U.S. patent application number 11/264444 was filed with the patent office on 2006-09-14 for antisense antiviral compounds and methods for treating a filovirus infection.
Invention is credited to Sina Bavari, Patrick L. Iversen, David A. Stein.
Application Number | 20060205693 11/264444 |
Document ID | / |
Family ID | 36319793 |
Filed Date | 2006-09-14 |
United States Patent
Application |
20060205693 |
Kind Code |
A1 |
Stein; David A. ; et
al. |
September 14, 2006 |
Antisense antiviral compounds and methods for treating a filovirus
infection
Abstract
The invention provides antisense antiviral compounds and methods
of their use and production in inhibition of growth of viruses of
the Filoviridae family, and in the treatment of a viral infection.
The compounds and methods relate to the treatment of viral
infections in mammals including primates by Ebola and Marburg
viruses. The antisense antiviral compounds are substantially
uncharged morpholino oligonucleotides having: a) a nuclease
resistant backbone, b) 15-40 nucleotide bases, and c) a targeting
sequence of at least 15 bases in length that hybridizes to a target
region selected from the following: i) the AUG start site region of
VP35, as exemplified by antisense compounds SEQ ID NO:21-26, ii)
the AUG start site region of VP24, as exemplified by antisense
compound SEQ ID NO:34, iii) the region 85 to 65 base pairs upstream
of the AUG start site of VP24, as exemplified by SEQ ID NO:39, iv)
the AUG start site region of polymerase L, as exemplified by
antisense compound SEQ ID NO: 17, and v) combinations of (i), (ii),
(iii), and/or (iv).
Inventors: |
Stein; David A.; (Corvallis,
OR) ; Iversen; Patrick L.; (Corvallis, OR) ;
Bavari; Sina; (Frederick, MD) |
Correspondence
Address: |
PERKINS COIE LLP
P.O. BOX 2168
MENLO PARK
CA
94026
US
|
Family ID: |
36319793 |
Appl. No.: |
11/264444 |
Filed: |
October 31, 2005 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
60624277 |
Nov 1, 2004 |
|
|
|
60671694 |
Apr 14, 2005 |
|
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|
Current U.S.
Class: |
514/81 |
Current CPC
Class: |
C12N 2310/31 20130101;
C12N 2310/11 20130101; A61P 31/14 20180101; C12N 15/1131 20130101;
C12N 2310/32 20130101; C12N 2310/3513 20130101 |
Class at
Publication: |
514/081 |
International
Class: |
A61K 48/00 20060101
A61K048/00 |
Claims
1. An antiviral compound, useful in treating a Filovirus infection,
comprising an oligonucleotide analog having a) a nuclease-resistant
backbone, b) 15-40 nucleotide bases, and c) a targeting sequence of
at least 15 bases in length that hybridizes to a target region
selected from the following: i) the AUG start site region of VP35,
as exemplified by antisense compounds SEQ ID NO:21-26, ii) the AUG
start site region of VP24, as exemplified by antisense compound SEQ
ID NO:34, iii) the region 85 to 65 base pairs upstream of the AUG
start site of VP24, as exemplified by SEQ ID NO:39, iv) the AUG
start site region of polymerase L, as exemplified by antisense
compound SEQ ID NO: 17, and v) combinations of (i), (ii), (iii),
and/or (iv).
2. The compound of claim 1, wherein the oligonucleotide analog has:
a) the capability of being actively taken up by mammalian host
cells, and b) the ability to form a heteroduplex structure with the
viral target region, wherein said heteroduplex structure is: i)
composed of the positive or negative sense strand of the virus and
the oligonucleotide compound, and ii) characterized by a Tm of
dissociation of at least 45.degree. C.
3. The compound of claim 1, wherein the oligonucleotide analog is
composed of morpholino subunits linked by uncharged,
phosphorous-containing intersubunit linkages that join a morpholino
nitrogen of one subunit to a 5' exocyclic carbon of an adjacent
subunit.
4. The compound of claim 3, wherein the morpholino subunits are
joined by phosphorodiamidate linkages in accordance with the
structure: ##STR2## where Y.sub.1.dbd.O, Z.dbd.O, Pj is a purine or
pyrimidine base-pairing moiety effective to bind, by base-specific
hydrogen bonding, to a base in a polynucleotide, and X is alkyl,
alkoxy, thioalkoxy, or alkyl amino.
5. The compound of claim 4 wherein X.dbd.NR.sub.2, and where each R
is independently hydrogen or methyl.
6. The compound of claim 1, wherein the oligonucleotide analog
hybridizes to a sequence selected from the group consisting of SEQ
ID NOs:1-14.
7. The compound of claim 1, wherein the viral target region
comprises one of the sequences selected from the group consisting
of SEQ ID NOs:1, 2 and 5.
8. The compound of claim 1, wherein the antisense compound has at
least 12 contiguous bases from one of the sequences selected from
the group consisting of SEQ ID NOs:15-58.
9. The compound of claim 1, wherein the targeting sequence
comprises one of the sequences selected from the group consisting
of SEQ ID NOs:17, 22 and 34.
10. The compound of claim 1, wherein the oligonucleotide analog is
conjugated to an arginine-rich polypeptide that enhances the uptake
of the compound into host cells.
11. The compound of claim 10, wherein the arginine-rich polypeptide
is selected from the group consisting of SEQ ID NOs:61-66.
12. A method of treating an Ebola or Marburg virus infection in a
mammalian host, by administering to the host, a therapeutically
effective amount of a composition of the type described in claim 1,
said method including in exemplary embodiments, administering a
composition having a combination of antisense compounds targeted
against different viral proteins, such as the VP35, VP24, and L
polymerase proteins.
13. A method of vaccinating a mammalian subject against Ebola virus
by pretreating the subject with the composition of claim 1, and
exposing the subject to the Ebola virus, preferably in an
attenuated form.
Description
[0001] This application claims priority to U.S. provisional Patent
Application No. 60/671,694 filed Apr. 14, 2005, and U.S.
provisional Patent Application No. 60/624,277 filed Nov. 1, 2004,
which are both incorporated herein in their entirety by
reference.
FIELD OF THE INVENTION
[0002] This invention relates to antisense oligonucleotide
compounds for use in treating an infection by a virus of the
Filoviridae family and antiviral treatment methods employing the
compounds. More specifically, it relates to treatment methods and
compounds for treating viral infections in mammals including
primates by Ebola and Marburg viruses. [0003] Agrawal, S., S. H.
Mayrand, et al. (1990). "Site-specific excision from RNA by RNase H
and mixed-phosphate-backbone oligodeoxynucleotides." Proc Natl Acad
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"Redirection of drug metabolism using antisense technology." Curr
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al. (1994). "An approach to the structure determination of nucleic
acid analogues hybridized to RNA. NMR studies of a duplex between
2'-OMe RNA and an oligonucleotide containing a single amide
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Bonham, M. A., S. Brown, et al. (1995). "An assessment of the
antisense properties of RNase H-competent and steric-blocking
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W., J. S. Rice, et al. (1997). "Solution structure of an
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J. M., J. L. Littig, et al. (2000). "Targeted elimination of
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hybridizes to complementary oligonucleotides obeying the
Watson-Crick hydrogen-bonding rules." Nature 365(6446): 566-8.
[0016] Feldmann, H., S. Jones, et al. (2003). "Ebola virus: from
discovery to vaccine." Nat Rev Immunol 3(8): 677-85. [0017]
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and replication of filoviruses. " Curr Top Microbiol Immunol 235:
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[0019] Felgner, P. L., T. R. Gadek, et al. (1987). "Lipofection: a
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et al. (1974). "Synthetic-analogues of polynucleotides XII.
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[0022] Geisbert, T. W. and L. E. Hensley (2004). "Ebola virus: new
insights into disease aetiopathology and possible therapeutic
interventions." Expert Rev Mol Med 6(20): 1-24. [0023] Geisbert, T.
W., L. E. Hensley, et al. (2003). "Treatment of Ebola virus
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[0024] Jahrling, P. B., T. W. Geisbert, et al. (1999). "Evaluation
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S224-34. [0025] Lesnikowski, Z. J., M. Jaworska, et al. (1990).
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"Cellular uptake of antisense morpholino oligomers conjugated to
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J. and J. W. LeDuc (1999). "An introduction to Ebola: the virus and
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BACKGROUND OF THE INVENTION
[0035] Minus-strand (-) RNA viruses are major causes of human
suffering that cause epidemics of serious human illness. In humans
the diseases caused by these viruses include influenza
(Orthomyxoviridae), mumps, measles, upper and lower respiratory
tract disease (Paramyxoviridae), rabies (Rhabdoviridae),
hemorrhagic fever (Filoviridae, Bunyaviridae and Arenaviridae),
encephalitis (Bunyaviridae) and neurological illness (Bomaviridae).
Virtually the entire human population is thought to be infected by
many of these viruses (e.g. respiratory syncytial virus) (Strauss
and Strauss 2002).
[0036] The order Mononegavirales is composed of four minus strand
RNA virus families, the Rhabdoviridae, the Paramyxoviridae, the
Filoviridae and the Bornaviridae. The viruses in these families
contain a single strand of non-segmented negative-sense RNA and are
responsible for a wide range of significant diseases in fish,
plants, and animals. Viruses with segmented (-) RNA genomes belong
to the Arenaviridae, Bunyaviridae and Orthomyxoviridae families and
possess genomes with two, three and seven or eight segments,
respectively.
[0037] The expression of the five to ten genes encoded by the
members of the Mononegavirales is controlled at the level of
transcription by the order of the genes on the genome relative to
the single 3' promoter. Gene order throughout the Mononegavirales
is highly conserved. Genes encoding products required in
stoichiometric amounts for replication are always at or near the 3'
end of the genome while those whose products are needed in
catalytic amounts are more promoter distal (Strauss and Strauss
2002). The segmented (-) RNA viruses encode genes with similar
functions to those encoded by the Mononegavirales. Other features
of virion structure and replication pathways are also shared among
the (-) RNA viruses.
[0038] For some (-) RNA viruses, effective vaccines are available
(e.g. influenza, mumps and measles virus) whereas for others there
are no effective vaccines (e.g. Ebola virus and Marburg virus). In
general, no effective antiviral therapies are available to treat an
infection by any of these viruses. As with many other human viral
pathogens, available treatment involves supportive measures such as
anti-pyretics to control fever, fluids, antibiotics for secondary
bacterial infections and respiratory support as necessary.
[0039] The development of a successful therapeutic for filoviruses
Ebola and Marburg virus is a long-sought and seemingly difficult
endeavor (Geisbert and Hensley 2004). Although they cause only a
few hundred deaths worldwide each year, filoviruses are considered
a significant world health threat and have many of the
characteristics commonly associated with biological weapons since
they can be grown in large quantities, can be fairly stable, are
highly infectious as an aerosol, and are exceptionally deadly
(Borio, Inglesby et al. 2002). Filoviruses are relatively simple
viruses of 19 Kb genomes and consist of seven genes which encode
nucleoprotein (NP), glycoprotein (GP), four smaller viral proteins
(VP24, VP30, VP35 and VP40), and the RNA-dependent RNA polymerase
(L protein) all in a single strand of negative-sensed RNA (Feldmann
and Kiley 1999). The development of an effective therapeutic for
Ebola virus has been hindered by a lack of reagents and a clear
understanding of filovirus pathogenesis, disparity between animal
models, and both the difficulty and danger of working with Ebola
virus in biosafety level (BSL)-4 conditions (Geisbert and Hensley
2004; Burnett, Henchal et al. 2005). Administration of type I
interferons, therapeutic vaccines, immune globulins, ribavirin, and
other nucleoside analogues have been somewhat successful in rodent
Ebola virus models, but not in infected nonhuman primates
(Jahrling, Geisbert et al. 1999; Geisbert and Hensley 2004;
Warfield, Perkins et al. 2004). Ebola virus frequently causes
severe disseminated intravascular coagulation and administration of
a recombinant clotting inhibitor has recently shown to protect 33%
of rhesus monkeys (Geisbert, Hensley et al. 2003; Geisbert and
Hensley 2004). Host-directed therapeutics alone have not proven to
be a sufficiently efficacious therapeutic approach. A
well-orchestrated sequence-specific attack on viral gene expression
is required for a highly successful anti-filovirus therapeutic and
treatment regimen.
[0040] In view of the severity of the diseases caused by (-) RNA
viruses, in particular members of the Filoviridae family of
viruses, and the lack of effective prevention or therapies, it is
therefore an object of the present invention to provide therapeutic
compounds and methods for treating a host infected with a (-) RNA
virus.
SUMMARY OF THE INVENTION
[0041] The invention includes, in one aspect, an anti-viral
antisense composition effective in inhibiting replication within a
host cell of an Ebola virus or Marburg virus. The composition
contains one or more antisense compounds that target viral RNA
sequences within a region of the positive-strand mRNA that includes
the region 5' and/or the 25-basepair region just downstream of the
AUG start site of the (i) VP35 polymerase, (ii) the L polymerase,
(iii) the VP24 membrane associated protein, (iv) the VP40
membrane-associated protein, and (v) the VP30 nucleoprotein. The
antiviral compound(s) in the composition include an oligonucleotide
analog having: [0042] a) a nuclease-resistant backbone, [0043] b)
15-40 nucleotide bases, and [0044] c) a targeting sequence of at
least 15 bases in length that hybridizes to a target region
selected from the following: [0045] i) the AUG start site region of
VP35, as exemplified by antisense compounds SEQ ID NOs:21-26,
[0046] ii) the AUG start site region of VP24, as exemplified by
antisense compound SEQ ID NO:34, [0047] iii) the region 85 to 65
base pairs upstream of the AUG start site of VP24, as exemplified
by SEQ ID NO:39, [0048] iv) the AUG start site region of polymerase
L, as exemplified by antisense compound SEQ ID NO:17, and [0049] v)
combinations of (i), (ii), (iii) and/or (iv). The oligonucleotide
analog also has: [0050] a) the capability of being actively taken
up by mammalian host cells, and [0051] b) the ability to form a
heteroduplex structure with the viral target region, wherein said
heteroduplex structure is: [0052] i) composed of the positive or
negative sense strand of the virus and the oligonucleotide
compound, and [0053] ii) characterized by a Tm of dissociation of
at least 45.degree. C.
[0054] The compound may be composed of morpholino subunits linked
by uncharged, phosphorus-containing intersubunit linkages, joining
a morpholino nitrogen of one subunit to a 5' exocyclic carbon of an
adjacent subunit. In one embodiment, the intersubunit linkages are
phosphorodiamidate linkages, such as those having the structure:
##STR1## where Y.sub.1.dbd.O, Z.dbd.O, Pj is a purine or pyrimidine
base-pairing moiety effective to bind, by base-specific hydrogen
bonding, to a base in a polynucleotide, and X is alkyl, alkoxy,
thioalkoxy, or alkyl amino e.g., wherein X.dbd.NR.sub.2, where each
R is independently hydrogen or methyl. The compound may contain one
or more cationic linkages wherein X.dbd.(1-piperazino).
[0055] The compound may also be a covalent conjugate of an
oligonucleotide analog moiety capable of forming such a
heteroduplex structure with the positive or negative sense strand
of the virus, and an arginine-rich polypeptide effective to enhance
the uptake of the compound into host cells. Exemplary polypeptides
have one of the sequences identified as SEQ ID NOs:61-66.
[0056] Exemplary compositions include one or more antisense
compounds that target a positive strand RNA region that includes:
[0057] (i) the AUG start site region of VP35, as exemplified by
antisense compounds SEQ ID NOs:21-26, [0058] (ii) the AUG start
site region of VP24, as exemplified by antisense compound SEQ ID
NO:34, [0059] (iii) the region 85 to 65 base pairs upstream of the
AUG start site of VP24, as exemplified by SEQ ID NO:39, [0060] (iv)
the AUG start site region of polymerase L, as exemplified by
antisense compound SEQ ID NO:17, and [0061] (v) combinations of (i)
, (ii), (iii) and/or (iv).
[0062] The antisense compound(s) in the composition preferably
target(s) at least 18, more preferably, at least 20 target base
pairs.
[0063] In another aspect, the invention includes a method of
treating an Ebola or Marburg virus infection in a mammalian host,
by administering to the host, a therapeutically effective amount of
a composition of the type described above. The method includes, in
exemplary embodiments, administering a composition having a
combination of antisense compounds targeted against different viral
proteins, such as the VP35, VP24, and L polymerase proteins.
[0064] In a related, more general aspect, the invention includes a
method of vaccinating a mammalian subject against Ebola or Marburg
virus by pretreating the subject with the composition of the
invention, and exposing the subject to the Ebola virus, preferably
in an attenuated form.
[0065] These and other objects and features of the invention will
become more fully apparent when the following detailed description
of the invention is read in conjunction with the accompanying
drawings.
BRIEF DESCRIPTION OF THE FIGURES
[0066] FIGS. 1A-1D show the repeating subunit segment of several
preferred morpholino oligonucleotides, designated A through D,
constructed using subunits having 5-atom (A), six-atom (B) and
seven-atom (C-D) linking groups suitable for forming polymers.
[0067] FIGS. 2A-2G show the backbone structures of various
oligonucleotide analogs with uncharged backbones and FIG. 2H shows
a cationic linkage structure.
[0068] FIGS. 3A-3C illustrate the components and morphology of a
filovirus (3A), and show the arrangement of viral genes in the
Ebola virus (Zaire) (3B), and the Marburg virus (3C).
[0069] FIGS. 4A-4B show the target regions of 6 antisense compounds
targeted against the VP35 gene in Ebola virus.
[0070] FIG. 5 is a plot showing cytotoxicity in Vero cell culture,
expressed as a percent control, as a function of antisense type and
concentration.
[0071] FIGS. 6A-6C are photomicrographs of Vero cells in culture
(6A) in the absence of Ebola virus infection and antisense
treatment; (6B) with Ebola virus infection but no antisense
treatment; and (6C) with Ebola virus infection and treatment with
VP35-AUG (SEQ ID NO:17) antisense compound.
[0072] FIG. 7 is a plot of treatment efficacy, expressed as a
fraction of mouse survivors 10 days post infection, as a function
of VP35 antisense length.
[0073] FIG. 8 is a plot of treatment efficacy, expressed as percent
survival, as a function of dose of various combinations of
antisense compounds.
[0074] FIG. 9A shows the schedule of the experimental protocol.
FIG. 9B plots the fraction of mouse survivors with various dose
schedules of antisense compounds.
[0075] FIG. 10 is a schematic of the treatment schedule for a trial
using PMO to treat Ebola infection in nonhuman primates.
[0076] FIG. 11 shows Ebola-specific PMOs protect mice from lethal
Ebola virus infection. (A) Survival of mice pretreated at 4 and 24
hours before EBOV infection with 500 .mu.g of PMOs targeting VP24
(.diamond-solid.), VP35 (.box-solid.), L (.tangle-solidup.), or
with an unrelated sequence (X). (B) Survival of mice pretreated
with 1 mg (.diamond.), 0.1 mg (.quadrature.), or 0.01 mg (.DELTA.)
of a combination of the VP24, VP35, and L) PMOs or 1 mg
(.diamond-solid.), 0.1 mg (.box-solid.), or 0.01 mg
(.tangle-solidup.) of VP35 PMO only or an unrelated sequence (X).
(C) Survival in mice treated 24 hours following EBOV infection with
1 mg (.diamond-solid.), 0.1 mg (.box-solid.), or 0.01 mg
(.tangle-solidup.) of the combination of PMOs or an unrelated
sequence (X). (D-G) C57B1/6 mice were challenged intraperitoneally
with 1000 plaque-forming units of EBOV following treatment with
PMOs. Immunoperoxidase stain is brown with hematoxylin
counterstain. Viral antigen within the spleen (100.times.) of a
mouse treated with scrambled PMO (D) or the EBOV PMOs (E) three
days after EBOV infection. Diffuse staining pattern in the livers
(600.times.) of the scrambled PMO-treated mice (F) on day 6 of EBOV
infection, compared to focal areas of infection in the mice treated
with the combination of PMOs (G).
[0077] FIG. 12 shows that treatment of guinea pigs with antisense
PMOs increases survival following lethal Ebola virus infection.
Hartley guinea pigs were treated intraperitoneally with 10 mg each
of VP24, VP35, and L PMO in PBS at -24 (.tangle-solidup.), +24
(.circle-solid.), or +96 (.box-solid.) hours post challenge.
Control guinea pigs were injected with PBS only (X). The guinea
pigs were infected subcutaneously with .about.1000 pfu of EBOV and
monitored for illness for 21 days. The data are presented as
percent survival for each group (n=6).
[0078] FIG. 13 shows that Ebola-specific PMOs reduce viral
replication in vivo. Viral titers in tissues from mice treated with
a combination of PMO and infected with 1000 pfu of EBOV. Samples of
the liver, spleen, and kidney were taken at 3 or 6 days post
challenge (dpc), macerated, and analyzed for viral titer using
plaque assay. The data are presented as the mean viral titer of 3
mice with error bars representing the standard deviation.
[0079] FIG. 14 shows the immune responses of PMO-treated mice
following survival of Ebola virus infection. (A) PMO-treated
C57BL/6 mice that have previously survived EBOV infection generate
EBOV-specific CD8.sup.+ responses. Pooled splenocytes from three
PMO-treated EBOV survivors were re-stimulated in vitro with
EBOV-specific VP35 or NP peptides, an irrelevant Lassa NP peptide
as a negative control, or PMA/ionomycin as a positive control. The
stimulated cells were stained after for 4 hours in culture with
anti-CD44 FITC, anti-IFN-.gamma. PE, and anti-CD8 Cy-Chrome. The
percent of CD44.sup.+, IFN-.gamma..sup.+ cells among CD8.sup.+
lymphocytes is indicated in the upper right quadrant of each plot.
These data are representative of the Ebola CD8 specific epitopes
observed after challenge. (B) Total serum anti-Ebola virus
antibodies were measured in surviving mice prior to or 4 weeks
following treatment and challenge. PMO mice were treated with the
combination of PMOs 24 and 4 hours before challenge and their
antibody responses are compared with mice treated with Ebola VLPs
24 hours before EBOV infection. The results are depicted as the
endpoint titers of the individual mice (circles). The horizontal
line in each column represents the geometric mean titer of the
group. (C) Mice that previously survived EBOV challenge following
PMO treatment were re-challenged with 1000 pfu of mouse-adapted
Ebola virus 4 weeks after the initial challenge. Results are
plotted as percent survival for the PMO-treated mice (black) and
naive control mice (n=10 per group).
[0080] FIG. 15 shows that treatment of rhesus macaques with
antisense PMOs provide protection against lethal Ebola virus
infection. (A) Survival following infection with 1000 pfu of EBOV
in monkeys treated with a combination of PMOs (.box-solid.) or
untreated monkeys (.largecircle.). The arrows indicate the monkeys
that died at the time indicated. (B-D) Viral titers (B), platelet
counts (C), or alkaline phosphatase levels (D) in the blood of the
PMO-treated monkeys [0646 (.diamond-solid.), 1438
(.tangle-solidup.), 1496 ( X), 1510 (.box-solid.)] or an untreated
monkey (.largecircle.).
[0081] FIG. 16 shows the increased antisense activity of PMOs with
cationic linkages targeting the EBOV VP24 mRNA in a cell free
translation assay. PMOs used were 537-AUG (SEQ ID NO:34), 164-AUG+
(SEQ ID NO:40), 165-5'-term (SEQ ID NO:39) and 166-5'-term+ (SEQ ID
NO:41).
DETAILED DESCRIPTION OF THE INVENTION
I. Definitions
[0082] The terms below, as used herein, have the following
meanings, unless otherwise indicated:
[0083] The terms "oligonucleotide analog" refers to an
oligonucleotide having (i) a modified backbone structure, e.g., a
backbone other than the standard phosphodiester linkage found in
natural oligo- and polynucleotides, and (ii) optionally, modified
sugar moieties, e.g., morpholino moieties rather than ribose or
deoxyribose moieties. The analog supports bases capable of hydrogen
bonding by Watson-Crick base pairing to standard polynucleotide
bases, where the analog backbone presents the bases in a manner to
permit such hydrogen bonding in a sequence-specific fashion between
the oligonucleotide analog molecule and bases in a standard
polynucleotide (e.g., single-stranded RNA or single-stranded DNA).
Preferred analogs are those having a substantially uncharged,
phosphorus containing backbone.
[0084] A substantially uncharged, phosphorus containing backbone in
an oligonucleotide analog is one in which a majority of the subunit
linkages, e.g., between 60-100%, are uncharged at physiological pH,
and contain a single phosphorous atom. The analog contains between
8 and 40 subunits, typically about 8-25 subunits, and preferably
about 12 to 25 subunits. The analog may have exact sequence
complementarity to the target sequence or near complementarity, as
defined below.
[0085] A "subunit" of an oligonucleotide analog refers to one
nucleotide (or nucleotide analog) unit of the analog. The term may
refer to the nucleotide unit with or without the attached
intersubunit linkage, although, when referring to a "charged
subunit", the charge typically resides within the intersubunit
linkage (e.g. a phosphate or phosphorothioate linkage).
[0086] A "morpholino oligonucleotide analog" is an oligonucleotide
analog composed of morpholino subunit structures of the form shown
in FIGS. 1A-1D, where (i) the structures are linked together by
phosphorus-containing linkages, one to three atoms long, joining
the morpholino nitrogen of one subunit to the 5' exocyclic carbon
of an adjacent subunit, and (ii) P.sub.i and P.sub.j are purine or
pyrimidine base-pairing moieties effective to bind, by
base-specific hydrogen bonding, to a base in a polynucleotide. The
purine or pyrimidine base-pairing moiety is typically adenine,
cytosine, guanine, uracil, thymine or inosine. The synthesis,
structures, and binding characteristics of morpholino oligomers are
detailed in U.S. Pat. Nos. 5,698,685, 5,217,866, 5,142,047,
5,034,506, 5,166,315, 5,521,063, and 5,506,337, all of which are
incorporated herein by reference.
[0087] The subunit and linkage shown in FIG. 1B are used for
six-atom repeating-unit backbones, as shown in FIG. 1B (where the
six atoms include: a morpholino nitrogen, the connected phosphorus
atom, the atom (usually oxygen) linking the phosphorus atom to the
5' exocyclic carbon, the 5' exocyclic carbon, and two carbon atoms
of the next morpholino ring). In these structures, the atom Y.sub.1
linking the 5' exocyclic morpholino carbon to the phosphorus group
may be sulfur, nitrogen, carbon or, preferably, oxygen. The X
moiety pendant from the phosphorus is any stable group which does
not interfere with base-specific hydrogen bonding. Preferred X
groups include fluoro, alkyl, alkoxy, thioalkoxy, and alkyl amino,
including cyclic amines, all of which can be variously substituted,
as long as base-specific bonding is not disrupted. Alkyl, alkoxy
and thioalkoxy preferably include 1-6 carbon atoms. Alkyl amino
preferably refers to lower alkyl (C.sub.1 to C.sub.6) substitution,
and cyclic amines are preferably 5- to 7-membered nitrogen
heterocycles optionally containing 1-2 additional heteroatoms
selected from oxygen, nitrogen, and sulfur. Z is sulfur or oxygen,
and is preferably oxygen.
[0088] A preferred morpholino oligomer is a
phosphorodiamidate-linked morpholino oligomer, referred to herein
as a PMO. Such oligomers are composed of morpholino subunit
structures such as shown in FIG. 1B, where X.dbd.NH.sub.2, NHR, or
NR.sub.2 (where R is lower alkyl, preferably methyl), Y.dbd.O, and
Z.dbd.O, and P.sub.i and P.sub.j are purine or pyrimidine
base-pairing moieties effective to bind, by base-specific hydrogen
bonding, to a base in a polynucleotide. Also preferred are
structures having an alternate phosphorodiamidate linkage, where,
in FIG. 1B, X.dbd.lower alkoxy, such as methoxy or ethoxy, Y.dbd.NH
or NR, where R is lower alkyl, and Z.dbd.O. A cationic linkage can
be introduced into the backbone by utilizing X.dbd.(1-piperazino)
as shown in FIG. 1B.
[0089] The term "substituted", particularly with respect to an
alkyl, alkoxy, thioalkoxy, or alkylamino group, refers to
replacement of a hydrogen atom on carbon with a
heteroatom-containing substituent, such as, for example, halogen,
hydroxy, alkoxy, thiol, alkylthio, amino, alkylamino, imino, oxo
(keto), nitro, cyano, or various acids or esters such as
carboxylic, sulfonic, or phosphonic. It may also refer to
replacement of a hydrogen atom on a heteroatom (such as an amine
hydrogen) with an alkyl, carbonyl or other carbon containing
group.
[0090] As used herein, the term "target", relative to the viral
genomic RNA, refers to at least one of the following: 1) a 125
nucleotide region that surrounds the AUG start codon of a viral
messenger RNA and/or; 2) the terminal 30 bases of the 3' terminal
end of the minus-strand viral RNA (e.g. virion RNA or vRNA) and/or;
3) the terminal 25 bases of viral mRNA transcripts
[0091] The term "target sequence" refers to a portion of the target
RNA against which the oligonucleotide analog is directed, that is,
the sequence to which the oligonucleotide analog will hybridize by
Watson-Crick base pairing of a complementary sequence. As will be
seen, the target sequence may be a contiguous region of the viral
positive-strand mRNA or the minus-strand vRNA.
[0092] The term "targeting sequence" is the sequence in the
oligonucleotide analog that is complementary (meaning, in addition,
substantially complementary) to the target sequence in the RNA
genome. The entire sequence, or only a portion, of the analog
compound may be complementary to the target sequence. For example,
in an analog having 20 bases, only 12-14 may be targeting
sequences. Typically, the targeting sequence is formed of
contiguous bases in the analog, but may alternatively be formed of
non-contiguous sequences that when placed together, e.g., from
opposite ends of the analog, constitute sequence that spans the
target sequence. For example, as will be seen, the target and
targeting sequences are selected such that binding of the analog to
a portion of a 125 nucleotide region associated with the AUG start
codon of the positive-sense RNA strand (i.e., mRNA) of the virus
acts to disrupt translation of the viral gene and reduce viral
replication.
[0093] The term "AUG start site region" includes a 125 nucleotide
region in both the 5' and 3' direction relative to the AUG start
codon of viral mRNAs. The region includes about 25 nucleotides
downstream (i.e., in a 3' direction) and 100 nucleotides upstream
(i.e., in a 5' direction) as exemplified by the targets sequences
shown as SEQ ID NOs: 1-6 for Ebola virus and SEQ ID NOs: 8-13 for
Marburg virus.
[0094] Target and targeting sequences are described as
"complementary" to one another when hybridization occurs in an
antiparallel configuration. A targeting sequence may have "near" or
"substantial" complementarity to the target sequence and still
function for the purpose of the present invention, that is, still
be "complementary." Preferably, the oligonucleotide analog
compounds employed in the present invention have at most one
mismatch with the target sequence out of 10 nucleotides, and
preferably at most one mismatch out of 20. Alternatively, the
antisense oligomers employed have at least 90% sequence homology,
and preferably at least 95% sequence homology, with the exemplary
targeting sequences as designated herein.
[0095] An oligonucleotide analog "specifically hybridizes" to a
target polynucleotide if the oligomer hybridizes to the target
under physiological conditions, with a T.sub.m substantially
greater than 45.degree. C., preferably at least 50.degree. C., and
typically 60.degree. C.-80.degree. C. or higher. Such hybridization
preferably corresponds to stringent hybridization conditions. At a
given ionic strength and pH, the T.sub.m is the temperature at
which 50% of a target sequence hybridizes to a complementary
polynucleotide. Again, such hybridization may occur with "near" or
"substantial" complementary of the antisense oligomer to the target
sequence, as well as with exact complementarity.
[0096] A "nuclease-resistant" oligomeric molecule (oligomer) refers
to one whose backbone is substantially resistant to nuclease
cleavage, in non-hybridized or hybridized form; by common
extracellular and intracellular nucleases in the body; that is, the
oligomer shows little or no nuclease cleavage under normal nuclease
conditions in the body to which the oligomer is exposed.
[0097] A "heteroduplex" refers to a duplex between an
oligonculeotide analog and the complementary portion of a target
RNA. A "nuclease-resistant heteroduplex" refers to a heteroduplex
formed by the binding of an antisense oligomer to its complementary
target, such that the heteroduplex is substantially resistant to in
vivo degradation by intracellular and extracellular nucleases, such
as RNAseH, which are capable of cutting double-stranded RNA/RNA or
RNA/DNA complexes.
[0098] A "base-specific intracellular binding event involving a
target RNA" refers to the specific binding of an oligonucleotide
analog to a target RNA sequence inside a cell. The base specificity
of such binding is sequence specific. For example, a
single-stranded polynucleotide can specifically bind to a
single-stranded polynucleotide that is complementary in
sequence.
[0099] An "effective amount" of an antisense oligomer, targeted
against an infecting filovirus, is an amount effective to reduce
the rate of replication of the infecting virus, and/or viral load,
and/or symptoms associated with the viral infection.
[0100] As used herein, the term "body fluid" encompasses a variety
of sample types obtained from a subject including, urine, saliva,
plasma, blood, spinal fluid, or other sample of biological origin,
such as skin cells or dermal debris, and may refer to cells or cell
fragments suspended therein, or the liquid medium and its
solutes.
[0101] The term "relative amount" is used where a comparison is
made between a test measurement and a control measurement. The
relative amount of a reagent forming a complex in a reaction is the
amount reacting with a test specimen, compared with the amount
reacting with a control specimen. The control specimen may be run
separately in the same assay, or it may be part of the same sample
(for example, normal tissue surrounding a malignant area in a
tissue section).
[0102] "Treatment" of an individual or a cell is any type of
intervention provided as a means to alter the natural course of the
individual or cell. Treatment includes, but is not limited to,
administration of e.g., a pharmaceutical composition, and may be
performed either prophylactically, or subsequent to the initiation
of a pathologic event or contact with an etiologic agent. The
related term "improved therapeutic outcome" relative to a patient
diagnosed as infected with a particular virus, refers to a slowing
or diminution in the growth of virus, or viral load, or detectable
symptoms associated with infection by that particular virus.
[0103] An agent is "actively taken up by mammalian cells" when the
agent can enter the cell by a mechanism other than passive
diffusion across the cell membrane. The agent may be transported,
for example, by "active transport", referring to transport of
agents across a mammalian cell membrane by e.g. an ATP-dependent
transport mechanism, or by "facilitated transport", referring to
transport of antisense agents across the cell membrane by a
transport mechanism that requires binding of the agent to a
transport protein, which then facilitates passage of the bound
agent across the membrane. For both active and facilitated
transport, the oligonucleotide analog preferably has a
substantially uncharged backbone, as defined below. Alternatively,
the antisense compound may be formulated in a complexed form, such
as an agent having an anionic backbone complexed with cationic
lipids or liposomes, which can be taken into cells by an
endocytotic mechanism. The analog also may be conjugated, e.g., at
its 5' or 3' end, to an arginine-rich peptide, e.g., a portion of
the HIV TAT protein, or polyarginine, to facilitate transport into
the target host cell as described (Moulton, Nelson et al. 2004).
The compound may also have one or more cationic linkages to enhance
antisense activity and/or cellular uptake. A preferred cationic
linkage is shown in FIG. 1B where X.dbd.(1-piperazino).
[0104] The term "filovirus" refers collectively to members of the
Filoviridae family of single stranded (-) RNA viruses including
Ebola and Marburg viruses listed in Table 1 below.
II. Targeted Viruses
[0105] The present invention is based on the discovery that
effective inhibition of single-stranded, negative-sense RNA ((-)
RNA)viruses can be achieved by exposing cells infected with the
virus to antisense oligonucleotide analog compounds (i) targeted
against the AUG start codon of the positive sense viral mRNAs or
the 3' termini of the negative strand viral RNA, and (ii) having
physical and pharmacokinetic features which allow effective
interaction between the antisense compound and the virus within
host cells. In one aspect, the oligomers can be used in treating a
mammalian subject infected with the virus.
[0106] The invention targets RNA viruses having genomes that are:
(i) single stranded, (ii) negative polarity, and (iii) less than 20
kb. The targeted viruses also synthesize a RNA species with
positive polarity, the positive-strand or sense RNA, as the
requisite step in viral gene expression. In particular, targeted
viruses include those of the Filoviridae family referred to herein
as filoviruses. Targeted viruses organized by family, genus and
species are listed in Table 1. Various physical, morphological, and
biological characteristics of each of the Filoviridae family, and
members therein, can be found, for example, in Textbook of Human
Virology, R. Belshe, ed., 2.sup.nd Edition, Mosby, 1991, in
"Viruses and Human Disease" (Strauss and Strauss 2002) and at the
Universal Virus Database of the International Committee on Taxonomy
of Viruses (www.ncbi.nlm.nih.gov/ICTVdb/index.htm). Some of the key
biological characteristics of each family are summarized below
following Table 1. TABLE-US-00001 TABLE 1 Targeted viruses of the
invention organized by family and genus Family Genus Virus
Filoviridae Marburg-like Marburg virus (MARV) Ebola-like Zaire
Ebola virus (ZEBOV) Sudan Ebola virus (SEBOV) Reston Ebola virus
(REBOV) Cote d'Ivoire Ebola (ICEBOV)
[0107] A. Filoviridae
[0108] The Filoviridae family is composed of two members, Ebola
virus (EBOV) and Marburg virus (MARV). Four species of Ebola have
been identified to date and are named by the location of where they
were identified including Ebola Ivory Coast (ICEBOV), Ebola Zaire
(ZEBOV), Ebola Sudan (SEBOV) and Ebola Reston (REBOV). Ebola Reston
is the only known filovirus that does not cause severe human
disease. The filovirus structure is pleomorphic with shapes varying
from long filaments to shorter contorted structures. The viral
filaments measure up to 14,000 nm in length and have uniform
diameter of 80 nm. The virus filament is envelope in a lipid
membrane. The virion contains one, single-stranded, negative sense
RNA.
[0109] The first filovirus was recognized in 1967 after laboratory
workers in Marburg Germany developed hemorrhagic fever following
studies involving handling tissues from green monkeys. The Marburg
outbreak led to 31 cases and seven deaths. The first Ebola virus
was identified in 1976 following outbreaks of Ebola hemorrhagic
fever in northern Zaire (now the Democratic Republic of Congo) and
southern Sudan. Eventually, two distinct viral isolates were
recognized. Ebola Zaire was lethal in 90% of the infected cases and
Ebola Sudan was lethal in 50% of the cases. A list of Ebola
hemorrhagic fever case is compiled for Ebola Zaire in TABLE 2.
TABLE-US-00002 TABLE 2 Chronological order of Ebola Zaire Outbreaks
Date Location Human Cases Deaths 1976 Zaire 318 280 (88%) 1977
Zaire 1 1 (100%) 1994 Gabon 49 29 (59%) 1995 Dem. Rep. Congo 315
255 (81%) 1996 Gabon 31 21 (68%) 1996 Gabon 60 45 (75%) 1996 South
Africa 2 1 (50%) 2001 Gabon and Congo 122 96 (79%)
[0110] The summary of these outbreak data include 899 cases
resulting in 728 deaths or an overall 81% rate of lethality
observed over a period of 25 years. A single case of Ebola Ivory
Coast was reported in 1994 and that infection was not lethal.
Finally, 4 outbreaks of Ebola Sudan from 1976 to 2001 produced 744
cases resulting in 398 deaths or an overall rate of lethality of
53%. These observations indicate Ebola Zaire is the virus of
greatest concern both in apparent prevalence and lethality. It
appears Ebola is transmitted to humans from ongoing life cycles in
animals other than humans which make it a zoonotic virus. Ebola can
replicate in various rodents such as mice, guinea pigs and some
species of bats. Some types of bats are native to areas where the
virus is found which suggests the bat may be the natural host and
viral reservoir. Once a human is infected, person-to-person
transmission is the means for further infections. During recorded
outbreaks, individuals that cared for or worked closely with
infected people were at high risk of becoming infected. Nosocomial
transmission has also been an important factor in the spread of
viral infection during outbreaks. In the laboratory setting, viral
spread through small-particle aerosols has been clearly
demonstrated.
[0111] The incubation period for Ebola hemorrhagic fever ranges
from 2 to 21 days. The clinical symptoms include abrupt onset of
fever, headache, joint and muscle aches, sore throat and weakness.
These symptoms are then followed by diarrhea, vomiting and stomach
pain which do not help in diagnosis of infection. Diagnosis is
suspected when this group of symptoms is observed in an area where
Ebola is known to be active. Patients who die usually have not
developed a significant immune response to the virus at the time of
death. There are no known treatments for filovirus infections.
[0112] The filovirus virus genome is approximately 19,000 bases of
single-stranded RNA that is unsegmented and in the antisense (i.e.
negative sense) orientation. The genome encodes 7 proteins from
monocistronic mRNAs complementary to the vRNA as shown in FIG. 3. A
review of filoviruses can be found in Fields Virology and (Strauss
and Strauss 2002).
[0113] Ebola Virus
[0114] Ebola virus (EBOV), a member of the family Filoviridae and
the order Mononegavirales, is an enveloped, nonsegmented
negative-strand RNA virus and is one of the most lethal human and
nonhuman primate pathogens recognized to date. Four subtypes of
Ebola virus have been identified, including Zaire (ZEBOV), Sudan
(SEBOV), Ivory Coast (ICEBOV), and Reston (REBOV) (Sanchez, Kiley
et al. 1993). Human infection with subtype Zaire causes a
fulminating, febrile, hemorrhagic disease resulting in extensive
mortality (Feldmann, Klenk et al. 1993; Peters and LeDuc 1999;
Feldmann, Jones et al. 2003).
[0115] Ebola virus particles have a filamentous appearance, but
their shape may be branched, circular, U- or 6-shaped, or long and
straight. Virions show a uniform diameter of approximately 80 nm,
but vary greatly in length. Ebola virus particles consist of seven
structural proteins. The glycoprotein (GP) of Ebola virus forms
spikes of approximately 7 nm, which are spaced at 5- to 10-nm
intervals on the virion surface.
[0116] Marburg Virus
[0117] Marburg virus (MARV) was first recognized in 1967, when an
outbreak of hemorrhagic fever in humans occurred in Germany and
Yugoslavia, after the importation of infected monkeys from Uganda.
Thirty-one cases of MARV hemorrhagic fever were identified that
resulted in seven deaths. The filamentous morphology of the virus
was later recognized to be characteristic, not only of additional
MARV isolates, but also of EBOV. MARV and EBOV are now known to be
distinctly different lineages in the family Filoviridae, within the
viral order Mononegavirales (Strauss and Strauss 2002).
[0118] Few natural outbreaks of MARV disease have been recognized,
and all proved self-limiting, with no more than two cycles of
human-to-human transmission. However, the actual risks posed by
MARV to global health cannot be assessed because factors which
restrict the virus to its unidentified ecological niche in eastern
Africa, and those that limit its transmissibility, remain unknown.
Concern about MARV is further heightened by its known stability and
infectivity in aerosol form. A recent (2005) epidemic in eastern
Africa caused at least 200 deaths and further increases the concern
about MARV.
[0119] B. Target Sequences
[0120] The filovirus structure is pleomorphic with shapes varying
from long filaments to shorter contorted structures. The viral
filaments measure up to 14,000 nm in length and have uniform
diameter of 80 nm. The virus filament is envelope in a lipid
membrane. The virion contains one, single-stranded, negative sense
RNA. The filovirus virus genome is approximately 19,000 bases of
single- stranded RNA that is unsegmented and in the antisense
orientation. The genome encodes 7 proteins from monocistronic mRNAs
complementary to the vRNA. A diagram of a representative filovirus
and its genome is provided in FIGS. 3A-3C (taken from Fields
Virology).
[0121] The targets selected were positive-strand (sense) RNA
sequences that span or are just downstream (within 25 bases) or
upstream (within 100 bases) of the AUG start codon of selected
Ebola virus proteins or the 3' terminal 30 bases of the
minus-strand viral RNA. Preferred protein targets are the viral
polymerase subunits VP35 and L, nucleoproteins NP and VP30, and
membrane-associated proteins VP24 and VP40. Among these early
proteins are favored, e.g., VP35 is favored over the later
expressed L polymerase. As will be seen, a preferred
single-compound target is VP35 that spans the AUG start site,
and/or targets a region within 100 bases upstream or 25 bases
downstream of the translational start site. Preferred combinations
of targets include the VP35-AUG target plus the VP24-AUG start site
(or the 100-base region upstream or 25-base-region downstream of
the start site) and or the L polymerase AUG start site (or the
100-base region upstream or 25-base-region downstream of the start
site).
[0122] Additional targets include the terminal 25 base pair region
of the viral mRNA transcripts as represented by the sequences
complementary to the SEQ ID NOs:42 and 43. These targets are
preferred because of their high degree of sequence conservation
across individual filovirus isolates.
[0123] The Ebola virus RNA sequences (Zaire Ebola virus, Mayinga
strain) can be obtained from GenBank Accession No. AF086833. The
particular targeting sequences shown below were selected for
specificity against the Ebola Zaire virus strain. Corresponding
sequences for Ebola Ivory Coast, Ebola Sudan and Ebola Reston
(GenBank Acc. No. AF522874) are readily determined from the known
GenBank entries for these viruses. Preferably targeting sequences
are selected that give a maximum consensus among the viral strains,
particularly the Zaire, Ivory Coast, and Sudan strains, or base
mismatches that can be accommodated by ambiguous bases in the
antisense sequence, according to well-known base pairing rules.
[0124] GenBank references for exemplary viral nucleic acid
sequences representing filovirus genomic segments are listed in
Table 3 below. The nucleotide sequence numbers in Table 3 are
derived from the GenBank reference for the positive-strand RNA of
Ebola Zaire (AF086833) and Marburg virus (Z29337). It will be
appreciated that these sequences are only illustrative of other
sequences in the Filoviridae family, as may be available from
available gene-sequence databases of literature or patent resources
(See e.g. www.ncbi.nlm.nih.gov). The sequences in Table 3 below,
identified as SEQ ID NOs: 1-14, are also listed in the Sequence
Listing table at the end of the specification.
[0125] The target sequences in Table 3 represent the 3' terminal 30
bases of the negative sense viral RNA or the 125 bases surrounding
the AUG start codons of the indicated filovirus genes. The
sequences shown are the positive-strand (i.e., antigenomic or mRNA)
sequence in the 5' to 3' orientation. It will be obvious that when
the target is the minus-strand vRNA, as in the case of the Str Inh
1 target (SEQ ID NOs: 15 and 44) the targeted sequence is the
complement of the sequence listed in Table 3.
[0126] Table 3 lists the targets for exemplary Ebola viral genes
VP35, VP24, VP30, VP40, L and NP. The proteins represent six of the
seven proteins encoded by Ebola. The target sequences for the AUG
start codons of the six genes are represented as SEQ ID NOs:1-6.
The corresponding set of target sequences for Marburg virus are
shown as SEQ ID NOs:8-13. The 3' terminal sequence of the
minus-strand viral RNA (SEQ ID NOs:7 and 14) can also be targeted.
The sequences shown in Table 3 for the 3' terminal minus-strand
targets (SEQ ID NOs:7 and 14) are the minus-strand sequences in a
5'-3' orientation for Ebola and Marburg viruses, respectively.
TABLE-US-00003 TABLE 3 Exemplary Filovirus Nucleic Acid Target
Sequences Nucle- SEQ GenBank otide ID Name No. Region Sequence (5'
to 3') NO VP35- AF086833 3029- AAUGAUGAAGAUUAAAACCUUCAUCA 1 AUG
3153 UCCUUACGUCAAUUGAAUUCUCUAGC ACUCGAAGCUUAUUGUCUUCAAUGUA
AAAGAAAAGCUGGUCUAACAAGAUGA CAACUAGAACAAAGGGCAGGG VP24- AF086833
10245- CGUUCCAACAAUCGAGCGCAAGGUUU 2 AUG 10369
CAAGGUUGAACUGAGAGUGUCUAGAC AACAAAAUAUUGAUACUCCAGACACC
AAGCAAGACCUGAGAAAAAACCAUGG CUAAAGCUACGGGACGAUACA VP30- AF086833
8409- AGAUCUGCGAACCGGUAGAGUUUAGU 3 AUG 8533
UGCAACCUAACACACAUAAAGCAUUG GUCAAAAAGUCAAUAGAAAUUUAAAC
AGUGAGUGGAGACAACUUUUAAAUGG AAGCUUCAUAUGAGAGAGGAC VP40- AF086833
4379- AAACCAAAAGUGAUGAAGAUUAAGAA 4 AUG 4503
AAACCUACCUCGGCUGAGAGAGUGUU UUUUCAUUAACCUUCAUCUUGUAAAC
GUUGAGCAAAAUUGUUAAAAAUAUGA GGCGGGUUAUAUUGCCUACUG L-AUG AF086833
11481- GUAGAUUAAGAAAAAAGCCUGAGGAA 5 11605
GAUUAAGAAAAACUGCUUAUUGGGUC UUUCCGUGUUUUAGAUGAAGCAGUUG
AAAUUCUUCCUCUUGAUAUUAAAUGG CUACACAACAUACCCAAUAC NP- AF086833 370-
UGAACACUUAGGGGAUUGAAGAUUCA 6 AUG 494 ACAACCCUAAAGCUUGGGGUAAAACA
UUGGAAAUAGUUAAAAGACAAAUUGC UCGGAAUCACAAAAUUCCGAGUAUGG
AUUCUCGUCCUCAGAAAAUCU Str. AF086833 30- UAAAAAUUCUUCUUUCUUUUUGUGUG
7 Ihn 1 UCCG 1(-) VP35- Z29337 2844- CUAAAAAUCGAAGAAUAUUAAAGGUU 8
AUG 2968 UUCUUUAAUAUUCAGAAAAGGUUUUU UAUUCUCUUCUUUCUUUUUGCAAACA
UAUUGAAAUAAUAAUUUUCACAAUGU GGGACUCAUCAUAUAUGCAAC VP24- Z29337
10105- UUCAUUCAAACACCCCAAAUUUUCAA 9 AUG 10229
UCAUACACAUAAUAACCAUUUUAGUA GCGUUACCUUUCAAUACAAUCUAGGU
GAUUGUGAAAAGACUUCCAAACAUGG CAGAAUUAUCAACGCGUUACA VP30- Z29337 8767-
GAAGAACAUUAAGUGUUCUUUGUUAG 10 AUG 8891 AAUUAUUCAUCCAAGUUGUUUUGAGU
AUACUCGCUUCAAUACAACUUCCCUU CAUAUUUGAUUCAAGAUUUAAAAUGC
AACAACCCCGUGGAAGGAGU VP40- Z29337 4467- UCCCAAUCUCAGCUUGUUGAAUUAAU
11 AUG 4591 UGUUACUUAAGUCAUUCUUUUUAAAA UUAAUUCACACAAGGUAGUUUGGGUU
UAUAUCUAGAACAAAUUUUAAUAUGG CCAGUUCCAGCAAUUACAACA L-AUG Z29337
11379- UCAUUCUCUUCGAUACACGUUAUAUC 12 11503
UUUAGCAAAGUAAUGAAAAUAGCCUU GUCAUGUUAGACGCCAGUUAUCCAUC
UUAAGUGAAUCCUUUCUUCAAUAUGC AGCAUCCAACUCAAUAUCCUG NP- Z29337 3-
CACACAAAAACAAGAGAUGAUGAUUU 13 AUG 127 UGUGUAUCAUAUAAAUAAAGAAGAAU
AUUAACAUUGACAUUGAGACUUGUCA GUCUGUUAAUAUUCUUGAAAAGAUGG
AUUUACAUAGCUUGUUAGAGU Str. Z29337 30- CAAAAUCAUCAUCUCUUGUUUUUGUG 14
Ihn 1 UGUC 1(-)
[0127] Targeting sequences are designed to hybridize to a region of
the target sequence as listed in Table 3. Selected targeting
sequences can be made shorter, e.g., 12 bases, or longer, e.g., 40
bases, and include a small number of mismatches, as long as the
sequence is sufficiently complementary to allow hybridization with
the target, and forms with either the virus positive-strand or
minus-strand, a heteroduplex having a T.sub.m of 45.degree. C. or
greater.
[0128] More generally, the degree of complementarity between the
target and targeting sequence is sufficient to form a stable
duplex. The region of complementarity of the antisense oligomers
with the target RNA sequence may be as short as 8-11 bases, but is
preferably 12-15 bases or more, e.g. 12-20 bases, or 12-25 bases.
An antisense oligomer of about 14-15 bases is generally long enough
to have a unique complementary sequence in the viral genome. In
addition, a minimum length of complementary bases may be required
to achieve the requisite binding Tm, as discussed below.
[0129] Oligomers as long as 40 bases may be suitable, where at
least the minimum number of bases, e.g., 8-11, preferably 12-15
bases, are complementary to the target sequence. In general,
however, facilitated or active uptake in cells is optimized at
oligomer lengths less than about 30, preferably less than 25, and
more preferably 20 or fewer bases. For PMO oligomers, described
further below, an optimum balance of binding stability and uptake
generally occurs at lengths of 18-25 bases.
[0130] The oligomer may be 100% complementary to the viral nucleic
acid target sequence, or it may include mismatches, e.g., to
accommodate variants, as long as a heteroduplex formed between the
oligomer and viral nucleic acid target sequence is sufficiently
stable to withstand the action of cellular nucleases and other
modes of degradation which may occur in vivo. Oligomer backbones
which are less susceptible to cleavage by nucleases are discussed
below. Mismatches, if present, are less destabilizing toward the
end regions of the hybrid duplex than in the middle. The number of
mismatches allowed will depend on the length of the oligomer, the
percentage of G:C base pairs in the duplex, and the position of the
mismatch(es) in the duplex, according to well understood principles
of duplex stability. Although such an antisense oligomer is not
necessarily 100% complementary to the viral nucleic acid target
sequence, it is effective to stably and specifically bind to the
target sequence, such that a biological activity of the nucleic
acid target, e.g., expression of viral protein(s), is
modulated.
[0131] The stability of the duplex formed between the oligomer and
the target sequence is a function of the binding T.sub.m and the
susceptibility of the duplex to cellular enzymatic cleavage. The
T.sub.m of an antisense compound with respect to
complementary-sequence RNA may be measured by conventional methods,
such as those described by Hames et al., Nucleic Acid
Hybridization, IRL Press, 1985, pp. 107-108 or as described in
Miyada C. G. and Wallace R. B., 1987, Oligonucleotide hybridization
techniques, Methods Enzymol. Vol. 154 pp. 94-107. Each antisense
oligomer should have a binding T.sub.m, with respect to a
complementary-sequence RNA, of greater than body temperature and
preferably greater than 50.degree. C. T.sub.m's in the range
60-80.degree. C. or greater are preferred. According to well known
principles, the T.sub.m of an oligomer compound, with respect to a
complementary-based RNA hybrid, can be increased by increasing the
ratio of C:G paired bases in the duplex, and/or by increasing the
length (in base pairs) of the heteroduplex. At the same time, for
purposes of optimizing cellular uptake, it may be advantageous to
limit the size of the oligomer. For this reason, compounds that
show high T.sub.m (50.degree. C. or greater) at a length of 20
bases or less are generally preferred over those requiring greater
than 20 bases for high T.sub.m values.
[0132] Table 4 below shows exemplary targeting sequences, in a
5'-to-3' orientation, that target the Ebola Zaire virus (GenBank
Acc. No. AF086833) according to the guidelines described above. The
sequences listed provide a collection of targeting sequences from
which additional targeting sequences may be selected, according to
the general class rules discussed above. SEQ ID NOs:16-43 are
antisense to the positive strand (mRNA) of the virus whereas SEQ ID
NO:15 is antisense to the minus strand viral RNA. TABLE-US-00004
TABLE 4 Exemplary Antisense Oligomer Sequences Targeting Ebola
Zaire Target SEQ GenBank No. ID Name AF086833 Sequence 5'-3' NO
Str. Inh. 1 1-22 (-) CGGACACACAAAAAGAAAGAAG 15 strand L-AUG
11588-11567 GTAGCCATTTAATATCAAGAGG 16 L'-AUG 11581-11600
TGGGTATGTTGTGTAGCCAT 17 L-29-AUG 11552-11573 CAAGAGGAAGAATTTCAACTGC
18 L + 4-AUG 11584-11604 GTATTGGGTATGTTGTGTAGC 19 L + 11-AUG
11591-11611 CGTCTGGGTATTGGGTATGTT 20 VP35-AUG 3136-3115
GTTGTCATCTTGTTAGACCAGC 21 VP35'-AUG 3133-3152 CCTGCCCTTTGTTCTAGTTG
22 VP35-22-AUG 3032-3053 GATGAAGGTTTTAATCTTCATC 23 VP35-19-AUG
3115-3133 GTCATCTTGTAGACCAGC 24 VP35-16-AUG 3118-3133
GTCATCTTGTTAGACC 25 VP35 + 3131-3152 CCTGCCCTTTGTTCTAGTTGTC 26
2-AUG NP-AUG 464-483 GGACGAGAATCCATACTCGG 27 NP + 4-AUG 473-495
CAGATTTTCTGAGGACGAGAATC 28 NP + 11-AUG 480-499 CATCCAGATTTTCTGAGGAC
29 NP + 18-AUG 487-507 CTCGGCGCCATCCAGATTTTC 30 NP-19-AUG 451-472
CATACTCGGAATTTTGTGATTC 31 VP40-AUG 4481-4498 GGCAATATAACCCGCCTC 32
VP30-AUG 8494-8512 CCATTTAAAAGTTGTCTCC 33 VP24-AUG 10331-10349
GCCATGGTTTTTTCTCAGG 34 VP24-28-AUG 10317-10336 CTCAGGTCTTGCTTGGTGTC
35 VP24 + 10348-10369 TGTATCGTCCCGTAGCTTTAGC 36 4-AUG VP24 +
10354-10372 GATTGTATCGTCCCGTAGC 37 10-AUG VP24 + 10361-10382
GGCGATATTAGATTGTATCGTC 38 19-AUG VP24-5'trm 10261-10280
TTCAACCTTGAAACCTTGCG 39 VP24(8+)- 10331-10349 GCCA + TGG + T + T +
40 AUG T + T + T + TC + TCAGG VP24- 10261-10280 +T + TCAACC + T +
41 5'trm(6+) TGAAACC + T + TGCG panVP35 3032-3053
GATGAAGGTTTTAATCTTCATC 42 Scrv3 4390-4407 TTTTTCTTAATCTTCATC 43
8288-8305
[0133] In Table 4, above, SEQ ID NOs:40 and 41 are shown with
cationic linkages (+) wherein X.dbd.(1-piperazino) as shown in FIG.
1B and FIG. 2H. Also in Table 4, above, SEQ ID NOs: 42 and 43
correspond to antisense oligomers that target the 5' terminal
nucleotide region of the Ebola virus VP35 mRNA (SEQ ID NO:42) and
the 5' terminal nucleotide region of both the Ebola virus VP40 and
VP30 mRNAs (SEQ ID NO:43).
[0134] Table 5 below shows exemplary targeting sequences, in a
5'-to-3' orientation, that target the Marburg virus (GenBank Acc.
No. Z29337) according to the guidelines described above. The
sequences listed provide a collection of targeting sequences from
which additional targeting sequences may be selected, according to
the general class rules discussed above. SEQ ID NOs:45-58 are
antisense to the positive strand (mRNA) of the virus whereas SEQ ID
NO:44 is antisense to the minus strand viral RNA. TABLE-US-00005
TABLE 5 Exemplary Antisense Oligomer Sequences Targeting Marburg
Virus Target SEQ GenBank ID Name No. Z29337 Sequence 5'-3' NO
(-)3'term 1-21 (-) GACACACAAAAACAAGAGATG 44 L-AUG 11467-11485
GCTGCATATTGAAGAAAGG 45 L + 7-AUG 11485`411506
CATCAGGATATTGAGTTGGATG 46 VP35-AUG 2932-2952 GTCCCACATTGTGAAAATTAT
47 VP35 + 2950-2971 CTTGTTGCATATATGATGAGTC 48 7-AUG NP-AUG 94-112
GTAAATCCATCTTTTCAAG 49 NP-6-AUG 97-120 CAAGCTATGTAAATCCATCTTTTC 50
NP + 4-AUG 106-124 CCTAACAAGCTATGTAAATC 51 NP-5'SL 68-88
TAACAGACTGACAAGTCTCAA 52 NP-5'UTR 44-64 CAATGTTAATATTCTTCTTTA 53
NP-5'UTRb 36-56 ATATTCTTCTTTATTTATATGT 54 VP30-AUG 8852-8873
GTTGCATTTTAAATCTTGAATC 55 VP35-5'UTR 2848-2867 CCTTTAATATTCTTCGATTT
56 VP24 + 10209-10231 GTTGTAACGCGTTGATAATTCTG 57 5-AUG NP-stem
58-77 CAAGTCTCAATGTCAATGTT 58 loop
III. Antisense Oligonucleotide Analog Compounds
[0135] A. Properties
[0136] As detailed above, the antisense oligonucleotide analog
compound (the term "antisense" indicates that the compound is
targeted against either the virus' positive-sense strand RNA or
negative-sense or minus-strand) has a base sequence target region
that includes one or more of the following: 1) 125 bases
surrounding the AUG start codons of viral mRNA and/or; 2) 30 bases
at the 3' terminus of the minus strand viral RNA and/or; 3) 25
bases at the 5' terminus of viral mRNA transcripts. In addition,
the oligomer is able to effectively target infecting viruses, when
administered to a host cell, e.g. in an infected mammalian subject.
This requirement is met when the oligomer compound (a) has the
ability to be actively taken up by mammalian cells, and (b) once
taken up, form a duplex with the target RNA with a T.sub.m greater
than about 45.degree. C.
[0137] As will be described below, the ability to be taken up by
cells requires that the oligomer backbone be substantially
uncharged, and, preferably, that the oligomer structure is
recognized as a substrate for active or facilitated transport
across the cell membrane. The ability of the oligomer to form a
stable duplex with the target RNA will also depend on the oligomer
backbone, as well as factors noted above, the length and degree of
complementarity of the antisense oligomer with respect to the
target, the ratio of G:C to A:T base matches, and the positions of
any mismatched bases. The ability of the antisense oligomer to
resist cellular nucleases promotes survival and ultimate delivery
of the agent to the cell cytoplasm.
[0138] Below are disclosed methods for testing any given,
substantially uncharged backbone for its ability to meet these
requirements.
[0139] B. Active or Facilitated Uptake by Cells
[0140] The antisense compound may be taken up by host cells by
facilitated or active transport across the host cell membrane if
administered in free (non-complexed) form, or by an endocytotic
mechanism if administered in complexed form.
[0141] In the case where the agent is administered in free form,
the antisense compound should be substantially uncharged, meaning
that a majority of its intersubunit linkages are uncharged at
physiological pH. Experiments carried out in support of the
invention indicate that a small number of net charges, e.g., 1-2
for a 15- to 20-mer oligomer, can in fact enhance cellular uptake
of certain oligomers with substantially uncharged backbones. The
charges may be carried on the oligomer itself, e.g., in the
backbone linkages, or may be terminal charged-group appendages.
Preferably, the number of charged linkages is no more than one
charged linkage per four uncharged linkages. More preferably, the
number is no more than one charged linkage per ten, or no more than
one per twenty, uncharged linkages. In one embodiment, the oligomer
is fully uncharged.
[0142] An oligomer may also contain both negatively and positively
charged backbone linkages, as long as opposing charges are present
in approximately equal number. Preferably, the oligomer does not
include runs of more than 3-5 consecutive subunits of either
charge. For example, the oligomer may have a given number of
anionic linkages, e.g. phosphorothioate or N3'.fwdarw.P5'
phosphoramidate linkages, or cationic linkages, such as
N,N-diethylenediamine phosphoramidates (Dagle, Littig et al. 2000)
or 1-piperazino phosphoramidates (FIG. 2H). The net charge is
preferably neutral or at most 1-8 net charges per oligomer.
[0143] In addition to being substantially or fully uncharged, the
antisense agent is preferably a substrate for a membrane
transporter system (i.e. a membrane protein or proteins) capable of
facilitating transport or actively transporting the oligomer across
the cell membrane. This feature may be determined by one of a
number of tests for oligomer interaction or cell uptake, as
follows.
[0144] A first test assesses binding at cell surface receptors, by
examining the ability of an oligomer compound to displace or be
displaced by a selected charged oligomer, e.g., a phosphorothioate
oligomer, on a cell surface. The cells are incubated with a given
quantity of test oligomer, which is typically fluorescently
labeled, at a final oligomer concentration of between about 10-300
nM. Shortly thereafter, e.g., 10-30 minutes (before significant
internalization of the test oligomer can occur), the displacing
compound is added, in incrementally increasing concentrations. If
the test compound is able to bind to a cell surface receptor, the
displacing compound will be observed to displace the test compound.
If the displacing compound is shown to produce 50% displacement at
a concentration of 10.times. the test compound concentration or
less, the test compound is considered to bind at the same
recognition site for the cell transport system as the displacing
compound.
[0145] A second test measures cell transport, by examining the
ability of the test compound to transport a labeled reporter, e.g.,
a fluorescence reporter, into cells. The cells are incubated in the
presence of labeled test compound, added at a final concentration
between about 10-300 nM. After incubation for 30-120 minutes, the
cells are examined, e.g., by microscopy, for intracellular label.
The presence of significant intracellular label is evidence that
the test compound is transported by facilitated or active
transport.
[0146] The antisense compound may also be administered in complexed
form, where the complexing agent is typically a polymer, e.g., a
cationic lipid, polypeptide, or non-biological cationic polymer,
having an opposite charge to any net charge on the antisense
compound. Methods of forming complexes, including bilayer
complexes, between anionic oligonucleotides and cationic lipid or
other polymer components, are well known. For example, the
liposomal composition Lipofectin.RTM. (Felgner, Gadek et al. 1987),
containing the cationic lipid DOTMA
(N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride) and
the neutral phospholipid DOPE (dioleyl phosphatidyl ethanolamine),
is widely used. After administration, the complex is taken up by
cells through an endocytotic mechanism, typically involving
particle encapsulation in endosomal bodies.
[0147] The antisense compound may also be administered in
conjugated form with an arginine-rich peptide linked covalently to
the 5' or 3' end of the antisense oligomer. The peptide is
typically 8-16 amino acids and consists of a mixture of arginine,
and other amino acids including phenyalanine and cysteine. The use
of arginine-rich peptide-PMO conjugates can be used to enhance
cellular uptake of the antisense oligomer (See, e.g. (Moulton,
Nelson et al. 2004; Nelson, Stein et al. 2005). Exemplary
arginine-rich peptides are listed as SEQ ID NOs:61-66 in the
Sequence Listing.
[0148] In some instances, liposomes may be employed to facilitate
uptake of the 30 antisense oligonucleotide into cells. (See, e.g.,
Williams, S. A., Leukemia 10(12): 1980-1989, 1996; Lappalainen et
al., Antiviral Res. 23:119, 1994; Uhlmann et al., "Antisense
oligonucleotides: A new therapeutic principle," Chemical Reviews,
Volume 90, No. 4, pages 544-584, 1990; Gregoriadis, G., Chapter 14,
Liposomes, Drug Carriers in Biology and Medicine, pp. 287-341,
Academic Press, 1979). Hydrogels may also be used as vehicles for
antisense oligomer administration, for example, as described in WO
93/01286. Alternatively, the oligonucleotides may be administered
in microspheres or microparticles. (See, e.g., Wu, G. Y. and Wu, C.
H., J. Biol. Chem. 262:4429-4432, 1987). Alternatively, the use of
gas-filled microbubbles complexed with the antisense oligomers can
enhance delivery to target tissues, as described in U.S. Pat. No.
6,245,747.
[0149] Alternatively, and according to another aspect of the
invention, the requisite properties of oligomers with any given
backbone can be confirmed by a simple in vivo test, in which a
labeled compound is administered to an animal, and a body fluid
sample, taken from the animal several hours after the oligomer is
administered, assayed for the presence of heteroduplex with target
RNA. This method is detailed in subsection D below.
[0150] C. Substantial Resistance to RNAseH
[0151] Two general mechanisms have been proposed to account for
inhibition of expression by antisense oligonucleotides. (See e.g.,
(Agrawal, Mayrand et al. 1990; Bonham, Brown et al. 1995;
Boudvillain, Guerin et al. 1997). In the first, a heteroduplex
formed between the oligonucleotide and the viral RNA acts as a
substrate for RNaseH, leading to cleavage of the viral RNA.
Oligonucleotides belonging, or proposed to belong, to this class
include phosphorothioates, phosphotriesters, and phosphodiesters
(unmodified "natural" oligonucleotides). Such compounds expose the
viral RNA in an oligomer:RNA duplex structure to hydrolysis by
RNaseH, and therefore loss of function.
[0152] A second class of oligonucleotide analogs, termed "steric
blockers" or, alternatively, "RNaseH inactive" or "RNaseH
resistant", have not been observed to act as a substrate for
RNaseH, and are believed to act by sterically blocking target RNA
nucleocytoplasmic transport, splicing or translation. This class
includes methylphosphonates (Toulme, Tinevez et al. 1996),
morpholino oligonucleotides, peptide nucleic acids (PNA's), certain
2'-O-allyl or 2'-O-alkyl modified oligonucleotides (Bonham, Brown
et al. 1995), and N3'.fwdarw.P5' phosphoramidates (Ding, Grayaznov
et al. 1996; Gee, Robbins et al. 1998).
[0153] A test oligomer can be assayed for its RNaseH resistance by
forming an RNA:oligomer duplex with the test compound, then
incubating the duplex with RNaseH under a standard assay
conditions, as described in Stein et al. After exposure to RNaseH,
the presence or absence of intact duplex can be monitored by gel
electrophoresis or mass spectrometry.
[0154] D. In Vivo Uptake
[0155] In accordance with another aspect of the invention, there is
provided a simple, rapid test for confirming that a given antisense
oligomer type provides the required characteristics noted above,
namely, high T.sub.m, ability to be actively taken up by the host
cells, and substantial resistance to RNaseH. This method is based
on the discovery that a properly designed antisense compound will
form a stable heteroduplex with the complementary portion of the
viral RNA target when administered to a mammalian subject, and the
heteroduplex subsequently appears in the urine (or other body
fluid). Details of this method are also given in co-owned U.S.
patent applications, Ser. No. 09/736,920, entitled "Non-Invasive
Method for Detecting Target RNA" (Non-Invasive Method), the
disclosure of which is incorporated herein by reference.
[0156] Briefly, a test oligomer containing a backbone to be
evaluated, having a base sequence targeted against a known RNA, is
injected into a mammalian subject. The antisense oligomer may be
directed against any intracellular RNA, including a host RNA or the
RNA of an infecting virus. Several hours (typically 8-72) after
administration, the urine is assayed for the presence of the
antisense-RNA heteroduplex. If heteroduplex is detected, the
backbone is suitable for use in the antisense oligomers of the
present invention.
[0157] The test oligomer may be labeled, e.g. by a fluorescent or a
radioactive tag, to facilitate subsequent analyses, if it is
appropriate for the mammalian subject. The assay can be in any
suitable solid-phase or fluid format. Generally, a solid-phase
assay involves first binding the heteroduplex analyte to a
solid-phase support, e.g., particles or a polymer or test-strip
substrate, and detecting the presence/amount of heteroduplex bound.
In a fluid-phase assay, the analyte sample is typically pretreated
to remove interfering sample components. If the oligomer is
labeled, the presence of the heteroduplex is confirmed by detecting
the label tags. For non-labeled compounds, the heteroduplex may be
detected by immunoassay if in solid phase format or by mass
spectroscopy or other known methods if in solution or suspension
format.
[0158] When the antisense oligomer is complementary to a
virus-specific region of the viral genome (such as those regions of
filovirus viral RNA or mRNA, as described above) the method can be
used to detect the presence of a given filovirus, or reduction in
the amount of virus during a treatment method.
[0159] E. Exemplary Oligomer Backbones
[0160] Examples of nonionic linkages that may be used in
oligonucleotide analogs are shown in FIGS. 2A-2G. In these figures,
B represents a purine or pyrimidine base-pairing moiety effective
to bind, by base-specific hydrogen bonding, to a base in a
polynucleotide, preferably selected from adenine, cytosine, guanine
and uracil. Suitable backbone structures include carbonate (2A,
R.dbd.O) and carbamate (2A, R.dbd.NH.sub.2) linkages (Mertes and
Coats 1969; Gait, Jones et al. 1974); alkyl phosphonate and
phosphotriester linkages (2B, R.dbd.alkyl or --O-alkyl)
(Lesnikowski, Jaworska et al. 1990); amide linkages (2C) (Blommers,
Pieles et al. 1994); sulfone and sulfonamide linkages (2D, R.sub.1,
R.sub.2.dbd.CH.sub.2); and a thioformacetyl linkage (2E) (Cross,
Rice et al. 1997). The latter is reported to have enhanced duplex
and triplex stability with respect to phosphorothioate antisense
compounds (Cross, Rice et al. 1997). Also reported are the
3'-methylene-N-methylhydroxyamino compounds of structure 2F.
[0161] Peptide nucleic acids (PNAs) are analogs of DNA in which the
backbone is structurally homomorphous with a deoxyribose backbone,
consisting of N-(2-aminoethyl) glycine units to which pyrimidine or
purine bases are attached. PNAs containing natural pyrimidine and
purine bases hybridize to complementary oligonucleotides obeying
Watson-Crick base-pairing rules, and mimic DNA in terms of base
pair recognition (Egholm, Buchardt et al. 1993). The backbone of
PNAs are formed by peptide bonds rather than phosphodiester bonds,
making them well-suited for antisense applications. The backbone is
uncharged, resulting in PNA/DNA or PNA/RNA duplexes which exhibit
greater than normal thermal stability. PNAs are not recognized by
nucleases or proteases.
[0162] A preferred oligomer structure employs morpholino-based
subunits bearing base-pairing moieties, joined by uncharged
linkages, as described above. Especially preferred is a
substantially uncharged phosphorodiamidate-linked morpholino
oligomer, such as illustrated in FIGS. 1A-1D. Morpholino
oligonucleotides, including antisense oligomers, are detailed, for
example, in co-owned U.S. Pat. Nos. 5,698,685, 5,217,866,
5,142,047, 5,034,506, 5,166,315, 5,185,444, 5,521,063, and
5,506,337, all of which are expressly incorporated by reference
herein.
[0163] Important properties of the morpholino-based subunits
include: the ability to be linked in a oligomeric form by stable,
uncharged backbone linkages; the ability to support a nucleotide
base (e.g. adenine, cytosine, guanine or uracil) such that the
polymer formed can hybridize with a complementary-base target
nucleic acid, including target RNA, with high T.sub.m, even with
oligomers as short as 10-14 bases; the ability of the oligomer to
be actively transported into mammalian cells; and the ability of
the oligomer:RNA heteroduplex to resist RNAse degradation.
[0164] Exemplary backbone structures for antisense oligonucleotides
of the invention include the .beta.-morpholino subunit types shown
in FIGS. 1A-1D, each linked by an uncharged, phosphorus-containing
subunit linkage. FIG. 1A shows a phosphorus-containing linkage
which forms the five atom repeating-unit backbone, where the
morpholino rings are linked by a 1-atom phosphoamide linkage. FIG.
1B shows a linkage which produces a 6-atom repeating-unit backbone.
In this structure, the atom Y linking the 5' morpholino carbon to
the phosphorus group may be sulfur, nitrogen, carbon or,
preferably, oxygen. The X moiety pendant from the phosphorus may be
fluorine, an alkyl or substituted alkyl, an alkoxy or substituted
alkoxy, a thioalkoxy or substituted thioalkoxy, or unsubstituted,
monosubstituted, or disubstituted nitrogen, including cyclic
structures, such as morpholines or piperidines. Alkyl, alkoxy and
thioalkoxy preferably include 1-6 carbon atoms. The Z moieties are
sulfur or oxygen, and are preferably oxygen.
[0165] The linkages shown in FIGS. 1C and 1D are designed for
7-atom unit-length backbones. In Structure 1C, the X moiety is as
in Structure 1B, and the moiety Y may be methylene, sulfur, or,
preferably, oxygen. In Structure 1D, the X and Y moieties are as in
Structure 1B. Particularly preferred morpholino oligonucleotides
include those composed of morpholino subunit structures of the form
shown in FIG. 1B, where X.dbd.NH.sub.2 or N(CH.sub.3).sub.2,
Y.dbd.O, and Z.dbd.O.
[0166] As noted above, the substantially uncharged oligomer may
advantageously include a limited number of charged linkages, e.g.
up to about 1 per every 5 uncharged linkages, more preferably up to
about 1 per every 10 uncharged linkages. Therefore a small number
of charged linkages, e.g. charged phosphoramidate or
phosphorothioate, may also be incorporated into the oligomers. A
preferred cationic linkage is 1-piperazino phosphoramidate as shown
in FIG. 2H.
[0167] The antisense compounds can be prepared by stepwise
solid-phase synthesis, employing methods detailed in the references
cited above. In some cases, it may be desirable to add additional
chemical moieties to the antisense compound, e.g. to enhance
pharmacokinetics or to facilitate capture or detection of the
compound. Such a moiety may be covalently attached, typically to a
terminus of the oligomer, according to standard synthetic methods.
For example, addition of a polyethyleneglycol moiety or other
hydrophilic polymer, e.g., one having 10-100 monomeric subunits,
may be useful in enhancing solubility. One or more charged groups,
e.g., anionic charged groups such as an organic acid, may enhance
cell uptake. A reporter moiety, such as fluorescein or a
radiolabeled group, may be attached for purposes of detection.
Alternatively, the reporter label attached to the oligomer may be a
ligand, such as an antigen or biotin, capable of binding a labeled
antibody or streptavidin. In selecting a moiety for attachment or
modification of an antisense oligomer, it is generally of course
desirable to select chemical compounds of groups that are
biocompatible and likely to be tolerated by a subject without
undesirable side effects.
IV. Inhibition of Filovirus Replication
[0168] A. Inhibition in Vero Cells:
[0169] PMO antisense compounds and the control PMO (SEQ ID NO:35)
were initially evaluated for cytotoxicity when incubated with Vero
cells (FIG. 5) in the absence of virus. Only one PMO (0-1-63-308)
was found to show dose dependent cytotoxicity in the concentration
range of 5 to 25.mu.M.
[0170] Viral titer data were obtained 10 days post-infection of
Vero cells. All inhibitors evaluated to date reduce the viral
titer, as measured by TCID.sub.50, to some degree (Table 6 below)
but the VP35-AUG inhibitor (SEQ ID NO:21) was the most inhibitory
against Ebola virus. The inoculum was taken from cells which
received the treatment after infection (15 .mu.M). No serum was
added to media during pre-incubation with inhibitor or during
infection. After the infection the inoculum was removed and
replaced the medium containing 2% serum. The VP35-AUG PMO produced
a 3 log reduction in viral titer relative to the no treatment
control group. The L-AUG PMO (SEQ ID NO:16) did not produce
reduction in viral titer. The L gene is active later in the viral
life cycle and the RNA becomes highly bound by NP, VP30 and VP45
proteins so this target may be inaccessible to the L-AUG PMO used
in this experiment. TABLE-US-00006 TABLE 6 Viral Titer Reduction in
Vero cells Treatment (PMO) TCID.sub.50 TCID.sub.50/ml Control (no
treatment) -5.5 3.16 .times. 10.sup.6 VP35-scr (SEQ ID NO: 60) -3.2
1.47 .times. 10.sup.4 Dscr (SEQ ID NO: 59) -3.8 6.81 .times.
10.sup.4 L-AUG (SEQ ID NO: 16) -4.2 1.47 .times. 10.sup.5 VP35-AUG
(SEQ ID NO: 21) -2.5 3.16 .times. 10.sup.3
[0171] Vero cells were pretreated with different concentrations of
the PMO (namely 0.1, 0.5, 1.0, 2.5, 5.0 and 10 .mu.M), infected
with EBOV for 1 h and the same concentration of PMO was added back
afterwards. The 1 .mu.M concentration of VP3 5-AUG (SEQ ID NO:21)
inhibitor reduced the cytopathic effect (CPE) significantly
compared to 0.5 .mu.M concentration. The reduction in CPE has been
repeatedly observed in culture and an example of these studies is
seen in FIGS. 6A-6C for non-infected (FIG. 6A), infected, no
treatment (FIG. 6B), and infected and treated (FIG. 6C).
[0172] B. Treatment in Infected Mice
[0173] These observations involved C57BL mice treated
intraperitoneally (IP) with PMO at -24 and -4 hours prior to viral
challenge at time 0. Each treatment group is composed of 10 male
mice. The Ebola Zaire infection involves 100 pfu injected IP and
death is the endpoint observed between days 7 and 10 post
infection. A summary of studies to date is provided in Table 7. The
dose.times.2 indicates the dose given at the two times prior to
viral infection. The VP35-AUGcon compound refers to the VP35-AUG
PMO that has been conjugated with the arginine-rich peptide
R.sub.9F.sub.2C (SEQ ID NO:61). TABLE-US-00007 TABLE 7 Summary of
Treatment in Mice Group Dose Survivors/challenged Saline na 1/10
Str. Ihn 1 (SEQ ID NO: 15) 0.5 mg .times. 2 0/10 VP35-AUG (SEQ ID
NO: 21) 0.5 mg .times. 2 6/10 Saline na 0/10 Str. Ihn 1 (SEQ ID NO:
15) 1.0 mg .times. 2 2/10 VP35-AUG (SEQ ID NO: 21) 1.0 mg .times. 2
7/10 Scramble (SEQ ID NO: 60) 1.0 mg .times. 2 1/10 VP35-AUG + Str
Inh 1 1.0 mg .times. 2 6/10 (SEQ ID NOs: 21 and 15) VP35-AUG-P003 +
VP35- 0.5 mg + 1.0 mg 9/10 AUG (SEQ ID NO: 21 + 61 and 21)
VP35-AUG-P003 (SEQ ID 0.5 mg .times. 2 9/10 NO: 21 + 61)
[0174] Mice that survived the viral challenge described in TABLE 7
were rechallenged with virus to determine the immunological
consequence of treatment. The results of the first studies are
summarized in TABLE 8. TABLE-US-00008 TABLE 8 Rechallenge Studies
in Mice Group Earlier dose Survivors/challenged Saline na 0/10 Str.
Ihn 1, 0-1-63-412 0.5 mg .times. 2 1/2 VP35, 0-1-63-413 0.5 mg
.times. 2 6/6 VP35, 0-1-63-413 1.0 mg .times. 2 7/7
[0175] All survivors from earlier Ebola challenge studies were
evaluated in re-challenge studies 2 to 4 weeks after the initial
viral exposure. The MOI for the re-challenge was identical to the
initial challenge. All of the re-challenged survivors from
therapeutic treatment with the PMO targeting VP35-AUG survived the
re-challenge. These observations suggest viral replication was
initiated in the viral challenge leading to a robust immune
response, essentially a perfect vaccination. In accordance with
another aspect, the invention includes a method of vaccinating a
mammalian subject against Ebola virus by (i) pretreating the
subject with antisense to Ebola virus, e.g., administering a VP35
antisense or compound combination at one or two times prior to
Ebola virus challenge, and (ii) challenging the individual with the
virus, preferably in an attenuated form incapable of producing
serious infection.
[0176] Similar treatment methods were aimed at determining the
optimal length for anti-Ebola PMO antisense, employing various
length VP35 antisense PMO. As seen from the data below (Table 9)
and the plot in FIG. 7, the 16-mer is less effective than the
19-mer which is less effective than the 22-mer which is in the same
order as the predicted Tm. TABLE-US-00009 TABLE 9 Studies to
Identify Optmal VP35-AUG Targeting Sequence Group AVI Number
Survivors/challenged* Saline NA 1/10 VP35scr SEQ ID NO: 60 1/10
VP35-16 SEQ ID NO: 25 3/10 VP35-19 SEQ ID NO: 24 5/10 VP35-22 SEQ
ID NO: 23 9/10 VP35'-AUG SEQ ID NO: 22 10/10; 9/10 *Observations as
of day 9 post challenge
[0177] Antisense compounds against six of the seven different genes
expressed by Ebola were evaluated in the mouse model in a
head-to-head experiment. (The GP gene was not included). As seen in
Table 10, below, the most effective PMOs target VP24 and VP35 with
L, VP40 and VP30 demonstrating less robust but significant activity
in reducing mortality. The mice treated with VP40 died later than
controls and those that survived appeared to be less active. These
data indicate differences in the efficacy for the different gene
targets. As single antisense compounds, the antisense against VP35
and VP24 are preferred therapeutic agents. TABLE-US-00010 TABLE 10
Comparison of Ebola Gene Targets Target SEQ ID NO
Survivors/challenged* NP-AUG 27 2/10 VP40-AUG 32 5/10 VP30-AUG 33
5/10 VP24-AUG 34 10/10; 5/10 L'-AUG 17 6/10; 2/10 VP35-22 23 9/10
Scramble 60 0/10; 0/10 PBS NA 1/10; 0/10 *Dose 0.5 mg IP at -24 and
-4 hours to challenge, second survival numbers are from repeat
experiment with fresh virus preparation.
[0178] In one embodiment, the antisense compound is administered in
a composition (or separately) in combination with one or more other
antisense compounds. One preferred combination is VP35-AUG (SEQ ID
NO:21) plus VP24-AUG (SEQ ID NO:34); another is VP35-AUG, VP24-AUG
and L-AUG (SEQ ID NOs:21, 34 and 16, respectively). As seen in
Table 11 below, and as plotted in FIG. 8, the dose response curves
for a combination of the 3 compounds (VP35-AUG, VP24-AUG and L-AUG,
each given IP at 0.5 mg/dose) is not different from 5 different
compounds (VP35-AUG, VP24-AUG, L-AUG, VP24-AUG and VP40-AUG). The
dose of 0.5 mg/mouse provides 100 percent survival from either
combination. Further, these data indicate the EC.sub.50 for
combination therapy is between 10 and 30 .mu.g/mouse and that the
EC.sub.90 is approximately 50 .mu.g/mouse. TABLE-US-00011 TABLE 11
Combination Treatment for Ebola Survivors/ Group SEQ ID NOs
Challenged PBS NA 0/10 NP-AUG, VP40-AUG, VP30- 27, 32-34 and 17
9/10 AUG, VP24-AUG, and L'-AUG NP-AUG, VP40-AUG, VP30- 27, 32-34,
17 and 21 10/10 AUG, VP24-AUG, L'-AUG and VP35-AUG VP35-AUG,
VP24-AUG and L'- 21, 34 and 17 10/10 AUG VP35-AUG, VP24-AUG, L'-
21, 34, 17, 32 and 33 10/10 AUG, VP40-AUG and VP30- AUG *Each agent
in the combination administered 0.5 mg via IP route.
[0179] The success with 100 percent survival from a single IP
injection 24 hours after Ebola infection (via IP route) indicates
the antisense mechanism can suppress virus after viral replication
has distributed throughout the body and that these agents can be
used as therapy for infected individuals (Table 12 and FIG. 9). The
comparison of dose-response in the -24 and -4 hour regimen between
VP35-AUG only and the 3 agent combination is clear evidence of
synergy. The combination could be more effective at 0.1.times. the
dose than a single agent. TABLE-US-00012 TABLE 12 Comparison of
Dose Regimens -24 and -4 -4 hours +24 Treatment Dose (mg) hours
only hours VP35-AUG 0.5 9/10 (SEQ ID NO: 21) 0.05 4/10 VP35-AUG,
VP24-AUG 0.5 10/10 10/10 10/10 and L'-AUG 0.05 10/10 4/10 5/10 (SEQ
ID NOs: 21, 34 0.005 0/10 4/10 & 17)
V. Treatment Method
[0180] The antisense compounds detailed above are useful in
inhibiting Ebola viral infection in a mammalian subject, including
human subjects. Accordingly, the method of the invention comprises,
in one embodiment, contacting a cell infected with the virus with
an antisense agent effective to inhibit the replication of the
virus. In one embodiment, the antisense agent is administered to a
mammalian subject, e.g., human or domestic animal, infected with a
given virus, in a suitable pharmaceutical carrier. It is
contemplated that the antisense oligonucleotide arrests the growth
of the RNA virus in the host. The RNA virus may be decreased in
number or eliminated with little or no detrimental effect on the
normal growth or development of the host.
[0181] A. Identification of the Infective Agent
[0182] The specific Ebola strain causing the infection can be
determined by methods known in the art, e.g. serological or
cultural methods, or by methods employing the antisense oligomers
of the present invention.
[0183] Serological identification employs a viral sample or culture
isolated from a biological specimen, e.g., stool, urine,
cerebrospinal fluid, blood, etc., of the subject. Immunoassay for
the detection of virus is generally carried out by methods
routinely employed by those of skill in the art, e.g., ELISA or
Western blot. In addition, monoclonal antibodies specific to
particular viral strains or species are often commercially
available.
[0184] Another method for identifying the Ebola viral strain
employs one or more antisense oligomers targeting specific viral
strains. In this method, (a) the oligomer(s) are administered to
the subject; (b) at a selected time after said administering, a
body fluid sample is obtained from the subject; and (c) the sample
is assayed for the presence of a nuclease-resistant heteroduplex
comprising the antisense oligomer and a complementary portion of
the viral genome. Steps (a)-(c) are carried for at least one such
oligomer, or as many as is necessary to identify the virus or
family of viruses. Oligomers can be administered and assayed
sequentially or, more conveniently, concurrently. The viral strain
is identified based on the presence (or absence) of a heteroduplex
comprising the antisense oligomer and a complementary portion of
the viral genome of the given known virus or family of viruses.
Preferably, a first group of oligomers, targeting broad families,
is utilized first, followed by selected oligomers complementary to
specific genera and/or species and/or strains within the broad
family/genus thereby identified. This second group of oligomers
includes targeting sequences directed to specific genera and/or
species and/or strains within a broad family/genus. Several
different second oligomer collections, i.e. one for each broad
virus family/genus tested in the first stage, are generally
provided. Sequences are selected which are (i) specific for the
individual genus/species/strains being tested and (ii) not found in
humans.
[0185] B. Administration of the Antisense Oligomer
[0186] Effective delivery of the antisense oligomer to the target
nucleic acid is an important aspect of treatment. In accordance
with the invention, routes of antisense oligomer delivery include,
but are not limited to, various systemic routes, including oral and
parenteral routes, e.g., intravenous, subcutaneous,
intraperitoneal, and intramuscular, as well as inhalation,
transdermal and topical delivery. The appropriate route may be
determined by one of skill in the art, as appropriate to the
condition of the subject under treatment. For example, an
appropriate route for delivery of a antisense oligomer in the
treatment of a viral infection of the skin is topical delivery,
while delivery of a antisense oligomer for the treatment of a viral
respiratory infection is by inhalation. The oligomer may also be
delivered directly to the site of viral infection, or to the
bloodstream.
[0187] The antisense oligomer may be administered in any convenient
vehicle which is physiologically acceptable. Such a composition may
include any of a variety of standard pharmaceutically accepted
carriers employed by those of ordinary skill in the art. Examples
include, but are not limited to, saline, phosphate buffered saline
(PBS), water, aqueous ethanol, emulsions, such as oil/water
emulsions or triglyceride emulsions, tablets and capsules. The
choice of suitable physiologically acceptable carrier will vary
dependent upon the chosen mode of administration.
[0188] In some instances, liposomes may be employed to facilitate
uptake of the antisense oligonucleotide into cells. (See, e.g.,
Williams, S. A., Leukemia 10(12): 1980-1989, 1996; Lappalainen et
al., Antiviral Res. 23:119, 1994; Uhlmann et al., "Antisense
oligonucleotides: A new therapeutic principle," Chemical Reviews,
Volume 90, No. 4, pages 544-584, 1990; Gregoriadis, G., Chapter 14,
Liposomes, Drug Carriers in Biology and Medicine, pp. 287-341,
Academic Press, 1979). Hydrogels may also be used as vehicles for
antisense oligomer administration, for example, as described in WO
93/01286. Alternatively, the oligonucleotides may be administered
in microspheres or microparticles. (See, e.g., Wu, G. Y. and Wu, C.
H., J. Biol. Chem. 262:4429-4432, 1987). Alternatively, the use of
gas-filled microbubbles complexed with the antisense oligomers can
enhance delivery to target tissues, as described in U.S. Pat. No.
6,245,747.
[0189] Sustained release compositions may also be used. These may
include semipermeable polymeric matrices in the form of shaped
articles such as films or microcapsules.
[0190] The antisense compound is generally administered in an
amount and manner effective to result in a peak blood concentration
of at least 200-400 nM antisense oligomer. Typically, one or more
doses of antisense oligomer are administered, generally at regular
intervals, for a period of about one to two weeks. Preferred doses
for oral administration are from about 5-1000 mg oligomer or
oligomer cocktail per 70 kg individual. In some cases, doses of
greater than 500 mg oligomer/patient may be necessary. For i.v.,
i.p or s.q. administration, preferred doses are from about 100-1000
mg oligomer or oligomer cocktail per 70 kg body weight. The
antisense oligomer may be administered at regular intervals for a
short time period, e.g., daily for two weeks or less. However, in
some cases the oligomer is administered intermittently over a
longer period of time. Administration may be followed by, or
concurrent with, administration of an antibiotic or other
therapeutic treatment. The treatment regimen may be adjusted (dose,
frequency, route, etc.) as indicated, based on the results of
immunoassays, other biochemical tests and physiological examination
of the subject under treatment.
EXAMPLES
Materials and Methods:
[0191] Synthesis of PMOs. PMOs were designed with sequence homology
near or overlapping the AUG start site of Ebola virus VP35
(VP35'-AUG, SEQ ID NO:22), VP24 (VP24-AUG, SEQ ID NO:36), and L
(L'-AUG, SEQ ID NO: 17). Unrelated, scrambled PMOs (SEQ ID NOs: 59
and 60) were used as a control in all experiments. The PMOs were
synthesized by AVI Biopharma, Inc. (Corvallis, Oreg.), as
previously described (Summerton and Weller 1997).
[0192] In vitro translation assay. The protein coding sequence for
firefly luciferase, without the initiator-Met codon ATG, was
subcloned into the multiple cloning site of plasmid pCiNeo
(Promega). Subsequently, complementary oligonucleotides for Ebola
virus VP35 (-98 to +39 bases 3020 to 3157), Ebola virus VP24 (-84
to +43 or bases 10261 to 10390), Ebola virus L (-80 to +49 or bases
11501 to 11632) were duplexed and subcloned into Nhe 1 and Sal 1
sites. RNA was generated from the T7 promoter with T7 Mega script
(Ambion, Inc., Austin, Tex.). The in vitro translations were
carried out by mixing different concentrations of PMO with 6 nM
RNA. A sigmoidal curve to determine the EC.sub.50 values was
generated with the observed luciferase light emission (n=3 per PMO
concentration) and the PMO concentration.
[0193] Ebola virus infection of PMO-treated animals. C57B1/6 mice,
aged 8-10 weeks of both sexes, were obtained from National Cancer
Institute, Frederick Cancer Research and Development Center
(Frederick, Md.). Mice were housed in microisolator cages and
provided autoclaved water and chow ad libitum. Mice were challenged
by intraperitoneal injection with .about.1000 pfu of mouse-adapted
Ebola virus diluted in phosphate buffered saline (PBS) (Bray, Davis
et al. 1998). Mice were treated with a combination of 1 mg, 0.1, or
0.01 mg of each of the VP24-AUG, L'-AUG and VP35'-AUG PMOs (SEQ ID
NOs:34, 17 and 22, respectively) or the scramble control PMO (SEQ
ID NO:60) either split between two equivalent doses at 24 and 4
hours prior to Ebola virus challenge or a single dose 24 hours
after challenge. C57B1/6 mice were challenged intraperitoneally
with 1000 plaque-forming units of mouse-adapted Ebola virus (Bray,
Davis et al. 1998). Hartley guinea pigs were treated
intraperitoneally with 10 mg of each of the VP24-AUG, VP35'-AUG,
and L'-AUG PMOs 24 hours before or 24 or 96 hours after
subcutaneous challenge with 1000 pfu of guinea-pig adapted Ebola
virus (Connolly, Steele et al. 1999). Female rhesus macaques of 3-4
kg in weight were challenged with .about.1000 pfu of Ebola virus
('95 strain) (Jahrling, Geisbert et al. 1999) by intramuscular
injection following PMO treatment. The monkeys were treated from
days -2 through day 9 via a combination of parenteral routes as
shown in FIG. 10. The dose of the VP24-AUG PMO was 12.5-25 mg at
each injection and the dose of the VP35'-AUG and L'-AUG PMOs ranged
from 12.5-100 mg per injection.
Example 1
Antiviral Efficacy of Ebola Virus-Specific PMOs in Rodents
[0194] To determine the in vivo efficacy of the Ebola
virus-specific PMOs, the survival of mice treated with 500 .mu.g
doses of the individual PMOs (VP24-AUG, L'-AUG and VP35'-AUG, SEQ
ID NOs:34, 17 and 22, respectively) at 24 and 4 hours before
challenge with 1000 plaque-forming units (pfu) of mouse-adapted
Ebola virus was determined. The VP35'-AUG, VP24-AUG and L'-AUG PMOs
exhibited a wide range of efficacy against lethal EBOV infection
and the VP35'-specific PMO provided nearly complete protection
(FIG. 11A). Next, we performed a dose response experiment with the
VP35 PMO and found that reducing the dose of the PMO from 1,000 to
100 .mu.g reduced the efficacy substantially (FIG. 11B). Hence, to
further enhance efficacy, we decided to use a combination of all
three PMOs. This combination of PMOs administered 24 and 4 h before
lethal Ebola virus challenge resulted in robust protection and
showed substantial enhancement in protection afforded by the VP35
PMO alone, especially at lower doses (FIG. 11B). To determine the
efficacy of the combination of PMOs in a post-challenge treatment
regimen, mice were injected with 1,000 pfu of Ebola virus and were
treated the next day with the PMOs (FIG. 11C). Mice that were given
a single dose of 1,000 .mu.g 24 h after the lethal challenge and
survival was scored for 14 days. Again, Ebola virus-infected mice
were fully protected and lower doses showed substantial protection
as compared to the control PMO. To determine the effectiveness of
the PMO treatment in Ebola virus-infected guinea pigs, the
combination of PMOs was administered 24 hours before or 24 or 96
hours after EBOV infection. Survival was greatly increased in
guinea pigs receiving the PMOs either 24 or 96 hours after
infection, as compared to untreated or pretreated guinea pigs as
shown in FIG. 12.
[0195] Examination of tissues shortly following infection showed
that treatment of mice with the combination of Ebola virus-specific
PMO slowed viral spread compared to mice treated with the scrambled
PMO. Three days after the infection, multiple foci of infected
cells were easily observed in the spleens of the mice treated with
the scrambled PMO (FIG. 13D). In contrast, very few EBOV-infected
cells could be found in the spleens of the anti-EBOV PMO-treated
mice (FIG. 13E). Six days after viral inoculation, the infection
was fulminant in the spleens of all animals (data not shown) and
had spread to the livers of both mice treated with scrambled and
combination PMOs (FIGS. 13F and 13G). However, the extent of the
infection was limited in the combination PMO-treated mice, and,
unlike the scrambled PMO-treated mice, EBOV antigen was not
detectable within their hepatocytes, (FIGS. 13F and 13G). The
observed pattern of antigen staining within the tissues was
corroborated by the viral titers as shown in FIG. 14.
[0196] To determine whether mice treated with the PMO therapeutics
generated immune responses to Ebola virus, they were tested for
Ebola virus-specific cell-mediated and humoral immune responses.
Four weeks after infection, the mice demonstrated both CD4+ and
CD8+ T cell responses to multiple Ebola virus peptides, including
NP and VP35 as shown in FIG. 15A. They also generated strong serum
Ebola virus-specific antibody responses that were similar to the
post-challenge antibody responses of mice protected by a
therapeutic Ebola virus-like particle vaccine as shown in FIG. 15B
(Warfield, Perkins et al. 2004). To study if the generated immune
responses were protective, PMO-treated mice were rechallenged with
another dose of 1,000 pfu of Ebola virus four weeks after surviving
the initial challenge and these mice were completely protected from
a second lethal Ebola virus infection as shown in FIG. 15C.
Example 2
Antiviral Efficacy of Ebola Virus-Specific PMOs in Non-Human
Primates
[0197] Based on the encouraging results both in vitro and in
rodents, a trial in nonhuman primates was performed. Four rhesus
monkeys were treated with PMO from two days prior to Ebola virus
infection through day 9 of the infection. The naive control monkey
in this experiment received no treatment and succumbed to Ebola
virus infection on day 10 as shown in FIG. 16A. Of 12 rhesus
monkeys that have been infected in the inventors' laboratory with
the same seed stock of virus, all died of Ebola virus between days
7 and 10 as shown in FIG. 16A. One of the PMO-treated monkeys
succumbed to the infection on day 10. A second PMO-treated monkey
cleared the EBOV infection from its circulation between days 9 and
14, but was unable to recover from disease and died on day 16 as
shown in FIGS. 16A and 16B. The two surviving monkeys had no
symptoms of disease beyond mild depression until day 35, at which
time they were euthanized. Incorporating historical controls, there
were significant differences in survival curves between groups
(p=0.0032). The mean survival time for the treatment group was 14.3
days with a standard error of 2.1 days. The mean survival time for
the control group was 8.3 days with a standard error of 0.2 days.
The overall survival rate demonstrated a significant p value of
0.0392, when compared to historical data.
[0198] There were early clinical signs or laboratory values that
correlated with survival. The laboratory tests that most closely
predicted survival were viral titers, platelet counts, and
liver-associated enzymes in the blood. The monkeys that did not
survive infection had detectable virus by day 5, in stark contrast
to the PMO-treated monkeys that survived, which had little to no
viremia on day 5 (FIG. 16B). As expected in a hemorrhagic disease,
both the PMO-treated and naive monkeys exhibited thrombocytopenia.
However, the PMO-treated monkeys that survived did not have
platelet counts far below 100,000 at any time, and their platelet
counts began to recover coincident with viral clearance (FIG. 16C).
Similarly, all the monkeys experienced increases in their
liver-associated enzyme levels, including alkaline phosphatase.
However, the levels in the surviving monkeys did not climb as high
as those that succumbed to the infection, and they returned to
normal levels within the month after the EBOV infection (FIG. 16D).
No correlation was found between survival and multiple other
hematological values, body temperature, serum cytokines, or fibrin
degradation products. Since the surviving PMO-treated monkeys had
low to undetectable viremias following infection, we assessed the
immune responses of the surviving monkeys. By 28 days after Ebola
virus challenge, the surviving rhesus monkeys had high levels of
both anti-EBOV antibodies and T cell responses, similar to the
PMO-protected mice.
Example 3
Increased Antisense of Activity Using PMO with Cationic
Linkages
[0199] Two PMOs were synthesized using cationic linkages for a
subset of the oligomer linkages as shown in Sequence Listing for
SEQ ID NOs:40 and 41. These oligomers incorporated the cationic
linkage (1-piperazino phosphoramidate) shown in FIG. 2H at the
positions indicated with a "+". These two PMOs target the EBOV VP24
mRNA. A cell free translation assay was performed using the
VP24:luciferase mRNA as the input RNA. PMO with and without
cationic linkages were compared for their ability to inhibit
luciferase expression and the results are shown in FIG. 16.
Compared to the uncharged PMO with the same base sequence, the PMOs
with between 6 and 8 cationic linkages demonstrated between 10 and
100-fold increased antisense activity in this assay.
[0200] Based on the experiments performed in support of the
invention as described above in the Examples, efficacious
anti-filovirus PMOs have been identified. The antiviral PMOs
demonstrate favorable anti-Ebola viral activity both in vitro and
in vivo in both rodents and non-human primates. Together, the
compounds and methods of the present invention provide a highly
efficacious therapeutic treatment regimen for lethal Ebola virus
infections. PMOs have already been tested in clinical trials and
have appropriate pharmacokinetic and safety profiles for use in
humans (Arora and Iversen 2001). The results presented here have
far-reaching implications for the treatment of highly lethal Ebola
virus hemorrhagic fever, as well as diseases caused by other
filovirus biothreats including Marburg virus. TABLE-US-00013 SEQ
AVI ID No. Name Target Sequences (5'-3') NO NA VP35-AUG
AAUGAUGAAGAUUAAAACCUUCAUCAUC 1 CUUACGUCAAUUGAAUUCUCUAGCACUC
GAAGCUUAUUGUCUUCAAUGUAAAAGAA AAGCUGGUCUAACAAGAUGACAACUAGA
ACAAAGGGCAGGG NA VP24-AUG CGUUCCAACAAUCGAGCGCAAGGUUUCAA 2
GGUUGAACUGAGAGUGUCUAGACAACAAA AUAUUGAUACUCCAGACACCAAGCAAGAC
CUGAGAAAAAACCAUGGCUAAAGCUACGG GACGAUACA NA VP30-AUG
AGAUCUGCGAACCGGUAGAGUUUAGUUGC 3 AACCUAACACACAUAAAGCAUUGGUCAAA
AAGUCAAUAGAAAUUUAAACAGUGAGUGG AGACAACUUUUAAAUGGAAGCUUCAUAUG
AGAGAGGAC NA VP40-AUG AAACCAAAAGUGAUGAAGAUUAAGAAAAA 4
CCUACCUCGGCUGAGAGAGUGUUUUUUCA UUAACCUUCAUCUUGUAAACGUUGAGCAA
AAUUGUUAAAAAUAUGAGGCGGGUUAUAU UGCCUACUG NA L-AUG
GUAGAUUAAGAAAAAAGCCUGAGGAAGAU 5 UAAGAAAAACUGCUUAUUGGGUCUUUCCG
UGUUUUAGAUGAAGCAGUUGAAAUUCUUC CUCUUGAUAUUAAAUGGCUACACAACAUA
CCCAAUAC NA NP-AUG UGAACACUUAGGGGAUUGAAGAUUCAACA 6
ACCCUAAAGCUUGGGGUAAAACAUUGGAA AUAGUUAAAAGACAAAUUGCUCGGAAUCA
CAAAAUUCCGAGUAUGGAUUCUCGUCCUC AGAAAAUCU NA Str. Ihn 1(-)
UAAAAAUUCUUCUUUCUUUUUGUGUGUC 7 CG NA VP35-AUG
CUAAAAAUCGAAGAAUAUUAAAGGUUUUC 8 UUUAAUAUUCAGAAAAGGUUUUUUAUUCU
CUUCUUUCUUUUUGCAAACAUAUUGAAAU AAUAAUUUUCACAAUGUGGGACUCAUCAU
AUAUGCAAC NA VP24-AUG UUCAUUCAAACACCCCAAAUUUUCAAUCA 9
UACACAUAAUAACCAUUUUAGUAGCGUUA CCUUUCAAUACAAUCUAGGUGAUUGUGAA
AAGACUUCCAAACAUGGCAGAAUUAUCAA CGCGUUACA NA VP30-AUG
GAAGAACAUUAAGUGUUCUUUGUUAGAAU 10 UAUUCAUCCAAGUUGUUUUGAGUAUACUC
GCUUCAAUACAACUUCCCUUCAUAUUUGA UUCAAGAUUUAAAAUGCAACAACCCCGUG
GAAGGAGU NA VP40-AUG UCCCAAUCUCAGCUUGUUGAAUUAAUUGU 11
UACUUAAGUCAUUCUUUUUAAAAUUAAUU CACACAAGGUAGUUUGGGUUUAUAUCUAG
AACAAAUUUUAAUAUGGCCAGUUCCAGCA AUUACAACA NA L-AUG
UCAUUCUCUUCGAUACACGUUAUAUCUUU 12 AGCAAAGUAAUGAAAAUAGCCUUGUCAUG
UUAGACGCCAGUUAUCCAUCUUAAGUGAA UCCUUUCUUCAAUAUGCAGCAUCCAACUC
AAUAUCCUG NA NP-AUG CACACAAAAACAAGAGAUGAUGAUUUUGU 13
GUAUCAUAUAAAUAAAGAAGAAUAUUAAC AUUGACAUUGAGACUUGUCAGUCUGUUAA
UAUUCUUGAAAAGAUGGAUUUACAUAGCU UGUUAGAGU NA Str. Ihn 1(-)
CAAAAUCAUCAUCUCUUGUUUUUGUGUG 14 UC Ebola Virus Oligomer Targeting
Sequences (5'-3') 305 Str. Inh. 1 CGGACACACAAAAAGAAAGAAG 15 309
L-AUG GTAGCCATTTAATATCAAGAGG 16 538 L'-AUG TGGGTATGTTGTGTAGCCAT 17
1156 L-29-AUG CAAGAGGAAGAATTTCAACTGC 18 1157 L + 4-AUG
GTATTGGGTATGTTGTGTAGC 19 1158 L + 11-AUG CGTCTGGGTATTGGGTATGTT 20
413 VP35-AUG GTTGTCATCTTGTTAGACCAGC 21 539 VP35'-AUG
CCTGCCCTTTGTTCTAGTTG 22 565 VP35-22- GATGAAGGTTTTAATCTTCATC 23 AUG
540 VP35-19- GTCATCTTGTAGACCAGC 24 AUG 541 VP35-16-
GTCATCTTGTTAGACC 25 AUG 1151 VP35 + 2-AUG CCTGCCCTTTGTTCTAGTTGTC 26
534 NP-AUG GGACGAGAATCCATACTCGG 27 1147 NP + 4-AUG
CAGATTTTCTGAGGACGAGAATC 28 1148 NP + 11-AUG CATCCAGATTTTCTGAGGAC 29
1149 NP + 18-AUG CTCGGCGCCATCCAGATTTTC 30 1150 NP-19-AUG
CATACTCGGAATTTTGTGATTC 31 535 VP40-AUG GGCAATATAACCCGCCTC 32 536
VP30-AUG CCATTTAAAAGTTGTCTCC 33 537 VP24-AUG GCCATGGTTTTTTCTCAGG 34
1152 VP24-28- CTCAGGTCTTGCTTGGTGTC 35 AUG 1153 VP24 + 4-AUG
TGTATCGTCCCGTAGCTTTAGC 36 1154 VP24 + 10- GATTGTATCGTCCCGTAGC 37
AUG 1155 VP24 + 19- GGCGATATTAGATTGTATCGTC 38 AUG 0165 VP24-5'trm
TTCAACCTTGAAACCTTGCG 39 0164 VP24(8+)- GCCA + TGG + T + T + T + T +
40 AUG T + TC + TCAGG 0166 VP24- +T + TCAACC + T + TGAAACC + 41
5'trm(6+) T + TGCG NA panVP35 GATGAAGGTTTTAATCTTCATC 42 NA Scrv3
TTTTTCTTAATCTTCATC 43 Marburg Virus Oligomer Targeting Sequences
(5'-3') NA (-)3'term GACACACAAAAACAAGAGATG 44 NA L-AUG
GCTGCATATTGAAGAAAGG 45 0177 L + 7-AUG CATCAGGATATTGAGTTGGATG 46 NA
VP35-AUG GTCCCACATTGTGAAAATTAT 47 0178 VP35 + 7-AUG
CTTGTTGCATATATGATGAGTC 48 NA NP-AUG GTAAATCCATCTTTTCAAG 49 0173
NP-6-AUG CAAGCTATGTAAATCCATCTTTTC 50 0174 NP + 4-AUG
CCTAACAAGCTATGTAAATC 51 0176 NP-5'SL TAACAGACTGACAAGTCTCAA 52 NA
NP-5'UTR CAATGTTAATATTCTTCTTTA 53 0175 NP-5'UTRb
ATATTCTTCTTTATTTATATGT 54 NA VP30-AUG GTTGCATTTTAAATCTTGAATC 55 NA
VP35-5'UTR CCTTTAATATTCTTCGATTT 56 0179 VP24 + 5-AUG
GTTGTAACGCGTTGATAATTCTG 57 NA NP-stem loop CAAGTCTCAATGTCAATGTT 58
Control Oligomers 183 DSscr AGTCTCGACTTGCTACCTCA 59 542 Scr
TGTGCTTACTGTTATACTACTC 60 Peptide Conjugates* NA R9F2C
NH.sub.2-RRRRRRRRRFFC-CO.sub.2H 61 NA RXR4
NH.sub.2-RXRRXRRXRRXRXB-CO.sub.2H 62 NA P008RX8
NH.sub.2-RXRXRXRXRXRXRXRXB-CO.sub.2H 63 NA RX4
NH.sub.2-RXRXRXRXB-CO.sub.2H 64 NA RXR2 NH.sub.2-RXRRXRXB-CO.sub.2H
65 NA RXR3 NH.sub.2-RXRRXRRXRXB-CO.sub.2H 66 *"X" and "B" denote
6-aminohexanoic acid and beta-alanine, respectively. **SEQ ID NOs:
40 and 41 incorporated the cationic linkage (1-piperazino
phosphoramidate) as shown in FIG. 2H, at the positions indicated
with a "+".
[0201]
Sequence CWU 1
1
66 1 125 RNA Zaire ebolavirus 1 aaugaugaag auuaaaaccu ucaucauccu
uacgucaauu gaauucucua gcacucgaag 60 cuuauugucu ucaauguaaa
agaaaagcug gucuaacaag augacaacua gaacaaaggg 120 caggg 125 2 125 RNA
Zaire ebolavirus 2 cguuccaaca aucgagcgca agguuucaag guugaacuga
gagugucuag acaacaaaau 60 auugauacuc cagacaccaa gcaagaccug
agaaaaaacc auggcuaaag cuacgggacg 120 auaca 125 3 125 RNA Zaire
ebolavirus 3 agaucugcga accgguagag uuuaguugca accuaacaca cauaaagcau
uggucaaaaa 60 gucaauagaa auuuaaacag ugaguggaga caacuuuuaa
auggaagcuu cauaugagag 120 aggac 125 4 125 RNA Zaire ebolavirus 4
aaaccaaaag ugaugaagau uaagaaaaac cuaccucggc ugagagagug uuuuuucauu
60 aaccuucauc uuguaaacgu ugagcaaaau uguuaaaaau augaggcggg
uuauauugcc 120 uacug 125 5 124 RNA Zaire ebolavirus 5 guagauuaag
aaaaaagccu gaggaagauu aagaaaaacu gcuuauuggg ucuuuccgug 60
uuuuagauga agcaguugaa auucuuccuc uugauauuaa auggcuacac aacauaccca
120 auac 124 6 125 RNA Zaire ebolavirus 6 ugaacacuua ggggauugaa
gauucaacaa cccuaaagcu ugggguaaaa cauuggaaau 60 aguuaaaaga
caaauugcuc ggaaucacaa aauuccgagu auggauucuc guccucagaa 120 aaucu
125 7 30 RNA Zaire ebolavirus 7 uaaaaauucu ucuuucuuuu uguguguccg 30
8 125 RNA Lake victoria marburgvirus 8 cuaaaaaucg aagaauauua
aagguuuucu uuaauauuca gaaaagguuu uuuauucucu 60 ucuuucuuuu
ugcaaacaua uugaaauaau aauuuucaca augugggacu caucauauau 120 gcaac
125 9 125 RNA Lake victoria marburgvirus 9 uucauucaaa caccccaaau
uuucaaucau acacauaaua accauuuuag uagcguuacc 60 uuucaauaca
aucuagguga uugugaaaag acuuccaaac auggcagaau uaucaacgcg 120 uuaca
125 10 124 RNA Lake victoria marburgvirus 10 gaagaacauu aaguguucuu
uguuagaauu auucauccaa guuguuuuga guauacucgc 60 uucaauacaa
cuucccuuca uauuugauuc aagauuuaaa augcaacaac cccguggaag 120 gagu 124
11 125 RNA Lake victoria marburgvirus 11 ucccaaucuc agcuuguuga
auuaauuguu acuuaaguca uucuuuuuaa aauuaauuca 60 cacaagguag
uuuggguuua uaucuagaac aaauuuuaau auggccaguu ccagcaauua 120 caaca
125 12 125 RNA Lake victoria marburgvirus 12 ucauucucuu cgauacacgu
uauaucuuua gcaaaguaau gaaaauagcc uugucauguu 60 agacgccagu
uauccaucuu aagugaaucc uuucuucaau augcagcauc caacucaaua 120 uccug
125 13 125 RNA Lake victoria marburgvirus 13 cacacaaaaa caagagauga
ugauuuugug uaucauauaa auaaagaaga auauuaacau 60 ugacauugag
acuugucagu cuguuaauau ucuugaaaag auggauuuac auagcuuguu 120 agagu
125 14 30 RNA Lake victoria marburgvirus 14 caaaaucauc aucucuuguu
uuuguguguc 30 15 22 DNA Artificial sequence Synthetic oligomer 15
cggacacaca aaaagaaaga ag 22 16 22 DNA Artificial sequence Synthetic
oligomer 16 gtagccattt aatatcaaga gg 22 17 20 DNA Artificial
sequence Synthetic oligomer 17 tgggtatgtt gtgtagccat 20 18 22 DNA
Artificial sequence Synthetic oligomer 18 caagaggaag aatttcaact gc
22 19 21 DNA Artificial sequence Synthetic oligomer 19 gtattgggta
tgttgtgtag c 21 20 21 DNA Artificial sequence Synthetic oligomer 20
cgtctgggta ttgggtatgt t 21 21 22 DNA Artificial sequence Synthetic
oligomer 21 gttgtcatct tgttagacca gc 22 22 20 DNA Artificial
sequence Synthetic oligomer 22 cctgcccttt gttctagttg 20 23 22 DNA
Artificial sequence Synthetic oligomer 23 gatgaaggtt ttaatcttca tc
22 24 18 DNA Artificial sequence Synthetic oligomer 24 gtcatcttgt
agaccagc 18 25 16 DNA Artificial sequence Synthetic oligomer 25
gtcatcttgt tagacc 16 26 22 DNA Artificial sequence Synthetic
oligomer 26 cctgcccttt gttctagttg tc 22 27 20 DNA Artificial
sequence Synthetic oligomer 27 ggacgagaat ccatactcgg 20 28 23 DNA
Artificial sequence Synthetic oligomer 28 cagattttct gaggacgaga atc
23 29 20 DNA Artificial sequence Synthetic oligomer 29 catccagatt
ttctgaggac 20 30 21 DNA Artificial sequence Synthetic oligomer 30
ctcggcgcca tccagatttt c 21 31 22 DNA Artificial sequence Synthetic
oligomer 31 catactcgga attttgtgat tc 22 32 18 DNA Artificial
sequence Synthetic oligomer 32 ggcaatataa cccgcctc 18 33 19 DNA
Artificial sequence Synthetic oligomer 33 ccatttaaaa gttgtctcc 19
34 19 DNA Artificial sequence Synthetic oligomer 34 gccatggttt
tttctcagg 19 35 20 DNA Artificial sequence Synthetic oligomer 35
ctcaggtctt gcttggtgtc 20 36 22 DNA Artificial sequence Synthetic
oligomer 36 tgtatcgtcc cgtagcttta gc 22 37 19 DNA Artificial
sequence Synthetic oligomer 37 gattgtatcg tcccgtagc 19 38 22 DNA
Artificial sequence Synthetic oligomer 38 ggcgatatta gattgtatcg tc
22 39 20 DNA Artificial sequence Synthetic oligomer 39 ttcaaccttg
aaaccttgcg 20 40 19 DNA Artificial sequence Synthetic oligomer 40
gccatggttt tttctcagg 19 41 20 DNA Artificial sequence Synthetic
oligomer 41 ttcaaccttg aaaccttgcg 20 42 22 DNA Artificial sequence
Synthetic oligomer 42 gatgaaggtt ttaatcttca tc 22 43 18 DNA
Artificial sequence Synthetic oligomer 43 tttttcttaa tcttcatc 18 44
21 DNA Artificial sequence Synthetic oligomer 44 gacacacaaa
aacaagagat g 21 45 19 DNA Artificial sequence Synthetic oligomer 45
gctgcatatt gaagaaagg 19 46 22 DNA Artificial sequence Synthetic
oligomer 46 catcaggata ttgagttgga tg 22 47 21 DNA Artificial
sequence Synthetic oligomer 47 gtcccacatt gtgaaaatta t 21 48 22 DNA
Artificial sequence Synthetic oligomer 48 cttgttgcat atatgatgag tc
22 49 19 DNA Artificial sequence Synthetic oligomer 49 gtaaatccat
cttttcaag 19 50 24 DNA Artificial sequence Synthetic oligomer 50
caagctatgt aaatccatct tttc 24 51 20 DNA Artificial sequence
Synthetic oligomer 51 cctaacaagc tatgtaaatc 20 52 21 DNA Artificial
sequence Synthetic oligomer 52 taacagactg acaagtctca a 21 53 21 DNA
Artificial sequence Synthetic oligomer 53 caatgttaat attcttcttt a
21 54 22 DNA Artificial sequence Synthetic oligomer 54 atattcttct
ttatttatat gt 22 55 22 DNA Artificial sequence Synthetic oligomer
55 gttgcatttt aaatcttgaa tc 22 56 20 DNA Artificial sequence
Synthetic oligomer 56 cctttaatat tcttcgattt 20 57 23 DNA Artificial
sequence Synthetic oligomer 57 gttgtaacgc gttgataatt ctg 23 58 20
DNA Artificial sequence Synthetic oligomer 58 caagtctcaa tgtcaatgtt
20 59 20 DNA Artificial sequence Synthetic oligomer 59 agtctcgact
tgctacctca 20 60 22 DNA Artificial sequence Synthetic oligomer 60
tgtgcttact gttatactac tc 22 61 12 PRT Artificial sequence Synthetic
arginine-rich peptide 61 Arg Arg Arg Arg Arg Arg Arg Arg Arg Phe
Phe Cys 1 5 10 62 14 PRT Artificial sequence Synthetic
arginine-rich peptide 62 Arg Xaa Arg Arg Xaa Arg Arg Xaa Arg Arg
Xaa Arg Xaa Xaa 1 5 10 63 17 PRT Artificial sequence Synthetic
arginine-rich peptide 63 Arg Xaa Arg Xaa Arg Xaa Arg Xaa Arg Xaa
Arg Xaa Arg Xaa Arg Xaa 1 5 10 15 Xaa 64 9 PRT Artificial sequence
Synthetic arginine-rich peptide 64 Arg Xaa Arg Xaa Arg Xaa Arg Xaa
Xaa 1 5 65 8 PRT Artificial sequence Synthetic arginine-rich
peptide 65 Arg Xaa Arg Arg Xaa Arg Xaa Xaa 1 5 66 11 PRT Artificial
sequence Synthetic arginine-rich peptide 66 Arg Xaa Arg Arg Xaa Arg
Arg Xaa Arg Xaa Xaa 1 5 10
* * * * *
References