U.S. patent application number 10/117267 was filed with the patent office on 2003-03-06 for compounds, processes and intermediates for synthesis of mixed backbone oligomeric compounds.
This patent application is currently assigned to Isis Pharmaceuticals, Inc.. Invention is credited to Maier, Martin A., Manoharan, Muthiah.
Application Number | 20030045698 10/117267 |
Document ID | / |
Family ID | 22946217 |
Filed Date | 2003-03-06 |
United States Patent
Application |
20030045698 |
Kind Code |
A1 |
Manoharan, Muthiah ; et
al. |
March 6, 2003 |
Compounds, processes and intermediates for synthesis of mixed
backbone oligomeric compounds
Abstract
Synthetic processes are provided wherein mixed backbone
oligomeric compounds are prepared having at least one
phosphodiester internucleoside linkage in addition to one or more
phosphorothioate, phosphoramidate and boranophosphate
internucleoside linkages. Novel H-phosphonate intermediates are
also disclosed that are useful in the synthetic processes. The
synthetic processes use a novel oxidation step to oxidize
H-phosphonate internucleoside linkages to phosphodiester
internucleoside linkages without degradation of adjacent
phosphorothioate, phosphoramidate and boranophosphate
internucleoside linkages. Also provided are synthetic intermediates
useful in such processes.
Inventors: |
Manoharan, Muthiah;
(Carlsbad, CA) ; Maier, Martin A.; (Carlsbad,
CA) |
Correspondence
Address: |
WOODCOCK WASHBURN LLP
ONE LIBERTY PLACE, 46TH FLOOR
1650 MARKET STREET
PHILADELPHIA
PA
19103
US
|
Assignee: |
Isis Pharmaceuticals, Inc.
|
Family ID: |
22946217 |
Appl. No.: |
10/117267 |
Filed: |
April 5, 2002 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10117267 |
Apr 5, 2002 |
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09726096 |
Nov 29, 2000 |
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09726096 |
Nov 29, 2000 |
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09250075 |
Feb 12, 1999 |
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6207819 |
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Current U.S.
Class: |
536/23.1 ;
544/243; 544/244 |
Current CPC
Class: |
C07H 21/00 20130101;
C07B 2200/11 20130101 |
Class at
Publication: |
536/23.1 ;
544/243; 544/244 |
International
Class: |
C07H 021/04; C07F
009/6512 |
Claims
What is claimed is:
1. A chimeric oligomeric compound having the formula:
5'--Nu--(L.sub.4--Nu).sub.z1--(L.sub.5--Nu).sub.z2--(L.sub.6
-Nu).sub.z3--3' wherein: each L.sub.4, L.sub.5, and L.sub.6 is,
independently, an internucleoside linkage selected from
phosphodiester, phosphorothioate, secondary phosphoramidate,
tertiary phosphoramidate or boranophosphate, with the provision
that L.sub.4 and L.sub.6 are different from L.sub.5 and that one of
L.sub.4, L.sub.5 and L.sub.6 are other than phosphodiester and
phosphorothioate; each z.sub.1, z.sub.2, and z.sub.3 is,
independently, an integer greater than 1; each Nu is a nucleoside
having the formula: 9wherein: Bx is a heterocyclic base moiety;
each R.sub.1 is, independently, H, hydroxyl, a protected hydroxyl,
a 2'-substituent group or a protected 2'-substituent group; and
said 5'- and said -3' ends of said chimeric oligomeric compound
are, independently, hydroxyl, a protected hydroxyl, a linkage to a
solid support, an activated phosphate group, an activated phosphite
group, a reactive group for forming an internucleotide linkage, a
nucleotide, a nucleoside, or an oligonucleotide with the proviso
that when one or both of said L.sub.4 and L.sub.6 is independently
a phosphoramidate then at least one R.sub.1 is other than H.
2. The chimeric oligomeric compound of claim 1 wherein each L.sub.4
and L.sub.6 is a phosphoramidate internucleotide linkage and each
L.sub.5 is a phosphorothioate internucleoside linkage.
3. The chimeric oligomeric compound of claim 1 wherein each L.sub.4
and L.sub.6 is a phosphoramidate internucleotide linkage and each
L.sub.5 is a phosphodiester internucleoside linkage.
4. The chimeric oligomeric compound of claim 1 wherein each L.sub.4
and L.sub.6 is a boranophosphate internucleotide linkage and each
L.sub.5 is a phosphodiester internucleoside linkage.
5. The chimeric oligomeric compound of claim 1 wherein each
L.sub.4, L.sub.5 and L.sub.6 is a phosphoramidate, phosphorothioate
or phosphodiester internucleoside linkage.
6. The chimeric oligomeric compound of claim 1 wherein each L.sub.4
and L.sub.6 is a phosphodiester internucleotide linkage and each
L.sub.5 is a phosphorothioate internucleoside linkage.
7. The chimeric oligomeric compound of claim 1 wherein each L.sub.4
and L.sub.6 is a boranophosphate internucleotide linkage and each
L.sub.5 is a phosphorothioate internucleoside linkage.
8. The chimeric oligomeric compound of claim 1 wherein each R.sub.1
is independently --O--CH.sub.2CH.sub.2--O--CH.sub.3,
--O--CH.sub.2CH.sub.2--- O--N(R.sub.6)(R.sub.7) or
--O--CH.sub.2CH.sub.2 --O--CH.sub.2CH.sub.2--N(R- .sub.6)(R.sub.7),
wherein each of R.sub.6and R.sub.7 is, independently, H or
C.sub.1-C.sub.10alkyl.
9. The chimeric oligomeric compound of claim 8 wherein each R.sub.6
and R.sub.7 is --CH.sub.3.
10. A chimeric oligomeric compound having the formula:
5'--Nu--(L.sub.4-Nu).sub.z1--(L.sub.5--Nu).sub.z2--(L.sub.6
--NU).sub.z3--(L.sub.7--Nu).sub.z4--3' wherein: each L.sub.4,
L.sub.5, L.sub.6, and L.sub.7 is, independently, an internucleoside
linkage selected from phosphodiester, phosphorothioate, secondary
phosphoramidate, tertiary phosphoramidate or boranophosphate, with
the provision that L.sub.4 and L.sub.6 are different from L.sub.5
and that one of L.sub.4, L.sub.5 and L.sub.6 are other than
phosphodiester and phosphorothioate; each z.sub.1, z.sub.2,
z.sub.3, and z.sub.4 is, independently, an integer greater than 1;
each Nu is a nucleoside having the formula: 10wherein: Bx is a
heterocyclic base moiety; each R.sub.1 is, independently, H,
hydroxyl, a protected hydroxyl, a 2'-substituent group or a
protected 2'-substituent group; and said 5'- and said -3' ends of
said chimeric oligomeric compound are, independently, hydroxyl, a
protected hydroxyl, a linkage to a solid support, an activated
phosphate group, an activated phosphite group, a reactive group for
forming an internucleotide linkage, a nucleotide, a nucleoside, or
an oligonucleotide with the proviso that when one or both of said
L.sub.4 and L.sub.6 is independently a phosphoramidate then at
least one R.sub.1 is other than H.
11. The chimeric oligomeric compound of claim 10 wherein L.sub.4 is
a phosphoramidate internucleotide linkage, L.sub.5 and L.sub.7 are,
independently, a phosphodiester internucleotide linkage and L.sub.6
is a phosphorothioate internucleotide linkage
12. A chimeric oligomeric compound having the formula:
5'--Nu--(L.sub.4--Nu).sub.z1--(L.sub.5--Nu).sub.z2--(L.sub.6--Nu).sub.z3--
-(L.sub.7--Nu).sub.z4(L.sub.8--Nu).sub.z5--3' wherein: each
L.sub.4, L.sub.5, L.sub.6, L.sub.7, and L.sub.8 is, independently,
an internucleoside linkage selected from phosphodiester,
phosphorothioate, secondary phosphoramidate, tertiary
phosphoramidate or boranophosphate, with the provision that L.sub.4
and L.sub.6 are different from L.sub.5 and that one of L.sub.4,
L.sub.5 and L.sub.6 are other than phosphodiester and
phosphorothioate; each z.sub.1, z.sub.2, z.sub.3, z.sub.4 and
Z.sub.5 is, independently, an integer greater than 1; each Nu is a
nucleoside having the formula: 11wherein: Bx is a heterocyclic base
moiety; each R.sub.1 is, independently, H, hydroxyl, a protected
hydroxyl, a 2'-substituent group or a protected 2'-substituent
group; and said 5'- and said -3' ends of said chimeric oligomeric
compound are, independently, hydroxyl, a protected hydroxyl, a
linkage to a solid support, an activated phosphate group, an
activated phosphite group, a reactive group for forming an
internucleotide linkage, a nucleotide, a nucleoside, or an
oligonucleotide with the proviso that when one or both of said
L.sub.4 and L.sub.6 is independently a phosphoramidate then at
least one R.sub.1 is other than H.
13. The chimeric oligomeric compound of claim 12 wherein L.sub.4 is
a phosphoramidate internucleotide linkage, L.sub.5 and L.sub.7 are,
independently, a phosphodiester internucleotide linkage, L.sub.6 is
a phosphorothioate internucleotide linkage and L.sub.8 is a
phosphoramidate internucleotide linkage.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of patent application
Ser. No. 09/726,096, filed Nov. 29, 2000, which is a divisional of
patent application Ser. No. 09/250,075, filed Feb. 12, 1999, each
of which is incorporated herein by reference in its entirety.
FIELD OF THE INVENTION
[0002] The present invention is directed to methods for oxidizing
an H-phosphonate internucleoside linkage in a compound which has at
least one 2'-substituent group. This invention further relates to
methods for the preparation of mixed backbone oligomeric compounds
having internucleoside linkages including phosphodiester,
phosphorothioate, phosphoramidate and boranophosphate linkages. The
present invention also relates to synthetic intermediates useful in
such methods. Also included are mixed backbone oligomeric compounds
having phosphodiester and boranophosphate internucleoside linkages
or phosphodiester and boranophosphate internucleoside linkages in
combination with other internucleoside linkages such as
phosphorothioate and phosphoramidate internucleoside linkages. The
methods of the present invention include a novel oxidation step
that allows oxidation of a region having one or more H-phosphonate
internucleoside linkages to phosphodiester internucleoside linkages
without degradation of adjacent phosphorothioate, phosphoramidate
or boranophosphate internucleoside linkages.
BACKGROUND OF THE INVENTION
[0003] Oligonucleotides and their analogs have been developed and
used in molecular biology in a variety of procedures as probes,
primers, linkers, adapters, and gene fragments. Modifications to
oligonucleotides used in these procedures include labeling with
nonisotopic labels, e.g., fluorescein, biotin, digoxigenin,
alkaline phosphatase or other reporter molecules. Other
modifications have been made to the ribose phosphate backbone to
increase the nuclease stability of the resulting analog. Examples
of such modifications include incorporation of methyl phosphonate,
phosphorothioate, or phosphorodithioate linkages, and 2'-O-methyl
ribose sugar units. Further modifications include those made to
modulate uptake and cellular distribution. With the success of
these compounds for both diagnostic and therapeutic uses, there
exists an ongoing demand for improved oligonucleotides, their
analogs and synthetic processes for their preparation.
[0004] It is well known that most of the bodily states in
multicellular organisms, including most disease states, are
effected by proteins. Such proteins, either acting directly or
through their enzymatic or other functions, contribute in major
proportion to many diseases and regulatory functions in animals and
man. For disease states, classical therapeutics has generally
focused upon interactions with such proteins in efforts to moderate
their disease-causing or disease-potentiating functions. In newer
therapeutic approaches, modulation of the actual production of such
proteins is desired. By interfering with the production of
proteins, the maximum therapeutic effect may be obtained with
minimal side effects. It is therefore a general object of such
therapeutic approaches to interfere with or otherwise modulate gene
expression, which would lead to undesired protein formation.
[0005] One method for inhibiting specific gene expression is via
the use of oligonucleotides, especially oligonucleotides which are
complementary to a specific target messenger RNA (MRNA) sequence.
Several oligonucleotides are currently undergoing clinical trials
for such use. Phosphorothioate oligonucleotides are presently being
used as such antisense agents in human clinical trials for various
disease states, including use as antiviral agents.
[0006] Transcription factors interact with double-stranded DNA
during regulation of transcription. Oligonucleotides can serve as
competitive inhibitors of transcription factors to modulate their
action. Several recent reports describe such interactions.
Bielinska, et al., Science, 1990, 250, 997-1000; and Wu, et al.,
Gene, 1990, 89, 203-209.
[0007] In addition to their use as indirect and direct regulators
of proteins, oligonucleotides and their analogs also have found use
in diagnostic tests. Such diagnostic tests can be performed using
biological fluids, tissues, intact cells or isolated cellular
components. As with inhibition of gene expression, diagnostic
applications utilize the ability of oligonucleotides and their
analogs to hybridize with a complementary strand of nucleic acid.
Hybridization is the sequence-specific hydrogen bonding of
oligomeric compounds via Watson-Crick and/or Hoogsteen base pairs
to RNA or DNA. The bases of such base pairs are said to be
complementary to one another.
[0008] Oligonucleotides and their analogs are also widely used as
research reagents. They are useful for understanding the function
of many other biological molecules as well as in the preparation of
other biological molecules. For example, the use of
oligonucleotides and their analogs as primers in PCR reactions has
given rise to an expanding commercial industry. PCR has become a
mainstay of commercial and research laboratories, and applications
of PCR have multiplied. For example, PCR technology now finds use
in the fields of forensics, paleontology, evolutionary studies and
genetic counseling. Commercialization has led to the development of
kits which assist non-molecular biology-trained personnel in
applying PCR. Oligonucleotides and their analogs, both natural and
synthetic, are employed as primers in such PCR technology.
[0009] Oligonucleotides and their analogs are also used in other
laboratory procedures. Several of these uses are described in
common laboratory manuals such as Molecular Cloning, A Laboratory
Manual, Second Ed., Sambrook et al, Eds., Cold Spring Harbor
Laboratory Press, 1989; and Current Protocols In Molecular Biology,
Ausubel et al., Eds., Current Publications, 1993. Such uses include
as synthetic oligonucleotide probes, in screening expression
libraries with antibodies and oligomeric compounds, DNA sequencing,
in vitro amplification of DNA by the polymerase chain reaction, and
in site-directed mutagenesis of cloned DNA. See Book 2 of Molecular
Cloning, A Laboratory Manual, supra. See, also, "DNA-protein
interactions and The Polymerase Chain Reaction" in Vol. 2 of
Current Protocols In Molecular Biology, supra.
[0010] Oligonucleotides and their analogs can be synthesized to
have customized properties that can be tailored for desired uses.
Thus a number of chemical modifications have been introduced into
oligomeric compounds to increase their usefulness in diagnostics,
as research reagents and as therapeutic entities. Such
modifications include those designed to increase binding to a
target strand (i.e., increase their melting temperatures, Tm), to
assist in identification of the oligonucleotide or an
oligonucleotide-target complex, to increase cell penetration, to
stabilize against nucleases and other enzymes that degrade or
interfere with the structure or activity of the oligonucleotides
and their analogs, to provide a mode of disruption (terminating
event) once sequence-specifically bound to a target, and to improve
the pharmacokinetic properties of the oligonucleotide.
[0011] The chemical literature discloses numerous processes for
coupling nucleosides through phosphorous-containing covalent
linkages to produce oligonucleotides of defined sequence. One such
method utilizes H-phosphonate monomers to prepare oliogmeric
compounds. The standard H-phosphonate method has been used for the
synthesis of uniformly modified oligomeric compounds containing
phosphodiester, phosphorothioate or phosphoramidate internucleoside
linkages. The method has not been effective for the synthesis of
mixed backbone oligomers because during the oxidation step
previously oxidized regions in an oligomer are degraded. Such
degradation has been observed for the oxidation of oligomers having
phosphorothioate and or phosphoramidate internucleoside linkages
when further H-phosphonate internucleoside linkages are oxidized to
phosphodiester linkages.
[0012] H-phosphonate methods and techniques are disclosed in
numerous publications. See, Mackie and Hogrefe, Glen Research,
H-phosphonate Chemistry, Glen Research Corp, Va.; Wada et al, J.
Am. Chem. Soc., 1997, 119, 12710-12721; and Sergueev et al., J. Am.
Chem. Soc., 1998, 120, 9417-9427.
[0013] Phosphoramidate oligodeoxynucleotides have been prepared
using H-phosphonate chemistry. Dagle et al., Nucleic Acids
Research, 1991, 19, 1805-1810.
[0014] 2'-Methoxymethyl oligonucleotides have been prepared using
H-phosphonate monomers. Bizdena et al., Collect. Czech. Chem.
Commun., 1996, 61, 283-286.
SUMMARY OF THE INVENTION
[0015] The present invention provides methods for oxidizing
H-phosphonate internucleoside linkages in a compound which bears at
least one 2'-substituent group. This oxidation is effected by an
oxidizing solution comprising an oxidizing agent, an aprotic
solvent, a base and water.
[0016] The present invention also provides methods for the
preparation of mixed backbone oligomeric compounds of formula:
1
[0017] wherein:
[0018] each Z is, independently, a phosphodiester,
phosphorothioate, phosphoramidate or boranophosphate
internucleoside linkage;
[0019] each T.sub.1 and T.sub.2 is, independently, hydroxyl or a
protected hydroxyl;
[0020] Bx is a heterocyclic base moiety;
[0021] each R.sub.1 is, independently, H, hydroxyl, a protected
hydroxyl, a 2'-substituent group or a protected 2'-substituent
group; and
[0022] n is an integer greater than 1;
[0023] provided that at least one of said Z is a phosphodiester
internucleoside linkage and at least another of said Z is a
phosphorothioate, phosphoramidate or boranophosphate
internucleoside linkage;
[0024] comprising the steps of:
[0025] (a) providing a compound of formula: 2
[0026] wherein:
[0027] Pg is an acid labile hydroxyl protecting group; and
[0028] T.sub.3 is a base labile hydroxyl protecting group or a
covalent attachment to a solid support;
[0029] (b) deblocking said acid labile hydroxyl protecting group to
form a deblocked hydroxyl group;
[0030] (c) treating said deblocked hydroxyl group with a further
compound having the formula: 3
[0031] and a condensing reagent in a solvent under conditions of
time, temperature and pressure effective to form an extended
compound having an added H-phosphonate internucleoside linkage;
[0032] (d) optionally treating said extended compound with a
capping agent to form a capped compound;
[0033] (e) optionally treating said capped compound with a
silylating agent to give a silylated compound;
[0034] (f) optionally treating said extended compound, said capped
compound, or said silylated compound with an oxidizing solution
inert to phosphodiester, phosphorothioate, phosphoramidate or
boranophosphate internucleoside linkages, thereby oxidizing said
H-phosphonate internucleoside linkages to phosphodiester,
phosphorothioate, phosphoramidate or boranophosphate
internucleoside linkages;
[0035] (g) optionally repeating steps (b), (c), (d), (e) and (f) to
form a protected oligomeric compound; and
[0036] (h) treating said protected oligomeric compound with a
deblocking solution to form said mixed backbone oligomeric
compound.
[0037] In a preferred embodiment, the mixed backbone oligomeric
compound comprises contiguous regions of phosphodiester and
phosphorothioate internucleoside linkages.
[0038] In another preferred embodiment, the mixed backbone
oligomeric compound comprises contiguous regions of phosphodiester
and phosphoramidate internucleoside linkages.
[0039] In a further preferred embodiment, the oxidizing solution
comprises an oxidizing agent, an aprotic organic solvent, a base
and water.
[0040] In one embodiment of the present invention the oxidizing
solution comprises from about 18% to 45% oxidizing agent. In a
preferred embodiment the oxidizing solution comprises from about
26% to about 40% oxidizing agent. In a more preferred embodiment
the oxidizing solution comprises about 33% oxidizing agent.
[0041] The present invention also provides compounds of formula:
4
[0042] wherein:
[0043] T.sub.4 is hydroxyl or a protected hydroxyl;
[0044] Bx is a heterocyclic base moiety; and
[0045] R.sub.2 has one of formula I or II: 5
[0046] wherein:
[0047] E is C.sub.1-C.sub.10 alkyl, N(R.sub.4)(R.sub.5) or
N.dbd.C(R.sub.4)(R.sub.5);
[0048] R.sub.3is OX, SX, or N(X).sub.2;
[0049] each R.sub.4 and R.sub.5 is, independently, H,
C.sub.1-C.sub.10 alkyl, a nitrogen protecting group, or R.sub.4 and
R.sub.5, together, are a nitrogen protecting group, or R.sub.4 and
R.sub.5 are joined in a ring structure that can include at least
one additional heteroatom selected from a group consisting of
nitrogen and oxygen;
[0050] each X is, independently, H, C.sub.1-C.sub.8 alkyl,
C.sub.1-C.sub.8 haloalkyl, C(.dbd.NH)N(H)Z, C(.dbd.O)N(H)Z or
OC(.dbd.O)N(H)Z;
[0051] Z is H or C.sub.1-C.sub.8 alkyl;
[0052] L.sub.1, L.sub.2 and L.sub.3 comprise a ring system having
from about 4 to about 7 carbon atoms or having from about 3 to
about 6 carbon atoms and at least 1 heteroatom, said heteroatom
being selected from a group consisting of oxygen, nitrogen and
sulfur, said ring system being aliphatic, unsaturated aliphatic,
aromatic, or saturated or unsaturated heterocyclic;
[0053] Y is alkyl or haloalkyl having 1 to about 10 carbon atoms,
alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to
about 10 carbon atoms, aryl having 6 to about 14 carbon atoms,
N(R.sub.4)(R.sub.5) OR.sub.4, halo, SR.sub.4 or CN;
[0054] each q.sub.1 is, independently, an integer from 2 to 10;
[0055] each q.sub.2 is, independently, 0 or 1;
[0056] p is an integer from 1 to 10; and
[0057] r is an integer from 1 to 10,
[0058] provided that when p is 0, r is an integer greater than
1.
[0059] In a preferred embodiment R.sub.2 is a 2'-substituent group.
In another preferred embodiment the 2'-substituent group is
--O--CH.sub.2CH.sub.2--O--CH.sub.3,
--O--CH.sub.2CH.sub.2--O--N(R.sub.6)(- R.sub.7) or
--O--CH.sub.2CH.sub.2--O--CH.sub.2CH.sub.2--N(R.sub.6)(R.sub.7- ),
wherein each of R.sub.6 and R.sub.7 is, independently, H or
C.sub.1-C.sub.10 alkyl. In a further preferred embodiment each
R.sub.6 and R.sub.7 is --CH.sub.3.
[0060] The present invention also provides chimeric oligomeric
compounds having the formula:
5'--Nu--(L.sub.4--Nu).sub.z1--(L.sub.5--Nu).sub.z2--(L.sub.6--Nu).sub.z3---
3'
[0061] wherein:
[0062] each L.sub.4, L.sub.5, and L.sub.6 is, independently, an
internucleoside linkage selected from phosphodiester,
phosphorothioate, phosphoramidate or boranophosphate, with the
provision that L.sub.4 and L.sub.6 are different from L.sub.5 and
that one of L.sub.4, L.sub.5 and L.sub.6 are other than
phosphodiester and phosphorothioate;
[0063] each z.sub.1, z.sub.2, and z.sub.3 is, independently, an
integer greater than 1;
[0064] each Nu is a nucleoside having the formula: 6
[0065] wherein:
[0066] Bx is a heterocyclic base moiety;
[0067] each R.sub.1 is, independently, H, hydroxyl, a protected
hydroxyl, a 2'-substituent group or a protected 2'-substituent
group; and
[0068] said 5'- and said -3' ends of said chimeric oligomeric
compound are, independently, hydroxyl, a protected hydroxyl, a
linkage to a solid support, an activated phosphate group, an
activated phosphate group, a reactive group for forming an
internucleotide linkage, a nucleotide, a nucleoside, or an
oligonucleotide.
[0069] In one embodiment, each L.sub.4 and L.sub.6 is a
phosphoramidate internucleotide linkage and each L.sub.5 is a
phosphorothioate internucleoside linkage.
[0070] In another embodiment, each L.sub.4 and L.sub.6 is a
phosphoramidate internucleotide linkage and each L.sub.5 is a
phosphodiester internucleoside linkage.
[0071] In yet another embodiment, each L.sub.4 and L.sub.6 is a
boranophsphate internucleotide linkage and each L.sub.5 is a
phosphodiester internucleoside linkage.
[0072] In a further embodiment, each L.sub.4, L.sub.5 and L.sub.6
is phosphoramidate, phosphorothioate or phosphodiester.
[0073] It is preferred that each R.sub.1 be, independently,
--O--CH.sub.2CH.sub.2--O--CH.sub.3,
--O--CH.sub.2CH.sub.2--O--N(R.sub.6)(- R.sub.7) or
--O--CH.sub.2CH.sub.2--O--CH.sub.2CH.sub.2--N(R.sub.6)(R.sub.7- ).
It is also preferred that each of R.sub.6and R.sub.7 be,
independently, H or C.sub.1-C.sub.10 alkyl.
[0074] It is further preferred that each R.sub.6 and R.sub.7 be
-CH.sub.3.
DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS
[0075] The present invention provides compounds and methods for the
preparation of mixed backbone oligomeric , or chimeric, compounds
having phosphodiester internucleoside linkages in addition to
phosphorothioate and/or phosphoramidate internucleoside linkages.
The methods also include incorporation of boranophosphate
internucleoside linkages into oligomeric compounds of the
invention. The methods utilize H-phosphonate intermediates that are
coupled together forming contiguous regions of one or more
H-phosphonate internucleoside linkages. Each contiguous region is
subsequently oxidized to phosphodiester, phosphorothioate,
phosphoramidate or boranophosphate internucleoside linkages prior
to further elongation. Mixed backbone oligomeric compounds are
prepared in this manner by oxidizing adjacent regions with
different reagents. Oligomeric compounds of the invention are
prepared using novel oxidation steps that oxidize a region of one
or more H-phosphonate internucleoside linkages without degrading
existing linkages that have been previously oxidized.
[0076] The H-phosphonate method of oligomer synthesis has been used
for the preparation of oligonucleotides and their analogs having a
variety of internucleotide linkages. These internucleotide linkages
have included phosphorothioate, phosphoramidate, methyl phosphate,
methylphosphonate, alkylphosphonate, S-aryl phosphorothioate,
acylphosphonate, phosphorofluoridate, phosphorodithioate,
selenophosphate, (hydroxymethyl)phosphonate and
boranophosphate.
[0077] As used herein, the term "chimeric oligomeric compound" or
"mixed backbone oligomeric compound" refers to oligomeric compounds
comprising nucleoside monomer subunits and containing at least two
different internucleoside linkages. The mixed backbone oligomeric
compounds of the present invention may contain a plurality of
nucleoside monomer subunits that are joined together by more than
one type of internucleoside linkages. At least one internucleoside
linkage is a phosphodiester linkage and at least one other linkage
is a phosphorothioate, a phosphoramidate or a boranophosphate
internucleoside linkage. Thus the term "oligomeric compound"
includes oligonucleosides, oligonucleotides, their analogs, and
synthetic oligonucleotides.
[0078] In some preferred embodiments, a first monomer attached to a
solid support is elongated using H-phosphonate monomers. The
methods of the present invention have been used with automated DNA
synthesizers to synthesize mixed backbone oligomeric compounds of
desired length and sequence. Some oligomeric compounds have been
synthesized having only phosphodiester and phosphorothioate
internucleoside linkages. Other oligomeric compounds have been
synthesized having phosphodiester, phosphorothioate and
phosphoramidate internucleoside linkages. Example 14 illustrates
the synthesis of a boranophosphate mixed backbone oligomeric
compound. Table I illustrates selected oligomeric compounds that
were synthesized using methods and intermediates of the present
invention.
[0079] In preferred embodiments, the methods of the present
invention are employed for use in iterative solid phase
oligonucleotide synthetic regimes. Representative solid phase
techniques are those typically employed for DNA and RNA synthesis
utilizing standard H-phosphonate chemistry. The H-phosphonate
method of oligonucleotide synthesis is disclosed in U.S. Pat. No.
5,149,798, issued Sep. 22, 1992, and U.S. Pat. No. 5,548,076,
issued Aug. 20, 1996. The entire disclosure of each is incorporated
herein by reference. A preferred synthetic solid phase synthesis
utilizes H-phosphonates as activated phosphate compounds. In this
technique, an H-phosphonate monomer is reacted with a free hydroxyl
on the growing oligomer chain to produce an intermediate phosphite
compound, which is subsequently oxidized to the P.sup.v state. This
technique is commonly used for the synthesis of several types of
linkages including phosphodiester, phosphorothioate, and
phosphoramidate linkages. Oxidation of H-phosphonate linkages to
phosphodiester linkages using standard H-phosphonate chemistry
results in the degradation of phosphorothioate and phosphoramidate
linkages when present in a growing oligomeric compound. This
degradation of adjacent linkages within an oligomeric compound has
been a limitation to the use of standard H-phosphonate chemistry
with mixed backbone syntheses.
[0080] Typically, the first step in such a process is attachment of
a monomer or higher order subunit containing a protected
5'-hydroxyl to a solid support, usually through a linker, using
standard methods and procedures known in the art. See, e.g.,
Oligonucleotides And Analogues A Practical Approach, Ekstein, F.
Ed., IRL Press, N.Y., 1991, hereby incorporated by reference in its
entirety. The support-bound monomer or higher order first synthon
is then treated to remove the 5'-protecting group. Typically, this
is accomplished by treatment with acid. The solid support bound
monomer is then reacted with a second monomer or higher order
synthon having a reactive group for forming an internucleoside
linkage. In preferred embodiments the coupling reaction is
performed under anhydrous conditions in the presence of a
condensing reagent.
[0081] After the addition of each monomer or higher order synthon,
a capping step is performed to cap unreacted hydroxyl groups. It is
generally preferable to perform a capping step either prior to or
after oxidation or sulfurization of the internucleoside linkage.
Such a capping step is generally known to be beneficial by
preventing shortened oligomer chains, by blocking chains that have
not reacted in the coupling cycle. One representative reagent used
for capping is acetic anhydride. Other suitable capping reagents
and methodologies can be found in U.S. Pat. No. 4,816,571, issued
Mar. 28, 1989, hereby incorporated by reference in its
entirety.
[0082] As used herein an "oxidizing solution" comprises a mixture
of reagents effective to oxidize an H-phosphonate internucleoside
linkage or silylated derivative thereof to a phosphodiester,
phosphorothioate, phosphoramidate or boranophosphate
internucleoside linkage. Such oxidation can be performed on a
region of an oligomeric compound without causing degradation of
other previously oxidized portions of the same oligomeric compound.
Oxidation of each type of internucleoside linkage is illustrated in
the examples below. Oxidation of the internucleoside linkage can be
performed iteratively after each coupling step, or can be performed
after a desired number or sequence of monomers have been coupled.
This allows for the preparation of gapmer-type oligomeric compounds
having one or more regions of one type of linkage with one or more
other regions having another type of linkage. A representative
example of a gapmer is an oligomeric compound having a
phosphorothioate region at the 3' and 5' ends with a phosphodiester
region located internally.
[0083] Treatment of the growing oligomeric compound with an acid
removes the 5'-hydroxyl protecting group enabling another synthetic
iteration. The growing oligomeric compound is extended with
subsequent oxidation at selected stages with selected oxidation
agents until an oligomeric compound of desired length is
produced.
[0084] The completed oligomer is then cleaved from the solid
support. The cleavage step can precede or follow deprotection of
protected functional groups. The term "deblocking solution" as used
herein is meant to encompass solutions routinely used for the
deblocking of oligomeric compounds prepared either by solution or
solid phase techniques. A common solution used for deblocking of
oligomers synthesized on solid support is aqueous ammonia.
[0085] As used herein "heterocyclic base moiety" is intended to
include nucleobases. Nucleobases useful in the compounds and
methods described herein include but are not limited to adenine,
guanine, cytosine, uridine, and thymine, as well as other
non-naturally occurring and natural nucleobases such as xanthine,
hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives
of adenine and guanine, 2-propyl and other alkyl derivatives of
adenine and guanine, 5-halo uracil and cytosine, 6-azo uracil,
cytosine and thymine, 5-uracil (pseudo uracil), 4-thiouracil,
8-halo, oxa, amino, thiol, thioalkyl, hydroxyl and other
8-substituted adenines and guanines, 5-trifluoromethyl and other
5-substituted uracils and cytosines, 7-methylguanine. Further
naturally- and non-naturally-occurring nucleobases include those
disclosed in U.S. Pat. No. 3,687,808 (Merigan et al.); in Sanghvi,
in Antisense Research and Application, Chapter 15, S. T. Crooke and
B. Lebleu, Eds., CRC Press, 1993; in Englisch et al., Angewandte
Chemie, International Edition, 1991, 30, 613-722 (particularly,
pages 622 and 623); in the Concise Encyclopedia of Polymer Science
and Engineering, J. I. Kroschwitz, Ed., John Wiley & Sons,
1990, pages 858-859; and in Cook, Anti-Cancer Drug Design, 1991, 6,
585-607, each of which is hereby incorporated by reference in its
entirety. The term "nucleosidic base moiety" is further intended to
include heterocyclic compounds that can serve as nucleosidic bases,
including certain `universal bases` that are not nucleosidic bases
in the most classical sense but serve as nucleosidic bases.
Especially mentioned as a universal base is 3-nitropyrrole.
[0086] As used herein, the term "2'-substituent group" includes
2'-sugar modifications. 2.varies.0-Sugar modifications of the
present invention include fluoro, O-alkyl, O-alkylamino,
O-alkylalkoxy, protected O-alkylamino, O-alkylaminoalkyl, O-alkyl
imidazole, and polyethers of the formula (O-alkyl).sub.m, where m
is 1 to about 10. Preferred among these polyethers are linear and
cyclic polyethylene glycols (PEGs), and PEG-containing groups, such
as crown ethers and those which are disclosed by Ouchi et al., Drug
Design and Discovery 1992, 9, 93; Ravasio et al., J. Org. Chem.
1991, 56, 4329; and Delgardo et. al., Critical Reviews in
Therapeutic Drug Carrier Systems 1992, 9, 249, each of which is
hereby incorporated by reference in its entirety. Further sugar
modifications are disclosed in Cook, Anti-Cancer Drug Design, 1991,
6, 585-607. Fluoro, O-alkyl, O-alkylamino, O-alkyl imidazole,
O-alkylaminoalkyl, and alkyl amino substitutions are described in
U.S. patent application Ser. No. 08/398,901, filed Mar. 6, 1995,
entitled "Oligomeric Compounds having Pyrimidine Nucleotide(s) with
2' and 5' Substitutions," hereby incorporated by reference in its
entirety.
[0087] Additional 2'-sugar modifications of use in the present
invention include 2'-SR and 2'-NR.sub.2 groups, where each R is,
independently, hydrogen, a protecting group or substituted or
unsubstituted alkyl, alkenyl, or alkynyl. 2'-SR nucleosides are
disclosed in U.S. Pat. No. 5,670,633, issued Sep. 23, 1997, hereby
incorporated by reference in its entirety. Incorporation of 2'-SR
monomer synthons is disclosed by Hamm et al., J. Org. Chem., 1997,
62, 3415-3420. 2'-NR.sub.2 nucleosides are disclosed by Goettingen,
J. Org. Chem., 1996, 61, 6273-6281; and Polushin et al.,
Tetrahedron Lett., 1996, 37, 3227-3230.
[0088] Some representative 2'-sugar modifications amenable to the
present invention include those having one of formula I or II:
7
[0089] wherein:
[0090] E is C.sub.1-C.sub.10 alkyl, N(R.sub.4)(R.sub.5) or
N.dbd.C(R.sub.4)(R.sub.5);
[0091] each R.sub.4 and R.sub.5 is, independently, H,
C.sub.1-C.sub.10 alkyl, a nitrogen protecting group, or R.sub.4 and
R.sub.5, together, are a nitrogen protecting group, or R.sub.4 and
R.sub.5 are joined in a ring structure that can include at least
one additional heteroatom selected from a group consisting of
nitrogen and oxygen;
[0092] R.sub.3 is OX, SX, or N(X).sub.2;
[0093] each X is, independently, H, C.sub.1-C.sub.8 alkyl,
C.sub.1-C.sub.8 haloalkyl, C(.dbd.NH)N(H)Z, C(.dbd.O)N(H)Z or
OC(.dbd.O)N(H)Z;
[0094] Z is H or C.sub.1-C.sub.8 alkyl;
[0095] L.sub.1, L.sub.2 and L.sub.3 comprise a ring system having
from about 4 to about 7 carbon atoms, or having from about 3 to
about 6 carbon atoms and at least one heteroatom, said heteroatom
being selected from a group consisting of oxygen, nitrogen and
sulfur, said ring system being aliphatic, unsaturated aliphatic,
aromatic, or saturated or unsaturated heterocyclic;
[0096] Y is alkyl or haloalkyl having 1 to about 10 carbon atoms,
alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to
about 10 carbon atoms, aryl having 6 to about 14 carbon atoms,
N(R.sub.4)(R.sub.5) OR.sub.4, halo, SR.sub.4 or CN;
[0097] each q.sub.1 is, independently, from 2 to 10;
[0098] each q.sub.2 is, 0 or 1;
[0099] p is from 1 to 10; and
[0100] r is from 1 to 10, provided that when p is 0, r is greater
than 1.
[0101] Representative 2'-sugar substituents of formula I are
disclosed in U.S. patent application Ser. No. 09/130,973, filed
Aug. 7, 1998, entitled "Capped 2'-Oxyethoxy Oligonucleotides,"
hereby incorporated by reference in its entirety.
[0102] Representative cyclic 2'-sugar substituents of formula II
are disclosed in U.S. patent application Ser. No. 09/123,108, filed
Jul. 27, 1998, entitled "RNA Targeted 2'-Modified Oligonucleotides
that are Conformationally Preorganized," hereby incorporated by
reference in its entirety.
[0103] Sugars wherein the ring oxygen atom is replaced by other
atoms are also amenable to the present invention. Representative
substitutions for the ring oxygen include S, CH.sub.2, CHF, and
CF.sub.2. See, e.g., Secrist et al., Abstract 21, Program &
Abstracts, Tenth International Roundtable, Nucleosides, Nucleotides
and their Biological Applications, Park City, Utah, Sep. 16-20,
1992, hereby incorporated by reference in its entirety.
[0104] As used herein, the term "alkyl" includes, but is not
limited to, straight chain, branched chain, and alicyclic
hydrocarbon groups. Alkyl groups of the present invention may be
substituted. Representative alkyl substituents are disclosed in
U.S. Pat. No. 5,212,295, at column 12, lines 41-50, hereby
incorporated by reference in its entirety. As used herein, the term
"lower alkyl" is intended to mean alkyl having 6 or fewer
carbons.
[0105] As used herein, the term "aralkyl" denotes alkyl groups
which bear aryl groups, for example, benzyl groups. The term
"alkaryl" denotes aryl groups which bear alkyl groups, for example,
methylphenyl groups. As used herein the term "aryl" denotes
aromatic cyclic groups including but not limited to phenyl,
naphthyl, anthracyl, phenanthryl, and pyrenyl.
[0106] As used herein, the term "alkanoyl" has its accustomed
meaning as a group of formula --C(.dbd.O)--alkyl. A preferred
alkanoyl group is the acetyl group.
[0107] In general, the term "hetero" denotes an atom other than
carbon, preferably but not exclusively nitrogen, oxygen or sulfur.
Accordingly, the term "heterocycloalkyl" denotes an alkyl ring
system having one or more heteroatoms, i.e., non-carbon atoms.
Preferred heterocycloalkyl groups include, for example, morpholino
groups. As used herein, the term "heterocycloalkenyl" denotes a
ring system having one or more double bonds and one or more
heteroatoms. Preferred heterocycloalkenyl groups include, for
example, pyrrolidino groups.
[0108] In a preferred embodiment of the present invention, oligomer
synthesis is performed on an automated synthesizer utilizing a
solid support. Solid supports are substrates which are capable of
serving as the solid phase in solid phase synthetic methodologies,
such as those described in U.S. Pat. Nos. 4,415,732; 4,458,066;
4,500,707; 4,668,777; 4,973,679; 5,132,418; 4,725,677 and Re.
34,069. Linkers are known in the art as short molecules which serve
to connect a solid support to functional groups, e.g., hydroxyl
groups, of initial synthon molecules in solid phase synthetic
techniques. Suitable linkers are disclosed in, for example,
Oligonucleotides And Analogues A Practical Approach, Ecstein, F.,
Ed., IRL Press, N.Y., 1991, Chapter 1, pages 1-23.
[0109] Solid supports according to the invention include those
generally known in the art to be suitable for use in solid phase
methodologies including, for example, controlled pore glass (CPG),
oxalyl-controlled pore glass (see, e.g., Alul et al., Nucleic Acids
Research 1991, 19, 1527, hereby incorporated by reference in its
entirety), TentaGel Support; an aminopolyethyleneglycol derivatized
support (see, e.g., Wright et al., Tetrahedron Letters 1993, 34,
3373, hereby incorporated by reference in its entirety) and Poros;
a copolymer of polystyrene/divinylbenzene.
[0110] In some embodiments of the invention, each of T.sub.1 and
T.sub.2 is, independently, a protected hydroxyl group, and T.sub.3
is a hydroxyl protecting group. A wide variety of hydroxyl
protecting groups can be employed in the methods of the invention.
Preferably, the protecting group is stable under either acidic or
basic conditions. This enables removal of a base-stable protecting
group under acidic conditions, and removal of an acid-stable
protecting group under basic conditions. In general, protecting
groups render chemical functionalities inert to specific reaction
conditions, and can be appended to and removed from such
functionalities in a molecule without substantially damaging the
remainder of the molecule. Representative hydroxyl protecting
groups are disclosed by Beaucage et al., Tetrahedron 1992, 48,
2223-2311, and also in Greene and Wuts, Protective Groups in
Organic Synthesis, Chapter 2, 2d ed, John Wiley & Sons, N.Y.,
1991, each of which is hereby incorporated by reference in its
entirety. Preferred protecting groups include dimethoxytrityl
(DMT), monomethoxytrityl (MMT), 9-phenylxanthen-9-yl (Pixyl) and
9-(p-methoxyphenyl)xanthen-9-yl (Mox).
[0111] In some preferred embodiments of the invention amino groups
are appended to alkyl or other groups such as, for example,
2'-alkoxy groups. Such amino groups are also commonly present in
naturally-occurring and non-naturally-occurring nucleobases. It is
generally preferred that these amino groups be in protected form
during the synthesis of oligomeric compounds of the invention.
Representative amino protecting groups suitable for these purposes
are discussed in Greene and Wuts, Protective Groups in Organic
Synthesis, Chapter 7, 2d ed, John Wiley & Sons, N.Y., 1991.
Generally, as used herein, the term "protected," when used in
connection with a molecular moiety such as "nucleobase," indicates
that the molecular moiety contains one or more functionalities
protected by protecting groups.
[0112] There are currently many useful condensing reagents known to
the art skilled that are amenable to the H-phosphonate method of
oligonucleotide synthesis. Wada et al., J. Am. Chem. Soc., 1997,
119, 12710-12721. Useful condensing reagents include, but are not
limited to, acid chlorides, chlorophosphates, carbonates, carbonium
type compounds and phosphonium type compounds. In a preferred
embodiment the condensing reagent is selected from a group
consisting of pivaloyl chloride, adamantyl chloride, 2,4,6
-triisopropyl-benzenesulfonyl chloride, 2-chloro-5,5-dimethyl-2
-oxo-1,3,2-dioxaphosphinane, diphenyl phosphorochloridate,
bis(2-oxo-3 -oxazolidinyl)phosphinic chloride,
bis(pentafluorophenyl)carbonate, 2-(1H-benzotriazole- 1
-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate,
O-(azabenzotriazol- 1 -yl)- 1,1,3,3-tetramethyl uronium
hexafluorophosphate, 6-(trifluoromethyl)benzotriazol-1
-yl-oxy-tris-pyrrolidino-phosphonium hexafluorophosphate,
bromo-tris-pyrrolidino-phosphonium hexafluorophosphate,
benzotriazole-1-yl-oxy-tris-pyrrolidino-phosphonium
hexafluorophosphate and 2-(benzotriazol-1 -yloxy)- 1,3-dimethyl-2
-pyrrolidin- 1 -yl- 1,3,2-diazaphospholidinium
hexafluorophosphate.
[0113] Sulfurizing agents used during oxidation to form
phosphorothioate and phosphorodithioate linkages, when they are the
only linkages present, include Beaucage reagent (Iyer et. al., J.
Chem. Soc., 1990, 112, 1253-1254; and Iyer et. al., J. Org. Chem.,
1990, 55, 4693-4699); tetraethylthiuram disulfide (Vu and
Hirschbein, Tetrahedron Lett., 1991, 32, 3005-3008); dibenzoyl
tetrasulfide (Rao, et. al., Tetrahedron Lett., 1992, 33,
4839-4842); di(phenylacetyl)disulfide (Kamer, Tetrahedron Lett.,
1989, 30, 6757-6760); Bis(O,O-diisopropoxy phosphinothioyl)disulfi-
des (Stec et al, Tetrahedron Lett., 1993, 34, 5317-5320); 3-ethoxy-
1,2,4-dithiazoline-5-one (Nucleic Acids Research, 1996 24,
1602-1607; and Nucleic Acids Research, 1996 24, 3643-3644);
bis(p-chlorobenzenesulfonyl)- -disulfide (Nucleic Acids Research,
1995 23, 4029-4033); sulfur, and sulfur in combination with ligands
such as triaryl, trialkyl, triaralkyl, or trialkaryl phosphines.
Each of the foregoing references is hereby incorporated by
reference in its entirety.
[0114] Useful oxidizing agents used to form the phosphodiester or
phosphorothioate linkages, when they are the only linkages present,
include iodine/tetrahydrofuran/water/pyridine, hydrogen
peroxide/water, tert-butyl hydro peroxide or any peracid like
m-chloroperbenzoic acid. In the case of oxidation using a sulfur
species, the reaction is performed under anhydrous conditions with
the exclusion of air, in particular oxygen, whereas in the case of
oxidation the reaction can be performed under aqueous
conditions.
[0115] The oxidation of H-phosphonate internucleoside linkages,
without simultaneous degradation of existing, previously oxidized
linkages, is performed using a novel oxidizing solution. The
oxidizing solution comprises particular compounds/reagents
dependent upon what oxidized linkages are being prepared from the
H-phosphonate linkages. In general, the oxidation solution
comprises an oxidizing agent, an aprotic organic solvent, and a
base.
[0116] Bases are present in the oxidizing solution to assist in the
oxidation process. Selected bases have a pka ranging from about 9
to about 12, which is believed to be the optimum range for
deprotonation of H-phosphonate or water without causing cleavage of
the backbone of the oligomeric compound. While not wanting to be
bound by theory, it is believed that bases within this pKa range,
and present in the oxidation solution in a concentration of from
about 0.01 to about 0.8 M, are necessary for oxidation of
H-phosphonate linkages without simultaneous degradation of existing
oxidized linkages. A more preferred range for the concentration of
the base is from about 0.05 to about 0.2 M in the oxidation
solution. Representative bases that are useful in the present
invention include 4-(dimethylamino)pyridine (DMAP), triethylamine
(TEA) and N,N-diisopropylethylamine (DIEA).
[0117] Many aprotic organic solvents known to those skilled in the
art are amenable to the present invention. Some representative
aprotic organic solvents include pyridine, acetonitrile and
dimethylformamide.
[0118] The choice of oxidizing agent is dependent on the particular
internucleoside linkage that is desired for the region of
H-phosphonate internucleoside linkages that is being oxidized.
Representative oxidizing agents useful for the preparation of
phosphodiester internucleoside linkages include carbon
tetrachloride, carbon tetrabromide, N-chlorosuccinimide and
N-bromosuccinimide. In addition to an oxidizing agent, water is a
necessary component of the oxidizing solution for preparing
phosphodiester linkages.
[0119] Phosphorothioate internucleoside linkages are prepared using
an oxidizing agent that oxidizes phosphorus by addition of sulfur
rather than oxygen. Elemental sulfur has been used to sulfrize
H-phosphonate to form phosphorothioate internucleoside linkages as
illustrated in the examples below. The use of elemental sulfur in
the oxidizing solution affords the desired phosphorothioate
internucleoside linkages while leaving unaffected any preexisting
oxidized linkages in the same oligomeric compound.
[0120] The selective oxidation of H-phosphonate internucleoside
linkages to phosphodiester, phosphorothioate, phosphoramidate and
boranophosphate internucleoside linkages in a mixed backbone
oligomeric compound is dependent on the oxidizing solution. The
oxidizing solution must not affect preexisting linkages in the
oligomeric compound that is undergoing oxidation. The oxidizing
solution is a mixture of an oxidizing agent, an aprotic solvent and
a base. For phosphodiester linkages water is also a component of
the oxidizing solution. The concentration of reagents in the
oxidizing solution for a given oxidation can vary. Optimal
concentration of reagents can be discerned by the art-skilled
without undue experimentation.
[0121] The composition and concentration of reagents in the
oxidizing solution used to oxidize an H-phosphonate linkages in a
mixed backbone oligomeric compound is variable dependent on whether
the desired oxidized linkage is phosphodiester, phosphorothioate or
phosphoramidate. In the case of boranophosphate internucleoside
linkages, a silylation step is also involved. The two main
components are the base and the oxidizing agent. For phosphodiester
and phosphorothioate internucleoside linkages, an aprotic organic
solvent is also used. Water is also used in the oxidizing solution
when phosphodiester linkages are prepared. The oxidizing solution
used for preparing phosphodiester internucleoside linkages in a
mixed backbone oligomeric compound of the invention generally has
from about 18% to about 45% oxidizing agent, from about 2% to about
15% water, from about 40% to about 80% aprotic organic solvent, and
from about 0.01 M to about 0.8 M base dissolved in the aprotic
organic solvent. A more preferred range of concentrations is from
about 26% to about 40% oxidizing agent, from about 4% to about 10%
water, from about 50% to about 70% aprotic organic solvent, and
from about 0.04 M to about 0.4 M base dissolved in the aprotic
organic solvent. Even more preferred is about 33% oxidizing agent,
about 7% water, about 60% aprotic organic solvent, and from about
0.05 M to about 0.2 M base dissolved in the aprotic organic
solvent.
[0122] The oxidizing solution used for preparing phosphorothioate
internucleoside linkages in a mixed backbone oligomeric compound of
the invention generally has from about 1% to about 15% oxidizing
agent, about 40% to about 60% solvent that will solubilize the
oxidizing agent, from about 40% to about 60% aprotic organic
solvent, and from about 0.01 M to about 0.8 M base dissolved in the
aprotic organic solvent. A more preferred range of concentrations
is from about 1% to about 10% oxidizing agent, about 40% to about
60% solvent that will solubilize the oxidizing agent, from about
40% to about 60% aprotic organic solvent, and from about 0.02 M to
about 0.5 M base dissolved in the aprotic organic solvent. Even
more preferred is about 3% to about 8% oxidizing agent, about 40%
to about 60% solvent that will solubilize the oxidizing agent, from
about 40% to about 60% aprotic organic solvent, and from about 0.04
M to about 0.1 M base dissolved in the aprotic organic solvent.
[0123] The oxidizing solution used for preparing phosphoramidate
internucleoside linkages in a mixed backbone oligomeric compound of
the invention generally has a primary or secondary amine in
combination with an oxidizing agent. An oxidizing agent that acts
as a solvent for the primary or secondary amine is preferable. A
preferred oxidizing agent is carbon tetrachloride. The oxidizing
solution has from about 1% to about 15% of the primary or secondary
amine, and from about 85% to about 99% oxidizing agent. A preferred
concentration is about 1% to about 10% of the primary or secondary
amine, and from about 90% to about 99% oxidizing agent. A more
preferred concentration of primary or secondary amine is about 2%
to about 5% by volume in the oxidizing solution.
[0124] The conversion of H-phosphonate internucleoside linkages to
the boranophosphate (O.dbd.P--BH.sub.3) internucleoside linkages
requires an additional silylation step prior to the oxidation step.
Sergueev et al., J. Am. Chem. Soc., 1998, 120, 9417-9427. A number
of silylating agents have been shown to be effective in the
silylation step including chlorotrimethyl-silane, N,
O-bis-(trimethylsilyl)acetamide, heptamethyldisilazane and N,
O-bis-(trimethylsilyl)trifluoroacetamide. The silylation step is
followed by oxidation with borane-N,N-diisopropyle- thylamine
(BH.sub.3.times.DIEA, 0.1 mmol to 1 mmol), borane-2-chloro-pyridine
or borane-aniline.
[0125] In one aspect of the present invention, the compounds of the
invention are used to modulate RNA or DNA encoding a protein whose
formation or activity is to be modulated. The targeting portion of
the composition to be employed is, thus, selected to be
complementary to the preselected portion of DNA or RNA. That is,
the targeting portion of the composition is hybridizable to the
preselected portion of DNA.
[0126] The methods of the present invention can be used to prepare
oligomeric compounds that are used in diagnostics, therapeutics,
and as research reagents and kits. They can be used in
pharmaceutical compositions by including a suitable
pharmaceutically acceptable diluent or carrier. They further can be
used for treating organisms having a disease characterized by the
undesired production of a protein. The organism should be contacted
with an oligonucleotide having a sequence that is capable of
specifically hybridizing with a strand of nucleic acid encoding the
undesirable protein. Treatments of this type can be practiced on a
variety of organisms ranging from unicellular prokaryotic and
eukaryotic organisms to multicellular eukaryotic organisms. Any
organism that utilizes DNA-RNA transcription or RNA-protein
translation as a fundamental part of its hereditary, metabolic or
cellular control is susceptible to therapeutic and/or prophylactic
treatment in accordance with the invention. Seemingly diverse
organisms such as bacteria, yeast, protozoa, algae, all plants and
all higher animal forms, including warm-blooded animals, can be
treated. Further, each cell of multicellular eukaryotes can be
treated, as they include both DNA-RNA transcription and RNA-protein
translation as integral parts of their cellular activity.
Furthermore, many of the organelles (e.g., mitochondria and
chloroplasts) of eukaryotic cells also include transcription and
translation mechanisms. Thus, single cells, cellular populations or
organelles can also be included within the definition of organisms
that can be treated with therapeutic or diagnostic
oligonucleotides.
[0127] As will be recognized, the steps of the methods of the
present invention need not be performed any particular number of
times or in any particular sequence. Additional objects,
advantages, and novel features of this invention will become
apparent to those skilled in the art upon examination of the
following examples thereof, which are intended to be illustrative
and not intended to be limiting.
EXAMPLE 1
General Procedure
Solid Phase Synthesis of Mixed Backbone Oligomeric Compounds Using
2'-O- methoxyethyl-3'-H-phosphonate monomers
[0128] Reagents
[0129] Selected solvents and reagents were purchased from Aldrich
Chemical Company and J. T. Baker Company. Phosphorus trichloride,
pivaloyl chloride, N-methylmorpholine, triethylamine,
diazabicyclo[5.4.0]undec-7-e- ne and 1,2,4-triazole were purchased
from Fluka. Pivaloyl chloride was distilled prior to its use for
solid phase synthesis. The 5'-O-DMT-2'-O-methoxyethyl
mononucleosides were prepared as per known literature methods.
Martin, Helv. Chim. Acta, 1995, 78, 486-504; Altmann et al.,
Chimia, 1996, 50, 168-176; Altmann et al., Biochem. Soc. Trans.,
1996, 24, 630-637; and Altmann et al., Nucleosides Nucleotides,
1997, 16, 917-926. Unmodified H-phosphonate mononucleotides, and
the capping reagent isopropylphosphite were purchased from Glen
Research.
[0130] Solid Phase Synthesis
[0131] Solid phase synthesis was carried out using an Applied
Biosystems (Perkin Elmer Corporation) DNA/RNA synthesizer 380B and
controlled pore glass (5'-O-DMT-2'-MOE mononucleoside-3'-succinate:
R. I. Chemical, Costa Mesa, Calif.) or primer support
(5'-O-DMT-2'-MOE mononucleoside-3'-succin- ate: Pharmacia) as the
solid supports. The H-phosphonate method of oligonucleotide
synthesis is disclosed in U.S. Pat. No. 5,149,798, issued Sep. 22,
1992, and U.S. Pat. No. 5,548,076, issued Aug. 20, 1996. The entire
disclosure of each is incorporated herein by reference.
[0132] The synthesis cycle was based on the H-phosphonate method
and included three reaction steps and several washing steps as
follows:
[0133] (i) Deblocking (DMT cleavage) with dichloroacetic acid (3%)
in dichloromethane;
[0134] Washing with acetonitrile; and
[0135] Washing with acetonitrile/pyridine (1: 1).
[0136] (ii) Coupling of the 5'-O-DMT-H-phosphonate mononucleotide
with the deblocked nucleotide using 10 equivalents of
mononucleotide and 40 equivalents of pivaloylchloride (0.2 M) in
acetonitrile/pyridine (1:1); and
[0137] Washing with acetonitrile/pyridine (1:1).
[0138] (iii) Capping (optional) of unreacted 5'-hydroxy functions
using 16 equivalents of isopropylphosphite and 64 equivalents of
pivaloylchloride (0.2 M) in acetonitrile/ pyridine (1:1);
[0139] Washing with acetonitrile/pyridine (1:1); and
[0140] Washing with acetonitrile.
[0141] Cleavage from the solid support and deprotection of the
oligonucleotides was carried out using aqueous ammonia (25-28%) for
1.5 hours on a column followed by heating at 55.degree. C. for 6
hours.
Oxidation Procedures
[0142] Phosphodiester Internucleoside Linkages in Mixed Backbone
Oligomeric Compounds
[0143] Mixed backbone oligomeric compounds were prepared having
phosphodiester linkages as well as phosphorothioate and/or
phosphoramidate linkages. The oxidation of H-phosphonate
internucleoside linkages to phosphodiester linkages was performed
with reagents inert to existing phosphorothioate and
phosphoramidate linkages. One oxidation solution that was effective
to convert H-phosphonate to phosphodiester and that was inert to
existing phosphorothioate and phosphoramidate internucleoside
linkages was triethylamine (0.1 M) or 4-(dimethylamino)pyridine
(DMAP, 0.1 M) in pyridine/carbon tetrachloride/water (9:5:1). The
reaction time for this oxidation step was 60 to 120 minutes.
[0144] The standard oxidation procedures used for H-phosphonate
synthesis are based on various formulations containing iodine as
the oxidation reagent. However, when preparing mixed backbone
oligomeric compounds having in addition to phosphodiester one or
both of phosphorothioate and phosphoramidate internucleoside
linkages present, the use of iodine significantly affects product
homogeneity leading to partial degradation of phosphorothioate
linkages or replacement of phosphoramidate linkages with
phosphodiester linkages.
[0145] The mild oxidation procedures shown in the reaction scheme
below illustrate the facile preparation of mixed backbone
oligomeric compounds. The oxidation of one or more consecutive
internucleoside linkages from H-phosphonate to phosphodiester is
performed under reaction conditions which are inert to
phosphorothioate or phosphoramidate internucleoside linkages. 8
[0146] Phosphorothioate Internucleoside Linkages
[0147] Phosphorothioate linkages were prepared via oxidation of
H-phosphonate linkages using 5% elemental sulfur in carbon
disulfide/pyridine/triethylamine (10:10:1). Prior to sulfurization,
the solid support was thoroughly washed with acetonitrile and dried
under vacuum. The reaction time was 60 to 120 minutes.
[0148] For oligomeric compounds containing phosphorothioate and
phosphoramidate linkages the oxidation is performed using 5%
elemental sulfur and DMAP (0.1 M) or triethylamine (0.1 M) in
carbon disulfide/pyridine(1:1). Prior to sulfurization, the solid
support is thoroughly washed with acetonitrile and dried under
vacuum. The reaction time is 60-120 min.
[0149] Phosphoramidate Internucleoside Linkages
[0150] Oligomeric compounds containing phosphoramidate linkages
were prepared via oxidation of the corresponding H-phosphonate
oligomer blocks on the solid support using a mixture of a primary
or secondary amine in carbon tetrachloride (10%:90%, v/v). Prior to
oxidation, the solid support was thoroughly washed with
acetonitrile and dried under vacuum. The reaction time was 60 to
120 minutes.
[0151] Boranophosphate Internucleoside Linkages
[0152] Oligomeric compounds containing boranophosphate linkages are
prepared by treatment of H-phosphonate internucleoside linkages
with N,O-bis(trimethylsilyl)trifluoroacetamide (0.3 M) in dry
tetrahydrofuran for 20 to 30 minutes, washing with tetrahydrofuran
and then treating with borane-N,N-diisopropyl-ethylamine
(BH.sub.3:DIEA, 0.1 mmol:1 mmol), borane-2-chloropyridine or
borane-aniline. Prior to oxidation, the solid support is thoroughly
washed with acetonitrile and dried under vacuum. The reaction time
is 60 to 240 minutes.
EXAMPLE 2
[0153] 5'-O-DMT-2'-MOE-Thymidine-3'-H-Phosphonate
[0154] To a stirred solution of 1,2,4-triazole (7.75 g, 0.112 mole)
and N-methylmorpholine (33.4 g, 0.33 mole) in dichloromethane (330
mL) was added phosphorus trichloride (4.53 g, 0.033 mole). After
stirring for 30 minutes at room temperature the mixture was cooled
down to .degree. C. Subsequently 5'-O-DMT-2'-MOE-thymidine (4 g,
6.6 mmole) in dichloromethane (100 mL) was added dropwise over a
period of 20 minutes. After stirring for another 20 min, the
mixture was allowed to warm up to room temperature and poured into
aqueous triethylammonium bicarbonate buffer (350 mL, pH 8.5) with
stirring. The mixture was transferred to a separatory funnel and
separated. The aqueous phase was extracted once with
dichloromethane (300 mL) and the combined organic phases were
washed with another triethylammonium bicarbonate buffer (350 mL).
After drying the organic phase over sodium sulfate, the solvent was
evaporated and the crude product was dried under vacuum. The crude
product was purified by silica gel column chromatography using a
step gradient of 0.5% triethylamine in dichloromethane to 0.5%
triethylamine in dichloromethane/methanol (9:1). The combined
product fractions were evaporated to a foam and evaporated twice
with acetonitrile to remove excess triethylamine. Subsequently the
purified product was dissolved in dichloromethane (300 mL), washed
twice each with 0.2 M diazabicyclo[5.4.0]undec-7-ene bicarbonate
buffer (350 mL, pH 8.7), dried over sodium sulfate and evaporated
to a foam. Prior to its use for solid phase synthesis the product
was dried under high vacuum to give 4.62 g (85%) of the title
compound.
[0155] .sup.31P-NMR (CDCl.sub.3, using 2% H.sub.3PO.sub.4 as an
external standard) 4.22 ppm.
EXAMPLE 3
[0156] 5'-O-DMT-2'-MOE-N-6-Benzoyladenosine-3'-H-Phosphonate
[0157] To a stirred solution of 8.03 g (0.116 mole) 1,2,4-triazole
and 34.6 g (0.342 mole) N-methylmorpholine in 340 mL
dichloromethane 4.7 g (0.0342 mole) of phosphorus trichloride were
added. The mixture was stirred for 30 min at room temperature and
cooled down to 0.degree. C. Subsequently,
5'-O-DMT-2'-MOE-N-6-benzoyladenosine (5 g, 6.84 mmole) in
dichloromethane (100 mL) was added dropwise over a period of 20
minutes. After stirring for another 20 minutes, the mixture was
allowed to warm up to room temperature and poured into aqueous
triethylammonium bicarbonate buffer (350 mL, pH 8.5) with stirring.
The mixture was transferred to a separatory funnel and separated.
The aqueous phase was extracted once with dichloromethane (300 mL)
and the combined organic phases were washed with triethylammonium
bicarbonate buffer (350 mL, pH 8.5). The organic phase was dried
over sodium sulfate, filtered, concentrated under vacuum, and the
residue dried under vacuum. The crude material was purified by
silica gel column chromatography using a step gradient of 0.5%
triethylamine in dichloromethane to 0.5% triethylamine in
dichloromethane/ methanol (9:1). The combined product fractions
were evaporated to a foam and coevaporated twice with acetonitrile
to remove trace triethylamine. Subsequently, the purified product
was dissolved in dichloromethane (350 mL), washed twice with
diazabicyclo[5.4.0]undec-7-en- e bicarbonate buffer (0.2 M, 350 mL,
pH 8.7), dried over sodium sulfate, and evaporated to a foam. Prior
to its use for solid phase synthesis the product was dried under
high vacuum to give 5.5 g (90%) of the title compound. .sup.31pNMR
(CDCl.sub.3, external standard: 85% H.sub.3PO.sub.4): 3.77 ppm.
EXAMPLE 4
[0158]
5.varies.0-O-DMT-2'-MOE-N-4-benzoyl-5-methyl-cytidine-3'-H-phosphon-
ate
[0159] To a stirred solution of 1,2,4-triazole (8.29 g, 0.12 mole)
and N-methylmorpholine (35.7 g, 0.353 mole) in dichloromethane (350
mL) phosphorus trichloride (4.85g, 35.3 mmole) was added. The
mixture was stirred for 30 minutes at room temperature and cooled
down to 0.degree. C. Subsequently
5'-O-DMT-2'-MOE-N-4-benzoylcytidine (5 g, 7.06 mmole) in
dichloromethane (100 mL) was added dropwise over a period of 20
minutes. After stirring for another 20 minutes the mixture was
allowed to warm up to room temperature and poured into aqueous
triethylammonium bicarbonate buffer (350 mL, pH 8.5) with stirring.
The mixture was transferred to a separatory funnel and separated.
The aqueous phase was extracted once with dichloromethane (300 mL)
and the combined organic phases were washed with aqueous
triethylammonium bicarbonate buffer (350 mL, pH 8.5). The organic
phase was dried over sodium sulfate, filtered, evaporated under
vacuum and the resulting residue dried under high vacuum. The crude
product was purified by silica gel column chromatography using a
step gradient of 3% triethylamine in dichloromethane to 3%
triethylamine in dichloromethane/methanol (9:1). The combined
product fractions were evaporated to a foam and evaporated twice
with acetonitrile to remove trace triethylamine. Subsequently the
purified product was dissolved in dichloromethane (300 mL), washed
twice with diazabicyclo[5.4.0]undec-7-en- e bicarbonate buffer (300
mL, 0.2 M, pH 8.7), dried over sodium sulfate, and evaporated to a
foam. Prior to its use for solid phase synthesis the product was
dried under high vacuum to give 3.9 g (63%) of the title compound.
.sup.31P-NMR (CDCl.sub.3, using 85% H.sub.3PO.sub.4 as an external
standard): 3.76 ppm.
EXAMPLE 5
[0160] 5'-O-DMT-2'-MOE-N-2-Isobutyrylguanosine-3'-H-phosphonate
[0161] To a stirred solution of 1,2,4-triazole (11.84 g, 0.171
mole) and N-methylmorpholine (50.98 g, 0.504 mole) in
dichloromethane (350 mL), phosphorus trichloride (6.92 g, 0.050
mole) was added. The mixture was stirred for 30 minutes at room
temperature and cooled down to -20.degree. C.
5'-O-DMT-2'-MOE-isobutyrylguanosine (6 g, 8.4 mmole) in
dichloromethane (100 mL) was added dropwise over a period of 20
minutes. After stirring for another 20 minutes, the mixture was
allowed to warm to room temperature and poured into aqueous
triethylammonium bicarbonate buffer (350 mL, pH 8.5) with stirring.
The mixture was transferred to a separatory funnel and separated.
The aqueous phase was extracted once with dichloromethane (300 mL)
and the combined organic phases were washed with aqueous
triethylammonium bicarbonate buffer (350 mL, pH 8.5). After drying
the organic phase over sodium sulfate, the solvent was evaporated
and the crude product was dried under vacuum. The crude product was
purified by silica gel column chromatography using a step gradient
of 3% triethylamine in dichloromethane to 3% triethylamine in
dichloromethane/methanol (9:1). The combined product fractions were
evaporated to a foam and coevaporated twice with acetonitrile to
remove trace triethylamine. Subsequently the purified product was
dissolved in dichloromethane (50 mL), washed twice with
diazabicyclo[5.4.0]undec-7-ene bicarbonate buffer (50 mL, 0.2 M, pH
8.7), dried over sodium sulfate, and evaporated to a foam. Prior to
its use for solid phase synthesis the product was dried under high
vacuum to give 0.8 g (12%) of the title compound. .sup.31P-NMR
(CDCl.sub.3, external standard: 85% H.sub.3PO.sub.4): 3.68 ppm.
EXAMPLE 6
[0162] Synthesis of Uniform 2'-MOE-Modified Phosphodiester
Oligonucleotides
[0163] The solid phase synthesis of a uniform phosphodiester
oligonucleotide (SEQ ID No: 8, 20-mer) containing T, C, A and G
nucleobases and having a 2'-methoxyethoxy (MOE) on each ribosyl
sugar moiety, was performed on a 1 .mu.mole scale using
5'-O-DMT-2'-MOE-5-methy- lcytidine-3'-succinyl CPG as the solid
support. The synthesis cycle is described in the General Procedures
above. After completion of synthesis the oligomer was oxidized
using iodine (0.1 M) in pyridine/water (98:2) and washed with
acetonitrile/pyridine (1:1) and acetonitrile. Deprotection and
cleavage from the solid support was performed with aqueous ammonia
(25-28%), as described in the General Procedures. Analysis of the
crude product by electrospray mass spectrometry gave a relative
molecular mass of 8023.5 (calculated mass: 8022.3).
EXAMPLE 7
[0164] Synthesis of 2'-MOE-Modified Gapmer Phosphodiester
Oligonucleotides
[0165] The solid phase synthesis of a uniform phosphodiester
oligonucleotide (SEQ ID No.: 2, 18-mer) containing T, C, A and G
nucleobases and having a 2'-MOE group on 4 of the ribosyl sugar
moieties at the 5' end of the oligonucleotide and on 5 ribosyl
sugar moieties at the 3' end of the oligonucleotide was performed
in a 1 .mu.mole scale using 5'-O-DMT-2'-MOE-thymidine-3'-succinyl
CPG as the solid support. The synthesis cycle is described in the
General Procedures of Example 1. After synthesis the oligomer was
oxidized using iodine (0.1 M) in pyridine/water (98:2) and washed
with acetonitrile/pyridine (1:1) and acetonitrile. Deprotection and
cleavage from the solid support was performed with aqueous ammonia
(25-28%), as described in the General Procedures. Analysis of the
crude product by electrospray mass spectrometry gave a relative
molecular mass of 6435.5 (calculated mass: 6440.7).
EXAMPLE 8
[0166] Synthesis of 2'-MOE-Modified Gapmer Phosphorothioate
Oligonucleosides
[0167] The solid phase synthesis of a uniform phosphorothioate
oligonucleotide (SEQ ID No: 6, 19-mer) containing T, C, A and G
nucleobases and having a 2'-MOE group on 5 of the ribosyl sugar
moieties at the 5' end of the oligonucleotide and on 6 ribosyl
sugar moieties at the 3' end of the oligonucleotide was performed
in a 1 .mu.mole scale using
5.varies.0-O-DMT-2'-MOE-thymidine-3'-succinyl CPG as the solid
support. The synthesis cycle is described in the General
Procedures. After completion of synthesis the oligomer was oxidized
using elemental sulfur (5%) in carbon
disulfide/pyridine/triethylamine (10:10:1) and washed with carbon
disulfide, acetonitrile/pyridine (1:1) and acetonitrile.
Deprotection and cleavage from the solid support was carried out
with aqueous ammonia (25-28%), as described in the General
Procedures. Analysis of the crude product by electrospray mass
spectrometry gave a relative molecular mass of 6873.4 (calculated
mass: 6874.8).
EXAMPLE 9
[0168] Synthesis of a 2'-MOE-Modified Gapmer Oligomeric Compounds
With a PO-PS-PO Mixed Backbone
[0169] The solid phase synthesis of a gapped oligomer (SEQ ID No:
9, 20-mer) having phosphodiester internucleoside linkages on the 3'
and the 5' ends with phosphorothioate internucleoside linkages
between nucleosides 6-15 and having a 2'-MOE group on 6 of the
ribosyl sugar moieties at each of the 5' and 3' ends of the gapped
oligomer with internal ribosyl moieties being deoxyribo moieties,
was performed on a 1 .mu.mole scale using
5'-O-DMT-2'-MOE-adenosine-3'-succinyl CPG as the solid support. The
synthesis cycle is described in the General Procedures of Example
1. After the first 5 couplings the oligomer was oxidized using 0.1
M DMAP in pyridine/carbontetrachloride/water (9:5: 1). Prior to
synthesis of the next segment, the solid support was thoroughly
washed with acetonitrile/pyridine (1:1) and acetonitrile. After
incorporation of nine additional H-phosphonate monomers (to give a
15-mer) the oligomer was oxidized using elemental sulfur (5%) in
carbondisulfide/ pyridine/triethylamine (10:10:1), as described in
the General Procedures. Prior to synthesis of the next segment, the
solid support was thoroughly washed with carbondisulfide,
acetonitrile/pyridine (1:1) and acetonitrile. After completion of
solid phase synthesis, the support-bound oligomer was finally
treated with DMAP (0.1 M) in pyridine/carbontetrachloride/water
(9:5:1) and washed with acetonitrile/pyridine (1:1) and
acetonitrile. Deprotection and cleavage from the solid support was
performed with aqueous ammonia (25-28%), as described in the
General Procedures. Analysis of the crude product by electrospray
mass spectrometry gave a relative molecular mass of 7425.9
(calculated mass: 7426.0).
EXAMPLE 10
[0170] Synthesis of a 2'-MOE-Modified Gapmer Oligomeric Compounds
With PN-PS-PN Mixed Backbone
[0171] The solid phase synthesis of a gapmer oligomer (SEQ ID No:
4, 19-mer) having two dimethylaminoethyl (DMAE) phosphoramidate
internucleoside linkages on the 3' and the 5' ends with
phosphorothioate internucleoside linkages between nucleosides 4-16
and having a 2'-MOE group on 3 of the ribosyl sugar moieties at the
5'end and on 4 of the ribosyl sugar moieties at the 5' end of the
oligomeric compound with internal ribosyl moieties being deoxyribo
moieties was performed in a 1 .mu.mole scale using
5'-O-DMT-2'-MOE-thymidine-3'-succinyl CPG as the solid support. The
synthesis cycle is described in the General Procedures. After the
first 2 couplings the oligomer was oxidized using 2
-dimethylaminoethylamine (10%) in carbontetrachloride. Prior to
synthesis of the next segment, the solid support was thoroughly
washed with acetonitrile. After incorporation of fourteen
additional H-phosphonate monomers (to give a 17-mer) the oligomer
was oxidized using elemental sulfur (5%) in
carbondisulfide/pyridine/ triethylamine (10:10:1), as described in
the General Procedures. Prior to synthesis of the next segment, the
solid support was thoroughly washed with carbondisulfide,
acetonitrile/pyridine (1:1) and acetonitrile. After completion of
solid phase synthesis, the support-bound oligomer was finally
treated with 2-dimethylaminoethylamine (10%) in
carbontetrachloride. Deprotection and cleavage from the solid
support was performed with aqueous ammonia (25-28%), as described
in the General Procedures.
EXAMPLE 11
[0172] Synthesis of a 2'-MOE-Modified Gapmer Oligomeric Compounds
With PN-PO-PS-PO Mixed Backbone
[0173] The solid phase synthesis of a gapmer oligomer (SEQ ID No:
10, 20-mer) having DMAE phosphoramidate internucleoside linkages
between nucleosides 1-3 on the 5' end, phosphodiester
internucleoside linkages between nucleosides 3 to 6 and 15 to 20,
phosphorothioate internucleoside linkages between nucleosides 6 to
15, 2'-MOE group on 6 of the ribosyl sugar moieties at the 5' and
the 3' end of the oligomeric compound, and with remaining ribosyl
units being 2' -deoxy ribosyls, was performed in a 1 .mu.mole scale
using 5'-O-DMT-2'-MOE-adenosine-3'-succinyl CPG as the solid
support. The synthesis cycle is described in the General Procedures
of Example 1. After the first 5 couplings the oligomer was oxidized
using triethylamine (0.1 M) in pyridine/carbontetrachloride/water
(9:5:1). Prior to synthesis of the next segment, the solid support
was thoroughly washed with acetonitrile/pyridine (1:1) and
acetonitrile. After introduction of nine additional H-phosphonate
monomers (to give an 15-mer) the oligomer was oxidized using
elemental sulfur (5%) in carbondisulfide/ pyridine/triethylamine
(10:10:1), as described in the General Procedures. Prior to
synthesis of the next segment, the solid support was thoroughly
washed with carbondisulfide, acetonitrile/pyridine (1:1) and
acetonitrile. After introduction of three additional H-phosphonate
monomers (to give an 18-mer) the oligomer was oxidized using
triethylamine (0.1 M) in pyridine/carbontetrachloride/water (9:5:1)
and washed thoroughly with acetonitrile/pyridine (1:1) and then
acetonitrile. After completion of solid phase synthesis, the
support-bound oligomer was finally treated with 2
-dimethyl-aminoethylami- ne (10%) in carbontetrachloride.
Deprotection and cleavage from the solid support was performed with
aqueous ammonia (25-28%), as described in the General Procedures.
Analysis of the crude product by electrospray mass spectrometry
gave a relative molecular mass of 7566.3 (calculated mass:
7566.3).
EXAMPLE 12
[0174] Synthesis of a 2'-MOE-Modified Gapmer Oligorieric Compounds
PN-PO-PS-PO-PN Mixed Backbone
[0175] The solid phase synthesis of a gapmer oligomer (SEQ ID No:
11, 20-mer) having DMAE phosphoramidate internucleoside linkages
between nucleosides 1-3 on the 5' end and 18-20 on the 3' end,
phosphodiester internucleoside linkages between nucleosides 3 to 6
and 15 to 18, phosphorothioate internucleoside linkages between
nucleosides 6 to 15, 2'-MOE group on 6 of the ribosyl sugar
moieties at the 5' and the 3' end of the oligonucleotide, and with
remaining ribosyl units being 2'-deoxy ribosyls was performed in a
1 .mu.mole scale using 5'-O-DMT-2'-MOE-adenosine-3'-succinyl CPG as
the solid support. The synthesis cycle is described in the General
Procedures of Example 1. After the first 2 couplings the oligomer
was oxidized, using 2-dimethylaminoethylamine (10%) in
carbon-tetrachloride. Prior to synthesis of the next segment, the
solid support was thoroughly washed with acetonitrile. After
introduction of three additional H-phosphonate monomers (to give a
6-mer) the oligomer was oxidized using DMAP (0.1 M) in
pyridine/carbontetrachloride/water (9:5:1) and thoroughly washed
with acetonitrile/pyridine (1:1) and then acetonitrile. After
introduction of nine additional H-phosphonate monomers (to give a
15-mer) the oligomer was oxidized using elemental sulfur (5%) in
carbondisulfide/pyridine/ triethylamine (10:10:1). Prior to
synthesis of the next segment, the solid support was thoroughly
washed with carbondisulfide, acetonitrile/pyridine (1:1), and
acetonitrile. After introduction of three additional H-phosphonate
monomers (to give an 18-mer) the oligomer was oxidized using DMAP
(0.1 M) in pyridine/carbontetrachloride/water (9:5:1) and
thoroughly washed with acetonitrile/pyridine (1:1) and
acetonitrile. After completion of solid phase synthesis, the
support-bound oligomer was treated with 2-dimethylaminoethylamine
(10%) in carbontetrachloride. Deprotection and cleavage from the
solid support was performed with aqueous ammonia (25-28%). Analysis
of the crude product by electrospray mass spectrometry gave a
relative molecular mass of 7704.6 (calculated mass: 7706.6).
[0176] Table I below shows the oligomeric compounds prepared
according to the procedures described in the examples above.
1TABLE 1 SEQ ID No. Sequence 5'-3' Mr.sub.calc Mr.sub.found 1
T*T*T* T*T*T* T*T*T* T*T*T* T*T*T* 7429.5 7424.8 T*T*T* T*T 2
T*T*T* T*GA CAC GGC AT*T* T*T*T* 6440.7 6435.5 3
T*.sub.NT*.sub.NT*.sub.N G.sub.SA.sub.SC.sub.S
A.sub.SC.sub.SG.sub.S G.sub.SC.sub.SA.sub.S C.sub.SC.sub.SA.sub.S
6886.0 n.a. T*.sub.NT*.sub.NT*.sub.N T* 4 T*.sub.NT*.sub.NT*.sub.S
G.sub.SA.sub.SC.sub.S A.sub.SC.sub.SG.sub.S G.sub.SC.sub.SA.sub.S
C.sub.SC.sub.SA.sub.S 6777.8 n.a. T*.sub.ST*.sub.NT*.sub.N T* 5
T*.sub.ST*.sub.ST*.sub.S T*.sub.ST*.sub.ST*.sub.S
T*.sub.ST*.sub.ST*.sub.- S T*.sub.ST*.sub.ST*.sub.S 6625.8 6626.0
T*.sub.ST*.sub.ST*.sub.S T*.sub.ST*.sub.S 6
T*.sub.SA*.sub.SA*.sub.S T*.sub.ST*.sub.SC.sub.S
G.sub.SA.sub.SA.sub.S C.sub.SG.sub.SG.sub.S C.sub.ST*.sub.SA*.sub.S
6874.8 6873.4 T*.sub.SA*.sub.SA*.sub.ST*.sub.S 7
T*.sub.SA*.sub.SA*.sub.S T*.sub.ST*.sub.SC.sub.S
G.sub.SA.sub.SA.sub.S C.sub.SG.sub.SG.sub.S C.sub.SA*.sub.SA*.sub.S
6892.9 6891.0 A*.sub.SA*.sub.SA*.sub.ST*.sub.S 8 T*C*T* G*A*G*
T*A*G* C*A*G* A*G*G* 8022.3 8023.5 A*G*C* T*C* 9 A*T*G*
C*A*T*.sub.S T.sub.SC.sub.ST.sub.S G.sub.SC.sub.SC.sub.S
C.sub.SC.sub.SC* 7426.0 7425.9 A*A*G* G*A* 10 A*.sub.NT*.sub.NG*
C*A*T*.sub.S T.sub.SC.sub.ST.sub.S G.sub.SC.sub.SC.sub.S
C.sub.SC.sub.SC* 7566.3 7566.3 A*A*G* G*A* 11 A*.sub.NT*.sub.NG*
C*A*T*.sub.S T.sub.SC.sub.ST.sub.S G.sub.SC.sub.SC.sub.S
C.sub.SC.sub.SC* 7706.6 7704.6 A*A*G*.sub.N G*.sub.NA* *=
2'-methoxyethoxy (MOE); .sub.S= phosphorothioate internucleoside
linkage; and .sub.N= dimethylaminoethyl phosphoramidate
internucleoside linkage.
EXAMPLE 13
[0177] General Procedure for the Synthesis of 2'-MOE-Modified
Gapmers With PN-PS-PN Mixed Backbone
[0178] The solid phase synthesis of a 2'-MOE gapped oligomer having
phosphoramidate internucleoside linkages at the 5' and 3' ends and
internal deoxyribo moieties having phosphorothioate linkages is
performed on a 1 mmole scale using a 5'-O-DMT-2'-nucleoside
attached via a succinyl linking group to CPG as the solid support.
The synthesis cycle is as described above in the general procedures
of Example 1. After coupling a desired number of further
nucleosides to the solid support bound nucleoside the resulting
oligomer is oxidized using 2-dimethylaminoethylamine (10%) in
carbon tetrachloride. Prior to further elongation the solid support
is washed with acetonitrile. After coupling of a desired number of
further nucleosides oxidation to for phosphorothioate
internucleoside linkages is performed using elemental sulfur (5%)
and 4-(dimethylamino)pyridine (0.1 M) in carbon disulfide/pyridine
(1:1). The solid support is again washed with carbon disulfide,
acetonitrile/pyridine (1:1) and acetonitrile. After addition of a
desired number of further nucleosides, the support-bound oligomer
is treated with 10% 2-dimethylaminoethylamine in carbon
tetrachloride. Deprotection and cleavage from the solid support is
performed with aqueous ammonia (25-28%) to give the desired
oligomeric compound.
EXAMPLE 14
[0179] General Procedure for the Synthesis of 2'-MOE-Modified
Gapmers With PBH.sub.3-PS-PBH.sub.3 Mixed Backbone
[0180] The solid phase synthesis of a 2'-MOE gapped oligomer having
boranophosphate internucleoside linkages at the 5' and 3' ends and
internal deoxyribo moieties having phosphorothioate linkages is
performed on a 1 mmole scale using a 5'-O-DMT-2'-nucleoside
attached via a succinyl linking group to CPG as the solid support.
The synthesis cycle is as described above in the general procedures
of Example 1. After coupling a desired number of further
nucleosides to the solid support bound nucleoside the resulting
oligomeric compound is treated with
N,O-bis(trimethylsilyl)trifluoroacetamide (0.3 M) in dry
tetrahydrofuran for 30 minutes and washed with tetrahydrofuran.
Subsequently, the support-bound oligomer is treated with
borane-N,N-diisopropylethylamine (0.5 M) complex in dry
tetrahydrofuran for 2 hours at room temperature. Prior to synthesis
of the next segment, the solid support is washed with acetonitrile.
After coupling of a desired number of further nucleosides, the
H-phosphonate internucleoside linkages are oxidized to
phosphorothioate internucleoside linkages using elemental sulfur
(5%) and 4-(dimethylamino)pyridine (0.1 M) in carbon
disulfide/pyridine (1:1). Prior to elongation of the oligomer the
solid support is washed with carbon disulfide,
acetonitrile/pyridine (1:1) and acetonitrile. After coupling of a
desired number of further nucleosides the H-phosphonate
internucleoside linkages are treated at room temperature with
N,O-bis(trimethylsilyl)trifluoroacetamide (0.3 M) in dry
tetrahydrofuran for 30 minutes and washed with tetrahydrofuran.
Subsequently, the support-bound oligomer is treated with 0.5 M
borane-N,N-diisopropylethyla- mine complex in dry tetrahydrofuran
for 2 hours at room temperature. Deprotection and cleavage from the
solid support is performed with aqueous ammonia (25-28%).
Biological Assays
Procedure A
[0181] ICAM-1 Expression
[0182] Targeted oligomeric compounds were prepared and assayed
using HUVEC cells to determine their ability to inhibit the
expression of ICAM- 1. HUVEC cells were washed three times with
Opti-MEM (Life Technologies, Inc.) that was prewarmed to 37.degree.
C. Oligomeric compounds were premixed with Lipofectin (10.mu.g/mL,
Life Technologies, Inc.) in Opti-MEM, serially diluted to the
desired concentrations, and applied to washed cells. Basal and
untreated (no oligomeric compounds added) control cells were also
treated with Lipofectin. Cells were incubated for 4 hours at
37.degree. C., at which time the medium was removed and replaced
with standard growth medium with or without TNF-a (5 mg/mL, R&D
Systems). Incubation at 37.degree. C. was continued for different
times as indicated below.
[0183] A fluorescence-activated cell sorter was used to quantitate
ICAM- 1 protein expression. The cells were removed from the plate
surface by brief trypsinization with trypsin (0.25%) in PBS.
Trypsin activity was quenched with a solution of bovine serum
albumin (2%) and sodium azide (0.2%) in PBS (+Mg/Ca). Cells were
pelleted by centrifugation (1000 rpm, Beckman GPR centrifuge),
resuspended in PBS, and stained with ICAM-1 specific antibody (3
.mu.L/105 cells), CD54-PE (Pharmingin). The antibodies were
incubated with the cells for 30 minutes at 4.degree. C. in the
dark, under gentle agitation. Cells were washed by centrifugation
procedures and then resuspended in FacsFlow buffer (0.3 mL, Becton
Dickinson) with formaldehyde (0.5%, Polysciences).
[0184] Expression of cell surface ICAM-1 was determined by flow
cytometry using a Becton Dickinson FACScan. The percentage of
ICAM-1 expression in the control was calculated as follows:
[(oligomeric compound-treated ICAM-1 value)-(basal ICAM-1
value)/(non-treated ICAM- 1 value) - (basal ICAM- 1 value))]. In
one study, 2'-O-(2-methoxy)ethyl-modified anti-intercellular
adhesion molecule 1 (ICAM-1) oligomeric compounds were shown to
selectively increase the ICAM- 1 MRNA level and inhibit formation
of the ICAM-1 translation initiation complex in human umbilical
vein endothelial cells (Baker et al., The Journal of Biological
Chemistry, 1997, 272, 11994-12000).
[0185] ICAM-1 expression data reveal that the uniform
phosphorothioate MOE oligomer T*C*T* G*A*G* T*A*G* C*A*G*
(*=2'-methoxyethoxy (MOE)) sequence synthesized by amidite
chemistry and the same compound synthesized by H-phosphonate
chemistry are efficacious in HUVEC cells in controlling ICAM-1
expression. The oligomers are presumably working by a direct
binding RNase H independent mechanism. Both compounds synthesized
from different chemistries display dose response in inhibiting
ICAM-1 expression between 3 and 100 nM range.
Procedure B
[0186] c-raf MRNA Expression in A549 Cells
[0187] Gapmers designed in this study are based on the parent
sequence of ATG CAT TCT GCC CCC AAG GA (SEQ ID No. 9) which is a
uniform deoxy phosphorothioate. This sequence is an antisense
oligomeric compound targeted to mouse c-raf. c-raf m-RNA expression
assay was carried out according to a reported procedure (Monia et
al., Nature Medicinek, 1996, 2, 668). Human A549 lung carcinoma
cells were obtained from the American Type Tissue Collection. These
were grown in Dulbecco's modified Eagle's medium containing 1 g of
glucose/liter (DMEM) and FCS (10%) and routinely passaged when
90-95% confluent.
[0188] Assay for Oligonucleoside Inhibition of c-raf Protein
Synthesis
[0189] A549 cells were plated in 6-well plates (Falcon Labware,
Lincoln Park, N.J.) and 24-48 hours later (when 80-90% confluent)
treated with 1 .mu.M phorbol 12,13-dibutyrate (PDBu) for 18 hours.
This procedure removes greater than 75% of immunoreactive c-raf
protein from the cells. Cells were then washed three times with
DMEM (3 mL) (to remove PDBu), and DMEM (1 mL) containing DOTMA/DOPE
solution (20 .mu.g/mL, LipofectinR, Bethesda Research Laboratories)
was added. Oligonucleoside gapmers were then added to the required
concentration (for our initial screen, 1 .mu.M) from a 10 .mu.M
stock solution, and the two solutions were mixed by swirling of the
dish. The cells were incubated at 37.degree. C. for 4 hours, washed
once with DMEM+FCS (10%) to remove the DOTMA/DOPE solution, and
then additional DMEM (3 mL) +10% FCS was added and the cells were
allowed to recover for another 10 hours. Total RNA is prepared 24
hours after the experiment and analyzed for c-raf and G3PDH mRNA
levels after normalization to G3PDH MRNA.
[0190] Results
[0191] Gapped oligomeric compounds (SEQ ID NO.: 9, 10 and 11, Table
1) inhibit c-raf MRNA expression in A549 cells in a dose dependent
manner between 50-400 nM range. The duration of the effect in
reducing c-raf expression is much longer for P=N containing Gapmers
as expected from the improved nuclease resistance.
[0192] It is intended that each of the patents, applications,
printed publications, and other published documents mentioned or
referred to in this specification be herein incorporated by
reference in their entirety.
[0193] Those skilled in the art will appreciate that numerous
changes and modifications may be made to the preferred embodiments
of the invention and that such changes and modifications may be
made without departing from the spirit of the invention. It is
therefore intended that the appended claims cover all such
equivalent variations as fall within the true spirit and scope of
the invention.
* * * * *