U.S. patent application number 12/941705 was filed with the patent office on 2011-03-10 for modulation of oligonucleotide cpg-mediated immune stimulation by positional modification of nucleosides.
This patent application is currently assigned to IDERA PHARMACEUTICALS, INC.. Invention is credited to SUDHIR AGRAWAL.
Application Number | 20110059067 12/941705 |
Document ID | / |
Family ID | 22746395 |
Filed Date | 2011-03-10 |
United States Patent
Application |
20110059067 |
Kind Code |
A1 |
AGRAWAL; SUDHIR |
March 10, 2011 |
MODULATION OF OLIGONUCLEOTIDE CPG-MEDIATED IMMUNE STIMULATION BY
POSITIONAL MODIFICATION OF NUCLEOSIDES
Abstract
The invention provides methods for modulating the immune
response caused by CpG dinucleotide-containing compounds. The
methods according to the invention enables both decreasing the
immunostimulatory effect for antisense applications, as well as
increasing the immunostimulatory effect for immunotherapy
applications.
Inventors: |
AGRAWAL; SUDHIR;
(SHREWSBURY, MA) |
Assignee: |
IDERA PHARMACEUTICALS, INC.
|
Family ID: |
22746395 |
Appl. No.: |
12/941705 |
Filed: |
November 8, 2010 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11274043 |
Nov 15, 2005 |
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12941705 |
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09845623 |
Apr 30, 2001 |
7115579 |
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11274043 |
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60201578 |
May 1, 2000 |
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Current U.S.
Class: |
424/130.1 ;
424/184.1 |
Current CPC
Class: |
C07H 21/00 20130101;
A61P 11/06 20180101; C12N 15/113 20130101; A61P 35/00 20180101;
A61K 38/00 20130101; C12N 15/117 20130101; C12N 2310/317 20130101;
A61P 37/06 20180101; A61P 11/00 20180101; A61P 31/00 20180101; C12N
2310/332 20130101; A61P 17/00 20180101; C12N 2310/33 20130101; Y10S
514/885 20130101; C12N 2310/335 20130101; A61P 37/00 20180101; C12N
2310/336 20130101; C12N 2310/334 20130101; A61P 29/00 20180101;
A61P 37/02 20180101; C12N 2310/18 20130101; A61K 2039/55561
20130101; C12N 2310/315 20130101; C12N 2310/3183 20130101; A61P
37/08 20180101; A61P 37/04 20180101 |
Class at
Publication: |
424/130.1 ;
424/184.1 |
International
Class: |
A61K 39/00 20060101
A61K039/00; A61K 39/395 20060101 A61K039/395; A61P 37/00 20060101
A61P037/00; A61P 35/00 20060101 A61P035/00; A61P 29/00 20060101
A61P029/00; A61P 37/08 20060101 A61P037/08; A61P 31/00 20060101
A61P031/00; A61P 17/00 20060101 A61P017/00; A61P 11/00 20060101
A61P011/00; A61P 11/06 20060101 A61P011/06; A61P 37/04 20060101
A61P037/04 |
Claims
1. A method for the therapeutic treatment of a mammal having a
disease the method comprising: inducing an immune response in a
mammal by administering a compound having an increased
immunostimulatory effect, the compound comprising a 5'-CpG-3'
dinucleotide, wherein C is cytosine and G is guanosine or a
substituted guanosine, and an immunomodulatory moiety, wherein the
immunomodulatory moiety is selected from the group consisting of
abasic nucleoside, 1,3-propanediol linker, nitropyrrole,
nitroindole, deoxyuridine, inosine, isoguanosine, 2-aminopurine,
nebularine, 7-deazaguanosine, 4-thiodeoxyuridine, 4-thiothymidine,
d-isoguanosine, d-iso-5-methylcytosine, P-base, and 3'-3' linkage,
wherein the compound is 6 to 50 nucleotides in length, the compound
does not have antisense activity, and wherein the increased
immunostimulatory effect is relative to a compound lacking the
immunomodulatory moiety.
2. The method according to claim 1 wherein the compound has the
structure 5'-Yn . . .
Y6-Y5-Y4-Y3-Y2-Y1-CG-X1-X2-X3-X4-X5-X6-X7-X8-X9 . . . Xm-3',
wherein C is cytosine, G is guanosine or a substituted guanosine,
and each X and Y is independently a nucleoside or an
immunomodulatory moiety, and n is a number from -6 to +20, and m is
a number from -9 to +20.
3. The method according to claim 2 wherein the compound has only
one immunomodulatory moiety for each CpG dinucleotide present in
the oligonucleotide.
4. The method according to claim 3 wherein the compound has only
one immunomodulatory moiety.
5. The method according to claim 1, wherein the mammal is a
human.
6. The method according to claim 2, wherein the mammal is a
human.
7. The method according to claim 1, wherein the compound is 12 to
35 nucleotides in length.
8. The method according to claim 1, wherein the administration of
the compound is parenteral, oral, sublingual, transdermal, topical,
intranasal, intratracheal, or intrarectal.
9. The method according to claim 1, wherein the compound is
administered at a sufficient dosage to attain a blood level of
oligonucleotide from about 0.01 micromolar to about 10
micromolar.
10. The method according to claim 1, wherein dosage of compound is
from about 0.1 mg per patient per day to about 200 mg per kg body
weight per day.
11. The method according to claim 1, wherein the compound is
administered in combination with a vaccine.
12. The method according to claim 6, further comprising
administering an adjuvant.
13. The method according to claim 1, wherein the substituted
guanosine is 7-deazaguanosine or inosine.
14. The method according to claim 1, wherein the compound is
administered in combination with an antibody, cytotoxic, antisense
oligonucleotide, gene therapy vector, DNA vaccine or adjuvant.
15. The method according to claim 1 wherein the disease or disorder
to be treated is cancer, an autoimmune disorder, airway
inflammation, inflammatory disorders, skin disorders, allergy,
asthma or a disease caused by a pathogen.
Description
BACKGROUND OF THE INVENTION
Related Applications
[0001] This application is a continuation of U.S. patent
application Ser. No. 11/274,043 filed on Nov. 15, 2005, which is a
continuation of Ser. No. 09/845,623, filed on Apr. 30, 2001, which
claims the benefit of U.S. Provisional Patent Application Ser. No.
60/201,578, filed on May 1, 2000. Each of the patent applications
listed above is hereby incorporated by reference in its
entirety.
FIELD OF THE INVENTION
[0002] The invention relates to the therapeutic use of
oligonucleotides, both in the antisense approach, and as
immunostimulatory agents.
SUMMARY OF THE RELATED ART
[0003] Oligonucleotides have become indispensable tools in modern
molecular biology, being used in a wide variety of techniques,
ranging from diagnostic probing methods to PCR to antisense
inhibition of gene expression. This widespread use of
oligonucleotides has led to an increasing demand for rapid,
inexpensive and efficient methods for synthesizing
oligonucleotides.
[0004] The synthesis of oligonucleotides for antisense and
diagnostic applications can now be routinely accomplished. See
e.g., Methods in Molecular Biology, Vol 20: Protocols for
Oligonucleotides and Analogs pp. 165-189 (S. Agrawal, Ed., Humana
Press, 1993); Oligonucleotides and Analogues: A Practical Approach,
pp. 87-108 (F. Eckstein, Ed., 1991); and Uhlmann and Peyman, supra.
Agrawal and Iyer, Curr. Op. in Biotech. 6: 12 (1995); and Antisense
Research and Applications (Crooke and Lebleu, Eds., CRC Press, Boca
Raton, 1993). Early synthetic approaches included phosphodiester
and phosphotriester chemistries. Khorana et al., J. Molec. Biol.
72: 209 (1972) discloses phosphodiester chemistry for
oligonucleotide synthesis. Reese, Tetrahedron Lett. 34: 3143-3179
(1978), discloses phosphotriester chemistry for synthesis of
oligonucleotides and polynucleotides. These early approaches have
largely given way to the more efficient phosphoramidite and
H-phosphonate approaches to synthesis. Beaucage and Caruthers,
Tetrahedron Lett. 22: 1859-1862 (1981), discloses the use of
deoxynucleoside phosphoramidites in polynucleotide synthesis.
Agrawal and Zamecnik, U.S. Pat. No. 5,149,798 (1992), discloses
optimized synthesis of oligonucleotides by the H-phosphonate
approach.
[0005] Both of these modern approaches have been used to synthesize
oligonucleotides having a variety of modified internucleotide
linkages. Agrawal and Goodchild, Tetrahedron Lett. 28: 3539-3542
(1987), teaches synthesis of oligonucleotide methylphosphonates
using phosphoramidite chemistry. Connolly et al., Biochemistry 23:
3443 (1984), discloses synthesis of oligonucleotide
phosphorothioates using phosphoramidite chemistry. Jager et al.,
Biochemistry 27: 7237 (1988), discloses synthesis of
oligonucleotide phosphoramidates using phosphoramidite chemistry.
Agrawal et al., Proc. Anti. Acad. Sci. USA.about.: 7079-7083
(1988), discloses synthesis of oligonucleotide phosphoramidates and
phosphorothioates using H-phosphonate chemistry.
[0006] More recently, several researchers have demonstrated the
validity of the antisense approach to therapeutic treatment of
disease. Crooke, Antisense Nucleic Acid Drug Dev. 8: vii-viii,
discloses the successful marketing approval of a phosphorothioate
oligonucleotide for the treatment of human cytomegalovirus induced
retinitis. Unfortunately, the use of phosphorothioate
oligonucleotides has become more complex than originally expected.
Certain effects caused by phosphorothioate oligonucleotides could
not be explained by the expected antisense mechanism. For example,
McIntyre et al., Antisense Res. Dev. 3: 309-322 (1993) teaches that
a "sense" phosphorothioate oligonucleotide causes specific immune
stimulation. This and other side effects have complicated the
picture for phosphorothioate oligonucleotides.
[0007] On the other hand, the observation that phosphodiester and
phosphorothioate oligonucleotides can induce immune stimulation has
created interest in developing this side effect as a therapeutic
tool. These efforts have focused on phosphorothioate
oligonucleotides containing the dinucleotide CpG. Kuramoto et al.,
Jpn. J. Cancer Res. 83: 1128-1131 (1992) teaches that
phosphodiester oligonucleotides containing a palindrome that
includes a CpG dinucleotide can induce interferon-alpha and gamma
synthesis and enhance natural killer activity. Krieg et al., Nature
371: 546-549 (1995) discloses that phosphorothioate CpG-containing
oligonucleotides are immunostimulatory. Liang et al., J. Clin.
Invest. 98: 1119-1129 (1996) discloses that such oligonucleotides
activate human B cells. Moldoveanu et aL, Vaccine 16: 1216-1224
(1998) teaches that CpG-containing phosphorothioate
oligonucleotides enhance immune response against influenza virus.
McCluskie and Davis, The Journal of Immunology 161: 4463-4466
(1998) teaches that CpG-containing oligonucleotides act as potent
adjuvants, enhancing immune response against hepatitis B surface
antigen.
[0008] These reports make clear that there is a need to be able to
modulate the immune response caused by CpG-containing
oligonucleotides. Ideally, such modulation should include
decreasing the immunostimulatory effect for antisense applications,
as well as increasing the immunostimulatory effect for
immunotherapy applications.
BRIEF SUMMARY OF THE INVENTION
[0009] The invention provides methods for modulating the immune
response caused by CpG dinucleotide-containing compounds. The
methods according to the invention enable both decreasing the
immunostimulatory effect for antisense applications, as well as
increasing the immunostimulatory effect for immunotherapy
applications. Thus, the invention further provides compounds having
optimal levels of immunostimulatory effect for either application
and methods for making and using such oligonucleotides.
[0010] The present inventor has surprisingly discovered that
positional modification of CpG-containing oligonucleotides
dramatically affects their immunostimulatory capabilities. In
particular, 2' or 3' sugar or base modifications of
oligonucleotides, or introduction of a modified internucleoside
linkage, at particular positions 5' or 3', including 5' or 3' end
modifications, to the CpG dinucleotide either enhances or reduces
their immunostimulatory effect in a reproducible and predictable
manner.
[0011] In a first aspect, the invention provides a method for
modulating the immunostimulatory effect of a CpG dinucleotide
containing compound by introducing an immunomodulatory moiety at a
position either 5' to or 3' to the CpG dinucleotide.
[0012] In a second aspect, the invention provides compounds having
increased or reduced immunostimulatory effect, the compounds
comprising a CpG dinucleotide and an immunomodulatory moiety,
wherein the increased or reduced immunomodulatory effect is
relative to a similar compound lacking the immunomodulatory
moiety.
[0013] In a third aspect, the invention provides a method for
obtaining an antisense-specific reduction in the expression of a
gene in a mammal, including a human, the method comprising
administering to the mammal an oligonucleotide that is
complementary to the gene and which comprises a CpG dinucleotide
and an immunomodulatory moiety, wherein the oligonucleotide has
less immunostimulatory effect than a similar oligonucleotide
lacking the immunomodulatory moiety.
[0014] In a fourth aspect, the invention provides a method for
inducing an immune response in a mammal, including a human, the
method comprising administering to the mammal a compound comprising
a CpG dinucleotide and an immunomodulatory moiety, wherein the
compound has greater immunostimulatory effect than a similar
compound lacking the immunomodulatory moiety.
BRIEF DESCRIPTION OF THE DRAWINGS
[0015] FIG. 1 shows preferred embodiments of immunomodulatory
moieties according to the invention. Note that the Figures use X3X4
for the 3' side and X1X2 for the 5' side. This use is illustrative
for this figure only and should not be used to interpret the
claims, which use the Y and X designations taught in this
specification.
[0016] FIG. 2 (SEQ ID NOs 1-3, respectively, in order of
appearance) shows a modified compound according to the invention
and results of spleen assays using this compound.
[0017] FIG. 3 (SEQ ID NOs 4-6, respectively, in order of
appearance) shows another modified compound according to the
invention and results of spleen assays using this compound.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0018] The invention relates to the therapeutic use of
oligonucleotides, both in the antisense approach, and as
immunostimulatory agents. The patents and publications cited herein
reflect the level of knowledge in the field and are hereby
incorporated by reference in their entirety. In the event of
conflict between any teaching of any reference cited herein and the
present specification, the latter shall prevail, for purposes of
the invention.
[0019] The invention provides methods for modulating the immune
response caused by CpG dinucleotide-containing compounds. The
methods according to the invention enable both decreasing the
immunostimulatory effect for antisense applications, as well as
increasing the immunostimulatory effect for immunotherapy
applications. Thus, the invention further provides oligonucleotides
having optimal levels of immunostimulatory effect for either
application and methods for making and using such
oligonucleotides.
[0020] The present inventor has surprisingly discovered that
positional modification of CpG-containing oligonucleotides
dramatically affects their immunostimulatory capabilities. In
particular, 2' or 3' sugar or base modifications of
oligonucleotides, or introduction of a modified internucleoside
linkage, at particular positions 5' or 3' to the CpG dinucleotide,
including 5' or 3' end modifications, or combinations thereof,
either enhances or reduces their immunostimulatory effect in a
reproducible and predictable manner.
[0021] In a first aspect, the invention provides a method for
modulating the immunostimulatory effect of a CpG dinucleotide
containing compound by introducing an immunomodulatory moiety at a
position either 5' to or 3' to the CpG dinucleotide. Preferred
compounds according to this aspect of the invention generally
include additional oligonucleotide sequences.
[0022] In certain preferred embodiments the method is used to make
an oligonucleotide that is complementary to a gene or gene
transcript. In certain preferred embodiments, the oligonucleotide
has antisense activity. In some preferred embodiments, only one
immunomodulatory moiety is introduced into the oligonucleotide for
each CpG dinucleotide present in the oligonucleotide. In some
preferred embodiments, only one immunomodulatory moiety is
introduced into the oligonucleotide.
[0023] In certain preferred embodiments, the oligonucleotide made
according to this aspect of the invention does not have antisense
activity and/or is not complementary to a gene.
[0024] As herein, the term "complementary" means having the ability
to hybridize to a genomic region, a gene, or an RNA transcript
thereof under physiological conditions. Such hybridization is
ordinarily the result of base-specific hydrogen bonding between
complementary strands, preferably to form Watson-Crick or Hoogsteen
base pairs, although other modes of hydrogen bonding, as well as
base stacking can also lead to hybridization. As a practical
matter, such hybridization can be inferred from the observation of
specific gene expression inhibition.
[0025] As used herein, "antisense activity" means that the
oligonucleotide, when introduced into a cell or an animal, causes a
reduction in the expression of the gene to which it is
complementary.
[0026] The method according to this aspect of the invention can be
conveniently carried out using any of the well-known synthesis
techniques by simply using an appropriate immunomodulatory moiety
monomer synthon in the synthesis process in a cycle following,
immediately or otherwise the incorporation of the CpG dinucleotide.
Preferred monomers include phosphoramidites, phosphotriesters and
H-phosphonates.
[0027] For purposes of the invention, "introducing an
immunomodulatory moiety into position Y2" simply means synthesizing
an oligonucleotide that has an immunomodulatory moiety at such a
position, with reference to the following structure:
TABLE-US-00001 5'-Yn . . . Y6-Y5-Y4-Y3-Y2-Y1-CG-X1-X2-X3-X4-X5-
X6-X7-X8-X9 . . . Xm-3',
[0028] wherein C is cytosine, G is guanosine, a substituted
guanosine, including inosine and 7-deazaguanosine, and each X and Y
is independently a nucleoside or an immunomodulatory moiety, and n
is a number from -6 to +20, and m is a number from -9 to +20.
[0029] Procedures for synthesis of oligonucleotides are well known
in the art.
[0030] In a second aspect, the invention provides compounds having
increased or reduced immunostimulatory effect, the compounds
comprising a CpG dinucleotide and an immunomodulatory moiety,
wherein the increased or reduced immunomodulatory effect is
relative to a similar compound lacking the immunomodulatory moiety.
Preferred compounds according to this aspect of the invention
generally include additional oligonucleotide sequences. Preferably,
such oligonucleotide sequences will have from about 6 to about 50
nucleotides, most preferably from about 12 to about 35
nucleotides.
[0031] Certain preferred compounds according to the invention have
the structure:
TABLE-US-00002 5'-Yn . . . Y6-Y5-Y4-Y3-Y2-Y1-CG--X1-X2-X3-X4-X5-
X6-X7-X8-X9 . . . Xm-3',
[0032] wherein C is cytosine, G is guanosine, a substituted
guanosine, including inosine and 7-deazaguanosine, and each X and Y
is independently a nucleoside or an immunomodulatory moiety, and n
is a number from -6 to +20, and m is a number from -9 to +20.
[0033] In particularly preferred embodiments, the base sequence
that is modified to provide the compound is
TABLE-US-00003 5'-CTATCTGACGTTCTCTGT-3' (SEQ ID NO 1) or
5'-CCTACTAGCGTTCTCATC-3' (SEQ ID NO 4)
Preferred immunomodulatory moieties include one or more abasic
nucleoside, 1,3-propanediol linker (substituted or unsubstituted),
and/or modified base-containing nucleosides, including
nitropyrrole, nitroindole, deoxyuridine, inosine, isoguanosine,
2-aminopurine, nebularine, 7-deazaguanosine, 4-thiodeoxyuridine,
4-thiothymidine, d-isoguanosine, d-iso-5-methylcytosine, P-base,
and 3'-3' linkage. As a general rule, introduction of an
immunomodulatory moiety at position Y6, Y5, Y4, or Y3, or a
combination thereof, increases the immunostimulatory effect of the
oligonucleotide. Generally, introduction of an immunomodulatory
moiety at position Y2 maintains immunostimulatory effect.
Generally, introduction of an immunomodulatory moiety at position
Y1 maintains or reduces immunostimulatory effect. Generally,
introduction of an immunomodulatory moiety at position C abolishes
immunostimulatory effect. Generally, introduction of an
immunomodulatory moiety at position G abolishes immunostimulatory
effect, except for 7-deazaguanosine, which maintains
immunostimulatory effect. Generally, introduction of an
immunomodulatory moiety at position X1 maintains or reduces
immunostimulatory effect. Generally, introduction of an
immunomodulatory moiety at position X2 has little impact on
immunostimulatory effect. Generally, introduction of an
immunomodulatory moiety at position X3 maintains or increases
immunostimulatory effect. Generally, introduction of an
immunomodulatory moiety at position X4, X5, X6, X7-Xm, or any
combination thereof, increases immunostimulatory effect.
[0034] Certain preferred oligonucleotides according to this aspect
of the invention are complementary to a gene or gene transcript.
More preferably, such oligonucleotides have antisense activity. In
some preferred embodiments, the oligonucleotide has only one
immunomodulatory moiety for each CpG dinucleotide present in the
oligonucleotide. In some preferred embodiments, the oligonucleotide
has only one immunomodulatory moiety. In other preferred
embodiments, the compounds according to this aspect of the
invention do not have antisense activity and/or are not
complementary to a gene.
[0035] In a third aspect, the invention provides a method for
obtaining an antisense-specific reduction in the expression of a
gene in a mammal, including a human, the method comprising
administering to the mammal an oligonucleotide that is
complementary to the gene and which comprises a CpG dinucleotide
and an immunomodulatory moiety, wherein the oligonucleotide has
less immunostimulatory effect than a similar oligonucleotide
lacking the immunomodulatory moiety.
[0036] In some preferred embodiments, the oligonucleotide has only
one immunomodulatory moiety for each CpG dinucleotide present in
the oligonucleotide. In some preferred embodiments, the
oligonucleotide has only one immunomodulatory moiety.
[0037] In the methods according to this aspect of the invention,
preferably, administration of antisense oligonucleotides should be
parenteral, oral, sublingual, transdermal, topical, intranasal,
intratracheal, or intrarectal. Administration of the therapeutic
compositions can be carried out using known procedures at dosages
and for periods of time effective to reduce symptoms or surrogate
markers of the disease. When administered systemically, the
therapeutic composition is preferably administered at a sufficient
dosage to attain a blood level of oligonucleotide from about 0.001
micromolar to about 10 micromolar. For localized administration,
much lower concentrations than this may be effective, and much
higher concentrations may be tolerated. Preferably, a total dosage
of oligonucleotide will range from about 0.1 mg oligonucleotide per
patient per day to about 200 mg oligonucleotide per kg body weight
per day. It may be desirable to administer simultaneously, or
sequentially a therapeutically effective amount of one or more of
the therapeutic compositions of the invention to an individual as a
single treatment episode. In a preferred embodiment, after the
composition of matter is administered, one or more measurement is
taken of biological effects selected from the group consisting of
complement activation, mitogenesis and inhibition of thrombin dot
formation.
[0038] The method according to this aspect of the invention is
useful in animal models of disease or gene expression, and is
further useful for the therapeutic treatment of human or animal
disease.
[0039] In a fourth aspect, the invention provides a method for
inducing an immune response in a mammal, including a human, the
method comprising administering to the mammal a compound comprising
a CpG dinucleotide and an immunomodulatory moiety, wherein the
compound has greater immunostimulatory effect than a similar
compound lacking the immunomodulatory moiety.
[0040] In the methods according to this aspect of the invention,
preferably, administration of compounds should be parenteral, oral,
sublingual, transdermal, topical, intranasal, intratracheal, or
intrarectal. Administration of the therapeutic compositions can be
carried out using known procedures at dosages and for periods of
time effective to reduce symptoms or surrogate markers of the
disease. When administered systemically, the therapeutic
composition is preferably administered at a sufficient dosage to
attain a blood level of oligonucleotide from about 0.001 micromolar
to about 10 micromolar. For localized administration, much lower
concentrations than this may be effective, and much higher
concentrations may be tolerated. Preferably, a total dosage of
oligonucleotide will range from about 0.1 mg oligonucleotide per
patient per day to about 200 mg oligonucleotide per kg body weight
per day. It may be desirable to administer simultaneously, or
sequentially a therapeutically effective amount of one or more of
the therapeutic compositions of the invention to an individual as a
single treatment episode. In a preferred embodiment, after the
composition of matter is administered, one or more measurement is
taken of biological effects selected from the group consisting of
complement activation, mitogenesis and inhibition of thrombin clot
formation.
[0041] In certain preferred embodiments, compounds according to the
invention are administered in combination with vaccines,
antibodies, cytotoxics, antisense oligonucleotides, gene therapy
vectors, DNA vaccines and/or adjuvants to enhance the specificity
or magnitude of the immune response. Either the compound or the
vaccine, or both may optionally be linked to an immunogenic
protein, such as keyhole limpet hemocyanin, cholera toxin B
subunit, or any other immunogenic carrier protein. Any of the
plethora of adjuvants may be used, including, without limitation,
Freund's complete adjuvant. For purposes of this aspect "in
combination with" means in the course of treating the same `disease
in the same patient, and includes administering the oligonucleotide
and/or the vaccine and/or the adjuvant in any order, including
simultaneous administration, as well as temporally spaced order of
up to several days apart. Such combination treatment may also
include more than a single administration of the oligonucleotide,
and/or independently the vaccine, and/or independently the
adjuvant. The administration of the oligonucleotide and/or vaccine
and/or adjuvant may be by the same or different routes.
[0042] The method according to this aspect of the invention is
useful for model studies of the immune system, and is further
useful for the therapeutic treatment of human or animal
disease.
[0043] For purposes of all aspects of the invention, the term
"oligonucleotide" includes polymers of two or more
deoxyribonucleotides, or any modified nucleoside, including
2'-halo-nucleosides, 2' or 3' substituted, 2' or 3'-O-substituted
ribonucleosides, deazanucleosides or any combination thereof. Such
monomers may be coupled to each other by any of the numerous known
internucleoside linkages. In certain preferred embodiments, these
internucleoside linkages may be phosphodiester, phosphotriester,
phosphorothioate, or phosphoramidate linkages, 2'-5' linkages of
any of the forgoing, or combinations thereof. The term
oligonucleotide also encompasses such polymers having chemically
modified bases or sugars and/or having additional substituents,
including without limitation lipophilic groups, intercalating
agents, diamines and adamantane. The term oligonucleotide also
encompasses PNA, LNA and oligonucleotides comprising non-pentose
sugar (e.g. hexose) backbones or backbone sections. For purposes of
the invention the terms "2'-O-substituted" and "3'-O-substituted"
mean (respectively) substitution of the 2' (or 3') position of the
pentose moiety with a halogen (preferably Cl, Br, or F), or an
-O-lower alkyl group containing 1-6 saturated or unsaturated carbon
atoms, or with a -O-aryl or allyl group having 2-6 carbon atoms,
wherein such alkyl, aryl or allyl group may be unsubstituted or may
be substituted, e.g., with halo, hydroxy, trifluoromethyl, cyano,
nitro, acyl, acyloxy, alkoxy, carboxyl, carbalkoxyl, or amino
groups; or such 2' substitution may be with a hydroxy group (to
produce a ribonucleoside), an amino or a halo group, but not with a
2' (or 3') H group. For purposes of all aspects of the invention,
the terms "CpG" or "CpG dinucleotide" means the dinucleotide
5'-deoxycytidine-deoxyguanidine or deoxyguanidine analog-3',
wherein p is an internucleotide linkage, and wherein the sugar
backbone of the dinucleotide may be ribose, deoxyribose, or 2'
substituted ribose, or combinations thereof. In preferred
embodiments of the first three aspects of the invention, p is
selected from phosphodiester, phosphorothioate, alkylphosphonate,
phosphotriester, stereospecific (Rp or Sp) phosphorothioate or
alkylphosphonate, and 2'-5' covalent linkages of any of the above.
The non-phosphodiester, non-phosphorothioate embodiments will
further reduce immunostimulatory effects. In preferred embodiments
of the last three aspects of the invention, p is selected from
phosphodiester, phosphorothioate and phosphorodithioate.
[0044] The following examples are intended to further illustrate
certain preferred embodiments of the invention, and are not
intended to limit the scope of the invention.
EXAMPLE 1
Modulation of Immunostimulatory Effect in Vitro
[0045] To study the impact of site of chemical modification of
PS-oligos containing CpG motif, we chose two oligonucleotides.
Oligo 1 and Oligo 2, each of which contains one CpG motif To
evaluate the immunostimulatory activity of oligonucleotides in the
present study, we will use a mouse spleen cell proliferation
assay.
[0046] Mouse spleen lymphocytes are cultured with oligonucleotides
at concentration of 0.1, 1, and 10 .mu.g/mL. Oligo 1 and Oligo 2
will induce a dose dependent effect on cell proliferation. At 0.1
.mu.g/mL, the proliferation index will increase. Substitution of
5'-flanking deoxynucleoside (Y1) of CpG motif of Oligo 1 or Oligo 2
with an immunomodulatory moiety according to the invention will
result in complete suppression of cell proliferation at all
concentrations used (FIG. 1). At 0.1 .mu.g/mL, cell proliferation
index will be similar to medium alone. Substitution of the
3'-flanking deoxynucleoside (X1) of CpG motif of Oligo 1 or Oligo 2
with 2'-OMe will not have such an impact on cell proliferation, but
may reduce it slightly. Similar substitutions are made in Oligo 1
or Oligo 2 in the 3'-flanking region to CpG motif. Oligos are
synthesized in which a deoxynucleoside is substituted with an
immunomodulatory moiety according to the invention at position X3,
X4, X5 or X6. The proliferation index of these oligos will
increase.
EXAMPLE 2
Effect of Immunomodulatory Moieties on Spleen Weight
[0047] After observing that above substitutions in modulates its
immunostimulatory activity based on cell culture assay, we
administer oligonucleotides listed in Table 1 intraperitonealy to
mice and measure the spleen weights to confirm that the
substitutions have similar effects in vivo. Administration of Oligo
1 or Oligo 2 will cause substantial increase in spleen weight.
Substitution of a deoxynucleotide away from CpG motif towards
5'-end, positions Y6, Y5, Y4 or Y3 will cause progressive increase
in spleen weights confirming an increase in their immunostimulatory
activity. Substitutions of a deoxynucleoside toward the 3'-end of
the CpG motif, in general, will cause less significant increase in
spleen weight. Data are shown in FIGS. 2 and 3.
EXAMPLE 3
Synthesis of Oligonucleotides Containing Immunomodulatory
Moieties
[0048] Oligonucleotides are synthesized on 1 micromolar scale using
an automated DNA synthesizer (Expedite 8909, PerSeptive Biosystems,
Foster City, Calif.). Standard deoxynucleoside phosphoramidites are
obtained from PerSeptive Biosystems. 1',2'-dideoxyribose
phosphoramidite, propyl-1-phosphoramidite,
2'-deoxy-5-nitroindole-ribofuranosyl phosphoramidite, deoxyuridine
phosphoramidite, dP phosphoramidite, d-2-aminopurine
phosphoramidite, d-nebularine phosphoramidite and d-7-deazaguanine
phosphoramidite are obtained from Glen Research (Sterling, Va.).
Deoxyinosine phosphoramidite is obtained from ChemGenes (Ashland,
Mass.). Normal coupling cycles are used for all phosphoramidites.
Beaucage reagent is used as an oxidant to obtain phosphorothioate
modification. After synthesis, oligonucleotides are deprotected by
incubating CPG-bound oligonucleotide with concentrated ammonium
hydroxide solution for 1.5-2 hours at room temperature and then
incubating the ammonium hydroxide supernatant for 12 hours at 55
degrees C. The ammonium hydroxide solution is evaporated to dryness
in a speed-vac and 5'-DMTr-oligonucleotides are purified by HPLC on
a C18 reverse-phase matrix using a solvent system of 0.1 M ammonium
acetate and 1:5 ratio 0.1 M ammonium acetate in acetonitrile. Then
the oligonucleotides are treated with 80% acetic acid to remove the
DMTr group, converted to sodium form and desalted by dialysis
against distilled water. Oligonucleotides are lyophilized and
redissolved in water. Characterization is achieved by denaturing
PAGE and MALDI-TOF mass spectrometry.
Sequence CWU 1
1
6118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 1ctatctgacg ttctctgt 18218DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 2ctanntgacg ttctctgt 18318DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 3ctatctgang ttctctgt 18418DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 4cctactagcg ttctcatc 18518DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 5cctnntagcg ttctcatc 18618DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 6cctactagng ttctcatc 18
* * * * *