U.S. patent application number 12/643578 was filed with the patent office on 2010-07-08 for antiviral oligonucleotides targeting rsv.
Invention is credited to Jean-Marc JUTEAU, Andrew VAILLANT.
Application Number | 20100173980 12/643578 |
Document ID | / |
Family ID | 31997929 |
Filed Date | 2010-07-08 |
United States Patent
Application |
20100173980 |
Kind Code |
A1 |
VAILLANT; Andrew ; et
al. |
July 8, 2010 |
ANTIVIRAL OLIGONUCLEOTIDES TARGETING RSV
Abstract
Random sequence oligonucleotides that have antiviral activity
are described, along with their use as antiviral agents. In many
cases, the oligonucleotides are greater than 40 nucleotides in
length. Also described are methods for the prophylaxis or treatment
of a viral infection in a human or animal, and a method for the
prophylaxis treatment of cancer caused by oncoviruses in a human or
animal. The methods typically involve administering to a human or
animal in need of such treatment, a pharmacologically acceptable,
therapeutically effective amount of at least oligonucleotide that
does not act by a sequence complementary mode of action.
Inventors: |
VAILLANT; Andrew; (Roxboro,
CA) ; JUTEAU; Jean-Marc; (Blainville, CA) |
Correspondence
Address: |
OGILVY RENAULT LLP
1, Place Ville Marie, SUITE 2500
MONTREAL
QC
H3B 1R1
CA
|
Family ID: |
31997929 |
Appl. No.: |
12/643578 |
Filed: |
December 21, 2009 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10661415 |
Sep 12, 2003 |
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12643578 |
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PCT/IB03/04573 |
Sep 11, 2003 |
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10661415 |
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60430934 |
Dec 5, 2002 |
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60410264 |
Sep 13, 2002 |
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Current U.S.
Class: |
514/44R |
Current CPC
Class: |
Y02A 50/385 20180101;
C12N 2310/315 20130101; C12N 2310/321 20130101; A61K 38/00
20130101; Y02A 50/393 20180101; C12N 15/11 20130101; A61P 35/00
20180101; A61K 45/06 20130101; C12N 15/115 20130101; A61P 31/12
20180101; C12N 2310/351 20130101; A61P 31/18 20180101; C12N
2310/3125 20130101; A61P 25/28 20180101; Y02A 50/387 20180101; A61P
25/00 20180101; A61P 31/16 20180101; A61P 31/20 20180101; Y02A
50/30 20180101; A61K 31/7088 20130101; A61P 31/22 20180101; A61P
31/14 20180101; A61K 31/7088 20130101; A61K 2300/00 20130101; C12N
2310/321 20130101; C12N 2310/3521 20130101 |
Class at
Publication: |
514/44.R |
International
Class: |
A61K 31/7088 20060101
A61K031/7088; A61P 31/12 20060101 A61P031/12 |
Claims
1. A method for the prophylaxis or treatment of a RSV or
parainfluenza virus infection in a subject, comprising
administering to a subject in need of such treatment a
therapeutically effective amount of a pharmacological acceptable
oligonucleotide of at least 20 nucleotides in length, wherein said
oligonucleotide comprises at least 19 phosphorothioated linkages,
does not comprise a CpG motif, does not have a complement in the
genomic sequence of RSV or parainfluenza virus, and wherein the
anti-viral activity of said oligonucleotide occurs principally by a
non-sequence complementary mode of action.
2. The method of claim 1, wherein said oligonucleotide is a
heteropolymer comprised of two different nucleic acids selected
from the group consisting of adenosine, guanosine, cytosine and
thymine.
3. The method of claim 1, wherein said oligonucleotide is a
heteropolymer comprised of alternating adenosine and cytosine
residues.
4. The method of claim 1, wherein said oligonucleotide is SEQ ID
NO:24.
5. The method of claim 1, wherein said oligonucleotide is a
heteropolymer comprised of alternating adenosine and guanosine
residues.
6. The method of claim 1, wherein said oligonucleotide is SEQ ID
NO:26.
7. The method of any of claims 1 to 6, wherein said oligonucleotide
comprises at least one phosphodiester linkage.
8. The method of any of claims 1 to 6, wherein said oligonucleotide
comprises at least one modification to its chemical structure.
9. The method of any of claims 1 to 6, wherein said oligonucleotide
comprises at least one 2' modification to the ribose moiety.
10. The method of any of claims 1 to 6, wherein said
oligonucleotide comprises at least one 2'-O methyl modification to
the ribose moiety.
11. The method of any of claims 1 to 6, wherein said
oligonucleotide comprises at least one 2'-O (2-methoxyethyl)
modification to the ribose moiety.
12. The method of any of claims 1 to 6, wherein said
oligonucleotide has all ribose moieties modified with a 2'
modification.
13. The method of any of claims 1 to 6, wherein said
oligonucleotide has all ribose moieties modified with a 2'-O methyl
modification.
14. The method of any of claims 1 to 6, wherein said
oligonucleotide has all ribose moieties modified with a 2'-O
(2-methoxyethyl) modification.
15. The method of any of claims 1 to 6, wherein said
oligonucleotide comprises at least one methylphosphonate
linkage.
16. The method of any of claims 1 to 6, wherein said
oligonucleotide comprises at least one phosphorodithioated
linkage.
17. The method of any of claims 1 to 6, wherein said
oligonucleotide comprises at least one locked nucleic acid.
18. The method of any of claims 1 to 6, wherein said
oligonucleotide is a concatamer consisting to two or more
oligonucleotide sequences joined by a linker.
Description
RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 10/661,415, filed Sep. 12, 2003, entitled ANTIVIRAL
OLIGONUCLEOTIDES TARGETING RSV, which is a continuation-in-part of
PCT Appl. PCT/IB03/04573, filed Sep. 11, 2003; said application
Ser. No. 10/661,415 also claims the benefit of U.S. Provisional
Appl. 60/430,934, filed Dec. 5, 2002 and of U.S. Provisional Appl.
60/410,264, filed Sep. 13, 2002, all of which are incorporated
herein by reference in their entireties, including drawings.
FIELD OF THE INVENTION
[0002] The present invention relates to oligonucleotides having
antiviral activities and their use as therapeutic agents in viral
infections caused by human and animal viruses and in cancers caused
by oncogene viruses and in other diseases whose etiology is
viral-based.
BACKGROUND OF THE INVENTION
[0003] The following discussion is provided solely to assist the
understanding of the reader, and does not constitute an admission
that any of the information discussed or references cited
constitute prior art to the present invention.
[0004] Many important infectious diseases afflicting mankind are
caused by viruses. Many of these diseases, including rabies,
smallpox, poliomyelitis, hepatitis, yellow fever, immune
deficiencies and various encephalitic diseases, are frequently
fatal. Others are significant in that they are highly contagious
and create acute discomfort such as influenza, measles, mumps and
chickenpox, as well as respiratory or gastrointestinal disorders.
Others such as rubella and cytomegalovirus can cause congenital
abnormalities. Finally there are viruses, known as oncoviruses,
which can cause cancer in humans and animals.
[0005] Among viruses, the family of Herpesviridae is of great
interest. The Herpesviridae are a ubiquitous class of icoshedral,
double stranded DNA viruses. Of over 100 characterized members of
Herpesviridae (HHV), only eight infect humans. The best known among
these are Herpes simplex type 1 (HSV-1), Herpes simplex type 2
(HSV-2), Varicella zoster (chicken pox or shingles),
cytomegalovirus (CMV) and Epstein-Barr virus (EBV). The prevalence
of Herpes viruses in humans is high, affecting at least one third
of the worldwide population; and in the United States, 70-80% of
the population have some kind of Herpes infection. While the
pathology of Herpes infections are usually not dangerous, as in the
case of HSV-1 which usually only causes short lived lesions around
the mouth and face, these viruses are also known to be the cause of
more dangerous symptoms, which vary from genital ulcers and
discharge to fetal infections which can lead to encephalitis (15%
mortality) or disseminated infection (40% mortality).
[0006] Herpes viruses are highly disseminated in nature and highly
pathogenic for man. For example, Epstein-Barr virus (EBV) is known
to cause infectious mononucleosis in late childhood or adolescence
or in young adults. The hallmarks of acute infectious mononucleosis
are sore throat, fever, headache, lymphadenopathy, enlarged tonsils
and atypical, dividing lymphocytes in the peripheral blood. Other
manifestations frequently include mild hepatitis, splenomegaly and
encephalitis. EBV is also associated with two forms of cancer:
Burkitt's lymphoma (BL) and the nasopharyngeal carcinoma (NPC). In
endemic areas of equatorial Africa, BL is the most common childhood
malignancy, accounting for approximately 80% of cancers in
children. While moderately observed in North American Caucasians,
NPC is one of the most common cancers in Southern China with age
incidence of 25 to 55 years. EBV, like the cytomegalovirus, is also
associated with post-transplant lymphoproliferative disease, which
is a potentially fatal complication of chronic immunosuppression
following solid organ or bone marrow transplantation.
[0007] Other diseases are also associated with HSV, including skin
and eye infections, for example, chorioretinitis or
keratoconjunctivitis. Approximately 300,000 cases of HSV infections
of the eye are diagnosed yearly in the United States.
[0008] AIDS (acquired immunodeficiency syndrome) is caused by the
human immunodeficiency virus (HIV). By killing or damaging cells of
the body's immune system, HIV progressively destroys the body's
ability to fight infections and certain cancers. There are
currently approximately 42 million people living with HIV/AIDS
worldwide. A total of 3.1 million people died of HIV/AIDS related
causes in 2002. The ultimate goal of anti-HIV drug therapy is to
prevent the virus from reproducing and damaging the immune system.
Although substantial progress has been made over the past fifteen
years in the fight against HIV, a cure still eludes medical
science. Today, physicians have more than a dozen antiretroviral
agents in three different drug classes to manage the disease.
Typically, drugs from two or three classes are prescribed in a
variety of combinations known as HAART (Highly Active
AntiRetroviral Treatment). HAART therapies typically comprise two
nucleoside reverse transcriptase inhibitors drugs with a third
drug, either a protease inhibitor or a non-nucleoside reverse
transcriptase inhibitor. Clinical studies have shown that HAART is
the most effective means of reducing viral loads and minimizing the
likelihood of drug resistance.
[0009] While HAART has been shown to reduce the amount of HIV in
the body, commonly known as viral load, tens of thousands of
patients encounter significant problems with this therapy. Some
side effects are serious and include abnormal fat metabolism,
kidney stones, and heart disease. Other side effects such as
nausea, vomiting, and insomnia are less serious, but still
problematic for HIV patients that need chronic drug therapy for a
lifetime.
[0010] Currently approved anti-HIV drugs work by entering an HIV
infected CD4+ T cell and blocking the function of a viral enzyme,
either the reverse transcriptase or a protease. HIV needs both of
these enzymes in order to reproduce. However, HIV frequently
mutates and become resistant, rendering reverse transcriptase or
protease inhibitor drugs ineffective. Once resistance occurs, viral
loads increase and dictate the need to switch the ineffective agent
for another antiretroviral agent. Unfortunately, when a virus
becomes resistant to one drug in a class, other drugs in that class
may become less effective. This phenomenon known as
cross-resistance, occurs because many anti-HIV drugs work in
similar manners. The occurrence of drug cross-resistance is highly
undesirable because it reduces the available number of treatment
options for patients.
[0011] There is therefore a great need for the development of other
antiviral agents effective against HIV that work through other
mechanisms of action against which the virus has not developed
resistance. This is becoming especially important in view of recent
data showing that 1 out of 10 patients newly diagnosed with HIV in
Europe, is infected with a strain of HIV already resistant to at
least one of the approved drug on the market.
[0012] Respiratory syncytial virus (RSV) causes upper and lower
respiratory tract infections. It is a negative-sense, enveloped RNA
virus and is highly infectious. It commonly affects young children
and is the most common cause of lower respiratory tract illness in
infants. RSV infections are usually associated with
moderate-to-severe cold-like symptoms. However, severe lower
respiratory tract disease may occur at any age, especially in
elderly or immunocompromised patients. Children with severe
infections may require oxygen therapy and, in certain cases,
mechanical ventilation. According to the American Medical
Association, an increasing number of children are being
hospitalized for bronchiolitis, often caused by RSV infection. RSV
infections also account for approximately one-third of
community-associated respiratory virus infections in patients in
bone marrow transplant centers. In the elderly population, RSV
infection has been recently recognized to be very similar in
severity to influenza virus infection.
[0013] Influenza (INF), also known as the flu, is a contagious
disease that is caused by the influenza virus. It attacks the
respiratory tract in humans (nose, throat, and lungs). An average
of about 36,000 people per year in the United States die from
influenza, and 114,000 per year require hospitalization as a result
of influenza.
[0014] In all infectious diseases, the efficacy of a given therapy
often depends on the host immune response. This is particularly
true for herpes viruses, where the ability of all herpes viruses to
establish latent infections results in an extremely high incidence
of reactivated infections in immunocompromised patients. In renal
transplant recipients, 40% to 70% reactivate latent HSV infections,
and 80% to 100% reactivate CMV infections. Such viral reactivations
have also been observed with AIDS patients.
[0015] The hepatitis B virus (HBV) is a DNA virus that belongs to
the Hepadnaviridae family of viruses. HBV causes hepatitis B in
humans. It is estimated that 2 billion people have been infected (1
out of 3 people) in the world. About 350 million people remain
chronically infected and an estimated 1 million people die each
year from hepatitis B and its complications. HBV can cause lifelong
infection, cirrhosis of the liver, liver cancer, liver failure, and
death. The virus is transmitted through blood and bodily fluids.
This can occur through direct blood-to-blood contact, unprotected
sex, use of unsterile needles, and from an infected woman to her
newborn during the delivery process. Most healthy adults (90%) who
are infected will recover and develop protective antibodies against
future hepatitis B infections. A small number (5-10%) will be
unable to get rid of the virus and will develop chronic infections
while 90% of infants and up to 50% of young children develop
chronic infections when infected with the virus. Alpha-interferon
is the most frequent type of treatment used. Significant side
effects are related to this treatment including flu-like symptoms,
depression, rashes, other reactions and abnormal blood counts.
Another treatment option includes 3TC which also has many side
effects associated with its use. In the last few years, there has
been an increasing number of reports showing that patients treated
with 3TC are developing resistant strains of HBV. This is
especially problematic in the population of patients who are
co-infected with HBV and HIV. There is clearly an urgent need to
develop new antiviral therapies against this virus.
[0016] Hepatitis C virus (HCV) infection is the most common chronic
bloodborne infection in the United States where the number of
infected patients likely exceeds 4 million. This common viral
infection is a leading cause of cirrhosis and liver cancer, and is
now the leading reason for liver transplantation in the United
States. Recovery from infection is uncommon, and about 85 percent
of infected patients become chronic carriers of the virus and 10 to
20 percent develop cirrhosis. It is estimated that there are
currently 170 million people worldwide who are chronic carriers.
According to the Centers for Disease Control and Prevention,
chronic hepatitis C causes between 8,000 and 10,000 deaths and
leads to about 1,000 liver transplants in the United States alone
each year. There is no vaccine available for hepatitis C. Prolonged
therapy with interferon alpha, or the combination of interferon
with Ribavirin, is effective in only about 40 percent of patients
and causes significant side effects.
[0017] Today, the therapeutic outlook for viral infections in
general is not favourable. In general, therapies for viruses have
mediocre efficacies and are associated with strong side effects
which either prevent the administration of an effective dosage or
prevent long term treatment. Three clinical situations which
exemplify these problems are herpesviridae, HIV and RSV
infections.
[0018] In the case of herpesviridae, there are five major
treatments currently approved for use in the clinic: idoxuridine,
vidarabine, acyclovir, foscarnet and ganciclovir. While having
limited efficacy, these treatments are also fraught with side
effects. Allergic reactions have been reported in 35% of patients
treated with idoxuridine, vidarabine can result in
gastrointestional disturbances in 15% of patients and acyclovir,
foscarnet and ganciclovir, being nucleoside analogs, affect DNA
replication in host cells. In the case of ganciclovir, neutropenia
and thrombocytopenia are reported in 40% of AIDS patients treated
with this drug.
[0019] While there are many different drugs currently available for
the treatment of HIV infections, all of these are associated with
side effects potent enough to require extensive supplemental
medication to give patients a reasonable quality of life. The
additional problem of drug resistant strains of HIV (a problem also
found in herpesviridae infections) usually requires periodic
changing of the treatment cocktail and in some cases, makes the
infection extremely difficult to treat.
[0020] The treatment of RSV infections in young infants is another
example of the urgent need for new drug development. In this case,
the usual line of treatment is to deliver Ribavirin by inhalation
using a small-particule aerosol in an isolation tent. Not only is
Ribavirin only mildly effective, but its uses is associated with
significant side effects. In addition, the potential release of the
drug has caused great concern in hospital personnel because of the
known teratogenicity of Ribavirin.
[0021] It is clear that for any new emerging antiviral drug being
developed, it would be highly desirable to incorporate the three
following features: 1--improved efficacy; 2--reduced risks of side
effects and 3--a mechanism of action which is difficult for the
virus to overcome by mutation.
[0022] Several attempts to inhibit particular viruses by various
antisense approaches have been made.
[0023] Zamecnik et al. have used ONs specifically targeted to the
reverse transcriptase primer site and to splice donor/acceptor
sites (Zamecnik, et at (1986) Proc. Natl. Acad. Sci. USA 83:4143-)
(Goodchild & Zamecnik (1989) U.S. Pat. No. 4,806,463).
[0024] Crooke and coworkers. (Crooke et al. (1992) Antimicrob.
Agents Chemother. 36:527-532) described an antisense against
HSV-1.
[0025] Draper et al. (1993) (U.S. Pat. No. 5,248,670) have reported
antisense oligonucleotides having anti-HSV activity containing the
Cat sequence and hybridizing to the HSV-1 genes UL13, UL39 and
UL40.
[0026] Kean et al. (Biochemistry (1995) 34:14617-14620) have tested
antisense methylphosphonate oligomers as anti-HSV agents.
[0027] Peyman et al. (Biol Chem Hoppe Seyler (1995) March;
376:195-198) have reported testing specific antisense
oligonucleotides directed against the IE110 and the UL30 mRNA of
HSV-1 for their antiviral properties.
[0028] Oligonucleotides or oligonucleotide analogs targeting CMV
mRNAs coding for IE1, IE2 or DNA polymerase were reported by
Anderson et at (1997) (U.S. Pat. No. 5,591,720)
[0029] Hanecak et at (1999) (U.S. Pat. No. 5,952,490) have
described modified oligonucleotides having a conserved G quartet
sequence and a sufficient number of flanking nucleotides to
significantly inhibit the activity of a virus such as HSV-1.
[0030] Jairath et al (Antiviral Res. (1997) 33:201-213) have
reported antisense oligonucleotides against RSV.
[0031] Torrence et at (1999) (U.S. Pat. No. 5,998,602) have
reported compounds comprising an antisense component complementary
to a single stranded portion of the RSV antigenomic strand (the
mRNA strand), a linker and a oligonucleotide activator of RNase
L.
[0032] Qi et al. (Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi
(2000) 14:253-256) have reported testing antisense PS-ODNs in
Coxsackie virus 83.
[0033] International publication WO9203051 (Roizman and Maxwell)
describes methylphosphonate antisense oligomers which are
complementary to vital regions of HSV viral genome or mRNA
transcripts thereof which exhibit antiviral activity.
[0034] Guanosine/thymidine or guanosine-rich phosphorothioate
oligodeoxynucleotides (GT-PS-ODNs) have been reported to have
antiviral activity. The article stated that "several different
PS-containing GT-rich ODNs (B106-140, I100-12, and G106-57) all 26
or 27 nt in length, were just as effective at reducing HIV-2 titers
as GT-rich ODNs consisting of 36 (B106-96, B106-97) or 45 nt (Table
4)." (Fennewald et al., Antiviral Res. (1995) 26:37-54).
[0035] In U.S. Pat. No. 6,184,369, anti-HIV, anti-HSV, and anti-CMV
oligonucleotides containing a high percentage of guanosine bases
are described. In preferred embodiments, the oligonucleotide has a
three dimensional structure and this structure is stabilized by
guanosine tetrads. In a further embodiment, the oligonucleotide
compositions of the invention have two or more runs of two
contiguous deoxyguanosines The patent claims a G-rich ODN that
includes at least two G residues in at least two positions.
[0036] Cohen et al. (U.S. Pat. Nos. 5,264,423 and 5,276,019)
described the inhibition of replication of HIV, and more
particularly to PS-ODN analogs that can be used to prevent
replication of foreign nucleic acids in the presence of normal
living cells. Cohen et al describe antiviral activity of antisense
PS-ODNs specific to a viral sequence. They also describe testing
polyA, polyT and polyC PS-ODN sequences of 14, 18, 21 and 28-mers
and indicate an antiviral effect of those PS-ODNs.
[0037] Matsukura et al. (Matsukura et at (1987) Proc Natl Acad Sci
USA 84:7706-7710) later published the result described in Cohen et
al, US patents above.
[0038] Gao et at (Gao et at (1989) J Biol Chem 264 :11521-11526),
describe the inhibition of replication of HSV-2, by PS-ODNs by
testing of polyA, polyT and polyC PS-ODN sequences in sizes of 7,
15, 21 and 28 nucleotides.
[0039] Archambault, Stein and Cohen (Archambault et at (1994) Arch
Virol 139:97109) report that a PS-ODN polyC of 28 nucleotides is
not effective against HSV-1.
[0040] Stein et al (Stein et al. (1989) AIDS Res Hum Retrovir
5:639-646), published results concerning additional data on
anti-HIV ODNs, generally of 21-28 nucleotides in length.
[0041] Marshal et al. (Marshall et al. (1992) Proc. Natl. Acad.
Sci. USA 89:6265-6269) describe anti-HIV-1 effect of
phosphorothioate and phosphorothioate poly-C oligos of 4-28
nucleotides in length.
[0042] Stein & Cheng (Stein et al. (1993) Science
261:1004-1012), in a review article, mention the antiviral activity
of non specific ODNs of 28 nucleotides, stating that "the anti-HIV
properties of PS oligos are significantly influenced by
non-sequence-specific effects, that is, the inhibitory effect is
independent of the base sequence."
[0043] In a review article Lebedeva & Stein (Lebedeva et at
(2001) Annul Rev Pharmacol 41:403-419) report a variety of
non-specific protein binding activity of PS-ODNs, including viral
proteins. They state that "these molecules are highly biologically
active, and it is often relatively easy to mistake artifact for
antisense".
[0044] Rein et al. (U.S. Pat. No. 6,316,190) reported a GT rich ON
decoy linked to a fusion partner and binding to the HIV
nucleocapsid, which can be used as an antiviral compound.
Similarly, Campbell et al. (Campbell et al (1999) J. Virol. 73
:2270-2279) reported PO-ODN with a TGTGT motif binding specifically
to the nucleocapsid of HIV but with no references to an antiviral
activity.
[0045] Feng at al. (Feng et al. (2002) J. Virol. 76 :11757-11762)
described A(n) and TG(n) PO-ODNs binding to the recombinant HIV
nucleocapsid but with no data nor references to an anti-HIV
activity.
[0046] Antisense ODNs developed as anticancer agents, antiviral
agents, or to treat others diseases are typically approximately 20
nucleotides in length. In a review article (Stein, Calif., (2001)
J. Clin. Invest. 108:641-644), it is affirmed that "the length of
an antisense oligonucleotide must be optimized: If the antisense
oligonucleotide is either too long or too short, an element of
specificity is lost. At the present time, the optimal length for an
antisense oligonucleotide seems to be roughly 16-20 nucleotides".
Similarly, in another review article (Crooke, ST (2000) Methods
Enzymol. 313:3-45) it is stated that "Compared to RNA and RNA
duplex formation, a phosphorothioate oligodeoxynucleotide has a
T.sub.m approximately -2.2.degree. lower per unit. This means that
to be effective in vitro, phosphorothioate oligodeoxynucleotides
must typically be 17- to .about.20-mer in length . . . ".
[0047] Caruthers and co-workers (Marshall et al. (1992) Proc. Natl.
Acad. Sci. USA 89:6265-6269) reported anti-HIV activity of
phosphorodithioate ODNs (PS2-ODNs) for a 12mer polycytidine-PS2-ODN
and for a 14mer PS2-ODN. No other sizes were tested for anti-HIV
activity. They also reported the inhibition of HIV reverse
transcriptase (RT) for 12, 14, 20 and 28mer polycytidine-PS2-ODNs.
Later, (Marshal et al (1993) Science 259:1564-1570) reported
results showing sequence specific inhibition of the HIV RT. The
same group published data for PS2-ODNs in several patents. In U.S.
Pat. Nos. 5,218,103 and 5,684,148, PS2-ODN structure and synthesis
is described. In U.S. Pat. Nos. 5,452,496, 5,278,302, and 5,695,979
inhibition of HIV RT is described for PS2-ODNs not longer than 15
bases. In U.S. Pat. Nos. 5,750,666 and 5,602,244, antisense
activity of PS2-ODNs is described.
SUMMARY OF THE INVENTION
[0048] The present invention involves the discovery that
oligonucleotides (ONs), e.g., oligodeoxynucleotides (ODNs), can
have a broadly applicable, non-sequence complementary antiviral
activity. Thus, it is not necessary for the oligonucleotide to be
complementary to any viral sequence or to have a particular
distribution of nucleotides in order to have antiviral activity.
Such an oligonucleotide can even be prepared as a randomer, such
that there will be at most a few copies of any particular sequence
in a preparation, e.g., in a 15 micromol randomer preparation 32 or
more nucleotides in length.
[0049] In addition, the inventors discovered that different length
oligonucleotides have varying antiviral effect, and further that
the length of antiviral oligonucleotide that produces maximal
antiviral effect is in the range of 40-120 nucleotides. In view of
the present discoveries concerning antiviral properties of
oligonucleotides, this invention provides oligonucleotide antiviral
agents that can have activity against numerous different viruses,
and can even be selected as broad-spectrum antiviral agents. Such
antiviral agents are particularly advantageous in view of the
limited antiviral therapeutic options currently available.
[0050] Therefore, the ONs, e.g., ODNs, of the present invention are
useful in therapy for treating or preventing viral infections or
for treating or preventing tumors or cancers induced by viruses,
such as oncoviruses (e.g., retroviruses, papillomaviruses, and
herpesviruses), and in treating or preventing other diseases whose
etiology is viral-based. Such treatments are applicable to many
types of patients and treatments, including, for example, the
prophylaxis or treatment of viral infections in immunosuppressed
human and animal patients.
[0051] In a first aspect, the invention provides an antiviral
oligonucleotide formulation that includes at least one antiviral
oligonucleotide, e.g., at least 6 nucleotides in length, adapted
for use as an antiviral agent, where the antiviral activity of the
oligonucleotide occurs principally by a non-sequence complementary
mode of action. Such a formulation can include a mix of different
oligonucleotides, e.g., at least 2, 3, 5, 10, 50, 100, or even
more.
[0052] As used herein in connection with oligonucleotides or other
materials, the term "antiviral" refers to an effect of the presence
of the oligonucleotides or other material in inhibiting production
of viral particles, i.e., reducing the number of infectious viral
particles formed, in a system otherwise suitable for formation of
infectious viral particles for at least one virus. In certain
embodiments of the present invention, the antiviral
oligonucleotides will have antiviral activity against multiple
different virus.
[0053] The term "antiviral oligonucleotide formulation" refers to a
preparation that includes at least one antiviral oligonucleotide
that is adapted for use as an antiviral agent. The formulation
includes the oligonucleotide or oligonucleotides, and can contain
other materials that do not interfere with use as an antiviral
agent in vivo. Such other materials can include without restriction
diluents, excipients, carrier materials, and/or other antiviral
materials.
[0054] As used herein, the term "pharmaceutical composition" refers
to an antiviral oligonucleotide formulation that includes a
physiologically or pharmaceutically acceptable carrier or
excipient. Such compositions can also include other components that
do not make the composition unsuitable for administration to a
desired subject, e.g., a human.
[0055] In the context of the present invention, unless specifically
limited the term "oligonucleotide (ON)" means oligodeoxynucleotide
(ODN) or oligodeoxyribonucleotide or oligoribonucleotide. Thus,
"oligonucleotide" refers to an oligomer or polymer of ribonucleic
acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof. This
term includes oligonucleotides composed of naturally-occurring
nucleobases, sugars and covalent internucleoside (backbone)
linkages as well as oligonucleotides having non-naturally-occurring
portions which function similarly. Such modified or substituted
oligonucleotides are often preferred over native forms because of
desirable properties such as, for example, enhanced cellular
uptake, enhanced affinity for nucleic acid target and increased
stability in the presence of nucleases. Examples of modifications
that can be used are described herein. Oligonucleotides that
include backbone and/or other modifications can also be referred to
as oligonucleosides.
[0056] As used in connection with an antiviral formulation,
pharmaceutical composition, or other material, the phrase "adapted
for use as an antiviral agent" indicates that the material exhibits
an antiviral effect and does not include any component or material
that makes it unsuitable for use in inhibiting viral production in
an in vivo system, e.g., for administering to a subject such as a
human subject.
[0057] As used herein in connection with antiviral action of a
material, the phrase "non-sequence complementary mode of action"
indicates that the mechanism by which the material exhibits an
antiviral effect is not due to hybridization of complementary
nucleic acid sequences, e.g., an antisense effect. Conversely, a
"sequence complementary mode of action" means that the antiviral
effect of a material involves hybridization of complementary
nucleic acid sequences. Thus, indicating that the antiviral
activity of a material is "not primarily due to a sequence
complementary mode of action" means that the activity of the
oligonucleotide satisfies at least one of the 4 tests provided
herein (see Example, 10) for determining whether the antiviral
activity is "not primarily due to a sequence complementary mode of
action". In particular embodiments, the oligonucleotide satisfies
test 1, test 2, test 3, or test 4; the oligonucleotide satisfies a
combination of two of the tests, i.e., tests 1 & 2; tests 1
& 3; tests 1 & 4, tests 2 & 3, tests 2 & 4, or
tests 3 & 4; the oligonucleotide satisfies a combination of 3
of the tests, i.e., tests 1, 2, and 3, tests 1, 2, and 4, tests 1,
3, and 4, or tests 2, 3, and 4; the oligonucleotide satisifies all
of tests 1, 2, 3, and 4.
[0058] As used herein in connection with administration of an
antiviral material, the term "subject" refers to a living higher
organism, including, for example, animals such as mammals, e.g.,
humans, non-human primates, bovines, porcines, ovines, equines,
dogs, and cats; birds; and plants, e.g., fruit trees.
[0059] A related aspect concerns an antiviral oligonucleotide
randomer formulation, where the antiviral activity of the randomer
occurs principally by a non-sequence complementary mode of action.
Such a randomer formulation can, for example, include a mixture of
randomers of different lengths, e.g., at least 2, 3, 5, 10, or more
different lengths.
[0060] As used herein in connection with oligonucleotide sequences,
the term "random" characterizes a sequence or an ON that is not
complementary to a viral mRNA, and which is selected to not form
hairpins and not to have palindromic sequences contained therein.
When the term "random" is used in the context of antiviral activity
of an oligonucleotide toward a particular virus, it implies the
absence of complementarity to a viral mRNA of that particular
virus. The absence of complementarity may be broader, e.g., for a
plurality of viruses, for viruses from a particular viral family,
or for infectious human viruses.
[0061] In the present application, the term "randomer" is intended
to mean a single stranded DNA having a wobble (N) at every
position, such as NNNNNNNNNN. Each base is synthesized as a wobble
such that this ON actually exists as a population of different
randomly generated sequences of the same size.
[0062] In another aspect, the invention provides an oligonucleotide
having antiviral activity against a target virus, where the
oligonucleotide is at least 29 nucleotides in length (or in
particular embodiments, at least 30, 32, 34, 36, 38, 40, 46, 50,
60, 70, 80, 90, 100, 110, or 120 nucleotides in length) and the
sequence of the oligonucleotide is not complementary to any portion
of the genome sequence of the target virus.
[0063] In another aspect, the invention provides an oligonucleotide
formulation, containing at least one oligonucleotide having
antiviral activity against a target virus, where the
oligonucleotide is at least 6 nucleotides in length (in particular
embodiments, at least 29, 30, 32, 34, 36, 38, 40, 46, 50, 60, 70,
80, 90, 100, 110, or 120 nucleotides in length) and the sequence of
oligonucleotide is less than 70% complementary to any portion of
the genomic nucleic acid sequence of the target virus and does not
consist essentially of polyA, polyC, polyG, polyT, Gquartet, or a
TG-rich sequence. In particular embodiments, the oligonucleotide
has less than 65%, 60%, 55%, 50%, 80% 90%, 95%, or 100%
complementarity to any portion of the genomic nucleic acid sequence
of the target virus.
[0064] As used in connection with the present oligos, the term
"TG-rich" indicates that the sequence of the antiviral
oligonucleotide consists of at least 70 percent T and G
nucleotides, or if so specified, at least 80, 90, or 95% T and G,
or even 100%.
[0065] Related aspects concern isolated, purified or enriched
antiviral oligonucleotides as described herein, e.g., as described
for antiviral oligonucleotide formulations, as well as other
oligonucleotide preparations, e.g., preparations suitable for in
vitro use.
[0066] Antiviral oligonucleotides useful in the present invention
can be of various lengths, e.g., at least 6, 10, 14, 15, 20, 25,
28, 29, 30, 35, 38, 40, 46, 50, 60, 70, 80, 90, 100, 110, 120, 140,
160, or more nucleotides in length. Likewise, the oligonucleotide
can be in a range, e.g., a range defined by taking any two of the
preceding listed values as inclusive end points of the range, for
example 10-20, 20-40, 30-50, 40-60, 40-80, 60-120, and 80-120
nucleotides. In particular embodiments, a minimum length or length
range is combined with any other of the oligonucleotide
specifications listed herein for the present antiviral
oligonucleotides.
[0067] The antiviral nucleotide can include various modifications,
e.g., stabilizing modifications, and thus can include at least one
modification in the phosphodiester linkage and/or on the sugar,
and/or on the base. For example, the oligonucleotide can include
one or more phosphorothioate linkages, phosphorodithioate linkages,
and/or methylphosphonate linkages; modifications at the 2'-position
of the sugar, such as 2'-O-methyl modifications, 2'-amino
modifications, 2'-halo modifications such as 2'-fluoro; acyclic
nucleotide analogs, and can also include at least one
phosphodiester linkage. Other modifications are also known in the
art and can be used. In oligos that contain 2'-O-methyl
modifications, the oligo should not have 2'-O-methyl modifications
throughout, as current results suggest that such oligos do not have
suitable activity. In particular embodiments, the oligonucleotide
has modified linkages throughout, e.g., phosphorothioate; has a 3'-
and/or 5'-cap; includes a terminal 3'-5' linkage; the
oligonucleotide is or includes a concatemer consisting of two or
more oligonucleotide sequences joined by a linker(s)
[0068] In particular embodiments, the oligonucleotide binds to one
or more viral proteins; the sequence of the oligonucleotide (or a
portion thereof, e.g., at least 1/2) is derived from a viral
genome; the activity of an oligonucleotide with a sequence derived
from a viral genome is not superior to a randomer oligonucleotide
or a random oligonucleotide of the same length; the oligonucleotide
includes a portion complementary to a viral sequence and a portion
not complementary to a viral sequence; the sequence of the
oligonucleotide is derived from a viral packaging sequence or other
viral sequence involved in an aptameric interaction; unless
otherwise indicated, the sequence of the oligonucleotide includes
A(x), C(x), G(x), T(x), AC(x), AG(x), AT(x), CG(x), CT(x), or
GT(x), where x is 2, 3, 4, 5, 6, . . . 60 . . . 120 (SEQ ID NOS
27-36, respectively) (in particular embodiments the oligonucleotide
is at least 29, 30, 32, 34, 36, 38, 40, 46, 50, 60, 70, 80, 90,
100, 110, or 120 nucleotides in length or the length of the
specified repeat sequence is at least a length just specified); the
oligonucleotide is single stranded (RNA or DNA); the
oligonucleotide is double stranded (RNA or DNA); the
oligonucleotide includes at least one Gquartet or CpG portion; the
oligonucleotide includes a portion complementary to a viral mRNA
and is at least 29, 37, or 38 nucleotides in length (or other
length as specified above); the oligonucleotide includes at least
one non-Watson-Crick oligonucleotide and/or at least one nucleotide
that participates in non-Watson-Crick binding with another
nucleotide; the oligonucleotide is a random oligonucleotide, the
oligonucleotide is a randomer or includes a randomer portion, e.g.,
a randomer portion that has a length as specified above for
oligonucleotide length; the oligonucleotide is linked or conjugated
at one or more nucleotide residues to a molecule that modifies the
characteristics of the oligonucleotide, e.g. to provide higher
stability (such as stability in serum or stability in a particular
solution), lower serum interaction, higher cellular uptake, higher
viral protein interaction, improved ability to be formulated for
delivery, a detectable signal, improved pharmacokinetic properties,
specific tissue distribution, and/or lower toxicity.
[0069] Oligonucleotides can also be used in combinations, e.g., as
a mixture. Such combinations or mixtures can include, for example,
at least 2, 4, 10, 100, 1000, 10000, 100,000, 1,000,000, or more
different oligonucleotides. Such combinations or mixtures can, for
example, be different sequences and/or different lengths and/or
different modifications and/or different linked or conjugated
molecules. In particular embodiments of such combinations or
mixtures, a plurality of oligonucleotides have a minimum length or
are in a length range as specified above for oligonucleotides. In
particular embodiments of such combinations or mixtures, at least
one, a plurality, or each of the oligonucleotides can have any of
the other properties specified herein for individual antiviral
oligonucleoties (which can also be in any consistent
combination).
[0070] The phrase "derived from a viral genome" indicates that a
particular sequence has a nucleotide base sequence that has at
least 70% identity to a viral genomic nucleotide sequence or its
complement (e.g., is the same as or complementary to such viral
genomic sequence), or is a corresponding RNA sequence. In
particular embodiments of the present invention, the term indicates
that the sequence is at least 70% identical to a viral genomic
sequence of the particular virus against which the oligonucleotide
is directed, or to its complementary sequence. In particular
embodiments, the identity is at least 80, 90, 95, 98, 99, or
100%.
[0071] The invention also provides an antiviral pharmaceutical
composition that includes a therapeutically effective amount of a
pharmacologically acceptable, antiviral oligonucleotide at least 6
nucleotides in length (or other length as listed herein), where the
antiviral activity of the oligonucleotide occurs principally by a
non-sequence complementary mode of action, and a pharmaceutically
acceptable carrier. In particular embodiments, the oligonucleotide
or a combination or mixture of oligonucleotides is as specified
above for individual oligonucleotides or combinations or mixtures
of oligonucleotides. In particular embodiments, the pharmaceutical
compositions are approved for administration to a human, or a
non-human animal such as a non-human primate.
[0072] In particular embodiments, the pharmaceutical composition is
adapted for the treatment, control, or prevention of a disease with
a viral etiology; adapted for treatment, control, or prevention of
a prion disease; is adapted for delivery by intraocular
administration, oral ingestion, enteric administration, inhalation,
cutaneous, subcutaneous, intramuscular, intraperitoneal,
intrathecal, intratracheal, or intravenous injection, or topical
administration. In particular embodiments, the composition includes
a delivery system, e.g., targeted to specific cells or tissues; a
liposomal formulation, another antiviral drug, e.g., a
non-nucleotide antiviral polymer, an antisense molecule, an siRNA,
or a small molecule drug.
[0073] In particular embodiments, the antiviral oligonucleotide,
oligonucleotide preparation, oligonucleotide formulation, or
antiviral pharmaceutical composition has an IC50 for a target virus
(e.g., any of particular viruses or viruses in a groups of viruses
as indicated herein) of 0.50, 0.20, 0.10, 0.09. 0.08, 0.07, 0.75,
0.06, 0.05, 0.045, 0.04, 0.035, 0.03, 0.025, 0.02, 0.015, or 0.01
.mu.M or less.
[0074] In particular embodiments of formulations, pharmaceutical
compositions, and methods for prophylaxis or treatment, the
composition or formulation is adapted for treatment, control, or
prevention of a disease with viral etiology; is adapted for the
treatment, control or prevention of a prion disease; is adapted for
delivery by a mode selected from the group consisting of
intraocular, oral ingestion, enterally, inhalation, or cutaneous,
subcutaneous, intramuscular, or intravenous injection delivery;
further comprises a delivery system, which can include or be
associated with a molecule increasing affinity with specific cells;
further comprises at least one other antiviral drug in combination;
and/or further comprises an antiviral polymer in combination.
[0075] As used herein in connection with antiviral oligonucleotides
and formulations, and the like, in reference to a particular virus
or group of viruses the term "targeted" indicates that the
oligonucleotide is selected to inhibit that virus or group of
viruses. As used in connection with a particular tissue or cell
type, the term indicates that the oligonucleotide, formulation, or
delivery system is selected such that the oligonucleotide is
preferentially present and/or preferentially exhibits an antiviral
effect in or proximal to the particular tissue or cell type.
[0076] As used herein, the term "delivery system" refers to a
component or components that, when combined with an oligonucleotide
as described herein, increases the amount of the oligonucleotide
that contacts the intended location in vivo, and/or extends the
duration of its presence at the target, e.g., by at least 20, 50,
or 100%, or even more as compared to the amount and/or duration in
the absence of the delivery system, and/or prevents or reduces
interactions that cause side effects.
[0077] As used herein in connection with antiviral agents and other
drugs or test compounds, the term "small molecule" means that the
molecular weight of the molecule is 1500 daltons or less. In some
cases, the molecular weight is 1000, 800, 600, 500, or 400 daltons
or less.
[0078] In another aspect, the invention provides a kit that
includes at least one antiviral oligonucleotide or oligonucleotide
formulation in a labeled package, where the antiviral activity of
the oligonucleotide occurs principally by a non-sequence
complementary mode of action and the label on the package indicates
that the antiviral oligonucleotide can be used against at least one
virus.
[0079] In particular embodiments the kit includes a pharmaceutical
composition that includes at least one antiviral oligonucletide as
described herein; the antiviral oligonucleotide is adapted for in
vivo use in an animal and/or the label indicates that the
oligonucleotide or composition is acceptable and/or approved for
use in an animal; the animal is a mammal, such as human, or a
non-human mammal such as bovine, porcine, a ruminant, ovine, or
equine; the animal is a non-human animal; the kit is approved by a
regulatory agency such as the U.S. Food and Drug Administration or
equivalent agency for use in an animal, e.g., a human.
[0080] In another aspect, the invention provides a method for
selecting an antiviral oligonucleotide, e.g., a non-sequence
complementary antiviral oligonucleotide, for use as an antiviral
agent. The method involves synthesizing a plurality of different
random oligonucleotides, testing the oligonucleotides for activity
in inhibiting the ability of a virus to produce infectious virions,
and selecting an oligonucleotide having a pharmaceutically
acceptable level of activity for use as an antiviral agent.
[0081] In particular embodiments, the different random
oligonucleotides comprises randomers of different lengths; the
random oligonucleotides can have different sequences or can have
sequence in common, such as the sequence of the shortest oligos of
the plurality; and/or the different random oligonucleotides
comprise a plurality of oligonucleotides comprising a randomer
segment at least 5 nucleotides in length or the different random
oligonucleotides include a plurality of randomers of different
lengths. Other oligonucleotides, e.g., as described herein for
antiviral oligonucleotides, can be tested in a particular
system.
[0082] In yet another aspect, the invention provides a method for
the prophylaxis or treatment of a viral infection in a subject by
administering to a subject in need of such treatment a
therapeutically effective amount of at least one pharmacologically
acceptable oligonucleotide as described herein, e.g., a
non-sequence complementary oligonucleotide at least 6 nucleotides
in length, or an antiviral pharmaceutical composition or
formulation containing such oligonucleotide. In particular
embodiments, the virus can be any of those listed herein as
suitable for inhibition using the present invention; the infection
is related to a disease or condition indicated herein as related to
a viral infection; the subject is a type of subject as indicated
herein, e.g., human, non-human animal, non-human mammal, plant, and
the like; the treatment is for a viral disease or disease with a
viral etiology, e.g., a disease as indicated in the Background
herein.
[0083] In particular embodiments, an antiviral oligonucleotide (or
oligonucleotide formulation or pharmaceutical composition) as
described herein is administered; administration is a method as
described herein; a delivery system or method as described herein
is used; the viral infection is of a DNA virus or an RNA virus; the
virus is a parvoviridae, papovaviridae, adenoviridae,
herpesviridae, poxyiridae, hepadnaviridae, or papillomaviridae; the
virus is a arenaviridae, bunyaviridae, calciviridae, coronaviridae,
filoviridae, flaviridae, orthomyxoviridae, paramyxoviridae,
picornaviridae, reoviridae, rhabdoviridae, retroviridae, or
togaviridae; the herpesviridae virus is EBV, HSV-1, HSV-2, CMV,
VZV, HHV-6, HHV-7, or HHV-8; the virus is HIV-1 or HIV-2; the virus
is RSV; the virus is an influenza virus, e.g., influenza A; the
virus is HBV; the virus is smallpox virus or vaccinia virus; the
virus is a coronavirus; the virus is SARS virus; the virus is West
Nile Virus; the virus is a hantavirus; the virus is a parainfluenza
virus; the virus is coxsackievirus; the virus is rhinovirus; the
virus is yellow fever virus; the virus is dengue virus; the virus
is hepatitis C virus; the virus is Ebola virus; the virus is
Marburg virus.
[0084] Similarly, in a related aspect, the invention provides a
method for the prophylactic treatment of cancer caused by
oncoviruses in a human or animal by administering to a human or
animal in need of such treatment, a pharmacologically acceptable,
therapeutically effective amount of at least one random
oligonucleotide of at least 6 nucleotides in length (or another
length as described herein), or a formulation or pharmaceutical
composition containing such oligonucleotide.
[0085] In particular embodiments, the oligonucleotide(s) is as
described herein for the present invention, e.g., having a length
as described herein; a method of administration as described herein
is used; a delivery system as described herein is used.
[0086] The term "therapeutically effective amount" refers to an
amount that is sufficient to effect a therapeutically or
prophylactically significant reduction in production of infectious
virus particles when administered to a typical subject of the
intended type. In aspects involving administration of an antiviral
oligonucleotide to a subject, typically the oligonucleotide,
formulation, or composition should be administered in a
therapeutically effective amount.
[0087] In another aspect, the discovery that non-sequence
complementary interactions produce effective antiviral activity
provides a method of screening to identify a compound that alters
binding of an oligonucleotide to a viral component, such as one or
more viral proteins (e.g., extracted or purified from a viral
culture of infected host organisms, or produced by recombinant
methods). For example, the method can involve determining whether a
test compound reduces the binding of oligonucleotide to one or more
viral components.
[0088] As used herein, the term "screening" refers to assaying a
plurality of compounds to determine if they possess a desired
property. The plurality of compounds can, for example, be at least
10, 100, 1000, 10,000 or more test compounds.
[0089] In particular embodiments, any of a variety of assay formats
and detection methods can be used to identify such alteration in
binding, e.g., by contacting the oligonucleotide with the viral
component(s) in the presence and absence of a compound(s) to be
screened (e.g., in separate reactions) and determining whether a
difference occurs in binding of the oligo the viral component(s) in
the presence of the compound compared to the absence of the
compound. The presence of such a difference is indicative that the
compound alters the binding of the random oligonucleotide to the
viral component. Alternatively, a competitive displacement can be
used, such that oligonucleotide is bound to the viral component and
displacement by added test compound is determined, or conversely
test compound is bound and displacement by added oligonucleotide is
determined.
[0090] In particular embodiments, the oligonucleotide is as
described herein for antiviral oligonucleotides; the
oligonucleotide is at least 6, 8, 10, 15, 20, 25, 29, 30, 32, 34,
36, 38, 40, 46, 50, 60, 70, 80, 90, 100, 110, or 120 nucleotides in
length or at least another length specified herein for the
antiviral oligonucleotides, or is in a range defined by taking any
two of the preceding values as inclusive endpoints of the range;
the test compound(s) is a small molecule; the test compound has a
molecular weight of less than 400, 500, 600, 800, 1000, 1500, 2000,
2500, or 3000 daltons, or is in a range defined by taking any two
of the preceding values as inclusive endpoints of the range; the
viral extract or component is from a virus as listed herein; at
least 100, 1000, 10,000, 20,000, 50,000, or 100,000 compounds are
screened; the oligonucleotide has an IC50 of equal to or less than
0.500, 0.200, 0.100, 0.075, 0.05, 0.045, 0.04, 0.035, 0.03, 0.025,
0.02, 0.015, or 0.01 .mu.M.
[0091] As used herein, the term "viral component" refers to a
product encoded by a virus or produced by infected host cells as a
consequence of the viral infection. Such components can include
proteins as well as other biomolecules. Such viral components, can,
for example, be obtained from viral cultures, infected host
organisms, e.g., animals and plants, or can be produced from viral
sequences in recombinant systems (prokaryotes and eukaryotes), as
well synthetic proteins having amino acid sequences corresponding
to viral encoded proteins. The term "viral culture extract" refers
to an extract from cells infected by a virus that will include
virus-specific products. Similarly, a "viral protein" refers to a
virus-specific protein, usually encoded by a virus, but can also be
encoded at least in part by host sequences as a consequence of the
viral infection.
[0092] In a related aspect, the invention provides an antiviral
compound identified by the preceding method, e.g., a novel
antiviral compound.
[0093] In a further aspect, the invention provides a method for
purifying oligonucleotides binding to at least one viral component
from a pool of oligonucleotides by contacting the pool with at
least one viral component, e.g., bound to a stationary phase
medium, and collecting oligonucleotides that bind to the viral
component(s). Generally, the collecting involves displacing the
oligonucleotides from the viral component(s). The method can also
involve sequencing and/or testing antiviral activity of collected
oligonucleotides (i.e., oligonucleotides that bound to viral
protein).
[0094] In particular embodiments, the bound oligonucleotides of the
pool are displaced from the stationary phase medium by any
appropriate method, e.g., using an ionic displacer, and displaced
oligonucleotides are collected. Typically for the various methods
of displacement, the displacement can be performed in increasing
stringent manner (e.g., with an increasing concentration of
displacing agent, such as a salt concentration, so that there is a
stepped or continuous gradient), such that oligonucleotides are
displaced generally in order of increased binding affinity. In many
cases, a low stringency wash will be performed to remove weakly
bound oligonucleotides, and one or more fractions will be collected
containing displaced, tighter binding oligonucleotides. In some
cases, it will be desired to select fractions that contain very
tightly binding oligonucleotides (e.g., oligonucleotides in
fractions resulting from displacement by the more stringent
displacement conditions) for further use.
[0095] Similarly, the invention provides a method for enriching
oligonucleotides from a pool of oligonucleotides binding to at
least one viral component, by contacting the pool with one or more
viral proteins, and amplifying oligonucleotides bound to the viral
proteins to provide an enriched oligonucleotide pool. The
contacting and amplifying can be performed in multiple rounds,
e.g., at least 1, 2, 3, 4, 5, 10, or more additional times using
the enriched oligonucleotide pool from the preceding round as the
pool of oligonucleotides for the next round. The method can also
involve sequencing and testing antiviral activity of
oligonucleotides in the enriched oligonucleotide pool following one
or more rounds of contacting and amplifying.
[0096] The method can involve displacing oligonucleotides from the
viral component (e.g., viral protein bound to a solid phase medium)
with any of a variety of techniques, such as those described above,
e.g., using a displacement agent. As indicated above, it can be
advantageous to select the tighter binding oligonucleotides for
further use, e.g., in further rounds of binding and amplifying. The
method can further involve selecting one or more enriched
oligonucleotides, e.g., high affinity oligonucleotides, for further
use. In particular embodiments, the selection can include
eliminating oligonucleotides that have sequences complementary to
host genomic sequences (e.g., human) for a particular virus of
interest. Such elimination can involve comparing the
oligonucleotide sequence(s) with sequences from the particular host
in a sequence database(s), e.g., using a sequence alignment program
(e.g., a BLAST search), and eliminating those oligonucleotides that
have sequences identical or with a particular level of identity to
a host sequence. Eliminating such host complementary sequences
and/or selecting one or more oligonucleotides that are not
complementary to host sequences can also be done for the other
aspects of the present invention.
[0097] In the preceding methods for identifying, purifying, or
enriching oligonucleotides, the oligonucleotides can be of types as
described herein. The above methods are advantageous for
identifying, purifying or enriching high affinity oligonucleotides,
e.g., from an oligonucleotide randomer preparation.
[0098] In a related aspect, the invention concerns an antiviral
oligonucleotide preparation that includes one or more
oligonucleotides identified using a method of any of the preceding
methods for identifying, obtaining, or purifying antiviral
oligonucleotides from an initial oligonucleotide pool, where the
oligonucleotides in the oligonucleotide preparation exhibit higher
mean binding affinity with one or more viral proteins than the mean
binding affinity of oligonucleotides in the initial oligonucleotide
pool.
[0099] In particular embodiments, the mean binding affinity of the
oligonucleotides is at least two-fold, 3-fold, 5-fold, 10-fold,
20-fold, 50-fold, or 100-fold greater than the mean binding
affinity of oligonucleotides in the initial oligonucleotide pool,
or even more; the median of binding affinity is at least two-fold,
3-fold, 5-fold, 10-fold, 20-fold, 50-fold, or 100-fold greater
relative to the median of the binding affinity of the initial oligo
pool, where median refers to the middle value.
[0100] In yet another aspect, the invention provides an antiviral
polymer mix that includes at least one antiviral oligonucleotide
and at least one non-nucleotide antiviral polymer. In particular
embodiments, the oligonucleotide is as described herein for
antiviral oligonucleotides and/or the antiviral polymer is as
described herein or otherwise known in the art or subsequently
identified.
[0101] In yet another aspect, the invention provides an
oligonucleotide randomer, where the randomer is at least 6
nucleotides in length. In particular embodiments the randomer has a
length as specified above for antiviral oligonucleotides; the
randomer includes at least one phosphorothioate linkage, the
randomer includes at least one phosphorodithioate linkage or other
modification as listed herein; the randomer oligonucleotides
include at least one non-randomer segment (such as a segment
complementary to a selected virus nucleic acid sequence), which can
have a length as specified above for oligonucleotides; the randomer
is in a preparation or pool of preparations containing at least 5,
10, 15, 20, 50, 100, 200, 500, or 700 micromol, 1, 5, 7, 10, 20,
50, 100, 200, 500, or 700 mmol, or 1 mole of randomer, or a range
defined by taking any two different values from the preceding as
inclusive end points, or is synthesized at one of the listed scales
or scale ranges.
[0102] Likewise, the invention provides a method for preparing
antiviral randomers, by synthesizing at least one randomer, e.g., a
randomer as described above.
[0103] As indicated above, for any aspect involving a viral
infection or risk of viral infection or targeting to a particular
virus, in particular embodiments the virus is as listed above.
[0104] The expression "human and animal viruses" is intended to
include, without limitation, DNA and RNA viruses in general. DNA
viruses include, for example, parvoviridae, papovaviridae,
adenoviridae, herpesviridae, poxyiridae, hepadnaviridae, and
papillomaviridae. RNA viruses include, for example, arenaviridae,
bunyaviridae, calciviridae, coronaviridae, filoviridae, flaviridae,
orthomyxoviridae, paramyxoviridae, picornaviridae, reoviridae,
rhabdoviridae, retroviridae, or togaviridae.
[0105] In connection with modifying characteristics of an
oligonucleotide by linking or conjugating with another molecule or
moiety, the modifications in the characteristics are evaluated
relative to the same oligonucleotide without the linked or
conjugated molecule or moiety.
[0106] Additional embodiments will be apparent from the Detailed
Description and from the claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0107] FIG. 1. Plaque reduction assay conducted in VERO cells using
HSV-1 (strain KOS). Infected cells are treated with increasing
concentrations of REP 1001 (a), REP 2001 (b) or REP 3007 (c).
IC.sub.50 values calculated from linear regressions are reported in
each graph.
[0108] FIG. 2. Relationship between PS-ODN size and IC.sub.50
against HSV-1. IC.sub.50 values from FIG. 1 are plotted against the
specific size of each PS-ODN tested in FIG. 1.
[0109] FIG. 3. Plaque reduction assay conducted in VERO cells using
HSV-1 (strain KOS). Infected cells are treated with increasing
concentrations of REP 2001 (a), REP 2002 (b) or REP 3003 (c), REP
2004 (d), REP 2005 (e), REP 2006 (f) and Acyclovir (g). IC.sub.50
values calculated from linear regressions are reported in each
graph.
[0110] FIG. 4. Relationship between PS-ODN size and IC.sub.50
against HSV-1. IC.sub.50 values from FIG. 3 are plotted against the
specific size of each PS-ODN tested in FIG. 3 which showed
anti-HSV-1 activity. The IC.sub.50 for Acyclovir is indicated for
reference to a clinical correlate.
[0111] FIG. 5. Plaque reduction assay conducted in VERO cells using
HSV-1 (strain KOS). A broad range of PS-ODN randomer sizes were
tested in increasing concentrations; REP 2003 (a), REP 2009 (b),
REP 2010 (c), REP 2011 (d), REP 2012 (e), REP 2004 (f), REP 2006
(g), REP 2007 (h) and REP 2008 (i). IC.sub.50 values calculated
from linear regressions are reported in each graph.
[0112] FIG. 6. UV backshadowing of PS-ODN randomers tested in FIG.
5 separated by acrylamide gel electrophoresis.
[0113] FIG. 7. Relationship between PS-ODN randomer size and
IC.sub.50 against HSV-1. IC.sub.50 values from FIG. 5 are plotted
against the specific size of each PS-ODN tested in FIG. 5 which
showed anti-HSV-1 activity.
[0114] FIG. 8. Plaque reduction assay conducted in VERO cells using
HSV-1 (strain KOS). Unmodified ODNs, PS-ODNs with a random sequence
and PS-ODNs targeting the start codon of HSV-1 IE110 were tested in
increasing concentrations. REP 2013 (a), REP 2014 (b), REP 2015
(c), REP 2016 (d), REP 2017 (e), REP 2018 (f), REP 2019 (g), REP
2020 (h) and REP 2021 (i). IC.sub.50 values calculated from linear
regressions are reported in each graph.
[0115] FIG. 9. UV backshadowing of PS-ODN randomers tested in FIG.
8 separated by acrylamide gel electrophoresis.
[0116] FIG. 10. Relationship between PS-ODN randomer, PS-ODN random
sequence, PS-ODN HSV-1 IE110 sequence and IC.sub.50 against HSV-1.
IC.sub.50 values from FIG. 8 are plotted against the specific size
of each PS-ODN tested in FIG. 8 which showed anti-HSV-1 activity.
Additional IC.sub.50 values from FIG. 5 are included for comparison
against PS-ODN randomers.
[0117] FIG. 11. Plaque reduction assay conducted in VERO cells
using HSV-1 (strain KOS). A PS-ODN having 2-0 methyl modifications
to the 4 ribose sugars at each end of the oligo (REP 2024, [a]); a
ODN having methylphosphonate modifications to the 4 ester linkages
at each end of the oligo (REP 2026 [b]); and RNA PS-ODNs 20 bases
(REP2059 [c]) and 30 bases (REP2060 [d]) in length were tested in
increasing concentrations. IC.sub.50 values calculated from linear
regressions are reported in each graph.
[0118] FIG. 12. Plaque reduction assay conducted in human
fibroblast cells using HSV-2 (strain MS2). Infected cells are
treated with increasing concentrations of REP 1001 (a), REP 2001
(b) or REP 3007 (c). IC.sub.50 values calculated from linear
regressions are reported in each graph.
[0119] FIG. 13. Relationship between. PS-ODN size and IC.sub.50
against HSV-2. IC.sub.50 values from FIG. 12 are plotted against
the specific size of each PS-ODN tested in FIG. 12.
[0120] FIG. 14. Plaque reduction assay conducted in VERO cells
using HSV-2 (strain MS2). Infected cells are treated with
increasing concentrations of REP 2001 (a), REP 2002 (b) or REP 2003
(c), REP 2004 (d), REP 2005 (e), REP 2006 (f) and acyclovir (g).
IC.sub.50 values calculated from linear regressions are reported in
each graph.
[0121] FIG. 15. Relationship between PS-ODN size and IC.sub.50
against HSV-2. IC.sub.50 values from FIG. 14 are plotted against
the specific size of each PS-ODN tested in FIG. 14 which showed
anti-HSV-2 activity. The IC.sub.50 for acyclovir is provided for
reference to a clinical correlate.
[0122] FIG. 16. Plaque reduction assay conducted in VERO cells
using CMV (strain AD169). Infected cells are treated with
increasing concentrations of REP 2004 (a) or REP 2006 (b).
IC.sub.50 values calculated from linear regressions are reported in
each graph. The relationship between PS-ODN size and IC.sub.50
against CMV is plotted in (c). IC.sub.50 values from figure (a) and
(b) are plotted against the specific size of each PS-ODN
tested.
[0123] FIG. 17. Plaque reduction assay conducted in VERO cells
using CMV (strain AD169). Three clinical CMV therapies were tested:
Gancyclovir (a), Foscarnet (b) and Cidofovir (c). A broad range of
PS-ODN randomer sizes were also tested in increasing
concentrations; REP 2003 (d), REP 2004 (e), REP 2006 (f) and REP
2007 (g). Finally, REP 2036 (Vitravene) was tested as synthesized
in house (h) and as commercially available (i). IC.sub.50 values
calculated from linear regressions are reported in each graph.
[0124] FIG. 18. Relationship between PS-ODN size and IC.sub.50
against CMV. IC.sub.50 values from FIG. 17 are plotted against the
specific size of each PS-ODN tested in FIG. 17 which showed
anti-CMV activity.
[0125] FIG. 19. CPE assay conducted in MT4 cells using HIV-1
(strain NL4-3). Infected cells are treated with increasing
concentrations of REP 2004 (a) or REP 2006 (b). IC.sub.50 values
calculated from linear regressions are reported in each graph.
Cytotoxicity profiles in uninfected MT4 cells are presented for REP
2004 (c) and REP 2006 (d).
[0126] FIG. 20. Relationship between PS-ODN size and IC.sub.50
against HIV-1. IC.sub.50 values from FIG. 1 are plotted against the
specific size of each PS-ODN tested in FIG. 1.
[0127] FIG. 21. Replication assay conducted in 293A cells using
recombinant wild type HIV-1NL4-3 (strain CNDO). Infected cells are
treated with increasing concentrations of Amprenavir (a), Indinavir
(b), Lopinavir (c), Saquinavir (d), REP 2003 (e), REP 2004 (f), REP
2006 (g) and REP 2007 (h). Both curves (black and dotted lines)
represent dose response curves against strain CNDO.
[0128] FIG. 22. (a) IC.sub.50 values from FIG. 21 and (b),
relationship between PS-ODN size and IC.sub.50 against recombinant
HIV-1. IC.sub.50 values from (a) are plotted against the specific
size of each PS-ODN tested in FIG. 21.
[0129] FIG. 23. Replication assay conducted in 293A cells using
recombinant multi drug resistant HIV-1 (strain MDRC4). Infected
cells are treated with increasing concentrations of Amprenavir (a),
Indinavir (b), Lopinavir (c), Saquinavir (d), REP 2003 (e), REP
2004 (f), REP 2006 (g) and REP 2007 (h). Dose response curves for
CNDO (wild type) are indicated in dotted lines and for MDRC4 (drug
resistant) are indicated in solid lines.
[0130] FIG. 24. IC50 values from FIGS. 21 and 23 showing fold
increases in IC50 values between wild type (CNDO) and drug
resistant (MDRC4) strains of recombinant HIV-1.
[0131] FIG. 25. CPE assay conducted in Hep2 cells using RSV (strain
A2). Infected cells are treated with increasing concentrations of
REP 2004 (a), REP 2006 (b), REP 2007 (c) or Ribavirin (d).
IC.sub.50 values calculated from linear regressions are reported in
each graph. Cytotoxicity profiles in uninfected Hep2 cells are
presented for REP 2004 (e), REP 2006 (f), REP 2007 (g) or Ribavirin
(h).
[0132] FIG. 26. Relationship between PS-ODN size and IC.sub.50
against RSV. IC.sub.50 values from FIG. 25 are plotted against the
specific size of each PS-ODN tested in FIG. 25 which showed
anti-RSV activity.
[0133] FIG. 27. CPE assay conducted in LLC-MK2 cells using
Coxsackievirus B2 (strain Ohio-1). Infected cells are treated with
increasing concentrations of REP 2006 (a). The cytotoxicity profile
for REP 2006 is shown in (b).
[0134] FIG. 28. A) FP interaction assay showing the ability of
PS-ODN randomers (REP 2003, 2004, 2006 and 2007) to compete the
interaction of a 20 base PS-ODN randomer bait from FBS. Larger
randomers compete more efficiently. B) and C) Serum protection and
improved delivery of REP2006 in 293 A cells with DOTAP and
Cytofectin. D) and E) Serum protection of REP 2006 encapsulated
with DOTAP or cytofectin measured by FP.
[0135] FIG. 29. Determination of viral lysate binding to baits of
different sizes by fluorescence polarization. REP 2032-FL, REP
2003-FL and REP 2004-FL were tested for lysate binding in lysates
from HSV-1 (a), HIV-1 (b) or RSV (c).
[0136] FIG. 30. Determination of affinity of PS-ODN randomers for
viral lysates by fluorescence polarization. Using REP 2004-FL as
the bait, complex formation with HSV-1 lysate (a), HIV-1 lysate (b)
or RSV lysate (c) was challenged with increasing concentrations of
REP 2003, REP 2004, REP 2006 or REP 2007.
[0137] FIG. 31. REP 2004-FL can bind to HIV-1 p24gag and HIV-1
gp41. The ability of REP 2004-FL to interact with increasing
amounts of these two purified proteins is tested by fluorescence
polarization.
[0138] FIG. 32. Effect of bait size on p24 and gp41 binding. Baits
of increasing sizes are tested for their ability to bind to p24gag
and gp41 by fluorescence polarization.
[0139] FIG. 33. The ability of double stranded PS-ODNs to bind to
viral lysates is tested by fluorescence polarization. Single
stranded (ss) or double stranded (ds) phosphorothioated REP 2017
(fluorescently labeled) was prepared as well as its non-thioated
analog (2017U). These baits were tested for binding to HSV-1 and
HIV-1 viral lysates.
[0140] FIG. 34. The delivery of fluorescently tagged PS-ODNs into
cells was measured by incubating 293A cells in the presence of 250
nM REP 2004-FL for 4 h. Following the incubation, cells were lysed
and the relative fluorescence released from the cells upon lysis
was measured by fluorometry.
[0141] FIG. 35. The ability of 20-mer PS-ODNs of different sequence
compositions to bind to viral lysates is measured by fluorescence
polarization. PS-ODNs 3' labeled with FITC are incubated in the
presence of 1 ug of HSV-1 (a), HIV-1 (b) or RSV (c) lysates. The
binding profiles for these PS-ODNs is similar in all three viral
lysates (see FIG. 35).
[0142] FIG. 36. Indirect determination of viral load in infected
supernatants from vaccinia infected VERO cells by measuring the CPE
induced by these supernatants in naive cells. REP 2004, 2006 and
2007 were tested at 10 uM while Cidofovir was tested at 50 uM).
[0143] FIG. 37. (A) IC50 values generated from a plaque reduction
assay conducted in VERO cells using HSV-1 (strain KOS). Infected
cells are treated with increasing concentrations of REP 2006 (N40),
REP 2028 (G40) (SEQ ID NO: 21), REP 2029 (A40) (SEQ ID NO: 202, REP
2030 (T40) (SEQ ID NO: 23), and REP 2031 (C40) (SEQ ID NO: 22) to
generate IC50 values. (B) HSV-1 PRA generated IC50 values of the
following: N40 (REP 2006), AC20 (SEQ ID NO: 24) (REP 2055, TC20
(SEQ ID NO: 25) (REP 2056), or AG20 (SEQ ID NO: 26) (REP 2057).
SELECTED ABBREVIATIONS
[0144] ON: Oligonucleotide [0145] ODN: Oligodeoxynucleotide [0146]
PS: Phosphorothioate [0147] PRA: Plaque reduction assay [0148] PFU:
Plaque forming unit [0149] INF A: Influenza A virus [0150] HIV:
Human immunodeficiency virus (includes both HIV-1 and HIV-2 if not
specified) [0151] HSV: Herpes simplex virus (includes both HSV-2
and HSV-3 if not specified) [0152] RSV: Respiratory syncytial virus
[0153] COX: Coxsackievirus [0154] DHBV: Duck hepatitis B virus
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
[0155] The present invention is concerned with the identification
and use of antiviral oligonucleotides that act by a non-sequence
complementary mechanism, and includes the discovery that for many
viruses, the antiviral activity is greater for larger
oligonucleotides, and are typically optimal for oligonucleotides
that are 40 nucleotides or more in length.
[0156] As described in the Background, a number of antisense
oligonucleotides (ONs) have been tested for antiviral activity.
However, such antisense ONs are sequence-specific, and typically
are about 16-20 nucleotides in length.
[0157] As demonstrated by the results in Examples 1 and 2, the
antiviral effect of random PS-ODNs is not sequence specific.
Considering the volumes and concentrations of PS-ODNs used in those
tests, it is almost theoretically impossible that a particular
random sequence is present at more than 1 copy in the mixture. This
means than there can be no antisense effect in these PS-ODNs
randomers. In the latter example, should the antiviral effect be
caused by the sequence-specificity of the PS-ODNs, such effect
would thus have to be caused by only one molecule, a result that
does not appear possible. For example, for an ON randomer 40 bases
in length, any particular sequence in the population would
theoretically represent only 1/4.sup.40 or 8.27.times.10.sup.-25 of
the total fraction. Given that 1 mole=6.022.times.10.sup.23
molecules, and the fact that our largest synthesis is currently
done at the 15 micromole scale, all possible sequences will not be
present and also, each sequence is present most probably as only
one copy. Of course, one skilled in the art applying the teaching
of the present invention could also use sequence specific ONs, but
utilize the non-sequence complementary activity discovered in the
present invention. Accordingly, the present invention is not to be
restricted to non-sequence complementary ONs, but disclaims what
has been disclosed in the prior art regarding sequence-specific
antisense ONs for treating viral infections.
[0158] For applicable viruses (including, for example, those for
which data is described herein), as the size of the randomer
increases, so does its antiviral potency. It should be pointed out
that due to limitations in current phosphoramidite-based DNA
synthesis, the larger PS-ODNs (e.g., 80- and 120-mers) have a
significant contamination of fragments smaller than the desired
size. The weaker effects (on a per base basis) seen with larger
oligos (80 and 120 bp) may reflect the lower concentration of
full-length randomers in these populations and may also reflect a
decreased uptake into the cell. It may be possible to achieve much
larger increases in antiviral activity if larger randomers (>40
bases) of reasonable purity (75% full length) were synthesized or
purified, and/or if the cellular uptake of any of these ODNs is
facilitated by a delivery system.
[0159] In the present invention, randomers (or other
oligonucleotides) may block viral replication by several
mechanisms, including but not limited to the following: 1
preventing the adsorption or receptor interaction of virions, thus
preventing infection, 2. doping the virus assembly or the packaging
of viral genomes into capsids (competing with viral DNA or RNA for
packaging), resulting in defective virions, 3. disrupting and or
preventing the formation of capsids during packaging or the
interaction of capsid proteins with other structural proteins,
resulting in inhibition of viral release or causing the release of
defective virions, 4. binding to key viral components and
preventing or reducing their activity, 5. binding to key host
components required for viral proliferation.
[0160] Without being limited on the mechanism by which the present
viral inhibition is achieved, as indicated above there are several
possible mechanisms that could explain and/or predict the
inhibitory properties of ONs against viral replication. The first
of these is that the general aptameric effect of ONs is allowing
for their attachment, either to proteins on the cell surface or to
viral proteins, preventing viral adsorption and fusion. The size
threshold for effect may be a result of a certain cumulative charge
required for interaction.
[0161] A second possible mechanism is that ONs may function within
the cell by preventing packaging and/or assembly of the virus. ONs
above a certain size threshold may compete or interfere with the
normal capsid/nucleic acid interaction, preventing the packaging of
a functional viral genome inside new viruses. Alternatively, ONs
may prevent the formation of a normal capsid, which could prevent
normal viral budding, alter viral stability, or prevent proper
virion disassembly upon internalization.
[0162] While the mechanism of action is not yet entirely clear,
assay results demonstrate that the present ONs can exhibit greater
efficacy in viral inhibition compared to the clinical correlates,
acyclovir, gancyclovir, Ribavirin, and protease inhibitors. ONs in
accordance with the present invention could thus be used for
treating or preventing viral infection. The viral infections
treated could be those caused by human, animal, and plant
viruses
[0163] Broad Spectrum Antiviral Activity
[0164] According to the conclusions discussed above and the data
reported herein, it appeared that random ONs and ON randomers could
have broad-spectrum antiviral activity with viruses where assembly
and/or packaging and/or encapsidation of the viral genome is a
required step in replication. Therefore to test this hypothesis,
several PS-ODN randomers of different sizes were selected to be
tested in cellular models of various viral Infections. A number of
such tests are described herein in the Examples, including tests
with CMV, HIV-1, RSV, Coxsackie virus B2, DHBV, Hantavirus,
Parainfluenza virus, and Vaccinia virus, as well as the tests on
HSV-1 and HSV-2 described in Examples 1 and 2. Despite the high
activity level exhibited for some of the tested oligonucleotides,
an oligo delivery system such as DOTAP, lipofectamine or
oligofectamine could result in much greater efficacies, especially
with the larger (.gtoreq.40 bases) randomers.
[0165] Conclusions on Broad Spectrum Antiviral Activity
[0166] The efficacy studies with different viruses demonstrate that
random ONs and randomers display inhibitory properties against a
variety of different viruses. Moreover, these studies support the
conclusion that larger randomers display greater efficacy for viral
inhibition than smaller randomers. This suggests a common size
and/or charge dependent mechanism for the random ONs or ON
randomers activity in all encapsidating viruses.
[0167] While HSV and CMV are both double-stranded DNA viruses of
the herpesviridae family, HIV is a RNA virus from the retroviridae,
and RSV a RNA virus from the paramyxoviridae. Given the fact that
ON randomers can inhibit viral function in a variety of different
viruses, without being limited to the mechanisms listed, as
discussed above the following mechanisms are reasonable: A) ONs/ON
randomers are inhibiting viral infection via an aptameric effect,
preventing viral fusion with the plasma membrane; and/or B) ONs/ON
randomers are preventing or doping the assembly of virions or the
packaging of viral DNA within capsids resulting in defective
virions; and/or C) ONs/ON randomers are interfering with host
proteins or components required in the assembly and/or packaging
and/or gene expression of the virus.
[0168] Requirement for Antiviral Activity
[0169] Since a randomized DNA sequence seems to be sufficient for
viral inhibition, it was interesting to see if antiviral activity
could be maintained in the absence of the phosphorothioate
modification and also if the efficacy was augmented by either
choosing a random sequence or a specific sequence found in the
viral genome.
[0170] Accordingly, DNA and RNA modifications were investigated
with respect to their effect on the antiviral efficacy of the
randomers. Since randomers work via a non-sequence complementary
mechanism, these experiments were designed to test the slight
changes in nucleic acid conformation and charge distribution on
antiviral efficacy.
[0171] To test if ODNs with different nucleotide/nucleoside
modifications could inhibit HSV-1, REP 2024, 2026, 2059, and 2060
were tested in the HSV-1 PRA as described in the Examples. REP 2024
(a PS-ODN with a 2-O-Methyl modification to the ribose on 4 bases
at both termini of the ODN), REP 2026 (a PO-ODN with
methylphosphonate modifications to the linkages between the 4 bases
at both termini of the ODN), REP 2059 (RNA PS-ODN randomer 20 bases
in length), and REP 2060 (RNA PS-ODN randomer 30 bases in length)
showed anti-HSV-1 activity (see FIG. 11).
[0172] In the latter example, should the antiviral effect be caused
only by the ONs consisting of DNA phosphorothioate backbone, such
effect would thus be caused by only one molecule. But other
backbones and modifications gave positive antiviral activity. Of
course, one skilled in the art applying the teaching of the present
invention could also use different chemistry ONs. A modification of
the ON, such as, but not limited to, a phosphorothioate
modification, appears to be beneficial for antiviral activity. This
is most likely due to the needed charge of ONs and/or the
requirement for stabilization of DNA both in the media and
intracellularly, and it may also be due to the chirality of the
PS-ODNs.
[0173] Compound REP 2026 showed an antiviral activity while having
a central portion comprising unmodified PO-nucleotides and 4
methylphosphonate linkages at both termini protecting from
degradation. This indicates that PO-ODNs can be used as antivirals
while protected from degradation. This protection can be achieved
by modifying nucleotides at termini and/or by using a suitable
delivery system as described later.
[0174] In general, the sequence composition of the DNA used has
little effect on the overall efficacy, whether randomer, random
sequence or a specific HSV-1 sequence. However, at intermediate
lengths, HSV-1 sequence was almost 3.times. more potent than a
random sequence (see FIG. 10). This data suggests that while
specific antisense functionality exists for specific HSV sequences,
the non-antisense mechanism (non-sequence complementary mechanism)
elucidated herein may represent the predominant part of this
activity. Indeed, as the ON grows to 40 bases, essentially all of
the antiviral activity can be attributed to a non-antisense
effect.
[0175] Lower Toxicity of Randomer
[0176] One goal of using an ON randomer is to lower the toxicity.
It is known that different sequences may trigger different
responses in the animal, such as general toxicity, interaction with
serum proteins, and interaction with immune system (Monteith et al
(1998) Toxicol Sci 46:365-375). The mixture of ONs may thus
decrease toxic effects because the level of any particular sequence
will be very low, so that no significant interaction due to
sequence or nucleotide composition is likely.
Pharmaceutical Compositions
[0177] The ONs of the invention may be in the form of a therapeutic
composition or formulation useful for treating (or prophylaxis of)
viral diseases, which can be approved by a regulatory agency for
use in humans or in non-human animals, and/or against a particular
virus or group of viruses. These ONs may be used as part of a
pharmaceutical composition when combined with a physiologically
and/or pharmaceutically acceptable carrier. The characteristics of
the carrier may depend on the route of administration. The
pharmaceutical composition of the invention may also contain other
active factors and/or agents which enhance activity.
[0178] Administration of the ONs of the invention used in the
pharmaceutical composition or formulation or to practice the method
of treating an animal can be carried out in a variety of
conventional ways, such as intraocular, oral ingestion, enterally,
inhalation, or cutaneous, subcutaneous, intramuscular,
intraperitoneal, intrathecal, intratracheal, or intravenous
injection.
[0179] The pharmaceutical composition or oligonucleotide
formulation of the invention may further contain other
chemotherapeutic drugs for the treatment of viral diseases, such
as, without limitation, Rifampin, Ribavirin, Pleconaryl, Cidofovir,
Acyclovir, Pencyclovir, Gancyclovir, Valacyclovir, Famciclovir,
Foscarnet, Vidarabine, Amantadine, Zanamivir, Oseltamivir,
Resquimod, antiproteases, HIV fusion inhibitors, nucleotide HIV RT
inhibitors (e.g., AZT, Lamivudine, Abacavir), non-nucleotide HIV RT
inhibitors, Doconosol, Interferons, Butylated Hydroxytoluene (BHT)
and Hypericin. Such additional factors and/or agents may be
included in the pharmaceutical composition, for example, to produce
a synergistic effect with the ONs of the invention.
[0180] The pharmaceutical composition or oligonucleotide
formulation of the invention may further contain a polymer, such
as, without restriction, polyanionic agents, sulfated
polysaccharides, heparin, dextran sulfate, pentosan polysulfate,
polyvinylalcool sulfate, acemannan, polyhydroxycarboxylates,
cellulose sulfate, polymers containing sulfonated benzene or
naphthalene rings and naphthalene sulfonate polymer, acetyl
phthaloyl cellulose, poly-L-lysine, sodium caprate, cationic
amphiphiles, cholic acid. Polymers are known to affect the entry of
virions in cells by, in some cases, binding or adsorbing to the
virion itself. This characteristic of antiviral polymers can be
useful in competing with ONs for the binding, or adsorption to the
virion, the result being an increased intracellular activity of the
ONs compared to its extracellular activity.
[0181] Exemplary Delivery System
[0182] We monitored the uptake of PS-ODN randomers by exposing
cultured cells to fluorescently labeled randomers and then examined
the fluorescence intensity in lysed cells after two rounds of
washing. The cellular uptake of cells exposed to 250 nM REP 2004-FL
was tested with no delivery and after encapsulation in one of the
following lipid based delivery systems; Lipofectamine.TM.
(Invitrogen), Polyfect.TM. (Qiagen) and Oligofectamine.TM.
(Invitrogen). After 4 hours, cells were washed twice with PBS and
lysed using MPER lysis reagent (PROMEGA). FIG. 34 shows the
relative fluorescence yield from equivalent numbers of exposed
cells with and without delivery. We observe than in the presence of
all three delivery agents tested, there was a significant increase
in the intracellular PS-ODN concentration compared to no
delivery.
[0183] In keeping with the test results, the use of a delivery
system can significantly increase the antiviral potency of ON
randomers. Additionally, they will serve to protect these compounds
from serum interactions, reducing side effects and maximizing
tissue and cellular distribution.
[0184] Although PS-ODNs are more resistant to endogenous nucleases
than natural phosphodiesters, they are not completely stable and
are slowly degraded in blood and tissues. A limitation in the
clinical application of PS oligonucleotide drugs is their
propensity to activate complement on i.v. administration. In
general, liposomes and other delivery systems enhance the
therapeutic index of drugs, including ONs, by reducing drug
toxicity, increasing residency time in the plasma, and delivering
more active drug to disease tissue by extravasation of the carriers
through hyperpermeable vasculature. Moreover in the case of PS-ODN,
lipid encapsulation prevents the interaction with potential
protein-binding sites while in circulation (Klimuk et al. (2000) J
Pharmacol Exp Ther 292:480-488).
[0185] According to our results described herein, an approach is to
use a delivery system such as, but without restriction, lipophilic
molecules, polar lipids, liposomes, monolayers, bilayers, vesicles,
programmable fusogenic vesicles, micelles, cyclodextrins, PEG,
iontophoresis, powder injection, and nanoparticles (such as PIBCA,
PIHCA, PHCA, gelatine, PEG-PLA) for the delivery of ONs described
herein. The purpose of using such delivery systems are to, among
other things, lower the toxicity of the active compound in animals
and humans, increase cellular delivery, lower the IC50, increase
the duration of action from the standpoint of drug delivery and
protect the oligonucleotides from non-specific binding with serum
proteins.
[0186] We have shown that the antiviral activity of PS-ODN
randomers increases with increasing size. Moreover this activity is
correlated with increased affinity for viral proteins (in a viral
lysate). Since it is well known in the art that the
phosphorothioate modification increases the affinity of protein-DNA
interaction, we tested the ability of increasingly larger PS-ODN
randomers to bind to fetal bovine serum (FBS) (FIG. 28a) using the
same FP-based assay used for measuring interaction with viral
lysates. In this assay, 250 ug of non-heat inactivated FBS was
complexed with a fluorescently labeled 20 base PS-ODN randomer,
under conditions where the binding (mP value) was saturated.
Unlabelled PS-ODN randomers of increasing size (REP 2003, REP 2004,
REP 2006 and REP 2007) were used to compete the interaction of FBS
with the labeled bait. The results of this test clearly show that
as the size of the PS-ODN randomer increases, so does its affinity
for FBS. This result suggests that the most highly active
anti-viral PS-ODNs will also be the ones to bind with the highest
affinity to proteins.
[0187] It is known in the art that one of the main therapeutic
problems for phosphorothioate antisense oligonucleotides is their
side effects due mainly to this increased interaction with proteins
(specifically with serum proteins) as described by Kandimalla and
co-workers (Kandimalla et al. (1998) Bioorg. Med. Chem. Lett.
8:2103-2108). Our data suggests substantial benefits by a suitable
delivery system capable of delivering antiviral ONs into the cell
while preventing their interaction with serum proteins.
[0188] To demonstrate the benefits of a delivery system, we tested
two different delivery technologies which are liposomal based;
Cytofectin and DOTAP. We measured the delivery of the PS-ODN
randomer REP 2006 (encapsulated with either Cytofectin or DOTAP)
into 293A cells in the presence of high concentrations of serum
(50%) by measuring the intracellular concentration of labeled REP
2006 by fluorometry (FIG. 28b, c). These results show that delivery
increases the intracellular concentration of REP 2006, and also
that, in the case of DOTAP, the levels of intracellular REP 2006
after 24 hours were markedly increased. Finally, we measured the
protection of REP2006 from serum protein interactions by DOTAP
(28d) and cytofectin (28e) in our in vitro FP-based interaction
assay. Unencapsulated REP 2006 was able to compete bound
fluorescent oligo from serum but when REP 2006 was encapsulated
with either DOTAP or cytofectin it was no longer able to compete
for serum binding. These data suggest that encapsulation protects
oligos from serum interaction and will result in a more effective
therapeutic effect with fewer side effects.
[0189] Another potential benefit in using a delivery system is to
protect the ONs from interactions, such as adsorption, with
infective virions in order to prevent amplification of viral
infection through different mechanisms such as increased cellular
penetration of virions.
[0190] Another approach is to accomplish cell specific delivery by
associating the delivery system with a molecule(s) that will
increase affinity with specific cells, such molecules being without
restriction antibodies, receptor ligands, vitamins, hormones and
peptides.
[0191] Additional options for delivery systems are provided
below.
[0192] Linked ODN
[0193] In certain embodiments, ONs of the invention are modified in
a number of ways without compromising their ability to inhibit
viral replication. For example, the ONs are linked or conjugated,
at one or more of their nucleotide residues, to another moiety.
Thus, modification of the oligonucleotides of the invention can
involve chemically linking to the oligonucleotide one or more
moieties or conjugates which enhance the activity, cellular
distribution or cellular uptake, increase transfer across cellular
membranes specifically or not, or protecting against degradation or
excretion, or providing other advantageous characteristics. Such
advantageous characteristics can, for example, include lower serum
interaction, higher viral-protein interaction, the ability to be
formulated for delivery, a detectable signal, improved
pharmacokinetic properties, and lower toxicity. Such conjugate
groups can be covalently bound to functional groups such as primary
or secondary hydroxyl groups. For example, conjugate moieties can
include a steroid molecule, a non-aromatic lipophilic molecule, a
peptide, cholesterol, bis-cholesterol, an antibody, PEG, a protein,
a water soluble vitamin, a lipid soluble vitamin, another ON, or
any other molecule improving the activity and/or bioavailability of
ONs.
[0194] In greater detail, exemplary conjugate groups of the
invention can include intercalators, reporter molecules,
polyamines, polyamides, polyethylene glycols, polyethers, SATE,
t-butyl-SATE, groups that enhance the pharmacodynamic properties of
oligomers, and groups that enhance the pharmacokinetic properties
of oligomers. Typical conjugate groups include cholesterols,
lipids, phospholipids, biotin, phenazine, folate, phenanthridine,
anthraquinone, acridine, fluoresceins, rhodamines, coumarins,
fluorescent nucleobases, and dyes.
[0195] Groups that enhance the pharmacodynamic properties, in the
context of this invention, include groups that improve oligomer
cellular uptake and/or enhance oligomer resistance to degradation
and/or protect against serum interaction. Groups that enhance the
pharmacokinetic properties, in the context of this invention,
include groups that improve oligomer uptake, distribution,
metabolism or excretion. Exemplary conjugate groups are described
in International Patent Application PCT/US92/09196, filed Oct. 23,
1992, which is incorporated herein by reference in its
entirety.
[0196] Conjugate moieties can include but are not limited to lipid
moieties such as a cholesterol moiety (Letsinger et al., Proc.
Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan
et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether,
e.g., hexyl-5-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci.,
1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let.,
1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl.
Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g.,
dodecandiol or undecyl residues (Saison-Behmoaras et at., EMBO J.,
1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259,
327-330; Svinarchuk et at., Biochimie, 1993, 75, 49-54), a
phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium
1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et at.,
Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids
Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol
chain (Manoharan et at., Nucleosides & Nucleotides, 1995, 14,
969-973), or adamantane acetic acid (Manoharan et at., Tetrahedron
Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et at.,
Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine
or hexylaminocarbonyl-oxycholesterol moiety (Crooke et al., J.
Pharmacol Exp. Ther., 1996, 277, 923-937.
[0197] The present oligonucleotides may also be conjugated to
active drug substances, for example without limitation, aspirin,
warfarin, phenylbutazone, ibuprofen, suprofen, fenbufen,
ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine,
2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a
benzothiadiazide, chlorothiazide, a diazepine, indomethicin, a
barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an
antibacterial or an antibiotic.
[0198] Exemplary U.S. patents that describe the preparation of
exemplary oligonucleotide conjugates include, for example, U.S.
Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313;
5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584;
5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439;
5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779;
4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013;
5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136;
5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873;
5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475;
5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481;
5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and
5,688,941, each of which is incorporated by reference herein in its
entirety.
[0199] Another approach is to prepare antiviral ONs as lipophilic
pro-oligonucleotides by modification with enzymatically cleavable
charge neutralizing adducts such as s-acetylthio-ethyl or
s-pivasloylthio-ethyl (Vives et al., 1999, Nucl Acids Res 27:
4071-4076). Such modifications have been shown to increase the
uptake of ONs into cells.
[0200] Design of Non-Specific ONs
[0201] In another approach, an antiviral ON demonstrating low,
preferably the lowest possible, homology with the human (or other
subject organism) genome is designed. The goal is to obtain an ON
that will show the lowest toxicity due to interactions with human
or animal genome sequence(s) and mRNAs. The first step is to
produce the desired length sequence of the ON, e.g., by aligning
nucleotides A, C, G, T in a random fashion, manually or, more
commonly, using a computer program. The second step is to compare
the ON sequence with a library of human sequences such as GenBank
and/or the Ensemble Human Genome Database. The sequence generation
and comparison can be performed repetitively, if desired, to
identify a sequence or sequences having a desired low homology
level with the subject genome. Desirably, the ON sequence is at the
lowest homology possible with the entire genome, while also
preferably minimizing self interaction.
[0202] Non-Specific ONs with Antisense Activity
[0203] In another approach, an antiviral non-specific sequence
portion(s) is/are coupled with an antisense sequence portion(s) to
increase the activity of the final ON. The non-specific portion of
the ONs is described in the present invention. The antisense
portion is complementary to a viral mRNA.
[0204] Non-Specific ONs with a G-rich Motif Activity
[0205] In another approach, an antiviral non-specific sequence
portion(s) is/are coupled with a motif portion(s) to improve the
activity of the final ON. The non-specific portion of the ON is
described in the present invention. The motif portion can, as
non-limiting examples, include, CpG, Gquartet, and/or CG that are
described in the literature as stimulators of the immune system.
Agrawal et al. (2001) Curr. Cancer Drug Targets 3:197-209.
[0206] Non-Watson-Crick ONs
[0207] Another approach is to use an ON composed of one type or
more of non-Watson-Crick nucleotides/nucleosides. Such ONs can
mimic PS-ODNs with some of the following characteristics similar to
PS-ODNs: a) the total charge; b) the space between the units; c)
the length of the chain; d) a net dipole with accumulation of
negative charge on one side; e) the ability to bind to proteins; f)
the ability to bind viral proteins, g) the ability to penetrate
cells, h) an acceptable therapeutic index, i) an antiviral
activity: The ON has a preferred phosphorothioate backbone but is
not limited to it. Examples of non-Watson-Crick
nucleotides/nucleosides are described in Kool, 2002, Acc. Chem.
Res. 35:936-943; and Takeshita et al., (1987) J. Biol. Chem.
262:10171-10179 where ODNs containing synthetic abasic sites are
described.
[0208] Antiviral Polymer
[0209] Another approach is to use a polymer mimicking the activity
of phosphorothioate ODNs. As described in the literature, several
anionic polymers were shown to have antiviral inhibitory activity.
These polymers belong to several classes: (1) sulfate esters of
polysaccharides (dextrin and dextran sulfates; cellulose sulfate);
(2) polymers containing sulfonated benzene or naphthalene rings and
naphthalene sulfonate polymers; (3) polycarboxylates (acrylic acid
polymers); and acetyl phthaloyl cellulose (Neurath et al. (2002)
BMC Infect Dis 2:27); and (4) abasic oligonucleotides (Takeshita et
al., 1987, J. Biol. Chem. 262:10171-10179). Other examples of
non-nucleotide antiviral polymers are described in the literature.
The polymers described herein mimic PS-ODNs described in this
invention and have the following characteristics similar to
PS-ODNs: a) the length of the chain; b) a net dipole with
accumulation of negative charge on one side; c) the ability to bind
to proteins; d) the ability to bind viral protein, e) an acceptable
therapeutic index, f) an antiviral activity. In order to mimic the
effect of a PS-ODN, the antiviral polymer may preferably be a
polyanion displaying similar space between its units as compared to
a PS-ODN. It may also have the ability to penetrate cells alone or
in combination with a delivery system.
[0210] Antiviral Activity of Double-Stranded PS-ODNs
[0211] A random sequence (REP 2017) and its complement (either PS
modified or unmodified) are fluorescently labeled as described
elsewhere and tested for their ability to bind to purified HSV-1
and HIV-1 proteins by fluorescence polarization as described in the
present invention. Hybridization was verified by acrylamide gel
electrophoresis. Unmodified REP 2017 (2017U), either single (ss) or
double stranded (ds), had no binding activity in either HSV-1 or
HIV-1 lysates. However, PS modified REP 2017, either single
stranded or double stranded, was capable of HSV-1 and HIV-1
interaction (see FIG. 33).
[0212] According to our results described herein, an approach is to
use double stranded ONs as effective antiviral agents.
Preferentially such ONs have a phosphorothioate backbone but may
also have other and/or additional modifications which increase
either their delivery and/or antiviral activity and/or stability as
described herein for single stranded ONs.
[0213] In Vitro Assay for Drug Discovery
[0214] An in vitro assay is developed based on fluorescence
polarization to measure the ability of PS-ODNs to bind to viral
components, e.g., viral proteins. When a protein (or another
interactor) binds to the fluorescently labeled bait, the three
dimensional tumbling of the bait in solution is retarded. The
retardation of this tumbling is measured by an inherent increase in
the polarization of excited light from the labeled bait. Therefore,
increased polarization (reported as a dimensionless measure [mP])
is correlated with increased binding.
[0215] One methodology is to use as bait a PS-ODN randomer labeled
at the 3' end with FITC using an inflexible linker
(3'-(6-Fluorescein) CPG). This PS-ODN randomer is diluted to 2 nM
in assay buffer (10 mM Tris, pH7.2, 80 mM NaCl, 10 mM EDTA, 100 mM
b-mercaptoethanol and 1% tween 20). This oligo is then mixed with
an appropriate interactor. In this case, we use lysates of sucrose
gradient purified HSV-1 (strain MacIntyre), HIV-1 (strain Mn) or
RSV (strain A2) suspended in 0.5 M KCl and 0.5% Triton X-100 (HSV-1
and HIV-1) or 10 mM Tris, pH7.5, 150 mM NaCl, 1 mM EDTA and 0.1%
Triton X-100 (RSV). Following bait interaction, the complexes are
challenged with various unlabelled PS-ODNs to assess their ability
to displace the bait from its complex.
[0216] In FIG. 29, we show a preliminary test with three baits of
different sizes; 6 (REP 2032-FL), 10 (REP 2003-FL) and 20 bases
(REP 2004-FL). These baits were tested for their ability to
interact with HSV-1 (FIG. 29a), HIV-1 (FIG. 29b) and RSV (FIG. 29c)
lysates. In the presence of any of the viral lysates the degree of
binding was dependent on the size of the bait used, with 2004-FL
displaying the largest shift in mP (binding) in the presence of
viral lysate. We note that this is similar to the size dependent
antiviral efficacy of PS-ODN randomers. This bait was then used to
assess the ability of PS-ODNs of different sizes to compete the
interaction of the bait with the lysate.
[0217] In FIG. 30, the interaction of REP 2004-FL with HSV-1 (FIG.
30a), HIV-1 (FIG. 30b) and RSV (FIG. 30c) lysates is challenged
with PS-ODNs of increasing size. For each viral lysate tested, we
note that REP 2003 is unable to compete the bait away from the
lysate. The bait interaction was very strong as revealed by the
relatively weak competition elicited by the REP 2004 (unlabeled
bait) competitor. However, it was observed that as the size of the
competitor PS-ODN increased above 20 bases, its ability to displace
the bait became more robust. This indicates an increased affinity
to protein components in the viral lysate as the PS-ODN randomer
size increases. This phenomenon mirrors the increased antiviral
activity of larger PS-ODN randomers against HSV-1, HSV-2, CMV,
HIV-1 and RSV.
[0218] The similarity between the efficacy in bait competition and
antiviral activity of PS-ODN randomers indicates that this assay
paradigm is a good predictor of antiviral activity. This assay is
robust, easy to perform and very stable, making it a very good
candidate for a high throughput screen to identify novel antiviral
molecules based not on specific target identification but on their
ability to interact with one or more components, e.g., viral
proteins.
[0219] While the exemplary method described herein utilizes
fluorescence polarization to measure interaction with the viral
lysate, numerous techniques are known in the art for monitoring
protein interactions, and can be used in the present methods. These
include without restriction surface plasmon resonance, fluorescence
resonance energy transfer (FRET), enzyme linked immunosorbent assay
(ELSIA), gel electrophoresis (to measure mobility shift),
isothermal titration and differential scanning microcalorimetry and
column chromatography. These other different techniques can be
applied to measure the interaction of ONs with a viral lysate or
component, and thus can be useful in screening for compounds which
have anti-viral activity.
[0220] The method described herein is used to screen for novel
compounds from any desired source, for example, from a library
synthesized by combinatorial chemistry or isolated by purification
of natural substances. It can be used to a) determine appropriate
size, modifications, and backbones of novel ONs; b) test novel
molecules including novel polymers; predict a particular virus'
susceptibility to novel ONs or novel compounds; or d) determine the
appropriate suite of compounds to maximally inhibit a particular
virus.
[0221] The increased lysate affinity with larger sized PS-ODN
randomers suggests that the antiviral mechanism of action of PS-ODN
randomers is based on an interaction with one or more viral protein
components which prevents either the infection or correct
replication of virions. It also suggests that this interaction is
charge (size) dependent and not dependent on sequence. As these
PS-ODN randomers have a size dependent activity across multiple
viruses spanning several different families, we suggest that PS-ODN
randomers interfere with common, charge dependent protein-protein
interactions, protein-DNA/RNA interactions, and/or other
molecule-molecule interactions. These interactions can include (but
are not limited to): [0222] a. The interaction between individual
capsid subunits during capsid formation. [0223] b. The interaction
between the capsid/nucleocapsid protein and the viral genome.
[0224] c. The interaction between the capsid and glycoproteins
during budding. [0225] d. The interaction between the glycoprotein
and its receptor during infection. [0226] e. The interaction
between other viral key components involved in viral
replication.
[0227] These multiple, simultaneous inhibitions of protein-protein
interactions represent a novel mechanism for antiviral
inhibition.
[0228] Effect of PS-ODN Sequence Composition on Lysate
[0229] We monitored the ability of PS-ODNs of different sequences
to interact with several viral lysates. In each case, a 20-mer
PS-ODN is labeled at the 3' end with FITC as previously described
herein. The PS-ODNs tested consisted of A20 (SEQ ID NO: 12), T20
(SEQ ID NO: 15), G20 (SEQ ID NO: 13), C20 (SEQ ID NO: 14), AC10
(SEQ ID NO: 16), AG10 (SEQ ID NO: 17), TC10 (SEQ ID NO: 18), TG10
(SEQ ID NO: 19), REP 2004 and REP 2017. Each of these sequences is
diluted to 4 nM in assay buffer and incubated in the presence of 1
ug of HSV-1, HIV-1 or RSV lysate. Interaction is measured by
fluorescence polarization.
[0230] The profile of interaction with all sequences tested is
similar in all viral lysates, indicating that the nature of the
binding interaction is very similar. Within each lysate, the
PS-ODNs of uniform composition (A20 (SEQ ID NO:12), G20 (SEQ ID
NO:13), T20 (SEQ ID NO:15), C20 (SEQ ID NO:14)) were the weakest
interactors with A20 (SEQ ID NO:12 being the weakest interactor of
these by a significant margin. For the rest of the PS-ODNs tested,
all of them displayed a similar, strong interaction with the
exception of TG10 (SEQ ID NO:19), which consistently displayed the
strongest interaction in each lysate (see FIG. 35).
[0231] Target Identification for PS-ODN Randomers in HIV-I
[0232] The ability of PS-ODN randomers to bind to purified HIV-1
proteins is tested by fluorescence polarization as described in
example 9. Increasing quantities of purified HIV-1 p24 or purified
HIV-1 gp41 were reacted with REP 2004-FL (see FIG. 31). We note
that for both these proteins, there is a protein concentration
dependent shift in fluorescence polarization, indicating an
interaction with both these proteins.
[0233] The ability of a range of sizes of PS-ODN randomers to bind
to these proteins was also tested using fluorescent versions of REP
2032, REP 2003, REP 2004, REP 2006 and REP 2007 (see FIG. 32). We
observe that for p24, there is no size dependent interaction with
p24 (see FIG. 32a) however; we did see an increase in gp41 binding
in PS-ODN randomers larger than 20 bases versus those less than 20
bases (see FIG. 32b). This suggests when PS-ODN randomer length
increases above 20 bases, multiple copies of gp41 can bind to
individual randomers, increasing their polarization.
[0234] This is a significant observation as it demonstrates the
potential of larger ONs to sequester structural proteins during
viral synthesis and limit their availability for the formation of
new virions.
[0235] High Affinity Oligonucleotides
[0236] Another approach is a method to enrich or purify antiviral
ON(s) having a higher affinity for viral components, such as viral
proteins, than the average affinity of the ONs in a starting pool
of ONs. The method will thus provide one or more non-sequence
complementary ON(s) that will exhibit increased affinity to one or
more viral components, e.g., having a three-dimensional shape
contributing to such elevated binding affinity. The rationale is
that while ON(s) will act as linear molecules in binding with viral
components, they can also fold into a 3-dimensional shape that can
enhance the interaction with such viral components. Without being
limited to the specific technique, high affinity ONs can be
purified or enriched in the following ways.
[0237] One method for purifying a high affinity ON, or a plurality
of high affinity ONs, involves using a stationary phase medium with
bound viral protein(s) as an affinity matrix to bind ONs, which can
then be eluted under increasingly stringent conditions (e.g.,
increasing concentration of salt or other chaotropic agent, and/or
increasing temperature and/or changes in pH). Such a method can,
for example, be carried out by: [0238] (a) loading a pool of ONs
onto an exchange column having a viral protein or several viral
proteins or a viral lysate bound to a stationary phase; [0239] (b)
displacing (eluting) bound ONs from the column, e.g., by using a
displacer solution such as an increasing salt solution; [0240] (c)
collecting fractions of eluted ONs at different salt concentration;
[0241] (d) cloning and sequencing eluted ONs from different
fractions, more preferably from a fraction(s) at high salt
concentration, such that the ONs eluted at the high salt
concentration have a greater binding affinity with the viral
protein(s); and [0242] (e) Testing the activity of sequenced ON(s)
in assays such binding and/or viral inhibition assay, e.g., a
fluorescence polarization-binding assay as described herein and/or
in a cellular viral inhibition assay and/or in an animal viral
inhibition assay.
[0243] In a second example, a method derived and modified from the
SELEX methodology (Morris et al (1998) Biochemistry 95:2902-2907)
can be used for purifying the high affinity ON. One implementation
of such a method can be performed as: [0244] (a) providing a
starting ON pool material, for example, a collection of synthetic
random ONs containing a high number of sequences, e.g., one hundred
trillion (10.sup.14) to ten quadrillion (10.sup.16) different
sequences. Each ON molecule contains a segment of random sequence
flanked by primer-binding sequences at each end to facilitate
polymerase chain reaction (PCR). Because the nucleotide sequences
of essentially all of the molecules are unique, an enormous number
of structures are sampled in the population. These structures
determine each molecule's biochemical properties, such as the
ability to bind a given viral target molecule; [0245] (b)
contacting ONs with a viral protein or several viral proteins or a
viral lysate; [0246] (c) selecting ONs that bind to viral
protein(s), using a partition technique(s) that can partition bound
and unbound ONs, such as native gel shifts and nitrocellulose
filtration. Either of these methods physically separates the bound
species from the unbound species, allowing preferential recovery of
those sequences that bind best. Also, to select ON (s) that bind to
a small protein, it is desirable to attach the target to a solid
support and use that support as an affinity purification matrix.
Those molecules that are not bound get washed off and the bound
ones are eluted with free target, again physically separating bound
and unbound species; [0247] (d) amplifying the eluted binding
ON(s), e.g., by using PCR using primers hybridizing with both
flanking sequences of ONs; [0248] (e) steps (b) (c) and (d) can be
performed multiple times (i.e., multiple cycles or rounds of
enrichment and amplification) in order to preferentially recover
ONs that display the highest binding affinity to viral protein(s).
After several cycles of enrichment and amplification, the
population is dominated by sequences that display the desired
biochemical property; [0249] (f) cloning and sequencing one or more
ONs selected from an enrichment cycle, e.g., the last such cycle;
and [0250] (g) testing the binding and/or activity of sequenced
ON(s) in assays, e.g., in a fluorescence polarization binding assay
as described herein and/or in a cellular viral inhibition assay
and/or in an animal viral inhibition assay.
[0251] Another approach is to apply a modification of a split
synthesis methodology to create one-bead one-PS-ODN and one-bead
one-PS2-ODN libraries as described in Yang et al (2002) Nucl. Acids
Res. 30(e132):1-8. Binding and selection of specific beads to viral
proteins can be done. Sequencing both the nucleic acid bases and
the positions of any thioate/dithioate linkages can be carried out
by using a PCR-based identification tag of the selected beads. This
approach can allow for the rapid and convenient identification of
PS-ODNs or PS2-ODNs that bind to viral proteins and that exhibit
potent antiviral properties.
[0252] Once the specific sequences that bind to the viral proteins
with high affinity are determined (e.g., by amplification and
sequencing of individual sequences), one or more such high affinity
sequences can be selected and synthesized (e.g., by either chemical
or enzymatic synthesis) to provide a preparation of high affinity
ON(s), which can be modified to improve their activity, including
improving their pharmacokinetic properties. Such high affinity ONs
can be used in the present invention.
[0253] Prion Diseases
[0254] Another approach is used in an alternative embodiment of the
present invention for the treatment, the control of the
progression, or the prevention of prion disease. This fatal
neurodegenerative disease is infectious and can affect both humans
and animals. Structural changes in the cellular prion protein, PrPC
to its scrapie isoform, PrPSC, are considered to be the obligatory
step in the occurrence and propagation of the prion disease.
Amyloid polymers are associated with neuropathology of the prion
disease.
[0255] The incubation of a prion protein fragment and double
stranded nucleic acid results in the formation of amyloid fibres
(Nandi et al (2002), J Mol Biol 322: 153-161). ONs having affinity
to proteins such as phosphorothioates are used to compete or
inhibit the interaction of double stranded nucleic acid with the
PrPC and consequently stop the formation of the amyloid polymers.
Such ONs of different sizes and different compositions can be used
in an appropriate delivery form to treat patients suffering from
prion diseases or for prophylaxis in high risk situations. Such
interfering ONs can be identified by measuring folding changes of
amyloid polymerase as described by Nandi et al. (supra) in the
presence of test ONs.
[0256] Putative Viral Etiologies
[0257] Another approach is used in another embodiment of the
present invention for the treatment or prevention of diseases or
conditions with putative viral etiologies as described without
limitation in the following examples. Viruses are putative causal
agents in diseases and conditions that are not related to a primary
viral infection. For example, arthritis is associated with HCV
(Olivieri et al. (2003) Rheum Dis Clin North Am 29:111-122),
Parvovirus 819, HIV, HSV, CMV, EBV, and VZV (Stahl et al. (2000)
Clin Rheumatol 19:281-286). Other viruses have also been identified
as playing a role in different diseases. For example, influenza A
in Parkinson's disease (Takahashi et al. (1999), Jpn J Infect Dis
52:89-98), Coronavirus, EBV and other viruses in Multiple Sclerosis
(Talbot et at (2001) Curr Top Microbiol Immunol 253:247-71); EBV,
CMV and HSV-6 in Chronic Fatigue Syndrome (Lerner et al. (2002)
Drugs Today 38:549-561); and paramyxoviruses in asthma (Walter et
at (2002) J Clin Invest 110:165-175) and in Paget's disease; and
HBV, HSV, and influrenza in Guillain-Barre Syndrome.
[0258] Because of these etiologies, inhibition of the relevant
virus using the present invention can delay, slow, or prevent
development of the corresponding disease or condition, or at least
some symptoms of that disease.
[0259] Oligonucleotide Modifications and Synthesis
[0260] As indicated in the Summary above, modified oligonucleotides
are useful in this invention. Such modified oligonucleotides
include, for example, oligonucleotides containing modified
backbones or non-natural internucleoside linkages. Oligonucleotides
having modified backbones include those that retain a phosphorus
atom in the backbone and those that do not have a phosphorus atom
in the backbone.
[0261] Such modified oligonucleotide backbones include, for
example, phosphorothioates, chiral phosphorothioates,
phosphorodithioates, phosphotriesters, aminoalkylphosphotri-esters,
methyl and other alkyl phosphonates including 3'-alkylene
phosphonates, 5'-alkylene phosphonates and chiral phosphonates,
phosphinates, phosphoramidates including 3'-amino phosphoramidate
and aminoalkylphosphoramidates, thionophosphoramidates,
thionoalkylphosphonates, thionoalkylphosphotriesters,
selenophosphates, carboranyl phosphate and borano-phosphates having
normal 3'-5' linkages, 2'-5' linked analogs of these, and those
having inverted polarity wherein one or more internucleotide
linkages is a 3' to 3', 5' to 5' or 2' to 2' linkage.
Oligonucleotides having inverted polarity typically include a
single 3' to 3' linkage at the 3'-most internucleotide linkage L e.
a single inverted nucleoside residue which may be abasic (the
nucleobase is missing or has a hydroxyl group in place thereof).
Various salts, mixed salts and free acid forms are also
included.
[0262] Preparation of Oligonucleotides with Phosphorus-Containing
linkages as indicated above are described, for example, in U.S.
Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196;
5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;
5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925;
5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799;
5,587,361; 5,194,599; 5,565,555; 5,527,899; 5,721,218; 5,672,697
and 5,625,050, each of which is incorporated by reference herein in
its entirety.
[0263] Some exemplary modified oligonucleotide backbones that do
not include a phosphorus atom have backbones that are formed by
short chain alkyl or cycloalkyl internucleoside linkages, mixed
heteroatom and alkyl or cycloalkyl internucleoside linkages, or one
or more short chain heteroatomic or heterocyclic internucleoside
linkages. These include those having morpholino linkages (formed in
part from the sugar portion of a nucleoside); siloxane backbones;
sulfide, sulfoxide and sulfone backbones; formacetyl and
thioformacetyl backbones; methylene formacetyl and thioformacetyl
backbones; riboacetyl backbones; alkene containing backbones;
sulfamate backbones; methyleneimino and methylenehydrazino
backbones; sulfonate and sulfonamide backbones; amide backbones;
and others having mixed N, O, S and CH.sub.2 component parts.
Particularly advantageous are backbone linkages that include one or
more charged moieties. Examples of U.S. patents describing the
preparation of the preceding oligonucleotides include U.S. Pat.
Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141;
5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677;
5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240;
5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070;
5,663,312; 5,633,360; 5,677,437; 5,792,608; 5,646,269 and
5,677,439, each of which is incorporated by reference herein in its
entirety.
[0264] Modified oligonucleotides may also contain one or more
substituted sugar moieties. For example, such oligonucleotides can
include one of the following 2'-modifications: OH; F; O-, S-, or
N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or
O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be
substituted or unsubstituted C.sub.1 to C.sub.10 alkyl or C.sub.2
to C.sub.10 alkenyl and alkynyl, or 2'-O--(O-carboran-1-yl)methyl.
Particular examples are O[(CH.sub.2).sub.nO).sub.mCH.sub.3,
O(CH.sub.2).about.OCH.sub.3, O(CH.sub.2).sub.nNH.sub.2,
O(CH.sub.2).sub.nCH.sub.3, O(CH.sub.2).sub.nONH.sub.2, and
O(CH.sub.2).sub.nON [(CH.sub.2).sub.nCH.sub.3)].sub.2, where n and
m are from 1 to 10. Other exemplary oligonucleotides include one of
the following 2'-modifications: C.sub.1 to C.sub.10 lower alkyl,
substituted lower alkyl, alkenyl, alkynyl, alkaryl, aralkyl,
O-alkaryl or O-aralkyl, SH, SCH.sub.3, OCN, Cl, Br, CN, CF.sub.3.
OCF.sub.3, SOCH.sub.3, SO.sub.2CH.sub.3, ONO.sub.2, NO.sub.2,
N.sub.3, NH.sub.2, heterocycloalkyl, heterocycloalkaryl,
aminoalkylamino, polyalkylamino, substituted silyl, a reporter
group, an intercalator, a group for improving the pharmacokinetic
properties of an oligonucleotide, or a group for improving the
pharmacodynamic properties of an oligonucleotide. Examples include
2'-methoxyethoxy (2'-O--CH.sub.2CH.sub.2OCH.sub.3, also known as
2'-O-(2-methoxyethyl) or 2'-MOE) (Martin et al., Helv. Chim. Acta,
1995, 78, 486-504) i.e., an alkoxyalkoxy group;
2'-dimethyl-laminooxyethoxy, i.e., a
O(CH.sub.2).sub.2ON(CH.sub.3).sub.2 group, also known as 2'-DMAOE;
and 2'-dimethylaminoethoxyethoxy (also known as
2'-.beta.-dimethylaminoethoxyethyl or 2'-DMAEOE), i.e.,
2'-O--CH.sub.2--O--CH.sub.2--N(CH.sub.2).sub.2.
[0265] Other modifications include Locked Nucleic Acids (LNAs) in
which the 2'-hydroxyl group is linked to the 3' or 4' carbon atom
of the sugar ring thereby forming a bicyclic sugar moiety. The
linkage can be a methelyne (--CH.sub.2--).about. group bridging the
2' oxygen atom and the 4' carbon atom wherein n is 1 or 2. LNAs and
preparation thereof are described in WO 98/39352 and WO 99/14226,
which are incorporated herein by reference in their entireties.
[0266] Other modifications include sulfur-nitrogen bridge
modifications, such as locked nucleic acid as described in Orum et
al. (2001) Curr. Opin. Mol. Ther. 3:239-243.
[0267] Other modifications include 2'-methoxy (2'-OCH.sub.3),
2'-methoxyethyl (2'O--CH.sub.2--CH.sub.3), 2'-aminopropoxy
(2'-OCH.sub.2CH.sub.2CH.sub.2NH.sub.2), 2'-allyl
(2'-CH.sub.2--CH.dbd.CH.sub.2), 2'-O-allyl
(2'-O--CH.sub.2CH.dbd.CH.sub.2) and 2'-fluoro (2'-F). The
2'-modification may be in the arabino (up) position or ribo (down)
position. Similar modifications may also be made at other positions
on the oligonucleotide, particularly the 3' position of the sugar
on the 3' terminal nucleotide or in 2'-5' linked oligonucleotides
and the 5' position of the 5' terminal nucleotide. Oligonucleotides
may also have sugar mimetics such as cyclobutyl moieties in place
of the pentofuranosyl sugar. Exemplary U.S. patents describing the
preparation of such modified sugar structures include, for example,
U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044;
5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811;
5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873;
5,646,265; 5,658,873; 5,670,633; 5,792,747; and 5,700,920, each of
which is incorporated by reference herein in its entirety.
[0268] Still other modifications include an ON concatemer
consisting of multiple oligonucleotide sequences joined by a
linker(s). The linker may, for example, consist of modified
nucleotides or non-nucleotide units. In some embodiments, the
linker provides flexibility to the ON concatemer. Use of such ON
concatemers can provide a facile method to synthesize a final
molecule, by joining smaller oligonucleotide building blocks to
obtain the desired length. For example, a 12 carbon linker (C12
phosphoramidite) can be used to join two or more ON concatemers and
provide length, stability, and flexibility.
[0269] As used herein, "unmodified" or "natural" bases
(nucleobases) include the purine bases adenine (A) and guanine (G),
and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
Oligonucleotides may also include base modifications or
substitutions. Modified bases include other synthetic and
naturally-occurring bases such as 5-methylcytosine (5-me-C),
5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine,
6-methyl and other alkyl derivatives of adenine and guanine,
2-propyl and other alkyl derivatives of adenine and guanine,
2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and
cytosine, 5-propynyl(--C.dbd.C--CH.sub.3) uracil and cytosine and
other alkynyl derivatives of pyrimidine bases, 6-azo uracil,
cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil,
8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other
8-substituted adenines and guanines, 5-halo particularly 5-bromo,
5-trifluoromethyl and other 5-substituted uracils and cytosines,
7-methylguanine and 7-methyladenine, 2-F-adenine, 2-amino-adenine,
8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine
and 3-deazaguanine and 3-deazaadenine. Additional modified bases
include tricyclic pyrimidines such as phenoxazine
cytidine(1H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one),
phenothiazine cytidine
(1H-pyrimido[5,4-b][1,4]benzothiazin-2(3H)-one), G-clamps such as a
substituted phenoxazine cytidine (e.g.
9-(2-aminoethoxy)-H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one),
carbazole cytidine (2H-pyrimido[4,5-b]indol-2-one), pyridoindole
cytidine (H-pyrido[3',':4,5]pyrrolo[2,3-d]pyrimidin-2-one).
Modified bases may also include those in which the purine or
pyrimidine base is replaced with other heterocycles, for example
7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone.
Further nucleobases include those described in U.S. Pat. No.
3,687,808, those disclosed in The Concise Encyclopedia Of Polymer
Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John
Wiley & Sons, 1990, those disclosed by Englisch et al.,
Angewandte Chemie, International Edition, 1991, 30, 613, and those
disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and
Applications, pages 289-302, Crooke, S. T. and Lebleu, B., ed., CRC
Press, 1993.
[0270] Another modification includes phosphorodithioate linkages.
Knowing that phosphorodithioate ODNs (PS2-ODNs) and PS-ODNs have a
similar binding affinity to proteins (Tonkinson et al. (1994)
Antisense Res. Dev. 4 :269-278)(Cheng et al. (1997) J. Mol. Recogn.
10:101-107) and knowing that a possible mechanism of action of ODNs
is binding to viral proteins, it could be desirable to include
phosphorodithioate linkages on the antiviral ODNs described in this
invention.
[0271] Another approach to modify ODNs is to produce stereodefined
or stereo-enriched ODNs as described in Yu at al (2000) Bioorg.
Med. Chem. 8:275-284 and in Inagawa et al. (2002) FEBS Lett.
25:48-52. ODNs prepared by conventional methods consist of a
mixture of diastereomers by virtue of the asymmetry around the
phosphorus atom involved in the internucleotide linkage. This may
affect the stability of the binding between ODNs and viral
components such as viral proteins. Previous data showed that
protein binding is significantly stereo-dependent (Yu et al.).
Thus, using stereodefined or stereo-enriched ODNs could improve
their protein binding properties and improve their antiviral
efficacy.
[0272] The incorporation of modifications such as those described
above can be utilized in many different incorporation patterns and
levels. That is, a particular modification need not be included at
each nucleotide or linkage in an oligonucleotide, and different
modifications can be utilized in combination in a single
oligonucleotide, or even in a single nucleotide.
[0273] Oligonucleotide Synthesis
[0274] The present oligonucleotides can by synthesized using
methods known in the art. For example, unsubstituted and
substituted phosphodiester (P.dbd.O) oligonucleotides can be
synthesized on an automated DNA synthesizer (e.g., Applied
Biosystems model 380B) using standard phosphoramidite chemistry
with oxidation by iodine. Phosphorothioates (P.dbd.S) can be
synthesized as for the phosphodiester oligonucleotides except the
standard oxidation bottle can be replaced by 0.2 M solution of
311-1,2-benzodithiole-3-one 1,1-dioxide in acetonitrile for the
step-wise thioation of the phosphite linkages. The thioation wait
step can be increased to 68 sec, followed by the capping step.
After cleavage from the CPG column and deblocking in concentrated
ammonium hydroxide at 55.degree. C. (18 h), the oligonucleotides
can be purified by precipitating twice with 2.5 volumes of ethanol
from a 0.5 M NaCl solution.
[0275] Phosphinate oligonucleotides can be prepared as described in
U.S. Pat. No. 5,508,270; alkyl phosphonate oligonucleotides can be
prepared as described in U.S. Pat. No. 4,469,863;
3'-Deoxy-3'-methylene phosphonate oligonucleotides can be prepared
as described in U.S. Pat. Nos. 5,610,289 and 5,625,050;
phosphoramidite oligonucleotides can be prepared as described in
U.S. Pat. No. 5,256,775 and U.S. Pat. No. 5,366,878;
alkylphosphonothioate oligonucleotides can be prepared as described
in published PCT applications PCT/US94/00902 and PCT/US93/06976
(published as WO 94/17093 and WO 94/02499, respectively);
3'-Deoxy-3'-amino phosphoramidate oligonucleotides can be prepared
as described in U.S. Pat. No. 5,476,925; Phosphotriester
oligonucleotides can be prepared as described in U.S. Pat. No.
5,023,243; borano phosphate oligonucleotides can be prepared as
described in U.S. Pat. Nos. 5,130,302 and 5,177,198;
methylenemethylimino linked oligonucleotides, also identified as
MMI linked oligonucleotides, methylenedimethyl-hydrazo linked
oligonucleotides, also identified as MDII linked oligonucleotides,
and methylenecarbonylamino linked oligonucleotides, also identified
as amide-3 linked oligonucleotides, and methyleneaminocarbonyl
linked oligo-nucleotides, also identified as amide-4 linked
oligonucleo-sides, as well as mixed backbone compounds having, for
instance, alternating MMI and P=0 or P.dbd.S linkages can be
prepared as described in U.S. Pat. Nos. 5,378,825, 5,386,023,
5,489,677, 5,602,240 and 5,610,289; formacetal and thioformacetal
linked oligonucleotides can be prepared as described in U.S. Pat.
Nos. 5,264,562 and 5,264,564; and ethylene oxide linked
oligonucleotides can be prepared as described in U.S. Pat. No.
5,223,618. Each of the cited patents and patent applications is
incorporated by reference herein in its entirety.
[0276] Oligonucleotide Formulations and Pharmaceutical
Compositions
[0277] The present oligonucleotides can be prepared in an
oligonucleotide formulation or pharmaceutical composition. Thus,
the present oligonucleotides may also be admixed, encapsulated,
conjugated or otherwise associated with other molecules, molecule
structures or mixtures of compounds, as for example, liposomes,
receptor targeted molecules, oral, rectal, topical or other
formulations, for assisting in uptake, distribution and/or
absorption. Exemplary United States patents that describe the
preparation of such uptake, distribution and/or absorption
assisting formulations include, for example, U.S. Pat. Nos.
5,108,921; 5,354,844; 5,416,016; 5,459,127; 5,521,291; 5,543,158;
5,547,932; 5,583,020; 5,591,721; 4,426,330; 4,534,899; 5,013,556;
5,108,921; 5,213,804; 5,227,170; 5,264,221; 5,356,633; 5,395,619;
5,416,016; 5,417,978; 5,462,854; 5,469,854; 5,512,295; 5,527,528;
5,534,259; 5,543,152; 5,556,948; 5,580,575; and 5,595,756, each of
which is incorporated herein by reference in its entirety.
[0278] The oligonucleotides, formulations, and compositions of the
invention include any pharmaceutically acceptable salts, esters, or
salts of such esters, or any other compound which, upon
administration to an animal including a human, is capable of
providing (directly or indirectly) the biologically active
metabolite or residue thereof. Accordingly, for example, the
disclosure is also drawn to prodrugs and pharmaceutically
acceptable salts of the compounds of the invention,
pharmaceutically acceptable salts of such prodrugs, and other
bioequivalents.
[0279] The term "prodrug" indicates a therapeutic agent that is
prepared in an inactive form that is converted to an active form
(i.e., drug) within the body or cells thereof by the action of
endogenous enzymes or other chemicals and/or conditions. In
particular embodiments, prodrug versions of the present
oligonucleotides are prepared as SATE [(S-acetyl-2-thioethyl)
phosphate] derivatives according to the methods disclosed in
Gosselin et al., WO 93/24510 and in Imbach et al., WO 94/26764 and
U.S. Pat. No. 5,770,713, which are hereby incorporated by reference
in their entireties.
[0280] The term "pharmaceutically acceptable salts" refers to
physiologically and pharmaceutically acceptable salts of the
present compounds: i.e., salts that retain the desired biological
activity of the parent compound and do not impart undesired
toxicological effects thereto. Many such pharmaceutically
acceptable salts are known and can be used in the present
invention.
[0281] For oligonucleotides, useful examples of pharmaceutically
acceptable salts include but are not limited to salts formed with
cations such as sodium, potassium, ammonium, magnesium, calcium,
polyamines such as spermine and spermidine, etc.; acid addition
salts formed with inorganic acids, for example hydrochloric acid,
hydrobromic acid, sulfuric acid, phosphoric acid, nitric acid and
the like; salts formed with organic acids such as, for example,
acetic acid, oxalic acid, tartaric acid, succinic acid, maleic
acid, fumaric acid, gluconic acid, citric acid, malic acid,
ascorbic acid, benzoic acid, tannic acid, palmitic acid, alginic
acid, polyglutamic acid, naphthalenesulfonic acid, methanesulfonic
acid, p-toluenesulfonic acid, naphthalenedisulfonic acid,
polygalacturonic acid, and the like; and salts formed from
elemental anions such as chlorine, bromine, and iodine.
[0282] The present invention also includes pharmaceutical
compositions and formulations which contain the antiviral
oligonucleotides of the invention. Such pharmaceutical compositions
may be administered in a number of ways depending upon whether
local or systemic treatment is desired and upon the area to be
treated. For example, administration may be topical (including
ophthalmic and to mucous membranes including vaginal and rectal
delivery); pulmonary, e.g., by inhalation or insufflation of
powders or aerosols, including by nebulizer; intratracheal;
intranasal; epidermal and transdermal; oral; or parenteral.
Parenteral administration includes intravenous, intraarterial,
subcutaneous, intraperitoneal or intramuscular injection or
infusion; or intracranial, e.g., intrathecal or intraventricular,
administration.
[0283] Pharmaceutical compositions and formulations for topical
administration may include transdermal patches, ointments, lotions,
creams, gels, drops, suppositories, sprays, liquids and powders.
Conventional pharmaceutical carriers, aqueous, powder or oily
bases, thickeners and the like may be necessary or desirable.
Coated condoms, gloves and the like may also be useful. Preferred
topical formulations include those in which the oligonucleotides of
the invention are in admixture with a topical delivery agent such
as lipids, liposomes, fatty acids, fatty acid esters, steroids,
chelating agents and surfactants. Preferred lipids and liposomes
include neutral (e.g. dioleoylphosphatidyl DOPE ethanolamine,
dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl
choline) negative (e.g. dimyristoylphosphatidyl glycerol DMPG) and
cationic (e.g. dioleoyltetramethylaminopropyl DOTAP and
dioleoylphosphatidyl ethanolamine DOTMA). Oligonucleotides may be
encapsulated within liposomes or may form complexes thereto, in
particular to cationic liposomes. Alternatively, oligonucleotides
may be complexed to lipids, in particular to cationic lipids.
Preferred fatty acids and esters include but are not limited
arachidonic acid, oleic acid, eicosanoic acid, laurie acid,
caprylic acid, capric acid, myristic acid, palmitic acid, stearic
acid, linoleic acid, linolenic acid, dicaprate, tricaprate,
monoolein, dilaurin, glyceryl 1-monocaprate,
1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or
a C.sub.1-10 alkyl ester (e.g. isopropylmyristate IPM),
monoglyceride, diglyceride or pharmaceutically acceptable salt
thereof.
[0284] Compositions and formulations for oral administration
include powders or granules, microparticulates, nanoparticulates,
suspensions or solutions in water or non-aqueous media, capsules,
gel capsules, sachets, tablets or minitablets. Thickeners,
flavoring agents, diluents, emulsifiers, dispersing aids or binders
may be desirable. Preferred oral formulations are those in which
oligonucleotides of the invention are administered in conjunction
with one or more penetration enhancers surfactants and chelators.
Exemplary surfactants include fatty acids and/or esters or salts
thereof, bile acids and/or salts thereof. Exemplary bile
acids/salts include chenodeoxycholic acid (CDCA) and
ursodeoxychenedeoxycholic acid (UDCA), cholic acid, dehydrocholic
acid, deoxycholic acid, glucholic acid, glycholic acid,
glycodeoxycholic acid, taurocholic acid, taurodeoxycholic acid,
sodium tauro-24,25-dihydro-fusidate, sodium glycodihydrofusidate.
Exemplary fatty acids include arachidonic acid, undecanoic acid,
oleic acid, lauric acid, caprylic acid, capric acid, myristic acid,
palmitic acid, stearic acid, linoleic acid, linolenic acid,
dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate,
1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or
a monoglyceride, a diglyceride or a pharmaceutically acceptable
salt thereof (e.g. sodium). Also preferred are combinations of
penetration enhancers, for example, fatty acids/salts in
combination with bile acids/salts. A particularly preferred
combination is the sodium salt of lauric acid, capric acid and
UDCA. Further exemplary penetration enhancers include
polyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether.
Oligonucleotides of the invention may be delivered orally in
granular form including sprayed dried particles, or complexed to
form micro or nanoparticles. Oligonucleotide complexing agents
include poly-amino acids; polyimines; polyacrytates;
polyalkylacrylates, polyoxethanes, polyalkylcyanoacrylates;
cationized gelatins, albumins, starches, acrylates,
polyethyleneglycols (PEG) and starches; polyalkylcyanoacrylates;
DEAE-derivatized polyimines, pollulans, celluloses, and starches.
Particularly advantageous complexing agents include chitosan,
N-trimethylchitosan, poly-L-lysine, polyhistidine, polyorithine,
polyspermines, protamine, polyvinylpyridine,
polythiodiethylamino-methylethylene P(TDAE), polyaminostyrene (e.g.
p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate),
poly(butylcyanoacrylate), poly(isobutylcyanoacrylate),
poly(isohexylcynaoacrylate), DEAE-methacrylate, DEAE-hexylacrylate,
DEAE-acrylamide, DEAE-albumin and DEAE-dextran, polymethylacrylate,
polyhexylacrylate, poly(D,L-lactic acid),
poly(DL-lactic-co-glycolic acid (PLGA), alginate, and
polyethyleneglycol (PEG).
[0285] Compositions and formulations for parenteral, intrathecal or
intraventricular administration may include sterile aqueous
solutions which may also contain buffers, diluents and other
suitable additives such as, but not limited to, penetration
enhancers, carrier compounds and other pharmaceutically acceptable
carriers or excipients.
[0286] Pharmaceutical compositions of the present invention
include, but are not limited to, solutions, emulsions, and
liposome-containing formulations. These compositions may be
generated from a variety of components that include, but are not
limited to, preformed liquids, self-emulsifying solids and
self-emulsifying semisolids.
[0287] The pharmaceutical formulations of the present invention,
which may conveniently be presented in unit dosage form, may be
prepared according to conventional techniques well known in the
pharmaceutical industry. Such techniques include the step of
bringing into association the active ingredients with the
pharmaceutical carrier(s) or excipient(s). In general the
formulations are prepared by uniformly and intimately bringing into
association the active ingredients with liquid carriers or finely
divided solid carriers or both, and then, if necessary, shaking the
product.
[0288] The compositions of the present invention may be formulated
into any of many possible dosage forms such as, but not limited to,
tablets, capsules, gel capsules, liquid syrups, soft gels,
suppositories, and enemas. The compositions of the present
invention may also be formulated as suspensions in aqueous,
non-aqueous or mixed media. Aqueous suspensions may further contain
substances which increase the viscosity of the suspension
including, for example, sodium carboxymethylcellulose, sorbitol
and/or dextran. The suspension may also contain stabilizers.
[0289] In one embodiment of the present invention the
pharmaceutical compositions may be formulated and used as foams.
Pharmaceutical foams include formulations such as, but not limited
to, emulsions, microemulsions, creams, jellies and liposomes. While
basically similar in nature these formulations vary in the
components and the consistency of the final product. The
preparation of such compositions and formulations is generally
known to those skilled in the pharmaceutical and formulation arts
and may be applied to the formulation of the compositions of the
present invention.
[0290] Emulsions
[0291] The formulations and compositions of the present invention
may be prepared and formulated as emulsions. Emulsions are
typically heterogenous systems of one liquid dispersed in another
in the form of droplets usually exceeding 0.1 .mu.m in diameter.
(Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and
Banker (lids.), 1988, Marcel Dekker, Inc., New York, N.Y., volume
1, p. 199; Rosoff, in Pharmaceutical Dosage Forms, Lieberman,
Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York,
N.Y., Volume 1, p. 245; Block in Pharmaceutical Dosage Forms,
Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New
York, N.Y., volume 2, p. 335; Higuchi et at., in Remington's
Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p.
301). Emulsions are often biphasic systems comprising of two
immiscible liquid phases intimately mixed and dispersed with each
other. In general, emulsions may be either water-in-oil (w/o) or of
the oil-in-water (o/w) variety. When an aqueous phase is finely
divided into and dispersed as minute droplets into a bulk oily
phase the resulting composition is called a water-in-oil (w/o)
emulsion. Alternatively, when an oily phase is finely divided into
and dispersed as minute droplets into a bulk aqueous phase the
resulting composition is called an oil-in-water (o/w) emulsion.
Emulsions may contain additional components in addition to the
dispersed phases and the active drug which may be present as a
solution in either the aqueous phase, oily phase or itself as a
separate phase. Pharmaceutical excipients such as emulsifiers,
stabilizers, dyes, and anti-oxidants may also be present in
emulsions as needed. Pharmaceutical emulsions may also be multiple
emulsions that are comprised of more than two phases such as, for
example, in the case of oil-in-water-in-oil (o/w/o) and
water-in-oil-in-water (w/o/w) emulsions. Such complex formulations
often provide certain advantages that simple binary emulsions do
not. Multiple emulsions in which individual oil droplets of an o/w
emulsion enclose small water droplets constitute a w/o/w emulsion.
Likewise a system of oil droplets enclosed in globules of water
stabilized in an oily continuous provides an o/w/o emulsion.
[0292] Emulsions are characterized by little or no thermodynamic
stability. Often, the dispersed or discontinuous phase of the
emulsion is well dispersed into the external or continuous phase
and maintained in this form through the means of emulsifiers or the
viscosity of the formulation. Either of the phases of the emulsion
may be a semisolid or a solid, as is the case of emulsion-style
ointment bases and creams. Other means of stabilizing emulsions
entail the use of emulsifiers that may be incorporated into either
phase of the emulsion. Emulsifiers may broadly be classified into
four categories: synthetic surfactants, naturally occurring
emulsifiers, absorption bases, and finely dispersed solids (Idson,
in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker
(Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p.
199).
[0293] Synthetic surfactants, also known as surface active agents,
have found wide applicability in the formulation of emulsions and
have been reviewed in the literature (Rieger, in Pharmaceutical
Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel
Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199).
Surfactants are typically amphiphilic and comprise a hydrophilic
and a hydrophobic portion. The ratio of the hydrophilic to the
hydrophobic nature of the surfactant has been termed the
hydrophile/lipophile balance (HLB) and is a valuable tool in
categorizing and selecting surfactants in the preparation of
formulations. Surfactants may be classified into different classes
based on the nature of the hydrophilic group: non-ionic, anionic,
cationic and amphoteric (Rieger, in Pharmaceutical Dosage Forms,
Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New
York, N.Y., volume 1, p. 285).
[0294] Naturally occurring emulsifiers used in emulsion
formulations include lanolin, beeswax, phosphatides, lecithin and
acacia. Absorption bases possess hydrophilic properties such that
they can soak up water to form w/o emulsions yet retain their
semisolid consistencies, such as anhydrous lanolin and hydrophilic
petrolatum. Finely divided solids have also been used as good
emulsifiers especially in combination with surfactants and in
viscous preparations. These include polar inorganic solids, such as
heavy metal hydroxides, nonswelling clays such as bentonite,
attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum
silicate and colloidal magnesium aluminum silicate, pigments and
nonpolar solids such as carbon or glyceryl tristearate.
[0295] A large variety of non-emulsifying materials are also
included in emulsion formulations and contribute to the properties
of emulsions. These include fats, oils, waxes, fatty acids, fatty
alcohols, fatty esters, humectants, hydrophilic colloids,
preservatives and antioxidants (Block, in Pharmaceutical Dosage
Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker,
Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical
Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel
Dekker, Inc., New York, N.Y., volume 1, p. 199).
[0296] Hydrophilic colloids or hydrocolloids include naturally
occurring gums and synthetic polymers such as polysaccharides (for
example, acacia, agar, alginic acid, carrageenan, guar gum, karaya
gum, and tragacanth), cellulose derivatives (for example,
carboxymethylcellulose and carboxypropylcellulose), and synthetic
polymers (for example, carbomers, cellulose ethers, and
carboxyvinyl polymers). These disperse or swell in water to form
colloidal solutions that stabilize emulsions by forming strong
inter-facial films around the dispersed-phase droplets and by
increasing the viscosity of the external phase.
[0297] Since emulsions often contain a number of ingredients such
as carbohydrates, proteins, sterols and phosphatides that may
readily support the growth of microbes, these formulations often
incorporate preservatives. Commonly used preservatives included in
emulsion formulations include methyl paraben, propyl paraben,
quaternary ammonium salts, benzalkonium chloride, esters of
p-hydroxybenzoic acid, and boric acid, Antioxidants are also
commonly added to emulsion formulations to prevent deterioration of
the formulation. Antioxidants used may be free radical scavengers
such as tocopherols, alkyl gallates, butylated hydroxyanisole,
butylated hydroxytoluene, or reducing agents such as ascorbic acid
and sodium metabisulfite, and antioxidant synergists such as citric
acid, tartaric acid, and lecithin.
[0298] The application of emulsion formulations via dermatological,
oral and parenteral routes and methods for their manufacture have
been reviewed in the literature (Idson, in Pharmaceutical Dosage
Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker,
Inc., New York, N.Y., volume 1, p. 199). Emulsion formulations for
oral delivery have been very widely used because of reasons of ease
of formulation, efficacy from an absorption and bioavailability
standpoint. (Rosoff, in Pharmaceutical Dosage Forms, Lieberman,
Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York,
N.Y., volume 1, p. 245; Idson, in Pharmaceutical Dosage Forms,
Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New
York, N.Y., volume 1, p. 199). Mineral-oil base laxatives,
oil-soluble vitamins and high fat nutritive preparations are among
the materials that have commonly been administered orally as o/w
emulsions.
[0299] In one embodiment of the present invention, the compositions
of oligonucleotides are formulated as microemulsions. A
microemulsion may be defined as a system of water, oil and
amphiphile which is a single optically isotropic and
thermodynamically stable liquid solution (Rosoff, in Pharmaceutical
Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel
Dekker, Inc., New York, N.Y., volume 1, p. 245). Typically
micro-emulsions are systems that are prepared by first dispersing
an oil in an aqueous surfactant solution and then adding a
sufficient amount of a fourth component, generally an intermediate
chain-length alcohol to form a transparent system. Therefore,
microemulsions have also been described as thermodynamically
stable, isotropically clear dispersions of two immiscible liquids
that are stabilized by interfacial films of surface-active
molecules (Leung and Shah, in: Controlled Release of Drugs:
Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH
Publishers, New York, pages 185-215). Microemulsions commonly are
prepared via a combination of three to five components that include
oil, water, surfactant, cosurfactant and electrolyte. Whether the
microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w)
type is dependent on the properties of the oil and surfactant used
and on the structure and geometric packing of the polar heads and
hydrocarbon tails of the surfactant molecules (Schott, in
Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton,
Pa., 1985, p. 271).
[0300] The phenomenological approach utilizing phase diagrams has
been extensively studied and has yielded a comprehensive knowledge,
to one skilled in the art, of how to formulate microemulsions
(Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and
Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1,
p. 245; Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger
and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y.,
volume 1, p. 335). Compared to conventional emulsions,
microemulsions offer the advantage of solubilizing water-insoluble
drugs in a formulation of thermodynamically stable droplets that
are formed spontaneously.
[0301] Surfactants used in the preparation of microemulsions
include, but are not limited to, ionic surfactants, non-ionic
surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol
fatty acid esters, tetraglycerol monolaurate (ML31O), tetraglycerol
monooleate (MO0310), hexaglycerol monooleate (PO310), hexaglycerol
pentaoleate (PO500), decaglycerol monocaprate (MCA750),
decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750),
decaglycerol decaoleate (DA0750), alone or in combination with
cosurfactants. The cosurfactant, usually a short-chain alcohol such
as ethanol, 1-propanol, and 1-butanol, serves to increase the
interfacial fluidity by penetrating into the surfactant film and
consequently creating a disordered film because of the void space
generated among surfactant molecules. Microemulsions may, however,
be prepared without the use of cosurfactants and alcohol-free
self-emulsifying microemulsion systems are known in the art. The
aqueous phase may typically be, but is not limited to, water, an
aqueous solution of the drug, glycerol, PEG300, PEG400,
polyglycerols, propylene glycols, and derivatives of ethylene
glycol. The oil phase may include, but is not limited to, materials
such as Captex 300, Captex 355, Capmul MCM, fatty acid esters,
medium chain (C8-C12) mono, di, and tri-glycerides,
polyoxyethylated glyceryl fatty acid esters, fatty alcohols,
polyglycolized glycerides, saturated polyglycolized C8-C10
glycerides, vegetable oils and silicone oil.
[0302] Microemulsions are particularly of interest from the
standpoint of drug solubilization and the enhanced absorption of
drugs. Lipid based microemulsions (both o/w and w/o) have been
proposed to enhance the oral bioavailability of drugs, including
peptides (Constantinides et al., Pharmaceutical Research, 1994, 11,
1385-1390; Ritschet, Met/i. Find. Exp. Clin. Pharmacol., 1993, 13,
205). Micro-emulsions afford advantages of improved drug
solubilization, protection of drug from enzymatic hydrolysis,
possible enhancement of drug absorption due to surfactant-induced
alterations in membrane fluidity and permeability, ease of
preparation, ease of oral administration over solid dosage forms,
improved clinical potency, and decreased toxicity (Constantinides
et at., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J.
Pharm. Set, 1996, 85, 138-143). Often microemulsions may form
spontaneously when their components are brought together at ambient
temperature. This may be particularly advantageous when formulating
thermolabile drugs, peptides or oligonucleotides. Microemulsions
have also been effective in the transdermal delivery of active
components in both cosmetic and pharmaceutical applications. It is
expected that the microemulsion compositions and formulations of
the present invention will facilitate the increased systemic
absorption of oligonucleotides and nucleic acids from the
gastrointestinal tract, as well as improve the local cellular
uptake of oligonucleotides and nucleic acids within the
gastrointestinal tract, vagina, buccal cavity and other areas of
administration.
[0303] Microemulsions of the present invention may also contain
additional components and additives such as sorbitan monostearate
(Grill 3), Labrasol, and penetration enhancers to improve the
properties of the formulation and to enhance the absorption of the
oligonucleotides and nucleic acids of the present invention.
Penetration enhancers used in the microemulsions of the present
invention may be classified as belonging to one of five broad
categories--surfactants, fatty acids, bile salts, chelating agents,
and non-chelating non-surfactants (Lee et al., Critical Reviews in
Therapeutic Drug Carrier Systems, 1991, p. 92).
[0304] Liposomes
[0305] There are many organized surfactant structures besides
microemulsions that have been studied and used for the formulation
of drugs. These include monolayers, micelles, bilayers and
vesicles. Vesicles offer specificity and extended duration of
action for drug delivery. Thus, as used herein, the term "liposome"
refers to a vesicle composed of amphiphilic lipids arranged in a
spherical bilayer or bilayers, i.e., liposomes are unilamellar or
multilamellar vesicles which have a membrane formed from a
lipophilic material and an aqueous interior. The aqueous portion
typically contains the composition to be delivered. In order to
cross intact mammalian skin, lipid vesicles must pass through a
series of fine pores, each with a diameter less than 50 nm, under
the influence of a suitable transdermal gradient. Therefore, it is
desirable to use a liposome which is highly deformable and able to
pass through such fine pores. Additional factors for liposomes
include the lipid surface charge, and the aqueous volume of the
liposomes.
[0306] Further advantages of liposomes include; liposomes obtained
from natural phospholipids are biocompatible and biodegradable;
liposomes can incorporate a wide range of water and lipid soluble
drugs; liposomes can protect encapsulated drugs in their internal
compartments from metabolism and degradation (Rosoff, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245).
[0307] For topical administration, there is evidence that liposomes
present several advantages over other formulations. Such advantages
include reduced side-effects related to high systemic absorption of
the administered drug, increased accumulation of the administered
drug at the desired target, and the ability to administer a wide
variety of drugs, both hydrophilic and hydrophobic, into the skin.
Compounds including analgesics, antibodies, hormones and
high-molecular weight DNAs have been administered to the skin,
generally resulting in targeting of the upper epidermis.
[0308] Liposomes fall into two broad classes. Cationic liposomes
are positively charged liposomes which interact with the negatively
charged DNA molecules to form a stable complex. The positively
charged DNA/liposome complex binds to the negatively charged cell
surface and is internalized in an endosome. Due to the acidic pH
within the endosome, the liposomes are ruptured, releasing their
contents into the cell cytoplasm (Wang et at., Biochem. Biophys.
Res. Commun., 1987, 147, 980-985).
[0309] Liposomes which are pH-sensitive or negatively-charged,
entrap DNA rather than complex with it. Since both the DNA and the
lipid are similarly charged, repulsion rather than complex
formation occurs. The DNA is thus entrapped in the aqueous interior
of these liposomes. pH-sensitive liposomes have been used, for
example, to deliver DNA encoding the thymidine kinase gene to cell
monolayers in culture (Zhou et al., Journal of Controlled Release,
1992, 19, 269-274).
[0310] One major type of liposomal composition includes
phospholipids other than naturally-derived phosphatidylcholine.
Neutral liposome compositions, for example, can be formed from
dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl
phosphatidylcholine (DPPC). Anionic liposome compositions generally
are formed from dimyristoyl phosphatidylglycerol, while anionic
fusogenic liposomes are formed primarily from dioleoyl
phosphatidylethanolamine (DOPE). Another type of liposomal
composition is formed from phosphatidylcholine (PC) such as, for
example, soybean PC, and egg PC. Another type is formed from
mixtures of phospholipid and/or phosphatidylcholine and/or
cholesterol.
[0311] Several studies have assessed the topical delivery of
liposomal drug formulations to the skin. Application of liposomes
containing interferon to guinea pig skin resulted in a reduction of
skin herpes sores while delivery of interferon via other means
(e.g. as a solution or as an emulsion) were ineffective (Weiner et
at., Journal of Drug Targeting, 1992, 2, 405-410). Further, an
additional study tested the efficacy of interferon administered as
part of a liposomal formulation to the administration of interferon
using an aqueous system, and concluded that the liposomal
formulation was superior to aqueous administration (du Plessis et
al., Antiviral Research, 1992, 18, 259-265).
[0312] Non-ionic liposomal systems have also been examined to
determine their utility in the delivery of drugs to the skin, in
particular systems comprising non-ionic surfactant and cholesterol.
Non-ionic liposomal formulations comprising Novasone.TM. I
(glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether)
and Novasome.TM. II (glyceryl
distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used
to deliver cyclosporin-A into the dermis of mouse skin. Results
indicated that such non-ionic liposomal systems were effective in
facilitating the deposition of cyclosporin-A into different layers
of the skin (Hu et at. S.T.P. Pharma. Sci., 1994, 4, 6, 466).
[0313] Liposomes also include "sterically stabilized" liposomes, a
term which, as used herein, refers to liposomes comprising one or
more specialized lipids that, when incorporated into liposomes,
result in enhanced circulation lifetimes relative to liposomes
lacking such specialized lipids. Examples of sterically stabilized
liposomes are those in which part of the vesicle-forming lipid
portion of the liposome include one or more glycolipids, such as
monosialoganglioside F.sub.M1, or is derivatized with one or more
hydrophilic polymers, such as a polyethylene glycol (PEG) moiety.
Without being bound by any particular theory, it is believed that
for sterically stabilized liposomes containing gangliosides,
sphingomyelin, or PEG-derivatized lipids, the increase in
circulation half-life of these sterically stabilized liposomes is
due to a reduced uptake into cells of the reticuloendothelial
system (RES) (Allen et at., FEBS Lett., 1987, 223, 42; Wu et al.,
Cancer Research, 1993, 53, 3765).
[0314] Various liposomes that include one or more glycolipids have
been reported in Papahadjopoulos et al., Ann. N.Y. Acad. Sci.,
1987, 507, 64 (monosiatoganglioside G.sub.M1, galactocerebroside
sulfate and phosphatidylinositol); Gabizon et at., Proc. Natl.
Acad. Sci. USA., 1988, 85, 6949,;Allen et al., U.S. Pat. No.
4,837,028 and International Application Publication WO 88/04924
(sphingomyelin and the ganglioside G.sub.M1 or a galactocerebroside
sulfate ester); Webb et al., U.S. Pat. No. 5,543,152
(sphingomyelin); Lim et al., WO 97/13499
(1,2-sn-dimyristoylphosphatidylcholine).
[0315] Liposomes that include lipids derivatized with one or more
hydrophilic polymers, and methods of preparation are described, for
example, in Sunamoto et al., Bull. Chem. Soc. Jpn., 1980, 53, 2778
(a nonionic detergent, 2C.sub.1215G, that contains a PEG moiety);
Ilium et al., FEBS Lett., 1984, 167, 79 (hydrophilic coating of
polystyrene particles with polymeric glycols); Sears, U.S. Pat.
Nos. 4,426,330 and 4,534,899 (synthetic phospholipids modified by
the attachment of carboxylic groups of polyalkylene glycols (e.g.,
PEG)); Klibanov et al., FEBS Lett., 1990, 268, 235
(phosphatidylethanolamine (PE) derivatized with PEG or PEG
stearate); Blume et al., Biochimica et Biophysica Acta, 1990, 1029,
91 (PEG-derivatized phospholipids, e.g., DSPE-PEG, formed from the
combination of distearoylphosphatidylethanolamine (DSPE) and PEG);
Fisher, European Patent No. EP 0 445 131 B1 and WO 90/04384
(covalently bound PEG moieties on liposome external surface);
Woodle et al., U.S. Pat. Nos. 5,013,556 and 5,356,633, and Martin
et al., U.S. Pat. No. 5,213,804 and European Patent No. EP 0 496
813 B1 (liposome compositions containing 1-20 mole percent of PE
derivatized with PEG); Martin et al., WO 91/05545 and U.S. Pat. No.
5,225,212 and in Zalipsky et al., WO 94/20073 (liposomes containing
a number of other lipid-polymer conjugates); Choi et al., WO
96/10391 (liposomes that include PEG-modified ceramide lipids);
Miyazaki et al., U.S. Pat. No. 5,540,935, and Tagawa et al., U.S.
Pat. No. 5,556,948 (PEG-containing liposomes that can be further
derivatized with functional moieties on their surfaces).
[0316] Liposomes that include nucleic acids have been described,
for example, in Thierry et al., WO 96/40062 (methods for
encapsulating high molecular weight nucleic acids in liposomes);
Tagawa et al., U.S. Pat. No. 5,264,221 (protein-bonded liposomes
containing RNA); Rahman et al., U.S. Pat. No. 5,665,710 (methods of
encapsulating oligodeoxynucleotides in liposomes); Love et al., WO
97/04787 (liposomes that include antisense oligonucleotides).
[0317] Another type of liposome, transfersomes are highly
deformable lipid aggregates which are attractive for drug delivery
vehicles. (Cevc et al., 1998, Biochim Biophys Acta.
1368(2):201-15.) Transfersomes may be described as lipid droplets
which are so highly deformable that they can penetrate through
pores which are smaller than the droplet. Transfersomes are
adaptable to the environment in which they are used, for example,
they are shape adaptive, self-repairing, frequently reach their
targets without fragmenting, and often self-loading. Transfersomes
can be made, for example, by adding surface edge-activators,
usually surfactants, to a standard liposomal composition.
[0318] Surfactants
[0319] Surfactants are widely used in formulations such as
emulsions
[0320] (including microemulsions) and liposomes. The most common
way of classifying and ranking the properties of the many different
types of surfactants, both natural and synthetic, is by the use of
the hydrophile/lipophile balance (HLB). The nature of the
hydrophilic group (also known as the "head") provides the most
useful means for categorizing the different surfactants used in
formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel
Dekker, Inc., New York, N.Y., 1988, p. 285).
[0321] If the surfactant molecule is not ionized, it is classified
as a nonionic surfactant. Nonionic surfactants are widely used in
pharmaceutical and cosmetic products and are usable over a wide
range of pH values, and with typical HLB values from 2 to about 18
depending on structure. Nonionic surfactants include nonionic
esters such as ethylene glycol esters, propylene glycol esters,
glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose
esters, and ethoxylated esters; and nonionic alkanolamides and
ethers such as fatty alcohol ethoxylates, propoxylated alcohols,
and ethoxylated/propoxylated block polymers are also included in
this class. The polyoxyethylene surfactants are the most commonly
used members of the nonionic surfactant class.
[0322] Surfactant molecules that carry a negative charge when
dissolved or dispersed in water are classified as anionic. Anionic
surfactants include carboxylates such as soaps, acyl lactylates,
acyl amides of amino acids, esters of sulfuric acid such as alkyl
sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl
benzene sulfonates, acyl isothionates, acyl laurates and
sulfosuccinates, and phosphates. The alkyl sulfates and soaps are
the most commonly used anionic surfactants.
[0323] Surfactant molecules that carry a positive charge when
dissolved or dispersed in water are classified as cationic.
Cationic surfactants include quaternary ammonium salts and
ethoxylated amines, with the quaternary ammonium salts used most
often.
[0324] Surfactant molecules that can carry either a positive or
negative charge are classified as amphoteric. Amphoteric
surfactants include acrylic acid derivatives, substituted
alkylamides, N-alkylbetaines and phosphatides.
[0325] The use of surfactants in drug products, formulations and in
emulsions has been reviewed in Rieger, in Pharmaceutical Dosage
Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).
[0326] Penetration Enhancers
[0327] In some embodiments, penetration enhancers are used in or
with a composition to increase the delivery of nucleic acids,
particularly oligonucleotides, to the skin of animals. Most drugs
are present in solution in both ionized and nonionized forms.
However, usually only lipid soluble or lipophilic drugs readily
cross cell membranes. It has been discovered that even
non-lipophilic drugs may cross cell membranes if the membrane to be
crossed is treated with a penetration enhancer. In addition to
aiding the diffusion of non-lipophilic drugs across cell membranes,
penetration enhancers also enhance the permeability of lipophilic
drugs.
[0328] Penetration enhancers may be classified as belonging to one
of five broad categories, i.e., surfactants, fatty acids, bile
salts, chelating agents, and non-chelating nonsurfactants (Lee et
al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.
92). Each of these classes of penetration enhancers is described
below in greater detail.
[0329] Surfactants: In connection with the present invention,
surfactants (or "surface-active agents") are chemical entities
which, when dissolved in an aqueous solution, reduce the surface
tension of the solution or the interfacial tension between the
aqueous solution and another liquid, with the result that
absorption of oligonucleotides through the mucosa is enhanced.
These penetration enhancers include, for example, sodium lauryl
sulfate, polyoxyethylene-9-lauryl ether and
polyoxyethylene-20-cetyl ether) (Lee et at., CriticalReviews in
Therapeutic Drug Carrier Systems, 1991, p. 92); and
perfluorochemical emulsions, such as FC-43. Takahashi et al., J.
Pharm. Pharmacol., 1988, 40, 252), each of which is incorporated
herein by reference in its entirety.
[0330] Fatty acids: Various fatty acids and their derivatives which
act as penetration enhancers include, for example, oleic acid,
lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic
acid, stearic acid, linoleic acid, linolenic acid, dicaprate,
tricaprate, monoolein (1-monooleoyl-rac-glycerol), dilaurin,
caprylic acid, arachidonic acid, glycerol 1-monocaprate,
1-dodecylazacycloheptan-2-one, acylcarnitines, acylcholines,
C.sub.1-10 alkyl esters thereof (e.g., methyl, isopropyl and
t-butyl), and mono- and diglycerides thereof (i.e., oleate,
laurate, caprate, myristate, palmitate, stearate, linoleate, etc.)
(Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems,
1991, p. 92; Muranishi, Critical Reviews in Therapeutic Drug
Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm.
Pharmacol., 1992, 44, 651-654), each of which is incorporated
herein by reference in its entirety.
[0331] Bile salts: The physiological role of bile includes the
facilitation of dispersion and absorption of lipids and fat-soluble
vitamins (Brunton, Chapter 38 in: Goodman & Gilman's The
Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al.
Eds., McGraw-Hill, New York, 1996, pp. 934-935). Various natural
bile salts, and their synthetic derivatives, act as penetration
enhancers. Thus the term "bile salts" includes any of the naturally
occurring components of bile as well as any of their synthetic
derivatives. The bile salts of the invention include, for example,
cholic acid (or its pharmaceutically acceptable sodium salt, sodium
cholate), dehydrocholic acid (sodium dehydrocholate), deoxycholic
acid (sodium deoxycholate), glucholic acid (sodium glucholate),
glycholic acid
[0332] (sodium glycocholate), glycodeoxycholic acid (sodium
glycodeoxycholate), taurocholic acid (sodium taurocholate),
taurodeoxycholic acid (sodium taurodeoxycholate), chenodeoxycholic
acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA),
sodium tauro-24,25-dihydro-fusidate (STDHF), sodium
glycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (Lee
et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991,
page 92; Swinyard, Chapter 39 In: Remington's Pharmaceutical
Sciences, 18th Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa.,
1990, pages 782-783; Muranishi, Critical Reviews in Therapeutic
Drug Carrier Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharm.
Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm:. Sci., 1990,
79, 579-583).
[0333] Chelating Agents: In the present context, chelating agents
can be regarded as compounds that remove metallic ions from
solution by forming complexes therewith, with the result that
absorption of oligonucleotides through the mucosa is enhanced. With
regards to their use as penetration enhancers in the present
invention, chelating agents have the added advantage of also
serving as DNase inhibitors, as most characterized DNA nucleases
require a divalent metal ion for catalysis and are thus inhibited
by chelating agents (Jarrett, J. Chromatogr., 1993, 618, 315-339).
Without limitation, chelating agents include disodium
ethylenediaminetetraacetate (EDTA), citric acid, salicylates (e.g.,
sodium salicylate, 5-methoxysalicylate and homovanilate), N-acyl
derivatives of collagen, laureth-9 and N-amino acyl derivatives of
beta-diketones (enamines)(Lee et al., Critical Reviews in
Therapeutic Drug Carrier Systems, 1991, page 92; Muranishi,
Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7,
1-33; Buur et al., J. Control Rel., 1990, 14, 43-51).
[0334] Non-chelating non-surfactants: As used herein, non-chelating
non-surfactant penetration enhancing compounds are compounds that
do not demonstrate significant chelating agent or surfactant
activity, but still enhance absorption of oligonucleotides through
the alimentary mucosa (Muranishi, Critical Reviews in Therapeutic
Drug Carrier Systems, 1990, 7, 1-33). Examples of such penetration
enhancers include unsaturated cyclic ureas, 1-alkyl- and
1-alkenylazacyclo-alkanone derivatives (Lee et al., Critical
Reviews in Therapeutic Drug Carrier Systems, 1991, page 92); and
nonsteroidal anti-inflammatory agents such as diclofenac sodium,
indomethacin and phenylbutazone (Yamashita et al J. Pharm.
Pharmacol., 1987, 39, 621-626).
[0335] Agents that enhance uptake of oligonucleotides at the
cellular level may also be added to the pharmaceutical and other
compositions and formulations of the present invention. For
example, cationic lipids, such as lipofectin (Junichi et al, U.S.
Pat. No. 5,705,188), cationic glycerol derivatives, and
polycationic molecules, such as polylysine (Lollo et al., PCT
Application WO 97/30731), are also known to enhance the cellular
uptake of oligonucleotides.
[0336] Other agents may be utilized to enhance the penetration of
the administered nucleic acids, including glycols such as ethylene
glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and
terpenes such as limonene and menthone.
[0337] Carriers
[0338] Certain compositions of the present invention also
incorporate carrier compounds in the formulation. As used herein,
"carrier compound" or "carrier" can refer to a nucleic acid, or
analog thereof, which is inert (i.e., does not possess biological
activity per se) but is recognized as a nucleic acid by in vivo
processes that reduce the bioavailability of a nucleic acid having
biological activity by, for example, degrading the biologically
active nucleic acid or promoting its removal from circulation. The
coadministration of a nucleic acid and a carrier compound, often
with an excess of the latter substance, can result in a substantial
reduction of the amount of nucleic acid recovered in the liver,
kidney or other extracirculatory reservoirs. For example, the
recovery of a partially phosphorothioate oligonucleotide in hepatic
tissue can be reduced when it is coadministered with polyinosinic
acid, dextran sulfate, polycytidic acid or 4-acetamido-4'
isothiocyano-stilbene-2,2-disulfonic acid (Miyao et al.,
AntisenseRes. Dev., 1995, 5, 115-121; Takakura et al., Antisense
& Nucl. Acid Drug Dev., 1996, 6, 177-183), each of which is
incorporated herein by reference in its entirety.
[0339] Excipients
[0340] In contrast to a carrier compound, a "pharmaceutical
carrier" or "excipient" is a pharmaceutically acceptable solvent,
suspending agent or any other pharmacologically inert vehicle for
delivering one or more nucleic acids to an animal, and is typically
liquid or solid. A pharmaceutical carrier is generally selected to
provide for the desired bulk, consistency, etc., when combined with
a nucleic acid and the other components of a given pharmaceutical
composition, in view of the intended administration mode. Typical
pharmaceutical carriers include, but are not limited to, binding
agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or
hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and
other sugars, microcrystalline cellulose, pectin, gelatin, calcium
sulfate, ethyl cellulose, polyacrylates or calcium hydrogen
phosphate, etc.); lubricants (e.g., magnesium stearate, talc,
silica, colloidal silicon dioxide, stearic acid, metallic
stearates, hydrogenated vegetable oils, corn starch, polyethylene
glycols, sodium benzoate, sodium acetate, etc.); disintegrants
(e.g., starch, sodium starch glycotate, etc.); and wetting agents
(e.g., sodium lauryl sulphate, etc.).
[0341] Pharmaceutically acceptable organic or inorganic excipients
suitable for non-parenteral administration which do not
deleteriously react with nucleic acids can also be used to
formulate the compositions of the present invention. Suitable
pharmaceutically acceptable carriers include, but are not limited
to, water, salt solutions, alcohols, polyethylene glycols, gelatin,
lactose, amylose, magnesium stearate, talc, silicic acid, viscous
paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the
like.
[0342] Formulations for topical administration of nucleic acids may
include sterile and non-sterile aqueous solutions, non-aqueous
solutions in common solvents such as alcohols, or solutions of the
nucleic acids in liquid or solid oil bases. The solutions may also
contain buffers, diluents and other suitable additives.
Pharmaceutically acceptable organic or inorganic excipients
suitable for non-parenteral administration which do not
deleteriously react with nucleic acids can be used.
[0343] Other Pharmaceutical Composition Components
[0344] The present compositions may additionally contain other
components conventionally found in pharmaceutical compositions, at
their art-established usage levels. Thus, for example, the
compositions may contain additional, compatible,
pharmaceutically-active materials such as, for example,
antipruritics, astringents, local anesthetics or anti-inflammatory
agents, or may contain additional materials useful in physically
formulating various dosage forms of the compositions of the present
invention, such as dyes, flavoring agents, preservatives,
antioxidants, opacifiers, thickening agents and stabilizers.
However, such materials, when added, should not unduly interfere
with the biological activities of the components of the
compositions of the present invention. The formulations can be
sterilized and, if desired, mixed with auxiliary agents, e.g.,
lubricants, preservatives, stabilizers, wetting agents,
emulsifiers, salts for influencing osmotic pressure, buffers,
colorings, flavorings and/or aromatic substances and the like which
do not deleteriously interact with the nucleic acid(s) of the
formulation.
[0345] Aqueous suspensions may contain substances which increase
the viscosity of the suspension including, for example, sodium
carboxymethylcellulose, sorbitol and/or dextran, and/or
stabilizers.
[0346] Certain embodiments of the invention provide pharmaceutical
compositions containing (a) one or more antiviral oligonucleotides
and (b) one or more other chemotherapeutic agents which function by
a different mechanism. Examples of such chemotherapeutic agents
include but are not limited to daunorubicin, daunomycin,
dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin,
bleomycin, mafosfamide, ifosfamide, cytosine arabinoside,
bis-chloroethylnitrosurea, busulfan, mitomycin C, actinomycin D,
mithramycin, prednisone, hydroxyprogesterone, testosterone,
tamoxifen, dacarbazine, procarbazine, hexamethylmelamine,
pentamethylmetamine, mitoxantrone, amsacrine, chlorambucil,
methylcyclohexylnitrosurea, nitrogen mustards, melphalan,
cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine,
5-azacytidine, hydroxyurea, deoxycoformycin,
4-hydroxyperoxycyclophosphoramide, 5-fluorouracil (5-FU),
5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine,
taxol, vincristine, vinblastine, etoposide (VP-16), trimetrexate,
irinotecan, topotecan, gemcitabine, teniposide, cisplatin, and
diethylstilbestrol (DES). See, generally, The Merck Manual of
Diagnosis and Therapy, 15th Ed. 1987, pp. 1206-1228, Berkow et al.,
eds., Rahway, N.J. When used with the compounds of the invention,
such chemotherapeutic agents may be used individually (e.g., 5-FU
and oligonucleotide), sequentially (e.g., 5-FU and oligonucleotide
for a period of time followed by MTX and oligonucleotide), or in
combination with one or more other such chemotherapeutic agents
(e.g., 5-EU, MTX and oligonucleotide, or 5-FU, radiotherapy and
oligonucleotide). Anti-inflammatory drugs, including but not
limited to nonsteroidal anti-inflammatory drugs and
corticosteroids, and antiviral drugs, including but not limited to
Ribavirin, cidofovir, vidarabine, acyclovir and ganciclovir, may
also be combined in compositions of the invention. See, generally,
The Merck Manual of Diagnosis and Therapy, 15th Ed., Berkow et al.,
eds., 1987, Rahway, N.J., pages 2499-2506 and 46-49, respectively).
Other non-oligonucleotide chemotherapeutic agents are also within
the scope of this invention. Two or more combined compounds may be
used together or sequentially.
EXAMPLES
Example 1
Herpes Simplex Virus
[0347] Herpes simplex virus (HSV) affects a significant proportion
of the human population. It was found in the present invention that
random ODNs or ODN randomers inhibited the infectivity of viruses
such as HSV. Using cellular HSV replication assays in VERO cells
(susceptible to HSV-1 (strain KOS) and HSV-2 (strain MS2)
infection) it was found that a single stranded PS-ODN complementary
to the HSV origin of replication inhibited replication of HSV-1 and
HSV-2. Surprisingly, control PS-ODNs complementary to human (343
ARS) and plasmid (pBR322/pUC) origins also inhibited viral
infectivity. Experiments with random sequence PS-ODNs and PS-ODN
randomers demonstrated that inhibition of viral infection increased
with increasing ODN size. These data show that ONs are potent
antiviral agents useful for therapeutic treatment of viral
infection.
[0348] The inventors have theorized that a potential mechanism for
blocking the spread of viruses such as HHVs was to prevent the
replication of its DNA. With this in mind, phosphorothioate
oligonucleotides (ODNs) complementary to the origin of replication
of HSV1 and HSV2 were introduced into infected cells. These ODNs
would cause DNA triplex formation at the viral origin of
replication, blocking the association of necessary trans-acting
factors and viral DNA replication. Surprising results are presented
herein of these experiments which show that, in an experimental
paradigm, the potency of ODNs in inhibiting viral infection
increases as their size (length) increases.
[0349] Inhibition of HSV-1
[0350] The ability of PS-ODNs to inhibit HSV-1 is measured in a
plaque reduction assay (PRA). Immortalized African Green Monkey
kidney (VERO) cells are cultured at 37.degree. C. and 5% CO.sub.2
in MEM (minimal essential medium) plus 10% fetal calf serum
supplemented with gentamycin, vancomycin and amphoterecin B. Cells
are seeded in 12 well plates at a density which yields a confluent
monolayer of cells after 4 days of growth. Upon reaching
confluency, the media is changed to contain only 5% serum plus
supplements as described above and cells are then exposed to HSV-1
(strain KOS, approximately 40-60 PFU total) in the presence of the
test compound for 90 minutes. After viral exposure, the media is
replaced with new "overlay" media containing 5% serum, 1% human
immunoglobulins, supplements as described above and the test
compound. Plaque counting is performed 3-4 days post infection
following formalin fixation and cresyl violet staining of infected
cultures.
[0351] All ONs (except where noted otherwise) were synthesized at
the University of Calgary Core DNA Services lab. ONs (see table 1)
are prepared on a 1 or 15 micromol synthesis scale, deprotected and
desalted on a 50 cm Sephadex G-25 column. The resulting ONs are
analyzed by UV shadowing gel electrophoresis and are determined to
contain .about.95% of the full length, n-1 and n-2 oligo and up to
5% of shorter oligo species (these are assumed to have random
deletions). For random oligo synthesis, adenine, guanosine,
cytosine and thymidine amidites are mixed together in equimolar
quantities to maximize the randomness of incorporation at each
position of the ODNs during synthesis.
[0352] To test if PS-ODNs could inhibit HSV-1, REP 1001, 2001 and
3007 are tested in the HSV-1 PRA. It is expected that only REP 2001
will show any activity as this PS-ODN is directed against the
origin of replication in HSV (the other two are directed against
replication origins in humans and plasmids). However all three
PS-ODNs showed anti-HSV-1 activity (see FIG. 1). Moreover, the
potentcy of the anti-HSV-1 effect is dependent on the size of the
oligo (see FIG. 2).
[0353] To confirm the size dependence and relative sequence
independence of PS-ODNs on anti-HSV-1 activity, we tested PS-ODNs
that vary in size (REP 2002, 2003, 2004, 2005 and 2006). These
PS-ODNs are rendered inert with respect to sequence specific
effects by synthesizing each base as a "wobble" (N) so that each
PS-ODN actually represents a population of different random
sequences with the same size, these PS-ODNs are termed "randomers".
When these oligos are tested in the HSV-1 PRA, we find that oligos
10 bases or lower have no detectable anti-HSV-1 activity but as the
size of the PS-ODN increases above 10 bases, the potency also
increases (IC.sub.50 decreases, see FIGS. 3 and 4). We also note
that PS-ODNs greater than 20 bases had IC.sub.50 values
significantly lower than a clinically accepted anti-HSV-1 drug,
acyclovir (see FIG. 4).
[0354] To better define the effective size range for PS-ODN
anti-HSV-1 activity, we tested PS-ODN randomers covering a broader
range of sizes from 10 to 120 bases (see FIGS. 5 and 6). We
discovered that oligos 12 bases and larger have detectable
anti-HSV-1 activity and that the efficacy against HSV-1 also
increases with increased PS-ODN randomer length at least up to 120
bases. However, the increases in efficacy per base increase in size
are smaller in PS-ODN randomers greater than 40 bases (see FIG.
7).
[0355] To compare the efficacy of non-PS-ODN randomers, a random
sequence PS-ODN and a HSV-1 specific sequence PS-ODN, we tested
these three types of modifications in ODNs 10, 20 and 40 bases in
size (see FIGS. 8 and 9). Unmodified ODN randomers have no
detectable anti-HSV-1 activity at tested sizes (see FIG. 8a-c).
Both random sequence and specific HSV-1 sequence PS-ODNs show size
dependent anti-HSV-1 activity (no activity is observed at 10 bases
for either of these modifications, see FIG. 8d and g). A comparison
of random sequence, specific HSV-1 sequence and randomer PS-ODNs
(see FIG. 10) shows that for PS-ODNs 20 bases in length, there is
an enhancement of anti-HSV-1 activity with the specific HSV-1
sequence but that at 40 bases in length, all modifications, whether
randomer, random sequence or specific HSV-1 sequence were equally
efficacious against HSV-1.
[0356] To the best of our knowledge, this is the first time IC50s
for HSV-1 as low as 0.059 .mu.M and 0.043 .mu.M are reported for
PS-ODNs.
Example 2
Inhibition of HSV-2
[0357] The ability of PS-ODNs to inhibit HSV-2 is measured by PRA.
Immortalized African Green Monkey kidney (VERO) cells are cultured
at 37.degree. C. and 5% CO.sub.2 in MEM plus 10% fetal calf serum
supplemented with gentamycin, vancomycin and amphoterecin B. Cells
are seeded in 12 well plates at a density which yields a confluent
monolayer of cells after 4 days of growth. Upon reaching
confluency, the media is changed to contain only 5% serum plus
supplements as described above and cells are then exposed to HSV-2
(strain MS2, approximately 40-60 PFU total) in the presence of the
test compound for 90 minutes. After viral exposure, the media is
replaced with new "overlay" media containing 5% serum, 1% human
immunoglobulins, supplements as described above and the test
compound. Plaque counting is performed 3-4 days post infection
following formalin fixation and cresyl violet staining of infected
cultures.
[0358] To test if PS-ODNs could inhibit HSV-2, REP 1001, 2001 and
3007 are tested in the HSV-2 PRA. It is expected that only REP 2001
will show any activity as this PS-ODN is directed against the
origin of replication in HSV-1/2 (the other two are directed
against replication origins in humans and plasmids), however all
three PS-ODNs showed anti-HSV-2 activity (see FIG. 12). Moreover,
the potency of the anti-HSV-2 effect is dependent on the size of
the PS-ODN and independent of the sequence (see FIG. 13).
[0359] To confirm the size dependence and sequence independence of
PS-ODNs on anti-HSV-2 activity, we test PS-ODNs that vary in size
(REP 2001, 2002, 2003, 2004, 2005 and 2006). These PS-ODNs are
rendered inert with respect to sequence specific effects by
synthesizing each base as a "wobble" (N) so that each PS-ODN
actually represents a population of different random sequences with
the same size, these PS-ODNs are termed "randomers". When these
PS-ODNs are tested in the HSV-2 PRA, we find that PS-ODNs 10 bases
or lower had no detectable anti-HSV-2 activity but as the size of
the PS-ODN increases above 10 bases, the potency also increases
(IC.sub.50 decreases, see FIGS. 14 and 15). We also noted that
PS-ODNs greater than 20 bases had IC.sub.50 values significantly
lower than a clinically accepted anti-HSV-2 drug, Acyclovir.TM.
(see FIG. 15).
[0360] To the best of our knowledge, this is the first time an IC50
for HSV-2 as low as 0.012 .mu.M has been reported for a PS-ODN.
[0361] To determine if non-specific sequence composition has an
effect on ON antiviral activity, several PS-ODNs of equivalent size
but differing in their sequence composition were tested for
anti-HSV1 activity in the HSV-1 PRA. The PS-ODNs tested were REP
2006 (N20), REP 2028 (G40) (SEQ ID NO: 21), REP 2029 (A40) (SEQ ID
NO: 20), REP 2030 (T40) (SEQ ID NO: 23) and REP 2031 (C40) (SEQ ID
NO: 22). The IC.sub.50 values generated from the HSV-1 PRA (see
FIG. 37) show that REP 2006 (N40) was clearly the most active of
all sequences tested while REP 2029 (A40) (SEQ ID NO: 20) was the
least active. We also note that, all the other PS-ODNs were
significantly less active than N40 with their rank in terms of
efficacy being N40>C40 (SEQ ID NO: 22)>T40>(SEQ ID NO: 23)
A40 (SEQ ID NO: 20)>>G40 (SEQ ID NO: 21).
[0362] We also tested the efficacy of different PS ODNs having
varying sequence composition with two different nucleotides (see
FIG. 37b). The PS-ODN randomer (REP 2006) was significantly more
efficacious against HSV-1 than AC20 (SEQ ID NO: 24)(REP 2055), TC20
(SEQ ID NO: 25) (REP 2056) or AG20 (SEQ ID NO: 26) (REP 2057) with
their efficacies ranked as follows: N40>AG(20) (SEQ ID NO:
26)>AC(20) (SEQ ID NO: 24)>TC(20) (SEQ ID NO: 25). This data
suggests that although the anti-viral effect is non-sequence
complementary, certain non-specific sequence compositions (i.e. C40
(SEQ ID NO: 22) and N40) have the most potent anti-viral activity.
We suggest that this phenomenon can be explained by the fact that,
while retaining intrinsic protein binding ability, sequences like
C40 (SEQ ID NO: 22), A40 (SEQ ID NO: 20), T40 (SEQ ID NO: 23) and
G40 (SEQ ID NO: 21) bind fewer viral proteins with high affinity,
probably due to some restrictive tertiary structure formed in these
sequences. On the other hand, due to the random nature of N40, it
retains its ability to bind with high affinity to a broad range of
anti-viral proteins which contributes to its robust anti-viral
activity.
Example 3
Inhibition of CMV
[0363] The ability of PS-ODNs to inhibit CMV is measured in a
plaque reduction assay (PRA). This assay is identical to the assay
used for testing anti-HSV-1 and anti-HSV-2 except that CMV (strain
AD169) is used as the viral innoculum and human fibroblasts were
used as cellular host.
[0364] To test the size dependence and sequence independence of
PS-ODNs on anti-CMV activity, we test PS-ODN randomers that vary in
size (see FIG. 16a, b). When these PS-ODNs are tested in the CMV
PRA, we find that as the size of the PS-ODN increases, the potency
also increases (IC.sub.50 decreases, see FIG. 16c).
[0365] To more clearly elucidate the effective size range for
PS-ODN anti-CMV activity, we tested PS-ODN randomers covering a
broader range of sizes from 10 to 80 bases. We also included
several clinically accepted small molecule CMV treatments
(Gancyclovir, Foscarnet and Cidofovir) as well as 2 versions of a
marketed antisense treatment for CMV retinitis, (Vitravene.TM.;
commercially available and synthesized by the University of
Calgary) (see FIG. 17). We discovered that while increased PS-ODN
randomer size leads to increased efficacy, this effect saturates at
40 bases (see FIG. 18). Moreover, the 20, 40 and 80 base PS-ODN
randomers are all significantly more efficacious than any of the
small molecule treatments tested (FIG. 17). In addition, 40 and 80
base PS-ODN randomers are more efficacious than Vitravene.TM..
[0366] To the best of our knowledge, this is the first time an IC50
for CMV as low as 0.067 .mu.M has been reported for a PS-ODN.
Example 4
Inhibition of HIV-1
[0367] The ability of PS-ODN randomers to inhibit HIV-1 is measured
by two different assays:
[0368] Cytopathic Effect (CPE)
[0369] Cytopathic effect is monitored using MTT dye to report the
extent of cellular metabolism. Immortalized human lymphocyte (MT4)
cells are cultured at 37.degree. C. and 5% CO.sub.2 in MEM plus 10%
fetal calf serum supplemented with antibiotics. Cells are seeded in
96 well plates in media containing the appropriate test compound
and incubated for 2 hours. After preincubation with the test
compound, HIV-1 (strain NL 4-3) was added to the wells (0.0002
TCID.sub.50/cell). After 6 days of additional incubation, CPE is
monitored by MTT conversion. Cytotoxicity is measured by incubating
the drugs for 6 days in the absence of viral inoculation. For
transformation of MTT absorbance values into survival, the
absorbance of uninfected, untreated cells is set to 100% and the
absorbance of infected, untreated cells is set to 0%.
[0370] Replication Assay (RA)
[0371] The ability of HIV to replicate is monitored in immortalized
human embryonic kidney (293A) cells. These cells are cotransfected
with two plasmids. One plasmid contains a recombinant wild type
HIV-1 genome (NL 4-3) having its env gene disrupted by a luciferase
expression cassette (identified as strain CNDO), the other plasmid
contains the env gene from murine leukemia virus (MLV). These two
plasmids provide all the protein factors in trans to produce a
mature chimeric virus having all the components from HIV-1 except
the protein products provided in trans from the MLV env gene.
Virions produced from these cells are infectious and replicative
but cannot produce another generation of infectious virions because
they will lack the env gene products.
[0372] 24 hours after transfection, these cells are trypsinized and
plated in 96 well plates. After the cells have adhered, the media
is washed and replaced with media containing the test compound.
Virus production is allowed to proceed for an additional 24 hours.
The supernatant is then harvested and used to reinfect naive 293A
cells. Naive cells that are infected are identified by the
luciferase gene product. The number of luciferase positive cells is
a measure of the extent of replication and/or infection by the
recombinant HIV-1. This assay is also adapted to test the
resistance to many clinically accepted anti-HIV-1 drugs by using a
HIV-1 genome with several point mutations known to induce
resistance to several different classes of anti-HIV drugs.
Percentage inhibition is set to 100% for no detectable luciferase
positive cells and 0% for the number of positive cells in infected,
untreated controls.
[0373] To test the size dependence and sequence independence of
PS-ODNs on anti-HIV-1 activity, we test PS-ODN randomers that vary
in size. When these PS-ODN randomers are tested the HIV-1 CPE
assay, we find that as the size of the PS-ODN increases the potency
also increases (IC.sub.50 decreases, see FIGS. 19a, b and 20). We
also noted that the PS-ODN randomers exhibited no significant
toxicity to the host cells in this assay (see FIG. 19c,d).
[0374] To the best of our knowledge, this is the first time an IC50
for HIV-1 as low as 0.011 .mu.M has been reported for a PS-ODN.
[0375] To more clearly elucidate the effective size range for
PS-ODN anti-HIV-1 activity, we tested more PS-ODN randomers
covering a broader range of sizes from 10 to 80 bases by RA using
wild-type HIV-I (recombinant NL 4-3 (CNDO)). In addition, we tested
four protease inhibitors currently used in the clinic (aprenavir,
indinavir, lopinavir and saquinavir). We discovered that PS-ODN
randomers 10 bases and larger have anti-HIV-1 activity and that the
efficacy against HIV-1 also increases with increased PS-ODN
randomer length but is saturated at 40 bases (see FIG. 21e-h and
FIG. 22b). Moreover, the 40 and 80 base PS-ODN randomers were
almost equivalent in efficacy with the 4 clinical controls (see
FIG. 21a-d and 22a).
[0376] To the best of our knowledge, this is the first time an IC50
for HIV-1 as low as 0.014 .mu.M has been reported for a PS-ODN.
[0377] To test the ability of PS-ODN randomers to inhibit a drug
resistant strain of HIV, we duplicated the above test using the
recombinant MDRC4 strain of HIV-1. This recombinant strain exhibits
significant resistance to at least 16 different clinically accepted
drugs from all classes: nucleotide RT inhibitors, non-nucleotide RT
inhibitors and protease inhibitors. All the PS-ODN randomers
perform as well against the resistant strain as they do against the
wild type strain (see FIG. 23e-h). However, three of the four
protease inhibitors show a reduction in their efficacy against the
mutant strain (see FIG. 23a-d and 24), such that the 40 and 80 base
PS-ODN randomers are now more potent against this resistant strain
than these drugs.
Example 5
Inhibition of RSV
[0378] The ability of PS-ODN randomers to inhibit RSV is measured
by monitoring CPE with alamar blue (an indirect measure of cellular
metabolism). Human larynx carcinoma (Hep2) cells are cultured at
37.degree. C. and 5% CO.sub.2 in MEM plus 5% fetal calf serum.
Cells are seeded in 96 well plates at a density which yields a
confluent monolayer of cells after 5-6 days of growth. The day
after plating, cells were infected with RSV (strain A2, 10.sup.8.2
TCID.sub.50/ml) in the presence of the test compound in a reduced
volume for 2 hours. Following inoculation, the media was changed
and was supplemented with test compound. 6 days after infection,
CPE was monitored by measuring the fluorescent conversion of alamar
blue. Toxicity of test compounds in Hep2 cells was monitored by
treating uninfected cells for 7 days and measuring alamar blue
conversion in these cells. The alamar blue readings in uninfected,
untreated cells were set to 100% survival and the readings in
infected, untreated cells were set to 0% survival.
[0379] To confirm the size dependence and sequence independence of
PS-ODNs on anti-RSV activity, we test PS-ODN randomers that vary in
size. In addition, we tested the clinically accepted treatment for
RSV infection, Ribavirin (Virazole.TM.). When tested in the RSV CPE
assay, we find that as the size of the PS-ODN randomer increases,
the potency also increases but saturates at 40 bases in size (see
FIG. 25a-c and 26). We also noted that 20, 40 and 80 base PS-ODN
randomers had IC.sub.50 values significantly lower than a
clinically accepted anti-RSV drug, Ribavirin (see FIG. 25a-d and
26). PS-ODN randomers exhibited no toxicity in Hep2 cells while
Ribavirin was significantly toxic (therapeutic index=2.08, see FIG.
25e-h).
[0380] To the best of our knowledge, this is the first time an IC50
for RSV-1 as low as 0.015 .mu.M has been reported for a PS-ODN.
Example 6
Inhibition of Coxsackie virus B2
[0381] The ability of PS-ODN randomers to inhibit COX B2 is
measured monitoring CPE with alamar blue (an indirect measure of
cellular metabolism). Rhesus monkey kidney (LLC-MK2) cells are
cultured at 37.degree. C. and 5% CO.sub.2 in MEM plus 5% fetal calf
serum. Cells are seeded in 96 well plates at a density which yields
a confluent monolayer of cells after 5-6 days of growth. The day
after plating, cells were infected with COX B2 (strain Ohio-1,
10.sup.7.8TCID.sub.50/ml) in the presence of the test compound in a
reduced volume for 2 hours. Following inoculation, the media was
changed and was supplemented with test compound. 6 days after
infection, CPE was monitored by measuring the fluorescent
conversion of alamar blue. Toxicity of test compounds in LLC-MK2
cells was monitored by treating uninfected cells for 7 days and
measuring alamar blue conversion in these cells. The alamar blue
readings in uninfected, untreated cells were set to 100% survival
and the readings in infected, untreated cells were set to 0%
survival.
[0382] We tested the anti-COX 82 activity of REP 2006 in the COX 82
CPE assay. We found that, while exhibiting some slight toxicity in
LLC-MK2 cells (see FIG. 27b), this PS-ODN randomer was able to
partially rescue infected LLC-MK2 cells from COX 82 infection (see
FIG. 27a).
Example 7
Inhibition of Vaccinia Virus
[0383] We used the vaccinia infection model as a measure of the
potential efficacy of our compounds against poxviruses, including
smallpox virus. The ability of PS-ODN randomers to inhibit Vaccinia
is measured by monitoring CPE with alamar blue (an indirect measure
of cellular metabolism). Vero cells are cultured at 37.degree. C.
and 5% CO.sub.2 in MEM plus 5% fetal calf serum. Cells are seeded
in 96 well plates at a density which yields a confluent monolayer
of cells after 5-6 days of growth. The day after plating, cells
were infected with Vaccinia (10.sup.7.9TCID.sub.50/ml) in the
presence of the test compound in a reduced volume for 2 hours.
Following inoculation, the media was changed and was supplemented
with test compound (all at 10 uM, except for Cidofovir which was
used at 50 uM). Five days after infection, the supernatants were
harvested. The viral load in the supernatant was determined by
reinfection of VERO cells with supernatant diluted 1:100 and the
monitoring of CPE 7 days after reinfection by measuring the
fluorescent conversion of alamar blue.
[0384] We tested PS-ODN randomers that vary in size (REP 2004, 2006
and 2007). In addition, we tested a known effective treatment for
Vaccinia infection, Cidofovir (Vistide.TM.). When tested in the
Vacinnia CPE assay, we find that treatment with REP 2004, 2006 and
2007 all displayed antiviral activity (i.e. resulted in
supernatants which showed a decreased CPE upon reinfection) but
that this activity was weaker than that seen for Cidofovir (see
FIG. 36).
Example 8
Inhibition of DHBV, Parainfluenza-3 virus, and Hanta Virus
[0385] Because DHBV, Parainfluenza-3 virus and Hanta virus do not
readily generate measurable plaques or CPE, we tested the efficacy
of REP 2006 in these viruses using a fluorescence focus forming
unit (FFFU) detection. In this assay, REP 2006 (at a final
concentration of 10 uM) is mixed with the virus which is then
adsorbed onto the cells. After adsorption, infected cells are
allowed to incubate for an additional 7-14 days at which point they
are fixed in methanol. Regions of viral replication are detected by
immunofluorescence microscopy against the appropriate viral
antigen. For each of the three viruses tested, the specific
experimental conditions and results are described below:
TABLE-US-00001 FFFU count Antibody for FFFU count (10 uM REP Virus
Cellular Host FFFU detection (no drug) 2006) DHBV (HBV Primary duck
Mouse anti-DHBV 163 +/- 38.5 0 surrogate) hepatocytes IgG
Parainfluenza-3 LLC-MK2 Mouse anti-PI3 288 +/- 126 0 cells IgG
Hanta Virus VERO E6 Mouse anti- 232.3 +/- 38.17 0 (Strain cells
SinNombre Prospect Hill) nucleoprotein IgG
[0386] This initial data shows that at 10 uM, REP 2006 is effective
in inhibiting DHBV, Parainfluenza-2 and Hanta Virus. We anticipate
that given the robust response in the preliminary test that
IC.sub.50 values will be lower. These data support the efficacy of
PS-ODN randomers for the treatment of human infections of Hanta
Virus and Hepatitis B (closely related to DHBV) as well as
providing a rationale for the immediate treatment of pediatric
bronchiolitis caused by RSV and Parainfluenza-3, which may not
require differential diagnosis for treatment to begin.
Example 9
Currently Non-Responsive Viruses
[0387] To date we have not observed a detectable anti-viral
efficacy with PS-ODN randomers (up to 10 uM) without using a
delivery system, a drug combination, or a chemical modification in
the following viral systems:
TABLE-US-00002 Assay Virus Strain Cellular Host paradigm Influenza
A H3N2 MDCK cells Plaque reduction Corona virus MHV2 (mouse)
NCTC-1496 cells Plaque (SARS surrogate) MHV-A59 (mouse) DBT cells
reduction HCoV-OC43 HRT-18 cells (human) BVDV (HCV NA BT cells CPE
by surrogate) alamar blue Rhinovirus HGP HeLa cells CPE by alamar
blue Adenovirus Human Ad5 293A cells Plaque reduction
[0388] Under the current testing procedures, we did not demonstrate
activity. However, the lack of antiviral activity may be due to a
lower cellular penetration of the PS-ODN under the conditions of
the assays. Nonetheless, additional testing is underway to achieve
efficacious results with these viruses. These viruses may respond
to PS-ODN when using a delivery system such as a liposomal
formulation, in order to increase its intracellular concentration.
Also in a combination with another antiviral drug, such as
described herein, PS-ODNs may exhibit an antiviral efficacy for
these viruses. A chemical modification to increase intracellular
concentration may also be useful to render PS-ODNs active against
these viruses.
[0389] Since we have good evidence that the charge characteristics
of a PS-ODN are important for the inhibition of viruses from
several different families, we expect that this charge dependent
mechanism for the inhibition of viral activity has the potential to
inhibit the activity of all encapsidating viruses. The corollary to
this is that the lack of detected anti-viral efficacy against those
viruses listed in Example 9 suggests that the interaction between
the PS-ODN and the structural proteins of these viruses is not
strong enough to prevent the interaction of viral proteins during
the replication of these viruses. One way of achieving efficacy
against these viruses is to alter the charge characteristics of the
DNA or anti-viral polymer (e.g., substituting phosphorodithioate
for phosphorothioate linkages in DNA) so their affinity for viral
proteins is increased.
Example 10
Tests for Determining if an Oligonucleotide Acts Predominantly by a
Non-Sequence Complementary Mode of Action
[0390] An ON, e.g., ODN, in question shall be considered to be
acting predominantly by a non-sequence complementary mode of action
if it meets the criterion of any one of the 3 tests outlined
below.
Test #1--Effect of Partial Degeneracy on Antiviral Efficacy
[0391] This test serves to measure the antiviral activity of a
particular ON sequence when part of its sequence is made
degenerate. If the degenerate version of the ON having the same
chemistry retains its activity as described below, is it deemed to
be acting predominantly by a non-sequence complementary mode of
action. ONs will be made degenerate according to the following
rule:
[0392] L.sub.ON=the number of bases in the original ON
[0393] X=the number of bases on each end of the oligo to be made
degenerate (but having the same chemistry as the original ON)
[0394] If L.sub.ON is even, then X=L.sub.ON/4
[0395] If L.sub.ON is odd, then X=integer (L.sub.ON/4)+1
[0396] Each degenerate base shall be synthesized according to any
suitable methodology, e.g., the methodology described herein for
the synthesis of PS-ODN randomers.
[0397] If the ON is claimed to have an anti-viral activity against
a member of the herpesviridae, retroviridae, or paramyxoviridae
families, the IC.sub.50 generation will be performed using the
assay described herein for that viral family preferably using the
viral strains indicated. If the ON is claimed to have an anti-viral
activity against a member of a particular virus family not
mentioned above, then the IC50 values shall be generated by a test
of antiviral efficacy accepted by the pharmaceutical industry. IC50
values shall be generated using a minimum of seven concentrations
of compound, with three or more points in the linear range of the
dose response curve. Using this test, the IC.sub.50 of said ON
shall be compared to its degenerate counterpart. If the IC.sub.50
of the degenerate ON is less than 2-fold greater than the original
ON for an ON of 25 bases and less, or is less than 10-fold greater
than the original ON for ONs 26 bases or more (based on minimum
triplicate measurements, standard deviation not to exceed 15% of
mean) then the ON shall be deemed to be functioning predominantly
by a non-sequence complementary mode of action.
Test #2--Comparison of Efficacy with Randomer
[0398] This test serves to compare the anti-viral efficacy of an ON
with the antiviral efficacy of a randomer ON of equivalent size and
the same chemistry in the same virus or viral family.
[0399] If the ON is claimed to have an anti-viral activity against
a member of the herpesviridae, retroviridae, or paramyxoviridae
families, the IC.sub.50 generation will be performed using the
assay described herein for that viral family preferably using the
viral strains indicated. If the ON is claimed to have an anti-viral
activity against a member of a particular virus family not
mentioned above, then the IC50 values shall be generated by a test
of antiviral efficacy accepted by the pharmaceutical industry. IC50
values shall be generated using a minimum of seven concentrations
of compound, with three or more points in the linear range of the
dose response curve. Using this test, the IC.sub.50 of the ON shall
be compared to an ON randomer of equivalent size and the same
chemistry. If the IC.sub.50 of the degenerate ON is less than
2-fold greater than the original ON for an ON of 25 bases and less,
or is less than 10-fold greater than the original ON for ONs 26
bases or more (based on minimum triplicate measurements, standard
deviation not to exceed 15% of mean) then the ON shall be deemed to
be functioning predominantly by a non-sequence complementary mode
of action.
Test #3--Comparison of Efficacy in a Different Viral Family
[0400] This test serves to compare the efficacy of an ON against a
target virus whose genome is homologous to the ON with the efficacy
of the ON against a second virus whose genome has no homology to
ON. In many cases, the different virus will be selected from a
different viral family than the viral family of the target virus.
The comparison of the relative activities of the ON in the target
virus and the second virus is accomplished by using the activities
of a randomer of the same length and chemistry in the both viruses
to normalize the IC.sub.50 values for the ON obtained in the two
viruses.
[0401] Thus, if the ON is claimed to have an anti-viral activity
against a certain virus, then the IC.sub.50 generation will be
determined in this virus using one of the assays described herein
for the herpesviridae, retroviridae, or paramyxoviridae families,
or other assay known in the art. Similarly, IC.sub.50 generation
will be performed for the ON against a second virus using one of
the assays as described herein for a virus whose genome has no
homology to the sequence of the ON. IC.sub.50 generation is also
performed for a randomer of equivalent size and chemistry against
each of the viruses. The IC.sub.50 efficacies of the randomer
against the two viruses are used to normalize the IC.sub.50 values
for the specific ON as follows: [0402] 1. An algebraic
transformation is applied to the IC.sub.50 of the ON and the
randomer in the first (homologous) virus such that the IC.sub.50 of
the randomer is now 1. [0403] 2. An algebraic transformation is
applied to the IC.sub.50 of the ON and the randomer in the second
(non-homologous) virus such that the IC.sub.50 of the randomer in
now 1. [0404] 3. The fold difference in the IC50s for the ON in the
homologus versus the non-homologous virus is calculated by dividing
the transformed IC50 of the ON in the non-homologous virus by the
transformed IC50 of the ON in the homologous virus.
[0405] For an ON less than 25 bases in length, the ON shall be
deemed to be acting by a non-sequence complementary mode of action
if the fold difference is less than 2. For an ON 25 bases or more
in length, the ON shall be deemed to be acting by a non-sequence
complimentary mode of action if the fold difference in less than
10.
TEST #4: Efficacy in a Different Viral Family
[0406] This test serves to determine if an ON has a drug like
activity in a virus where the sequence of said ON is not homologous
to any portion of the viral genome. Thus the ON shall be tested
using one of the assays described herein for the herpesviridae,
retroviridae or paramyxoviridae such that the sequence of the ON
tested is not homologous to any portion of the genome of the virus
to be used. An IC.sub.50 value shall be generated using a minimum
of seven concentrations of the ON, with three or more points in the
linear range. If the resulting dose response curve indicates a drug
like activity (which can be typically be seen as a decay or
sigmoidal curve, having reduced anti-viral efficacy with decreasing
concentrations of ON) and the IC.sub.50 generated from said curve
is less than 1 uM, the ON shall be deemed to have a drug like
activity. If the ON is deemed to have a drug like activity in a
virus to which the ON is not complementary and thus can have no
complementary sequence dependent activity, it shall be considered
to be acting by a non-sequence complementary mode of action.
Thresholds Used in these Tests
[0407] There is no scientific or empirical basis, either in the
academic or industrial fields, to design an antisense ON which is
longer than 25 bases. In addition, to our knowledge, there has
never been an ON formulation administered in any human trials that
used an ON longer than 25 nucleotides.
[0408] Given these facts, we have established two different
thresholds which we use to define a sequence as acting
predominantly by a non-sequence complimentary mode of action. For
oligos 25 bases and less, the ON must have an antiviral activity
which is at least 2-fold greater than a randomer or a degenerate ON
of the same chemistry in order to be considered to acting
predominantly by an antisense mechanism. If an antisense ON is not
at least twice as good as a randomer or a degenerate ON, then we
conclude that more than half of its activity can be attributed to a
non-antisense mode of action.
[0409] For ONs 26 bases and larger, the ON must have an antiviral
activity which is at least 10-fold (1 log) greater than a randomer
or a degenerate ON of the same chemistry to be considered to be
acting by an antisense mechanism. Our rationale for this larger
threshold it that, given the current state of the art for ON design
for antisense, it is reasonable to assume that oligos that are 26
bases and larger and claimed to have an antiviral activity were
designed with the knowledge of the invention contained herein (the
optimal length of antisense ONs is generally accepted to be between
16 and 21 bases).
[0410] The thresholds described in tests 1 to 3 above are the
default thresholds. If specifically indicated, other thresholds can
be used in the comparison tests 1 to 3 described above. Thus for
example, for ONs under 25 bases in length and/or ONs 25 or more
bases in length, if specifically indicated the threshold for
determining whether an ON is acting principally by a non-sequence
complementary mode of action can be any of 10-fold, 8-fold, 6-fold,
5-fold, 4-fold, 3-fold, 2-fold, 1.5-fold, or equal. The threshold
described in test 4 above is also a default threshold. If
specifically indicated, the threshold for determining whether an ON
is acting principally by a non-sequence complementary mode of
action in test 4 can be an IC.sub.50 of less than 1 uM, 0.8 uM, 0.6
uM, 0.5 uM, 0.4 uM, 0.3 uM, 0.2 uM or 0.1 uM. Similarly, though the
default is that satisfying any one of the above 4 tests is
sufficient, if specifically indicated, the ON can be required to
satisfy any two (e.g., tests 1 & 2, 1 & 3, 1 & 4, 2
& 3, 2& 4 and 3 & 4) or any three (e.g., tests 1 &
2 & 3, 1 & 3 & 4, and 2 & 3 & 4) or all 4 of
the tests at a default threshold, or if specifically indicated, at
another threshold as indicated above.
Antiviral Assay for Herpesviridae
[0411] A plaque reduction assay performed as follows:
[0412] For HSV-1 or HSV-2, VERO cells (ATCC# CCL-81) are grown to
confluence in 12 well tissue culture plates (NUNC or equivalent) at
37 deg C. and 5% CO.sub.2 in the presence of MEM supplemented with
10% heat inactivated fetal calf serum and gentamycin, vancomycin
and amphoterecin B. Upon reaching confluency, the media is changed
to contain 5% fetal calf serum and antibiotics as detailed above
supplemented with either HSV-1 (strain KOS, 40-60 PFU total) or
HSV-2 (strain MS2, 40-60 PFU total). Viral adsorbtion proceeds for
90 minutes, after which cells are washed and replaced with new
"overlay" media containing 5% fetal calf serum and 1% human
immunoglobins. Three to four days after adsorbtion, cells are fixed
by formalin and plaques are counted following formalin
fixation.
[0413] For CMV, human fibroblasts are grown as specified for VERO
cells in the HSV-1/2 assay. Media components and adsorbtion I
overlay procedures are identical with the following exceptions:
[0414] 1. CMV (strain AD169, 40-60 PFU total) is used to infect
cells during the adsorbtion. [0415] 2. In the overlay media, 1%
human immunoglobins are replaced by 4% sea-plaque agarose.
[0416] For other herpesviridae, testing is to be conducted in a
plaque assay described above using an appropriate cellular host and
40-60 PFU of virus during the adsorbtion.
[0417] This test is only valid if identifiable plaques are present
in the absence of compound at the end of the test.
[0418] IC.sub.50 is the concentration at which 50% of the plaques
are present compared to the untreated control.
[0419] Compound to be tested is present during the adsorption and
in the overlay.
[0420] Antiviral Assay for Retroviridae
[0421] Detection of total p24 in the supernatant of HIV-1 infected
cells is performed as follows:
[0422] Human PBMCs are infected with a primary isolate of HIV-1 in
the presence the compound. The cells are then incubated for an
additional 7 days in fresh medium supplemented with the compound
after which the levels of p24 in the supernatant are measured using
a commercial p24 ELISA kit (BIOMERIEUX or equivalent.)
[0423] This test is only valid if there is an accumulation of p24
in the tissue culture supernatant in the infected, untreated
cells.
[0424] IC.sub.50 is the concentration at which the amount of p24
detectable is 50% of the p24 present in the untreated control.
[0425] Compound to be tested is present during the adsorption and
in the media after adsorption.
Antiviral Assay for Paramyxoviridae
[0426] For RSV, A measurement of CPE is performed as follows:
[0427] Hep2 cells were plated in 96 well plates and allowed to grow
overnight in MEM plus 5% fetal calf serum at 37 deg C. and 5%
CO.sub.2. The next day, cells are infected with RSV (strain A2,
10.sup.8.2 TCID.sub.50/ml in 100 ul/well) by adsorbtion for 2
hours. Following adsorbtion, media is changed and after 7 days
growth, CPE is measured by conversion of Alamar Blue dye to its
fluorescent adduct by living cells.
[0428] This test is only valid if CPE measurement (as measured by
Alamar Blue conversion) in infected cells in the absence of
compound is 10% of the conversion measured in uninfected cells.
[0429] For purposes of IC.sub.50 comparison, 100% CPE is set at the
conversion level seen in infected cells and 0% CPE is set at the
conversion seen in uninfected cells. Therefore IC.sub.50 is the
concentration of compound which generates 50% CPE.
[0430] Compound to be tested is present during the adsorption and
in the media after adsorption.
[0431] All patents and other references cited in the specification
are indicative of the level of skill of those skilled in the art to
which the invention pertains, and are incorporated by reference in
their entireties, including any tables and figures, to the same
extent as if each reference had been incorporated by reference in
its entirety individually.
[0432] One skilled in the art would readily appreciate that the
present invention is well adapted to obtain the ends and advantages
mentioned, as well as those inherent therein. The methods,
variances, and compositions described herein as presently
representative of preferred embodiments are exemplary and are not
intended as limitations on the scope of the invention. Changes
therein and other uses will occur to those skilled in the art,
which are encompassed within the spirit of the invention, are
defined by the scope of the claims.
[0433] It will be readily apparent to one skilled in the art that
varying substitutions and modifications may be made to the
invention disclosed herein without departing from the scope and
spirit of the invention. For example, variations can be made to
synthesis conditions and compositions of the oligonucleotides.
Thus, such additional embodiments are within the scope of the
present invention and the following claims.
[0434] The invention illustratively described herein suitably may
be practiced in the absence of any element or elements, limitation
or limitations which is not specifically disclosed herein. Thus,
for example, in each instance herein any of the terms "comprising",
"consisting essentially of" and "consisting of" may be replaced
with either of the other two terms. The terms and expressions which
have been employed are used as terms of description and not of
limitation, and there is no intention that in the use of such terms
and expressions of excluding any equivalents of the features shown
and described or portions thereof, but it is recognized that
various modifications are possible within the scope of the
invention claimed. Thus, it should be understood that although the
present invention has been specifically disclosed by preferred
embodiments and optional features, modification and variation of
the concepts herein disclosed may be resorted to by those skilled
in the art, and that such modifications and variations are
considered to be within the scope of this invention as defined by
the appended claims.
[0435] In addition, where features or aspects of the invention are
described in terms of Markush groups or other grouping of
alternatives, those skilled in the art will recognize that the
invention is also thereby described in terms of any individual
member or subgroup of members of the Markush group or other
group.
[0436] Also, unless indicated to the contrary, where various
numberical values are provided for embodiments, additional
embodiments are described by taking any 2 different values as the
endpoints of a range. Such ranges are also within the scope of the
described invention.
[0437] Thus, additional embodiments are within the scope of the
invention and within the following claims.
TABLE-US-00003 TABLE 1 DESCRIPTION OF OLIGONUCLEOTIDES REP 1001
20mer from human automonously replicating sequence SEQUENCE T T G A
T A A A T A G T A C T A G G A C (SEQ ID NO: 1) PS ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? REP 2001 22mer from HSV-1 origin of
replication SEQUENCE G A A G C G T T C G C A C T T C G T C C C A
(SEQ ID NO: 2) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP
3007 16mer from pUC19/pBR322 origin of replication SEQUENCE C T T G
C G G T A T T C G G A A (SEQ ID NO: 3) PS ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? REP 2002 5mer randomer SEQUENCE N N N N N PS ? ? ? ? ? REP
2032 6mer randomer SEQUENCE N N N N N N PS ? ? ? ? ? ? REP 2003
10mer randomer SEQUENCE N N N N N N N N N N PS ? ? ? ? ? ? ? ? ? ?
REP 2009 12mer randomer SEQUENCE N N N N N N N N N N N N PS ? ? ? ?
? ? ? ? ? ? ? ? REP 2010 14mer randomer SEQUENCE N N N N N N N N N
N N N N N PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2011 16mer randomer
SEQUENCE N N N N N N N N N N N N N N N N PS ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? REP 2012 18mer randomer SEQUENCE N N N N N N N N N N N N N
N N N N N PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2004 20mer
randomer SEQUENCE N N N N N N N N N N N N N N N N N N N N PS ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2005 30mer randomer SEQUENCE
N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N PS ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2006
40mer rendomer SEQUENCE N N N N N N N N N N N N N N N N N N N N N N
N N N N N N N N N N N N N N N N N N PS ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2007 80mer
randomer SEQUENCE N N N N N N N N N N N N N N N N N N N N N N N N N
N N N N N N N N N N N N N N N N N N N N N N PS ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? N N N N N N N N N N N N N 60 ? ? ? ? ? ? ? ? ? ? ? ? ?
SEQUENCE N N N N N N N N N N N N N N N N N N N N 80 PS ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2008 120mer randomer SEQUENCE N N N
N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N
N N N N N N N N N N PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? N N N N N N N N N
N N N N 60 ? ? ? ? ? ? ? ? ? ? ? ? ? SEQUENCE N N N N N N N N N N N
N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N
N N PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? N N N N N N N N N N N N N 120 ? ?
? ? ? ? ? ? ? ? ? ? ? REP 2013 10mer randomer SEQUENCE N N N N N N
N N N N no modifica- tion REP 2014 20mer randomer SEQUENCE N N N N
N N N N N N N N N N N N N N N N no modifica- tion REP 2015 40mer
randomer SEQUENCE N N N N N N N N N N N N N N N N N N N N N N N N N
N N N N N N N N N N N N N N N no modifica- tion REP 2016 10mer
random sequence SEQUENCE T C C G A A G A C G (SEQ ID NO: 4) PS ? ?
? ? ? ? ? ? ? ? REP 2017 20mer random sequence SEQUENCE A C A C C T
C C G A A G A C G A T A A C (SEQ ID NO: 5) PS ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? REP 2018 40mer random sequence SEQUENCE C T A C A
G A C A T A C A C C T C C G A A G A C G A T A A C A C T A G A C A T
A (SEQ ID NO: 6) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2019 10mer sequence centered
around start codon of HSV-1 IE110 protein (NCBI accession # X04814)
SEQUENCE PS ##STR00001## REP 2020 20mer sequence centered around
start codon of HSV-1 IE110 protein (NCBI accession # X04614)
SEQUENCE PS ##STR00002## REP 2021 40mer sequence centered around
start codon of HSV-1 IE110 protein (NCBI accession # X04814)
SEQUENCE PS ##STR00003## REP 2024 40mer randomer SEQUENCE N N N N N
N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N N
N PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? 2-OMe ? ? ? ? ? ? ? ? REP 2026 40mer randomer
SEQUENCE N N N N N N N N N N N N N N N N N N N N N N N N N N N N N
N N N N N N N N N N N PCH3 ? ? ? ? ? ? ? ? REP 2036 21mer
Commercially marketed antisense against CMV (vitravine/fomvinsen)
SYNTHESIZED INTERNALLY SEQUENCE G C G T T T G C T C T T C T T C T T
G C G (SEQ ID NO: 10) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
REP 2038 .COPYRGT. 21mer commercially marketed antisense against
CMV (vitravine/fomvinsen) COMMERCIAL PRODUCT (cGMP) SEQUENCE G C G
T T T G C T C T T C T T C T T G C G (SEQ ID NO: 11) PS ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? A20 20 mer SEQUENCE A A A A A A A A A
A A A A A A A A A A A-FITC (SEQ ID NO: 12) PS ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? G20 20 mer SEQUENCE G G G G G G G G G G G G G G G
G G G G G-FITC (SEQ ID NO: 13) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? C20 20 mer SEQUENCE C C C C C C C C C C C C C C C C C C C
C-FITC (SEQ ID NO: 14) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
T20 20 mer SEQUENCE T T T T T T T T T T T T T T T T T T T T-FITC
(SEQ ID NO: 15) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? AC10 20
mer SEQUENCE A C A C A C A C A C A C A C A C A C A C-FITC (SEQ ID
NO: 16) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? AG10 20 mer
SEQUENCE A G A G A G A G A G A G A G A G A G A G-FITC (SEQ ID NO:
17) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? TC10 20 mer SEQUENCE
T C T C T C T C T C T C T C T C T C T C-FITC (SEQ ID NO: 18) PS ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? TG10 20 mer SEQUENCE T G T G T
G T G T G T G T G T G T G T G-FITC (SEQ ID NO: 19) PS ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? REP 2029 40 mer SEQUENCE A A A A A A A A
A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A
(SEQ ID NO: 20) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2028 40 mer SEQUENCE G G G G G
G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G
G (SEQ ID NO: 21) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2031 40 mer SEQUENCE C C C C
C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C
C C (SEQ ID NO: 22) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2030 40 mer SEQUENCE T T T
T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T
T T T (SEQ ID NO: 23) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2055 40 mer SEQUENCE A C
A C A C A C A C A C A C A C A C A C A C A C A C A C A C A C A C A C
A C A C (SEQ ID NO: 24) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2058 40 mer SEQUENCE T
C T C T C T C T C T C T C T C T C T C T C T C T C T C T C T C T C T
C T C T C (SEQ ID NO: 25) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2057 40 mer SEQUENCE
A G A G A G A G A G A G A G A G A G A G A 0 A G A G A G A G A G A G
A G A G A G (SEQ ID NO: 26) PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2059 20mer RNA
randomer SEQUENCE N N N N N N N N N N N N N N N N N N N N PS ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? REP 2060 30mer RNA randomer
SEQUENCE N N N N N N N N N N N N N N N N N N N N N N N N N N N N N
N PS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
Sequence CWU 1
1
36120DNAHomo sapiens 1ttgataaata gtactaggac 20222DNAHuman
herpesvirus 1 2gaagcgttcg cacttcgtcc ca 22316DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 3cttgcggtat tcggaa 16410DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 4tccgaagacg 10520DNAArtificial SequenceDescription
of Artificial Sequence Synthetic oligonucleotide 5acacctccga
agacgataac 20640DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 6ctacagacat acacctccga
agacgataac actagacata 40710DNAHuman herpesvirus 1 7cccccatgga
10820DNAHuman herpesvirus 1 8tacgaccccc atggagcccc 20940DNAHuman
herpesvirus 1 9tccagccgca tacgaccccc atggagcccc gccccggagc
401021DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 10gcgtttgctc ttcttcttgc g
211121DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 11gcgtttgctc ttcttcttgc g
211220DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 12aaaaaaaaaa aaaaaaaaaa
201320DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 13gggggggggg gggggggggg
201420DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 14cccccccccc cccccccccc
201520DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 15tttttttttt tttttttttt
201620DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 16acacacacac acacacacac
201720DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 17agagagagag agagagagag
201820DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 18tctctctctc tctctctctc
201920DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 19tgtgtgtgtg tgtgtgtgtg
202040DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 20aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
aaaaaaaaaa 402140DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 21gggggggggg gggggggggg
gggggggggg gggggggggg 402240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 22cccccccccc
cccccccccc cccccccccc cccccccccc 402340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 23tttttttttt tttttttttt tttttttttt tttttttttt
402440DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 24acacacacac acacacacac acacacacac
acacacacac 402540DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 25tctctctctc tctctctctc
tctctctctc tctctctctc 402640DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 26agagagagag
agagagagag agagagagag agagagagag 4027120DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 27aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
aaaaaaaaaa aaaaaaaaaa 60aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
aaaaaaaaaa aaaaaaaaaa 12028120DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 28cccccccccc
cccccccccc cccccccccc cccccccccc cccccccccc cccccccccc 60cccccccccc
cccccccccc cccccccccc cccccccccc cccccccccc cccccccccc
12029120DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 29gggggggggg gggggggggg gggggggggg
gggggggggg gggggggggg gggggggggg 60gggggggggg gggggggggg gggggggggg
gggggggggg gggggggggg gggggggggg 12030120DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 30tttttttttt tttttttttt tttttttttt tttttttttt
tttttttttt tttttttttt 60tttttttttt tttttttttt tttttttttt tttttttttt
tttttttttt tttttttttt 12031240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 31acacacacac
acacacacac acacacacac acacacacac acacacacac acacacacac 60acacacacac
acacacacac acacacacac acacacacac acacacacac acacacacac
120acacacacac acacacacac acacacacac acacacacac acacacacac
acacacacac 180acacacacac acacacacac acacacacac acacacacac
acacacacac acacacacac 24032240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 32agagagagag
agagagagag agagagagag agagagagag agagagagag agagagagag 60agagagagag
agagagagag agagagagag agagagagag agagagagag agagagagag
120agagagagag agagagagag agagagagag agagagagag agagagagag
agagagagag 180agagagagag agagagagag agagagagag agagagagag
agagagagag agagagagag 24033240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 33atatatatat
atatatatat atatatatat atatatatat atatatatat atatatatat 60atatatatat
atatatatat atatatatat atatatatat atatatatat atatatatat
120atatatatat atatatatat atatatatat atatatatat atatatatat
atatatatat 180atatatatat atatatatat atatatatat atatatatat
atatatatat atatatatat 24034240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 34cgcgcgcgcg
cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg 60cgcgcgcgcg
cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg
120cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg
cgcgcgcgcg 180cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg cgcgcgcgcg
cgcgcgcgcg cgcgcgcgcg 24035240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 35ctctctctct
ctctctctct ctctctctct ctctctctct ctctctctct ctctctctct 60ctctctctct
ctctctctct ctctctctct ctctctctct ctctctctct ctctctctct
120ctctctctct ctctctctct ctctctctct ctctctctct ctctctctct
ctctctctct 180ctctctctct ctctctctct ctctctctct ctctctctct
ctctctctct ctctctctct 24036240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 36gtgtgtgtgt
gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt 60gtgtgtgtgt
gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt
120gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt
gtgtgtgtgt 180gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt
gtgtgtgtgt gtgtgtgtgt 240
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