines, secondary amines, tertiary amines, quaternary ammonium salts, imidazoles, and guanidine groups; R is an alkyl chain having from 1 to 2 carbon atoms; R is selected from the group consisting of hydrogen, branched and unbranched lower- alkyl groups having from 1 to 5 carbon atoms, -CH2C5H5, and -(CH2)_zCOR3, wherein z is an integer ranging from 0 to 3 and R3 is as defined above; a is an integer ranging from about 3 to about 16; b is an integer ranging from about 2 to about 5; c is an integer ranging from about 0 to about 3; d is an integer ranging from about 2 to about 5; e is an integer ranging from about 0 to about 3; f is an integer ranging from about 2 to about 9; g is an integer ranging from about 2 to about 5; h is an integer ranging from about 0 to about 3; i is an integer ranging from about 3 to about 12; and the ratio of cations in the polycationic polymer to anions in the polyanionic oligonucleotide pair ranges from about 0.7: 1 to about 1.5: 1, respectively.

BRIEF DESCRIPTION OF THE FIGURES

Figure 1 illustrates an HPLC purification of the compounds of the present invention. Figure 1(A) is graph of an anion-exchange HPLC purification of the activated oligonucleotide TTTATT-iodoacetyl oligonucleotide. Figure 1(B) is a graph of an anion-exchange HPLC purification of the peptide-oligonucleotide conjugate, TTTATT-Cys-(Leu-Lys)2-Lys-(Leu-Lys)2-Cys-S-S-tBu. Figure 1(C) is a graph of a reverse-phase HPLC desalting of the peptide-oligonucleotide conjugate, TTTATT-Cys-(Leu-Lys)2-Lys-(Leu-Lys)2-Cys-S-S-tBu. Figure 1(D) is a graph of a reverse-phase HPLC purification of the oligonucleotide- peptide-oligonucleotide bridged conjugate, TTTATT-

Cys-(Leu-Lys)2-Lys-(Leu-Lys)2-Cys-CATTTC.

Figure 2 is a photograph illustrating gel electrophoresis analysis of intermediates and the product of bridged conjugate synthesis for a Leu-Lys-type peptide.

Figure 3 is a photograph illustrating gel electrophoresis analysis of intermediates and the product of cyclic conjugate synthesis for a Leu-Lys-type peptide.

Figure 4 illustrates reverse-phase HPLC purification of the compounds of the present invention. Figure 4(A) is a graph of a purification of the peptide-oligonucleotide conjugate, TTTATT- Cys-(rfe/tαOm)ιo-Cys-S-S-tBu. Figure 4(B) is a graph of a purification of the oligonucleotide-peptide-oligonucleotide conj ugate ,

TTTATT-Cys-(ώ./tαOrn) i o-Cys-CATTTC .

Figure 5 illustrates gel electrophoresis analysis of intermediates and the product of bridged conjugate synthesis for a deltaOm peptide.

Figure 6 illustrates gel electrophoresis analysis of intermediates and the product of cyclic conjugate synthesis for a deltaOm peptide.

DETAD ED DESCRIPTION OF THE INVENTION

The present invention pertains to cyclic polycationic polymer- oligonucleotide conjugates comprising a polycationic polymer covalently bonded at each end to the 3'- and 5'- terminal nucleotides of a polyanionic oligonucleotide via one or more cross-linking agents. The cations in the polycationic polymer, such as cationic side chains in a polycationic peptide, are attached to the backbone of the polymer in a specific and repetitive manner mimicking the pattern of attachment of the anions (phosphate groups) in the nucleic acids of the polyanionic oligonucleotide. Each positively charged group in the polycationic polymer is positioned to be close to a negatively charged phosphate group in the oligonucleotide to neutralize the negative charges in the oligonucleotide through electrostatic interactions. The peptide can also interact with nucleic acid targets through electrostatic interactions or hydrogen bonds thereby increasing binding affinity. Different functional groups may also be introduced into the peptide to give additional properties to these compounds.

Unlike single linkage peptide-oligonucleotide conjugates, the conformations of the polycationic peptides are more restricted in cyclic conjugates enabling the peptide to interact with the target. This restriction in conformation of the polycationic polymer is inherent in the design of the present invention. This restriction occurs because the polycationic polymer is covalently linked at both ends to the termini of the oligonucleotide which forms a relatively rigid structure when hybridized to the target single-stranded RNA or double-stranded DNA and because the spacing between the positively charged groups on the polycationic polymer is similar to the spacing between the negatively charged groups (phosphates) on the oligonucleotide. The ability to synthesize the cyclic conjugates from two 6-mer oligonucleotides bridged by a polycationic peptide suggests that the peptide helps the hybridization through interaction with a target oligonucleotide, since hybridization to the target is required in the ligation reaction.

The cyclic conjugates of the present invention are a new class of oligonucleotides having unique properties. For example, the cyclic conjugates have an enhanced strength of hybridization of the oligonucleotides to the target nucleic acid because the ionic repulsion inherent between the two or three polyanionic oligonucleotide strands is reduced. Furthermore, the polycationic bridge may catalyze degradation of the target RNA strand, see Perello, M., Barbier, B., and

Brack, A., "Hydrolysis of Oligoribonucleotides by alpha-helical Basic Peptides", Int. J. Peptide Protein Res. 38 (1991), pp. 154-160. The cyclic conjugates also have enhanced stability in vivo because degradation is minimized when the 3'- and 5'-termini of the oligonucleotides, individually or simultaneously, are blocked by linkage to the polycationic polymer. The ability of the cyclic conjugates to enter cells is also enhanced because uncharged oligonucleotides can more readily penetrate through cellular membranes. Chemotherapeutic agents such as intercalators, cell targeting agents, transmembrane delivery agents, and nucleases may also be coupled to the polycationic polymer to further enhance the activity of the cyclic conjugates.

As set out above, the cyclic polycationic polymer-oligonucleotide conjugates of the present invention comprise a polycationic polymer covalently bonded at each end to the 3'- and 5'- terminal nucleotides of a polyanionic oligonucleotide via a cross-linking agent. The polycationic polymers may be represented by the formulae:

R₂- [XR₁CHCO] _a-R₃ (I) NH₂ or the formula:

R₂ - [ XR₆COXCHCO ] _a-R₃ (II) R₇ R4 -R5 or the formula:

R₂- [XCHCOXR₆CO ] _a-R₃ (HI) R5-R4 R₇ or the formula:

R₂- [ [NH (CH₂ ) _b] _c [NH (CH₂ ) _d ] _e] f [NH ( CH₂ ) _g] _h-NHR₂ ( IV) or the formula:

R₂-[XCHCO]i-R₃ (V) R4-R5 or the formula:

_R2-CX_R6COXC„COX_R6CO,_a-_R3 (VI) R₇ R4R5 R₇ or the formula:

(VII)

R5R4 R₇ R5R4 or the formula:

_R2-_tXC„COXC„COX_R6COX_R6C_01a-_R3 R5R4 R5R4 R₇ R₇

In Formulas I-VIII, group C is carbon. In DNA sequences, C is cytosine.

The polyanionic oligonucleotides in the present invention may be any natural or synthetic oligonucleotide known in the art. The polyanionic oligonucleotides may be oligodeoxyribonucleic acids (normal DNA), oligoribonucleic acids (normal RNA), backbone-modified oligonucleotides such as methylated RNA and phosphorothioate oligodeoxyribonucleic acids (-OP(S)(O)O-), and combinations of normal and backbone-modified oligonucleotides. The oligonucleotide sequence may be a sense strand or an antisense strand (complementary to either a DNA or RNA sequence, i.e. , the sense strand, of the gene to be inhibited). Preferably, the oligonucleotide sequence is an antisense strand. Antisense carriers and backbone- odified oligonucleotides are more fully described in Stein et al. , New Jersey Medicine, 87, pp. 1011-1015 (1990), Stein et ah, Journal of Liquid Chromatography, 11, pp. 2005-2017 (1988), and Miller, Bio /Technolog , 9, pp. 358-362 (1991), which disclosures are incorporated herein by reference. While the polyanionic oligonucleotides of the present invention are not limited to any specific number of nucleotide monomers, the polyanionic oligonucleotide preferably comprises from about 6 to about 20 nucleotides, more preferably from about 8 to about 16 nucleotides, and most preferably from about 10 to about 14 nucleotides.

The polycationic polymers in the present invention may be natural or synthetic polypeptides, pseudopeptides, or polyamines. The cations in the polycationic polymer are attached to the backbone of the polymer in a specific and repetitive manner mimicking the pattern of attachment of the anions in the oligonucleotide. Preferably, the cation is selected from the group consisting of primary amines, secondary amines, tertiary amines, quaternary ammonium salts, imidazoles, and guanidine groups.

Pseudopeptides contain backbone modifications such as amide bond surrogates. The term "surrogate" as used herein refers to an amide bond modification which involves replacement of a naturally occurring amide bond by an unnatural bond. Nonlimiting examples of amide bond modifications include ketones (-COCH2-), thioesters (-COS-), substituted amides (-CONR-), esters (-COO-), thioamides (-CSNH-), amines (-CH2NH-), alkyl groups (-CH2CH2-), sulfides (-CH2S-), sulfoxides (-CH2SO-), sulfones (-CH2SO2-), alkene groups (-CH=CH-), and unnatural amide groups (-NHCO-). The term "pseudopeptide" as used herein refers to a peptide analog containing an amide backbone modification. The term "pseudopeptide" also refers to a peptide analog having amide bonds employing side chain amines instead of a/pΛα-amines. Peptide backbone modifications are generally employed to confer stability to a peptide against enzymatic or proteolytic degradation such as to prepare an orally active peptide or a peptide having sustained activity. Amino acids containing amide bond modifications are termed pseudoamino acids. Peptide backbone modifications are well known in the art and are discussed in detail in "Chemistry and Biochemistry of

Amino Acids, Peptides, and Proteins", Volume 7, B. Weinstein, Ed., Ch. 5, Marcel Dekker, New York, New York (1983), which disclosure is incorporated herein by reference. In a first embodiment, the polycationic polymers are represented by the formula:

R₂-[XR₁CHCO]_a-R₃ (I)

NH₂

In Formula (I), the polycationic polymer is a pseudopeptide containing the monomer -XRjCH(NH2)CO-. Group X is a heteroatom selected from the group consisting of -NH-, -O-, and -S-. The terminal heteroatom group X on the side chain of the monomer forms amide, ester, or thioester bonds for peptide or polymer formation instead of the alpha-amine group. The alpha-a ine group in the monomer is used as the repeating cationic group to form ion pairs with the anionic groups in the oligonucleotide. Preferably, group X is -NH-.

Group Rj is a lower-alkyl spacer group which may be varied to provide the desired number of carbon atoms in the skeleton of the repeating monomer. Group R\ is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 4 carbon atoms in the chain. Preferably, group Ri contains from 2 to 3 carbon atoms in the chain.

Groups R2 and R3 are terminal end capping groups covalently bonded to the terminal nitrogen, oxygen, or sulfur group in the polycationic polymer of Formula (I) and are cross-linking agents covalently linking the polycationic polymer to the oligonucleotide. Group R2 will generally contain a carbonyl group for coupling R2 to group X via an amide, ester, or thioester bond.

For example, R2 may be an acyl group having from 1 to about 15 carbon atoms, preferably from 1 to about 10 carbon atoms, and more preferably from 1 to about 6 carbon atoms. Group R3 will generally contain an amine, hydroxyl, or sulfhydryl group for coupling R3 to the carbonyl group of the polycationic polymer of

Formula (I) via an amide, ester, or thioester bond and a hydroxyl or sulfhydryl group to form an ester or thioester bond with the phosphate group on the oligonucleotide.

The cross-linking agents which may be employed in the present invention are those agents which will covalently link the polycationic polymer to the oligonucleotide without interfering with the ion-pairing of the polycationic polymer and the oligonucleotide. Groups R2 and R3 may be a single cross-linking agent such as glycine or cysteine, and preferably is cysteine. Groups R2 and R3 may also be a combination of compounds to form a cross- linking agent such as aminolink agents, succinate cross-linking agents, cysteine. and maleimide. Nonlimiting examples of aminolink agents include 1 ,6-hexanolamine, and 2,3-dihydroxy-l- aminopropane. Aminolink agents contain a hydroxyl group at one end of a chain to form an ester bond with the phosphate group on the oligonucleotide and an amine group at the other end of the chain to form an amide bond with a carbonyl group. Nonlimiting examples of succinate cross-linking agents include those agents derived from ethylene glycotø(sulfo succinimidylsuccinate) (Sulfo-EGS), and maleimidobenzoyl-sulfosuccinimide ester (sulfo-MBS). Cysteine may also be coupled to the succinate cross-linking agent and then further coupled to the polycationic polymer via the terminal amine or carbonyl group. In one embodiment, the combination of cross-linking agents is an aminolink agent coupled to the oligonucleotide and further coupled to a succinate cross-linking agent, the succinate cross-linking agent is in turn coupled to a cysteine, which is in turn coupled by its carbonyl group to group X in the polycationic polymer of

Formula (I).

In a second embodiment, the polycationic polymers are represented by the formula:

R₂- [XR₆COXCHCO] _a-R₃ (II)

R₇ R4-R5

In Formula (II), the polycationic polymer is a polypeptide or pseudopeptide containing the monomer -XR6(R7)COXCH(R4-R5)CO- which comprises two different types of amino acids or pseudo amino acids. Groups X, R2, and R3 are defined as set out above. A first amino acid or pseudoamino acid (- XCH(R4~R5)CO-) contains a side chain (-R4-) having a cationic group (-R5), such as an amine group, imidazole group, or a guanidine group, which is used as the repeating cationic group to form ion pairs with the oligonucleotide. The άlpha- amine group or group X in this first amino acid forms the amide, ester, or thioester bonds for peptide or polymer formation. A second amino acid or pseudoamino acid (-XR-g(R7)CO-) is coupled to the first amino acid and is used as a spacer group to provide the desired skeleton size of the repeating monomer unit. R7 may be a functionalized side chain for attaching additional groups to the polycationic polymer such as cross-linking agents and chemotherapeutic agents. Group R4 is a lower-alkyl side chain group to which cationic group R5 is coupled. The length of the side chain may be varied to provide the desired number of carbon atoms in the chain. Group R4 is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 5 carbon atoms in the chain. Preferably, group R4 contains from 2 to 4 carbon atoms in the chain.

Group R5 is a cationic group attached to lower-alkyl side chain group R4. The type of cationic group employed in R5 may be varied to optimize the ion-pairing properties with the particular oligonucleotide. Group R5 is selected from the group consisting of primary amines, secondary amines, tertiary amines, quaternary ammonium salts, imidazoles, and guanidine groups (-NHC(=NH)NH2)- Preferably, group R5 is selected from the group consisting of primary amines, secondary amines, and guanidine groups (-NHC(=NH)NH2). More preferably, group R5 is a guanidine group (-NHC(=NH)NH2).

Group R6 is a lower-alkyl spacer group which may be varied to provide the desired number of carbon atoms in the skeleton of the repeating monomer. Group Rg is an alkyl chain having from 1 to 2 carbon atoms in the chain. Preferably, group Rg contains 1 carbon atom in the chain.

Group R7 may be hydrogen; a side chain such as those found in alanine, leucine, isoleucine, valine, or phenylalanine; or a functionalized side chain. When group R→β contains two carbon atoms, group R7 may be attached to either carbon atom. Group R7 is selected from the group consisting of hydrogen, branched and unbranched lower-alkyl groups having from 1 to 5 carbon atoms, -CH2C6H5, and -(CH2)_zCOR3. Preferably, the branched and unbranched lower- alkyl groups have from 1 to 4 carbon atoms, more preferably from 1 to 3 carbon atoms. The integer z may range from 0 to 3, preferably from 0 to 2. Group R3 is as defined above. When R7 contains a functionalized side chain such as an acyl group (-(CH2)_zCOR3), additional groups (R3 groups) may be attached to the polycationic polymer such as cross-linking agents and chemotherapeutic agents. Preferably, group R7 is selected from the group consisting of hydrogen and branched and unbranched lower-alkyl groups having from 1 to 5 carbon atoms. More preferably, group R7 is selected from the group consisting of hydrogen and branched and unbranched lower-alkyl groups having from 1 to 3 carbon atoms. Most preferably, group R7 is hydrogen. In a third embodiment, the polycationic polymers are represented by the formula:

In Formula (III), the polycationic polymer is a variation of the polycationic polymer set out above in Formula (II). The polycationic polymer in Formula (HI) is a polypeptide or pseudopeptide containing the monomer -XCH Rj- R5)COXR₍5(R7)CO-, wherein the C-terminal and N-terminal positions of the two different types of amino acids or pseudo amino acids set out above in Formula (II) are reversed. Groups X and R2 through R7 are defined as set out above.

In a fourth embodiment, the polycationic polymers are represented by the formula:

R₂-[[NH(CH₂)_b]_c[NH(CH₂)_d]e]_f[NH(CH₂)_g]_h-NHR₂ (IV)

In Formula (IV), the polycationic polymer is a polyamine containing the monomer -NH(CH2)b- or the monomer -NH(CH2)d", or both. The monomer

-NH(CH2)g- permits the polycationic polymers of Formula (IV) to contain an odd number of monomers. Each group R2 may be the same or different and is defined as set out above. The secondary amine groups in the polyamines are an integral part of the skeleton of the polycationic polymer and are used as the repeating cationic group to form ion pairs with the oligonucleotide. In general, these polyamines are derived by hydride reduction of the amide bonds in the corresponding polypeptides to give polyamines of the spermidine and spermine type. For example, the peptide beto-alanine-^α α-aminobutyric acid-beta- alanine-carboxy amide yields spermine upon reduction. Different sequences of these amino acids or other combinations of amino acids, including cysteine, may be used to generate any desired polyamine. Alternatively, commercially available polyamines may be suitably derivatized with the R2 groups. In a fifth embodiment, the polycationic polymers are represented by the formula:

R₂- [XCHCO] -R₃ (V)

R4-R5

In Formula (V), the polycationic polymer is a peptide containing the monomer -XCH(R4-R5)CO-. Groups X and R2 through R5 are defined as set out above. In this embodiment, the monomer -XCH(R4-R5)CO- is preferably arginine and R2 and R3 are cysteine.

In a sixth embodiment, the polycationic polymers are represented by the formula:

^R2-^[ R₇ ^cox Rr4R5r R₇ ^oia-^R3

In Formula (VI), the polycationic polymer is a polypeptide or pseudopeptide containing the monomer -XR6(R7)COXCH(R4R5)COXR6(R7)CO- which comprises three amino acids or pseudo amino acids of two different types.

Groups X and R2 through R7 are defined as set out above. A first amino acid or pseudoamino acid (-XCH(R4-R5)CO-) contains a side chain (-R4-) having a cationic group (-R5), such as an amine group, imidazole group, or a guanidine group, which is used as the repeating cationic group to form ion pairs with the oligonucleotide. The alpha-amine group or group X in this first amino acid forms the amide, ester, or thioester bonds for peptide or polymer formation. A second amino acid or pseudoamino acid (-XR6(R7)CO-) is coupled to the first amino acid and is used as a spacer group to provide the desired skeleton size of the repeating monomer unit. R7 may be a functionalized side chain for attaching additional groups to the polycationic polymer such as cross-linking agents and chemotherapeutic agents. In a seventh embodiment, the polycationic polymers are represented by the formula:

R₂- [XCHCOXR₆COXCHCO] _a-R₃ (VII)

R5R4 R₇ R₅R4

In Formula (VII), the polycationic polymer is a variation of the polycationic polymer set out above in Formula (VI). The polycationic polymer in Formula (VII) is a polypeptide or pseudopeptide containing the monomer - XCH(R5R4)COXR6(R7)COXCH(R5R4)CO-, wherein the C-terminal and N- terminal positions of the amino acids or pseudo amino acids set out above in Formula (VI) are reversed. Groups X and R2 through R7 are defined as set out above.

In an eighth embodiment, the polycationic polymers are represented by the formula:

(VI11)

In Formula (VIII), the polycationic polymer is a polypeptide or pseudopeptide containing the monomer

-XCH(R5R4)COXCH(R5-R4)COXR6(R7)COXR6(R7)CO- which comprises four amino acids or pseudo amino acids of two different types. Groups X and R2 through R7 are defined as set out above. A first amino acid or pseudoamino acid (- XCH(R4-R5)CO-) and a second amino acid or pseudoamino acid (-XR (R )CO-) are as described above for the polycationic polymers represented by formulae II, III, VI, and VII.

The integer a may range from about 3 to about 16, preferably from about 3 to about 10, and more preferably from about 4 to about 8. The integer b may range from about 2 to about 5, preferably from about 2 to about 4, and more preferably from about 3 to about 4. The integer c may range from about 0 to about 3, preferably from about 1 to about 3, and more preferably from about 2 to about

3. The integer d may range from about 2 to about 5, preferably from about 2 to about 4, and more preferably from about 3 to about 4. The integer e may range from about 0 to about 3, preferably from about 1 to about 3, and more preferably from about 2 to about 3. The integer f may range from about 2 to about 9, preferably from about 2 to about 5, and more preferably from about 2 to about 3. The integer g may range from about 2 to about 5, preferably from about 2 to about 4, and more preferably from about 3 to about 4. The integer h may range from about 0 to about 3, preferably from about 1 to about 3, and more preferably from about 2 to about 3. The integer i may range from about 3 to about 12, preferably from about 3 to about 7, more preferably from about 5 to about 7, and most preferably 7.

In general, the ratio of cations in the polycationic polymer to anions in the polyanionic oligonucleotide pair will range from about 0.7:1 to about 1.5:1, preferably from about 0.8: 1 to about 1.3: 1 , and more preferably from about 0.9:1 to about 1.2: 1, respectively. Cyclic conjugates containing an excess of cations may have useful properties such as enhanced uptake of the cyclic conjugate into cells or into the nucleus of cells or may have ribonuclease-like activity, Perello, M.,

Barbier, B., and Brack, A., "Hydrolysis of Oligoribonucleotides by alpha-helical Basic Peptides", Int. J. Peptide Protein Res. 38 (1991), pp. 154-160.

The term "branched lower-alkyl chain" means a lower-alkyl chain or skeleton to which is attached branching lower-alkyl groups having from about 1 to about 4 carbon atoms, preferably from about 1 to about 3 carbon atoms. The substituent groups attached to the lower-alkyl chain or branching lower-alkyl groups may be selected from the group consisting of hydroxyl, sulfhydryl, halogen, and lower-alkoxy groups having from 1 to 4 carbon atoms. The term halogen, as used herein, refers to the chemically related elements consisting of fluorine, chlorine, bromine, and iodine.

The cyclic conjugates of the present invention have high specificity because the sequence of each particular antisense oligonucleotide can be selected to be complementary to a specific target according to Watson-Crick or Hoogsteen base pairing. The cyclic conjugates also have high affinity hybridization because the ion-pairing properties of the polycationic polymer chain lowers the ionic repulsion between the two polyanionic oligonucleotides, as demonstrated by analogy with methylphosphonate oligonucleotides, R. S. Quartin and J. G. Wetmur, "Effect of Ionic Strength on the Hybridization of Oligodeoxynucleotides With Reduced Charge Due to Methylphosphonate Linkages to Unmodified Oligodeoxynucleotides Containing the Complementary Sequence", Biochemistry 2£ (1989) pp. 1040-1047, and as shown by R. Eritja, A. Pons, M. Escareller, E. Giralt, and F. Albericio, "Synthesis of Defined Peptide-Oligonucleotide Hybrids Containing a Nuclear Transport Signal Sequence", Tetrahedron 47 (1991), pp. 4113-4120. Because hybridization strength (i.e. , T_m or melting temperature) is dependent upon the length and sequence of an oligonucleotide, shorter antisense chains of the strong affinity cyclic conjugates of the present invention may be sufficient for hybridizing a particular oligonucleotide with a target nucleic acid.

The cyclic conjugates also have enhanced stability in vivo because exonuclease digestion is minimized when both the 3'- and 5' -termini are blocked such as by linking the polycationic polymers of the present invention to the oligonucleotide. Similarly, polypeptide degradation is minimized when both the amino-terminus and carboxy-terminus are blocked by linkage to the oligonucleotide, thereby limiting exopeptidase digestion. Endopeptidase digestion is also minimized when pseudopeptide bonds are employed in the polypeptide.

The cyclic conjugates have enhanced bioavailability because the ability of the oligonucleotides to penetrate through cellular membranes is enhanced when the negative charges on the antisense DNA are ion-paired, by analogy to methylphosphonate and other non-ionic antisense oligonucleotides, P. S. Miller, K. B. McParland, K. Jayaraman, and P. O. P. Ts'o, "Biochemical and Biological Effects of Nonionic Nucleic Acid Methylphosphonates", Biochemistry 20 (1981), pp. 1874-1880. Additional hydrophobic groups such as valine, phenylalanine, iήtercalators, and other groups may be coupled to, or incorporated in, the polycation polymer to enhance permeability.

Alternatively, an excess of cations in the oligonucleotide-conjugate can be used to enhance permeability. Enhanced oligonucleotide uptake occurs through binding of the positively charged paired-ion oligonucleotide to the negatively charged outer membrane of the cell followed by endocytosis, P. L. Schell, "Uptake of Polynucleotides by Mammalian Cells XIV: Stimulation of the Uptake of Polynucleotides by Poly(L-lysine)", Biochim. Biophys. Acta 340, (1974) pp. 323-333). A combination of hydrophobic and positively charged groups may be synergistic with regard to the ability of the antisense substance to reach the necessary compartments in vivo, such as the nuclei of cells, R. Eritja, A. Pons, M. Escareller, E. Giralt, and F. Albericio, "Synthesis of Defined Peptide- Oligonucleotide Hybrids Containing a Nuclear Transport Signal Sequence",

Tetrahedron 47 (1991), pp. 4113-4120.

The cyclic conjugates have low toxicity because the metabolic degradation products of polypeptide conjugates are amino acids and nucleotides. Concern has been expressed about the toxicity of phosphorothioate and other backbone-modified DNA-analogs, S. Agrawal, J. Goodchild, M. P. Civeira, A. H. Thornton, P. S. Sarin, and P. C. Zamecnik, "Oligodeoxynucleoside Phosphoramidates and Phosphorothioates as Inhibitors of Human Immunodeficiency Virus", Proc. Natl. Acad. Sci. USA 85, (1988) pp. 7079-7083; Y. Cheng, W. Gao, and F. Han, "Phosphorothioate Oligonucleotides as Potential Antiviral Compounds Against Human Immunodeficiency Virus and Herpes Viruses", Nucleosides & Nucleotides JO (1991), pp. 155-166. Increasing the potency of the antisense oligonucleotide should result in a better therapeutic index.

The cost per dose of the cyclic conjugates should be reasonable especially for a high potency product because, in the preferred size range of 5-25 nucleotide monomers, oligodeoxyribonucleotides and polypeptides are routinely synthesized on automated instruments.

The present invention extends to methods for preparing the cyclic conjugates. The cyclic conjugates may be synthesized using standard techniques and apparatus known to those skilled in the art. The ultimate cyclic conjugates are readily prepared using methods generally known in the chemical and biochemical arts.

In general, the polycationic peptides can be synthesized by standard peptide chemistry coupling reactions such as by N-Fmoc [N-(9-fluorenyl- methoxycarbonyl] chemistry on a peptide synthesizer. In one embodiment, the amino acids may be coupled to a PAL™ support by BOP [benzotriazolyl-N- oxytris(dimethylamino) phosphonium hexafluorophosphate] and HOBt (1- hydroxybenzotriazole). The side chain protecting groups may be removed by TFA (trifluoroacetic acid) at the time when the peptide is cleaved from the solid support. The peptide product may be purified by reverse-phase HPLC and the identity of the product may be confirmed by amino acid analysis, peptide sequencing, and mass spectrometry.

A pair of sense or antisense oligonucleotides having a primary amine group coupled through its 5'- or 3'-terminus, or through an internal position, may be synthesized on an automated DNA synthesizer using commercially available reagents. After HPLC purification and removal of the protecting groups, each oligonucleotide may then be coupled, in a stepwise manner, to opposite ends of the polycationic polymer via a cross-linking agent such as a succinimide-mediated chemical reaction. The oligonucleotide-peptide-oligonucleotide bridged conjugate may then be cyclized in a ligation reaction using kinase and ligase enzymes in the presence of a complementary single-stranded DNA. The intermediate and final products may be purified by chromatographic and electrophoretic methods.

In a specific embodiment, the invention is directed at a method for preparing cyclic polycationic polymer-oligonucleotide conjugates comprising a polycationic polymer covalently bonded at each end to the 3'- and 5¹- terminal nucleotides of a polyanionic oligonucleotide via a cross-linking agent, wherein the polycationic polymer may be represented by the formulae:

R₂-[XR₁CHCO]_a--R₃ (I) NH₂ or the formula:

(ID

or the formula:

R₂-[XCHCOXRgCO]_a-R₃ (III)

I I

R5-R4 R₇ or the formula:

R₂-[[NH(CH₂)_b]_c[NH(CH₂)_d]_e]_f[NH(CH₂)g]_h-NHR₂ (IV) or the formula:

R₂-[XCHCO]i-R₃ (V) R4-R5 or the formula:

_R2-_[XR6COXC„COX_R6CO_]a-_R3 (VI) R₇ R4R5 R₇ or the formula:

(VII)

or the formula:

R₂-[XCHCOXCHCOXR₆COXR₆CO]_a-R₃ (VIII)

R5R4 R5R4 R₇ R₇ wherein X is selected from the group consisting of -NH-, -O-, and -S-; R\ is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 4 carbon atoms in the chain; R2 and R3 are cross-linking agents covalently linking the polycationic polymer to the oligonucleotide; R4 is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 5 carbon atoms in the chain; R5 is selected from the group consisting of primary amines, secondary amines, tertiary amines, quaternary ammonium salts, imidazoles, and guanidine groups; R$ is an alkyl chain having from 1 to 2 carbon atoms; R7 is selected from the group consisting of hydrogen, branched and unbranched lower- alkyl groups having from 1 to 5 carbon atoms, -CH2C6H5, and -(CH2)_zCOR3, wherein z is an integer ranging from 0 to 3 and R3 is as defined above; a is an integer ranging from about 3 to about 16; b is an integer ranging from about 2 to about 5; c is an integer ranging from about 0 to about 3; d is an integer ranging from about 2 to about 5; e is an integer ranging from about 0 to about 3; f is an integer ranging from about 2 to about 9; g is an integer ranging from about 2 to about 5; h is an integer ranging from about 0 to about 3; i is an integer ranging from about 3 to about 12; and the ratio of cations in the polycationic polymer to anions in the polyanionic oligonucleotide pair ranges from about 0.7:1 to about

1.5: 1, respectively; which comprises the steps of:

(1) providing the polyanionic oligonucleotides;

(2) providing the polycationic polymer; (3) coupling the polyanionic oligonucleotides to the polycationic polymer via the cross linking agents; and

(4) ligating the pair of oligonucleotides coupled to the ends of the polycationic polymer.

The cyclic conjugates may be prepared using sandard techniques and equipment known to those skilled in the art. The apparatus useful in accordance with the present invention comprises apparatus well known in the chemical and biochemical arts, and therefore the selection of the specific apparatus will be apparent to the artisan.

The cyclic conjugates of the present invention may be used together with pharmaceutically acceptable carriers to provide pharmaceutical compositions which can be administered to mammals such as man in amounts effective to provide a variety of therapeutic activity. Suitable carriers include propylene glycol-alcohol-water, isotonic water, sterile water for injection (USP), emulphor™-alcohol- water, cremophor-EL™ or other suitable carriers known to those skilled in the art. Other suitable carriers include isotonic water, sterile water for injection (USP), alone or in combination with other solubilizing agents such as ethanol, propylene glycol, or other conventional solubilizing agents known to those skilled in the art.

Of course, the type of carrier will vary depending upon the mode of administration desired for the pharmaceutical composition as is conventional in the art. A preferred carrier is an isotonic aqueous solution of the inventive compound.

The compounds of the present invention can be administered to mammals, e.g., animals or humans, in amounts effective to provide the desired therapeutic effect. Since the activity of the compounds and the degree of the desired therapeutic effect vary, the dosage level of the compound employed will also vary. The actual dosage administered will also be determined by such generally recognized factors as the body weight of the patient and the individual hypersensitiveness of the particular patient. Thus, the unit dosage for a particular patient (human) can be as low as about 0.001 mg/kg, or about 0.1 mg in a 100 kg person, which the practitioner may titrate to the desired effect.

The compounds of the present invention can be administered parenterally, in the form of sterile solutions or suspensions, such as intravenously, intramuscularly or subcutaneously in the carriers previously described.

For parental therapeutic administration, the compounds of the present invention may be incorporated into a sterile solution or suspension. These preparations should contain at least about 0.1% of the inventive compound, by weight, but this amount may be varied to between about 0.1 % and about 50% of the inventive compound, by weight of the parental composition. The exact amount of the inventive compound present in such compositions is such that a suitable dosage level will be obtained. Preferred compositions and preparations according to the present invention are prepared so that a paranteral dosage unit contains from between about 0.1 milligrams to about 100 milligrams of the inventive compound.

The sterile solutions or suspensions may also include the following adjuvants: a sterile diluent, such as water for injection, saline solution, fixed oils, polyethylene glycol, glycerine, propylene glycol, or other synthetic solvent; antibacterial agents, such as benzyl alcohol or methyl paraben; antioxidants, such as ascorbic acid or sodium metabisulfite; chelating agents, such as ethylenediaminetetraacetic acid (EDTA); buffers, such as acetates, citrates or phosphates; and agents for the adjustment of tonicity, such as sodium chloride or dextrose. The parental preparatio s may be enclosed in ampules, disposable syringes, or multiple dose vials made of glass or plastic.

It is especially advantageous to formulate the pharmaceutical compositions in dosage unit forms for ease of administration and uniformity of dosage. The term dosage unit forms as used herein refers to physically discrete units suitable for use as a unitary dosage, each unit containing a predetermined quantity of active ingredient calculated to produce the desired therapeutic effect in association with the pharmaceutical carrier.

The present invention is further illustrated by the following examples which are not intended to limit the effective scope of the claims. All parts and percentages in the examples and throughout the specification and claims are by weight of the final composition unless otherwise specified.

Examples

Materials and Methods

T4 DNA ligase (EC 6.5.1.1.) in the storage buffer (Tris-HCl,

20 mmol/1; KC1, 60 mmol/1; bovine serum albumin, 500 mg/ml; pH 7.6. Ligation buffer for T4 DNA ligase, 10-times concentrated: Tris-HCl, 660 mmol/1; MgCl2, 50 mmol/1; dithioerythritol, 10 mmol/1; ATP, 10 mmol/1; pH 7.5.

Polynucleotide kinase from E. coli (EC 2.7.1.78) in the storage buffer (TrisHCl, 50 mmol/1; dithioerythritol, 1 mmol/1; EDTA, 0.1 mmol/1; ATP, μmol/1; glycerol 50% (v/v); pH ca. 7.5. phosphorylation buffer for direct phosphorylation, 10-times concentrated: Tris-HCl, 500 mmol/1; MgCl2, 100 mmol/1; EDTA, 1 mmol/1; dithioerythritol, 50 mmol/1; spermidine, 1 mmol/1; pH 8.2 (at 25°C) Alkaline phosphatase (EC. 3.1.3.1.) in the storage buffer (Triethanolamine, 30 mmol/1; NaCl, 3 mol/1; MgCl2, 1 mmol/1; ZnCl2, 0.1 mmol/1; pH ca. 7.6. Dephosphorylation buffer, 10-times concentrated: Tris-HCl, 500 mmol/1; EDTA, 1 mmol/1; pH 8.5 (20°C).

Preparation of 6-mers

Oligonucleotides were synthesized by phosphoramidite methods using the Model 380B DNA synthesizer (Applied Biosystems, Foster city, CA). The 6-mer with 5' aminolinker (H2N-CATTTC) was coupled to the 5' end of the oligonucleotide on the instrument. The other 6-mer was with 3' aminolinker (TTTATT-NH2). After synthesis, each oligonucleotide-resin was dried under vacuum overnight. The oligonucleotide with 5' aminolinker was cleaved from the solid support using 5ml of concentrated ammonium hydroxide at 55 °C for 24 hours, and the oligonucleotide with 3' aminolinker was cleaved from the solid support using 5ml of concentrated ammonium hydroxide at 55 °C for 8 hours. The supernatant was dried under vacuum. Each oligonucleotide was purified by HPLC. Purification was on a Nucleogen 60-7 DEAE column (4 xl25mm) using a gradient of 100% A for 5 minutes, then 0.5%/minute of B. Mobile phase A was 60% 20 mM sodium acetate, pH 6.5 and 40% acetonitrile. Mobile phase B was mobile phase A containing 0.7M lithium chloride. The flow rate was 1 ml/min. Desalting was on a Hamilton PRP-1 (4.1 x 150 mm) column using a gradient of increasing acetonitrile in 0.1 M triethylammonium acetate buffer, pH 9.7.

Preparation of TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-S-S-fBu Conjugate

(Scheme I)

6-mer Oligonucleotide with 3' aminolinker (3.6 units, A260) and 2.5 mg N-iodoacetoxysuccinimide in 50 μ\ of DMSO were mixed in 100 μl of 0.1 M sodium bicarbonate for 2 hours. The TTTATT-iodoacetyl oligonucleotide was purified by anion-exchange chromatography on a Nucleogen 60-7 DEAE column (4 xl25mm). Mobile phase A was 60% 20 mM sodium acetate, pH 6.5 and 40% acetonitrile. Mobile phase B was mobile phase A containing 0.7M lithium chloride. The gradient was 100% A for 5 minutes, then 0.5%/minute of B. The flow rate was 1 ml/min. The eluent corresponding to the peak at 37.66 minutes

(Figure 1A) was collected which was TTTATT-iodoacetyl oligonucleotide. About 2 mg of Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-S-S-tBu dissolved in water was added into TTTATT-iodoacetyl oligonucleotide solution from the anion-exchange chromatography. The mixture was reacted for 12 hours at room temperature and then put into speed vacuum to remove acetonitrile and product 6-mer TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-S-S-tBu was isolated by same anion-exchange chromatography on the same column and gradient (Figure IB). Desalting by reverse phase chromatography on an PRP-1 (4.1 x 150 mm) column, the TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-S-S-tBu peak was 52.36 minutes (Figure 1C). Mobile phase A was 95% TEAA buffer pH 9.7 and 5% acetonitrile. Mobile phase B was 5% TEAA buffer pH 9.7 and 95% acetonitrile . The gradient was 100% A for 5 minutes, then 0.5%/minute of B. The flow rate was 1 ml/min.

Scheme I Preparation of Bridged Oligonucleotide-Peptide Conjugate

3' N-Iodoacetoxy- 3'

TTTATT\/\/\/\NH2 ► TTTATT\/\/\/\NHCOCH2l succinimide

t-Bu-S-S-Cys-(Lys-Leu)2-Lys-(Lys-Leu)2-Cys-SH

3^*

TTTATT\/\/\ΛNHCOCH2l

3' TTTATT\/\/\/\NHCOCH2S t-Bu-S-S-Cys-Lys-Leu-Lys-Leu-Lys-Lys-Leu-Lys-Leu-Cys

Tributylphosphine

3' TTTATT\A/\/\NHCOCH₂S

H-S-Cys-Lys-Leu-Lys-Leu-Lys-Lys-Leu-Lys-Leu-Cys

ICH2CONH\/\/\/\CATTTC

3' CH₂CONH\/\/\/\CATTTC TTTATT\/\/\/\NHCOCH2

S-Cys-Lys-Leu-Lys-Leu-Lys-Lys-Leu-Lys-Leu-Cys-S Preparation of TTTATT-Cys(Leu-Lys)2-Lys(-Leu-Lys)2Cys-CATTTC

Conjugate (Scheme I)

6-mer Oligonucleotide with 3' aminolinker (2.0 units, A260) and 2.0 mg N-Iodoacetoxysuccinimide in 50 μl of DMSO were mixed in 100 μl of 0.1M sodium bicarbonate for 2 hours. lodoacetyl-CATTTC oligonucleotide was purified using the same method as for the TTTATT-iodoacetyl oligonucleotide. The retention time on anion-exchange for iodoacetyl-CATTTC oligonucleotide was 36.7 minutes. The single linkage conjugate TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-S-S-tBu (1.4 O.D.) collected directly from ion exchange buffer was put in speed vacuum to reduce the volume to 0.5 ml and pH of the solution was adjusted to 8.0 by IM NaHCO3. Then 15 μl of tributylphosphine in 0.5 ml dichloromethane was added into TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-S-S-tBu. The reaction was carried out under nitrogen for 4 hours to remove the t-butylthiol protecting group. Then iodoacetyl-CATTTC oligonucleotide was added and the pH of the final solution was adjusted again to 8.0. The reaction was carried out under nitrogen overnight at room temperature. TTTATT-Cys(--^u-Lys)2Lys(Leu-Lys)2Cys-CATTTC conjugate was isolated by reverse phase chromatography on a PRP-1 (4.1x150 mm) column. The condition was the same as for isolation of the single linkage conjugate. The retention time for the bridged conjugate was 37.57 minutes (Figure ID).

Pol acrylamide Gel Electrophoresis (PAGE)

All the conjugates were analyzed on a native 20% polyacrylamide gel. The running buffer was TrisBorate-EDTA, pH 8.3. The samples were suspended in 20 μl of loading buffer (99%) formamide), heated to 90 °C for 2 minutes, chilled on ice and loaded on the gel. The pictures were taken by Polaroid 667 film under UV shadowing (Figure 2).

Preparation of Cyclic Oligonucleotide-Peptide Conjugate

(Scheme II)

a) Transfer of a ³²P terminal phosphate group of ATP to the 5'hydroxylated terminus of bridged conjugate.

TTTATT-Cys(Leu-Lys)2Lys(Leu-Lys)2Cys-CATTTC 17 pmole (0.02 O.D.); 2 μl phosphorylation buffer, 10 x cone; 25 pmole (150 μCi) [gamma- ³²P] ATP were mixed and water added to a final volume of 19 μl followed by 50 units of polynucleotide kinase. It was mixed well and incubated for 30 minutes at 37° C. The reaction was stopped by heating to 95 °C for 10 minutes and cooling in an ice bath.

b) Formation of phosphodiester bonds between neighboring 3 '-hydroxyl- and 5'-phosphate ends of TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2CysCATTTC catalyzed by T4 DNA ligase.

5 μl (4 pmole) of above solution (bridged conjugate with 5' phosphate); 10 pmole (1 μl of a water solution 0.04 O.D./ml) of template (5ΑATAAAGAAATG3'); 2 μl of 10 x cone, ligation buffer and 7 μl of water were mixed and annealed in the water bath from 50 °C to 12 °C. The ligation reaction was carried out at 12°C for 2 hours by adding 5 units of T4 DNA ligase.

c) Dephosphorylation of uncyclized conjugate.

10 μl of above solution (a mixture of cyclic and uncyclic conjugate); 2 μl of 10 x cone, dephosphorylation buffer; 7 μl of water and 5 units alkaline phosphatase were incubated at 37 °C for 60 minutes.

Analysis of the reaction products was by autoradiography of a 20% polyacrylamide gel. (Figure 3).

Scheme π Cyclization of oligonucleotide-peptide by DNA T4 ligase

3^* CH₂CONH\/\/\/\CATTTC TTTATT\/\/\/\NHCOCH2

S-Cys-Lys-Leu-Lys-Leu-Lys-Lys-Leu-Lys-Leu-Cys-S

DNA T4 kinase

DNA T4 ligase 5'AATAAAGAAATG

3'

CH2CONH\/\/\/\CATTTCTTTATT\/\/\/\NHCOCH2

S-Cys-Lys-Leu-Lys-Leu-Lys-Lys-Leu-Lys-Leu-Cys-S Preparation of TTTATT-Cys(rfe/tα-Orn)κ)Cys-S-S-*Bu Corrugate

6-mer oligonucleotide with 3' aminolinker (3.6 units, A260) and 2.5 mg N-iodoacetoxysuccinimide in 50 μl of DMSO were mixed in 100 μl of 0.1 M sodium bicarbonate for 2 hours. The TTTATT-iodoacetyl oligonucleotide was purified by anion-exchange chromatography on a Nucleogen 60-7 DEAE column (4 x 125mm). Mobile phase A was 60% 20 mM sodium acetate, pH 6.5 and 40% acetonitrile. Mobile phase B was mobile phase A containing 0.7M lithium chloride. The gradient was 100% A for 5 minutes, then 0.5%/min of B. The flow rate was 1 ml/min. The eluent corresponding to the peak at 37.66 min (see Figure 1A) was collected which was TTTATT-iodoacetyl oligonucleotide. About 2 mg of Cys(de/taOrn)ioCys-S-S-tBu dissolved in water was added into TTTATT- iodoacetyl oligonucleotide solution from the anion-exchange chromatography. The mixture was reacted for 12 hours at room temperature and then put into speed vacuum to remove acetonitrile and product 6-mer

DNA-Cys(de/tfl-Orn)ιoCys-S-S-tBu was isolated by reverse phase chromatography on an PRP-1 (4.1 x 150 mm) column, the Cys(-- e/t-2-Orn)ιoCys-S-S-tBu peak was 30 minutes (Figure 4A). Mobile phase A was 95 % TEAA buffer pH 9.7 and 5% acetonitrile. Mobile phase B was 5% TEAA buffer pH 9.7 and 95% acetonitrile. The gradient was 100% A for 5 minutes, then 0.5%/min of B. The flow rate was 1 ml/min.

Preparation of TTTATT-Cys(rfeΛα-Orn)ιoCys-CATTTC Conjugate

6-mer oligonucleotide with 3' aminolinker (2.0 units, A260) and 2.0 mg N-iodoacetoxysuccinimide in 50 μl of DMSO were mixed in 100 μl of 0.1 M sodium bicarbonate for 2 hours. iodoacetyl-CATTTC oligonucleotide was purified using the same way as TTTATT-iodoacetyl oligonucleotide. The retention time on anion-exchange for iodoacetyl-CATTTC oligonucleotide was 36.7 minutes. The single linkage conjugate TTTATT-Cys(ώ?/m-Orn)ιoCys-S-StBu (0.6 O.D.) collected directly from reverse phase buffer was put in speed vacuum to reduce the volume to 0.5 ml and pH of the solution was adjusted to 8.0 by IM NaHCO3. Then 15 μl of tributylphosphine in 0.5 ml dichloromethane was added into TTTATT-Cys(^/tfl-Orn)ioCys-S-S-rBu. The reaction was carried out under nitrogen for 4 hours to remove the t-butylthiol protecting group. Then iodoacetyl- CATTTC oligonucleotide was added and the pH of the final solution was adjusted again to 8.0. The reaction was carried out under nitrogen overnight at room temperature. TTTATT-Cys(^/to-Orn)ιoCysCATTTC conjugate was isolated by reverse phase chromatography on a PRP-1 (4.1 x 150 mm) column. The condition was the same as for isolation of the single linkage conjugate. The retention time for the bridged conjugate was 22 minutes (Figure 4B) which is almost the same as 6-mer iodoacetyl-CATTTC oligonucleotide. Because anion-exchange chromatography gave a poor recovery of the desired product, further purification was carried out on polyacrylamide gel electrophoresis. The 22 minutes peak was loaded on a native 20% polyacrylamide gel. The running buffer was Tris-Borate-EDTA, pH 8.3. The samples were suspended in 20 μl of loading buffer (99% formamide), heated to 90 °C for 2 minutes, chilled on ice and loaded on the gel. The pictures were taken by Polaroid 667 film under UV shadowing (Figure 5). The TTTATT-Cys(rfe/tc-Orn)ioCys-CATTTC was separated from unreacted iodoacetyl-CATTTC oligonucleotide. Then the

TTTATT-Cys(de/tfl-Orn)ιoCys-CATTTC was extracted from the gel using IM lithium chloride and desalted by reverse phase chromatography on the same column and same condition.

Preparation of cyclic oligonucleotide-peptide conjugate π

(Scheme m)

a) Transfer of a ³²P terminal phosphate group of ATP to the 5'hydroxylated terminus of bridged conj ugate.

TTTATT-Cys(rfe/tα-Orn)ιoCysCATTTC 17 pmole (0.018 O.D.); 2 μl phosphorylation buffer, 10 x cone; 25 pmole (150 μCi) {gamma- ¥ ATP were mixed and water added to a final volume of 19 μl followed by 50 units of polynucleotide kinase. It was mixed well and incubated for 30 minutes at 37°C. The reaction was stopped by heating to 95 °C for 10 minutes and cooling in an ice bath.

b) Formation of phosphodiester bonds between neighboring 3 '-hydroxyl and 5 ' -phosphate ends of TTTATT-Cys(tfe/ttf-Orn) i øCys-C ATTTC catalyzed by T4

DNA ligase.

5 μl (4 pmole) of the above solution (bridged conjugate with 5' phosphate); 10 pmole (1 μl of a water solution 0.04 O.D./ml) of template (5ΑATAAAGAAATG3'); 2 μl of 10 x cone, ligation buffer and 7 μl of water were mixed and annealed in the water bath from 50°C to 12°C. The ligation reaction was carried out at 20 °C for 16 hours by adding 5 units of T4 DNA ligase. c) Dephosphorylation of uncyclized conjugate.

10 μl of the above solution (a mixture of cyclic and uncyclic conjugate); 2 μl of lOx cone. Dephosphorylation buffer; 7 μl of water and 5 units of alkaline phosphatase were incubated at 37°C for 60 minutes.

Analysis of the reaction products was by autoradiography of a 20% polyacrylamide gel. (Figure 6).

Scheme in Cyclization Of oligonucleotide-peptide by DNA T4 ligase

CH2CONH\A/\/\CATTTC TTTATT\/\/\/\NHCOCH2

S-Cys-Orn-Orn-Orn-Orn-Orn-Orn-Orn-Orn-Orn-Orn-Cys-S

DNA T4 kinase

DNA T4 ligase 5'AATAAAGAAATG

CH2CONH\/\/\/\CATTTCTTTATT\/\/\/\NHCOCH2-S S-Cys-Orn-Orn-Orn-Orn-Orn-Orn-Orn-Orn-Orn-Orn-Cys

26 Figure 1 illustrates an HPLC purification of the compounds of the present invention. Figure 1(A) is graph of an anion-exchange HPLC purification of the activated oligonucleotide TTTATT-iodoacetyl oligonucleotide. Figure 1(B) is a graph of an anion-exchange HPLC purification of the peptide-oligonucleotide conjugate, TTTATT-Cys-(Leu-Lys)2-Lys-(Leu-Lys)2-Cys-S-S-tBu. Figure 1(C) is a graph of a reverse-phase HPLC desalting of the peptide-oligonucleotide conjugate, TTTATT-Cys-(Leu-Lys)2-Lys-(Leu-Lys)2-Cys-S-S-tBu. Figure 1(D) is a graph of a reverse-phase HPLC purification of the oligonucleotide- peptide-oligonucleotide bridged conjugate, TTTATT- Cys-(Leu-Lys)2-Lys-(-Leu-Lys)2-Cys-CATTTC.

Figure 2 is a photograph illustrating gel electrophoresis analysis of intermediates and the product of bridged conjugate synthesis for a Leu-Lys-type peptide. Lane 1: 6-mer CATTTC with 5' aminolinker.

Lane 2: 6-mer TTTATT with 3' aminolinker. Lane 3: TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-CATTTC. Lane 4: TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-S-S-tBu.

Lane 1: Template 5'AATAAAGAAATG after 5' end labeling.

Lane 2: 5' end labeled 5'AATAAAGAAATG after dephosphorylation. Lane 3: TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-CATTTC after 5' end labeling.

Lane 4: 5' end labeled TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-CATTTC after dephosphorylation .

Lane 5: 5' end labeled TTTATT-Cys(Leu-Lys)2-Lys(Leu-Lys)2Cys-CATTTC after ligation by T4 DNA ligase and template DNA.

Lane 6: T4 DNA ligase treated conjugate (in Lane 5) after dephosphorylation.

Figure 4 illustrates reverse-phase HPLC purification of the compounds of the present invention. Figure 4(A) is a graph of a purification of the peptide-oligonucleotide conjugate, TTTATT- Cys-(de/tαOrn)ιo-Cys-S-S-tBu. Figure 4(B) is a graph of a purification of the oligonucleotide-peptide-oligonucleotide conjugate,

TTTATT-Cys-(de/tflOrn)io-Cys-C ATTTC. Figure 5 illustrates gel electrophoresis analysis of intermediates and the product of bridged conjugate synthesis for a deltaOm peptide. Lane 1: 6-mer TTTATT with 3" aminolinker.

Lane 2: Unreacted 6-mer CATTTC derivative (lower band) and TTTATT-Cys(£te/tα-Orn)ιoCys-C ATTTC (upper band). Lane 3: TTTATT-Cys(<2e/tα-Orn)ιoCys-S-S-tBu. Lane 4: Unreacted TTTATT-Cys(ώ-7tα-Orn)ιoCys.

Figure 6 illustrates gel electrophoresis analysis of intermediates and the product of cyclic conjugate synthesis for a deltaOm peptide. Lane 1: TTTATT-Cys(ώ,/tα-Orn)ιoCys-C ATTTC after 5' end labeling. Lane 2: 5' end labeled TTTATT-Cys(<-fe/ta-Orn)i()Cys-C ATTTC after dephosphorylation. Lane 3, 6: 5' end labeled TTTATT-Cys(ώ./tβ-Orn)ιoCys-C ATTTC after ligation by T4 DNA ligase and template DNA. Lane 4, 7: T4 DNA ligase treated conjugate (in Lane 3, 6) after dephosphorylation. Lane 5: blank.

Results and Discussion

The cyclization of a bridged oligonucleotide-cationic peptide conjugate by the ligase and a DNA template should be a valuable technique. This intramolecular reaction of an oligonucleotide-peptide conjugate was not studied before. From the intensities of the bands before and after phosphatase treatment

(Figure 3, lanes 5 and 6), most of the compound was still uncyclized when the peptide moiety was Cys(Leu-Lys)2-Lys(LeuLys)2Cys; the yield of cyclic molecules in this preliminary experiment was around 10% . When the peptide moiety was

Cys(de-tø-Orn)ιoCys, in which the length of the peptide chain is longer and more flexible because of using side chain to link each amino acid, the yield of cyclic oligonucleotidepeptide conjugate is higher, around 50%. Thus the selection of the polycationic polymer must be optimized with respect to the polyanionic oligonucleotide to which it is conjugated as well as with respect to the particular single or double stranded nucleic acid target.

Throughout this application, various publications have been referenced. The disclosures in these publications are incorporated herein by reference in order to more fully describe the state of the art. References

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2. Stein, C. A., and Cohen, J. S. (1989) Important advances in oncology. 79-97.

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4. Zon, G. (1988) Pharmaceutical Research 5, 539-549.

5. Crooke, S. T. (1992) Bio/Technology 10, 882-886.

6. Asseline, U., Delarue, M. , Lancelot, G., Toulme, F., Thuong,

N. T., Montenary-Garestier, T., and Helene, C. (1984) Proc. Natl. Acad. Sci. USA 81, 3297-3301.

7. Sun, J. S., Francois, J. C, Montenary-Garestier, T., Saison- Behmoaras, T., Roig, V., Chassignol, M., Thuong, N. T., and Helene, C. (1989)

Proc. Natl. Acad. Sci. USA 86, 9198-9202.

8. Francois, J. C, Saison-Behmoaras, T., Barbier, C, Chassignol, M., Thuong, N. T., and Helene, C. (1989) Proc. Natl. Acad. Sci. USA 86, 9702- 9706.

9. Stevenson, M., and Iversen, P. L. (1989) J. Gen. Virol. 70, 2673-2682.

While the invention has been particularly described in terms of specific embodiments, those skilled in the art will understand in view of the present disclosure that numerous variations and modifications upon the invention are now enabled, which variations and modifications are not to be regarded as a departure from the spirit and scope of the invention. Accordingly, the invention is to be broadly construed and limited only by the scope and spirit of the following claims.

Claims

We claim:

1. A cyclic polycationic polymer-oligonucleotide conjugate comprising a polycationic polymer covalently bonded at each end to the 3'- and 5'- terminal nucleotides of a polyanionic oligonucleotide via a cross-linking agent, wherein the polycationic polymer may be represented by the formulae:

R₂-[XR₁CHCO]_a-R₃ (I) NH₂ or the formula:

R₂-[XR₆COXCHCO]_a-R₃ (II) R₇ R4-R5 or the formula:

R₂-[XCHCOXR₆CO]_a-R₃ (III) R5-R4 R₇ or the formula:

R₂-[tNH(CH₂)_b]_c[NH(CH₂)_d]_e]_f[NH(CH₂)_g]_h-NHR₂ (IV) or the formula:

R₂-[XCHCO]i-R₃ (V) R4-R5 or the formula:

_R2-CX_R6COXC„COX_R6CO_]a-_R3 (VI) R₇ R4R5 R₇ or the formula:

(VII)

or the formula:

R₂-[XCHCOXCHCOXR₆COXR₆CO]_a-R₃ (VIII) R5R4 R5R4 R₇ R₇ wherein X is selected from the group consisting of -NH-, -O-, and -S-; Rj is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from

1 to 4 carbon atoms in the chain; R2 and R3 are cross-linking agents covalently linking the polycationic polymer to the oligonucleotide; R4 is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 5 carbon atoms in the chain; R5 is selected from the group consisting of primary amines, secondary amines, tertiary amines, quaternary ammonium salts, imidazoles, and guanidine groups; R5 is an alkyl chain having from 1 to 2 carbon atoms; R7 is selected from the group consisting of hydrogen, branched and unbranched lower- alkyl groups having from 1 to 5 carbon atoms, -CH2C5H5, and -(CH2)_zCOR3, wherein z is an integer ranging from 0 to 3 and R3 is as defined above; a is an integer ranging from about 3 to about 16; b is an integer ranging from about 2 to about 5; c is an integer ranging from about 0 to about 3; d is an integer ranging from about 2 to about 5; e is an integer ranging from about 0 to about 3; f is an integer ranging from about 2 to about 9; g is an integer ranging from about 2 to about 5; h is an integer ranging from about 0 to about 3; i is an integer ranging from about 3 to about 12; and the ratio of cations in the polycationic polymer to anions in the polyanionic oligonucleotide pair ranges from about 0.7: 1 to about 1.5: 1, respectively.

2. The cyclic conjugate according to claim 1, wherein the oligonucleotide comprises from about 6 to about 20 nucleotides.

3. The cyclic conjugate according to claim 2, wherein the oligonucleotide comprises from about 8 to about 16 nucleotides.

4. The cyclic conjugate according to claim 1, wherein X is -NH-.

5. The cyclic conjugate according to claim 1, wherein Rj has from 2 to 3 carbon atoms in the chain.

6. The cyclic conjugate according to claim 1, wherein R2 and R3 are cysteines.

7. The cyclic conjugate according to claim 1, wherein R4 has from

2 to 4 carbon atoms in the chain.

8. The cyclic conjugate according to claim 1, wherein group R5 is guanidine.

9. The cyclic conjugate according to claim 1, wherein group R has 1 carbon atom.

10. The cyclic conjugate according to claim 1 , wherein group R7 is selected from the group consisting of hydrogen and branched and unbranched lower-alkyl groups having from 1 to 5 carbon atoms.

11. The cyclic conjugate according to claim 1, wherein a is an integer ranging from about 3 to about 8, b is an integer ranging from about 2 to about 4, c is an integer ranging from about 1 to about 3, d is an integer ranging from about 2 to about 4, e is an integer ranging from about 1 to about 3, f is an integer ranging from about 2 to about 5, g is an integer ranging from about 2 to about 4, h is an integer ranging from about 1 to about 3, and i is an integer ranging from about 3 to about 7.

12. The cyclic conjugate according to claim 1, wherein the ratio of cations in the polycationic polymer to anions in the polyanionic oligonucleotide pair ranges from about 0.8: 1 to about 1.3: 1, respectively.

13. The cyclic conjugate according to claim 1, wherein the polycationic polymer may be represented by the formula:

Cys-(delta-Om)\_Q-Cys

14. A pharmaceutical composition comprising a pharmaceutically acceptable carrier and the cyclic conjugate according to claim 1.

15. A method for preparing a cyclic polycationic polymer- oligonucleotide conjugate comprising a polycationic polymer covalently bonded at each end to the 3'- and 5'- terminal nucleotides of a polyanionic oligonucleotide via a cross-linking agent, wherein the polycationic polymer may be represented by the formulae:

R₂-[XR₁CHCO]_a-R₃ (I)

NH₂ or the formula:

R₂-[XR₆COXCHCO]_a-R₃ (II)

R₇ R4-R5 or the formula:

or the formula:

R₂-[[NH(CH₂)_b]_c[NH(CH₂)_d]_e]_f[NH(CH₂)g]h-NHR₂ (IV) or the formula:

R₂-[XCHCO]i-R₃ (V) R₄-R₅ or the formula:

^-^COXCHCOX^CO,^ (VI) R₇ R4R5 R₇ or the formula:

(VII)

or the formula:

R₂-[XCHCOXCHCOXR₆COXR₆CO]_a-R₃ (VI11)

I I I I

R5R4 R5R4 R₇ R₇

wherein X is selected from the group consisting of -NH-, -O-, and -S-; R\ is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 4 carbon atoms in the chain; R2 and R3 are cross-linking agents covalently linking the polycationic polymer to the oligonucleotide; R4 is a substituted or unsubstituted branched or unbranched lower-alkyl chain having from 1 to 5 carbon atoms in the chain; R5 is selected from the group consisting of primary amines, secondary amines, tertiary amines, quaternary ammonium salts, imidazoles, and guanidine groups; Rβ is an alkyl chain having from 1 to 2 carbon atoms; R7 is selected from the group consisting of hydrogen, branched and unbranched lower- alkyl groups having from 1 to 5 carbon atoms, -CH2C5Η5, and -(CH2)_zCOR3, wherein z is an integer ranging from 0 to 3 and R3 is as defined above; a is an integer ranging from about 3 to about 16; b is an integer ranging from about 2 to about 5; c is an integer ranging from about 0 to about 3; d is an integer ranging from about 2 to about 5; e is an integer ranging from about 0 to about 3; f is an integer ranging from about 2 to about 9; g is an integer ranging from about 2 to about 5; h is an integer ranging from about 0 to about 3; i is an integer ranging from about 3 to about 12; and the ratio of cations in the polycationic polymer to anions in the polyanionic oligonucleotide pair ranges from about 0.7:1 to about 1.5:1, respectively; which comprises the steps of: (1) providing the polyanionic oligonucleotides;

(2) providing the polycationic polymer;

(3) coupling the polyanionic oligonucleotides to the polycationic polymer via the cross linking agents; and