Synthetic conjugate of CpG DNA and T-help/CTL peptide

Abstract

Highly effective vaccine compositions are constructed according to the methods of this invention. The methods are amenable to use with any peptidic antigen sequence and involve covalent attachment of an immunostimulatory nucleotide sequence to an antigenic peptide sequence. Preferred antigenic peptides are fusion peptides made up of one or more CTL epitope peptides in sequence fused to a T helper peptide.

Claims

1. A method of increasing the effectiveness of an antigenic peptide CTL epitope vaccine component, the method comprises conjugating a fusion peptide to a DNA oligomer, wherein the fusion peptide comprises a T-help epitope and an antigenic peptide CTL epitope, wherein the antigenic peptide CTL epitope is conjugated to the DNA oligomer, and wherein the antigenic peptide CTL epitope is amino acid residues 14-32 of SEQ ID NO:3 or amino acid residues 14-32 of SEQ ID NO:4.

2. The method of claim 1, wherein the DNA oligomer comprises a CpG sequence.

3. The method of claim 2, wherein the DNA oligomer is a phosphodiester CpG DNA.

4. The method of claim 2, wherein the DNA oligomer is a fully phosphorothioated backbone CpG DNA.

5. The method of claim 1, wherein the DNA oligomer comprises about 8 to about 300 nucleotide bases.

6. The method of claim 5, wherein the DNA oligomer comprises about 15 to about 100 nucleotide bases.

7. The method of claim 5, wherein the DNA oligomer comprises about 20 to about 25 nucleotide bases.

8. The method of claim 1, wherein the fusion peptide is synthetic.

Description

BRIEF DESCRIPTION OF THE FIGURES

(1) FIG. 1 shows the chemical synthetic scheme for the synthesis of Conjugates 1 and 2.

(2) FIG. 2 is a polyacrylamide gel. Lane 1=Oligo 1; lane 2=Oligo 2; lane 3=Conjugate 1; lane 4=Conjugate 2; lane 5=the maleimide propionic addition product of AKXVAAWTLKAAAILKEPVHGV (X=cyclohexylalanine; SEQ ID NO:1).

(3) FIG. 3 shows the chemical synthetic scheme for the synthesis of Conjugates 3-7.

(4) FIG. 4 is a polyacrylamide gel. Lane 1=Oligo 3; lane 2=Conjugate 2; lane 3=Conjugate 3; lane 4=Hyd-PADRE:I9V (AKXVAAWTLKAAAILKEPVHGV; X=cyclohexylalanine; SEQ ID NO:1).

(5) FIG. 5 shows percent lysis by splenocytes immunized once with 1 nmole Conjugate 3 or 50 nmole PADRE:I9V (AKXVAAWTLKAAAILKEPVHGV; X=cyclohexylalanine; SEQ ID NO:1) P (Tt) two-tail 0.03.

(6) FIG. 6 shows a partial synthetic scheme for synthesis of Conjugate 4 (SEQ ID NOs:2 and 9).

(7) FIG. 7 is a polyacrylamide gel. Lane 1=Oligo 3; lane 2=Conjugate 2.

(8) FIG. 8 shows a partial synthetic scheme for synthesis of Conjugate 5 (SEQ ID NOs:4 and 9).

(9) FIG. 9 is a polyacrylamide gel. Lane 1=Oligo 3; lane 2=Conjugate 6; lane 3=Conjugate 5.

(10) FIG. 10 shows a partial synthetic scheme for synthesis of Conjugate 6 (SEQ ID NOs:3 and 9).

(11) FIG. 11 is a polyacrylamide gel. Lane 1=Oligo 3; lane 2-Conjugate 6; lane 3=Conjugate 5.

(12) FIG. 12 shows percent lysis of human HIV-infected CD4.sup.+ T cells (diamonds, JA2; triangles and squares, R7). P (Tt) two-tail 0.03.

(13) FIG. 13 shows response to challenge by surrogate virus after a single immunization with 5 nmoles Conjugate 3 versus CpG alone. Each bar provides data from a single mouse. Each treatment was performed on three mice.

(14) FIG. 14 shows response to challenge by recombinant vaccinia virus expressing the HIV-pol gene after a single intranasal administration of 1 or 10 nmole Conjugate 3 versus 10 nmole CpG DNA or PADRE:I9V peptide alone. (P0.02, Wilcoxon Two Sample Test). Each bar represents data from a single mouse. Each treatment was performed on two or three mice as shown.

(15) FIG. 15 shows response to challenge by recombinant vaccinia virus expressing HIV-pol after subcutaneous and intraperitoneal immunization with 1 nmole Conjugate 3 or 1 nmole PADRE:I9V peptide plus CpG DNA. Each bar provides data from a single mouse. Each treatment was performed on three mice.

(16) FIG. 16 shows response to challenge by recombinant vaccinia virus expressing HIV-pol after immunization with 0.1 nmole Conjugate 3 or peptide+DNA, fusion peptide or CpG DNA alone. Each bar provides data from a single mouse. Each treatment was performed on multiple mice as shown.

(17) FIG. 17 is a set of three FACS results of cells stained to identify IFN- after immunization with Conjugate 4 (17C), peptide mix (17B) or DNA alone (17A).

(18) FIG. 18 shows percent cell lysis of targets by immune splenocytes after immunization with 0.1 nmole Conjugate 5 (Squares) or its individual components (diamonds). Targets were pre-loaded with I9V peptide (ILKEPVHGV; SEQ ID NO:5). P<0.03.

(19) FIG. 19 shows percent cell lysis of targets by immunized splenocytes after immunization with 0.1 nmole Conjugate 5 (Circles) or its individual components (Squares). Targets were pre-loaded with S9L peptide (SLYNTVATL; SEQ ID NO:6). P<0.01.

(20) FIG. 20 shows cell lysis of R7 cells that were infected with HIV by splenocytes immunized with Conjugate 5 (Bars) or with its individual components (Squares). P<0.01.

(21) FIG. 21 provides histograms of the flow cytometry analysis of immune splenocytes for reaction with an isotype control (21A), an irrelevant, control peptide (21B), Conjugate 5 (21C) or fusion peptide plus DNA, unconjugated (21D).

(22) FIG. 22 shows results of a chromium release assay performed using I9V-loaded JA2 cells as targets and cells from HHD II mice immunized with either Conjugate 7 or Conjugate 3.

(23) FIG. 23 presents percent cytotoxicity data for cells from HLA A2/Kb mice immunized with either Conjugate 3 or Conjugate 10.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

(24) This invention provides an efficient means to immunize or vaccinate against infectious disease or any other disease treatable or preventable by vaccination, for example, HIV, HCMV and cancer. The invention involves a method of covalently attaching an antigenic peptide (for example a human cytomegalovirus, HIV or cancer antigen) to a DNA sequence that acts as an adjuvant, enhancing response to the antigen. Such DNA sequences, known as immunostimulatory nucleotide sequences, are per se known and discussed in U.S. Pat. No. 6,514,948, the disclosures of which are hereby incorporated by reference.

(25) This invention involves covalent attachment of an immunostimulatory nucleic acid, such as a cytosine-phosphate-guanosine (CpG)-containing DNA sequence, to an antigenic peptidic sequence. The conjugates of this invention may be synthesized by reacting a DNA having a 5-end thiohexyl modification with an N-terminal maleimide propionic acid-modified peptidic sequence to form a conjugate or by reacting DNA having a 5-aldehyde modification to a peptide with a N-terminal hydrazine to form a conjugate linked by a hydrazone linkage. Preferred methods for their construction are illustrated in Examples 1-5. The fused vaccine compositions of this invention enhance the immune response in a mammal to the antigenic peptidic sequence and thereby increase the effectiveness of the antigen as a vaccine.

(26) Such DNA-peptide fusions may include any DNA sequence that acts to increase immune stimulation. DNA oligomers of any source are suitable, including bacterial, viral, insect, mammalian or any source at all, including synthetic DNA molecules and DNA molecules with either phosphodiester or phosphorothioate backbones. The particular sequence contained in the DNA is not of paramount importance because any sequence can be effective to stimulate immunity according to this invention, however nucleotide sequences with CpG DNA are preferred.

(27) In general, single-stranded DNA oligomers are used, preferably about 20 to about 25 nucleotides long, however, double-stranded DNA is contemplated for use with this invention. Double-stranded DNA conjugates can be made by first attaching single-stranded DNA to the peptide and then hybridizing the resulting conjugate to a complementary single-stranded DNA sequence. Longer or shorter DNA sequences may be used with this invention, including DNA sequences from about 8 to about 300 nucleotides long, or from about 15 to about 100 nucleotides long. Any convenient size or sequence of DNA may be used with this invention, however, it is generally preferred to use single-stranded DNA of about 10, 15, 20, 25, 30, 35, 40, or 50 nucleotides in length. DNA containing CpG sequences is preferred, but not necessary. Exemplary nucleic acids include, but are not limited to 5-tcgtcgttttgtcgttttgtcgtt-3 (phosphorothioate-substituted; SEQ ID NO:10) and 5-ggGGGACGATCGTCgggggG-3 (in which phosphorothioate linkages are denoted by lower case letters and phosphodiester linkages by upper case letters; SEQ ID NO:11). See Hartmann et al., J. Immunol. 164:1617-1624, 2000. Sequences having fully phosphorothioated backbones, partially phosphorothioated backbones, or fully phosphodiester backbones are suitable.

(28) In recent years, CpG DNA have been grouped into different classes called CpG-A and CpG-B by the Krieg group and CpG-D and CpG-K by Klinman and colleagues. See Verthelyi et al., J. Immunol. 166(4):2372-2377, 2001; Krug et al., Eur. J. Immunol. 31(7):2154-2163, 2001; Klinman et al., Microbes. Infect. 4(9):897-901, 2002; Gursel et al., J. Leukoc. Biol. 71(5):813-820, 2002. Any of these CpG sequences are suitable for use with this invention.

(29) An ODN known to have immunologic activity is referred to as ODN 2216. This is a mixed phosphodiester-phosphorothioate backbone of the sequence ggGGGACGATCGTCgggggG (SEQ ID NO:11) with small letters denoting phosphorothioate linkages and uppercase letters denoting phosphodiester linkages. This ODN is CpG A-class as defined by Krieg and collaborators. Additional motifs include pyrimidine NTTTTGT and its derivatives as described by Elias et al., J. Immunol. 171:3697-3704, 2003. In the context of induction of a T-helper 2 response, Tamura et al. have described ODN without CpG which function to elicit those classes of responses. These responses are not necessarily stimulatory for the types of CTL response here. Sano et al., J. Immunol. 170:2367-2373, 2003.

(30) The peptide moiety of the DNA-peptide compounds according to this invention may be any antigenic peptide from any source against which enhanced immune response is desired. It is contemplated that the invention will be used most frequently with viral and bacterial antigens, particularly from bacteria and viruses that are causative agents in infectious disease. Therefore, the invention may be used to create vaccine compositions for treatment and prophylaxis of such disease as HIV, human cytomegalovirus, tuberculosis or any infections disease. Peptide epitopes of bacterial or viral origin are especially preferred. As well, cancer antigens may be used in the present invention to enhance the efficacy of cancer vaccines, for either treatment or prophylaxis.

(31) The peptides may be of any convenient length so long as the antigenic function of the peptide is intact. Peptide CTL epitopes generally are about 8 to about 12 amino acids long, and therefore such peptides are contemplated for use with the invention and are preferred. Peptides shorter than 8 amino acids long, for example 5, 6 or 7 amino acids long, are not preferred but may be used, however longer peptide sequences are most suitable, including 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 40, 50, 100 or more amino acids in length, including multi-epitope peptides. See Alexander et al., J. Immunol. 168 (12):6189-6198, 2002), the disclosures of which are hereby incorporated by reference.

(32) Fusion peptides including an antigenic peptide as described above fused to another peptide sequence are specifically contemplated for use with the inventive methods and compounds. Especially preferred peptides include fusion peptides composed of a CTL epitope sequence and a helper T lymphocyte (CD4) epitope sequence fused together. Examples of suitable CD4 epitopes include the synthetic sequence PADRE, tetanus-specific peptides, peptides derived from the same antigen or other antigens from the virus that is to be targeted. Similarly, for cancer antigens, a CD4 peptide derived from the same antigen, or any other cell-antigen known in the art, and the like may be used. Linker peptide sequences at the N- or C-terminal end of the fusion or between the CTL and CD4 epitopes in the fusion also may be used. Such linker sequences generally are from about 1 to about 10 amino acids in length and preferably are about 2 to about 7 amino acids in length or more preferably from about 3 to about 5 amino acids in length and may comprise modified or non-traditional amino acids.

(33) Conjugate vaccine compounds may be made by providing a maleimide-substituted or hydrazine-substituted antigenic peptide of the formula

(34) ##STR00001##
wherein B is an antigenic peptide having about 8 to about 50 or more amino acid residues; providing a 5-end thiohexyl modified CpG DNA of the formula A-(CH.sub.2).sub.6SH or an aldehyde (Amidite-A) of the formula A-Amidite, wherein A is a CpG DNA oligomer having about 8 to about 300 nucleotide bases; reacting the peptide of step (a) and the DNA of step (b); and purifying the resulting conjugate vaccine compound of the formula

(35) ##STR00002##
wherein B is an antigenic peptide having about 8 to about 50-100 or more amino acid residues and A is a CpG DNA oligomer having about 8 to about 300 nucleotide bases. Compounds made by this method also form part of this invention. Preferred compounds and methods are those in which the antigenic peptide is a fusion peptide comprising PADRE and a CTL peptide epitope sequence. The CpG DNA oligomer may have a phosphodiester or fully phosphorothioated backbone.

(36) The biologic properties of peptides were studied in HLA A*0201/Kb mice. These model mice express the human HLA type and are well-known to successfully predict human clinical immune responses and demonstrate the usefulness of these molecules in modifying immunity to the antigen. The non-natural assembly of these peptide-DNA fusions was processed to result in an immunologic response with greater sensitivity of recognition compared to non-linked molecules.

(37) All references cited herein are incorporated by reference into this specification in their entirety. In light of the preceding description, one skilled in the art can practice the invention in its full scope. The following examples, therefore, are to be construed as illustrative only and not limiting in relation to the remainder of the disclosure.

EXAMPLES

Example 1

Synthesis of Peptide-Oligonucleotide (CpG DNA) Conjugates 1 & 2

(38) Synthesis of Conjugate 1 (a conjugate of CpG DNA Oligo 1 (SEQ ID NO:7) and PADRE:I9V fusion peptide (SEQ ID NO:1)) and Conjugate 2 (a conjugate of CpG DNA Oligo 2 (SEQ ID NO:8) and PADRE:I9V fusion peptide (SEQ ID NO:1)) was accomplished as follows. See FIG. 1.

(39) (1) Synthesis of Mal-Peptide

(40) All reagents were Peptide Synthesis Grade. Synthesis: Fmoc-Strategy, Manual. Wang Resin (substitution about 0.8 mmole/g) (Novabiochem, San Diego, Calif.).

(41) Fmoc-Val-OH was attached to the Wang resin (1 eq; substitution approximately 0.8 mmole by the symmetrical anhydride (5 eq)/DMAP (1 eq) method. The symmetrical anhydride was made using Fmoc-Val-OH and 1,3-diisopropylcarbodiimide (DIC) in a 2:1 ratio. A total of 0.4 g Fmoc-Val-Wang Resin (approximately 0.22 mmole) was produced. The Fmoc group was deblocked at each step of the growing peptide chain by 20% piperidine/DMF treatment. All the amino acids used during chain elongation were N.sup.-Fmoc-protected, however, amino acids with side chain functionalities were used with the additional protective groups: (a) histidine modified with trityl; (b) lysine and tryptophan modified with Boc; (c) glutamic acid and threonine modified with t-butyl. Coupling of all amino acids was done using 2-(1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium (HBTU)/DIEA reagents. Peptide chain elongation was continued using known methods to create the PADRE-I9V epitope fusion peptide (AKXVAAWTLKAAAILKEPVHGV; X=cyclohexylalanine; SEQ ID NO:1). After deprotection of the Fmoc group from the N-terminal alanine of the peptide chain assembled on the resin, maleimide propionic acid was introduced to the free amino group of the alanine in the presence of DIC/1-hydroxybenzotriazole reagent.

(42) The remaining protecting groups then were removed. Final cleavage was achieved by treating the peptide-linked resin with trifluoroacetic acid (TFA)/triisopropylsilane (TIS)/water (95/2.5/2.5) for two hours at room temperature. This was followed by methyl-t-butyl ether (MBTE) precipitation, filtration and drying of the product.

(43) ##STR00003##

(44) Approximately 440 mg crude product (about 40% pure Mal-peptide) of formula was obtained (X=cyclohexylalanine; SEQ ID NO:1).

(45) Purification was performed on a Shimadzu HPLC System consisting of LC-8A binary pumps and a SPD-10A UV detector using a VYDAC column (22250 mm; packing material: C-4, 10, 300 ). About 440 mg crude peptide (purity about 40%) was purified in 2 lots. Each lot of about 210-220 mg was dissolved in 40 ml of 20% acetic acid/H.sub.2O, filtered through a 0.45 filter, and loaded on a pre-equilibrated column through a solenoid valve (FCV-11AL; Shimadzu) from port B, attached to the line of LC-8A Pump-A.

(46) With detection at a wavelength of 220 nm, one column-volume of mobile phase A (about 80 mL) was run through the column at 8 ml/minute Mobile phase A consisted of 0.05% or 0.10% TFA in water filtered through 0.2 filter paper. A gradient of mobile phase A and mobile phase B (0.08% TFA and in acetonitrile/water (1:1)) then was run as shown in Table I, below, at 8 ml/minute.

(47) TABLE-US-00001 TABLE I HPLC Mobile Phase, Step One Gradient Conditions Time (min.) % A % B 0.01 80 20 50 55 45 60 0 100 70 0 100 70.01 80 20 80 Stop

(48) Fractions were collected. The peptide material eluted between 30 and 45 minutes. The desired fractions were pooled and subjected to analytical HPLC. The mobile phases were as described above, with a flow rate of 1 ml/minute. The column was a 4.6250 mm C-18 column (5, 300 ). After loading onto a pre-equilibrated column as described above, the gradient shown in Table II, below was run.

(49) TABLE-US-00002 TABLE II HPLC Mobile Phase, Step Two Gradient Conditions Time (min.) % A % B 0.01 50 50 25 0 100 30 0 100 30.01 50 50 39 Stop

(50) All fractions containing purified peptide were pooled and concentrated to one-third their original volume using a Rotavapor, then freeze-dried in a pre-weighed vial. About 70 mg peptide was obtained.

(51) This freeze-dried material was analyzed for purity using the same HPLC methodology as described above for step two and also by the following method. A sample was loaded onto a 4.6250 mm C-4 column (5, 300 ) and the gradient provided in Table III, below was run. Mobile phase C was 10% acetonitrile in 0.1 M triethylammonium acetate, pH 5.2-5.4 in water. Mobile phase D was 100% acetonitrile. By both HPLC methods, the synthetic peptide was greater than or equal to 85% pure.

(52) TABLE-US-00003 TABLE III HPLC Mobile Phase, Analysis. Gradient Conditions Time (min.) % C % D 0.01 100 0 20 40 60 25 40 60 25.01 100 0 30 Stop

(53) The synthetic peptide also was analyzed by mass spectroscopy on a Shimadzu-Kratos MALDI-TOF Kompact Probe instrument. The determined mass was within the stated error of the instrument (calculated mass=2478 amu, experimental mass=2477.9 amu).

(54) Oligo 1 (phosphodiester single-stranded CpG DNA (5-tccatgacgttcctgacgtt-3; SEQ ID NO:7), with the 5 end modified to thiohexyl) and Oligo 2 (fully phosphorothioated backbone, single-stranded CpG DNA (5-tccatgacgttcctgacgtt-3 (SEQ ID NO:8) with the 5 end modified to thiohexyl, ((CH.sub.2).sub.6SH) were analyzed by analytical HPLC according to method B above and found to be about 85% and 60% pure, respectively. The DNAs each were dissolved in 6.5 ml 0.1 M triethylammonium acetate, pH 7.0.

(55) Synthesis of Conjugate 1

(56) The conjugate reaction was carried out between PADRE:I9V (SEQ ID NO:1) and Oligo 1 above. All reagents were DNA synthesis grade. The peptide (5.0 mg, 2 eq) was dissolved in 0.1 M guanidine hydrochloride solution (5 mL), pH 6.5-7.0. Oligo 1(6.5 mg, 1 eq) was dissolved in 0.1 M TEAA (6.5 mL), pH 7.0. The above two solutions were mixed together under N.sub.2 atmosphere and stirred for 4 hours at room temperature. The reaction mixture was filtered through a 0.45 filter and passed through the preparative HPLC C-4, 10250 mm, column for desalting and purification (flow rate=4 mL/min; =260 nm; mobile phase A=10% ACN, 0.1M, TEAA, pH 5.2-5.4; mobile phase B=ACN). Mobile phase A and B were filtered through 0.2 filter paper. The column was equilibrated with one column volume (about 20 mL) mobile phase A. After loading the sample, the column was desalted with one column volume (about 20 mL). The desired product was eluted using the following gradient. See Table IV.

(57) TABLE-US-00004 TABLE IV HPLC Mobile Phase, Synthetic Conjugate Gradient Conditions Time (min.) % E % D 0.01 100 0 30 40 60 35 40 60 35.01 0 100 45 0 100 45 Stop

(58) The desired peak eluted at between 20-30 minutes of the gradient run. The peak was collected and concentrated on a Rotavapor to of its original volume, then freeze dried in a pre-weighed vial. About 3.0 mg of Conjugate 1 was obtained. The product was analyzed by HPLC using Method B as above and 8 M urea, 15% acrylamide PAGE as follows. The gel was run at 250 V for 30 minutes. The sample (10 L) was prepared in formamide, heated to 70.sub.CC for 5 minutes and loaded onto the gel with bromophenol blue tracking dye. The gel then was run at 250 V for about thirty minutes until the dye reached the bottom. The gel was stained using Gel Code Blue Stain Reagent. See FIG. 2.

(59) Synthesis of Conjugate 2

(60) The conjugate reaction was carried out between PADRE:I9V peptide (SEQ ID NO:1) and Oligo 2. Peptide (2.5 mg, 1 eq) was dissolved in 2 M urea (5 mL). Oligo 2 (6.5 mg, 1 eq) was dissolved in 2 M urea (6.5 mL). The above two solutions were mixed together under N.sub.2 atmosphere and stirred for four hours at room temperature. The reaction mixture was filtered through a 0.45 filter and passed through a preparative HPLC column for desalting and purification: flow rate=4 mL/minute; =260 nm; mobile phase A=10% ACN, 0.1 M TEAA, pH 5.2-5.4; mobile phase B=ACN. Mobile phases A and B were filtered through a 0.2 (Millipore) filter paper. The column was equilibrated with one column volume (about 20 mL) and the sample was loaded, then desalted with one column volume (about 20 mL). The gradient below was used to elute the desired product at between 20-30 minutes.

(61) TABLE-US-00005 TABLE V HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 30 40 60 35 40 60 35.01 0 100 45 0 100 45 Stop

(62) The desired peak was collected and concentrated on a Rotavapor to of its original volume, then freeze-dried in a pre-weighed vial. About 2.0 mg of Conjugate 2 was obtained. The product was analyzed by HPLC according to Method B (70-80% pure), and by PAGE according to Method C and produced a single band. See FIG. 2.

Example 2

Synthesis of PeptideOligonucleotide (CpG DNA) Conjugate 3

(63) Synthesis and purification of Hyd-PADRE:I9V (SEQ ID NO:1) conjugate with a fully phosphorothioated backbone, single-stranded CpG DNA (5-tccatgacgttcctgacgtt-3; SEQ ID NO:9) with 5 end modified to aldehyde, obtained from Trilink Technologies and referred to as Oligo 3, was accomplished as follows. All the reagents were peptide synthesis grade. Fmoc-Val-OH (>99%) was attached to the Wang resin (substitution about 0.8 mmole/g; 1 eq) by the symmetrical anhydride (5 eq)/DMAP (1 eq) method. Synthesis proceeded as using Fmoc-Val-OH and DIC in a 2:1 ratio. See FIG. 3.

(64) Synthesis was started with 0.4 g Fmoc-Val-Wang resin (approximately 0.22 mmole). The Fmoc group was deblocked at each step of the growing peptide chain by 20% piperidine/DMF treatment. All the amino acids used during chain elongation were N.sup.-Fmoc-protected, however amino acids with side chain functionalities were used with the additional protective groups: (histidine modified with trityl; lysine and tryptophan modified with Boc; glutamic acid and threonine modified with t-butyl). Coupling of all amino acids was done using HBTU/DIEA reagents. After deprotection of the Fmoc group from the N-terminal alanine of the peptide chain assembled on the resin, HDA was introduced to the free amino group of alanine in the presence of DIC/1-hydroxybenzotriazole reagent. Final cleavage was done by treating peptide-resin with TFA/TIS/water in a 95/2.5/2.5 ratio for two hours at room temperature. This was followed by MBTE precipitation, filtration and drying of the product. Approximately 440 mg of crude product (about 40% purity by analytical HPLC, Method A) was obtained.

(65) Purification was done on Shimadzu HPLC system with LC-8A binary pumps and SPD-10A UV Detector, using a VYDAC column (22250 mm; packing material, C-4, 10, 300 ). About 440 mg crude peptide (purity about 40%) was purified in 2 lots. Each lot of about 210-220 mg was dissolved in 40 ml of 20% acetic acid/H.sub.2O, filtered through a 0.45 filter, and loaded on a pre-equilibrated column through the solenoid valve FCV-11AL from port B, attached to the line of LC-8A Pump-A (flow rate=8 mL/minute; =220 nm; mobile phase=0.05% TFA, H.sub.2O; acetonitrile). Mobile phases A and B were filtered through 0.2 filter paper. The column was equilibrated with one column volume of mobile phase A (about 80 mL) and the sample loaded. One column volume of mobile phase A (about 80 mL) was followed by the gradient below.

(66) TABLE-US-00006 TABLE VI HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 80 20 50 55 45 60 0 100 70 0 100 70.01 80 20 80 Stop

(67) The desired peak eluted between 30 and 45 minutes of the gradient. The fractions were analyzed by analytical HPLC according to Method A: flow rate=1 mL/minute; =220 nm, column=C-18, 5, 300 , 4.6250 mm; mobile phase A=0.10% TFA, H.sub.2O; mobile phase B=0.08% TFA, 1:1 ACN/H.sub.2O.

(68) TABLE-US-00007 TABLE VII HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 50 50 25 0 100 30 0 100 30.01 50 50 39 Stop

(69) All the fractions containing pure peptide (85%) from all the four lots were pooled and concentrated on a Rotavapor to of its original volume, then freeze-dried in a pre-weighed vial. About 80 mg of peptide was obtained. This freeze dried material was again analyzed by analytical HPLC and mass analysis by method A above and method B: flow rate=1 mL/minute; =260 nm; column=C-4, 5 300 , 4.6250 mm; mobile phase A=10% acetonitrile, 0.1 M TEAA, pH 5.2-5.4; mobile phase B=ACN.

(70) TABLE-US-00008 TABLE VIII HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 20 40 60 25 40 60 25.01 100 0 0 Stop

(71) Mass analysis was carried out on a Shimadzu-Kratos MALDI-TOF Kompact Probe mass analyzer. The calculated mass was 2462 a.m.u. The experimental mass was 2462 a.m.u., which is within the stated error of the instrument.

(72) CpG-DNA fully phosphorothioated with 5-end modified to aldehyde (Oligo 3) was obtained from Trilink Technologies, analyzed by analytical HPLC as per Method B above and found to be 60% pure.

(73) Synthesis of Conjugate 3

(74) The peptide above, PADRE:I9V (SEQ ID NO:1; 4.2 mg, about 1.7 eq), was dissolved in 2 M urea solution (5 mL). Oligo 3 (SEQ ID NO:8; 13.4 mg, about 2 eq) was dissolved in 2 M urea (15 mL). The above two solutions were mixed together and stirred for three hours at room temperature. The reaction mixture was filtered through a 0.45 filter and passed through the preparative HPLC C-4, column (22250 mm) for desalting and purification: (flow rate=8 mL/minute; -260 nm; mobile phase A=10% ACN, 0.1 M TEAA, pH 5.1-5.2; mobile phase B=ACN). Mobile phases A and B were filtered through a 0.2 filter paper. The column was equilibrated with one column volume (about 80 mL) of mobile phase A and the sample loaded. One column volume (about 80 mL) was run through the column for desalting. The following gradient was used to elute the desired product.

(75) TABLE-US-00009 TABLE IX HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 50 50 50 50.01 0 100 60 Stop

(76) The desired peak eluted between 35-45 minutes of gradient run. The peak collected above was concentrated on a Rotavapor to of its original volume and then freeze dried in a pre-weighed vial. About 5.1 mg of Conjugate 3 was obtained. The product was analyzed by HPLC by Method B above and found to be 70-80% pure. Under PAGE, a single band was found using Method C: gel, 8 M urea, 15% acrylamide; pre-run at 250 V for 30 minutes; sample run, 10 L sample formamide, heated to 70.sub.CC for five minutes and loaded; tracking dye, bromophenol blue; run at 250 V until tracking dye reaches bottom (about 30 minutes). The gel was stained with Gel Code Blue StainReagent. See FIG. 4.

(77) Synthesis of Conjugate 3 (Batch-2)

(78) All reagents were DNA synthesis grade. Hyd-PADRE:I9V (SEQ ID NO:1; 4.1 mg, about 1.7 eq) was dissolved in 2 M urea solution (5 mL). Oligo 3 (SEQ ID NO:8; 13.5 mg, about 2 eq) was dissolved in 2 M urea (15 mL). The above two solutions were mixed together and stirred for three hours at room temperature. The reaction mixture was filtered through a 0.45 filter and passed through the preparative HPLC diphenyl column (10250 mm) for desalting and purification: flow rate=4 mL/minute; =260 nm; mobile phase A=10% ACN, 0.1 M TEAA, pH 5.1-5.2; mobile phase B=ACN. Mobile phases A and B were filtered through a 0.2 filter paper. The column was equilibrated with one column volume (about 20 mL) of mobile phase A and the sample loaded. One column volume (about 20 mL) was run through the column for desalting. The gradient below was used to elute the desired product.

(79) TABLE-US-00010 TABLE X HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 40 40 60 45 0 100 60 Stop

(80) The desired peak eluted between 20-30 minutes of the gradient run. The peak collected above was concentrated on Rotavapor to of its original volume and then freeze dried in a pre-weighed vial. About 7.0 mg of Conjugate 3 was obtained. The product was analyzed by HPLC by Method B above, using a diphenyl column, in place of the C-4 column and found to be 70-80% pure. The material formed a single band by PAGE, Method C.

(81) To demonstrate that the conjugate molecules are immunogenic, HLA A2/kb mice were immunized once subcutaneously with 1 nmole Conjugate 3. Fourteen days later, the spleens were retrieved. The CTL responses of the immune splenocytes were tested after one round of in vitro stimulation (IVS). FIG. 5 shows that administration of a single dose of 1 nmole Conjugate 3 results in 80% target cell lysis at an E:T ratio of 100, while administration of two doses of 50 nmoles PADRE:I9V fusion peptide (unconjugated; AKXVAAWTLKAAAILKEPVHGV; X=cyclohexylalanine; SEQ ID NO:1) resulted in only 8% cell lysis at the same E:T ratio. Targets were labeled with I9V peptide (SEQ ID NO:5) for both sets of animals. This demonstrates the ability of Conjugate 3 to be processed and to induce specific CTL responses. This experiment was repeated four times with similar results each time. Using a two-tailed T test, there was a significant difference of P<0.03 at all E:T ratios. An additional analysis using flow cytometry revealed that high frequencies of splenic T cells were stimulated by the incubation with the I9V peptide to produce IFN-. This IFN--producing population is present only after stimulation with the specific I9V peptide. Consistently, between 5 and 60% of the CD8.sup.+ T cell population were specific for I9V after immunization with Conjugate 3.

Example 3

Synthesis of Peptide-Oligonucleotide (CpG DNA) Conjugate 4

(82) Synthesis and purification of Hyd-KSS:PADRE: S9L; KSSAKXVAAWTLKAAASLYN TVATL; X=cyclohexylalanine; (SEQ ID NO:2; PADRE-HIVgag fusion) was performed as follows. Fully phosphorothioated backbone, single-stranded (ss) CpG DNA (5-CHOC.sub.6H.sub.5(CONH(CH.sub.5(CONH(CH.sub.2).sub.6O-tccatgacgttcctgacgtt 3; SEQ ID NO:9) with 5 end modified to aldehyde was obtained from Trilink Technologies and termed Oligo 3 in the text. See FIGS. 3 and 6.

(83) Synthesis of Conjugate 4

(84) The Conjugate reaction was carried out between Hyd-KSS:PADRE:S9L and 5-aldehyde substituted oligonucleotide with phosphorothioated backbone i.e. Oligo 3.

(85) Synthesis of Hyd-KSS:PADRE:S9L

(86) All the reagents were Peptide Synthesis Grade. Synthesis: Fmoc-Strategy, Manual. Wang resin (substitution about 0.8 mmole/g). Fmoc-Leu-OH (>99%) was attached to the Wang resin (1 eq) by the symmetrical anhydride (5 eq)/DMAP (1 eq) method as described above (symmetrical anhydride was made using Fmoc-Val-OH and DIC in a 2:1 ratio. Synthesis was started with 0.4 g Fmoc-Leu-Wang resin (approximately 0.22 mmole). The Fmoc-group was deblocked at each step of the growing peptide chain by 20% piperidine/DMF treatment. All the amino acids used during chain elongation were N.sup.-Fmoc-protected, however, amino acids with side chain functionalities were used with additional protective groups: asparagine modified with trityl; lysine and tryptophan modified with Boc; tyrosine, serine and threonine modified with t-butyl. Coupling of all amino acids was done using HBTU/DIEA reagents. After deprotection of the Fmoc-group from the N-terminal lysine of the peptide chain assembled on the resin, HDA (1 eq) was introduced to the free alpha amino group of lysine in the presence of DIC/1-hydroxybenzotriazole reagent. Final cleavage was done by treating the peptide-resin with TFA/thioanisole/ethanedithiol/water in a 90/5/2.5/2.5 ratio (2 hour treatment) at room temperature. This was followed by MTBE precipitation, filtration and drying of the product. Approximately 400 mg of crude product (about 40% Purity, analyzed by analytical HPLC, Method A) was obtained.

(87) Purification of Hyd-Peptide

(88) Purification was done on Shimadzu HPLC system consisting of LC-8A binary pumps and an SPD-10A UV Detector, using VYDAC column (22250 mm; packing material, C-4, 10, 300 ). About 400 mg crude peptide (purity about 40%) was purified in 2 lots. About 200 mg was dissolved in 40 mL 20% acetic acid/H.sub.2O, filtered through a 0.45 filter, and loaded onto a pre-equilibrated column through a solenoid valve FCV-11AL (Shimadzu) from port B, attached to the line of LC-8A Pump-A: flow rate=8 mL/minute; =220 nm; mobile phase=0.05% TFA, H.sub.2O; acetonitrile (ACN). Mobile phases A and B were filtered through a 0.2 filter paper. The column was equilibrated with one column volume of mobile phase A (about 80 mL) and the sample was loaded as above. One column volume of Mobile Phase A (about 80 ml) was run through the column, followed by the gradient below.

(89) TABLE-US-00011 TABLE XI HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 80 20 50 55 45 60 0 100 70 0 100 70.01 80 20 80 Stop

(90) The desired peak eluted between 30 and 45 minutes of the gradient run. The fractions were analyzed by analytical HPLC as per Method A: flow rate=1 mL/minute; , =220 nm; column=C-18, 5 300 , 4.6250 mm; mobile phase A=0.10% TFA, H.sub.2O; mobile phase B=0.08% TFA, 1:1 ACN/H.sub.2O.

(91) TABLE-US-00012 TABLE XII HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 50 50 25 0 100 30 0 100 30.01 50 50 39 Stop

(92) All the fractions containing pure peptide (85%) from all the four lots were pooled and concentrated on a Rotavapor to of its original volume, then freeze-dried in a pre-weighed vial. About 60 mg of peptide was obtained. This freeze dried material was analyzed by analytical HPLC (method A above and method B below) and mass analysis. Mass analysis was carried out on Shimadzu-Kratos MALDI-TOF Kompact Probe mass analyzer. The calculated mass was 2754 a.m.u. and the experimental mass was 2754.4 a.m.u., which is within the stated error of the instrument. HPLC method B: flow rate=1 mL/minute; =260 nm; column=diphenyl, 5, 300 , 4.6250 mm; mobile Phase A=10% ACN, 0.1 M TEAA, pH 5.0-5.1; mobile phase B=ACN.

(93) TABLE-US-00013 TABLE XIII HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 20 40 60 25 40 60 25.01 100 0 0 Stop

(94) Oligo 3

(95) CpG-DNA fully phosphorothioated with 5-end modified to aldehyde (CHO) was obtained from Trilink Technologies, analyzed by analytical HPLC by method B above and found to be about 60% pure.

(96) Synthesis of Conjugate 4

(97) All the reagents were DNA synthesis grade. Hyd-KSS-PADRE:S9L (SEQ ID NO:2; 4.7 mg, about 1.7 eq) was dissolved in 2 M urea solution (5 mL). Oligo 3 (14.7 mg, about 2.2 eq) was dissolved in 2 M Urea (15 mL). The two solutions were mixed together and stirred for 3 hours at room temperature. The reaction mixture was filtered through a 0.45 filter and passed through a preparative HPLC diphenyl column (10250 mm) for desalting and purification: flow rate=4 mL/min; =260 nm; mobile phase A=10% ACN, 0.1 M TEAA, pH 5.0-5.1; mobile phase B=ACN. Mobile phases A and B were filtered through 0.2 filter paper. The column was equilibrated with one column volume (about 20 mL) mobile phase A, and the sample was loaded. One column volume (about 20 mL) was run through the column for desalting. The gradient below was used to elute the desired product.

(98) TABLE-US-00014 TABLE XIV HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 40 40 60 45 0 100 60 Stop

(99) The desired peak eluted between 20-30 minutes of the gradient run. The desired peak collected above was concentrated on a Rotavapor to of its original volume and then freeze dried in a pre-weighed vial. About 6.0 mg of Conjugate 4 was obtained. This product was analyzed by HPLC (about 70-80% pure by method B above) and by PAGE (forming a single band by method C: gel preparation, 8 M urea, 15% acrylamide; pre-run, 250 V for 30 minutes; sample run, 10 L sample formamide, heated to 70.sub.CC for 5 minute and loaded, tracking dye, bromophenol; run, 250 V for about 30 minutes or until the dye reached the bottom; staining, Gel Code Blue Stain Reagent. See FIG. 7.

Example 4

Synthesis of Peptide-Oligonucleotide (CpG DNA) Conjugate 5

(100) Synthesis and purification of Hyd-PADRE:I9V:N:S9L (AKXVAAWTLKAAAILK EPVHGVNSLYNTVATL; X=cyclohexylalanine; SEQ ID NO:4; PADRE-HIVpol-Asn-HlVgag fusion) was performed as follows. Fully phosphorothioated backbone, single-stranded CpG DNA (5-3 tccatgacgttcctgacgtt; SEQ ID NO:9) with 5 end modified to aldehyde (CHO) was obtained from Trilink Technologies and is termed Oligo 3. The conjugate reaction was carried out between Hyd-PADRE:I9V:N:S9L (SEQ ID NO:4) and Oligo 3. See FIG. 8.

(101) Synthesis of Hyd-PADRE:I9V:N:S9L

(102) All the reagents were Peptide Synthesis Grade. Synthesis: Fmoc-Strategy, manual, using Wang resin (substitution about 0.8 mmole/g. Fmoc-Leu-OH (>99%) was attached to the Wang resin (1 eq) by the symmetrical anhydride (5 eq)/DMAP (1 eq) method as described above. The symmetrical anhydride was made using Fmoc-Val-OH and DIC in a 2:1 ratio. The synthesis was started with 0.4 g Fmoc-Leu-Wang resin (approximately 0.22 mmole). The Fmoc group was deblocked at each step of the growing peptide chain by 20% piperidine/DMF treatment. All the amino acids used during chain elongation were N.sup.-Fmoc-protected, however, amino acids with side chain functionalities were used with the following additional protective groups: asparagine and histidine modified with trityl; lysine and tryptophan modified with Boc; glutamic acid, tyrosine, serine and threonine modified with t-butyl. Coupling of all amino acids was done using HBTU/DIEA reagents. After deprotection of the Fmoc-group from the N-terminal alanine of the peptide chain assembled on the resin, HDA (1 eq) was introduced to the free amino group of alanine in the presence of DIC/HOBt reagent.

(103) Final cleavage was achieved by treating the peptide-resin with TFA/thioanisole/EDT/water in a 90/5/2.5/2.5 ratio (2 hour treatment) at room temperature. This was followed by MTBE precipitation, filtration and drying of the product. Approximately 450 mg of crude product (about 30% purity as determined by analytical HPLC, method A) was obtained. Purification was achieved using a Shimadzu HPLC system consisting of LC-8A binary pumps and a SPD-10A UV detector, using a VYDAC column (2250 mm; packing material, C-4, 10, 300 ) Sample was prepared as follows. Four hundred fifty milligrams crude peptide (purity about 40%) was purified in 2 lots. For each lot, 220-230 mg peptide was dissolved in 40 mL of 20% acetic acid/H.sub.2O and filtered through 0.45 filter, then loaded on a pre-equilibrated column through a solenoid valve FCV-11AL (Shimadzu) from port B, attached to the line of LC-8A Pump-A: flow rate=8 mL/minute; =220 nm; mobile phase A, 0.05% TFA, H.sub.2O; mobile phase B, ACN. Mobile phases A and B were filtered through 0.2 filter paper. One column volume of Mobile Phase A (about 80 mL) was used to equilibrate the column. The sample was loaded as described above. One column volume of mobile phase A (about 80 mL) was run through the column for desalting, followed by the gradient below.

(104) TABLE-US-00015 TABLE XV HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 87 13 50 62 38 60 0 100 70 0 100 70.01 87 13 80 Stop

(105) The desired peak eluted between 40 and 55 minutes of the gradient run. The collected fractions were analyzed by analytical HPLC per method A: flow rate=1 mL/minute; =220 nm; column=C-18, 5300 , 4.6250 mm; mobile phase A=0.10% TFA, H.sub.2O; mobile phase B=0.08% TFA, 1:1 ACN/H.sub.2O.

(106) TABLE-US-00016 TABLE XVI HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 50 50 25 0 100 30 0 100 30.01 50 50 39 Stop

(107) All fractions containing pure peptide 85%) from all the four lots were pooled and concentrated on a Rotavapor to of its original volume, then freeze-dried in a pre-weighed vial. About 60 mg of peptide was obtained. This freeze dried material was analyzed by analytical HPLC (method A above and method B below) and mass analysis using a Shimadzu-Kratos MALDI-TOF Kompact Probe mass analyzer.

(108) The calculated mass was 3539 a.m.u. and the experimental mass was 3539.2 a.m.u., which is within the stated error of the instrument. Method B: flow rate=1 mL/minute; =260 nm; column=diphenyl, 5, 300 , 4.6250 mm; mobile phase A=10% ACN, 0.1 M TEAA, pH 5.0-5.1; mobile phase B=ACN.

(109) TABLE-US-00017 TABLE XVII HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 20 40 60 25 40 60 25.01 100 0 0 Stop

(110) Oligo 3

(111) CpG-DNA fully phosphorothioated with 5-end modified to aldehyde was obtained from Trilink Technologies, analyzed by analytical HPLC by Method B above and found to be 60% pure.

(112) Synthesis of Conjugate 5

(113) All the reagents were DNA synthesis grade. Hyd-PADRE:I9V:N:S9L (SEQ ID NO:4; 7.2 mg, about 2 eq) was dissolved in 2M urea solution (7 mL). Oligo 3 (17.0 mg, about 2.5 eq) was dissolved in 2 M urea (17 mL). The two solutions were mixed together and stirred for 3 hours at room temperature. The reaction mixture was filtered through a 0.45 filter and passed through the preparative HPLC diphenyl column (10250 mm) for desalting and purification: flow rate=4 mL/min; =260 nm; mobile phase A=10% ACN, 0.1 M TEAA, pH 5.0-5.1; mobile phase B=ACN. Mobile phases A and B were filtered through 0.2 filter paper. The column was equilibrated with one column volume (about 20 mL) of mobile phase A and the sample loaded. One column volume (about 20 mL) was run through the column for desalting. The following gradient then was used to elute the desired product.

(114) TABLE-US-00018 TABLE XVIII HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 40 40 60 45 0 100 60 Stop

(115) The desired peak eluted between 20-32 minutes of the gradient run. The peak collected above was concentrated on a Rotavapor to of its original volume and then freeze dried in a pre-weighed vial. About 8.0 mg of Conjugate 5 was obtained. The product was analyzed by HPLC 70-80% pure by method B above) and by PAGE (method C), where it ran as a single band. Method C: 8 M urea, 15% acrylamide gel; pre-run at 250 V for 30 minutes; Samples prepared with 10 L sample formamide, heated to 70.sub.CC for 5 minutes and loaded with bromophenol blue tracking dye. The gel was run at 250 V for about 30 minutes or until the dye reached the bottom. Staining was done with Gel Code Blue StainReagent. See FIG. 9.

Example 5

Synthesis of Peptide-Oligonucleotide (CpG DNA) Conjugate 6

(116) Synthesis and purification of Hyd-PADRE:I9V:K:S9L (AKXVAAWTLKAAAILKEPV HGVKSLYNTVATL; SEQ ID NO:3). The conjugate reaction carried out between Hyd-PADRE:I9V:K:S9L and Oligo 3 (described above). See FIG. 10.

(117) Synthesis of Hyd-PADRE:I9V:K:S9L

(118) All the reagents were Peptide Synthesis Grade. Synthesis: Fmoc-Strategy, manual. Wang resin (substitution about 0.8 mmole/g). Fmoc-Leu-OH (>99%) was attached to the Wang resin (1 eq) by the symmetrical anhydride (5 eq)/DMAP (1 eq) method as described above using Fmoc-Val-OH and 1,3-DIC in a 2:1 ratio. The synthesis was started with 0.4 g Fmoc-Leu-Wang resin (approximately 0.22 mmole). The Fmoc group was deblocked at each step of the growing peptide chain by 20% piperidine/DMF treatment. All the amino acids used during chain elongation were N-Fmoc-protected, however amino acids with side chain functionalities were used with the additional protective groups: asparagine and histidine modified with trityl; lysine and tryptophan modified with Boc; glutamic acid, tyrosine, serine and threonine modified with t-butyl. Coupling of all amino acids was done using HBTU/DIEA reagents. After deprotection of the Fmoc group from the N-terminal alanine of the peptide chain assembled on the resin, HDA (1 eq) was introduced to the free amino group of alanine in the presence of DIC/HOBt reagent.

(119) Final cleavage was achieved by treating the peptide-resin with TFA/thioanisole/EDT/water in a 90/5/2.5/2.5 ratio (2 hour treatment) at room temperature. This was followed by MTBE precipitation, filtration and drying of the product. Approximately 450 mg of crude product (about 30% purity, by analytical HPLC, method A) was obtained.

(120) Purification of Hyd-Peptide

(121) Purification was done on a Shimadzu HPLC system consisting of LC-8A binary pumps and a SPD-10A UV detector, using a VYDAC column (22250 mm, packing material, C-4, 10, 300 A). Sample was prepared as follows. Approximately 450 mg crude peptide (purity about 40%) was purified in 2 lots. Each lot of about 220-230 mg peptide was dissolved in 40 mL 20% acetic acid/H.sub.2O and filtered through a 0.45 filter, then loaded on pre-equilibrated column through solenoid valve FCV-11AL (Shimadzu) from port B, attached to the line of LC-8A Pump-A: flow rate=8 mL/minute; =220 nm; mobile phase=0.05% TFA, H.sub.2O; mobile phase B=ACN. Mobile phases A and B were filtered through 0.2 filter paper. The column was equilibrated with one column volume of mobile phase A (about 80 mL) and the sample was loaded as described above. One column volume of mobile phase A (about 80 mL) was run through the column, followed by the gradient below.

(122) TABLE-US-00019 TABLE XIX HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 80 20 50 55 45 60 0 100 70 0 100 70.01 87 13 80 Stop

(123) The desired peak eluted between 25 and 40 minutes of the gradient run. The collected fractions were analyzed by analytical HPLC by Method A. All fractions containing pure peptide 85%) from all the four lots were pooled and concentrated on a Rotavapor to of its original volume, then freeze-dried in a pre-weighed vial. About 70 mg of peptide was obtained. This freeze-dried material was analyzed by analytical HPLC (methods A (85% pure) and B (85% pure) as described above) and mass analysis using a Shimadzu-Kratos MALDI-TOF Kompact Probe mass analyzer. The calculated mass was 3553 a.m.u. and the experimental mass was 3553.3 a.m.u., which is within the stated error of the instrument.

(124) Oligo 3

(125) CpG-DNA fully phosphorothioated with 5-end modified to aldehyde was obtained from Trilink Technologies, analyzed by analytical HPLC as per Method B above and found to be about 60% pure.

(126) Synthesis of Conjugate 6

(127) All the reagents were DNA synthesis grade. Hyd-PADRE:I9V:K:S9L (SEQ ID NO:3) (5.8 mg, about 1.6 eq) was dissolved in 2 M urea solution (6 mL). Oligo 3 (13.4 mg, about 2.0 eq) was dissolved in 2 M urea (14 mL). The two solutions were mixed together and stirred for 3 hours at room temperature. The reaction mixture was filtered through a 0.45 filter and passed through the preparative HPLC diphenyl column (10250 mm) for desalting and purification: flow rate=4 mL/min; =260 nm; mobile phase A=10% ACN, 0.1 M TEAA, pH 5.0-5.1; mobile phase B=ACN. Mobile phases A and B were filtered through 0.2 filter paper. The column was equilibrated with one column volume (about 20 mL) mobile phase A, and the sample loaded. One column volume (about 20 mL) was run through the column for desalting step, followed by the gradient below.

(128) TABLE-US-00020 TABLE XX HPLC Mobile Phase Gradient Conditions Time (min.) % A % B 0.01 100 0 40 40 60 45 0 100 60 Stop

(129) The desired peak eluted between 20-32 minutes of the gradient run. The peak collected above was concentrated on a Rotavapor to of its original volume and then freeze dried in a pre-weighed vial. About 7.0 mg Conjugate 6 was obtained. This product was analyzed by HPLC (about 70-80% pure by method B above) and by PAGE (Method C), where it ran as a single band. See FIG. 11.

Example 6

Recognition of Naturally Processed HIV Epitopes

(130) Splenic immune cells from mice immunized with Conjugate 3 (1 nmole) were subjected to one round of in vitro stimulation and tested for the ability to lyse HIV-infected CD4.sup.+ cells (R7 cells). R7 cells are capable of synthesizing HIV particles that express p24, a characteristic diagnostic protein. The cells were tested at E:T ratios of 4, 20 and 100. Results are shown in FIG. 12, which also shows results for control JA2 cells. P (T<=t)=0.03 using a two-tail T test. The epitope recognized after immunization with Conjugate 3 is only a small portion of the total amount of peptides presented on the surface of the cells. This assay demonstrates recognition in one of the best in vitro systems to demonstrate that the immunization leads to recognition of bond fide HIV-infected cells. These results therefore indicate that the inventive approach to immunization is suitable for use in a clinical situation in which individuals are infected with HIV, for example for therapeutic use, or for prophylaxis against HIV.

Example 7

Immunization Protects In Vivo Against Challenge with Vaccinia Virus Expressing the H1V-pol Gene

(131) Three mice were immunized with 5 nmole Conjugate 3 or CpG Sequence #1826 (control). Fourteen days after immunization, the mice were challenged by intraperitoneal administration of 110.sup.7 p.f.u. of recombinant vaccinia virus expressing the HIV-pol gene. After five days, the virus titer in the ovaries of the mice was determined. Results are shown in FIG. 13. There was an approximate six orders of magnitude difference in protection in the case of mice immunized with Conjugate 3 versus control.

(132) This study was repeated using intranasal immunization. See FIG. 14. These HLA A2/Kb mice were immunized with 1 nmole Conjugate 3, 10 nmole PADRE:I9V or 10 nmole CpG DNA. Fourteen days after immunization, all mice were challenged intranasally with 210.sup.7 p.f.u. recombinant vaccinia virus expressing HIV-pol. After five days, the virus titer in the mice ovaries was determined. The animals that were administered 10 nmoles of Conjugate 3 were significantly better at providing protection against the vaccinia virus challenge than animals immunized with the PADRE:I9V peptide or animals receiving only CpG DNA without peptide (P=0.02; Wilcoxon two sample test). The results therefore indicate that vaccination with Conjugate 3 protects against viral infection in vivo.

Example 8

Vaccination with Conjugate Versus Unconjugated Peptide

(133) HLA A2/Kb mice were immunized both subcutaneously and intraperitoneally with 1 nmole of Conjugate 3 or 1 nmole of PADRE:I9V peptide plus CpG DNA (unconjugated). Fourteen days later, the mice were challenged intraperitoneally with 110.sup.7 p.f.u. of recombinant vaccinia virus expressing HIV-pol. After five days, the virus titer in the ovaries of the challenged mice was determined. Using a two-tailed T test, the difference between these two vaccine strategies was significant at p<0.02. See FIG. 15. Immunization with one dose of 1 nmole of Conjugate 3 provided protection against challenge with vaccinia virus expressing HIV-pol, whereas immunization with 1 nmole of the peptide with unconjugated CpG DNA did not confer protection against viral challenge. Ten-fold higher doses of unconjugated peptide vaccine were required to reach the same level of protection when the vaccine was administered as a conjugate.

(134) A lower dose of Conjugate 3 (0.1 nmole) was tested in comparison to a mixture of the peptide and CpG DNA. Two immunizations fourteen days apart were administered to mice, followed by challenge with 110.sup.7 p.f.u. recombinant vaccinia virus expressing HIV-pol seven days after the second immunization. Five days later, the virus titer in the ovaries of the mice were determined. As is shown in FIG. 16, only the group vaccinated with Conjugate 3 received significant protection (P<0.02; Wilcoxon two sample test). Animals receiving either peptide, CpG DNA or both in combination were equivalently unprotected against viral challenge. Conjugate 3 was ten times more sensitive than peptide plus DNA (unconjugated) for protection against vaccinia virus infection.

(135) Conjugate 4, which is composed of CpG DNA #1826 (Oligo 3) linked using a HDA hydrazone linkage to PADRE followed by the HIV-gag CTL epitope SLYNTVATL (SEQ ID NO:6), was tested as described for Conjugate 3 above in comparison with unconjugated peptide. Chromium release assays and cytokine flow cytometry studies were carried out. One nanomole of the conjugate in a single immunization, followed by one in vitro stimulation, resulted in development of more than 23% HIV-gag CTL epitope-specific splenocytes (FIGS. 17B and 17A, respectively), greater than the mix of peptide plus DNA or DNA alone (FIG. 17C). This conjugate also caused cytotoxicity against peptide-sensitized targets and against the R7 cell line.

(136) Methods for flow cytometry were as follows. Mice were immunized subcutaneously with either 1 nmole Conjugate 4 or 1 nmole KSS:PADRE:S9L (SEQ ID NO:2) and 1 nmole CpG DNA. One day 14, splenocytes from immunized mice were stimulated in vitro for 7 days with irradiated S9L-loaded LPS blasts from syngeneic litter mates. After the incubation, the cell mix was incubated further with S9L or irrelevant (control) peptide for six hours. The cells were passed through a Ficoll-Hypaque gradient, and the live cells were washed with phosphate buffered saline. One million cells were stained with CD8-FITC, then fixed and permeabilized by Perm/Fix solution for 30 minutes at 4 C. The cells then were washed in permeabilizing buffer and incubated with either anti-IFN--APC or isotype-matched APC-labeled mAb. Two animals were analyzed for each vaccine and stimulation. See FIG. 17.

Example 9

HIV Immune Recognition after Multi-Epitope Peptide Vaccination

(137) Conjugate 5 was synthesized to contain CpG DNA components in a linear chain with the CTL epitopes separated by a non-native asparagine residue (SEQ ID NOs:4 and 9). The conjugate was modified at the amino terminus as for Conjugates 3 and 4 and was physically evaluated by HPLC and gel electrophoresis. The conjugate was dissolved in saline solution and administered to HLA A2/Kb mice, and compared to a fusion peptide of all three CTL epitopes mixed with CpG DNA or to CpG DNA alone. Each vaccination contained 0.1 nmole vaccine component.

(138) Fourteen days after vaccination, splenocytes from individual mice were incubated with either 19V-loaded (FIG. 18) or S9L LPS blasts (FIG. 19 under in vitro stimulation conditions. Cytolytic T cell responses were determined by chromium release assay using either I9V-loaded targets (FIG. 18) or S9L-loaded targets (FIG. 19). The data in FIG. 18 shows a statistically significant (P<0.03) difference between the conjugated vaccine according to the invention and a mixture of the peptide and CpG DNA. Recognition of the S9L-loaded targets required a greater amount of conjugate in the immunization (10 nmoles). Nevertheless, a statistically significant (P<0.02) difference was found between the group immunized with Conjugate 5 versus the mixture of peptide plus DNA.

(139) Additional targets were evaluated, including R7 cells that were infected with HIV. The level of recognition of the R7 target was higher with the multi-epitope peptide of Conjugate 5 than with Conjugate 3, even without conjugation. See FIG. 20. The comparison between the groups immunized with Conjugate 5 or a mixture of peptide plus DNA show that the difference in recognition of the R7 cells is significantly greater with Conjugate 5 (P<0.01). This demonstrates enhanced sensitivity of recognition of an HIV-infected cell line with Conjugate 5, and the level of recognition is much higher than with any of the conjugates containing one CTL epitope examined above.

(140) The conjugate strategy can be extended to a greater number of epitopes or different epitopes that cover or apply to a wide variety of HIV strains and HLA types. Therefore, any single epitope or any combination of epitopes can be included in the peptide portion of the conjugate vaccines according to this invention. For example, two or more CTL epitopes may be included as a linear chain, with or without spacers between the epitopes, or three, four, five, six or more epitopes as desired to provide coverage for multi-ethnic populations, for different viral strains, or both.

Example 10

Flow Cytometry Analysis of Immune Splenocytes

(141) Aliquots of the splenocytes evaluated above were evaluated by flow cytometry for expression of IFN- and for quantitation of the frequency of T cells specific for the relevant antigens. The immunization described in FIG. 18 was evaluated, with the modification that the splenocytes, instead of being incubated with cellular targets, were incubated with the I9V or irrelevant (control) peptide for six hours. The cells were passed through a Ficoll-Hypaque gradient and live cells were washed with phosphate-buffered saline. One million of the cells were stained with CD8-FITC. The cells then were fixed and permeabilized using Perm/Fix solution for 30 minutes at 4 C. Cells were washed in permeabilizing buffer and incubated with either anti-IFN--allophycocyanin (APC) or isotype-matched APC-labeled mAb. See FIGS. 21A, 21B, 21C and 21D.

(142) The data show that there was limited non-specific reaction of splenocytes to either an isotype control (FIG. 21A) or an irrelevant peptide (FIG. 21B), but that much more significant frequencies of reactive T cells were found after exposure to the I9V peptide in the case of immunization with the fusion peptide plus DNA, unconjugated (FIG. 20D), or with Conjugate 5 (FIG. 20C). The very high frequency of reactive T cells in FIG. 20C demonstrates a good correlation with the chromium release assay of FIGS. 17-19. The activity of Conjugate 5 is very high and affords a very high level of recognition by T cells, even after only one immunization. The extraordinary level of sensitivity in this well-recognized in vivo model for human cellular and humoral immune responses demonstrates the merit of this immunization approach.

Example 11

Effect of TH Epitope on Immunogenicity

(143) Because the adjuvant activity of CpG was remarkable, experiments were performed to investigate the need for both CTL and T.sub.H epitope components in chimeric peptides for vaccine. Conjugate 7, which is CpG (oligo 3) covalently attached to the I9V peptide, was synthesized. See FIG. 3.

(144) HHD II mice were immunized with 1 nmole of either Conjugate 7 or Conjugate 3 (which is the same as Conjugate 7 but also contains PADRE). A chromium release assay was performed using I9V-loaded JA2 cells as targets. See FIG. 22 for results. Conjugate 7 had less activity than Conjugate 3 against these cells (p<0.005).

(145) To address whether the defect in Conjugate 7 immunogenicity was the missing PADRE T.sub.H epitope, immunizations with Conjugate 7 plus PADRE T.sub.H were compared to immunizations with Conjugate 7 alone. Each of three mice were immunized with Conjugate 7 alone, Conjugate 7 together with the PADRE T.sub.H epitope, Conjugate 3, or the PADRE:I9V fusion peptide alone. FIG. 22 shows that the fusion peptide alone had little immunogenicity, while Conjugate 3 worked efficiently. Although Conjugate 7 had minimal immunogenicity when used alone, in combination with the free PADRE T.sub.H epitope, its immunogenicity was restored almost to the level of Conjugate 3. See FIG. 22. This demonstrates that both the T.sub.H and CTL epitopes should be present for maximal immunogenicity. Further, the majority of the stimulating activity of the PADRE epitope is caused by the sequence itself, rather than the artificial junction caused by chimerizing the CTL and T.sub.H epitopes, since Conjugate 3 and Conjugate 7 plus PADRE in trans have similar immunogenicity. Similar fusion peptides, including a fusion peptide composed of PADRE and an HPV-specific CTL epitope, have been administered to volunteers and women with cervical neoplasia without causing observable autoimmunity

Example 12

Human-specific ODN

(146) Conjugate 10, composed of PADRE fused to I9V (SEQ ID NO:1), is identical to Conjugate 3 except for the substitution of the CpG portion, which is a primate- and human-specific CpG-ODN (Oligo 4; SEQ ID NO:10). See Hartmann et al., J. Immunol. 164:1617-1624, 2000. The chemical yield and purity of this conjugate were similar to the others synthesized above using CpG 1826 (murine). Groups of three HLA A2/Kb mice were immunized with either Conjugate 3 and Conjugate 10 (1 nmole). Chromium release assay results in FIG. 23 show that both conjugates were recognized equivalently, providing additional evidence that these constructs are feasible for use in a clinical setting in human patients. The CpG-ODN used in Conjugate 10 also is known under the trade names ProMune or Vaxmune (Coley Pharmaceutical Group).

(147) TABLE-US-00021 TABLEXXI SummaryofConjugateStructuresandSequences SEQID NAME NO SEQUENCEORSTRUCTURE PADRE:19V 1 AKXVAAWTLKAAAILKEPVHGV,X= cyclohexylalanine KSS:PADRE:S9L 2 KSSAKXVAAWTLKAAASLYNTVATL,X= cyclohexylalanine PADRE:I9V:K:S9L 3 AKXVAAWTLKAAAILKEPVHGVKSLYNTVATL,X= cyclohexylalanine PADRE:I9V:N:S9L 4 AKXVAAWTLKAAAILKEPVHGVNSLYNTVATL,X= cyclohexylalanine I9V 5 ILKEPVHGV S9L 6 SLYNTVATL Oligo1 7 Phosphodiestersingle-strandedCpGDNA5-tccatgacgttcctgacgtt-3 withthe5 endmodifiedtothiohexyl Oligo2 8 Phosphorothioatedbackbone,single-strandedCpGDNA5- tccatgacgttcctgacgtt-3 withthe5 endmodifiedtothiohexyl Oligo3 9 Phosphorothioatedbackbone,single-strandedCpGDNA5-H-CO- C.sub.6H.sub.3-CO-NH-(CH.sub.2).sub.6-tccatgacgttcctgacgtt-3' (5-aldehydelinker: Amidite-A) Oligo4 10 5-tcgtcgttttgtcgttttgtcgtt-3 (phosphorothioate-substituted) Oligo5 11 5-ggGGGACGATCGTCgggggG-3 (phosphorothioate-substitutedat lowercaseletters) PADRE 12 AKXVAAWTLKAAA,X= cyclohexylalanine Conjugate1 NA PADRE-I9V+ Oligo1 Conjugate2 NA PADRE-I9V+ Oligo2 Conjugate3 NA PADRE:I9V+ Oligo3 Conjugate4 NA KSS:PADRE:S9L+ Oligo3 Conjugate5 NA PADRE:I9V:N:S9L+ Oligo3 Conjugate6 NA PADRE:I9V:K:S9L+ Oligo3 Conjugate7 NA AAA:I9V+ Oligo3 Conjugate10 NA PADRE:I9V+ Oligo4 Hyd NA NH.sub.2-NH-C.sub.6H.sub.3N-CO-

REFERENCES

(148) 1. Cho et al., IFN-alpha beta promote priming of antigen-specific CD8+ and CD4+ T lymphocytes by immunostimulatory DNA-based vaccines. J. Immunol. 168:4907-4913, 2002.

(149) 2. Cho et al., Immunostimulatory DNA-based vaccines induce cytotoxic lymphocyte activity by a T-helper cell-independent mechanism. Nat. Biotechnol. 18:509-514, 2000.

(150) 3. Hartmann et al., Delineation of a CpG phosphorothioate oligodeoxynucleotide for activation primate immune responses in vitro and in vivo. J. Immunol. 164:1617-1624, 2000.

(151) 4. Homer et al., Immunostimulatory DNA-based vaccines elicit multifaceted immune responses against HIV at systemic and mucosal sites. J. Immunol. 167:1584-1591, 2001.

(152) 5. Livingston et al., The Hepatitis B virus-specific CTL responses induced in humans by lipopeptide vaccination are comparable to those elicited by acute viral infection. J. Immunol. 159:1383-1392, 1997.

(153) 6. Schirmbeck et al., Antigenic epitopes fused to cationic peptide bound to oligonucleotides facilitate toll-like receptor 9-dependent, but CD4+ T cell help-independent priming of CD8+ T cells. J. Immunol. 171:5198-5207, 2003.

(154) 7. Tighe et al., Conjugation of protein to immunostimulatory DNA results in rapid, long-lasting and potent induction of cell-mediated and humoral immunity, Eur. J. Immunol. 30(7):1939-1947, 2000.

(155) 8. Tighe et al., Conjugation of immunostimulatory DNA to the short ragweed allergen and a 1 enhances its immunogenicity and reduces its allergenicity. J. Allergy Clin. Immunol. 106(1 Pt. 1):124-134, 2000.

(156) 9. Vitiello et al., Development of a lipopeptide-based therapeutic vaccine to treat chronic HBV infection. I. Induction of a primary cytotoxic T lymphocyte response in humans. J. Clin. Invest. 95:341-349, 1995.