# Patent

## Title
Content dependent inhibitors of cytidine deaminases and uses thereof

## Abstract

This invention relates to cytidine deaminase inhibitors (Cytidine deaminase inhibitors) of cytidine deaminases and uses thereof.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Application 60/568,490, filed May 6, 2004.


This invention was made with government support under Grants DK43739 and AI54369 and RR15934 awarded by the National Institutes of Health, and a grant from the Air Force Office for Scientific Research. Therefore, the government may have certain rights in the invention.


BACKGROUND OF THE INVENTION
Cytidine deaminases (CDAs) represent a novel class of enzymes involved in pyrimidine metabolism in both lower and higher organisms. The fundamental cytidine deaminase reaction requires a cytidine deaminase with bound Zn2+, which serves as a Lewis acid in a reaction that activates a water. The activated water serves as a nucleophile that attacks the C4 (sp2) position of the cytosine ring leading to a transition state that proceeds through a tetrahedral intermediate (sp3). A subsequent change from the enol to keto base tautamer results in an aprotic exocylic oxygen at C4, accompanied by the elimination of ammonia. The product is the uridine nucleoside. The reverse reaction is unfavorable and does not occur to any measurable extent on the enzyme.
The synthesis and inhibitory activity of cytidine deaminase inhibitors have been described in the art (Kim, C. H., et al., J Med Chem, 29(8):1374-80, 1996; Laliberte, J. Cancer Chemother Pharmacol, 30(1): 7-11, 1992; Driscoll, J. S., et al., J Med Chem, 34(11):3280-4, 1991; Xiang, S., et al., Biochemistry, 36(16):4768-74, 1997; Xiang, S., et al., Biochemistry, 35(5):1335-41, 1996; Xiang, S., et al., Biochemistry, 34(14):4516-23, 1995; Frick, L., et al., Biochemistry, 28(24):9423-30, 1989.)
Historically the development of the zebularine nucleoside was based on the need for an inhibitory agent to impair the function of cytidine deaminases that metabolize antileukemic nucleosides such as 5-aza-2′-deoxycytidine (5-aza-dC) and cytidine arabinoside (ara-C) (Foubister, V., Drug Discov Today 8(10):430-1, 2003.) Such undesirable cytidine deaminase activity renders these therapeutics ineffective as anti-leukemia drugs. By comparison to 5-aza-dC and ara-C, zebularine is considerably less cytotoxic and more chemically stable, up to pH 12, in aqueous solution (Barchi, J. J., Jr., J. Organic Chem., 57:536-541, 1992; Kelley, J. A., et al., J Med Chem, 29(11):2351-8, 1986). Interest in zebularine as a therapeutic has emerged due to its efficacy as an anti-DNA methyltransferase drug Cheng, J. C., et al., J Natl Cancer Inst, 95(5):399-409, 2003; Zhou, L., et al., J Mol Biol, 321(4):591-9, 2002). In many types of cancers, tumor suppressor genes become inactivated due to abnormal methylation of their promoter regions. Clinical studies have demonstrated that oral administration of zebularine can reactivate genes that naturally suppress cancer through a mechanism that inhibits methylation. However, in animal studies, the efficacy of zebularine in free nucleoside form was limited due to the very high oral doses needed (1 g per kg body weight in mouse models Foubister, V., Drug Discov Today, 8(10):430-1, 2003). Furthermore, zebularine is cytotoxic due to its non-specific action against the enzymes of pyrimidine metabolism and indiscriminate targeting of DNA methyltransferases. What is needed in the art are inhibitors that selectively target cytidine deaminases with the property that inhibition has little or no cytotoxicity.
In this regard, cytidine deaminases active on cytidine or deoxycytidine in RNA or DNA (respectively) and that belong to a family of enzymes known as APOBEC-1 Related Proteins (ARPs) have been shown to play a role in modifying nucleic acid sequences and thereby giving rise to altered protein expression and/or serving as antiviral agents. ARPs modify select cytidines or deoxycytidines in RNA or DNA through targeting sequence specific signals within 5′ and/or 3′ sequences flanking the modified base. The flanking sequences represent a unique context within which the target cytidine of deoxycytidine is embedded.
SUMMARY
The invention discloses context dependent inhibitors of cytidine deaminases, (Cytidine deaminase inhibitors) and methods for their use.



BRIEF DESCRIPTION OF THE DRAWINGS
The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several embodiments of the invention and together with the description, serve to explain the principles of the invention.
FIG. 1 shows a summary of the relevant chemical mechanism and stereochemical aspects of the fundamental cytidine deaminase reaction. The noteworthy aspect of the reaction is that it requires a cytidine deaminase with bound Zn2+, which serves as a Lewis acid in the reaction to activate water. Activated water serves as a nucleophile that attacks the C4 (sp2) position of the cytosine ring leading to a transition state that proceeds through a tetrahedral intermediate (sp3), for which the enzyme exhibits its greatest affinity. A change from enol to keto base tautamer results in a keto oxygen at C4, accompanied by the elimination of ammonia. The product is the uridine nucleoside. The reverse reaction is unfavorable and does not occur to any measurable extent on the enzyme.
FIG. 2 shows the stereochemical property of zebularine that makes it such an effective inhibitor of cytidine deaminase activity. The enzyme modifies the analog base in a mechanism-based manner. Specifically, when the zebularine nucleoside is bound by the enzyme active site, the de-oxo C4 position undergoes nucleophilic attack in a manner analogous to that observed for the cytidine substrate seen in FIG. 1. However, due to the absence of a suitable leaving group (i.e. hydrogen in lieu of ammonia), the enzyme remains trapped in complex with the C4-hydroxylated analog, which mimics the tetrahedral geometry of the transition state. Hence, the enzyme exhibits much greater affinity for the 3,4 dihydrouridine adduct than the zebularine ground-state. Therefore, an inhibitor need not be one that is chemically susceptible to nucleophilic attack, but can be one that mimics the chemical properties of the intermediate in geometry and charge.
FIG. 3 shows how representative substrate specificity is achieved for the cytidine deaminase APOBEC-1 whose target site interaction is conferred through direct interaction with an auxiliary factor, ACF. The latter complementation factor binds APOBEC-1, as well as an RNA sequence that flanks the deaminated site (C6666) known as the ‘mooring sequence. RNA recognition by ACF requires 3 tandem RNA recognition motifs (RRMs) that interact with high affinity (Kd= ̃8 nM) on the mooring sequence. Due to their sequence homology to APOBEC-1, APOBEC related proteins (ARPs) can require similar high-specificity auxiliary factors in substrate targeting. One analysis of the ARP known as the activation induced deaminase (AID) showed that deoxycytidine is targeted for modification within immunoglobulin genes in the context of single stranded DNA sequence (A/G-G-C-A/T (RGYW) or A/T-A/G-C-C/T (WRCY) within Ig genes for SHM, CSR and on reporter DNAs. However, many other sites were modified as well (Harris, R. S., Petersen-Mahrt, S. K. and Neuberger, M. S. (2002). Mol Cell 10, 1247-53; Petersen-Mahrt, S. K., et al., (2002). Nature 418, 99-104; Yu, K., et al., (2003). J. Biol. Chem. 279, 6496-6500. Targeting of deoxycytidines within the HIV-1 single stranded minus strand intermediates during viral reverse transcription demonstrated a target sequence preference of ACCC or GCCC in which the third C is deaminated (Zhang et al., (2003) Nature 424, 94-8; Lecossier et al., Science 300, 1112).
In the editosome deamination model, APOBEC-1 is the core editing enzyme of a macromolecular complex required for site specific C to U deamination of the mRNA encoding the serum lipoprotein apoB. By itself APOBEC-1 exhibits little RNA binding specificity; however, through interactions with APOBEC-1 complementation factor, ACF, the editing enzyme is guided to the correct target site to perform its natural biochemical C to U deamination function because ACF binds selective to the mooring sequence. This paradigm of auxiliary proteins and their selective interaction with target sequences is a theme with the ARP family described throughout.
FIG. 4 shows several other context dependent inhibitors (Cytidine deaminase inhibitors) of ARP-related cytidine deaminases other than zebularine.
FIG. 5 shows a description of the sequence environment employed for the synthesis and application of cytidine deaminase inhibitors containing embedded zebularine. The single stranded construct is envisioned for APOBEC-1, which entails incorporating specific sequences of the tripartite apoB mRNA substrate; Z marks the position of zebularine. A single-stranded or double-stranded “bubble” target provides a substrate mimic for AID.
FIG. 6 shows that the expression of CEM15 in 293T cells resulted in at least a 100-fold decrease in Vif-viral infectivity compared to particles generated in parental 293T cells. The low level of GFP expression from vif(−), CEM15+ particles is indistinguishable from background fluorescence in control cells [0.2%]. This assay is amenable to the use of existing HIV-1 proviral isotyped vectors that are deleted for different regions and different amounts of the HIV-1 genome. Deleted genes can be provided in trans by co-transfection of suitable expression plasmids.
FIG. 7 shows expression of AID transcripts in human B cell lymphoma lines. Total RNA was extracted from the cell lines indicated, reverse transcribed and subjected to PCR amplifications with primers to AID and α-actin as described (McCarthy et al. (Blood (94) Feb. 13, 2003). Amplified fragments were separated on 1.2% agarose gels. AID PCR products were then transferred onto Hybond nylon filters, hybridized to a 32P-labeled internal AID oligonucleotide, and the hybridization signal was detected using phosphorimager screens. Note the different AID band patterns present in the individual lymphoma lines. (wt, wild-type-size AID band (646 bp); sv1/sv2, bands compatible with size of known splice variants; *, potential novel splice variants.)
FIG. 8 shows retroviral expression of AID. His-tagged murine AID cDNA was cloned into the pMIG retroviral vector (Pear et al. Blood 92:378-3792, 1998) and retroviral particles were generated using the Phoenix-Eco packaging cell line. Viral supenatants were used to transduce in vitro activated B cell. Panel A: Day1 LPS-activated lymphoblasts were incubated with Phoenix-Eco virus-free supernatant (No virus), pMIG virus containing supernatants and pMIG-AID containing supernatants, in the presence of 4 μg/ml polybrene. At day 5 of culture, cells were harvested and analyzed by flow cytometry (FSC/SSC live-gated cells shown in plots). Transduction efficiencies average 30-40% with the pMIG virus, and 20-30% with pMIG-AID. Note that GFP expression is lower for pMIG-AID than for pMIG, probably because the AID in the first cistron position diminished expression of the IRES-GFP module (therefore, transduction efficiencies with pMIG-AD may be somewhat underestimated). Panel B: Day 5 cells from αCD40- (one experiment) and LPS-stimulated cultures transduced with either pMIG (open bars) or pMIG- were stained with PE-conjugated anti-IgG antibodies (αIgG1 for CD40 culture, αIgG2b/αIgG3 for the LPS cultures), analyzed by flow cytometry, and rates of IgG switching in transduced, GFP+ cells compared. Note how pMIG-AID transduction increases IgG switching rates by 2-4 folds, indicating expression of functional A/D.
FIG. 9 shows retroviral transduction of human B lymphoma cells. Cultured cells from the indicated lymphoma lines were transduced with an RD114-packaged GFP-expressing retrovirus using the flow-through method (Chuck et al. Hum Gene Ther 7:743-750, 1996). 48 hours after transduction, cells were analyzed by flow cytometry for GFP expression. Efficiencies vary between 20% and >80%.
FIG. 10 Ribbon representations of HsAPOBEC-1 and HsAID comparative models. (A) The dimeric APOBEC-1 model with polypeptide chains colored: purple and red (NTCD and NCCTD); and blue and green (NTCD and NCCTD). A central flap (cyan with hatched oval) connects the NTCD to the NCCTD. Each NTCD coordinates Zn2+ (dark green sphere). Trans-acting structure elements that form the purple active site are: T1 and L2 (green NCCTD), flap (cyan with hatched circle) and T3 (blue NTCD). The symmetry axis in black represents a proper dyad; the blue axes represent improper (pseudo) 2-fold rotations. (B) The dimeric AID structure as in 2B. The subunit interface of AID obeys D2 symmetry analogous to APOBEC-1, but axes were omitted for clarity.
FIG. 11 Stereo views of the HsAPOBEC-1 and HsAID active sites with bound RNA and DNA substrates depicted as ball-and-stick models (yellow). (A) The APOBEC-1 active site with bound apoB mRNA substrate 5′-GAUAU6666AA-3′. (B) The APOBEC-1 active site with bound DNA substrate 5′-d(ATCTC*CG)-3′, described as an rpoB mutation hot spot (13). (C) The AID active site with bound DNA substrate 5′-d(TAAGU*TA)-3′, described as an SHM hot spot (14). Residues mutated in HIGM2 syndrome are colored red. For all diagrams, the protein Cα backbone is drawn as a ribbon showing contributions of both polypeptides chains of the dimer (i.e. magnified views of FIGS. 10A and 10B). Basic residues (light blue), acidic residues (pale pink), and aromatic residues (gray) are drawn as stick representations. Predicted hydrogen bonds and ionic interactions with Zn2+ are depicted as black lines. The sites of base deamination are indicated by red arrowheads. For clarity, not all amino acids are shown.
FIG. 12 shows the product eluted in the synthesis of a context dependent inhibitor of DNA harboring 5-methyl-2′-deoxyzebularine. A sequence was synthesized was a 15-mer comprising: 5′-d(AGC-TAG-(dmZ)-TAA-GTT-AT)-3′ (SEQ ID NO: 22), where one of the edited positions has been replaced by 5-methyl-2′-deoxyzebularine denoted (dmZ) (Example 1). The product eluted as a single peak with a retention time of 44.3 min; failure sequences and impurities were clearly separated in this step. The DNA was detected at 260 nm and the pooled material was lyophilized to dryness. The yield was 25% (nearly 2 mg).
FIG. 13 shows MALDI/TOF mass spectrometry for 5-methyl-2′-deoxyzebularine. The major peak was observed at an m/z of 4532. This result demonstrates the existence of an oligomer of the correct molecular weight that represents the largest component of the sample.



DESCRIPTION OF THE PREFERRED EMBODIMENTS
The invention provides compounds that inhibit cytidine deaminase, as well as methods of using, identifying, and making such compounds. The compounds, cytidine deaminase inhibitors (also referred to as Cytidine deaminase inhibitors), are useful in preventing or treating a variety of diseases as well as aiding in combination with other treatment therapies. Described herein are cytidine deaminase inhibitors of cytidine deaminases, including APOBEC-1 and APOBEC-1 related proteins (ARPs).
Cytidine deaminase inhibitors comprise a polymeric substrate having a targeting function and an inhibiting moiety. The targeting polymeric substrate can be directed to a cytidine deaminase or a cytidine deaminase auxiliary protein. The inhibiting moiety can be a nucleoside. The nucleic acid sequence of the polymeric substrate can contain a sequence that binds the cytidine deaminase. For example, the sequence can be a RNA or DNA and can flank the zebularine nucleotide 5′, 3′ or both 5′ and 3′ (as is the case with the tripartite motif containing the mooring sequence within apoB mRNA i.e., the mooring sequence of APOBEC-1, is located 3′ of the edited site at C6666, a spacer sequence lies immediately 3′ of C6666 and an enhancer element lies immediately 5′ of C6666). Alternately, the polymeric substrate binds the auxiliary protein The cytidine deaminase inhibitor can inhibit a cytidine deaminase or an auxiliary protein, by, for example, complexing with the cytidine deaminase or the auxiliary protein in a manner that blocks the cytidine deaminase function. The cytidine deaminase inhibitors can also chemically or structurally alter the cytidine deaminase or auxiliary protein so as to inhibit its ability to deaminate.
Optimally, the chemical property of cytidine deaminase inhibitors that causes them to be effective inhibitors of cytidine deaminase activity is that the enzyme modifies the analog base in a mechanism-based manner. For example, when a zebularine nucleoside is bound by the enzyme active site, the de-oxo C4 position undergoes nucleophilic attack (FIG. 2) in a manner analogous to that observed for the cytidine substrate (FIG. 1). However, due to the absence of a suitable leaving group (such as ammonia), the enzyme remains trapped in complex with the hydroxylated analog, which mimics the tetrahedral geometry characteristic of the transition state. Hence, the enzyme exhibits much greater affinity for the 3,4 dihydrouridine adduct than the zebularine ground-state. However, the nature of the cytidine deaminase inhibitor need not be one that requires strict chemical reactivity (defined as geometric transformation). The cytidine deaminase inhibitor functions by mimicking the tetrahedral intermediate preferred by the enzyme as representative of the charge and geometry observed in the transition state. For example, 3,4,5,6-tetrahydrouridine embedded within the substrate can act in an inhibitory manner. There are several examples of cellular and viral mRNA editing reactions in mammalian cells. (Grosjean and Benne (1998) Modification and Editing of RNA, ASM Press, Washington D.C.; Smith et al. (1997) RNA 3: 1105-23). Two examples of such editing mechanisms are the adenosine to inosine and cytidine to uridine conversions. (Grosjean and Benne, 1998; Smith et al. Trends in Genetics 12:418-24, 1996; Krough et al. J. Mol. Biol. 235:1501-31, 1994). The latter enzymes can be expected to be inhibited by cytidine deaminase inhibitors with the form of nebularine (which is the purine version of zebularine). Editing can also occur on both RNA and on DNA, and typically these functions are performed by different types of deaminases.
Cytidine deaminases are responsible for cytidine to uridine conversions. This group of enzymes also includes deoxycytidine deaminases, which are responsible for deoxycytidine to uridine conversions. The term “cytidine deaminase” used throughout the application is interchangeable with “deoxycytidine deaminase.” “Cytidine deaminases” also include those deaminases active on both DNA and RNA. As described in the foregoing section, this simplification stems from the fact that APOBEC-1 and ARPs can act on single stranded RNA and/or single stranded DNA.
The most highly studied Cytidine Deaminase Active on RNA (CDAR), which acts upon polymeric nucleic acid substrates, is the apoB editing catalytic chain-1, APOBEC-1 (Wedekind, J. E., et al., Trends Genet, 19(4):207-16, 2003). The selectivity requirements of APOBEC-1 in editing of apoB RNA reporters was similar to that of the yeast enzyme CDD1 when the respective proteins were overexpressed in yeast (Dance et al., (2000) Nucleic Acids Res. 28, 424-49; Dance et al., (2001) Nucleic Acids Res. 29, 1772-80). Hence, the structure of CDD1 provided a tenable connection between known CDA and yeast cytosine deaminase (ScCD) enzymes, and the family of mammalian APOBEC related proteins. Consequently, four empirically derived deaminase structures were employed in comparative modeling of HsAPOBEC-1 and HsAID. Preparation of a structural template revealed major differences in the modes of substrate binding by CDA and ScCD enzymes. Comparative modeling of APOBEC-1 and AID suggested that the domain interface between subunits influences the positioning of ribose binding loops as in CDAs and that a variably-sized flap at the catalytic site regulates access based on substrate size, which was corroborated by functional data. Both AID and APOBEC-1 targeted DNA in vivo (Harris, R. S. (2002) Mol. Cell. 10, 1247-53; Petersen-Mahrt, S. K., (2002) Nature 418, 99-103.). However, APOBEC-1 did not substitute for AID in CSR or SHM (Eto, T., (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 12895-8) and AID could not substitute for APOBEC-1 in apoB mRNA editing (Muramatsu, M. (1999) J. Biol. Chem. 274, 18470-6) showing each enzyme has an inherent specificity for its own substrate. Specifically, models of APOBEC-1 and AID (FIGS. 10 and 11) indicated either DNA or RNA substrates could be accommodated by their active sites, but only in single-stranded form.
APOBEC-1 is the core editing enzyme of a macromolecular complex or editosome required for site specific C to U deamination of the mRNA encoding the serum lipoprotein apoB. By itself APOBEC-1 exhibits little RNA binding specificity; however, in the presence of the APOBEC-1 complementation factor (ACF) the editing enzyme is guided to the correct target site to perform its natural biochemical C to U deamination function (Mehta, A., et al., Mol Cell Biol 20, 1846-54, 2000). APOBEC-1 target specificity is conferred through direct interaction with ACF, which mediates contact with a flanking RNA ‘mooring sequence’ located 3′ of the edited site at C6666 (FIG. 3). RNA recognition by ACF requires 3 tandem RNA recognition motifs (RRMs) that interact with high affinity (Kd= ̃8 nM) on the mooring sequence (FIG. 3) (Smith, H. C., Cell Biol, 4:267-78, 1993; Mehta, A. and D. M. Driscoll, RNA, 8(1):69-82, 2002; Blanc, V., et al., J Biol Chem, 276: 46386-93, 2000.)
Due to the tripartite substrate sequence motif of apoB mRNA, which includes (i) a mooring sequence, (ii) an “enhancer” sequence and (iii) a “spacer” sequence, which collectively flank the C6666 editing site in apoB mRNA, the site appears unique compared to all other mammalian mRNA, rRNA and tRNA sequences. Hence the intermolecular interactions between APOBEC-1, ACF, and the RNA substrate can be selectively targeted by incorporating the unique tripartite sequence features into the cytidine deaminase inhibitor.
As a therapeutic, an understanding of APOBEC-1 is relevant to heart disease and stroke. Current lipid-lowering therapies, such as statins, have shown effective potency as inhibitors of hydroxymethylglutaryl (HMG)-CoA reductase, which catalyzes the committed step in the synthesis of cholesterol. The other lipid-lowering bile-acid-binding resin therapy has shown efficacy via sequestering the bile acids in the intestine, thereby interrupting the enterohepatic circulation of bile acids and increasing the elimination of cholesterol from the body. These are valid therapies for patients with hyperlipidemia. However, up to 30% of the patients have been observed to indicate adverse reactions to these therapies, showing that alternative therapies have a market. Moreover the latter therapies are less effective on patient suffering from metabolic syndrome.
Cholesterol is carried in the blood from one tissue to another as lipoprotein particles by specific carrier proteins called apolipoproteins. Apolipoprotein B (apoB) is an integral and non-exchangeable structural component of lipoprotein particles referred to as chylomicrons, very-low-density lipoprotein (VLDL) and low-density lipoprotein (LDL). ApoB circulates in human plasma as two isoforms, ApoB100 and apoB48. ApoB100 can be converted into ApoB48 by the enzyme APOBEC-1 (ApoB mRNA editing catalytic subunit-1). With the help of auxiliary factors, APOBEC-1 can stop the synthesis (production) of ApoB100 form and start the synthesis of ApoB48 form in cells. ApoB100 and ApoB48 play different roles in lipid metabolism. Various studies indicated that ApoB100-associated lipoproteins (VLDL and LDL) are much more atherogenic than ApoB48-associated lipoproteins.
Stimulating hepatic ApoB mRNA editing is a way to reduce serum LDL through the reduction in synthesis and secretion of ApoB100 containing VLDL. In most mammals (including humans), ApoB mRNA editing is carried out only in the small intestine. Studies found that the presence of substantial editing in liver is associated with a less atherogenic lipoprotein profile compared with animals that do not have liver editing activity. APOBEC-1 is expressed in all tissues that carry out ApoB mRNA editing. Human liver does not express APOBEC-1 but it does express sufficient auxiliary proteins to complement exogenous APOBEC-1 in ApoB mRNA editing in transfected cells. Therefore, induction of editing in human liver reduces apoB100 synthesis and thereby reduce the levels of circulating LDL cholesterol.
Based on population studies the etiology of atherosclerosis falls into four causalities (i) hypercholesterolemia (described above), (ii) pro-inflamatory reactions, (iii) pro clotting, and (iv) metabolic syndrome (Corestti, J. P. et al., (2003) Atherosclerosis 171, 351-8; Moss, A. J. (1999) Circulation 99, 2517-22, herein incorporated by reference in their entireties). Cytidine deaminase inhibitor-based compounds are indicated for the latter causality as it is intestinally derived B48 containing reminants of chylomicrons that are small and accumulate within the walls of arteries due to their heightened affinity and high abundance in the blood of approximately 25% of the total population at risk for atherogenic disease. Chylomicron reminants appear in blood maximally within 1-2 hours following a meal (as a consequence of intestinal absorption) and are present in proportion to the fat content of the meal.
The small intestine from all mammals edits 80-100% of apoB mRNA produced (Backus, J. W. (1990) Biochem. Biophys. Res. Commun. 170, 513-8; Greeve, J. (2003) J. Lipid Res. 34, 1367-83, herein incorporated by reference in their entireties) and secretes B48 chylomicrons assembled in response to the presence of dietary lipids into the lymphatic system. Transgenic apobec-1 gene knock-out mice do not edit apoB mRNA and as a consequence assemble chylomicrons on apoB100 protein. These mice have a normal phenotype (Farese, R. V. et al., (1996) PNAS USA 93, 6393-8; Nakamuta, M. et al., (1996) J. Biol. Chem. 271, 25981-8, herein incorporated by reference in their entireties), but do have an elevated risk of atherosclerosis due to the lack of hepatic editing. This leads to hepatic apoB100 VLDL secretion into the blood steam and subsequent metabolism to apoB100 LDL. cytidine deaminase inhibitors selective for APOBEC-1 inhibits apoB mRNA editing within intestinal cells thereby resulting in exclusive secretion of apoB100 containing chylomicrons that are metabolized to large particles that are cleared by the liver with reduced rates of artery wall accumulation.
In addition to the established apoB mRNA editing activity of APOBEC-1, C to U modifications have been detected in the tumors of approximately one quarter of individuals afflicted with the disease neurofibromatosis type I (NF1) (Skuse, G. R., et al., (1996) Nucleic Acids Res, 24, 478-85, herein incorporated by reference in its entirety). The translation product of NF1 mRNA, is a tumor suppressor GTPase activating protein (GAP), neurofibromin, which inhibits cell growth signaling mediated by the GTPase dependent Ras oncogene product. Due to the presence of a mooring-sequence-like segment downstream of C3916 in the neurofibromin mRNA, this site can be edited converting an Arg to an in-frame translation stop codon. If the product of the edited mRNA escapes nonsense mediated decay, the result is a truncated protein missing the C-terminal GAP domain providing a potential mechanism for disease. APOBEC-1 mRNA editing of neurofibromin mRNA appears to play a direct role in NF1 disease (Mukhopadhyay, D., et al., (2002) Am J Hum Genet, 70, 38-50, herein incorporated by reference in its entirety). Due to the unique tripartite motif in NF1 mRNA editing of C3916 in NF1 mRNA can be selectively inhibited by cytidine deaminase inhibitors. This is an instance where in the same enzyme (APOBEC-1) can be targeted by two different cytidine deaminase inhibitors (one mimicking NF1 and the other apoB RNA) with the possibility of tissue specific effects due to the differential affinity and competition of the cytidine deaminase inhibitor with the endogenous mRNA substrate that is selectively expressed in each tissue (e.g. NF1 cytidine deaminase inhibitor inhibits APOBEC-1 editing only in neuronal tissue and apoB cytidine deaminase inhibitor inhibits editing only in liver and intestine).
Unregulated transgenic expression of APOBEC-1 confers susceptibility to liver cancer (Sowden, M., (1996) J Biol Chem, 271:3011-7; Yamanaka, S., et al., (1995) PNAS USA, 92, 8483-7, herein incorporated by reference in its entirety), possibly as a result of nonspecific mRNA editing affecting the NAT1 translational repressor. Another novel mechanism leading to neoplasia that can be related to the observation that APOBEC-1-mediates stabilization of mRNA transcripts of c-myc (Anant, S. and Davidson, N. O. (2000) Mol Cell Biol, 20, 1982-92, herein incorporated by reference in its entirety). Although APOBEC-1 itself has marginal affinity for apoB mRNA, it has been demonstrated that it exhibits modest affinity for tandem AU-rich sequences. Disruption of this interaction by cytidine deaminase inhibitor compound can decrease c-myc stabilization, which could significantly impact the half-life of the proto oncogene product.
Two loci of APOBEC-1 related proteins (ARPs) were discovered in humans, as well as related proteins in mice and yeast (Dance, G. S., et al., (2001) Nucleic Acids Res, 29, 1772-80; Anant, S., et al., (2001) Am J Physiol Cell Physiol, 281, C1904-16; Jarmuz, A., et al., (2002) Genomics, 79, 285-96 all herein incorporated by reference in their entireties). A summary of human ARP proteins is provided in Table I and in Wedekind, J. E., et al., (2003) Trends in Genet, 19, 207-16. The cytidine deaminase inhibitors described herein can target the ARPs or their auxiliary proteins in a manner similar to APOBEC-1. For example, context dependent inhibitors applications are specifically indicated for metabolic syndrome, while apoB mRNA editing is indicated for treatment in the small intestine.
The activation-induced cytidine deaminase (AID) (e.g. a novel ARP) is required for somatic hypermutation (SHM) of immunoglobulin (Ig) genes in germinal center (GC) B cells (Muramatsu, M., et al., (1999) J Biol Chem, 274, 18470-6; Muramatsu, M., et al., (2000) Cell, 102, 553-63). AID is also known to be deficient in human patients afflicted with hyper IgM syndrome type II (Revy, P., et al., (2000) Cell, 102, 565-75). Although AID displays significant homology to APOBEC-1, it can act directly on DNA (Petersen-Mahrt, S. K., (2000) Nature, 418, 99-103; Harris, R. S., et al., (2002) Mol Cell, 10, 1247-53, herein incorporated by reference in their entireties). In GC B cells, SHM is usually restricted to Ig genes, however, AID is constitutively expressed in human B cell malignancies such as diffuse large B cell lymphomas (DLBCL) and some chronic lymphocytic leukemias (CLL), as well as in other lymphomas of both germinal center (GC) and non-GC origin (Greeve, J., et al., (2003) Blood, 101, 3574-80; McCarthy, H., et al., (2003) Blood, 101, 4903-8; Oppezzo, P., et al., (2003) Blood, 101, 4029-32, herein incorporated by reference in their entireties). In CLL samples, AID expression was specifically associated with poor prognostic features. Paradoxically, poor prognosis in CLL correlates with the absence of Ig gene SHM (Damle, R. N., et al., (1997) Blood, 94, 1840-7; Hamblin, T. J., et al., (1999) Blood, 94, 1848-54 herein incorporated by reference in their entireties), showing that AID function is altered in these cells. AID expression in the absence of ongoing SHM is also observed in certain diffuse large B-cell lymphomas (DLBCLs), specifically those defined as “activated B cell-like” based upon gene expression profiles and surface markers (Lossos, I. S., et al., (2000) PNAS USA, 97, 10209-13, herein incorporated by reference in its entirety). Here too, a worse outcome is associated with the non-mutating phenotype compared to DLBCLs in which ongoing Ig SHM is detected, such as those of GC-like phenotype (Rosenwald, A., et al., (2003) N Engl J Med, 346, 1937-47; Alizadeh, A. A., et al., (2000) Nature, 403, 503-11, herein incorporated by reference in their entireties).







TABLE 1







Genetic Location and Properties of human APOBEC-1 Related Proteins (ARPs)














Accession
Equivalent
Expressed
C to U


Gene
Locus
Number
Names
Sequence
Activity





APOBEC-1
12p13.1
AAD00185
—
Small & Large
apoB mRNA






Intestine


APOBEC-2
6p21
NP_006780
CAB44740/ARCD1
Cardiac &
—






Skeletal Muscle


AID
12p13
NP_065712
—
B lymphocytes
DNA


APOBEC-3A
22q13.1
NP_663745
Phorbolin-1
Keratinocytes
—


APOBEC-3B
22q13.1
Q9UH17
Phorbolin-3
Keratinocytes,
—





Phorbolin- 1-related
colon





Phorbolin-2





APOBEC-1L





ARCD-3


APOBEC-3C
22q13.1
CAB45271
Phorbolin-1
Spleen, testes,
—





ARCD-2/ARCD-4
heart, thymus,






prostate, ovary,






uterus, PBLs,


APOBEC-
22q13.1
NM_145298
—
uterus
—


3D + E


APOBEC-3D
22q13.1
BF841711
—
head and neck
—






cancers


APOBEC-3E
22q13.1
Pseudogene
ARCD-6
—
—


APOBEC-3F
22q13.1
BG_758984
ARCD-5
B lymphocytes
—


APOBEC-3G
22q13.1
NP_068594
Phorbolin-like-
Spleen, breast,
Viral





protein, MDS019,
heart, thymus,
DNA





HsCEM15
PBLs, colon,






stomach, kidney,






uterus, pancreas,






placenta, prostate


22q13.1
22q13.1
XP_092919
—
—
—


12q23
—
XP_115170
—
—
—









In subsets of DLBCL and CLL, AID expression is uncoupled from somatic hypermutation activity, a feature that correlates with more aggressive forms of these diseases. These characteristics show that AID function is aberrant in B cell cancers. In fact, oncogene mutations with patterns resembling SHM have been found at high frequency in B cell lymphomas. One explanation for these data is that loss of target specificity during the SHM process may be involved in the transformation and/or progression of B lymphoid malignancies. Constitutive AID expression in transgenic mice was shown to cause T cell lymphomas and pulmonary adenomas, formally demonstrating AID's oncogenic potential. Finally, and most significantly, transgenic expression of AID under a ubiquitous promoter induces T cell lymphomas and pulmonary adenomas, accompanied by extensive mutations in the c-myc protooncogene, confirming that AID can act as a bona fide oncogene when ectopically expressed (Okazaki, I. M., et al., (2003) J Exp Med, 197, 1173-81,). Hence, the oncogenic effect of AID appears to be attributable to loss of regulation over a “normal” DNA mutase activity, as a consequence of over-expression of AID isoforms with altered function, or defects in cofactors involved in determining specificity of SHM targeting. The consequence is genome-wide mutagenesis contributing to rapid accumulation of multiple oncogenic hits, resulting in accelerated tumor progression. Therefore, selectively disabling the deaminase activity of AID in neoplastic cells using a cytidine deaminase inhibitor is a useful therapeutic strategy.
Another ARP of immediate medical relevance is hsCEM15/APOBEC-3G (Table 1), which has been described as a broad antiviral agent that reduces the infectivity of the human lentivirus, HIV-1 (Mangeat, B., et al., 2003, Nature 424, 99-103). The virus contains a 10-kb single-stranded, positive-sense RNA genome that encodes three major classes of gene products. One class known as “auxiliary” proteins (Vpr, Vif, Vpu, Nef) are not required for efficient virus replication in at least some settings in cell culture. One of these proteins, Vif (virion infectivity factor), is required for efficient virus replication in vivo, as well as in certain host cell types in vitro (Fisher, A. G., et al., (1987) Science, 237:888-93; Strebel, K., et al., (1987) Nature, 328:728-30), because of its ability to overcome the action of a cellular antiviral system (Simon, J. H., et al., (1998) Nat Med, 4, 1397-400; Madani, N. and D. Kabat, (1998) J Virol, 72, :10251-5).
The in vitro replicative phenotype of vif-deleted molecular clones of HIV-1 is strikingly different in vif-permissive cells (such as 293T cells, and the SUPT1 and CEM-SS T cell lines), as compared to vif-non-permissive cells (such as primary T cells and macrophages). In the former cells, vif-deleted HIV-1 clones replicate with an efficiency that is essentially identical to that of wild-type virus, whereas in the latter cells, replication of vif-negative HIV-1 mutants is arrested due to a failure to accumulate reverse transcripts and to generate infectious proviral integrants in the host cell (Courcoul, M., et al., (1995) J Virol, 69, :2068-74; Simon, J. H. and M. H. Malim, (1996) J Virol, 70, 5297-305; von Schwedler, U., et al., (1993) J Virol, 67, 4945-55; Sova, P. and D. J. Volsky (1993) J Virol, 67, 6322-6). These defects are due to the expression of host cell protein CEM15 in vif-non-permissive cells (Sheehy, A. M., et al., (2002) Nature, 418, 646-50). The instability of viral reverse transcripts in vif-non-permissive cells in the absence of Vif, and the fact that both Vif and CEM15 are present in HIV-1 virions (Sheehy, A. M., et al., (2002) Nature, 418, 646-50; Camaur, D. (1996) J Virol, 70, 6106-11; Liu, H., et al., (1995) J Virol, 69, 7630-8), strongly suggests that the CEM15 antiviral activity may be derived from effects on viral RNA or reverse transcripts (viral DNA). This HIV RNA/DNA modification hypothesis is the most likely explanation for the CEM15 effect on viral infectivity. Due to the “broad” anti-viral activity described for CEM15, cytidine deaminase inhibitors can be used in the context of retroviral-based expression of exogenous nucleic acids.
The reason(s) for the modest success of retroviral mediated delivery of gene therapy (Chang, L. J. and E. E. Gay, (2001) Curr Gene Ther, 1, 237-51) can be at least in part due to the activity of enzymes like CEM15. It is likely that editing enzymes in general act to prevent retroviral infection through the body. ARPs and Adenosine Deaminase active on RNA (ADRA1 and ADAR2) are selectively expressed tissues and regions within tissues (Barbon, A. et al. (2003) Brain Res. Mol Brain Res. 117, 168-78; Sowden et al., (2000) J. Cell Sci. 115, 1027-39, herein incorporated by reference in their entireties). Each enzyme requires a unique flanking sequence context for cytidine, deoxycytidine or adenosine editing. CEM15 (Zhang et al., (2003) Nature 424, 94-8; Lecossier et al., Science 300, 1112) and ADAR1 (George, C. X. & Samuel, C. E. (1999) PNAS USA 96, 4621-26; Jayan, G. C. & Casey, J. I. (2002) J. Virol. 76, 12399-404, Casey, J. L. (2002) J. Virol. 76, 7385-97, herein incorporated by reference in their entireties) use target sequence and RNA secondary structure to edit viral RNA and DNA. Inactivating CEM15, ADARs or other ARPs with cytidine deaminase inhibitors can be used to selectively inhibit editing in tissues where these enzymes are expressed while allowing enzymes that were not targeted with cytidine deaminase inhibitors to remain active in other tissues. Tissues in which cytidine deaminase inhibitor therapy inactivated editing enzymes are not be able to edit retrovirus and thereby become more susceptible to gene therapy, whereas all other tissues are refractory to retroviral infection because their editing enzymes does not interact with the cytidine deaminase inhibitors and therefore remain active to modify and inactive the retroviral genome and transgenes. Cytidine deaminase inhibitor and retrovirus vectors are used in combination to not only enhance the efficiency of gene delivery but also enable retroviral delivery which are used tissue specifically.
The results of x-ray crystallographic structural studies and comparative modeling show that the overall molecular architecture and enzyme active sites of cytidine deaminases share common features that enable binding and activity on large nucleic acid substrates. Furthermore, these active sites are susceptible to inhibition by cytidine deaminase inhibitors that target all related enzymes indiscriminately. Therefore, embedding the cytidine deaminase inhibitor within specific polynucleotide target sequences preferred by each respective cytidine deaminase causes selective inhibition of the cytidine deaminase. In this context, it is possible to direct inhibition of only selected cytidine deaminase activities. The large size of the embedded cytidine deaminase inhibitor precludes interaction and cytotoxicity associated with many cytidine deaminases involved in pyrimidine metabolism.
DEFINITIONS
As used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an inhibitor” includes mixtures of the inhibitors.
Ranges may be expressed herein as from “about” one particular value, and/or to “about” another particular value. When such a range is expressed, another embodiment includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another embodiment. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint.
In this specification and in the claims which follow, reference will be made to a number of terms which shall be defined to have the following meanings:
“Optional” or “optionally” means that the subsequently described event or circumstance may or may not occur, and that the description includes instances where said event or circumstance occurs and instances where it does not.
Ranges may be expressed herein as from “about” one particular value, and/or to “about” another particular value. When such a range is expressed, another aspect includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another aspect. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint.
References in the specification and concluding claims to parts by weight of a particular element or component in a composition or article, denotes the weight relationship between the element or component and any other elements or components in the composition or article for which a part by weight is expressed. Thus, in a compound containing 2 parts by weight of component X and 5 parts by weight component Y, X and Y are present at a weight ratio of 2:5, and are present in such ratio regardless of whether additional components are contained in the compound.
A weight percent of a component, unless specifically stated to the contrary, is based on the total weight of the formulation or composition in which the component is included.
The terms “higher,” “increases,” “elevates,” “enhances,” or “elevation” refer to increases above basal levels, e.g., as compared to a control. The terms “low,” “lower,” “reduces,” “suppresses” or “reduction” refer to decreases below basal levels, e.g., as compared to a control. For example, basal levels are normal in vivo levels prior to, or in the absence of, or addition of an agent such as a cytidine deaminase inhibitor or another molecule or ligand.
The term “test compound” is defined as any compound to be tested for its ability (efficacy) to inhibit a cytidine deaminase molecule or a deoxycytidine deaminase molecule. Also, “test compounds” include drugs, molecules, and compounds that come from combinatorial libraries where thousands of such ligands are screened by drug class.
By “subject” is meant an individual. Preferably, the subject is a mammal such as a primate, and, more preferably, a human. The term “subject” can include domesticated animals, such as cats, dogs, etc., livestock (e.g., cattle, horses, pigs, sheep, goats, etc.), and laboratory animals (e.g., mouse, rabbit, rat, guinea pig, etc.).
The terms “control levels” or “control cells” are defined as the standard by which a change is measured, for example, the controls are not subjected to the experiment, but are instead subjected to a defined set of parameters, or the controls are based on pre- or post-treatment levels.
By “contacting” is meant an instance of exposure by close physical contact of at least one substance to another substance. For example, contacting can include contacting a substance, such as a pharmacologic agent, with a cell. A cell can be contacted with a test compound, for example, a cytidine deaminase inhibitor, or putative cytidine deaminase inhibitor by adding the agent to the culture medium (by continuous infusion, by bolus delivery, or by changing the medium to a medium that contains the agent) or by adding the agent to the extracellular fluid in vivo (by local delivery, systemic delivery, intravenous injection, bolus delivery, or continuous infusion). The duration of contact with a cell or group of cells is determined by the time the test compound is present at physiologically effective levels or at presumed physiologically effective levels in the medium or extracellular fluid bathing the cell.
“Treatment” or “treating” means to administer a composition to a subject or a system with an undesired condition or at risk for the condition. The condition can include a disease or a predisposition to a disease. The effect of the administration of the composition to the subject can have the effect of but is not limited to reducing or preventing the symptoms of the condition, a reduction in the severity of the condition, or the complete ablation of the condition.
By “effective amount” is meant a therapeutic amount needed to achieve the desired result or results, e.g., inhibiting editing of nucleic acids, interrupting selective cytidine deaminase activity, reducing viral production or infectivity, inhibiting class switch recombination, inhibiting somatic hypermutation, enhancing or blunting physiological functions, enhancing viral vector therapy, altering the qualitative or quantitative nature of the proteins expressed by cell or tissues, and eliminating or reducing disease causing molecules and/or the mRNA or DNA that encodes them, etc.
Herein, “inhibition” or “suppression” means to reduce activity as compared to a control (e.g., basal activity in the absence of such inhibition). It is understood that inhibition or suppression can mean a slight reduction in activity to the complete ablation of all activity. An “inhibitor” or “suppressor” can be anything that reduces the targeted activity. For example, suppression of CEM15 by a cytidine deaminase inhibitor can be determined by assaying the amount of CEM15 activity in the presence of the cytidine deaminase inhibitor to the amount of CEM15 activity in the absence of the cytidine deaminase inhibitor. In this example, if the amount of CEM15 activity is decreased in the presence of the context dependent inhibitor as compared to the amount of CEM15 activity in the absence of the context dependent inhibitor, the cytidine deaminase inhibitor can be said to suppress CEM15 activity.
Methods disclosed herein may refer to “systems.” It is understood that systems can be, for example, cells, columns, or batch processing containers (e.g., culture plates). A system is a set of components, any set of components that allows for the steps of the method to performed. Typically a system will comprise one or more components, such as a protein(s) or reagent(s). One type of system disclosed would be a cell that comprises both a cytidine deaminase and a cytidine deaminase inhibitor, for example. Another type of system would be one that comprises a cell (e.g., a cancer cell). A third type of system might be a chromatography column that has CEM15, AID, or other deaminase or putative deaminase, bound to the column.
“Context dependent inhibitor” or cytidine deaminase inhibitor means any inhibitor found within the context of a polymeric substrate that has a targeting function. The polymeric substrate can be a nucleic acid, but it is not limited to such molecules.
A “cytidine deaminase-positive cell” means any cell that expresses one or more cytidine deaminases or deoxycytidine deaminases. Such expression can be naturally occurring or the cell can include an exogenous nucleic acid that encodes one or more selected deaminases.
By “polymeric substrate” is meant a nucleic acid sequence into which the cytidine deaminase inhibitor has been incorporated. The polymeric substrate of the cytidine deaminase inhibitor can comprise an oligonucleotide or a polynucleotide, for example. The nucleic acid sequence can be 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 or more residues in length. Also, the nucleic acid sequence can be an RNA or a DNA sequence, can comprise naturally occurring or non-naturally occurring nucleotides, and can comprise double or single stranded sequences. A double stranded sequence can comprise a single stranded region such as a replication bubble, but is not limited to such duplex structures. Double-stranded need not imply Watson-Crick base pairing interactions as the sole feature that holds the two-stranded molecule together (e.g. there can be non-base-paired as well as base paired regions etc).
Variables such as R1-R10, W, X1, X2, Y, and Z used throughout the application are the same variables as previously defined unless stated to the contrary.
The term “alkyl group” as used herein is a branched or unbranched saturated hydrocarbon group of 1 to 24 carbon atoms, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, t-butyl, pentyl, hexyl, heptyl, octyl, decyl, tetradecyl, hexadecyl, eicosyl, tetracosyl and the like. A “lower alkyl” group is an alkyl group containing from one to six carbon atoms.
The term “alkenyl group” is defined as a hydrocarbon group of 2 to 24 carbon atoms and structural formula containing at least one carbon-carbon double bond.
The term “alkynyl group” is defined as a hydrocarbon group of 2 to 24 carbon atoms and a structural formula containing at least one carbon-carbon triple bond.
The term “halogenated alkyl group” is defined as an alkyl, alkenyl, or alkynyl group as defined above with one or more hydrogen atoms present on these groups substituted with a halogen (F, Cl, Br, I).
The term “cycloalkyl group” is defined as a non-aromatic carbon-based ring composed of at least three carbon atoms. Examples of cycloalkyl groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, etc. The term “heterocycloalkyl group” is a cycloalkyl group as defined above where at least one of the carbon atoms of the ring is substituted with a heteroatom such as, but not limited to, nitrogen, oxygen, sulphur, or phosphorous.
The term “aryl group” as used herein is any carbon-based aromatic group including, but not limited to, benzene, naphthalene, etc. The term “aromatic” also includes “heteroaryl group,” which is defined as an aromatic group that has at least one heteroatom incorporated within the ring of the aromatic group. Examples of heteroatoms include, but are not limited to, nitrogen, oxygen, sulfur, and phosphorus. The aryl group can be substituted or unsubstituted. The aryl group can be substituted with one or more groups including, but not limited to, alkyl, alkynyl, alkenyl, aryl, halide, nitro, amino, ester, ketone, aldehyde, hydroxy, carboxylic acid, or alkoxy.
The term “aralkyl” is defined as an aryl group having an alkyl, alkynyl, or alkenyl group as defined above attached to the aromatic group. An example of an aralkyl group is a benzyl group.
The term “amine group” is represented by the formula —NRR′, where R and R′ can be, independently, hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, or heterocycloalkyl group described above.
The term “amide group” is represented by the formula —C(O)NRR′, where R and R′ can be hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, or heterocycloalkyl group described above.
The term “ester” is represented by the formula —OC(O)R, where R can be an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, or heterocycloalkyl group described above.
The term “hydroxyl group” is represented by the formula —OH. The term “alkoxy group” is represented by the formula —OR, where R can be an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, or heterocycloalkyl group described above.
The term “aldehyde” is represented by the formula —C(O)H.
The term “keto group” is represented by the formula —C(O)R, where R is an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, or heterocycloalkyl group described above.
The term “acyl” is represented by the formula —OC(O)R, where R is hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, or heterocycloalkyl group described above.
The term “sulfone” is represented by the formula —S(O)2R, where R is hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, or heterocycloalkyl group described above.
The term “halo” is defined as F, Cl, Br, or I.
The term “monophosphate” (or monophosphoryl) is represented by the formula (RO)2(O)PO—, where each R can be, independently, hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, heterocycloalkyl group as described above, or the salt thereof.
The term “diphosphate” (or diphosphoryl) is a double phosphoanhydride bond represented by the formula (RO)2(O)P—O—P(O)(OR)O—, where each R can be, independently, hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, heterocycloalkyl group as described above, or the salt thereof.
The term “triphosphate” (or triphosphoryl) is a triple phosphoanhydride bond represented by the formula (RO)2(O)P—O—P(O)(OR)O—P(O)(OR)O—, where each R can be, independently, hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, heterocycloalkyl group as described above, or the salt thereof.
The term “phosphorothioate” is a P—S bond represented by the formula (RO)2(SR)PO—, where S is a sulfur (and can be a thiolate), and each R can be, independently, hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, heterocycloalkyl group as described above, or the salt thereof.
The term “phosphoroamidate” is a P—N bond represented by the formula (RO)2(NRR′)PO—, where each R and R′ can be, independently, hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, heterocycloalkyl group as described above, or the salt thereof.
The term “phosphonate” is a P—C bond represented by the formula (RO)2(CRR′)PO—, where each R and R′ can be, independently, hydrogen, an alkyl, alkenyl, alkynyl, aryl, aralkyl, cycloalkyl, halogenated alkyl, heterocycloalkyl group as described above, or the salt thereof.
A 2′-5′ (2′-to-5′) phosphodiester linkage is a phosphoanhydride linkage between the 2′-oxygen of the nucleotide ribose sugar and the 5′-phosphorus of the flanking nucleotide. This bond is chemically distant from the typical 3′-5′ phosphodiester bond observed in cellular (natural) DNA or RNA synthesis via polymerase enzymes. The linkage is resistant to cellular degradation enzymes.
R1-R10, W, X1, X2, Y, and Z can, independently, possess two or more of the groups listed above. For example, if R1 is a straight chain alkyl group, one of the hydrogen atoms of the alkyl group can be substituted with a hydroxyl group, an alkoxy group, etc. Depending upon the groups that are selected, a first group may be incorporated within second group or, alternatively, the first group may be pendant (i.e., attached) to the second group. For example, with the phrase “an alkyl group comprising an ester group,” the ester group may be incorporated within the backbone of alkyl group. Alternatively, the ester can be attached to the backbone of the alkyl group. The nature of the group(s) that is (are) selected will determine if the first group is embedded or attached to the second group.
Disclosed are compounds, compositions, and components that can be used for, can be used in conjunction with, can be used in preparation of, or are products of the disclosed methods and compositions. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combinations and permutation of these compounds may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a number of different nucleosides and polymeric substrates are disclosed and discussed, each and every combination and permutation of the nucleoside and the polymeric substrate are specifically contemplated unless specifically indicated to the contrary. Thus, if a class of molecules A, B, and C are disclosed as well as a class of molecules D, E, and F, and an example of a combination molecule, A-D is disclosed, then even if each is not individually recited, each is individually and collectively contemplated. Thus, in this example, each of the combinations A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C—F are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. Likewise, any subset or combination of these is also specifically contemplated and disclosed. Thus, for example, the sub-group of A-E, B-F, and C-E are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. This concept applies to all aspects of this disclosure including, but not limited to, steps in methods of making and using the disclosed compositions. Thus, if there are a variety of additional steps that can be performed it is understood that each of these additional steps can be performed with any specific embodiment or combination of embodiments of the disclosed methods, and that each such combination is specifically contemplated and should be considered disclosed.
Compounds and Compositions
Cytidine deaminases are a class of enzymes involved in pyrimidine metabolism. The mechanism for cytidine deaminase activity involves nucleophilic attack at the C4 position of the cytosine ring by water coordinated to Zn2+, where the zinc ion is bound to the enzyme. Thus, any nucleoside susceptible to nucleophilic attack or one that mimics the tetrahedral sp3 geometry of the intermediate (but need not be chemically reactive) can be used in any of the methods described herein as a component of a cytidine deaminase inhibitor. In one aspect, one or more cytidine deaminase inhibitors can be used in the polymeric substrate to inhibit cytidine deaminases.
The C4 position of cytosine is a sp2 carbon center, which is susceptible to nucleophilic attack by the enzyme. In one aspect, the cytidine deaminase inhibitor used herein is a nucleoside comprising a sp2 carbon center susceptible to nucleophilic attack giving rise to the enzyme's preferred sp3 intermediate. Methods for making a compound susceptible to nucleophilic attack and those whose geometry are preferred by the enzyme are known in the art. For example, attaching an electron-withdrawing group on the atom where nucleophilic attack is desired can be performed. As used herein, the term “electron-withdrawing group” is defined as any group that makes a compound more susceptible to nucleophilic when compared to the same compound that does not contain the electron-withdrawing group. In one aspect, the cytidine deaminase inhibitor is a nucleoside comprising a sp2 carbon center with an electron-withdrawing group attached to the sp2 carbon center. Examples of electron-withdrawing groups include, but are not limited to, a nitro group, a cyano group, an ester group, an aldehyde group, a keto group, a sulfone group, a carbonyl group, an imino group, an alkenyl, an amide group, a hydroxyl group, or a combination thereof. Two or more electron-withdrawing groups can be used in combination with one another. For example, the electron-withdrawing group can be an enol represented by the formula —C═C—OH, which is composed of an alkenyl group and a hydroxyl group. In this example, the enol can tautomerize to the corresponding keto compound —HC—C(O).
As described above, in one aspect, the cytidine deaminase inhibitor of cytidine deaminases described herein are susceptible to nucleophilic attack. In one aspect, the Cytidine deaminase inhibitor of cytidine deaminases are susceptible to nucleophilic attack by a metal-bound hydroxide such as, for example, zinc hydroxide.
In one aspect, the cytidine deaminase inhibitor of cytidine deaminases (or its family members the adenosine deaminases acting on RNA or ADARs, including those with activity on mRNA, tRNA or rRNA) used herein comprise a purine or pyrimidine. The terms “purine” and “pyrimidine” include any natural and non-natural purines and pyrimidines. When the Cytidine deaminase inhibitor of cytidine deaminases comprise a pyrimidine, nucleophilic attack can occur at the C4 position by the cytidine deaminase. Likewise, when the cytidine deaminase inhibitor of cytidine deaminases comprise a purine, nucleophilic attack can occur at the C6 position of the purine by the cytidine deaminase. In order to enhance nucleophilic attack at these positions, one or more electron-withdrawing groups can be placed at the C4 position of the pyrimidine or C6 position of the purine. However, the cytidine deaminase inhibitor can function by simply mimicking the sp3 intermediate at the C4 or C6 positions of pyrimidine or purine bases.
In one aspect, any of the nucleosides described herein are provided as the indicated enantiomer and substantially in the absence of its corresponding enantiomer (i.e., in enantiomerically enriched form). As used herein, the term “enantiomerically pure” refers to a nucleoside composition that includes at least approximately 95%, and preferably approximately 97%, 98%, 99%, or 100% of a single enantiomer of that nucleoside. In one aspect, the nucleoside is the naturally occurring D-enantiomer or the L-enantiomer.
In one aspect, the cytidine deaminase inhibitor of cytidine deaminases includes a nucleoside having the formula I or II




wherein

    
    
        R1, R2, and R3 can be, independently, hydrogen, hydroxyl, alkoxy, halo, alkyl, acyl, aryl, aralkyl, monophosphate, diphosphate, triphosphate, phosphorothioate, phosphoramidate, phosphonate, or a 2′-5′ phosphodiester linkage, N3, NR4R5, NO2, NOR6, CN, —C(O)NH2, SH, —S-alkyl, —S-aryl, Se-alkyl, Se-aryl, or a residue of the polymeric substrate, wherein at least one of R2 or R3 is hydroxyl;
        X1, X2, and Y can be, independently, hydrogen, hydroxyl, alkoxy, alkyl, acyl, aryl, aralkyl, NR4R5, or an electron-withdrawing group;
        wherein R4, R5, and R6 can be, independently, alkyl, aryl, aralkyl, alkaryl, acyl, or hydrogen; and
        Z can be nitrogen or CR7, wherein R7 is hydrogen, hydroxyl, alkoxy, halo, alkyl, acyl, aryl, or aralkyl.
    
    


Any of the Cytidine deaminase inhibitors described herein can be incorporated in the polymeric substrate. By “incorporated into” is meant bracketed by (1) the polymeric substrate, (2) at either terminus (e.g. 5′ or 3′) of the polymeric substrate, or (3) a combination thereof. In one aspect, when the context-dependent cytidine deaminase inhibitor having the formula I or II is bracketed by the polymeric substrate, R1 and R2 are a residue of the polymeric substrate. In another aspect, when the cytidine deaminase inhibitor having the formula I or II is the terminus of the polymeric substrate, R1 or R2 is a residue of the polymeric substrate. The term “residue” as used in the specification and claims, refers to any moiety of the polymeric substrate including the moiety attached to any of the nucleosides described herein after the nucleoside has been incorporated (e.g., within the polymeric substrate or at the terminus or both) into the polymeric substrate.
In one aspect, X in formulae I and II is any of the electron-withdrawing groups described above. In one aspect, when the nucleoside is formula I, R2 is hydroxyl and R3 can be hydroxyl, halo, or alkoxy. In another aspect, when the nucleoside has the formula I, X1 can be halo such as fluoro, chloro, bromo, or iodo, and X2 is hydroxyl. In a further aspect, when the nucleoside is I, Z is CH. The nucleoside having the formula I can have any combination of these aspects.
In another aspect, when the nucleoside has formula II, R2 is hydroxyl and R3 can be hydroxyl, halo, or alkoxy. In a further aspect, when the nucleoside has the formula II, X1 can be hydrogen, hydroxyl, or NR4R5. In another aspect, when the nucleoside has the formula II, Y is hydrogen. In yet another aspect, when the nucleoside has the formula II, Z can be nitrogen or CR7, wherein R7 can be hydrogen or hydroxyl. When R7 is hydroxyl, the resulting enol can tautomerize to the keto form. The nucleoside having the formula II can have any combination of these aspects.
In another aspect, any of the nucleosides described herein has at least one group capable of hydrogen bonding in a manner similar to cytosine or uracil. In one aspect, R2 and/or R3 in formulae I-VII, where formulae III-VII are discussed below, is a hydroxyl group. Nucleosides having at least one group capable of hydrogen bonding increases the nucleoside's affinity for the cytidine deaminase.
Mechanistic studies have indicated that cytidine deaminases exhibit greater affinity for the tetrahedral intermediate (sp3) than the corresponding s center prior to nucleophilic attack. In one aspect, the nucleosides described herein have at least one stable sp center that mimics the intermediate at C4 or C6 of pyrimidine or purine. In a related aspect, a compound such as cacodylic acid also known as dimethyl arsenic acid ((CH3)2—As—O2H) mimics the sp3 geometry and can serve as a cytidine deaminase inhibitor as long as it is tethered to the flanking sequences at 5′ and 3′ termini. The group at C4 need not be carbon, and can be replaced by As in the latter instance. In another aspect, the nucleoside has at least one sp3 carbon center, wherein the sp3 carbon center has at least one —WR group, wherein W is O, S, Se, or NR, wherein R is hydrogen, alkyl, aryl, aralkyl, alkenyl, alkynyl, or acyl as described above. In a further aspect, when the nucleoside includes a pyrimidine or purine, the nucleoside comprises a sp3 carbon center at C4 of the pyrimidine or C6 of the purine.
In one aspect, the cytidine deaminase inhibitor includes a nucleoside having the formula III or IV




wherein

    
    
        R1, R2, and R3 can be, independently, hydrogen, hydroxyl, alkoxy, halo, alkyl, acyl, aryl, aralkyl, monophosphate, diphosphate, triphosphate, phosphorothioate, phosphoramidate, phosphonate, or a 2′-5′ phosphodiester linkage, N3, N4R5, NO2, NOR6, CN, —C(O)NH2, SH, —S-alkyl, —S-aryl, Se-alkyl, Se-aryl, or a residue of the polymeric substrate, wherein at least one of R2 or R3 is hydroxyl;
        X1, X2, and Y can be, independently, hydrogen, hydroxyl, alkoxy, alkyl, acyl, aryl, aralkyl, NR4R5, or an electron-withdrawing group;
        W can be O, S, Se, or NR10;
        wherein R4, R5, R6, R8, R9, and R10 can be, independently, alkyl, aryl, aralkyl, alkaryl, acyl, or hydrogen; and
        Z can be nitrogen or CR7, wherein R7 is hydrogen, hydroxyl, alkoxy, halo, alkyl, acyl, aryl, or aralkyl.
    
    


In one aspect, X1 and X2 in formulae III and IV can be any of the electron-withdrawing groups described above. In one aspect, when the nucleoside is formula III, R2 is hydroxyl and R3 can be hydroxyl, halo, or alkoxy. In another aspect, when the nucleoside has the formulae III or IV, X1 can be halo such as fluoro, chloro, bromo, or iodo, and X2 is hydroxyl. In a further aspect, when the nucleoside is III, Z is CH. The nucleoside having the formulae III or IV can have any combination of these aspects.
Examples of nucleosides useful in the methods described herein include, but are not limited to, any of the phosphoramidites (distinct from phosphoramidates) manufactured by Glen Research Corporation. In one aspect, the nucleoside can be

    5′-dimethoxytrityl-N-acetyl-2′-O-acetyl-cytisine arabinoside, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-benzoyl-adenosine, 2′-O-methyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-benzoyl-cytidine, 2-′O-methyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-acetyl-cytidine, 2-′O-methyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-dimethylaminomethylidene-guanosine, 2′-O-methyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-uridine, 2′-O-Me-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-phenoxyacetyl-2′-adenosine, 2′-O-methyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N2-isopropylphenoxyacetyl-2′-O-methyl-guanosine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-benzoyl-2′-adenosine, 2′-O-methyl-3′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-N-benzoyl-2′-cytidine, 2′-O-methyl-3′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-N-acetyl-cytidine, 2′-O-methyl-3′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-N-dimethylformamidine-guanosine, 2′-O-methyl-3′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-uridine, 2′-O-methyl-3′-succinoyl-long chain alkylamino-CPG
    N-(6-(O-dimethoxytrityl)-hexyl)-(2-carboxamide)-phthalimidyl-lcaa-CPG
    5′-dimethoxytrityl-N-acetyl-adenosine, 2′-O-acetyl-3′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-N-acetyl-cytidine, 2′-acetate-3′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-N-acetyl-guanosine, 2′-O-acetyl-3′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-inosine, 2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-4-(2-cyanoethylthio)-uridine, 2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-5-Methyl-uridine, 2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-acetyl-5-methyl-cytidine, 2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-acetyl-2′-deoxypurineriboside, 2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N2-(diacetyl)-2,6-diaminopurineriboside, 2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-5-bromo-uridine, 2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-5-iodo-uridine, 2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-[6-methyl-pyrrolo-[2,3-d]-pyrimidine-2(3H)-one]-2′-O-triisopropylsilyloxymethyl-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-O-methyl-2′-deoxythymidine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-monomethoxytritylamino-2′-deoxythymidine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-benzoyl-3′-deoxyadenosine, 2′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-N-benzoyl-3′-deoxycytosine, 2′-succinoyl-long chain alkylamino-CPG 500
    5′-dimethoxytrityl-N-dimethylformamidine-3′-deoxyguanosine, 2′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-3′-deoxythymidine, 2′-succinoyl-long chain alkylamino-CPG
    5′-dimethoxytrityl-N-succinoyl-long chain alkylamino-CPG, 2′,3′-deoxyCytosine
    N6-diisobutylaminomethylidene-2′,3′-dideoxyadenosine, 5′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    N4-diisobutylaminomethylidene-2′,3′-dideoxycytidine, 5′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    N2-dimethylaminomethylidene-2′,3′-dideoxyguanosine, 5′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    2′,3′-dideoxythymidine, 5′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-phenoxyacetyl-2′-deoxyadenosine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-acetyl-2′-deoxycytidine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-p-isopropyl-phenoxyacetyl-deoxyguanosine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-benzoyl-5-methyl-2′-deoxycytidine, 2′-succinoyl-long chain alkylamino-CPG 500
    5′-dimethoxytrityl-N2,N6-bis(diisobutylaminomethylidene)-2,6-diamino-2′-deoxypurineriboside-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N4-ethyl-2′-deoxycytidine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-benzoyl-2′-deoxyadenosine, 3′-[(methyl)-(N,N-diisopropyl)]-phosphonamidite
    5′-dimethoxytrityl-N-isobutyryl-2′-deoxycytidine, 3′-[(methyl)-(N,N-diisopropyl)]-phosphonamidite
    5′-dimethoxytrityl-N4-acetyl-2′-deoxycytidine, 3′-[(methyl)-(N,N-diisopropyl)]phosphonamidite
    5′-dimethoxytrityl-N-isobutyryl-2′-deoxyguanosine, 3′-[(methyl)-(N,N-diisopropyl)]-phosphonamidite
    5′-dimethoxytrityl-2′-deoxythymidine, 3′-[(methyl)-(N,N-diisopropyl)]-phosphonamidite
    5′-dimethoxytrityl-N-phenoxyacetyl-2′-deoxyadenosine, 3′-[methyl-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-acetyl-2′-deoxycytidine, 3′-[methyl-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-p-isopropyl-phenoxyacetyl-guanosine, 3′-[methyl-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-2′-deoxythymidine, 3′-[(O-methyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-dimethoxytrityl-N-benzoyl-2′-deoxyadenosine, 3′-H-phosphonate, TEA salt
    5′-dimethoxytrityl-N-benzoyl-2′-deoxycytidine, 3′-H-phosphonate, DBU salt
    5′-dimethoxytrityl-N-isobutyryl-2′-deoxyguanosine, 3′-H-phosphonate, TEA salt
    5′-dimethoxytrityl-2′-deoxythymidine, 3′-H-phosphonate, TEA salt
    5′-Dimethoxytrityl-5-methyl-pyrimidin-2-one-2′-deoxyriboside, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite (5-Me-2′-deoxyZebularine)
    5′-Dimethoxytrityl-2′-deoxyNebularine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite (5-Me-2′-deoxyNebularine)
    5′-Dimethoxytrityl-N-acetyl-deoxyCytidine, 2′-fluoro-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-Dimethoxytrityl-deoxyUridine, 2′-fluoro-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-Dimethoxytrityl-Uridine, 2′-methylseleno-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-Dimethoxytrityl-N-benzoyl-3′-deoxyAdenosine, 2′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-Dimethoxytrityl-N-benzoyl-3′-deoxyCytidine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-Dimethoxytrityl-N-dimethylformamidine-3′-deoxyGuanosine,
    3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-Dimethoxytrityl-3′-deoxyThymidine, 2′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
    5′-Dimethoxytrityl-N-acetyl-2′-O-acetyl-Cytisine Arabinoside,
    3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite


In another aspect, the nucleoside can be zebularine, 5-methylzebularine, 4-fluorozebularine, 2′-deoxy, 2′-fluorozebularine, nebularine, 8-azanebularine, coformycin, 3,4,5,6-tetrahydro-2′-deoxyuridine, 5-fluorozebularine, diazepinone riboside, or inosine.
Also described herein are nucleosides that, when incorporated into a polymeric substrate, can facilitate the inhibition of cytidine deaminases. In one aspect, nucleoside has the formula V




wherein

    
    
        R1, R2, and R3 can be, independently, hydrogen, hydroxyl, alkoxy, halo, alkyl, acyl, aryl, aralkyl, monophosphate, diphosphate, triphosphate, phosphorothioate, phosphoramidate, phosphonate, or a 2′-5′ phosphodiester linkage, N3, NR4R5, NO2, NOR6, CN, —C(O)NH2, SH, —S-alkyl, —S-aryl, Se-alkyl, or Se-aryl, wherein at least one of R2 or R3 is hydroxyl;
        wherein R4, R5, and R6 can be, independently, alkyl, aryl, aralkyl, alkaryl, acyl, or hydrogen;
        X1 and X2 can be electron-withdrawing groups, and
        Z can be nitrogen or CR7, wherein R7 can be hydrogen, hydroxyl, alkoxy, halo, alkyl, acyl, aryl, or aralkyl,

wherein the nucleoside is not uracil, thymine, cytosine, zebularine.

    
    


Any of the electron-withdrawing groups described above can be used in formula V. In one aspect, X1 and X2 can be a nitro group, a halo group such as fluoro, chloro, bromo, or iodo, a cyano group, an ester group, an aldehyde group, a keto group, a sulfone group, an amide group, an imino group, an alkenyl group, a hydroxyl group, or a combination thereof. In another aspect, R1 and R2 are hydroxyl, and R3 can be hydroxyl, halo, or alkoxy. In a further aspect, Z is CH. The nucleoside having the formula V can have any combination of these aspects. In one aspect, the nucleoside having the formula V is 4-fluorozebularine or 2′-deoxy, 2′-fluorozebularine.
In another aspect, the nucleoside has the formula VI or VII




wherein

    
    
        R1, R2, and R3 can be, independently, hydrogen, hydroxyl, alkoxy, halo, alkyl, acyl, aryl, aralkyl, monophosphate, diphosphate, triphosphate, phosphorothioate, phosphoramidate, phosphonate, or a 2′-5′ phosphodiester linkage, N3, NR4R5, NO2, NOR6, CN, —C(O)NH2, SH, —S-alkyl, —S-aryl, Se-alkyl, or Se-aryl, wherein at least one of R2 or R3 is hydroxyl;
        X1 and X2 can be electron-withdrawing groups;
        W can be O, S, Se, or NR10;
        wherein R4, R5, R6, R8, R9, and R10 can be, independently, alkyl, aryl, aralkyl, alkaryl, acyl, or hydrogen; and
        Z can be nitrogen or CR7, wherein R7 can be hydrogen, hydroxyl, alkoxy, halo, alkyl, acyl, aryl, or aralkyl.
    
    


The nucleosides having the formulas VI and VII can be readily prepared by reacting nucleosides having the formula I with a nucleophile. For example, a nucleoside having the formula I can be reacted with an alcohol (R10OH) or alkoxide (R10O−) to produce a nucleoside having the formula VI or VII. In one aspect, X1 and X2 in formulae VI and VII can be any of the electron-withdrawing groups described above. In one aspect, when the nucleoside is formula VI or VII, R2 is hydroxyl and R3 can be hydroxyl, halo, or alkoxy. In another aspect, when the nucleoside has the formula VI or VII, X1 or X2 can be halo such as fluoro, chloro, bromo, or iodo. In a further aspect, when the nucleoside is VI or VII, Z is CH. The nucleoside having the formula VI or VII can have any combination of these aspects.
Disclosed are cytidine deaminase inhibitors that can comprise a nucleoside as described above, incorporated in a polymeric substrate, wherein the polymeric substrate targets a cytidine deaminase. The polymeric substrate can comprise an oligonucleotide or a polynucleotide, and can be 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 or more residues in length. Particularly, the nucleic acid residues can comprise up to about 18 residues.
The nucleic acids of the cytidine deaminase inhibitor can be any length, particularly from about 2 to about 1000 residues, or any amount in between, from about 5 to about 500 residues, from about 10 to about 100 residues, or from about 15 to about 50 residues, or in particular about 18-20 residues. Large oligos can be made from smaller pieces joined together by 5′-I to 3′-phosphorothioate ligation as described by Y. Z. Xu and E. T. Kool, Tetrahedron Lett., 1997, 38, 5595-5598, herein incorporated in its entirety by reference.
The nucleic acids of the cytidine deaminase inhibitor can comprise RNA residues from a single stranded RNA, a double stranded RNA, or a single stranded replication bubble. Alternatively, the nucleic acids also comprise DNA residues. The DNA residues can form a single stranded DNA, a double stranded DNA, or a single stranded replication bubble. Furthermore, the nucleic acids of the cytidine deaminase inhibitor can comprise stretches of RNA and DNA alternating on the same strand of a single stranded oligonucleotide, or on double strands. Furthermore, in a double stranded oligonucleotide, one strand can comprise RNA, while the other comprises DNA.
Optimally, the targeted cytidine deaminase can be APOBEC-1, which is encoded by the following nucleic acid sequence:








(SEQ ID NO: 2)











gatcccagag gaggaagtcc agagacagag caccatgact




 



tctgagaaag gagaagaatc gaaccctggg agtttgacgt



 



cttctatgac cccagagaac ttcgtaaaga ggcctgtctg



 



ctctacgaaa tcaagtgggg catgagccgg aagatctggc



 



gaagctcagg caaaaacacc accaatcacg tggaagttaa



 



ttttataaaa aaatttacgt cagaaagaga ttttcaccca



 



tccatcagct gctccatcac ctggttcttg tcctggagtc



 



cctgctggga atgctcccag gctattagag agtttctgag



 



tcggcaccct ggtgtgactc tagtgatcta cgtagctcgg



 



cttttttggc acatggatca acaaaatcgg caaggtctca



 



gggaccttgt taacagtgga gtaactattc agattatgag



 



agcatcagag tattatcact gctggaggaa ttttgtcaac



 



tacccacctg gggatgaagc tcactggcca caatacccac



 



ctctgtggat gatgttgtac gcactggagc tgcactgcat



 



aattctaagt cttccaccct gtttaaagat ttcaagaaga



 



tggcaaaatc atcttacatt tttcagactt catcttcaaa



 



actgccatta ccaaacgatt ccgccacaca tccttttagc



 



tacagggctg atacatcctt ctgtggcttg gagatgaata



 



ggatgattcc gtgtgtgtac tgattcaaga acaagcaatg



 



atgacccact aaagagtgaa tgccatttag aatctagaaa



 



tgttcacaag gtaccccaaa actctgtagc ttaaaccaac



 



aataaatatg tattacctct ggc






The targeted cytidine deaminase of the cytidine deaminase inhibitor can also be an APOBEC-related protein, such as AID. The full length nucleic acid sequence that encodes AID is:








(SEQ ID NO: 6)











atggacagcc tcttgatgaa ccggaggaag tttctttacc




 



aattcaaaaa tgtccgctgg gctaagggtc ggcgtgagac



 



ctacctgtgc tacgtagtga agaggcgtga cagtgctaca



 



tccttttcac tggactttgg ttatcttcgc aataagaacg



 



gctgccacgt ggaattgctc ttcctccgct acatctcgga



 



ctgggaccta gaccctggcc gctgctaccg cgtcacctgg



 



ttcacctcct ggagcccctg ctacgactgt gcccgacatg



 



tggccgactt tctgcgaggg aaccccaacc tcagtctgag



 



gatcttcacc gcgcgcctct acttctgtga ggaccgcaag



 



gctgagcccg aggggctgcg gcggctgcac cgcgccgggg



 



tgcaaatagc catcatgacc ttcaaagatt atttttactg



 



ctggaatact tttgtagaaa accatgaaag aactttcaaa



 



gcctgggaag ggctgcatga aaattcagtt cgtctctcca



 



gacagcttcg gcgcatcctt ttgcccctgt atgaggttga



 



tgacttacga gacgcatttc gtactttggg actttga






The cytidine deaminase inhibitor for AID can comprise WRZY (SEQ ID NO: 7),
wherein W is A or T, wherein R is a purine, wherein Z is the nucleoside, and wherein Y is a pyrimidine.
The cytidine deaminase inhibitor can also be directed towards CEM15. The full length nucleic acid that encodes CEM15 (APOBEC-3G) is represented by:








(SEQ ID NO: 10)









ctgccagggggagggccccagagaaaaccagaaagagggtgagagactga



 


ggaagataaagcgtcccagggcctcctacaccagcgcctgagcaggaagc


 


gggaggggccatgactacgaggccctgggaggtcactttagggagggctg


 


tcctaaaaccagaagcttggagcagaaagtgaaaccctggtgctccagac


 


aaagatcttagtcgggactagccggccaaggatgaagcctcacttcagaa


 


acacagtggagcgaatgtatcgagacacattctcctacaacttttataat


 


agacccatcctttctcgtcggaataccgtctggctgtgctacgaagtgaa


 


aacaaagggtccctcaaggccccctttggacgcaaagatctttcgaggcc


 


aggtgtattccgaacttaagtaccacccagagatgagattcttccactgg


 


ttcagcaagtggaggaagctgcatcgtgaccaggagtatgaggtcacctg


 


gtacatatcctggagcccctgcacaaagtgtacaagggatatggccacgt


 


tcctggccgaggacccgaaggttaccctgaccatcttcgttgcccgcctc


 


tactacttctgggacccagattaccaggaggcgcttcgcagcctgtgtca


 


gaaaagagacggtccgcgtgccaccatgaagatcatgaattatgacgaat


 


ttcagcactgttggagcaagttcgtgtacagccaaagagagctatttgag


 


ccttggaataatctgcctaaatattatatattactgcacatcatgctggg


 


ggagattctcagacactcgatggatccacccacattcactttcaacttta


 


acaatgaaccttgggtcagaggacggcatgagacttacctgtgttatgag


 


gtggagcgcatgcacaatgacacctgggtcctgctgaaccagcgcagggg


 


ctttctatgcaaccaggctccacataaacacggtttccttgaaggccgcc


 


atgcagagctgtgcttcctggacgtgattcccttttggaagctggacctg


 


gaccaggactacagggttacctgcttcacctcctggagcccctgcttcag


 


ctgtgcccaggaaatggctaaattcatttcaaaaaacaaacacgtgagcc


 


tgtgcatcttcactgcccgcatctatgatgatcaaggaagatgtcaggag


 


gggctgcgcaccctggccgaggctggggccaaaatttcaataatgacata


 


cagtgaatttaagcactgctgggacacctttgtggaccaccagggatgtc


 


ccttccagccctgggatggactagatgagcacagccaagacctgagtggg


 


aggctgcgggccattctccagaatcaggaaaactgaaggatgggcctcag


 


tctctaaggaaggcagagacctgggttgagcctcagaataaaagatcttc


 


ttccaagaaatgcaaacaggctgttcaccaccatctccagctgatcacag


 


acaccagcaaagcaatgcactcctgaccaagtagattcttttaaaaatta


 


gagtgcattactttgaatcaaaaatttatttatatttcaagaataaagta


 


ctaagattgtgctcaatacacagaaaagtttcaaacctactaatccagcg


 


acaatttgaatcggttttgtaggtagaggaataaaatgaaatactaaatc


 


tttctgtaaaaaaaaaa






Representative sequences recognized by CEM15 include first strand DNA or portions thereof, including ten or more sequences comprising those produced by reverse transcription from HIV-1:








(SEQ ID NO: 4)









ggtctctctggttagaccagatttgagcctgggagctctctggctaacta



 


gggaacccactgcttaagcctcaataaagcttgccttgagtgcttcaagt


 


agtgtgtgcccgtctgttgtgtgactctggtaactagagatccctcagac


 


ccttttagtcagtgtggaaaatctctagcagtggcgcccgaacagggact


 


tgaaagcgaaagggaaaccagaggagctctctcgacgcaggactcggctt


 


gctgaagcgcgcacggcaagaggcgaggggaggcgactggtgagtacgcc


 


aaaaattttgactagcggaggctagaaggagagagatgggtgcgagagcg


 


tcagtattaagcgggggagaattagatcgatgggaaaaaattcggttaag


 


gccagggggaaagaaaaaatataaattaaaacatatagtatgggcaagca


 


gggagctagaacgattcgcagttaatcctggcctgttagaaacatcagaa


 


ggctgtagacaaatactgggacagctacaaccatcccttcagacaggatc


 


agaagaacttagatcattatataatacagtagcaaccctctattgtgtgc


 


atcaaaggatagagataaaagacaccaaggaagctttagacaagatagag


 


gaagagcaaaacaaaagtaagaaaaaagcacagcaagcagcagctgacac


 


aggacacagcagccaggtcagccaaaattaccctatagtgcagaacatcc


 


aggggcaaatggtacatcaggccatatcacctagaactttaaatgcatgg


 


gtaaaagtagtagaagagaaggctttcagcccagaagtgatacccatgtt


 


ttcagcattatcagaaggagccaccccacaagatttaaacaccatgctaa


 


acacagtggggggacatcaagcagccatgcaaatgttaaaagagaccatc


 


aatgaggaagctgcagaatgggatagagtgcatccagtgcatgcagggcc


 


tattgcaccaggccagatgagagaaccaaggggaagtgacatagcaggaa


 


ctactagtacccttcaggaacaaataggatggatgacaaataatccacct


 


atcccagtaggagaaatttataaaagatggataatcctgggattaaataa


 


aatagtaagaatgtatagccctaccagcattctggacataagacaaggac


 


caaaagaaccctttagagactatgtagaccggttctataaaactctaaga


 


gccgagcaagcttcacaggaggtaaaaaattggatgacagaaaccttgtt


 


ggtccaaaatgcgaacccagattgtaagactattttaaaagcattgggac


 


cagcagctacactagaagaaatgatgacagcatgtcagggagtgggagga


 


cccggccataaggcaagagttttggctgaagcaatgagccaagtaacaaa


 


ttcagctaccataatgatgcaaagaggcaattttaggaaccaaagaaaga


 


ttgttaagtgtttcaattgtggcaaagaagggcacatagccagaaattgc


 


agggcccctaggaaaaagggctgttggaaatgtggaaaggaaggacacca


 


aatgaaagattgtactgagagacaggctaattttttagggaagatctggc


 


cttcctacaagggaaggccagggaattttcttcagagcagaccagagcca


 


acagccccaccatttcttcagagcagaccagagccaacagccccaccaga


 


agagagcttcaggtctggggtagagacaacaactccctctcagaagcagg


 


agccgatagacaaggaactgtatcctttaacttccctcagatcactcttt


 


ggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagct


 


ctattagatacaggagcagatgatacagtattagaagaaatgagtttgcc


 


aggaagatggaaaccaaaaatgatagggggaattggaggttttatcaaag


 


taagacagtatgatcagatactcatagaaatctgtggacataaagctata


 


ggtacagtattagtaggacctacacctgtcaacataattggaagaaatct


 


gttgactcagattggttgcactttaaattttcccattagtcctattgaaa


 


ctgtaccagtaaaattaaagccaggaatggatggcccaaaagttaaacaa


 


tggccattgacagaagaaaaaataaaagcattagtagaaatttgtacaga


 


aatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccataca


 


atactccagtatttgccataaagaaaaaagacagtactaaatggagaaaa


 


ttagtagatttcagagaacttaataagagaactcaagacttctgggaagt


 


tcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaa


 


cagtactggatgtgggtgatgcatatttttcagttcccttagatgaagac


 


ttcaggaagtatactgcatttaccatacctagtataaacaatgagacacc


 


agggattagatatcagtacaatgtgcttccacagggatggaaaggatcac


 


cagcaatattccaaagtagcatgacaaaaatcttagagccttttagaaaa


 


caaaatccagacatagttatctatcaatacatggatgatttgtatgtagg


 


atctgacttagaaatagggcagcatagaacaaaaatagaggagctgagac


 


aacatctgttgaggtggggacttaccacaccagacaaaaaacatcagaaa


 


gaacctccattcctttggatgggttatgaactccatcctgataaatggac


 


agtacagcctatagtgctgccagaaaaagacagctggactgtcaatgaca


 


tacagaagttagtgggaaaattgaattgggcaagtcagatttacccaggg


 


attaaagtaaggcaattatgtaaactccttagaggaaccaaagcactaac


 


agaagtaataccactaacagaagaagcagagctagaactggcagaaaaca


 


gagagattctaaaagaaccagtacatggagtgtattatgacccatcaaaa


 


gacttaatagcagaaatacagaagcaggggcaaggccaatggacatatca


 


aatttatcaagagccatttaaaaatctgaaaacaggaaaatatgcaagaa


 


cgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaa


 


aaaataaccacagaaagcatagtaatatggggaaagactcctaaatttaa


 


actacccatacaaaaggaaacatgggaaacatggtggacagagtattggc


 


aagccacctggattcctgagtgggagtttgtcaatacccctcctttagtg


 


aaattatggtaccagttagagaaagaacccatagtaggagcagaaacgtt


 


ctatgtagatggggcagctagcagggagactaaattaggaaaagcaggat


 


atgttactaatagaggaagacaaaaagttgtcaccctaactgacacaaca


 


aatcagaagactgagttacaagcaattcatctagctttgcaggattcggg


 


attagaagtaaatatagtaacagactcacaatatgcattaggaatcattc


 


aagcacaaccagataaaagtgaatcagagttagtcaatcaaataatagag


 


cagttaataaaaaaggaaaaggtctatctggcatgggtaccagcacacaa


 


aggaattggaggaaatgaacaagtagataaattagtcagtgctggaatca


 


ggaaagtactatttttagatggaatagataaggcccaagatgaacatgag


 


aaatatcacagtaattggagagcaatggctagtgattttaacctgccacc


 


tgtagtagcaaaagaaatagtagccagctgtgataaatgtcagctaaaag


 


gagaagccatgcatggacaagtagactgtagtccaggaatatggcaacta


 


gattgtacacatttagaaggaaaagttatcctggtagcagttcatgtagc


 


cagtggatatatagaagcagaagttattccagcagaaacagggcaggaaa


 


cagcatactttcttttaaaattagcaggaagatggccagtaaaaacaata


 


catacagacaatggcagcaatttcaccagtactacggttaaggccgcctg


 


ttggtgggcgggaatcaagcaggaatttggaattccctacaatccccaaa


 


gtcaaggagtagtagaatctatgaataaagaattaaagaaaattataggc


 


caggtaagagatcaggctgaacatcttaagacagcagtacaaatggcagt


 


attcatccacaattttaaaagaaaaggggggattggggggtacagtgcag


 


gggaaagaatagtagacataatagcaacagacatacaaactaaagaatta


 


caaaaacaaattacaaaaattcaaaattttcgggtttattacagggacag


 


cagagatccactttggaaaggaccagcaaagctcctctggaaaggtgaag


 


gggcagtagtaatacaagataatagtgacataaaagtagtgccaagaaga


 


aaagcaaagatcattagggattatggaaaacagatggcaggtgatgattg


 


tgtggcaagtagacaggatgaggattagaacatggaaaagtttagtaaaa


 


caccatatgtatgtttcagggaaagctaggggatggttttatagacatca


 


ctatgaaagccctcatccaagaataagttcagaagtacacatcccactag


 


gggatgctagattggtaataacaacatattggggtctgcatacaggagaa


 


agagactggcatctgggtcagggagtctccatagaatggaggaaaaagag


 


atatagcacacaagtagaccctgaactagcagaccaactaattcatctgt


 


attactttgactgtttttcagactctgctataagaaaggccttattagga


 


catatagttagccctaggtgtgaatatcaagcaggacataacaaggtagg


 


atctctacaatacttggcactagcagcattaataacaccaaaaaagataa


 


agccacctttgcctagtgttacgaaactgacagaggatagatggaacaag


 


ccccagaagaccaagggccacagagggagccacacaatgaatggacacta


 


gagcttttagaggagcttaagaatgaagctgttagacattttcctaggat


 


ttggctccatggcttagggcaacatatctatgaaacttatggggatactt


 


gggcaggagtggaagccataataagaattctgcaacaactgctgtttatc


 


catttcagaattgggtgtcgacatagcagaataggcgttactcaacagag


 


gagagcaagaaatggagccagtagatcctagactagagccctggaagcat


 


ccaggaagtcagcctaaaactgcttgtaccacttgctattgtaaaaagtg


 


ttgctttcattgccaagtttgtttcacaacaaaagccttaggcatctcct


 


atggcaggaagaagcggagacagcgacgaagacctcctcaaggcagtcag


 


actcatcaagtttctctatcaaagcagtaagtagtacatgtaatgcaacc


 


tatacaaatagcaatagcagcattagtagtagcaataataatagcaatag


 


ttgtgtggtccatagtaatcatagaatataggaaaatattaagacaaaga


 


aaaatagacaggttaattgatagactaatagaaagagcagaagacagtgg


 


caatgagagtgaaggagaaatatcagcacttgtggagatgggggtggaaa


 


tggggcaccatgctccttgggatattgatgatctgtagtgctacagaaaa


 


attgtgggtcacagtctattatggggtacctgtgtggaaggaagcaacca


 


ccactctattttgtgcatcagatgctaaagcatatgatacagaggtacat


 


aatgtttgggccacacatgcctgtgtacccacagaccccaacccacaaga


 


agtagtattggtaaatgtgacagaaaattttaacatgtggaaaaatgaca


 


tggtagaacagatgcatgaggatataatcagtttatgggatcaaagccta


 


aagccatgtgtaaaattaaccccactctgtgttagtttaaagtgcactga


 


tttggggaatgctactaataccaatagtagtaataccaatagtagtagcg


 


gggaaatgatgatggagaaaggagagataaaaaactgctctttcaatatc


 


agcacaagcataagaggtaaggtgcagaaagaatatgcatttttttataa


 


acttgatataataccaatagataatgatactaccagctatacgttgacaa


 


gttgtaacacctcagtcattacacaggcctgtccaaaggtatcctttgag


 


ccaattcccatacattattgtgccccggctggttttgcgattctaaaatg


 


taataataagacgttcaatggaacaggaccatgtacaaatgtcagcacag


 


tacaatgtacacatggaattaggccagtagtatcaactcaactgctgttg


 


aatggcagtctagcagaagaagaggtagtaattagatctgccaatttcac


 


agacaatgctaaaaccataatagtacagctgaaccaatctgtagaaatta


 


attgtacaagacccaacaacaatacaagaaaaagtatccgtatccagagg


 


ggaccagggagagcatttgttacaataggaaaaataggaaatatgagaca


 


agcacattgtaacattagtagagcaaaatggaatgccactttaaaacaga


 


tagctagcaaattaagagaacaatttggaaataataaaacaataatcttt


 


aagcaatcctcaggaggggacccagaaattgtaacgcacagttttaattg


 


tggaggggaatttttctactgtaattcaacacaactgtttaatagtactt


 


ggtttaatagtacttggagtactgaagggtcaaataacactgaaggaagt


 


gacacaatcacactcccatgcagaataaaacaatttataaacatgtggca


 


ggaagtaggaaaagcaatgtatgcccctcccatcagcggacaaattagat


 


gttcatcaaatattacagggctgctattaacaagagatggtggtaataac


 


aacaatgggtccgagatcttcagacctggaggaggagatatgagggacaa


 


ttggagaagtgaattatataaatataaagtagtaaaaattgaaccattag


 


gagtagcacccaccaaggcaaagagaagagtggtgcagagagaaaaaaga


 


gcagtgggaataggagctttgttccttgggttcttgggagcagcaggaag


 


cactatgggcgcacggtcaatgacgctgacggtacaggccagacaattat


 


tgtctggtatagtgcagcagcagaacaatttgctgagggctattgaggcg


 


caacagcatctgttgcaactcacagtctggggcatcaagcagctccaggc


 


aagaatcctggctgtggaaagatacctaaaggatcaacagctcctgggga


 


tttggggttgctctggaaaactcatttgcaccactgctgtgccttggaat


 


gctagttggagtaataaatctctggaacagatttggaataacatgacctg


 


gatggagtgggacagagaaattaacaattacacaagcttaatacattcct


 


taattgaagaatcgcaaaaccagcaagaaaagaatgaacaagaattattg


 


gaattagataaatgggcaagtttgtggaattggtttaacataacaaattg


 


gctgtggtatataaaaatattcataatgatagtaggaggcttggtaggtt


 


taagaatagtttttgctgtactttctatagtgaatagagttaggcaggga


 


tattcaccattatcgtttcagacccacctcccaaccccgaggggacccga


 


caggcccgaaggaatagaagaagaaggtggagagagagacagagacagat


 


ccattcgattagtgaacggatccttagcacttatctgggacgatctgcgg


 


agcctgtgcctcttcagctaccaccgcttgagagacttactcttgattgt


 


aacgaggattgtggaacttctgggacgcagggggtgggaagccctcaaat


 


attggtggaatctcctacagtattggagtcaggaactaaagaatagtgct


 


gttagcttgctcaatgccacagccatagcagtagctgaggggacagatag


 


ggttatagaagtagtacaaggagcttgtagagctattcgccacataccta


 


gaagaataagacagggcttggaaaggattttgctataagatgggtggcaa


 


gtggtcaaaaagtagtgtggttggatggcctactgtaagggaaagaatga


 


gacgagctgagccagcagcagatggggtgggagcagcatctcgagacctg


 


gaaaaacatggagcaatcacaagtagcaatacagcagctaccaatgctgc


 


ttgtgcctggctagaagcacaagaggaggaggaggtgggttttccagtca


 


cacctcaggtacctttaagaccaatgacttacaaggcagctgtagatctt


 


agccactttttaaaagaaaaggggggactggaagggctaattcactccca


 


acgaagacaagatatccttgatctgtggatctaccacacacaaggctact


 


tccctgattggcagaactacacaccagggccaggggtcagatatccactg


 


acctttggatggtgctacaagctagtaccagttgagccagataaggtaga


 


agaggccaataaaggagagaacaccagcttgttacaccctgtgagcctgc


 


atggaatggatgaccctgagagagaagtgttagagtggaggtttgacagc


 


cgcctagcatttcatcacgtggcccgagagctgcatccggagtacttcaa


 


gaactgctgacatcgagcttgctacaagggactttccgctggggactttc


 


cagggaggcgtggcctgggcgggactggggagtggcgagccctcagatgc


 


tgcatataagcagctgctttttgcctgtactgggtctctctggttagacc


 


agatttgagcctgggagctctctggctaactagggaacccactgcttaag


 


cctcaataaagcttgccttgagtgcttca






Other targets for CEM-15 can include the RNA and first strand DNA from: simian immunodeficiency virus (SIV), equine infectious anemia virus (EIAV), and murine leukemia virus, as well as other human lentiviruses, and retroviruses such as T-cell leukemia virus, spleen necrosis virus, and the pararetorvirus hepatitis B virus.
Mooring Sequences
Mooring sequences are the nucleic acid sequences recognized by cytidine deaminases. These sequences act as the recognition site for the enzyme, which can then deaminate a cytidine that is within a given length of the mooring sequence.
In APOBEC-1, RNA secondary structure does not appear to be required for apoB RNA editing. Instead, apoB mRNA editing requires an 11 nucleotide motif known as the mooring sequence. Placement of the mooring sequence 4-8 nucleotides 3′ of a cytidine within reporter RNAs is frequently sufficient for that RNA to support editing (Smith (1993) Seminars in Cell Biol. 4, 267-78; Sowden (1998) Nucl. Acids Res. 26, 1644-1652; Backus and Smith (1992) Nucl. Acids Res. 22, 6007-14; Backus and Smith (1991) Nucl. Acids Res. 19, 6781-86; Backus and Smith (1994) Biochim. Biophys. Acta 1217, 65-73; Backus and Smith (1994) Biochim. Biophys. Acta 1219, 1-14; Sowden et al., (1996) RNA 2, 274-88). The mooring sequence is left intact in edited mRNA and therefore its occurrence downstream of a cytidine is predictive of an editing site.
Alone APOBEC-1 exhibits only nominal affinity for AU-rich sequences within the region of the apoB mRNA mooring sequence (Anant and Davidson (2000) Mol. Cell. Biol. 20, 1982-1992, incorporated by reference in its entirety). The consensus sequence for APOBEC-1 binding is: 5′UUUN[A/U]U-3′ (SEQ ID NO: 11) The mooring sequence described by Smith (1993) Seminars in Cell Biology 4, 267-278), herein incorporated by reference) is:











5′-C*AAuu[uGauCAGUAUA]uu-3′
(SEQ ID NO: 12)







(where C* is the cytidine to be edited) and is highly conserved among 32 mammalian sequences (Hersberger et al & Innerarity, (1999) J. Biol. Chem. 274, 34590-34597, herein incorporated by reference in its entirety for teachings related to mooring sequences). Regions in lower case are specific “high affinity” sequences for APOBEC-1 binding. Regions in brackets define the “mooring sequence.” A cytidine deaminase inhibitor can utilize both the upstream sequence at the edited C (denoted by * and would be substituted with a zebularine or other cytidine deaminase inhibitor nucleotide) as well as downstream regions including the mooring sequence. The minimal sequence size capable of supporting editing (and hence and effective cytidine deaminase inhibitor of APOBEC-1 is ≧about a 26-mer) having a nucleic acid sequence:










5′-GAUA(Z*)AAUU[UGAUCAGUAUA]U-3′.
(SEQ ID NO: 13).







Auxiliary Proteins
Disclosed are cytidine deaminase inhibitors comprising a nucleoside incorporated in a polymeric substrate, wherein the polymeric substrate targets an auxiliary protein of a cytidine deaminase. An auxiliary protein of a cytidine deaminase is a protein that assists the cytidine deaminase in nucleic acid recognition, and specifically in recognized editing sites.
One example of an auxiliary protein of a cytidine deaminase is APOBEC-1 Complementing Factor (ACF). The nucleotide sequence recognized by ACF is the mooring sequence RNA disclosed above (SEQ ID NO: 13).
Another example of an auxiliary protein of a cytidine deaminase is APOBEC-1 Stimulating Protein (ASP). ASP recognizes the mooring sequence and is a spliced variant of ACF (Dance et al., 2002) J. Biol. Chem. 277, 12703-09). Additional ACF spliced variants are ACF45 and ACF43 that also bind to the mooring sequence (Sowden et al., (2004) J. Biol. Chem. 279, 197-206)
Other mRNA sequences targeted by APOBEC-1 which can be inhibited by cytidine deaminase inhibitor include, but are not limited, to NF1 (neurofibromin 1), whose targeted sequence is








(SEQ ID NO: 14)











5′-CCUUUAUUA(Z*)GAAUUGUGAUCACAUCCUCUG-3′,







wherein “Z” is the nucleoside residue.

Unregulated transgenic expression of APOBEC-1 confers susceptibility to liver cancer (Sowden, M., (1996) J Biol Chem, 271:3011-7; Yamanaka, S., et al., (1995) PNAS USA, 92, 8483-7, herein incorporated by reference in their entireties), possibly as a result of nonspecific mRNA editing affecting the NAT1 translational repressor. The following human NAT-1 (novel APOBEC-1 target) sequences are listed with each “mooring sequence” underlined.









(SEQ ID NO: 15)











5′-aagcaagttztttgatcagtttactcaaaca-3′




 








(SEQ ID NO: 16)











5′-aaatgctgczagaaattgatcagaataagga-3′




 








(SEQ ID NO: 17)











5′-ttacttgcazcaaactgatcagttttgagag-3′







Yamanaka et al. looked at several proteins and reported editing of protein tyrosine kinase (TEC). Only the latter was edited











Mouse TEC sequence









(SEQ ID NO: 18)











5′-aggtacgttztggatgatcagtacacaagttc-3′




 



Corresponding HUMAN TEC Sequence








(SEQ ID NO: 19)











5′-aggtatgttztggatgatcagtacacaagttc-3′







APOBEC-1 relies on auxiliary proteins for RNA recognition (Grosjean and Benne (1998); Teng (1993) Science 260:1816-19; Sowden (1998) Nucl. Acids Res. 26:1644-52; Inui (1994) J. Lipid Res. 35:1477-89; Dance (2001) Nucl. Acids Res. 29:1772-80). APOBEC-1 only has weak RNA binding activity of low specificity (Anant (1995) J. Biol Chem 270, 14768-75; MacGinnitie (1995) J. Biol Chem, 270, 14768-75). To edit apoB mRNA, APOBEC-1 requires, in addition to the mooring sequence described above, RNA binding proteins that bind apoB mRNA and to which APOBEC-1 can bind and orient itself to C6666. The components of the minimal editosome from defined in vitro system analyses are APOBEC-1 as a homodimeric cytidine deaminase (Lau, P. P., (1994) PNAS U.S.A. 91, 8522-8526) bound to the auxiliary protein ACF/ASP that serves as the editing-site recognition factor through its mooring-sequence-selective RNA-binding activity (Mehta, A., (2000) Mol. Cell. Biol. 20, 1846-1854; Lellek, H., (2000) J. Biol. Chem. 275, 19848-19856). Several other auxiliary protein candidates have also been described that had binding affinities for APOBEC-1 and/or apoB mRNA and that demonstrated the ability to modulate editing efficiency (Giannoni, F., et al., (1994) J. Biol. Chem. 269, 5932-5936; Yamanaka, S., et al., (1994) J. Biol. Chem. 269, 21725-21734; Yang, Y., et al., (1997) J. Biol. Chem. 272, 27700-27706; Lellek, H., et al., (2000) J. Biol. Chem. 275, 19848-19856; Teng, B., et al., (1993) Science 260, 1816-1819; Inui, Y., et al., (1994) J. Lipid Res. 35, 1477-1489; Anant, S. G., et al., (1997) Nucleic Acids Symp. Ser. 36, 115-118; Lau, P. P., et al., (1997) J. Biol. Chem. 272, 1452-1455).
ACF was isolated and cloned using biochemical fractionation and yeast two hybrid genetic selection (Mehta et al., (2000) Mol. Cell. Biol. 20, 1846-54; Lellek (2000) JBC 275:19848-56). Overexpression of 6His-tagged APOBEC-1 in mammalian cells enabled the intracellularly assembled editosome to be affinity purified (Yang Y. et al., (1997) J. Biol. Chem. 272, 27700-06). ACF associated with APOBEC-1 through 1M NaCl resistant interactions and that three other RNA binding proteins (100 kDa, 55 kDa and 44 kDa) with affinity for the mooring sequence co-purified with the editosome (Yang, Y. et al., (1997) J. Biol. Chem. 272, 27700-06). P100 and p55 were both mooring-sequence-selective RNA binding proteins but p44 was a general RNA binding protein. Additional studies utilizing yeast two hybrid analyses using APOBEC-1 affinity and antibodies developed against the editosome and ACF have demonstrated proteins such as hnRNP ABBP1 (Lau, P. et al., (1997) J. Biol Chem 272, 1452-55), the alternative splicing factor KSRP (Lellek et al., (2000) J. Biol Chem 275, 19848-56) and αI3 serum proteinase inhibitor as positive modulators of editing activity (Schock, D. et al., (1996) PNAS USA 93, 1097-1102) and hnRNP protein C (Greeve, J. et al., (1998) Biol. Chem. 379, 1063-73) and GRY-RBP (Blanc, V. et al., (2001) J. Biol Chem, 276, 10272-83; Lau, P. et al., (2001) Biochem. Biophys. Res. Commun. 282, 977-83) as negative modulators of apoB mRNA editing.
Disclosed are compositions comprising a cytidine deaminase inhibitor, such as those described above, and a pharmaceutical carrier.
The compositions can be administered in vivo in a pharmaceutically acceptable carrier. By “pharmaceutically acceptable” is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to a subject, along with a nucleic acid or vector, without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained. The carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
Delivery
The disclosed compositions can be delivered to the target cells in a variety of ways. For example, the compositions can be delivered through electroporation, or through lipofection, or through calcium phosphate precipitation. The delivery mechanism chosen will depend in part on the type of cell targeted and whether the delivery is occurring for example in vivo or in vitro.
Thus, the compositions, can comprise, for example, lipids such as liposomes, such as cationic liposomes (e.g., DOTMA, DOPE, DC-cholesterol) or anionic liposomes. Liposomes can further comprise proteins to facilitate targeting a particular cell, if desired. Administration of a composition comprising a compound and a cationic liposome can be administered to the blood afferent to a target organ or inhaled into the respiratory tract to target cells of the respiratory tract. Regarding liposomes, see, e.g., Brigham et al. (1989) Am. J. Resp. Cell. Mol. Biol. 1, 95-100); Felgner et al. (1987) PNAS USA 84, 7413-7417); U.S. Pat. No. 4,897,355. Furthermore, the compound can be administered as a component of a microcapsule that can be targeted to specific cell types, such as macrophages, or where the diffusion of the compound or delivery of the compound from the microcapsule is designed for a specific rate or dosage.
Disclosed are methods of treating a subject with cancer, or having a predisposition to cancer. Such cancers include, but are not limited to, those associated with AID, like B cell malignancies such as diffuse large B cell lymphomas and chronic lymphatic leukemia. The disorder can also be a T cell lymphoma or a pulmonary adenoma. Also included are those cancers associated with APOBEC-1, like colorectal cancer and neurofibromatosis. Also included are those cancers associated with CEM15, such as breast cancer. Cancers involving overexpression of other ARPs of listed in Wedekind et al. (2003) Trends in Genetics, herein incorporated by reference in it's entirety.
As used throughout, administration of a cytidine deaminase inhibitor can occur in conjunction with other therapeutic agents. Thus, the cytidine deaminase inhibitors of the present invention can be administered alone or in combination with one or more therapeutic agents. For example, a subject can be treated with a cytidine deaminase inhibitor alone, or in combination with chemotherapeutic agents, antibodies, antivirals, steroidal and non-steroidal anti-inflammatories, conventional immunotherapeutic agents, cytokines, chemokines, and/or growth factors. Combinations may be administered either concomitantly (e.g., as an admixture), separately but simultaneously (e.g., via separate intravenous lines into the same subject), or sequentially (e.g., one of the compounds or agents is given first followed by the second). Thus, the term “combination” or “combined” is used to refer to either concomitant, simultaneous, or sequential administration of two or more agents.
A cytidine deaminase inhibitor is an agent that inhibits editing of nucleic acids by cytidine deaminases. Additional genetic, pharmacologic, or metabolic agents or conditions also modulate the RNA or DNA editing or mutating function of the deaminase. Some of the conditions that modulate editing activity include: (i) changes in the diet, (ii) hormonal changes (e.g., levels of insulin or thyroid hormone), (iii) osmolarity (e.g., hyper or hypo osmolarity), (iv) ethanol, (v) inhibitors of RNA or protein synthesis and (vi) conditions that promote liver proliferation. Thus, the methods of the invention can comprise administering a cytidine deaminase inhibitor to the subject and using other conditions that reduce the efficiency of mRNA editing function or the efficacy of the cytidine deaminase.
Disclosed are methods of treating a condition, wherein the condition is a cancer. The cancer can be selected from the group consisting of lymphomas (Hodgkins and non-Hodgkins), B cell lymphoma, T cell lymphoma, myeloid leukemia, leukemias, mycosis fungoides, carcinomas, carcinomas of solid tissues, squamous cell carcinomas, adenocarcinomas, sarcomas, gliomas, blastomas, neuroblastomas, plasmacytomas, histiocytomas, melanomas, adenomas, hypoxic tumours, myelomas, AIDS-related lymphomas or sarcomas, metastic cancers, bladder cancer, brain cancer, nervous system cancer, squamous cell carcinoma of head and neck, neuroblastoma/glioblastoma, ovarian cancer, skin cancer, liver cancer, melanoma, squamous cell carcinomas of the mouth, throat, larynx, and lung, colon cancer, cervical cancer, cervical carcinoma, breast cancer, epithelial cancer, renal cancer, genitourinary cancer, pulmonary cancer, esophageal carcinoma, head and neck carcinoma, hematopoietic cancers, testicular cancer, colo-rectal cancers, prostatic cancer, or pancreatic cancer.
Cytidine deaminase inhibitors are of benefit to individuals who are over-expressing cytidine deaminases, as well as those individuals who would benefit from a reduction in their activity. Because cytidine deaminase inhibitors reduce the activity of cytidine deaminases, the mutation rate of certain nucleic acids recognized by the cytidine deaminase is reduced, and any subject that can benefit from a reduction in the activity of cytidine deaminases can be administered cytidine deaminase inhibitor. This includes those receiving exogenous nucleic acids via a viral vector, in which a reduction in the recognition of these viral vectors would be beneficial. Therefore, the cytidine deaminase inhibitors can be administered in combination with viral vectors. For example, inactivation of AID can permit introduction and function of the viral vector delivered therapeutic model, such as RNA, DNA, siRNA, or protein, so these two technologies can be used in tandem.
One skilled in the art will appreciate that the viral vector can comprise any viral vector useful in delivery of exogenous nucleic acids. For example, the viral vector can be a recombinant adenovirus vector, an adeno-associated viral vector, a lentiviral vector, a pseudotyped retroviral vector, a vaccinia vector, an alphavirus vector, or any other viral vector known in the art or described throughout.
In particular, the viral vector can be a retrovirus. A retrovirus is an animal virus belonging to the virus family of Retroviridae, including any types, subfamilies, genus, or tropisms. Retroviral vectors, in general, are described by Verma, I. M., Retroviral vectors for gene transfer. In Microbiology-1985, American Society for Microbiology, pp. 229-232, Washington, which is incorporated by reference herein in its entirety for the retroviral vectors taught and methods of making or using the same. Examples of methods for using retroviral vectors for exogenous nucleic acid delivery are described in U.S. Pat. Nos. 4,868,116 and 4,980,286; PCT applications WO 90/02806 and WO 89/07136; and Mulligan, (Science 260:926-932 (1993)); the teachings of which are incorporated herein by reference in their entirety for the methods taught herein. The retrovirus can be in the Oncovirinae subfamily of retroviruses, such as HTLV-I or HTLV-II (human T-cell leukemia virus type I and type II, respectively). Additionally, the retrovirus can be in the Lentivirinae subfamily of retroviruses, such as HIV-1, HIV-II, SIV, FIV, EIAV and CAEV (human immunodeficiency virus type I, human immunodeficiency virus type II, simian immunodeficiency virus, feline immunodeficiency virus, equine infectious anemia virus, and caprine arthritis-encephalitis virus, respectfully).
A retrovirus is essentially a package that has packed into it nucleic acid cargo. The nucleic acid cargo carries with it a packaging signal, which ensures that the replicated daughter molecules will be efficiently packaged within the package coat. In addition to the package signal, there are a number of molecules which are needed in cis, for the replication, and packaging of the replicated virus. Typically a retroviral genome contains the gag, pol, and env genes which are involved in the making of the protein coat. Retrovirus vectors typically contain a packaging signal for incorporation into the package coat, a sequence which signals the start of the gag transcription unit, elements necessary for reverse transcription, including a primer binding site to bind the tRNA primer of reverse transcription, terminal repeat sequences that guide the switch of RNA strands during DNA synthesis, a purine rich sequence 5′ to the 3′ LTR that serve as the priming site for the synthesis of the second strand of DNA synthesis, and specific sequences near the ends of the LTRs that enable the insertion of the DNA state of the retrovirus to insert into the host genome. The removal of the gag, pol, and env genes allows for about 8 kb of foreign sequence to be inserted into the viral genome, become reverse transcribed, and upon replication be packaged into a new retroviral particle. This amount of nucleic acid is sufficient for the delivery of a one to many genes depending on the size of each transcript. It is preferable to include either positive or negative selectable markers along with other genes in the insert.
Since the replication machinery and packaging proteins in most retroviral vectors have been removed (gag, pol, and env), the vectors are typically generated by placing them into a packaging cell line. A packaging cell line is a cell line which has been transfected or transformed with a retrovirus that contains the replication and packaging machinery, but lacks any packaging signal. When the vector carrying the DNA of choice is transfected into these cell lines, the vector containing the gene of interest is replicated and packaged into new retroviral particles, by the machinery provided in cis by the helper cell. The genomes for the machinery are not packaged because they lack the necessary signals.
Because cytidine deaminases are known to act upon viruses, inactivating these cytidine deaminases in the presence of viral vectors allows for tissue specific gene transfer and insertion for therapeutic purposes (i.e. retroviral DNA synthesis and genome incorporation). The infectivity of HIV-1 is markedly reduced in T lymphocytes that naturally express CEM15 (Sheehy et al., (2002) Nature, 418, 646-50). Recent research has demonstrated that CEM15 acts as a host cell defense mechanism by introducing numerous dC to dU and dG to dA mutations in the HIV-1 genome during it's replication, rendering the virus nonfunctional (Mangeat, B. et al., (2002) Nature 424, 99-103; Mariani, R. et al., (2003) Cell 114, 21-31; Zhang, H. et al., (2003) Nature 424, 94-8). A critical step for this activity is for CEM15 to incorporate into viral particles during their assembly (Mariani, R. et al., (2003) Cell 114, 21-31; Stopak, K. et al., (2003) Mol Cell 12, 591-601) and then, subsequent to infection, mutate single stranded DNA during viral replication Mangeat, B. et al., (2002) Nature 424, 99-103; Zhang, H. et al., (2003) Nature 424, 94-8; Stopak, K. et al., (2003) Mol Cell 12, 591-601). This defense mechanism can be blocked by the HIV protein known has Vif (Sheehy et al., (2002) Nature, 418, 646-50) which reduces the expression of CEM15 (Stopak, K. et al., (2003) Mol Cell 12, 591-601) and binds to CEM15 (Mariani, R. et al., (2003) Cell 114, 21-31; Yang, B. et al., (2003) J. Biol. Chem. 278, 6596-602), targeting it to the protein degradation pathway of the cell (Stopak, K. et al., (2003) Mol Cell 12, 591-601; Liu, B. et al., (2004) J. Virol. 78, 2072-81; Sheehy, A. M., et al., (2003) Nat. Med. 9, 1404-7). Viral particles produced from Vif positive HIV contain Vif (Ohagen, A. and Gabuzda, D. (2000) J. Virol. 74, 11055-66; Zhang, H. et al., (2000) J. Virol. 74, 8252-61; Simon, J. H. et al., (1996) J. Virol. 70, 5297-305; Khan, M. A. et al., (2001) J. Virol. 75, 7252-65) but contain low or no CEM15 (Mariani, R. et al., (2003) Cell 114, 21-31; Stopak, K. et al., (2003) Mol Cell 12, 591-601; Liu, B. et al., (2004) J. Virol. 78, 2072-81; Sheehy, A. M., et al., (2003) Nat. Med. 9, 1404-7) and consequently are infectious. These new understandings suggest that there are at least two times when CEM15 activity is critical in host defense from HIV infection. These are: early during infection when the viral RNA genome is replicated and late in infection when viral particles are being assembled. Both of these require CEM15 localization within the cytoplasm of the host cell and this has been confirmed by immunolocalization and biochemical fractionation.
The compositions comprising a cytidine deaminase inhibitor in a pharmaceutically acceptable carrier may be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like, although topical intranasal administration or administration by inhalant is typically preferred. As used herein, “topical intranasal administration” means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism or droplet mechanism, or through aerosolization of the nucleic acid or vector. The latter may be effective when a large number of animals is to be treated simultaneously. Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intubation. The exact amount of the compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the disorder being treated, the particular nucleic acid or vector used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.
Cytidine deaminase inhibitor for APOBEC-1, used to reduce apoB mRNA editing in the small intestine, can be administered orally, for example. RNA is stable to stomach acids, and the ribonucleases can have modified backbones in one embodiment. As disclosed herein, peptide sequences can be used with the RNA molecule during its synthesis (for example, using the TAT motif for enhanced uptake). It is also envisioned that peptide-oligos contain information, not only for compound entry, but also for targeting by employing peptidyl nuclear or cytoplasmic nuclear localization signals, such as PNAs, can be used.
In one aspect, the cytidine deaminase inhibitor molecule can be a PNA (peptide-RNA), for example. This molecule can serve to both stabilize the oligonucleotide as well as encoding a motif such as the cell transduction motif of ‘TAT’, for example, which permits the penetration of the cytidine deaminase inhibitor into cells. For example, the methodology to establish a peptide in covalent linkage to an oligonucleotide has been described by Glen Research (http://www.glenresearch.com) (Example 10). In another aspect, the cytidine deaminase inhibitor can be a non-peptidyl-oligo composed of an inert non-peptidyl based mimic. For example, any compound possessing one or non-protease digestable amino acid linkages (i.e., inert peptide bond) can be used in this aspect. The synthesis of the non-peptidyl-oligos can be performed using similar techniques described above for producing peptide-oligos. Examples of molecules having one or more inert peptide bonds are well known in the art and can be found, for example, in the HIV-1 protease inhibitor field. In one aspect, the non-peptidyl based mimic UIC-94017 disclosed in Koh et al., Antimicrobial Agents and Chemotherapy, vol. 47, no. 10, p. 3123-3129, October 2003, can be used herein.
In one example, nanoparticles are used such as those described by Lambert G, et al. (Drug Deliv Rev. 2001; 47, 99-112). Lambert et al. reviewed various assemblies to deliver anti sense oligonucleotides. For example, in vivo, polyalkylcyanoacrylate (PACA) nanoparticles were able to efficiently distribute the antisense molecules to the liver. Alginate nanosponges can concentrate the antisense molecules in the lungs. Antisense loaded to PACA nanoparticles were able to improve the treatment of RAS cells expressing the point mutated Ha-ras gene in mice.
The composition can include active components that can be delivered to a subject for which delivery to the intestine is desired. Examples of such additional components are numerous and are well known in the art. For example, there have been described various forms of composites which make possible active ingredients to be delivered to the intestine including for example those in the form of capsule (Japanese Patent Laid-Open Publication Nos. 41422/1992, 225922/1992, 179618/1994, and 327634/1995), those coated with monolayer (Japanese Patent Laid-Open Publication Nos. 368321/1992, and 2701/1995), and those coated with chitosan and a special polymer (Japanese Patent Laid-Open Publication Nos. 34927/1991, 69333/1992, and 217924/1992), herein incorporated in their entirety for methods of delivery to the intestine.
Intestinal absorption enhancers can be used as well. These fall within the following general classes: (1) calcium chelators, such as citrate and EDTA; and (2) surfactants, such as sodium dodecyl sulfate, bile salts, palmitoylcarnitine, and sodium salts of fatty acids, for example.
Parenteral administration of the composition, if used, is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Pat. No. 3,610,795, which is incorporated by reference herein in its entirety for the methods taught.
The compositions may be in solution or in suspension (for example, incorporated into microparticles, liposomes, or cells). These compositions may be targeted to a particular cell type via antibodies, receptors, or receptor ligands. The following references are examples of the use of this technology to target specific proteins to given tissue (Senter, et al., Bioconjugate Chem., 2:447-451, (1991); Bagshawe, K. D., (1989) Br. J. Cancer, 60, 275-281; Bagshawe, et al., (1988) Br. J. Cancer, 58, 700-703; Senter, et al., (1993) Bioconjugate Chem., 4, 3-9; Battelli, et al., (1992) Cancer Immunol. Immunother., 35, 421-425; Pietersz and McKenzie, (1992) Immunolog. Reviews, 129, 57-80; and Roffler, et al., (1991) Biochem. Pharmacol, 42, 2062-2065). Vehicles such as “stealth” and other antibody conjugated liposomes (including lipid mediated drug targeting to colonic carcinoma), receptor mediated targeting of DNA through cell specific ligands, lymphocyte directed tumor targeting, and highly specific therapeutic retroviral targeting of murine glioma cells in vivo. In general, receptors are involved in pathways of endocytosis, either constitutive or ligand induced. These receptors cluster in clathrin-coated pits, enter the cell via clathrin-coated vesicles, pass through an acidified endosome in which the receptors are sorted, and then either recycle to the cell surface, become stored intracellularly, or are degraded in lysosomes. The internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor-mediated endocytosis has been reviewed (Brown and Greene, (1991) DNA and Cell Biology 10, 6, 399-409).
Pharmaceutically Acceptable Carriers
Delivery of the cytidine deaminase inhibitors can be used therapeutically in combination with a pharmaceutically acceptable carrier. Pharmaceutical carriers are known to those skilled in the art. These most typically would be standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH. The compositions can be administered intramuscularly or subcutaneously. Other compounds will be administered according to standard procedures used by those skilled in the art.
Pharmaceutical compositions may include carriers, thickeners, diluents, buffers, preservatives, surface active agents and the like in addition to the molecule of choice. Pharmaceutical compositions may also include one or more active ingredients such as antimicrobial agents, anti-inflammatory agents, anesthetics, and the like.
The pharmaceutical composition may be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration may be topically (including opthamalically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection. The disclosed compounds can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally.
Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.
Formulations for topical administration may include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
Compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders may be desirable.
Some of the compositions may potentially be administered as a pharmaceutically acceptable acid- or base-addition salt, formed by reaction with inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and organic bases such as mono-, di-, trialkyl and aryl amines and substituted ethanolamines.
Therapeutic Uses
The dosage ranges for the administration of the compositions are those large enough to produce the desired effect in which the symptoms of the disorder are affected. The dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like. Generally, the dosage will vary with the age, condition, sex and extent of the disease in the patient and can be determined by one of skill in the art. The dosage can be adjusted by the individual physician in the event of any contraindications. Dosage can vary, and can be administered in one or more dose administrations daily, for one or several days.
Cytidine deaminase inhibitors that do not have a specific pharmaceutical function, but which may be used for tracking changes within cellular chromosomes or for the delivery of diagnostic tools for example can be delivered in ways similar to those described for the pharmaceutical products.
As described previously, cytidine deaminase inhibitors can be administered together with other forms of therapy. For example, the molecules can be administered with antibodies, antibiotics, or other cancer treatment protocols as described above, or viral vectors. When the cytidine deaminase inhibitor is in a vector, as described above, the vector containing the nucleic acid for therapeutic purposes can also contain the cytidine deaminase inhibitor.
Also disclosed are cells comprising a cytidine deaminase inhibitor or comprising a nucleic acid that encodes the cytidine deaminase inhibitor, such as those described above. Disclosed are cell lines comprising a cytidine deaminase inhibitor. The cytidine deaminase inhibitor can be contained in a vector, or can be part of the genome of the cell. The cytidine deaminase inhibitor can comprise a nucleoside incorporated in a polymeric substrate, wherein the polymeric substrate targets a cytidine deaminase or a cytidine deaminase auxiliary protein. The cytidine deaminase inhibitor can be any of those cytidine deaminase inhibitors described above.
The disclosed cell lines can be used in a variety of ways. For example, they can be used as tools to study cytidine deaminases. The cell line can be monitored in vitro for the inhibitory activity of cytidine deaminase inhibitors. The cell line can also be used for screening drugs that inhibit the efficacy of the cytidine deaminase inhibitor. Alternatively, cells of the cell line can be administered to a test animal and monitored for the effect thereof. The cell line can be used for drug discovery and for drug validation. Substances that are known or suspected of interacting with cytidine deaminase inhibitors can be administered to the cell line, and the effects thereof monitored. Combinations of the above can also be used to monitor the cause and effect relationship of various drug candidates. The disclosed cell lines can also be used as reagents to produce other beneficial cell lines, by for example, allowing the cell lines to multiply. These cell lines are useful as model systems for drug discovery and validation.
Methods of Using the Compositions
Disclosed are methods of inhibiting cytidine deaminases comprising contacting a cell containing the cytidine deaminase with a cytidine deaminase inhibitor under conditions that allow the inhibitor to inhibit the deaminase function of the cytidine deaminase. The step of contacting the cytidine deaminase with a cytidine deaminase inhibitor can occur either in vivo or in vitro.
By “inhibiting cytidine deaminases” is meant inhibiting the functionality of the enzyme, or inhibiting its ability to deaminate nucleic acids. The cytidine deaminase can be inhibited at 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90%, or 100% or greater or any amount in between, compared to a control cytidine deaminase or the normal functionality of the cytidine deaminase either in vivo or in vitro.
Also disclosed is a method of treating a subject with a disorder associated with a cytidine deaminase comprising administering to the subject a cytidine deaminase inhibitor as taught herein. The disorder associated with cytidine deaminase can be a disorder associated with AID. Such disorders include, but are not limited to, B cell malignancies such as diffuse large B cell lymphomas and chronic lymphatic leukemia. The disorder can also be a T cell lymphoma or a pulmonary adenoma.
The disorder associated with cytidine deaminase can also be a disorder associated with APOBEC-1. Such disorders include, but are not limited to cancers such as colorectal cancer, neurofibromatosis, atherosclerosis, steatosis (fatty liver disease) and metabolic syndrome.
The disorder can also be associated with CEM15. Such disorders include, but are not limited to, cancers such as breast cancer.
As discussed above, also disclosed are methods of promoting viral vector incorporation in a subject comprising the step of administering to the subject a therapeutic amount of a cytidine deaminase inhibitor. The cytidine deaminase inhibitor can be any cytidine deaminase inhibitors described herein.
Disclosed are methods of promoting incorporation of a viral vector in a subject comprising the steps of administering to the subject a therapeutic amount of a cytidine deaminase inhibitor and administering the viral vector to the subject. The cytidine deaminase inhibitor can be any of those cytidine deaminase inhibitors described above.
Cytidine deaminase inhibitors can induce nucleotide deamination in the sequence of the retroviral vector itself either during its reverse transcription, replication and/or during the expression of RNA from the transgene after the virus integrated into the cell's chromosomes. The gene that the retrovirus is carrying is mutated as well, thereby reducing or eliminating functional protein expression (an effect that appears as low efficiency of transduction by the virus). Also as described above, the sites that are affected are those that are exact or approximate target sites that enable binding of CEM15 directly or through an auxiliary protein of CEM15. The partial or total mutation of C's (or A's as would be the case of ADAR1) blunts the ability of the retroviruses to express functional proteins from its own genes and the gene(s) it carries and therefore the retrovirus is not able to integrate into the cells' chromsomes.
Also disclosed is a method of screening for a cytidine deaminase inhibitor comprising the steps of contacting a cytidine deaminase with an agent to be screened, wherein the agent is incorporated in a polymeric substrate, wherein the polymeric substrate targets the cytidine deaminase; and determining the level of cytidine deaminase activity. A reduction in cytidine deaminase activity, as compared to cytidine deaminase activity in the absence of the agent to be screened, indicating a cytidine deaminase inhibitor. A reduction in cytidine deaminase activity is defined as less than 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or greater or any amount in between reduction in activity compared to a control or to the normal level of activity ascribed to the cytidine deaminase.
In the screening methods, the cytidine deaminase can be in a cell, or can be in a transgenic animal. The method of screening can occur either in vivo, ex vivo, or in vitro. The polymeric substrate can comprise oligonucleotide residues. The polymeric substrate can be a nucleic acid that specifically targets the cytidine deaminase. Cytidine deaminase activity can be determined using a variety of techniques known in the art and taught by the following examples.
The present invention is more particularly described in the following examples which are intended as illustrative only since numerous modifications and variations therein will be apparent to those skilled in the art.
EXAMPLES
Example 1
Methods for Synthesizing Context Dependent Inhibitors Containing Zebularine
Sources of Deoxy Zebularine Phosphoramidite: synthesis of deoxyzebularine phosphoramidite (DNA) is known in the art (Cheng, J. C., et al., J Natl Cancer Inst, 95(5):399-409, 2003). Also, 5-methyl-2′-deoxyzebularine is commercially available from Glen Research. The base is rather unstable at high pH during which the exocylic amine undergoes deblocking at the end of the synthesis. Hence, the synthesis needs “ultramild CE phosphoramidites,” which can be purchased from Glen Research (http://www.glenres.com).
There are the following options for synthesis: DNA Phosphoramidites, CE phenoxyacetyl (Pac) protected dA, CE acetyl (Ac) protected dC, and CE 4-isopropyl-phenoxyacetyl (iPr-Pac) protected dG (thymine/uridine do not need to be deblocked since there is no exocylic amine).
The forementioned method was employed in the synthesis of a context dependent inhibitor of DNA harboring 5-methyl-2′-deoxyzebularine. As proof of principle, a sequence was synthesized was a 15-mer comprising: 5′-d(AGC-TAG-(dmZ)-TAA-GTT-AT)-3′ (SEQ ID NO: 22), where one of the edited positions has been replaced by 5-methyl-2′-deoxyzebularine denoted (dmZ). This product represents a substrate for the enzyme activation induced deaminase (AID) as reported by Goodman and colleagues (Bransteitter, R. et al (2003) Proc. Natl. Acad. Sci. USA 100, 4102-4107). The phosphoramidites used were those of the ultramild class, which were purchased from Glen Research. The phosphoramidites were coupled on a 1 μmole scale using a DNA Synthesizer with coupling times and procedures recommended by Glen Research for mild phosphoramidites. The DNA product was deblocked and the trityl group removed under mild conditions described by Glen Research. The partially lyophilized product was resuspended in 0.1 M Triethylammonium acetate (TEAA) buffer pH 7.0 (Buffer A) and subjected to HPLC purification using a 1.9×30 cm μ-Bondapack C18 column (Waters) operated at 7 ml min−1. The product eluted as a single peak (FIG. 12) with a retention time of 44.3 min; failure sequences and impurities were clearly separated in this step. The ion pairing elution buffer comprised Buffer A with 50% acetonitrile (Buffer B). The percent of Buffer B upon elution was 26%. The gradient started at 15% Buffer A and ended at 30% Buffer A in 70 min. Peak fractions were pooled and the pure product was lyophilized and desalted on a SepPak C18 cartridge (Waters). The DNA was detected at 260 nm and the pooled material was lyophilized to dryness. The yield was 25% (nearly 2 mg). The sample was resuspended in water and analyzed by MALDI/TOF mass spectrometry (FIG. 13). The major peak was observed at an m/z of 4532. This result demonstrates the existence of an oligomer of the correct MW that represents the largest component of the sample.
As another option to make RNA inhibitors containing 2′-OMe groups, the following options are available, although the deoxyzebularine must be used at the site of C-to-U conversion: 2′-OMe RNA Phosphoramidites, phenoxyacetyl (Pac) protected 2′-OMe-A, acetyl (Ac) protected 2′-OMe-C, and 4-isopropyl-phenoxyacetyl (iPr-Pac) protected 2′-OMe-G (regular 2′-OMe-uridine can be used).
The Cap A reagent to phenoxyacetic anhydride needs to be changed to be compatible with ultramild bases, and used with an “ultramild” solid phase support (page 22-23 of the Glen Catalog on the internet). 2′-OMe-U can be purchased as a starting material but 2′-OMe CPG has to be synthesized. Using these mild reagents allows the ammonia deblocking step to be reduced to 4 hours at room temp. On the Glen Research website, 0.05M potassium carbonate in methanol is recommended. Alternatively, ethanolic ammonium hydroxide can be used.
Apart from the above, no changes are needed to the synthesis. The zebularine phosphoramidite can be dissolved at the normal concentrations (0.1 M), filtered, and coupled for the same time as a normal deoxy phosphoramidite. However, careful purification is needed as the mild ammonia reduces, but does not eliminate, destruction of the zebularine base. “DMT-on” purification can be performed, along with initial purification on reverse-phase HPLC (C18) with buffers as follows: A: 0.1 M triethylammonium acetate pH 6.5+5% CH3CN; B: 0.1 M triethylammonium acetate pH 6.5+65% CH3CN; and 25 to 65% B, over 30 minutes. The desired DMT-on product elutes at about 12-15 minutes (failure sequences, which lack the hydrophobic group elute in the void volume).
The product is collected in bulk based on absorption at 260 nm, lyophilized to near dryness at −95° C. to remove TEAA buffer and the DMT group hydrolyzed by incubating in 80% acetic acid/20% water for 30 minutes. The solution is stopped by freezing in liquid N2 and acetic acid can be removed by lyophilization; adding 1 ml of water and evaporating (repeat 3 times) removes all the acid).
A normal oligonucleotide is pure at this stage, however this is not true with zeb-derivatives. A second reverse phase HPLC purification is required with a shallower gradient; 0-25% buffer B, over 30 minutes. A cluster of closely running peaks elute at around 10-15 minutes. The desired zeb product is usually the biggest, slowest running peak. Identity can be confirmed by MALDI-TOF MS or UV absorbance/fluorescence spectroscopy. zebularine absorbs at  ̃305 nm and zebularine oligos contain a shoulder (sometimes not very prominent) at this wavelength. Zebularine is also fluorescent, excitation at 305 gives fluorescence at about 390 nm. Yields are usually 20-30% compared to an oligonucleotide of the same length with only normal bases.
The phosphoramidite is stored desiccated at minus 20° C. (stable forever). Likewise the final zebularine-oligos are stable when stored frozen at −20° C.
Example 2
Alternate Methods for Synthesizing Cytidine Deaminase Inhibitors
One compound useful as a cytidine deaminase inhibitor can be 4-fluoro zebularine. One advantage of such an inhibitor is that it is more reactive than the parent compound. Conceptually, the nucleoside should hydrate at C4 like zebularine and 5-fluorozebularine. However, the hydrated tetrahedral carbon has F instead of H, and since F is more an isostere for the hydroxyl, the compound may not bind effectively at the active site. Other substitutions at 2′ are designed to influence the ribose sugar pucker to more closely mimic the conformers of RNA, as well as their hydrogen bonding properties. In this respect, 2′-Fluoro can be used. Due to its inert nature, this position does not require protection during chemical synthesis.
Example 3
Reduction in Small Intestinal apoB mRNA Editing to Reduce B48 Containing Chylomicron Remnants in Patients with Metabolic Syndrome
The nucleotide analog deoxyzebularine, in the context of single-stranded (ss) RNA or PNA oligonucleotides comparable to SEQ ID NO: 12, can be used to reduce apoB mRNA editing in the small intestine: Cholesterol is carried in the blood from one tissue to another as lipoprotein particles by specific carrier proteins called apolipoproteins. Apolipoprotein B (apoB) is an integral and non-exchangeable structural component of lipoprotein particles referred to as chylomicrons, very-low-density lipoprotein (VLDL) and low-density lipoprotein (LDL). ApoB circulates in human plasma as two isoforms, ApoB100 and apoB48. ApoB100 can be converted into ApoB48 by the enzyme APOBEC-1 (ApoB mRNA editing catalytic subunit-1). With the help of auxiliary factors, APOBEC-1 can stop the synthesis (production) of ApoB100 form and start the synthesis of ApoB48 form in cells. ApoB100 and ApoB48 play different roles in lipid metabolism. Various studies indicated that ApoB100-associated lipoproteins (VLDL and LDL) are much more atherogenic than ApoB48-associated lipoproteins.
Stimulating hepatic ApoB mRNA editing is a way to reduce serum LDL through the reduction in synthesis and secretion of ApoB100 containing VLDL. In most mammals (including humans), ApoB mRNA editing is carried out only in the small intestine. Studies found that the presence of substantial editing in liver is associated with a less atherogenic lipoprotein profile compared with animals that do not have liver editing activity. APOBEC-1 is expressed in all tissues that carry out ApoB mRNA editing. Human liver does not express APOBEC-1 but it does express sufficient auxiliary proteins to complement exogenous APOBEC-1 in ApoB mRNA editing in transfected cells. Therefore, induction of editing in human liver reduces apoB100 synthesis and thereby reduce the levels of circulating LDL cholesterol.
Example 4
AID and Context Dependent Inhibitors
The nucleotide analog deoxyzebularine[(1-β-D-2′-deoxyribofuranosyl)pyrimidin-2-one, dZ], in the context of single-stranded (ss) DNA oligonucleotides (or those comparable to FIG. 5) bearing SHM hotspots, is tested as a specific inhibitor of AID, while being inactive on deoxycytidine deaminases (dCDA) essential for pyrimidine metabolism. The in vivo substrate specificity of AID has been already established as the deamination of deoxycytidine (dC) at N4 in the context of single-stranded, but not doublestranded (ds) DNA (Bransteitter, R., et al., (2003) PNAS USA, 100, 4102-7; Pham, P., et al. (2003) Nature, 424, 103-7; (Ramiro, A. R., et al., (2003) Nat Immunol, 4, 452-6; Chaudhuri, J., et al., (2003) Nature, 422, 726-30; Dickerson, S. K., et al., (2003) J Exp Med, 197, 1291-6). Furthermore, ssDNA deamination demonstrates activity on the SHM consensus sequence WRCY (SEQ ID NO: 19), where W=A or T, R=purine and Y=pyrimidine. By substituting dC with dZ in the context hot spot ssDNA oligos, selectively “poisoning” AID by inhibiting oligo release from its active site is possible. Previously, the use of free dZ and Z were shown to be intracellular inhibitors of mammalian deoxycytidine deaminases and cytidine deaminases involved in pyrimidine metabolism and revealed anti-tumor properties Barchi, J. J., Jr., et al., (2003) J Enzyme Inhib, 9, :147-62). Enzymatic inhibition by dZ is derived not only from its ability to mimic the structure and hydrogen bonding properties of dC, but also through its reactivity with the Zn2+-dependent enzyme to form 3,4-dihydrodeoxyouridine, a mechanism based transition state mimic that binds the cytidine deaminase active site with a Ki of  ̃10-12 M. Furthermore, in the context of dsDNA, dZ forms a covalent adduct with DNA methyl transferases Wedekind, J. E., et al., (2003) Trends in Genet, 19, 207-16. However, because ssDNAs are targeted by neither deoxycytidine deaminases, cytidine deaminases nor DNA methyl transferases, an oligo of the form 5′-d(XnWRZYXn)-3′ (SEQ ID NO: 20) selectively inhibits AID (where X=any nucleotide and n=multiple variable sequences, the nature of which depends on the context required by each deaminase or its auxiliary protein. ‘n’ is an integer to reflect the length of any flanking nucleotides of identity X.
DNA oligonucleotides are chemically synthesized by use of an Applied Biosystems 392 DNA/RNA synthesizer. Due to the ability of zebularine, methods employ Ultramild CE deoxyphosphoramidites (Glen Research, VA) following the recommendations of the manufacturer. The 2′-deoxyzebularine phosphoramidite can be synthesized by the methods of Zhou and coworkers (Zhou, L., et al., (2002) J Mol Biol, 321, 591-9, and refs therein). DNA products are purified by reverse phase HPLC as the DMT-on and DMT-off adducts, as described by Wedekind and McKay (Wedekind, J. E. and D. B. McKay (2000) Methods Enzymol, 317, 149-68).
Sequences of dZ-containing oligos are derived from previous work that demonstrated AID is active on ssDNA bearing the SHM hotspot sequence WRCY. Therefore, test and control DNA oligos are of the form: 5′-(RGTW)n[WR(C/Z)Y](RGTW)n 3′ (SEQ ID NO: 21), where n=1, 2, 3 or 4; sequences are chosen to minimize secondary structure based on thermodynamic stability calculated with the DNA option of program RNA structure (Mathews, D. H. et al., (2002) J Mol Biol, 317, 191-203). AID expressing reporter cell lines is cultured for 1 hr in serum-free medium in the absence or presence of dC- or dZ-containing oligonucleotides at concentrations 10 nM-25 μM, and then transferred back into complete medium. SHM activity is measured by GFP reporter reversion rates; residual toxicity is assessed by measuring cell viability by propidium iodide exclusion. Verification of in vitro activity is followed by in vivo studies on transgenic mice (Jansen, B. and U. Zangemeister-Wittke (2002) Lancet Oncol, 3, 672-83; Juliano, R. L. et al., (2000) Curr Opin Mol Ther, 2, 297-303) data are available for optimal delivery conditions of antisense nucleotides in mice, resulting in efficient delivery to splenic B lymphocytes (Zhao, Q., et al., (1998) Antisense Nucleic Acid Drug Dev, 8, 451-8).
Example 5
CEM15/APOBEC-3G and Context Dependent Inhibitors
Cytidine deaminase inhibitors designed to target CEM15 are tested in cell culture for the purpose of improving retroviral infectivity, which has application to the expression of exogenous nucleic acids and application to laboratory infections. Viral infectivity is measured by use of vif (+) and vif (−) pseudotype viruses and host 293T cells either lacking or expressing the Context Dependent Inhibitor target CEM15. The inhibitory effect of CEM15 on the infectivity of vif+ and vif-HIV-1 particles by transient co-transfection of appropriate HIV-1 proviral DNA and CEM15 expression plasmids has been established (Sheehy, A. M., et al., (2000) Nature, 418, 646-50). An assay has been developed using a VSV G-protein pseudotyped lentiviral particles that corroborates prior results on CEM15 infectivity and is amenable to the rapid demarcation of the regions of HIV-1 DNA (or RNA) that are the targets of CEM15 deaminase activity. This methodology can be used in the identification of exact cytidine deaminase inhibitor substrates.
An Env-deleted HIV-1 proviral DNA vector (derived from pNL43; AIDS Reagent Repository) was modified by replacement of Nef with a GFP reporter gene and two in-frame stop codons were inserted that abolished Vif production (pHR-GFPΔvif) (confirmed by western blotting with anti-Vif antibodies (AIDs Reagent Repository). Stable, HA-tagged CEM15 expressing 293T cell lines were selected with puromycin and verified by western blotting with a HA specific monoclonal antibody (HA.11; BabCo). The expression of similar levels of full-length HA-tagged CEM15 (or mutant derivative thereof) are assayed in stable cell lines. Although structural modeling can predict focused mutations that impair deaminase activity without destabilizing the entire protein, expression of the mutants must be verified; the addition of the HA epitope tag has no effect on the ability of CEM15 to suppress infectivity (Sheehy, A. M., et al., (2000) Nature, 418, 646-50, 2000). Isogenic HIV-1 pro-viral DNAs are packaged into pseudotyped lentiviral particles by co-transfection with a plasmid encoding the VSV G-protein into 293T cells that lack endogenous CEM15 (−) or expressed wild type CEM15 (+) as controls. The resulting pseudotyped particles containing HIV-1 RNA of near full-length (with only a  ̃2 kb deletion) were quantified by reverse transcriptase (RT) assay; presence of p24Gag protein content can also be assayed by ELISA to normalize viral particles. A defined number (1×105 cpm of RT activity) of these particles were added to target, virus susceptible MT2 cells (5×105). To assess their infectivity, the percentage of cells that expressed the GFP indicator gene encoded by the packaged recombinant HIV-1 genome was quantified 24 hours later by flow cytometry (University of Rochester Core Facility). The results (FIG. 6) indicate that the expression of CEM15 in 293T cells resulted in at least a 100-fold decrease in vif (−) viral infectivity compared to particles generated in parental 293T cells. The low level of GFP expression from vif(−), CEM15+ particles is indistinguishable from background fluorescence in control cells [0.2%]. This assay is amenable to the use of existing HIV-1 proviral isotyped vectors that are deleted for different regions and different amounts of the HIV-1 genome. Deleted genes can be provided in trans by co-transfection of suitable expression plasmids. A recent comprehensive examination of viral proteins and host tRNALys3 derived from vif (−) virions revealed no significant biochemical or priming defects (Gaddis, N. C., et al., (2003) J Virol, 77, 5810-20).
The effect of cytidine deaminase inhibitor compounds on CEM15 can be tested by treating one or more of the cell types that express CEM15 with various concentrations of cytidine deaminase inhibitor (of the form in FIG. 5) followed by subsequent infection with HIV-1 pseudotyped virus containing reporter GFP. Within 48 hours post infection, cell culture supernatants containing viral particles are added to HeLa cells to test their infectivity, as evidenced by the appearance of green fluorescent cells in FACS analysis. Reduction or elimination of green fluorescent cells relative to that observed in infections from CEM15 (+) cells HIV-1 vif (−) that were not treated with cytidine deaminase inhibitor compounds are scored as a positive identification of cytidine deaminase inhibitor inhibition of CEM15 deaminase activity. Inhibition of GPF reversion by CEM15 is analogous to CEM15 (+) vif (+) cell/virus phenotype.
Example 6
AID Activity and SHM Specificity in Human Lymphoma Cell Lines
High levels of SHM on reporter constructs are strongly dependent on the presence of Ig cis-acting regulatory elements, such as the Eμ and Eκ enhancers (Betz A G, et al & Neuberger M S. 1994. Cell 77: 239-248; Bachl J, & Wabl M. 1996 Immunogenetics 45: 59-64; Bachl J et al. 1998. Proc Natl Acad Sci USA 95: 2396-2399 In particular, a GFP-mutant reversion substrate was shown to mutate over an order of magnitude more efficiently in the presence of a linked Eμ enhancer sequence (Bachl, et al., 1999 Eur J Immunol 166, 5051-64). This context-dependent specificity of SHM targeting is exploited to test whether lymphoma lines with different phenotypes also display differences in their Ig SHM targeting ability.
A number of lymphoma cell lines have been obtained including SUDHL-4 and 6, OCI Ly-3, -7, -10 and -19. Preliminary RT-PCR expression data on a subset of the lines show that they express different levels of AID mRNA (FIG. 1; wt, 646 bp band); PCR products of different size are also found in at least 4 of 6 lines tested. Interestingly, the Farage line, which is known not to undergo Ig SHM in vitro, displays predominantly the smaller PCR products with little if any wild-type. Two of the alternative products ( ̃940 bp and 530 bp) correspond to the expected sizes for two of the trAID isoforms already described, while the smallest 2 bands are novel. These PCR products are cloned and further characterized.
The role of AID and its isoforms is investigated in this set of lymphoma lines, using assays capable of distinguishing between Ig-targeted and non-Ig-targeted SHM. A modified SHM GFP reversion assay (Bachl J (1999) Eur. J. Immunol. 29, 1383-1389; Gabay C. (1999) Eur J Haematol 63, 180-191; Bachl J, et al., (2001) J Immunol 166, 5051-5057) has been developed. In this highly sensitive and quantitative assay, a mutation creating a stop codon embedded in a SHM hotspot sequence has been introduced in the GFP gene; as SHM targets this sequence, reversion occurs and the reverted cells are detected by their fluorescence.
The assay is modified so that the mutated GFP coding sequence from plasmid pI was transferred under the control of the mouse strong, ubiquitous promoter from the phosphoglycerate kinase-1 (pgk) gene, to generate the pgk-GFP* construct. A 0.7 kb fragment containing the entire Eμ core enhancer was inserted 3′ of the pgk polyadenylation site in the variant construct pgk-GFP*-Eμ. These constructs are stably transfected by electroporation in the lymphoma lines as well as the following control lines: —NIH3T3 wild type, as a negative control; —NIH3T3—AID transfectant, as positive control for pgk-GFP* reversion; the hypermutating murine pre-B cell line 18.81 (as positive control for Ig-specific SHM, pgk-GFP*-Eμ reversion).
Cotransfection of a pgk-neor antibiotic resistance gene followed by G418 selection is used to identify stably transfected clones. Presence of the GFP gene is assessed by PCR with GFP-specific primers. Individual clones are isolated and expanded (3-4/transfection, tested for comparable transcriptional activity), but large mixed pools of >50 transfectants are also maintained, which are analyzed in parallel to further control for potential integration-dependent effects and other sources of heterogeneity in the clonal transfectants. Reversion rates of reversion are quantified by flow cytometry at different time points, and the SHM activity on Eμ-bearing and non-Eμ-bearing plasmids compared as described by Bachl and colleagues. Sequencing of PCR-amplified GFP fragments from flow-sorted reverent GFP+ cells are used to further characterize the frequency and features of the mutations occurring in the individual lines.
Primary GC-like DLBCL samples have been shown to often display ongoing Ig SHM, while ABC-like DLBCL do not (Lossos I S, et al., (2000) Proc. Natl. Acad. Sci. USA 97, 10209-10213). However, this is not necessarily the case for the culture-adapted lymphoma lines described above, which could have diverged from their original phenotypes. Indeed, if non-specific SHM does promote a mutator-like phenotype, it can be expected to emerge during long-term culture even in lines with germinal center origin. Differences among cell lines in the targeting of SHM can be detected, with some lines showing Ig-specific SHM (reversion rate of pgk-GFP*-Eμ>>pgk-GFP*), and others non-Ig-specific SHM (reversion rate of pgk-GFP*-Eμ ̃pgk-GFP*).
Consistent with data indicating that the Farage line has no ongoing Ig SHM, this line expresses little wtAID mRNA, but instead several shorter isoforms. The Toledo line is known to display significant Ig variable gene heterogeneity, indicative of ongoing, Ig-targeted SHM. By analyzing lines with a range of SHM phenotypes, the role of AID in determining SHM specificity can be established. In particular, the extent by which a mutator phenotype is present in lymphoma lines can be established, and its relationship with the pattern of wtAID and trAID expression elucidated. Moreover, these same cell lines provide valuable model systems for other experiments described below. Lines displaying normal wtAID expression but lack of SHM specificity, suggest defects in AID accessory factors. Such lines represent useful models for the identification of such factors.
Example 7
Effect of AID Isoforms on SHM Targeting
In some primary CLL samples, lack of Ig gene SHM is accompanied by the expression of unusual alternatively spliced forms of AID mRNA; similar mRNAs are also found in some, but not all, lymphomas. If translated, these mRNAs give rise to truncated AID isoforms with extensive alterations or loss of the pseudocatalytic domain. It appears that some of these isoforms affect SHM targeting specificity. This could occur by two alternative mechanisms, either the isoforms act directly as non-specific mutators, or they do so by interfering with wtAID function, by generating heterodimers that are perhaps incapable of properly associating with targeting factors.
cDNAs from human wtAID and for presumptive trAID isoforms have already been cloned as described above; if the variant AID transcripts already identified is found to differ from the expected, CLL sample mRNAs are utilized to isolate the correct cDNAs. All RT-PCR products are first modified to bear protein tags for direct detection by shuttling them into appropriate plasmid vectors (6×His/Xpress- and HA-tag vectors are readily available). Different tags are appended to wtAID vs. trAIDs, to allow for specific immunoprecipitation experiments. The tagged cDNAs are then cloned into retroviral vectors. An effective system for retroviral delivery of wtAID using the MSCV-derived pMIG-IRES-GFP bicistronic vector has been established.
Because the AID functional assays utilize a GFP gain of function reporter, the retroviral vector is modified by replacing GFP with the dsRed2 fluorescent protein coding sequence (Clontech), thereby enabling AID expression detection by immunofluorescent microscopy and flow cytometry in the red channel (pMIG-IRES-Red). Thus, pMIG-IRES-GFP (wtAID) and -Red (both wtAID and trAIDs) vectors are generated. Correct expression of the expected products is tested by transduction of NIH3T3 cells followed by Western blot analysis.
Functional assays on the individual proteins are conducted in pgk-GFP* and pgk-GFP*-EμNIH3T3 reporter cells, transduced with the ds-Red expressing retroviral vectors. Transduced cells are analyzed by flow cytometry, with red fluorescence marking trAID-expressing cells, and green fluorescence showing revertants. Rates of reversion (GFP-positive/Red2-positive) are compared between reporters (pgk-GFP* and pgk-GFP*-Eμ) and between cells expressing wtAID or individual trAIDs. This reveals whether trAIDs retain any intrinsic activity.
The ability of trAIDs to affect wtAID activity and SHM targeting is established by inducing their expression in cell lines already expressing wtAID. Lymphoid cell lines are used expressing endogenous AID and confirmed to undergo Ig-targeted SHM such as the murine 18.81 cell line and one of the lymphoma lines described above. These lines are transduced with the various trAID-Red-encoding retroviral vectors, and SHM specificity measured on the basis of pgk-GFP* and pgk-GFP*-Eμ reversion rates as described above.
If a dominant effect of trAIDs on wtAID activity is observed, such as loss of SHM specificity in double-expressors, an interaction of wtAID and trAIDs is evaluated. NIH3T3 cells are simultaneously transduced with both pMIG-HA/wtAID-IRES-GFP and pMIG-His-Xpress/trAID-IRES-Red vectors; such procedure has been shown to successfully generate double-expressor cells. Double-fluorescent (green/red) cells are enriched by flow cytometry and expanded. To demonstrate heterodimerization, total cell protein lysates are prepared and reciprocal immunoprecipitation reactions are performed with anti-HA of anti-Xpress antibodies, according to the manufacturer's protocols. Immunoprecipitated products are separated by SDS-PAGE gels, and blotted onto nitrocellulose filters. The filters are detected with either anti-HA or anti-Xpress antibodies, followed by an HRP-conjugated secondary antibody and visualization by the West Pico Super Signal Chemiluminescent substrate (Pierce).
Unlike the murine lines described above, human lymphoma cell lines require a slightly more complex retroviral transduction protocol. Briefly, the pMIG retroviral vector DNAs are first transfected by lipofection into the Phoenix-ampho packaging cell line, and the retroviral supernatants derived from this first packaging cycle are then used to transduce the RD114 packaging cell line, which generates retroviruses with a Feline Leukemia Virus envelope able to efficiently transduce human cells. This “ping-pong,” sequential packaging method is required for maximum yields because the RD114 cell line does not transfect efficiently enough to be used directly. Retroviral supernatants from the second packaging cycle are then used for human cell line transduction; the infection rate in human lymphoma lines routinely averages from 20 to over 80% (FIG. 3).
Example 8
AID's Oncogenic Role in B Cell Neoplasias
The finding of T cell lymphomas and pulmonary adenomas in AID transgenics confirms the oncogenicity of AID. These transgenics did not acquire B cell malignancies, raising the question of whether AID expression in fact plays a pathogenetic role in B cell neoplasias. B cells can be tested to determine if they have the potential to be transformed through A/D-mediated oncogenesis, whether this is associated with initiation of tumorigenesis, and/or if AID expression only contributes to neoplastic progression.
In human activated B cell-like DLBCL, the presence of mutations in Ig genes suggests a post-germinal center origin. Sustained AID transcription in the absence of ongoing Ig SHM, coupled with the frequent finding of SHM-like oncogene mutations in these cells, clearly suggest a deregulation of AID targeting. To investigate AID's effects on B lymphocytes, as models of human lymphomagenesis, transgenic mice are generated that replicate the AID expression pattern observed in human ABC-like DLBCL.
The immunoglobulin IgH 3′ enhancer element (3′EH) is involved in the regulation of immunoglobulin gene expression and class switch recombination during B cell activation and terminal B cell differentiation. When linked to an Ig variable region promoter, the 3′EH hs (1,2) element has been shown to reliably direct transgene expression specifically in activated B cells and plasma cells. A transgenic expression vector containing the murine VH186.2 promoter and the 3′EH hs(1,2) enhancer is available. His-tagged wtAID cDNA is cloned into this vector (3′E-AID construct), and transgenic mice are generated by pronuclear microinjection of C57Bl/6 zygotes.
Transgenic mice are identified by PCR for the fusion gene containing AID cDNA and the human γ-globin 3′UTR/poly-A site present in the vector. Appropriate expression of the transgene in activated B cells will be established by RT-PCR on flow-sorted B cell subpopulations (resting, B220+, IgDhiIgMlo B cells; germinal center B220+/GL7+ cells; plasma cells, large B220lo, CD43+, sIg-cells) and by immunohistochemistry on splenic section using the anti-Xpress mAb and counterstains for GC cells (PNA+) and plasma cells (cytoplasmic Ighi). Transgene inducibility are also verified in vitro by culture of primary splenic B cells with activators (LPS, 20 μg/ml; anti-CD40 clone HM40-3, 2 μg/ml) known to induce 3′EH activity, followed by RT-PCR and Western blotting at different time points (day 0, 1, 2, 4 of activation). Transgenic AID activity are functionally assessed by breeding the 3′E-AID transgenics with AID-deficient mice; if AID activity is present, at least partial complementation of the defect in SHM and CSR is observed in these mice. 3′E-AID/A/D−/− mice are evaluated for their ability to undergo SHM by VH region sequencing using primers for Ig VHJ558 segments following sheep red blood cell immunization, and class switching by ELISA on pre- and post-immunization serum.
The ability of transgenic AID expression to induce B cell neoplasias is evaluated by monitoring the health status of transgenics as they age. Mice displaying signs of ongoing disease (cachexia, lack of activity, fur loss, hunched posture, etc) are sacrificed and their lymphoid tissues (bone marrow, spleen, peripheral and mesenteric lymph nodes and Peyer's patches) analyzed histologically and by flow cytometry with an array of antibodies specific to B cell- (CD19, CD21, CD23, IgM, IgD, Igκ/λ, GL-7), T cell- (CD3ε, CD4, CD8) and myeloid markers (Mac-1, Gr-1). Signs of B lymphoid expansion can be monitored; if this is observed, emergent clonality is established by Southern blot analysis of Ig gene rearrangements in the tissue's genomic DNA.
To distinguish potential effects of AID as a progression factor, transgenic mice are bred onto genetic backgrounds already predisposed to B cell lymphoma development. Initially, Eμ-bcl2 transgenic mice are used. This transgene results in rare, late (>12 months) lymphomas on a normal background, but dramatically accelerates lymphomagenesis when combined with another transgenic oncogene, such as Eμ-c-myc, suggesting that accumulation of multiple secondary mutagenic hits is required for disease progression in these mice. By generating double transgenics, any potential effect of AID expression in accelerating lymphoma development is established. In addition, should the effect of AID in the bcl2 background be weak, breeding with Eμ-c-myc transgenic mice, which display a more aggressive baseline phenotype, can also be used.
3′EH-hs(1,2)-dependent constructs are known to reliably express in activated B cells. The availability of AID-deficient mice allows the unequivocal determination of transgene expression and activity. Evidence of B cell malignancies following sustained AID expression, either as a primary event (in a normal background), or as a progression factor (in lymphoma-susceptible backgrounds) confirms that B lineage cells can be targets of AID-mediated transformation, and provide a valuable model for the study of the mechanisms of human AID-mediated lymphomagenesis. Lack of a cancer phenotype also can represent an informative result, as it suggests either an intrinsic protection of B lymphocytes against SHM mistargeting, or more likely, based on the strong evidence for SHM-like oncogene mutations in human lymphomagenesis, a role for still unidentified SHM effectors downstream of AID.
Example 9
Molecular Identification of Non-Ig Gene AID Targets in Lymphomas
A small number of oncogenes (c-myc, Pim1, Pax5, RhoH/TTF) have been found to bear hallmarks of SHM in human lymphoma samples. Additional important targets can exist whose mutation contributes to neoplastic development. In this experiment, a mutation screening method based on a genetic selection strategy that exploits bacterial DNA mismatch repair is used. This method has been used to identify single nucleotide polymorphism in human genomic DNA and has been modified herein.
These experiments take advantage of the mismatch repair detection (MRD) system, a novel, high-throughput bacterial positive genetic selection strategy for human disease related single nucleotide polymorphisms. In this example, the selection system is used as it was originally intended for screen mismatches in genomic DNA sequences.
Genomic DNA isolated from a non-B cell source (e.g. fibroblasts) and from lymphomas from AID-transgenic mice is digested with DpnII (average size  ̃0.3 kb) and cloned separately into two different plasmids. Unmethylated plasmids (grown in a dam methylase-deficient E. coli strain) containing the ‘control’ inserts (from normal tissue DNA) also encode an intact Cre recombinase, whereas the methylated plasmids contain putative mutated fragments from lymphoma cells and encode an inactive 5 nucleotide deletion mutant of Cre. Heteroduplexes formed in vitro between the two plasmid libraries by melting and reannealing are transformed into a bacterial strain that harbors an F′ episome carrying a ‘floxed’ tetracycline resistance gene. Repair of the mismatch uses the methylated strand as template, resulting in loss of the functional Cre recombinase gene and retention of the ‘floxed’ tetracycline resistance gene. Non-mismatched heteroduplexes, instead, induce no repair, express functional Cre, and result in TetR. LoxP-mediated deletion. The TetR clones obtained through the MRD process therefore contain exclusively fragments displaying sequence heterogeneity between the original samples, and will be subject to further selection and identification steps.
Example 10
Deaminase Inhibitors as Agents for AID-Targeted Pharmacological Intervention
AID, like other cytidine deaminases, is known to be inhibited by Zn2+ chelation. It has previously been shown that two types of Zn2+ chelators and metalloenzyme inhibitors, tetracyclines and hydroxamates, display a remarkable ability to inhibit CSR in vitro at therapeutic concentrations. Tetracyclines also inhibit antibody responses in vivo. Although A/D mRNA expression was not affected by tetracycline treatment in vitro), the possibility exists that the observed inhibitory activity reflected an indirect effect on CSR, rather than a direct inhibition of AID function. Because both tetracyclines and hydroxamates (and especially the former) are available drugs which could, if necessary, be rapidly applied in a clinical setting, they can be tested to determine if they are capable of directly inhibiting AID function in the model systems described above.
The same reporter cells lines and assays are used as described in Example 9. A/D activity on the GFP reversion assay is assayed in cells cultured in the presence of increasing concentrations of doxycycline (1-10 μg/ml) and the KB8301 hydroxamate (5-50 μM) (Becton Dickinson). Importantly, the assays are performed on cells expressing both endogenous (18.81, lymphoma lines) as well as exogenous AID (NIH3T3 transfectants); this controls for the possibility that either drug can act on some other component of the B cell SHM/CSR activation pathway (which is absent in NIH3T3). Assuming inhibition will be observed in all systems, additional agents are tested, including other tetracyclines and FDA-approved non-antibiotic tetracycline analogs (CMT series, from Collagenex Pharmaceuticals), as well as hydroxamates approved for cancer therapy, such as marimastat/BB2516/TA2516 (British Biotech/Schering Plough). The optimal agents, based on inhibitory activity and known pharmacological properties, can then be tested in the AID transgenic mice derived in Example 7, if appropriate, to establish their ability to arrest of delay tumor onset and/or progression.
Example 11
Making Peptide-Oligo Conjugates
One method of making a peptide-oligo conjugate is to use Fmoc chemistry and synthesize the peptide from an oligo synthesized on amino-CPG. Deprotection of peptides synthesized using Fmoc chemistry requires 50% TFA and t-boc synthesized peptides require HF. Another method is to use a heterobifunctional crosslinking reagent to link a synthetic peptide, containing an N-terminal lysine, to a 5′-Thiol modified oligo or conversely a 5′-amino modified oligo to a cysteine containing peptide. An example of a crosslinking reagent is N-Maleimido-6-aminocaproyl-(2′-nitro, 4′-sulfonic acid)-phenyl ester. Na+ (mal-sac-HNSA) from Bachem Bioscience (cat. # Q-1615). Reaction of this crosslinker with an amino group releases the dianion phenolate, 1-hydroxy-2-nitro-4-benzene sulfonic acid a yellow chromophore. The chromophore allows both quantitation of the coupling reaction as well as act as an aid in monitoring the separation of activated peptide from free crosslinking reagent using gel filtration.
Method A: Couple Peptide Amine to Oligo Thiol (Peptide MW should be >5,000 to be Excluded from Desalting Column).
The following is an example of one method that can be used to couple a peptide amine to an oligo thiol. Step 1: Synthesize a peptide with an N-terminal, or internal, lysine (The epsilon amino group is more reactive than an alpha amino group). This can be done for the TAT peptide. Step 2: Synthesize an oligonucleotide with a 5′ Thiol group. These are available from Glen Research. Step 3: React peptide with excess mal-sac-HNSA (pH 7.5 Sodium phosphate). Step 4: Separation of peptide-mal-sac conjugate from free crosslinker and buffer exchange (pH 6.0 Sodium phosphate) using a gel filtration column (NAP or eq.). (Peptide must be large enough to separate from the free linker which can be visualized as a yellow band. Do not collect yellow band with peptide. Step 5: Activate thiol modified oligo, desalt and buffer exchange (pH 6 Sodium phosphate) on NAP 5 column. Step 6: React activated peptide with Thiol modified oligo. Step 7: Purify Peptide-Oligo conjugate by ion exchange chromatography on Nucleogen DEAE-500-10 or eq. Elution order: free peptide, peptide-oligo, free oligo.
Method B: Couple Oligo Amine to Peptide Cysteine (Oligos>15mers are Excluded from Desalting Column).
The following is an example of one method that can be used to couple an oligo amine to a peptide cysteine. Use above procedure switching oligo for peptide. Step 1: Synthesize a peptide with an N-terminal, or internal, cysteine. In this method, Tat is a basic protein with numerous reactive lysine side-chains. Step 2: Synthesize an oligonucleotide with a 5′ amino modifier. Step 3: Purify oligo Trityl-on by RP HPLC or cartridge. Step 4: React oligo with excess mal-sac-HNSA (pH 7.5 Sodium phosphate). Step 5: Separation of oligo-mal-sac conjugate from free crosslinker and buffer exchange (pH 6 Sodium phosphate) using a gel filtration column (NAP or eq.). Note oligo must be large enough to separate from the free linker which can be visualized as a yellow band. Do not collect yellow band with oligo. Step 6: Dissolve peptide in pH 6.0 Sodium phosphate buffer and react with activated oligo. Step 7: Purify Peptide-Oligo conjugate by ion exchange chromatography on Nucleogen DEAE-500-10 or eq. Elution order: free peptide, peptide-oligo, free oligo.
Throughout this application, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.
It will be apparent to those skilled in the art that various modifications and variations can be made in the present invention without departing from the scope or spirit of the invention. Other embodiments of the invention will be apparent to those skilled in the art from consideration of the specification and practice of the invention disclosed herein. It is intended that the specification and examples be considered as exemplary only, with a true scope and spirit of the invention being indicated by the following claims.
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## Claims

1. A context-dependent cytidine deaminase inhibitor comprising a nucleoside incorporated in a polymeric substrate, wherein the polymeric substrate selectively targets a cytidine deaminase, further wherein the polymeric substrate comprises a mooring sequence.

2. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the nucleoside comprises a base, wherein the base of the nucleoside is susceptible to nucleophilic attack.

3. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the nucleoside comprises a base, wherein the base of the nucleoside comprises a sp2 carbon center susceptible to nucleophilic attack.

4. The context-dependent cytidine deaminase inhibitor of claim 3, wherein an electrophilic group is present at the sp2 carbon center.

5. The context-dependent cytidine deaminase inhibitor of claim 3, wherein the Sp2 carbon center is a carbonyl group, an imino group, or an alkenyl group.

6. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the nucleoside is susceptible to nucleophilic attack by a metal-bound hydroxide.

7. The context-dependent cytidine deaminase inhibitor of claim 6, wherein the metal-bound hydroxide is zinc hydroxide.

8. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the nucleoside comprises a pyrimidine.

9. The context-dependent cytidine deaminase inhibitor of claim 1, wherein when the nucleoside comprises a pyrimidine, and wherein nucleophilic attack occurs at C4 of the pyrimidine.

10. The context-dependent cytidine deaminase inhibitor of claim 9, wherein the pyrimidine has an electron-withdrawing group at C4.

11. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the nucleoside comprises a base, wherein the base of the nucleoside has at least one Sp3 carbon center.

12. The context-dependent cytidine deaminase inhibitor of claim 11, wherein the sp3 carbon center has at least one —OR group, wherein R is hydrogen, alkyl, aryl, aralkyl, alkenyl, alkynyl, or acyl.

13. The context-dependent cytidine deaminase inhibitor of claim 1, wherein when the nucleoside comprises a pyrimidine, the nucleoside comprises a sp3 carbon center at C4 of the pyrimidine.

14. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the nucleoside comprises a base, wherein the base of the nucleoside comprises at least one group capable of hydrogen bonding.

15. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the nucleoside is selected from the group consisting of 4-fluorozebularine, 2′-deoxy, 2′-fluorozebularine, 3,4,5,6-tetrahydro-2′-deoxyuridine, nebularine; 8-azanebularine; coformycin; or zebularine.

16. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the polymeric substrate comprises oligonucleotide residues.

17. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the targeted cytidine deaminase is APOBEC-1.

18. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the targeted cytidine deaminase is AID.

19. The context-dependent cytidine deaminase inhibitor of claim 18, comprising WRZY, wherein W is Adenine or Thymine, wherein R is a purine, wherein Z is the nucleoside, and wherein Y is a pyrimidine.

20. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the targeted cytidine deaminase is CEM15.

21. A composition comprising the context-dependent cytidine deaminase inhibitor of claim 1 and a pharmaceutical carrier.

22. A cell comprising the context-dependent cytidine deaminase inhibitor of claim 1.

23. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the targeted cytidine deaminase is APOBEC-3F.

24. The context-dependent cytidine deaminase inhibitor of claim 1, wherein the targeted cytidine deaminase is APOBEC-3B.