Novel phosphoramidate compounds and methods of use

Abstract

This invention provides compounds, compositions and methods for treating cancer, infectious disease, an autoimmune disorder or an inflammatory condition. Therapeutic compounds useful in the methods of this invention are 5′-phosphoramidatyl, 1,5-substituted pyrimidine compounds, derivatives, analogs and pharmaceutically acceptable salts thereof

Description

TECHNICAL FIELD

[0002] The present invention is in the field of medicinal chemistry and relates to other areas such as pharmacology, oncology and immunology. In particular, it provides compounds and methods to treat hyperproliferative disorders.

BACKGROUND

[0003] Throughout and within this disclosure, various publications, patents, published patent applications and references are identified by first author and date, within parentheses, patent number, publication number or by web address. If the complete bibliographic citation is not provided after the publication or reference, it is at the end of the specification, immediately preceding the claims. The disclosures of all publications, references and information provided at the web addresses are hereby incorporated by reference into this disclosure to more fully describe the state of the art to which this invention pertains.

[0004] Hyperproliferative cells grow at a rate over that of normal or healthy cells. The presence of these abnormal cells has been linked to many pathologies, e.g., cancer, infectious disease, autoimmune disorders and inflammatory conditions or diseases. In many instances, they are useful diagnostic indicators. In other instances, subcellular changes linked to progression toward the hyperproliferative state are useful prognostic indicators of disease progression or its curative treatment.

[0005] Cancer cells are hyperproliferative, i.e., characterized by uncontrolled growth, de-differentiation and genetic instability, that express as aberrant chromosome number, chromosome deletions, rearrangements, loss or duplication beyond the normal diploid number. (Wilson, J. D. et al. (1991)). This genomic instability may be caused by several factors. One of the best characterized is the enhanced genomic plasticity which occurs upon loss of tumor suppressor gene function (e.g., Almasan, A. et al. (1995a) and Almasan, A. et al. (1995b)). The genomic plasticity lends itself to adaptability of tumor cells to their changing environment, and may allow for the more frequent mutation, amplification of genes, and the formation of extrachromosomal elements (Smith, K. A. et al. (1995) and Wilson, J. D. et al. (1991)). These characteristics provide for mechanisms resulting in more aggressive malignancy because they allow tumors to rapidly develop resistance to natural host defense mechanisms, biologic therapies (See Wilson, J. D. et al. (1991) and Shepard, H. M. et al. (1988)), as well as to chemotherapeutics (See Almasan, A. et al. (1995a); and Almasan, A. et al. (1995b)).

[0006] The heterogeneity of malignant tumors with respect to their genetics, biology and biochemistry as well as primary or treatment-induced resistance to therapy mitigate against curative treatment. Moreover, many anticancer drugs display only a low degree of selectivity, causing often severe or even life threatening toxic side effects, thus preventing the application of doses high enough to kill all cancer cells. Searching for anti-neoplastic agents with improved selectivity to treatment-resistant pathological, malignant cells remains, therefore, a central task for drug development.

[0007] The function of tumor suppressor genes is a major focus of recent attempts to develop innovative therapeutics for the treatment cancer. The products of tumor suppressor gene expression are generally characterized as negative regulators of cell proliferation (Knudson, A. G. (1993) and Weinberg, R. A. (1995)). Thus, therapeutic approaches to date include gene therapies to restore inactive or missing tumor suppressor function in cancer cells to re-establish normal cellular function or induce apoptosis (Clayman, G. L. (2000) and Knudson, A. G. (1993)).

[0008] Loss of RB/p16 function can result in similar proinflammatory, proliferative and dedifferentiating effects on cells (Carson, R. A. and Haneji, N. (1999); Shim, J. et al. (2000); Wolff, B. and Naumann, M. (1999); DiCiommo et al. (2000)), and alteration in cell-cell interactions (Plath et al. (2000)). Inactivation of tumor suppressor function by somatic mutation or via interaction with virally-encoded proteins is proposed to contribute to the proliferative/inflammatory aspect of athersclerosis, restenosis or other hyperproliferative diseases (Tanaka, K. et al. (1999); Aoki, M. et al. (1999); Guevara, N. V. et al. (1999); and Iglesias, M. et al. (1998)). Finally, the expression of the proinflammatory cytokine, macrophage inhibitory factor (MIF), may be capable of inactivating p53 function in some cell types (Hudson, J. D. et al. (1999); Cordon-Cardo, C. and Prives, C. (1999); and Portwine, C. (2000)).

[0009] Functional loss of tumor suppressor genes also has been linked to inflammatory or autoimmune diseases that have cellular hyperproliferation as one of their characteristics (Cordan-Cardo, C. and Prives, C. (1999)) and/or defective apoptosis (programmed cell death) (Mountz, J. D. et al. (1994)). These include: rheumatoid arthritis, systemic lupus erythmatosus, psoriatic arthritis, reactive arthritis, Crohn's disease, ulcerative colitis and scleroderma. Table 1 lists literature examples which suggest that such a link may exist.

TABLE 1
Literature Examples Suggesting that Biological Expression of p53 Tumor
Suppressor Mutation/Inactivation Relates to Noncancer Hyperproliferative Disease,
Autoimmune Disease and Inflammation.
Impact	Disease Effect	Reference
Increased IL6	Proliferation	Han, et al. (1999)
	Inflammation
	Rheumatoid Arthritis
Increased metalloproteinases	Tissue Degradation	Sun, Y. et al.
(2000)
Increased proliferation of	Rheumatoid arthritis	Aupperle, K. R. et
al. synovial cells		(1998)
Genetic instability	Chronic inflammation	Tak, P. P. et al.
		(2000)
and disease progression	Ulcerative colitis	Lang, S. M. et al.
		(1999)
Increased expression of	Proliferation	Banerjee, D. et al.
E2F regulated genes	Drug resistance	(1998)
(TS, DHFR)	Multiple autoimmune
	and inflammatory diseases
Viral proteins expression	Athersclerosis	Tanaka, K. et al.
leading to p53 inactivation		(1999)
Increased angiogensis	Supports hyper-proliferative	Zhang, L. et al.
	States, ex. enabling	(2000)
	atheromaorpannus formation.

[0010] The hyperproliferative phenotype has also been linked to resistance to chemotherapy in cancer, infectious disease, autoimmune disease and inflammatory conditions. Some hyperproliferative cells overexpress an intracellular enzyme that is related to any of a loss of tumor suppressor gene product function, drug resistance or genetic instability. A number of cellular mechanisms are involved in drug resistance, e.g., altered metabolism of the drug, impermeability of the cell with regard to the active compound or accelerated drug elimination from the cell, altered specificity of an inhibited enzyme, increased production of a target molecule, increased repair of cytotoxic lesions, or the bypassing of an inhibited reaction by alternative biochemical pathways. Enzymes activated or overexpressed and related to drug resistance include, but are not limited to thymidylate synthase (TS) (Lönn, U. et al. (1996); Kobayashi, H. et al. (1995); Jackman, A. L. et al. (1995)), dihydrofolate reductase (Banerjee, D. et al. (1995) and Bertino, J. R. et al. (1996)), tyrosine kinases (TNF-α, Hudziak, R. M. et al. (1988)) and multidrug resistance (Stühlinger, M. et al. (1994)); Akdas, A. et al. (1996); and (Tannock, I. F. (1996)); and ATP-dependent multidrug resistance associated proteins (Simon, S. M. and Schnindler, M. (1994)). Alternatively, resistance to one drug may confer resistance to other, biochemically distinct drugs. Amplication of certain genes is involved in resistance to chemotherapy. Amplification of dihydrofolate reductase (DHFR) is related to resistance to methotrexate while amplification of the gene encoding thymidylate synthase is related to resistance to tumor treatment with 5-fluoropyrimidine.

[0011] Overexpression of enzymes encoded by human and animal pathogens, and in which the inhibitors have failed due to development of resistance, also has been linked to disease. Indeed, resistance to antibiotics is a major health care problem. In infectious disease, most drug resistance is enzyme mediated. Typically, an enzyme expressed by the infectious agent rapidly modifies the chemotherapeutic or antibiotic, thereby abolishing its therapeutic activitiy. Amplified expression of beta-lactamases accounts for more than one-third of all beta-lactam antibiotic resistant isolates (Felmingham and Washington (1999)), including the majority of resistant Haemophilis influenza (upper respiratory infections) and Moraxella catarrhalis (otitis media). In addition, genes conferring resistance to various alternative types of antibiotics occur in nature and have become increasing common in populations of infectious organisms. Recently, infectious agents carrying sets of genes simultaneously conferring resistance to multiple antibiotic agents have arisen making treatment by traditional antibiotic therapy difficult.

[0012] Thus, novel compounds and therapies are necessary overcome the limitations of current therapies. This invention satisfies this need and provides related advantages as well.

DISCLOSURE OF THE INVENTION

[0013] Novel phosphoramidatyl, 1,5-substituted pyrimidine compounds, derivatives, analogs, and pharmaceutically acceptable salts thereof and compositions containing the compounds are provided by this invention. The compounds can be combined with an additional therapeutic drug or therapy. The compounds and compositions are useful diagnostically and therapeutically.

[0014] This invention provides methods for treating cells or tissue involved in a pathology characterized by hyperproliferative cells. Examples of pathologies include, but are not limited to cancer, infectious disease, autoimmune disease and an inflammatory condition. The cells and/or tissue are contacted with an effective amount of one or more of a compound of this invention. Applicants have previously noted that some compounds of this class are effective in treating hyperproliferative disorders. See U.S. Pat. No. 6,339,151B1 and 6,245,750, issued Jan. 15, 2002 and Jun. 12, 2001, respectively and published international patent applications PCT/US00/19844; PCT/US00/20007; and PCT/US00/20008.

[0015] The methods can be practiced in vitro, ex vivo and in vivo. In one aspect, the cells or tissue are characterized by loss of tumor suppressor function. In another aspect, the pathological mcells overexpress an endogenous intracellular enzyme such as thymidylate synthase or a target enzyme. In yet a further aspect, the cells have become resistant to a chemotherapeutic drug, e.g., 5-fluorouracil (5FU). In another aspect, an infectious agent overexpresses a target enzyme which in turn confers resistance.

[0016] When practiced in vivo, the invention provides a method for treating a subject having a pathology characterized by hyperproliferative cells, e.g., cancer, an infectious disease, autoimmune disorder or an inflammatory condition, by delivering to the subject an effective amount of at least one or more of the 5′-phosphoramidatyl, 1,5-substituted pyrimidine, derivative, analog or pharmaceutically acceptable salt thereof. Methods for synthesizing the compounds are described herein and in Applicants' prior patent literature, e.g., PCT/US98/16607 and PCT/US99/01332, which describe the compounds as “ECTA” compounds or prodrugs.

[0017] The methods are further useful to treat or ameliorate the symptoms of a hyperproliferative disorder, e.g., cancer, infectious disease, autoimmune disease or an inflammatory condition, in a subject by administering to the subject an effective amount of a compound or composition of this invention.

[0018] Further provided are compositions and methods for reversing reistance to a chemotherapeutic by contacting the resistant cells or tissue with a compound of this invention. Yet further provided are methods and compositions for enhancing the efficacy of drugs that treat or ameliorate symptons associated with cancer, infectious disease, autoimmune disease or an inflammatory condition.

[0019] Assays for identifying agents, therapies and combinations thereof that inhibit the growth of pathological cells or tissue are also provided herein.

BRIEF DESCRIPTION OF THE FIGURES

[0020] FIG. 1 is a graph showing fluorescent products from incubation of Bromovinyl, 2′-Deoxyuridine Monophosphate (“BVdUMP”) with Recombinant Human Thymidylate Synthase (“rHuTS”). Incubation of BVdUMP with thymidylate synthase (“TS”) results in a time and enzyme dependent generation of fluorescent product(s). BVdUMP was incubated with the indicated amounts of rHuTS in the standard reaction mixture at 30° C. (Materials and Methods), except that N5, N10-methylenetetrahydrofolate was omitted from the reaction. The numbers adjacent to each data curve refer to TS enzyme units.

[0021] FIG. 2 shows the results of an experiment that demonstrates that preincubation with BVdUMP does not inactivate rHuTS. Human thymidylate synthase was pre-incubated in reaction mixtures with and without 125 μM BVdUMP. After 20 hours, BVdUMP was added to a concentration of 125 μM, dUMP to a final concentration of 125 μM, and N5, N10-methylene tetrahydrofolate was added to 70 μM. Thymidylate synthase activity was determined by measuring the increase in A340. Solid circles (preincubated reaction), Open circles (no preincubation).

[0022] FIGS. 3A and 3B show detection of BVdUMP in H630R10 cells treated with NB1011. H630 R10 cells were treated with 100 μM NB1011 for 5 days, then analyzed by LC/MS as described in Materials and Methods.

[0023] FIG. 4 demonstrates that NB1011 does not irreversibly inactivate TS in vivo. The effect of NB1011 on TS activity in intact cells is completely reversible. TS activity was measured in intact RKO cells by release of [3H]2O from 5-[3H]deoxyuridine as described in Materials and Methods. NB1011 was washed out of cells by replacing with fresh media, incubating for 60 minutes at 37 ° C., then repeating this procedure. Control and untreated cells were subjected to the same washing procedure.

[0024] FIGS. 5A and 5B show that there are marked similarities between in vitro efficacy requirements for NB1011 and anti-HER2. A), Data are taken from Tables 4, 5, and 8. B). Data from Shepard, et al. (1991). Vertical bars show standard error of means calculated using the Mann-Whitney U test.

[0025] FIG. 6 shows that NB1011 is highly active against Tomudex resistant cancers. Cytotoxicity vs. TDXR cell lines was measured in the alamarBlue assay, as described in Materials and Methods, below.

[0026] FIG. 7 shows transcript levels of thymidylate synthase in human normal and tumor colon tissues. RT-PCR analysis was performed as described in Materials and Methods, below. The ratio of TS mRNA in tumor vs. normal tissue samples, each normalized to β-actin was (left to right) 14.35, 7.31, 0.75, 59.5, 2.53, 24.1, and 4.0.

[0027] FIG. 8A shows that NB1011 inhibits growth of 5-FU resistant colon cancer. Treatment of nude mice bearing H630R10 (5FU Resistant) human colon carcinoma. Tumor measurements began on the first day of treatment (Day 1).

[0028] FIG. 8B shows long term response to NB1011. Analysis of pooled data at Day 25. Statistical analysis is described in the Materials and Methods section below.

[0029] FIG. 9 is a graph showing mRNA levels of TS in multiple human tissues. TS mRNA levels were determined by using RT-PCR. The DNA bands corresponding to thymidylate synthase were quantified and normalized to that of β-actin by Molecular Dynamics Storm. Column 1 to 20 indicate the TS mRNA level in human normal tissues. The expression levels are expressed as values relative to that of colon (column 16). Columns 21 and 22 show the average TS transcript levels in 7 matched colon normal and cancer tissues. The expression values were relative to that of normal colon tissues (column 21).

MODES FOR CARRYING OUT THE INVENTION

[0030] General Techniques

[0031] The practice of the present invention will employ, unless otherwise indicated, conventional techniques of organic chemistry, pharmacology, molecular biology (including recombinant techniques), cell biology, biochemistry, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature, such as, “MOLECULAR CLONING: A LABORATORY MANUAL” Second Edition (Sambrook et al., 1989); “OLIGONUCLEOTIDE SYNTHESIS” (M. J. Gait, ed., 1984); “ANIMAL CELL CULTURE” (R. I. Freshney, ed., 1987); the series “METHODS IN ENZYMOLOGY” (Academic Press, Inc.); “HANDBOOK OF EXPERIMENTAL IMMUNOLOGY” (D.M. Weir & C. C. Blackwell, eds.); “GENE TRANSFER VECTORS FOR MAMMALIAN CELLS” (J. M. Miller & M. P. Calos, eds., 1987); “CURRENT PROTOCOLS IN MOLECULAR BIOLOGY” (F. M. Ausubel et al., eds., 1987, and periodic updates); “PCR: THE POLYMERASE CHAIN REACTION” (Mullis et al., eds., 1994); “CURRENT PROTOCOLS IN IMMUNOLOGY” (J. E. Coligan et al., eds., 1991); and J. March, ADVANCED ORGANIC CHEMISTRY: REACTIONS, MECHANISMS AND STRUCTURE, 4th edition (John Wiley & Sons, NY (1992)).

[0032] Definitions

[0033] As used herein, certain terms may have the following defined meanings.

[0034] As used in the specification and claims, the singular form “a,” “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a cell” includes a plurality of cells, including mixtures thereof. Similarly, use of “a compound” for treatment or preparation of medicaments as described herein contemplates using one or more compounds of this invention for such treatment or preparation unless the context clearly dictates otherwise.

[0035] As used herein, the term “comprising” is intended to mean that the compositions and methods include the recited elements, but not excluding others. “Consisting essentially of” when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination. Thus, a composition consisting essentially of the elements as defined herein would not exclude trace contaminants from the isolation and purification method and pharmaceutically acceptable carriers, such as phosphate buffered saline, preservatives, and the like. “Consisting of” shall mean excluding more than trace elements of other ingredients and substantial method steps for administering the compositions of this invention. Embodiments defined by each of these transition terms are within the scope of this invention.

[0036] As used herein, the term “analog” is intended to mean a structural derivative of a compound that differs from it by at least one element. The term “derivative” is intended to mean a compound derived or obtained by another and containing the essential elements of the parent substance.

[0037] The term “alkyl” refers to and covers any and all groups which are known as normal alkyl, branched-chain alkyl and cycloalkyl. As used herein, “alkyl” is intended to include both branched, straight-chain, substituted or unsubstituted saturated aliphatic hydrocarbon groups having the specified number of carbon atoms. Examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, and s-pentyl.

[0038] Lower alkyl means the above-defined broad definition of alkyl groups having 1 to 6 carbons in case of normal lower alkyl, and as applicable 3 to 6 carbons for lower branch chained and cycloalkyl groups. Lower alkenyl is defined similarly having 2 to 6 carbons for normal lower alkenyl groups, and 3 to 6 carbons for branch chained and cyclo- lower alkenyl groups. Lower alkynyl is also defined similarly, having 2 to 6 carbons for normal lower allynyl groups, and 4 to 6 carbons for branch chained lower alkynyl groups.

[0039] “Haloalkyl” is intended to include both branched and straight-chain saturated aliphatic hydrocarbon groups having the specified number of carbon atoms, substituted with 1 or more halogen (for example —CVFW where v=1 to 3 and w=1 to (2v+1)). Examples of haloalkyl include, but are not limited to, trifluoromethyl, trichloromethyl, pentafluoroethyl, and pentachloroethyl.

[0040] “Carbocyclic” is intended to include saturated or unsaturated ring groups, such as cyclopropyl, cyclobutyl, or cyclopentyl. They may be substituted or unsubstituted.

[0041] The term “alkenyl” refers to and covers normal alkenyl, branch chain alkenyl and cycloalkenyl groups having one or more sites of unsaturation. Similarly, the term alkynyl refers to and covers substituted or unsubstituted normal alkynyl, and branch chain alkynyl groups having one or more triple bonds. “Alkynyl” is intended to include hydrocarbon chains of either a substituted or unsubstituted straight or branched configuration and one or more triple carbon-carbon bonds which may occur in any stable point along the chain, such as ethynyl and propynyl.

[0042] Some of the compounds of the present invention may have trans and cis (E and Z isomers. In addition, the compounds of the present invention may contain one or more chiral centers and therefore may exist in enantiomeric and diasteromeric forms. Still further oxi and related compounds of the present invention may exist in syn and anti isomeric forms. The scope of the present invention is intended to cover all such isomers per se, as well as mixtures of cis and trans isomers, mixtures of syn and anti isomers, mixtures of diastereomers and racemic mixtures of enantiomers (optical isomers) as well. In the present application, when no specific mention is made of the configuration (cis, trans, syn, anti, R or S) of a compound (or of an asymmetric carbon) then a mixture of such isomers, or either one of the isomers is intended. In a similar vein, when in the chemical structural formulas of this application a straight line representing a valence bond is drawn to an as etric carbon, then isomers of both R and S configuration, as well as their mixtures are intended. Defined stereochemistry about an asymmetric carbon is indicated in the formulas (where applicable) by a solid triangle showing beta configuration, or by a hashed line showing alpha configuration.

[0043] All numerical designations, e.g., pH, temperature, time, concentration, and molecular weight, including ranges, are approximations which are varied (+) or (−) by increments of 0.1. It is to be understood, although not always explicitly stated that all numerical designations are preceded by the term “about”. It also is to be understood, although not always explicitly stated, that the reagents described herein are merely exemplary and that equivalents of such are known in the art.

[0044] A “subject” is a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets.

[0045] An “effective amount” is an amount sufficient to effect beneficial or desired results. For example, a therapeutic amount is one that achieves the desired therapeutic effect. This amount may be the same or different from a prophylatically effective amount, which is an amount necessary to prevent onset of disease or disease symptoms. An effective amount can be administered in one or more administrations, applications or dosages.

[0046] A “pathological cell” is one that is pertaining to or arising from disease. In one aspect, a pathological cell is identified from normal or healthy cells by presence of an endogenous intracellular enzyme such as TS or an activating enzyme. In another aspect, the cell overexpresses the enzyme (such as TS). In yet another aspect, the cell has become resistant to prior drugs or therapy. In a further aspect, the cell has defective tumor suppressor function. In yet a further aspect, the expression of the activating enzyme occurs as a consequence of infection by a pathogenic organism.

[0047] Pathological cells can be hyperproliferative. A “hyperproliferative cell” means cells or tissue are dividing and growing at a rate greater than that when the cell or tissue is in a normal or healthy state. Examples of such include, but are not limited to cancer cells, cells associated with autoimmune or inflammatory conditions and cells associated with infectious disease, e.g., bacteria, parasites, virus, yeast, fungi, or plant or animal cells infected with an agent. Examples of viruses include but are not limited to Herpes, Varicella zoster, Hepatitis C and Epstein Barr virus. Examples of parasites include but are not limited to T. brucei, T. cruzi, and Plasmodium falciparum. Examples of bacteria include, but are not limited to, all gram positive and gram negative bacteria, especially, Staphylococcus, sp., Enterococcus sp., Myoplasma sp., E. coli sp., Psudomonas sp., Nisseria sp. In one embodiment, the infectious agents have become resistant to common antibiotics (see review by Murray, B. E. (1997)). In other embodiments, the infectious agent expresses a “target enzyme” not expressed by the host cell.

[0048] Hyperproliferative cells also include de-differentiated, immortalized, neoplastic, malignant, metastatic, and cancer cells such as sarcoma cells, leukemia cells, carcinoma cells, or adenocarcinoma cells. Specified cancers include, but are not limited to breast cancer cells, hepatoma cells, liver cancer cells, pancreatic carcinoma cells, esophageal carcinoma cells, bladder cancer cells, gastrointestinal cancer cells, ovarian cancer cells, skin cancer cells, prostate cancer cells, and gastric cancer cells.

[0049] In one aspect, hyperproliferative cells overexpress an intracellular enzyme that is related to any of a loss of tumor suppressor gene product function, e.g. loss or inactivation of retinoblastoma (RB) or p53, known to enhance expression of TS (Li, W. et al. (1995) or DHFR (Bertino, et al. (1996) and Li, W. et al. (1995)), drug resistance (e.g., amplification of the gene encoding TS is related to resistance to tumor treatment with 5-fluoropyrimidines), or genetic instability or associated with a pathological phenotype. Alternatively, resistance to one drug may confer resistance to other, biochemically distinct drugs.

[0050] The enzyme glutathione-S-transferase was shown to be occasionally elevated in some human tumors (Morgan, A. S. et al. (1998)), but nevertheless is excluded from an enzyme that is overexpressed as used herein because it is a member of a gene family encoding enzymes with overlapping specificities.

[0051] A “pathology characterized by hyperproliferative cells” includes but is not limited to cancer, infectious disease, neoplasia, autoimmune disorders and inflammatory conditions.

[0052] “Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.

[0053] Examples of stringent hybridization conditions include: incubation temperatures of about 25° C. to about 37° C.; hybridization buffer concentrations of about 6×SSC to about 10×SSC; formamide concentrations of about 0% to about 25%; and wash solutions of about 6×SSC. Examples of moderate hybridization conditions include: incubation temperatures of about 40° C. to about 50° C.; buffer concentrations of about 9×SSC to about 2×SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5×SSC to about 2×SSC. Examples of high stringency conditions include: incubation temperatures of about 55° C. to about 68° C.; buffer concentrations of about 1×SSC to about 0.1×SSC; formamide concentrations of about 55% to about 75%; and wash solutions of about 1×SSC, 0.1×SSC, or deionized water. In general, hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes. SSC is 0.15M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.

[0054] A polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) has a certain percentage (for example, 80%, 85%, 90%, or 95%) of “sequence identity” to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel et al., eds., 1987) Supplement 30, section 7.7.18, Table 7.7.1. Preferably, default parameters are used for alignment. A preferred alignment program is BLAST, using default parameters. In particular, preferred programs are BLASTN and BLASTP, using the following default parameters: Genetic code=standard; filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62; Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+SwissProtein+SPupdate+PIR. Details of these programs can be found at the following Internet address: http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST.

[0055] “In vivo” gene delivery, gene transfer, gene therapy and the like as used herein, are terms referring to the introduction of a vector comprising an exogenous polynucleotide directly into the body of an organism, such as a human or non-human mammal, whereby the exogenous polynucleotide is introduced to a cell of such organism in vivo.

[0056] The term “isolated” means separated from constituents, cellular and otherwise, in which the polynucleotide, peptide, polypeptide, protein, antibody, or fragments thereof, are normally associated with in nature. For example, with respect to a polynucleotide, an isolated polynucleotide is one that is separated from the 5′ and 3′ sequences with which it is normally associated in the chromosome. As is apparent to those of skill in the art, a non-naturally occurring polynucleotide, peptide, polypeptide, protein, antibody, or fragments thereof, does not require “isolation” to distinguish it from its naturally occurring counterpart. In addition, a “concentrated”, “separated” or “diluted” polynucleotide, peptide, polypeptide, protein, antibody, or fragments thereof, is distinguishable from its naturally occurring counterpart in that the concentration or number of molecules per volume is greater than “concentrated” or less than “separated” than that of its naturally occurring counterpart. A polynucleotide, peptide, polypeptide, protein, antibody, or fragments thereof, which differs from the naturally occurring counterpart in its primary sequence or for example, by its glycosylation pattern, need not be present in its isolated form since it is distinguishable from its naturally occurring counterpart by its primary sequence, or alternatively, by another characteristic such as glycosylation pattern. Although not explicitly stated for each of the inventions disclosed herein, it is to be understood that all of the above embodiments for each of the compositions disclosed below and under the appropriate conditions, are provided by this invention. Thus, a non-naturally occurring polynucleotide is provided as a separate embodiment from the isolated naturally occurring polynucleotide. A protein produced in a bacterial cell is provided as a separate embodiment from the naturally occurring protein isolated from a eukaryotic cell in which it is produced in nature.

[0057] “Host cell,” “target cell” or “recipient cell” are intended to include any individual cell or cell culture which can be or have been recipients for compounds or compositions of this invention, test agents, vectors or the incorporation of exogenous nucleic acid molecules, polynucleotides and/or proteins. It also is intended to include progeny of a single cell, and the progeny may not necessarily be completely identical (in morphology or in genomic or total DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation. The cells may be prokaryotic or eukaryotic, and include but are not limited to bacterial cells, yeast cells, animal cells, and mammalian cells, e.g., murine, rat, simian or human.

[0058] A “subject” is a vertebrate, preferably an animal or a mammal, more preferably a human. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets.

[0059] A “control” is an alternative subject or sample used in an experiment for comparison purpose. A control can be “positive” or “negative”. For example, where the purpose of the experiment is to determine a correlation of the efficacy of a novel compound for the treatment for a particular type of cancer, it is generally preferable to use a positive control (a compound known to exhibit the desired therapeutic effect) and a negative control (a subject or a sample that does not receive the therapy or receives a placebo).

[0060] The terms “cancer,” “neoplasm,” and “tumor,” used interchangeably and in either the singular or plural form, refer to cells that have undergone a malignant transformation that makes them pathological to the host organism. Primary cancer cells (that is, cells obtained from near the site of malignant transformation) can be readily distinguished from non-cancerous cells by well-established techniques, particularly histological examination. The definition of a cancer cell, as used herein, includes not only a primary cancer cell, but also any cell derived from a cancer cell ancestor. This includes metastasized cancer cells, and in vitro cultures and cell lines derived from cancer cells. When referring to a type of cancer that normally manifests as a solid tumor, a “clinically detectable” tumor is one that is detectable on the basis of tumor mass; e.g., by such procedures as CAT scan, magnetic resonance imaging (MRI), X-ray, ultrasound or palpation. Biochemical or immunologic findings alone may be insufficient to meet this definition.

[0061] A neoplasm is an abnormal mass or colony of cells produced by a relatively autonomous new growth of tissue. Most neoplasms arise from the clonal expansion of a single cell that has undergone neoplastic transformation. The transformation of a normal to a neoplastic cell can be caused by a chemical, physical, or biological agent (or event) that directly and irreversibly alters the cell genome. Neoplastic cells are characterized by the loss of some specialized functions and the acquisition of new biological properties, foremost, the property of relatively autonomous (uncontrolled) growth. Neoplastic cells pass on their heritable biological characteristics to progeny cells.

[0062] The past, present, and future predicted biological behavior, or clinical course, of a neoplasm is further classified as benign or malignant, a distinction of great importance in diagnosis, treatment, and prognosis. A malignant neoplasm manifests a greater degree of autonomy, is capable of invasion and metastatic spread, may be resistant to treatment, and may cause death. A benign neoplasm has a lesser degree of autonomy, is usually not invasive, does not metastasize, and generally produces no great harm if treated adequately.

[0063] Cancer is a generic term for malignant neoplasms. Anaplasia is a characteristic property of cancer cells and denotes a lack of normal structural and functional characteristics (undifferentiation).

[0064] A tumor is literally a swelling of any type, such as an inflammatory or other swelling, but modem usage generally denotes a neoplasm. The suffix “-oma” means tumor and usually denotes a benign neoplasm, as in fibroma, lipoma, and so forth, but sometimes implies a malignant neoplasm, as with so-called melanoma, hepatoma, and seminoma, or even a non-neoplastic lesion, such as a hematoma, granuloma, or hamartoma. The suffix “-blastoma” denotes a neoplasm of embryonic cells, such as neuroblastoma of the adrenal or retinoblastoma of the eye.

[0065] Histogenesis is the origin of a tissue and is a method of classifying neoplasms on the basis of the tissue cell of origin. Adenomas are benign neoplasms of glandular epithelium. Carcinomas are malignant tumors of epithelium. Sarcomas are malignant tumors of mesenchymal tissues.

[0066] One system to classify neoplasia utilizes biological (clinical) behavior, whether benign or malignant, and the histogenesis, the tissue or cell of origin of the neoplasm as determined by histologic and cytologic examination. Neoplasms may originate in almost any tissue containing cells capable of mitotic division. The histogenetic classification of neoplasms is based upon the tissue (or cell) of origin as determined by histologic and cytologic examination.

[0067] “Suppressing” tumor growth indicates a growth state that is curtailed compared to growth without any therapy. Tumor cell growth can be assessed by any means known in the art, including, but not limited to, measuring tumor size, determining whether tumor cells are proliferating using a 3H-thymidine incorporation assay, or counting tumor cells. “Suppressing” tumor cell growth means any or all of the following states: slowing, delaying, and “suppressing” tumor growth indicates a growth state that is curtailed when stopping tumor growth, as well as tumor shrinkage.

[0068] The term “culturing” refers to the in vitro propagation of cells or organisms on or in media of various kinds. It is understood that the descendants of a cell grown in culture may not be completely identical (morphologically, genetically, or phenotypically) to the parent cell. By “expanded” is meant any proliferation or division of cells.

[0069] An “autoimmune disorder” is any condition in which an organism produces antibodies or immune cells which recognize the organism's own molecules, cells or tissues. Non-limiting examples of autoimmune disorders include rheumatoid arthritis, Sjogren's syndrome, graft versus host disease, myasthenia gravis, and systemic lupus erythematosus.

[0070] An “inflammatory condition” shall mean those conditions that are characterized by a persistent inflammatory response with pathologic sequelae. This state is characterized by infiltration of mononuclear cells, proliferation of fibroblasts and small blood vessels, increased connective tissue, and tissue destruction. Chronic inflammatory diseases include Crohn's disease, psoriasis, and asthma, are also included within the term “inflammatory condition.” Autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus can also result in a chronic inflammatory state.

[0071] For the purpose of illustration only, treatment can be noted by reduction in the expression of an endogenous intracellular enzyme, e.g., TS, reduction in the numbers of infectious agents, the reduction in inflammation, reduction of self-recognizing immune factors. In a further aspect, treatment is noted by the amelioration or reduction of symptoms of the disease, e.g., reduction in pathological cell growth or turnover, cachexia, tumor burden or elevated levels of immunological factors associated with a pathological or unhealthy state.

[0072] Treatment of arthritic conditions can result in decreased blood vessel formation in cartilage, specifically joints, resulting in increased mobility and flexibility in these regions. Treatment of psoriasis, administrationwill reduce dermatological symptoms such as scabbing, flaking and visible blood vessels under the surface of the skin.

[0073] In vitro treatment includes induction of apoptosis, as well as clinical (histological) and sub-clinical (e.g., biochemical and genetic changes associated with a reversal or dimunition of the pathological state.) Clinical and sub-clinical evidence of “treatment” will vary with pathology, the individual or subject, the cell or tissue type and the treatment.

[0074] “An endogenous intracellular enzyme” is one that is expressed by the cell whose regulation or expression can vary. In one aspect, the enzyme selectively activates a compound of this invention to produce products that confers treatment. In one aspect, the enzyme is overexpressed in a diseased cell as compared to a normal healthy cell. An example of such is thymidylate synthase (TS).

[0075] The term “activating enzyme” as used herein means an enzyme that is expressed by a pathogen in its native or natural environment. It is intended to distinguish enzymes or other agents that are administered to activate a prodrug.

[0076] A “composition” is intended to mean a combination of active agent and another compound or composition, inert (for example, a solid support, a detectable agent or label) or active, such as an adjuvant.

[0077] A “pharmaceutical composition” is intended to include the combination of an active agent with a carrier, inert or active, making the composition suitable for diagnostic or therapeutic use in vitro, in vivo or ex vivo.

[0078] As used herein, the term “pharmaceutically acceptable carrier” encompasses any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, and emulsions, such as an oil/water or water/oil emulsion, and various types of wetting agents. The compositions also can include stabilizers and preservatives. For examples of carriers, stabilizers and adjuvants, see Martin, REMINGTON'S PHARMACEUTICAL SCIENCES, 15th Ed., Mack Publ. Co., Easton, Pa. (1975).

[0079] The Compounds

[0080] Therapeutic compounds for use in the methods of this invention are one or more 5′-phosphoramidatyl 1,5-substituted pyrimidines, derivatives, analogs or pharmaceutically acceptable salts thereof. The compounds of this invention are nucleoside analogs comprising a substituted or unsubstituted uracil base covalently joined to a sugar modified by at least the addition of a 5′-phosphoramidate containing an amino acid residue. In one aspect, one or more of the compounds are substituted at the 5-position with a group that is extractable from pyrimidine by an endogenous, intracellular enzyme. The substituent at the 1-position of uridine is selected from the group consisting of substituted sugar, substituted thio-sugar, substituted carbocyclic, substituted cycloalkyl, and substituted acyclic substituents. Examples of sugar groups include, but are not limted to, monosaccharide cyclic sugar groups such as those derived from oxetanes (4-membered ring sugars), furanoses (5-membered ring sugars), and pyranoses (6-membered ring sugars). Examples of furanoses include threo-furanosyl (from threose, a four-carbon sugar); erythro-furanosyl (from erythrose, a four-carbon sugar); ribo-furanosyl (from ribose, a five-carbon sugar); ara-furanosyl (also often referred to as arabino-furanosyl; from arabinose, a five-carbon sugar); xylo-furanosyl (from xylose, a five-carbon sugar); and lyxo-furanosyl (from lyxose, a five-carbon sugar), and nucleoside analogs thereof.

[0081] Examples of thio sugar groups include the sulfur analogs of the above sugar groups, in which the ring oxygen has been replaced with a sulfur atom. Examples of carbocyclic groups include C4 carbocyclic groups, C5 carbocyclic groups, and C6 carbocyclic groups which may further have one or more substituents, such as —OH groups.

[0082] Derivatives of the compounds of this invention include, for example, “deoxy”, “keto”, and “dehydro” derivatives as well as substituted derivatives. Derivatives also include salts, esters, and ethers of the above compounds. Salts of the compounds of the present invention may be derived from inorganic or organic acids and bases. Examples of acids include hydrochloric, hydrobromic, sulfuric, nitric, perchloric, fumaric, maleic, phosphoric, glycollic, lactic, salicyclic, succinic, toluene-p-sulfonic, tartaric, acetic, citric, methanesulfonic, ethanesulfonic, formic, benzoic, malonic, naphthalene-2-sulfonic and benzenesulfonic acids. Other acids, such as oxalic, while not in themselves pharmaceutically acceptable, can be employed in the preparation of salts useful as intermediates in obtaining the compounds of the invention and their pharmaceutically acceptable acid addition salts. Examples of bases include alkali metal (e.g., sodium) hydroxides, alkaline earth metal (e.g., magnesium) hydroxides, ammonia, and compounds of formula NW4+, wherein W is C1-4 alkyl.

[0083] Examples of salts include: acetate, adipate, alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, flucoheptanoate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, lactate, maleate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, oxalate, palmoate, pectinate, persulfate, phenylproprionate, picrate, pivalate, propionate, succinate, tartrate, thiocyanate, tosylate and undecanoate. Other examples of salts include anions of the compounds of the present invention compounded with a suitable cation such as Na+, NH4+, and NW4+ (wherein W is a C1-4 alkyl group).

[0084] For therapeutic use, salts of the compounds of the present invention will be pharmaceutically acceptable. However, salts of acids and bases which are non-pharmaceutically acceptable may also find use, for example, in the preparation or purification of a pharmaceutically acceptable compound.

[0085] Esters of the compounds identified by the method of this invention include carboxylic acid esters (i.e., —O—C(═O)R) obtained by esterification of the 2′-, 3′- and/or 5′-hydroxy groups, in which R is selected from (1) straight or branched chain alkyl (for example, n-propyl, t-butyl, or n-butyl), alkoxyalkyl (for example, methoxymethyl), aralkyl (for example, benzyl), aryloxyalkyl (for example, phenoxymethyl), aryl (for example, phenyl optionally substituted by, for example, halogen, C1-4alkyl, or C1-4alkoxy or amino); (2) sulfonate esters, such as alkylsulfonyl (for example, methanesulfonyl) or aralkylsulfonyl; (3) amino acid esters (for example, L-valyl or L-isoleucyl); (4) phosphonate esters and (5) mono-, di- or triphosphate esters. The phosphate esters may be further esterified by, for example, a C1-20 alcohol or reactive derivative thereof, or by a 2,3-di-(C6-24)acyl glycerol. In such esters, unless otherwise specified, any alkyl moiety present advantageously contains from 1 to 18 carbon atoms, particularly from 1 to 6 carbon atoms, more particularly from 1 to 4 carbon atoms. Any cycloalkyl moiety present in such esters advantageously contains from 3 to 6 carbon atoms. Any aryl moiety present in such esters advantageously comprises a phenyl group. Examples of lyxo-furanosyl compound derivatives of the present invention include, for example, those with chemically protected hydroxyl groups (e.g., with O-acetyl groups), such as 2′-O-acetyl-lyxo-furanosyl; 3′-O-acetyl-lyxo-furanosyl; 5′-O-acetyl-lyxo-furanosyl; 2′,3′-di-O-acetyl-lyxo-furanosyl and 2′,3′,5′-tri-O-acetyl-lyxo-furanosyl.

[0086] Ethers of the compounds of the present invention include methyl, ethyl, propyl, butyl, isobutyl, and sec-butyl ethers.

[0087] Compounds useful in the methods of this invention can be described as the L and D isomers of compounds having one of the following structures: 1

[0088] or tautomers thereof, wherein in Formula C, R12 or R13 may be the same or different and are selected from the group consisting of oxo, OH or NHNH2, wherein a is 0 or 1, providing that if a is 0 and R13 is oxo, then a double bond exits between position 3 and 4 and R12 is NHNH2; further providing that if a is 0 and R12 is oxo, then a double bond exists between position 2 and 3 and R13 is NHNH2; further providing that if a is 1, then R12 and R13 are both oxo.

[0089] While not wishing to be bound by any theory, in one aspect of the above formulae (A, B and C), R1 (at the 5-position) is or contains a leaving group which is a chemical entity that has a molecular dimension and electrophilicity compatible with extraction from the pyrimidine ring by an endogenous, intracellular enzyme (e.g., thymidylate synthase). An embodiment for the substituent in the R1 position is one that could undergo an allylic interchange.

[0090] Another example is an alkenyl group of the formula, i.e., (—CH═CH)n—R4, wherein n is 0 or an integer from 1 to 10, and R4 is a halogen such as I or Br, CN or mercury, or alternatively, R1 is or contains a group selected from hydrogen, alkyl, alkene, alkyne, hydroxy, —O-alkyl,—O-aryl, O-heteroaryl, —S-alkyl, —S-aryl, a cyanide, cyanate, thiocyanate halovinyl group, halomercuric group, —S-heteroaryl, —NH2, —NH-alkyl, —N(alkyl)2, —NHCHO, —NHOH, —NHO-alkyl, NH2CONHO—, and NHNH2. For example, when n is 0 or an integer from 1 to 10, R4 is CH2-O—A, wherein A is a 2

[0091] phosphoramide derivative, or a compound of the formula:

[0092] Alternatively, in the above formulae (A, B or C), R1 can be a moiety of the formula: 3

[0093] wherein, R4 is a toxophore.

[0094] In one aspect of Formula D, R2 is or contains a divalent electron conduit moiety. In one embodiment, R2 is or contains a mono- or polyunsaturated electron conduit acting to conduct electrons away from the pyrimidine ring and toward R4. In another embodiment, R2 is selected from the group consisting of an unsaturated hydrocarbyl group, an aromatic hydrocarbyl group comprising one or more unsaturated hydrocarbyl groups, and a heteroaromatic group comprising one or more unsaturated hydrocarbyl groups.

[0095] In a yet further aspect, m is 0 and R2 is selected from the group consisting of: 4

[0096] wherein R5 is independently the same or different and is selected from the group consisting of a linear or branched alkyl group having from 1 to 10 carbon atoms, a cycloalkyl group having from 3 to 10 carbon atoms, CN and a halogen.

[0097] In one embodiment of Formula D, R2 is an unsaturated hydrocarbyl group having a structure selected from the group consisting of: 5

[0098] In another embodiment of Formula D, R2 is an aromatic hydrocarbyl group having a structure selected from the group consisting of: 6

[0099] In yet another embodiment of Formula D, R2 is a heteroaromatic group having a structure selected from the group consisting of: 7

[0100] wherein J is a heteroatom, such as —O—, —S—, or —Se—, or a heteroatom group, such as —NH— or —NRALK—, where RALK is a linear or branched alkyl having 1 to 10 carbon atoms or a cycloalkyl group having 3 to 10 carbon atoms.

[0101] In an alternative embodiment of Formula D, R3 is a divalent spacer moiety, also referred to as a spacer unit. Divalent spacers include, but are not limited to, a moiety having a structure: 8

[0102] wherein R5 is the same or different and is independently a linear or branched alkyl group having from 1 to 10 carbon atoms, or a cycloalkyl group having from 3 to 10 carbon atoms.

[0103] In an alternative aspect of Formula D, R3 is a divalent spacer moiety having a structure selected from the group consisting of: 9

[0104] In yet another aspect of Formula D, R2 and R3, taken together form a structure selected from the group consisting of: 10

[0105] In one embodiment, R4 (R4 in Formula D or R1 in Formulae A, B or C) is or contains a leaving group that is activated or released by an intracellular enzyme. In one embodiment, R4 is or contains a group having a structure selected from the group consisting of F, Cl, Br, I, CN, SO3H, CO2H, CO2CH2CH3, CO2CH3, SI(CH3)3, CHO, NO2, CF3, CCl3, CH═C(R15)2 and a derivative of cisplatin, such as: 11

[0106] or a substituent selected from the structures: 12

[0107] wherein Xa and Xb are independently the same or different and are selected from the group consisting of Cl, Br, I, and a potent leaving group and wherein Ya, Yb or Yc are independently the same or different and are hydrogen or F and wherein Z, Za and Zb are independently the same or different and are selected from the group consisting of O and S; and with respect to Formula C, R14 is hydrogen or F, providing if R14 is F, then a is 1 and R12 and R13 are both oxo.

[0108] Q is a 5′ phosphoramidate derivative, analog or pharmaceutically acceptable salt of a sugar as defined above, e.g., Q is selected from the group consisting of: 13

[0109] In the above Formula F, R2 and R3 are independently the same or different and are selected from the group consisting of Br, Cl, F, I, H, OH, OC(═O)CH3, —O-and —O—Rg, wherein Rg is a hydroxyl protecting group other than acetyl. R7 is attached to Q at the 5′ position of Q and is an amino acid containing phosphoramidate group. Any of the members of Formulae F may be in any enantiomeric, diasteriomeric, or stereoisomeric form, including D-form, L-form, α-anomeric form, and β-anomeric form.

[0110] In a specific embodiment, Q has the formula: 14

[0111] wherein R2 and R3 are independently the same or different and are independently H, —OH, —OC(═O)CH3, or —O-Rg, wherein Rg is a hydroxyl protecting group other than acetyl. R7 is as defined above.

[0112] In a further specific embodiment, Q has the following structure: 15

[0113] In each of Formulae F, G, or H, R7 is a phosphoramidate group derived from an amino acid, including, for example, the twenty naturally occurring amino acids, e.g., alanine and tryptophan. In one embodiment, R7 is a phosphoramidate group derived from tryptophan, for example a group having the structure: 16

[0114] The above group, and methods for its preparation, are described in Abraham et al., (1996).

[0115] In another embodiment, R7 is or contains a group having the structure: 17

[0116] wherein R8 is a side chain of any amino acid, its derivative, its analogue or its isomer and wherein R9 is selected from the group consisting of hydrogen, an unbranched or branched acyclic alkyl group containing from 1 to 5 carbons, a cyclic saturated alkyl group containing from 3 to 8 carbons, an aryl group and an adamantyl group. In one aspect, R8 is a side chain of any amino acid, its derivative, its analogue or its isomer with the proviso that when R8 is alanine, R9 is not selected from the group consisting of methyl, ethyl, methyl-tert-butyl, iso-propyl, methyl-cyclopropyl, cyclohexyl and benzyl. In a further aspect, R8 is a side chain of any amino acid, its derivative, its analogue or its isomer with the proviso that when R9 is methyl, R8 is not selected from the group consisting of tryptophan, valine, glycine, leucine, phenylalanine and aspartic acid. In a further aspect, R8 is a side chain of alanine and R9 is selected from the group consisting of benzyl, methyl-cyclopropyl, cyclohexyl, iso-propyl, methyl-tert-butyl, cycloheptyl, cyclooctyl and methyl-adamantyl. In a further aspect, R8 is a side chain of alanine and R9 is selected from the group consisting of cycloheptyl, cyclooctyl and methyl-adamantyl. In a further aspect, R8 is a side chain of tryptophan and R9 is methyl.

[0117] In another aspect, R8 and R9 are defined as above, wherein the nucleoside or its analog thereof is 2′-deoxy. In one aspect, when R8 is alanine and R9 is methyl, then R1 is not bromovinyl. In another aspect, when R8 is alanine, R9 is methyl and R1 is not bromovinyl, then the nucleoside or analog is not 2′-deoxy.

[0118] In one embodiment, R7 is a phosphoramidate group derived from alanine, e.g., a group having the structure: 18

[0119] The above group, and methods for its preparation, are described in McGuigan et al. (1993) and McGuigan et al. (1996).

[0120] In further embodiments, R7 is or contains a substituent selected from the group consisting of: 19

[0121] It is intended, although not always stated that the compounds of this invention may be in any enantiomeric, diasteriomeric, or stereoisomeric form, including, D-form, L-form, α-anomeric form, and β-anomeric forms. The compounds may be in a salt form, or in a protected or prodrug form, or a combination thereof, for example, as a salt, an ether, or an ester.

[0122] In a further aspect, R7 is as defined above and R1 is a bromovinyl group or a group shown in Table 2, below.

[0123] Specific compounds having the L or D structures are shown in Table 2, below. Compounds are identified by structure and a numerical designation.

TABLE 2
20
R1       21
22       NB 1011
23       NB 1012
24       NB 1013
—CF3     NB 1014
25       NB 1016
26       NB 1017
—≡—SiMe3 NB 1018
—≡—H     NB 1019
—≡—C8H17 —
—C8H17   —

[0124] Further embodiments of compounds of this invention are provided below. 27

[0125] wherein Xd and Xe are independently the same or different and are selected from the group consisting of Cl, Br, I, and CN. In a more preferred aspect, Xd is Cl or Br and Xe is hydrogen.

[0126] A compound having the structure: 28

[0127] wherein Xf and Xg are independently the same or different and are selected from the group consisting of Cl, Br, I, and CN. In a preferred embodiment, Xf and Xg are the same and are each is Cl or Br.

[0128] A compound having the structure of the formula: 29

[0129] wherein Xh and Xi are independently the same or different and are selected from the group consisting of Cl, Br, I, and CN. In a preferred embodiment, Xh and Xl are independently the same or different and are Cl or Br and in a more preferred embodiment, Xh and Xl are both Br.

[0130] A compound having the structure: 30

[0131] wherein R8 is a lower straight or branched chain alkyl.

[0132] A compound having the structure: 31

[0133] wherein R8 and R9 are lower straight or branched chain alkyls and R10 is hydrogen or CH3.

[0134] A compound having the structure: 32

[0135] wherein R10 is hydrogen or CH3.

[0136] A compound having the structure: 33

[0137] wherein X is selected from the group consisting of CO2Et, Cl, and Br.

[0138] A compound having the structure: 34

[0139] wherein R1 is a side chain of any naturally occurring amino acid, its analogue or its isomer; and wherein R2 is selected from the group consisting of hydrogen, an unbranched or branched acyclic alkyl group containing from 1 to 5 carbons, a cyclic saturated alkyl group containing from 3 to 8 carbons and a benzyl group and its pharmaceutically acceptable salts.

[0140] A compound having the structure: 35

[0141] The compounds can be combined with a carrier, such as a pharmaceutically acceptable carrier, for use in vitro and in vivo.

[0142] Formulations for In Vivo Administration

[0143] While it is possible for the composition ingredient to be administered alone, it is preferable to present it as a pharmaceutical formulation comprising at least one active ingredient, as defined above, together with one or more pharmaceutically acceptable carriers therefore and optionally other therapeutic agents. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient.

[0144] Formulations of the present invention suitable for oral administration may be presented as discrete units such as capsules, cachets or tablets, each containing a predetermined amount of the active ingredient; as a powder or granules; as a solution or suspension in an aqueous or non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion. The active ingredient may also be presented a bolus, electuary or paste.

[0145] A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared by compressing in a suitable machine the active ingredient in a free-flowing form such as a powder or granules, optionally mixed with a binder (e.g., povidone, gelatin, hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (e.g., sodium starch glycolate, cross-linked povidone, cross-linked sodium carboxymethyl cellulose) and/or surface-active or dispersing agent. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent. The tablets may optionally be coated or scored and may be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile. Tablets may optionally be provided with an enteric coating, to provide release in parts of the gut other than the stomach.

[0146] Formulations suitable for topical administration in the mouth include lozenges comprising the active ingredient in a flavored basis, usually sucrose and acacia or tragacanth; pastilles comprising the active ingredient in an inert basis such as gelatin and glycerin or sucrose and acacia; and mouthwashes comprising the active ingredient in a suitable liquid carrier.

[0147] Pharmaceutical compositions for topical administration according to the present invention may be formulated as an ointment, cream, suspension, lotion, powder, solution, past, gel, spray, aerosol or oil. Alternatively, a formulation may comprise a patch or a dressing such as a bandage or adhesive plaster impregnated with active ingredients and optionally one or more excipients or diluents.

[0148] For diseases of the eye or other external tissues, e.g., mouth and skin, the formulations are preferably applied as a topical ointment or cream containing the active ingredient in an amount of, for example, about 0.075 to about 20% w/w, preferably about 0.2 to about 25% w/w and most preferably about 0.5 to about 10% w/w. When formulated in an ointment, the composition may be employed with either a paraffinic or a water-miscible ointment base. Alternatively, the ingredients may be formulated in a cream with an oil-in-water cream base.

[0149] If desired, the aqueous phase of the cream base may include, for example, at least about 30% w/w of a polyhydric alcohol, i.e., an alcohol having two or more hydroxyl groups such as propylene glycol, butane-1,3-diol, mannitol, sorbitol, glycerol and polyethylene glycol and mixtures thereof. The topical formulations may desirably include a compound that enhances absorption or penetration of the ingredients through the skin or other affected areas. Examples of such dermal penetration enhancers include dimethylsulfoxide and related analogs.

[0150] The oily phase of the emulsions of this invention may be constituted from known ingredients in a known manner. While this phase may comprise merely an emulsifier (otherwise known as an emulgent), it desirably comprises a mixture of at least one emulsifier with a fat or an oil or with both a fat and an oil. Preferably, a hydrophilic emulsifier is included together with a lipophilic emulsifier that acts as a stabilizer. It is also preferred to include both an oil and a fat. Together, the emulsifier(s) with or without stabilizer(s) make up the so-called emulsifying wax, and the wax together with the oil and/or fat make up the so-called emulsifying ointment base which forms the oily dispersed phase of the cream formulations.

[0151] Emulgents and emulsion stabilizers suitable for use in the formulation of the present invention include Tween 60, Span 80, cetostearyl alcohol, myristyl alcohol, glyceryl monostearate and sodium lauryl sulfate.

[0152] The choice of suitable oils or fats for the formulation is based on achieving the desired cosmetic properties, since the solubility of the active compound in most oils likely to be used in pharmaceutical emulsion formulations is very low. Thus, the cream should preferably be a non-greasy, non-staining and washable product with suitable consistency to avoid leakage from tubes or other containers. Straight or branched chain, mono- or dibasic alkyl esters such as di-isoadipate, isocetyl stearate, propylene glycol diester of coconut fatty acids, isopropyl myristate, decyl oleate, isopropyl palmitate, butyl stearate, 2-ethylhexyl palmitate or a blend of branched chain esters known as Crodamol CAP may be used, the last three being preferred esters. These may be used alone or in combination depending on the properties required. Alternatively, high melting point lipids such as white soft paraffin and/or liquid paraffin or other mineral oils can be used.

[0153] Formulations suitable for topical administration to the eye also include eye drops wherein the active ingredient is dissolved or suspended in a suitable carrier, especially an aqueous solvent for the ingredients. The ingredients are preferably present in such formulation in a concentration of about 0.5 to about 20%, advantageously about 0.5 to about 10%, particularly about 1.5% w/w.

[0154] Formulations for rectal administration may be presented as a suppository with a suitable base comprising, for example, cocoa butter or a salicylate.

[0155] Formulations suitable for vaginal administration may be presented as suppositories, tampons, creams, gels, pastes, foams or spray formulations containing in addition to the ingredients, such carriers as are known in the art to be appropriate.

[0156] Formulations suitable for nasal administration, wherein the carrier is a solid, include a coarse powder having a particle size, for example, in the range of about 20 to about 500 microns which is administered in the manner in which snuff is taken, i.e., by rapid inhalation through the nasal passage from a container of the powder held close up to the nose. Suitable formulations wherein the carrier is a liquid for administration as, for example, nasal spray, nasal drops, or by aerosol administration by nebulizer, include aqueous or oily solutions of the ingredients.

[0157] Formulations suitable for parenteral administration include aqueous and non-aqueous isotonic sterile injection solutions which may contain antioxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents, and liposomes or other microparticulate systems which are designed to target the compound to blood components or one or more organs. The formulations may be presented in unit-dose or multi-dose sealed containers, for example, ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, water for injections, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the kind previously described.

[0158] It should be understood that in addition to the ingredients particularly mentioned above, the formulations of this invention may include other agents conventional in the art having regard to the type of formulation in question, for example, those suitable of oral administration may include such further agents as sweeteners, thickeners and flavoring agents.

[0159] Compositions of the formula of the present invention may also be presented for the use in the form of veterinary formulations, which may be prepared by methods that are conventional in the art.

[0160] Methods of Treatment

[0161] Pathological cells, tissues and pathologies characterized by hyperproliferative cells are treated by contacting the cells or tissue associated with these pathologies with an effective amount of a compound of this invention. The contacting can be any one or more of in vitro, ex vivo and in vivo.

[0162] When practiced in vivo in a subject other than a human patient such as a mouse, the method provides an animal model for use in discovering alternative agents and therapies. In a human patient, the method treats pathologies characterized by hyperproliferative cells, e.g., cancer, infectious disease, an autoimmune disorder or inflammatory condition. Methods for detecting clinical and sub-clinical evidence of effective therapy are known in the art and described herein. In each of these methods, an effective amount of a compound of this invention is delivered or administered to the subject, e.g., mouse or human patient.

[0163] In one aspect, this invention is directed to methods for inhibiting the proliferation or growth of an infectious agent or a cell infected with the agent by contacting the agent or infected cell with a compound of this invention. The methods and compositions of this invention are useful to preferentially inhibit the growth or proliferation of cells that express or contain activating enzyme, for example microbial cells, virally infected cells or cells infected with other pathogens. Overexpression of the enzyme is not required, as specificity is related to the species-specificity of the compound to the activating enzyme expressed by the pathogen. The activating enzyme may or may not be expressed by the host cell. However, even if the cell expresses its own version of the enzyme, the compound is selective on the basis that it is preferentially activated by the version of the enzyme expressed by the infectious agent as compared to the version of the enzyme expressed by the host cell. The activating enzyme can be the wild-type or a mutated version which has developed resistance to prior art therapeutics (Hooker, et al. (1996)).

[0164] Examples of activating enzymes that are selective targets for the compounds and methods of this invention include, but are not limited to, thymidylate synthase (TS), dihydrofolate reductase (DHFR) and β-lactamase activating enzymes.

[0165] The concepts of this invention are illustrated using the activating enzyme thymidylate synthase and its expression in human tumor cells. However, the use of TS is merely illustrative and the claims are not to be construed as limited to systems which target TS. Thymidylate synthase was used herein as the target,. activating enzyme because of the high degree of characterization of its structure and function (Carreras and Santi (1995)), the fact that it is encoded by a single gene, not a gene family (compare for example the family of enzymes noted as glutathione-S-transferase (GST)). In addition, TS overexpression is the result of acquired resistance to chemotherapeutics. Similarly, in one embodiment, the activating enzyme can be expressed as a result of resistance to prior therapy.

[0166] Other target activating enzymes include, but are not limited to viral reverse transcriptases and proteases. Examples of viruses that encode these enzymes include the retroviruses (eg. HIV-1, both enzymes, see Turner B. G. and Summers M. F. (1999)), the picornaviruses (eg., Hepatitis A virus, Wang Q. M. (1999)), and Hepatitis C virus (Kwong A. D. et al. (1999)). Early clinical success observed with anti-HIVl reverse transciptase and protease inhibitors (reviewed by Shafer R. W. and Vuitton D. A. (1999)) has been tempered by the development of resistance, largely due to mutations in the virally-enoded enzymes (Catucci, M. et al. (1999); Mahalingam, B. et al. (1999); and Palmer, S. et al. (1999)). Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many anti-retroviral compounds in current clinical development. Hooker et al. (1996). In these cases of resistance, the viral enzymes retain their catalytic activity because the mutated version of the enzyme retains the structure of the wild-type active site of the enzyme. The compounds of this invention are specifically designed to interact with the active site and be converted by this interaction into a toxin. Accordingly, the drug resistant viral infections are sensitive to the compounds of this invention that require the activating enzyme to generate toxin in the infected cell. NB1011 1 is an example of such a compound, directed against TS expressed by mammalian and human cells as well as pathogens.

[0167] Co-Administration

[0168] Co-administration of these compounds with other agents may provide unexpected synergistic therapeutic benefit. In the co-administration methods, the compounds are also useful in reducing deleterious side-effects of known therapies and therapeutic agents, as well as yet to be discovered therapies and therapeutic agents. In one aspect, the compounds are combined with a nucleoside transport inhibitor. Suitable nucleoside transport inhibitors include one or more selected from the group consisting of dipyridamole (DP), p-nitrobenzylthioinosine (NBMPR), 6-benzylaminopurine, 2′,3′-dideoxyguanosine, 8-bromoadenine, 9-[(2-hydroxyethoxy)methyl]guanine (Acyclovir), 9-[(1,3-dihydroxy-2-propoxy) methyl]guanine (Ganciclovir), adenine, hypoxanthine, allopurinol, dilazep, cytochalasin B, lidoflaxine, mioflazine, phloretin, phloridzine, and benzylisoquinoline alkaloids.

[0169] Suitable benzylisoquinoline alkaloids are selected from the group consisting of papaverine, ethaverine, laudanosine, noscarpine, and berberine. Additional operative combinations include, but are not limited to agents or drugs that neutralize or prevent the production of tumor necrosis factor-α (TNF-α) such as an anti-TNF-α antibody or soluble TNF-α receptor that treat or ameliorate the symptoms associated with autoimmune diseases.

[0170] Other examples include, but are not limited to corticosteriods, non-steroidal anti-inflammatory drugs (N-SAIDS), and anti-rheumatic drugs.

[0171] The use of operative combinations is contemplated to provide therapeutic combinations that may lower total dosage of each component than may be required when each individual therapeutic method, compound or drug is used alone. A reduction in adverse effects may also be noted. Thus, the present invention also includes methods involving co-administration of the compounds described herein with one or more additional active agents or methods. Indeed, it is a further aspect of this invention to provide methods for enhancing other therapies and/or pharmaceutical compositions by co-administering a compound of this invention. In co-administration procedures, the agents may be administered concurrently or sequentially. In one embodiment, the compounds described herein are administered prior to the other active agent(s), therapy or therapies. The pharmaceutical formulations and modes of administration may be any of those described herein or known to those of skill in the art.

[0172] In another aspect, the invention provides a method to enhance the cytotoxity of a compound of this invention against a pathological tissue or cell, containing contacting the cell or tissue with an effective amount of a nucleoside inhibitor compound. It further provides a methods to inhibit the growth of a pathological tissue or, e.g., a cell hyperproliferative cell by contacting the cell with an effective amount of a composition comprising an one or more compounds of this invention.

[0173] Reversing Resistance

[0174] Resistance to chemotherapeutics can be reversed by contacting the resistant cell with an effective amount of a compound of this invention, in vitro or in vivo. Subsequent to successful treatment, the prior (or original chemotherapeutic) can be re-utilized.

[0175] Use of Compounds for Preparing Medicaments

[0176] The compounds of the present invention are also useful in the preparation of medicaments to treat a variety of pathologies, e.g., infectious diseases, cancers, autoimmune diseases or inflammatory conditions. The methods and techniques for preparing medicaments of a compound are known in the art. For the purpose of illustration only, pharmaceutical formulations and routes of delivery are detailed below.

[0177] Thus, one of skill in the art would readily appreciate that any one or more of the compounds described more fully below, including the many specific embodiments, can be used by applying standard pharmaceutical manufacturing procedures to prepare medicaments to treat the many disorders described herein. Such medicaments can be delivered to the subject by using delivery methods known in the pharmaceutical arts.

[0178] Pharmaceutical Delivery

[0179] Various delivery systems are known and can be used to administer a compound or an agent of the invention, e.g., encapsulation in liposomes, microparticles, microcapsules, receptor-mediated endocytosis and the like. Methods of delivery include but are not limited to, intra-arterial, intramuscular, intravenous, intranasal, and oral routes. In a specific embodiment, it may be desirable to administer the pharmaceutical compositions locally to the area in need of treatment; this may be achieved by, for example and not by way of limitation, local infusion during surgery, by injection, or by means of a catheter. To determine patients that can be beneficially treated, a tissue sample can be removed from the patient and the cells are assayed for sensitivity to the agent.

[0180] Therapeutic amounts can be empirically determined and will vary with the pathology being treated, the subject being treated and the efficacy and toxicity of the compound as well as whether the compound is used alone or in combination with other agents of therapeutic methods. When delivered to an animal, the method is useful to further confirm efficacy of the agent. One example of an animal model is MLR/MpJ-lpr/lpr (“MLR-lpr”) (available from Jackson Laboratories, Bal Harbor, Me.). MLR-lpr mice develop systemic autoimmune disease.

[0181] Administration in vivo can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most effective means and dosage of administration are known to those of skill in the art and will vary with the composition used for therapy, the purpose of the therapy, the target cell being treated, and the subject being treated. Single or multiple administrations can be carried out with the dose level and pattern being selected by the treating physician.

[0182] Suitable dosage formulations and methods of administering the agents can be readily determined by those of skill in the art. For example, the compounds are administered at about 0.01 mg/kg to about 200 mg/kg, alternatively at about 0.1 mg/kg to about 100 mg/kg, or alternatively at about 0.5 mg/kg to about 50 mg/kg. When the compounds described herein are co-administered with another agent (e.g., as sensitizing agents) or therapy, the effective amount may be less than when the agent is used alone.

[0183] The pharmaceutical compositions can be administered orally, intranasally, parenterally or by inhalation therapy, and may take the form of tablets, lozenges, granules, capsules, pills, ampoules, suppositories or aerosol form. They may also take the form of suspensions, solutions and emulsions of the active ingredient in aqueous or nonaqueous diluents, syrups, granulates or powders. In addition to an agent of the present invention, the pharmaceutical compositions can also contain other pharmaceutically active compounds or a plurality of compounds of the invention.

[0184] More particularly, an agent of the present invention also referred to herein as the active ingredient, may be administered for therapy by any suitable route including oral, rectal, nasal, topical (including transdermal, aerosol, buccal and sublingual), vaginal, parenteral (including subcutaneous, intramuscular, intravenous and intradermal) and pulmonary. It will also be appreciated that the preferred route will vary with the condition and age of the recipient, and the disease being treated.

[0185] Ideally, the agent should be administered to achieve peak concentrations of the active compound at sites of disease. This may be achieved, for example, by the intravenous injection of the agent, optionally in saline, or orally administered, for example, as a tablet, capsule or syrup containing the active ingredient.

[0186] Desirable blood levels of the agent may be maintained by a continuous infusion to provide a therapeutic amount of the active ingredient within disease tissue.

[0187] Screening Assays

[0188] This invention also provides screening assays to identify therapeutic potentisl of known and new compounds and combinations.

[0189] In one aspect, the assay requires contacting a first sample comprising suitable cells or tissue (“control sample”) with an effective amount of a compound of this invention and contacting a second sample of the suitable cells or tissue (“test sample”) with the agent to be assayed. In a further aspect, the test agent is contacted with a third sample of cells or tissue comprising normal counterpart cells or tissue to the control and test samples and selecting agents that treat the second sample of cells or tissue but does not adversely effect the third sample. For the purpose of the assays described herein, a suitable cell or tissue is one involved in hyperproliferative disorders such as cancer, infectious disease, autoimmune disease or a chronic inflammatory condition. Examples of such include, but are not limited to cell or tissue infected with an infectious agent, cells or tissue obtained by biopsy, blood, breast cells, colon cells, liver cells, synovial fluid, a chondrocyte or an immune cell, such as a T cell, a macrophage, and an NK cell.

[0190] In a further aspect, the cells are tissue are characterized by the loss of a native tumor suppressor function. In a yet further aspect, the cells or tissue express a target enzyme or overexpress an endogenous intracellular enzyme. In a still further aspect, the cells or tissue have developed resistance to a drug such as 5-FU.

[0191] For example, the compound or agent to be tested can be activated by an endogenous intracellular enzyme that is overexpressed or differentially expressed in a pathological cell as compared to its normal counterpart. An example of such an enzyme includes, but is not limited to thymidylate synthase. Alternatively, a cell genetically modified to differentially express the enzyme or enzymes (containing the appropriate species of enzyme) can be used. Transfection of host cells with polynucleotides encoding the enzyme can be either transient or permanent using procedures well known in the art and described by Chen, L. et al. (1996), Hudziak, R. M. et al. (1988), or Carter, P. et al. (1992), and in the experimental section below. The cells can be prokaryotic (bacterial such as E. coli) or eukaryotic. The cells can be mammalian or non-mammalian cells, e.g., mouse cells, rat cells, human cells, fungi (e.g., yeast) or parasites (e.g., Pneumocystis or Leishmania) which cause disease.

[0192] Suitable vectors for insertion of the CDNA are commercially available from Stratagene, La Jolla, Calif. and other vendors. The amount of expression can be regulated by the number of copies of the expression cassette introduced into the cell or by varying promoter usage. The level of expression of enzyme in each transfected cell line can be monitored by immunoblot and enzyme assay in cell lysates, using monoclonal or polyclonal antibody previously raised against the enzyme for immunodetection. (Chen, L. et al. (1996)). Enzymatic assays to detect the amount of expressed enzyme also can be performed as reviewed by Carreras, C. W. and Santi, D. V. (1995) or the method described in the experimental section below.

[0193] In a further aspect, more than one species of enzyme is used to separately transduce separate host cells, so that the effect of the candidate drug with an enzyme can be simultaneously compared to its effect on another enzyme or a corresponding enzyme from another species.

[0194] The compounds and/or compositions can be directly added to the cell culture media and the target cell or the culture media is then assayed for the amount of label released from the candidate compound if the compound contains a detectable label. Alternatively, cellular uptake may be enhanced by packaging the compound into liposomes using the method described in Lasic, D. D. (1996) or combined with cytofectins as described in Lewis, J. G. et al. (1996).

[0195] In yet a further aspect, the assay requires at least two cell types, the first being a suitable control cell. The second cell type is of the same type or tissue as the control cell but differs in that pathogenesis toward disease has begun. In one aspect, pathogenesis is determined enzymatically by noting enhanced or over expression of an endogenous intracellular enzyme that activates the compound into a toxic entity. Amplification of genes associated with drug resistance can be detected and monitored by a modified polymerase chain reaction (PCR) as described in Kashini-Sabet, et al. (1988), Houze, T. A. et al. (1997), U.S. Pat. No. 5,085,983, or the method described herein. Acquired drug resistance can be monitored by the detection of cytogenetic abnormalities, such as homogeneous chromosome staining regions and double minute chromosomes both of which are associated with gene amplification. Alternative assays include direct or indirect enzyme activity assays, each of which are associated with gene amplification (e.g., Carreras, C. W. and Santi, D. V. (1995)) and other methodologies (e.g. polymerase chain reaction or immunohistochemistry (Johnson, P. G. et al. (1997)). These methods also provides the means to detect subclinical evidency of therapy or a therapeutic effect.

[0196] The assays are useful to predict whether a subject will be suitably treated by this invention by delivering a compound or composition to a sample containing the cell to be treated and assaying for treatment which will vary with the pathology. In one aspect, the cell or tissue is obtained from the subject or patient by biopsy. Applicants provide kits for determining whether a pathological cell or a patient will be suitably treated by this therapy by providing at least one composition of this invention and instructions for use.

[0197] This invention further provides a method for screening for compounds that are selectively converted to a toxin by an activating enzyme by providing cells that express an activating enzyme and contacting the cells with a candidate compound. At least one test cell expresses the pathogen's version of the enzyme (wild-type or mutated) and another test cell is a cell sample from the host organism which may, or may not express its own version of the enzyme. One then assays for conversion of the compound into toxic agents by the activating enzyme produced by the pathogen. As used herein, the test cells can be prokaryotic or eukaryotic cells infected with the pathogen or alternatively, transformed to express the activating enzyme. For example, a prokaryotic E. coli which does not endogenously express the activating enzyme TS is a suitable host cell or target cell. Alternatively, the test cell can be an infected cell isolated from the subject, or a cultured cell infected with the pathogen. The cell can have a control counterpart (lacking the target enzyme), or in a separate embodiment, a counterpart genetically modified to differentially express the target enzyme, or enzymes (containing the appropriate species of target enzyme). More than one species of enzyme can be used to separately transduce separate host cells, so that the effect of the candidate drug on a target enzyme can be simultaneously compared to its effect on another enzyme or a corresponding enzyme from another species.

[0198] In another embodiment, a third target cell is used as a positive control because it receives an effective amount of a compound, such as, for example, the compounds shown below, which have been shown to be potent compounds.

[0199] In another embodiment, transformed cell lines, such as ras-transformed NIH 3T3 cells (ATCC, 10801 University Blvd., Manassas, Va., 20110-2209, U.S.A.) are engineered to express variable and increasing quantities of the target enzyme of interest from cloned cDNA coding for the enzyme. Transfection is either transient or permanent using procedures well known in the art and described in Sambrook, et al., supra. Suitable vectors for insertion of the cDNA are commercially available from Stratagene, La Jolla, Calif. and other vendors. The level of expression of enzyme in each transfected cell line can be monitored by immunoblot and enzyme assay in cell lysates, using monoclonal or polyclonal antibody previously raised against the enzyme for immuno-detection. The amount of expression can be regulated by the number of copies of the expression cassette introduced into the cell or by varying promoter usage. Enzymatic assays to detect the amount of expressed enzyme also can be performed as reviewed by Carreras and Santi (1995), supra, or the methods described below.

[0200] The test cells can be grown in small multi-well plates and is used to detect the biological activity of test compounds. For the purposes of this invention, the successful candidate drug will block the growth or kill the pathogen but leave the control cell type unharmed.

[0201] The candidate compound can be directly added to the cell culture media or previously conjugated to a ligand specific to a cell surface receptor and then added to the media. Methods of conjugation for cell specific delivery are well known in the art, see e.g., U.S. Pat. Nos. 5,459,127; 5,264,618; and published patent specification WO 91/17424 (published Nov. 14, 1991). The leaving group of the candidate compound can be detectably labeled, e.g., with tritium. The target cell or the culture media is then assayed for the amount of label released from the candidate compound. Alternatively, cellular uptake may be enhanced by packaging the compound into liposomes using the method described in Lasic, D. D. (1996) or combined with cytofectins as described in Lewis, J. G. et al. (1996).

[0202] Compounds, agents and combinations thereof, identified by this method are further provided herein.

[0203] In one embodiment, the assay of the effect of the compound is provided by analysis of intracellular metabolites of the compound. In this embodiment, the compound contains a detectable label that is monitored during conversion of the compound to toxic agent by the activating enzyme. In an alternative embodiment, the candidate compound is detectably labeled, e.g., e.g., fluorescent marker, or a radioisotope. In a further aspect, the detectable label comprises at least two or more variable isotopes of the same atom, e.g., bromine. In this embodiment, one can assay for the modification of the compound into toxic byproducts by mass spectrometry of the reaction products. One means to accomplish this assay is by use of mass spectrometry as described in more detail below.

[0204] Using the above screen, one also can pre-screen several compounds against samples taken from a subject such as a human patient. One can use the screen to determine the most effective compound and therapy for each pathology or pathogen and subject.

[0205] Kits

[0206] Applicants also provide kits for determining whether a pathological cell, tissue or patient will be suitably treated by this therapy. Additionally, kits for performance of the assays are provided. These kits contain at least one compound or composition of this invention and instructions for use.

[0207] The following examples are intended to illustrate, but not limit, the invention.

MATERIALS AND METHODS

General Synthesis Procedures

[0208] Synthesis of Nueleoside Compounds

[0209] Synthesis of 5-substituted pyrimidine derivatives can be accomplished by methods known in the art, for example as described in Applicant's patent literature, PCT/US98/16607 and PCT/US99/01332.

[0210] One method requires treatment of 5-chloromercuri-2′-deoxyuridine with haloalkyl compounds, haloacetates or haloalkenes in the presence of Li2PdCl4 to form, through an organopalladium intermediate, the 5-alkyl, 5-acetyl or 5-alkene derivative, respectively (Wataya, Y. et al. (1979) and Bergstrom, D. E. et al. (1984)). Another example of C5-modification of pyrimidine nucleosides and nucleotides is the formation of C5-trans-styryl derivatives by treatment of unprotected nucleotide with mercuric acetate followed by addition of styrene or ring-substituted styrenes in the presence of Li2PdCl4 (Bigge, et al. (1980)).

[0211] Pyrimidine deoxyribonucleoside triphosphates can be derivatized with mercury at the 5 position of the pyrimidine ring by treatment with mercuric acetate in acetate buffer at 50° for 3 hours (Dale, et al. (1973)). Such treatment also would be expected to be effective for modification of monophosphates. Alternatively, a modified triphosphate can be converted enzymatically to a modified monophosphate, for example, by controlled treatment with alkaline phosphatase followed by purification of monophosphate. Other moieties, organic or nonorganic, with molecular properties similar to mercury but with preferred pharmacological properties could be substituted. For general methods for synthesis of substituted pyrimidines see, for example, U.S. Pat. Nos. 4,247,544, 4,267,171, and 4,948,882 and Bergstrom, D. E. et al. (1981). The above methods would also be applicable to the synthesis of derivatives of 5-substituted pyrimidine nucleosides and nucleotides containing sugars other than ribose or 2′-deoxyribose, for example 2′-3′-dideoxyribose, arabinose, furanose, lyxose, pentose, hexose, heptose, and pyranose. An example of a 5-position substituent is the halovinyl group, e.g. (E)-5-(2-bromovinyl)-2′-deoxyuridylate (Barr, P. J. et al. (1983)).

[0212] Alternatively, 5-bromodeoxyuridine, 5-iododeoxyuridine, and their monophosphate derivatives are available commercially from Glen Research, Sterling, Va. (USA), Sigma-Aldrich Corporation, St. Louis, Mo. (USA), Moravek Biochemicals, Inc., Brea, Calif. (USA), ICN, Costa Mesa, Calif. (USA) and New England Nuclear, Boston, Mass. (USA). Commercially-available 5-bromodeoxyuridine and 5-iododeoxyuridine can be converted to their monophosphates either chemically or enzymatically, through the action of a kinase enzyme using commercial available reagents from Glen Research, Sterling, Va. (USA) and ICN, Costa Mesa, Calif. (USA). These halogen derivatives could be combined with other substituents to create novel and more potent antimetabolites.

[0213] In one aspect, the structures at the 5-position of the compound, analogs and derivatives thereof are referred to as the tethers because they connect a proposed leaving group (toxophore) to the heterocycle.

[0214] In another aspect, the tether also contains a spacer between the toxin and the pyrimidine ring can be unsaturated, e.g., vinyl, allyl, and propargyl units are simple, small, and readily accessible synthetically. The vinyl and allyl units have the advantage that they can be prepared in either of two non-interconvertible geometric isomeric forms. Alternatively, synthesis based on the structure of BVdU monophosphate and features a proposed leaving group/toxin directly attached to the terminus of a (poly)vinyl substituent at C5 of the pyrimidine ring. This is the vinyl tether approach. A yet further approach is based on the structure of TFPe-dUMP and is similar to the vinyl tether approach but has a methylene unit separating the proposed leaving group/toxin and the unsaturated unit and thus contains an allyl or propargyl unit. This is the allyl tether approach.

[0215] 5-Alkylidenated 5,6-dihydrouracils similar in structure to the intermediate common to both the vinyl and allyl tether approach mechanisms have been synthesized recently (Anglada, J. M. et al. 1996). A C5 methylene intermediate produced by the enzyme thymidylate synthase TS was demonstrated by trapping studies (Barrett, J. E. et al. (1998)).

[0216] The compounds of Formula B are defined by the structure of the uracil base, or modified uracil base present. These classes are compounds where: 1) the base is a furano-pyrimidinone derivative of uracil; 2) the base is 6-fluoro uracil; 3) the base is 4-hydrazone substituted uracil derivative; and 4) the base is uracil. In one aspect, the uracil or modified uracil derived base is used to synthesize compounds substituted with toxic leaving groups at the 5 position, attached by an electron conduit tether at this 5 position, and including an appropriate spacer moiety between the electron conduit and the toxic leaving group. The compounds can be unphosphorylated, 5′ monophosphate, 5′ phosphodiester, or 5′ protected (“masked”) deoxyuridines or comparable derivatives of alternative carbohydrate moieties, as described below. Protected 5-substituted deoxyuridine monophosphate derivatives are those in which the phosphate moiety has been blocked through the attachment of suitable chemical protecting groups. In another embodiment, 5-substituted uracil or uridine derivatives are administered to cells containing nucleoside kinase activity, wherein the 5-substituted uracil/uridine derivative is converted to a 5-substituted uridine monophosphate derivative. Uridine derivatives may also be modified to increase their solubility, cell penetration, and/or ability to cross the blood-brain barrier.

[0217] Synthesis of Compounds with Propargyl Tethers

[0218] The synthesis of propargylic and allylic alcohol-equipped 2′-deoxyuridines are reported in the literature. For example, Barr, P. J. and Robins, M. J. (1981) and Balzarini, J. et al. (1985).

[0219] Both 5-mercuri- (Ruth, J. L. et al. (1978)) and 5-iodouridines (Robins, M. J. et al. (1981)) readily condense with alkenes and alkynes in the presence of a palladium catalyst to afford C5 tether-equipped uridines. The latter route is the more often employed (Robins, M. J. et al. (1982) and Asakura, S. et al. (1988) and (1990)). High-yielding condensations of protected 5-iodo-2′-deoxyuridines with t-butyidimethylsilyl propargyl ether (Graham, D. et al. (1998); De Clercq, E. et al. (1983), methyl propargyl ether (Tolstikov, V. V. et al. (1997)) and even propargyl alcohol itself (Chaudhuri, N. C. et al. (1995) and Goodwin, J. T. et al. (1993)) have been achieved. The 3-hydroxy-1-propynyl substituent introduced by the latter reaction can also be accessed by DIBAL-H reduction of a methacrylate group (Cho, Y. M. et al. (1994)), itself arising from the same Heck reaction used in the synthesis of BVdU. These palladium-catalyzed reactions can be used to condense very long and elaborately-functionalized propargyl-based tethers to 5-iodo-2′-deoxyuridines. (Livak, K. J. et al. (1992) and Hobbs, F. W. Jr. (1989)). (Z)-Allyl-based tethers are generated by the partial hydrogenation of a propargylic precursor over Undiar catalyst (Robins, M. J. et al. (1983)) whereas the (E)-allyl-based ones are best prepared by Heck coupling of an (E)-tributylstannylated ethylene (Crisp, G. T. (1989)).

[0220] Closely following the literature procedures, a t-butyldimethylsilyl propargyl ether-equipped 3′, 5′-di-O-protected 2′-deoxyuridine (Graham, D. et al. (1998), and De Clercq, E. et al. (1983)) can be prepared and a portion of it, converted to the corresponding (Z)-allyl ether, (Robins, M. J. et al. (1983)) is reduced. Because the TBAF-mediated removal of a TBDMS group generates an oxyanion that can be functionalized in situ, these TBDMS-protected propargyl- and (Z)-allytic-tethered nucleosides can serve as convenient precursors to some of the toxophore-equipped targets. For the (E)-allyl alcohol equipped nucleoside, the known O-tetrahydropyranyl ether derivative is prepared by the literature Heck coupling of an (E)-tributylstannylated ethylene (Crisp, G. T. (1989)). 36

[0221] Using a two step literature protocol (Phelps, M. E. et al. (1980) and Hsiao, L. Y. et al. (1981)), the propargylic and (E) and (Z)-allylic alcohols are converted to their corresponding bis-aziridinyl phosphoramidates or thiophosphoramidates. 37

[0222] Synthesis of Furano-Pyrimidinones

[0223] Synthesis of furano-pyrimidinones begins with synthesis of a C5 propargylic—alcohol-equipped 2′-deoxyuridine. Furano-pyrimidinone compounds are then be formed from the O-tetrahydropyranyl ether derivative described above. Synthesis proceeds by reaction of the second carbon of the propargyl bond with the oxygen attached to the C4 position of the pyrimidine ring to yield a fluorescent furano-pyrimidinone which can be readily separated from the reaction mix. Such compounds provide an additional basis for synthesis of compounds through various combinations of specific electron conduits, spacers and toxic leaving groups. 38

[0224] Furo[2,3-d]pyrimidinone nucleosides (represented by the above generic structure) were prepared by condensing 2′,3′-di-O-p-toluoyl or 2′,3′-di-O-acetyl-5-iodo-2′-deoxyuridine with 1-(tetrahydropyranyloxy)-2-propyne (Jones, R. G. and Mann, M. J. (1953)) under conditions known to promote the formation of these fluorescent compounds (Robins, M. J. et al.(1983)). Base-catalyzed removal of the carbohydrate protecting groups gave the 6-(tetrahydropyran-2-yloxymethyl)-substituted bicyclic nucleoside which was either subjected to standard acidic THP group hydrolysis (TFA in CH2Cl2) or was regioselectively 5′-phosphoramidated by the same procedure used to prepare BVdU-PA and 5FUdR-PA. After the phosphoramidation, the THP group can be removed by acidic hydrolysis.

[0225] Compounds Based on Furano-Pyrimidinones

[0226] Examples of synthesis of compounds having a structure of the class shown are as follows. 39

[0227] Proposed toxic R4 leaving groups can be attached to the furan-2 methyl alcohol using methods similar to those employed to attach toxic leaving groups to the hydroxyl on the C5 propargyl uridine compound, as explained above. A variety of alternative toxic leaving groups are envisioned. In addition, modifications to the length and composition of the R2 electron conduit component and of the composition of the R3 spacer element are also envisioned.

[0228] Compounds based on furano-pyrimidinones can also consist of variously modified phosphoramidates. A method for synthesis of such phosphoramidate compounds is accomplished by reacting a 2-deoxy 3′-hydroxy, 5′-hydroxy unprotected nucleotide with a phosphochloridate in the presence of an HCI scavenger. In one aspect, the phosphochloridate comprises a phosphorus substituent which is derived from an amino acid such as alanine. For example, the phosphochloridate can be phenyl-L-methoxyalanine phosphorochloridate.

[0229] C6 Fluoro Uridine and C4 Hydrazone Based Compounds

[0230] The introduction of fluorine at the C6 position can be synthesized by following the synthetic descriptions of Krajewskas and Shugar (1982), who describe the synthesis of a number of 6 substituted uracil and uridine analogs.

[0231] Chemistry facilitating substitutions at the C4 position of the pyrimidine base are known by those skilled in the art. Examples of literature descriptions include Wallis, et al. (1999); Negishi, et al. (1996), Barbato, et al. (1991), Barbato, et al. (1989) and Holy et al. (1999). These synthetic techniques also enable combinations of substitutions, for instance at the C4 and C5 positions of the pyrimidine ring (Pluta, et al. (1999)) or the C2 and C4 positions of the pyrimidine ring (Zeid, et al. (1999)). 40

[0232] In another embodiment of the invention, compounds are synthesized by addition of alternative electron conduits, spacer moieties and toxic leaving groups to either the C6 fluoro-uridine base or the C4 hydrazone modified pyrimidine. Methods described above for synthesis of 2-deoxyuridine based compounds can again be employed for the synthesis of such molecules.

[0233] Synthesis of Nucleoside Phenyl Methoxyalaninyl Phosphoramidates

[0234] The use of phosphoramidates as phosphate prodrugs for nucleotides was reported by McGuigan, C. et al. (1993) and McGuigan, C. et al. (1994). The phospharamidates were synthesized by reacting 2′,3′-dideoxynucleosides with phenyl methoxyalaninyl phosphorochloridate (PMPC).

[0235] Since only one hydroxyl group is present, these reactions usually proceed smoothly. In compounds where more than one hydroxyl group is present, the appropriately protected nucleoside may be required. Since the 5′-OH group of 2′-deoxynucleosides is much less hindered than the 3′-OH group, selective phosphoramidation with PMPC is possible under carefully controlled conditions. Both BVdU and 5FUdR condensed with PMPC in the presence of N-methylimidazole in anhydrous CH2Cl2 to give the corresponding phosphoramidates. In both cases, the desired product was readily separable from the starting material using column chromatography on silica gel. The synthetic scheme is summarized below. 41

EXAMPLES 1 AND 2

Synthesis of Compounds with Propargyl Tethers

[0236] Using the general synthetic procedure described supra, bis-aziridin-1-yl-phosphinic acid 3-[2-deoxyuridin-5-yl]-prop-2-ynyl ester was synthesized and analyzed by 1H NMR to yield the following result: 1H NMR ((CD3)2SO). Salient features: δ8.28 (d, 1, H6), 6.10 (pseudo-t, 1, H1′), 5.26 (m, exchanges with D2O, 1, 3′-OH), 5.13 (m, exchanges with D2O, 1, 5′-OH), 4.81 (q or dd, 2, propargyl-CH2), 4.24 (m, 1, H3′), 3.57 (m, 2, 5′-CH2), 2.15-2.0 (m, 8, aziridine-CH2).

[0237] Bis-aziridin-1-yl-phosphinothioic acid 3-[2-deoxyuridin-5-yl]-prop-2-ynyl ester was also synthesized and analyzed by 1H NMR to yield the following result: 1H NMR ((CD3)2SO). Salient features: δ8.29 (d, 1, H6), 6.10 (pseudo-t, 1, H1′), 5.22 (m, exchanges with D2O, 1, 3′-OH), 5.10 (m, exchanges with D2O, 1, 5′-OH), 4.88 (q or dd, 2, propargyl-CH2), 4.31 (m, 1, H3′), 3.52 (m, 2, 5′-CH2), 2.15-2.0 (m, 8, aziridine-CH2).

EXAMPLES 3 TO 8

Synthesis of Furano-pyrimidinones

[0238] Using the general synthetic procedure described supra, the following compounds were prepared.

Example 3

[0239] 3-(2-Deoxy-β-D-ribofuranosyl)-6-(tetrahydropyran-2-yloxymethyl)furo[2,3-d]pyrimidin-2(3H)-one. 1H NMR ((CD3)2SO) δ8.80 (s, 1, H4), 6.74 (s, 1, H5), 6.16 (pseudo-t, 1, H1′), 5.27 (d, exchanges with D2O, 1, 3′-OH), 5.12 (t, exchanges with D2O, 1, 5′-OH), 4.72 (m, 1, THP-H2), 4.56 (q, 2, CH2OTHP), 3.92 (m, 1, H4′), 3.64 (m, 2, 5′-CH2), 2.40 (m, 1, H2′a), 2.03 (m, 1, H2′b), 1.68 and 1.50 (m, 8, THP). Low-resolution mass spectrum (DCI—NH3) on bis-TMS derivative, m/z 323 (B+TMS+H+), 511 (MH+), 583 (M+TMS+).

Example 4

[0240] 3-(2-Deoxy-β-D-ribofuranosyl)-6-(hydroxymethyl)furo[2,3-d]pyrimidin-2(3H)-one. 1H NMR ((CD3)2SO) δ12.0 (bs, 1, OH), 8.24 (s, 1, H4), 6.53 (s, 1, H5), 5.51 (pseudo-t, 1, H1′), 4.42 (m, 2, CH2OH). Low-resolution mass spectrum (DCI—NH3), m/z 167 (B+2H+), 184 (B+NH4+).

Example 5

[0241] 1-[6-(Tetrahydropyran-2-yloxymethyl)furo[2,3-d]pyrimidin-2(3H)-on-3 -yl]-2-deoxy-β-D-ribofuranos-5-yl phenyl methoxy-L-alaninylphosphoramidate. 1HNMR ((CD3)2SO) complicated due to presence of diastereomers. Salient features: δ8.62 and 8.59 (each s, each 1, H4), 7.4-7.1 (m, 5, PhO), 6.61 and 6.60 (each s, each 1, H5), 6.25 (m, 1, H1′), 4.56 (q, 2, propargyl-CH2), 3.56 and 3.54 (each s, each 3, CO2Me), 2.0 (m, 1, H2′b), 1.22 (m, 3, alaninyl-α-Me). Low-resolution mass spectrum (DCI—NH3), m/z 167 (B+2H+), 184 (B+H++NH4+-THP).

Example 6

[0242] 1-[6-(Hydroxymethyl)furo[2,3-d]pyrimidin-2(3H)-on-3-yl]-2-deoxy-β-D-ribofuranos-5-yl phenyl methoxy-L-alaninylphosphoramidate. 1H NMR (CDCl3) complicated due to presence of diastereomers. Salient features: δ8.5 (s, 1, H4), 7.4-7.1 (m, 5, PhO), 6.36 and 6.30 (each s, each 1, H5), 6.23 (m, 1, H1′), 3.67 and 3.65 (each s, each 3, CO2Me), 2.69 (m, 1, H2′a), 2.10 (m, 1, H2′b), 1.35 (m, 3, alaninyl-α-Me). Low-resolution mass spectrum (DCI—NH3), m/z 525 (MH+), 595 (MNH4+).

Example 7

[0243] The 4-nitrophenyl ether derivative of 5-(3-hydroxy-1-propynyl)-2′-deoxyuridine was prepared according to standard ether synthesis as shown below. 42

Example 8

5-[3-(4-Nitrophenoxy)-1-propynyl]-2′-deoxyuridine

[0244] A solution of pre-dried 5-(3-hydroxy-1 -propynyl)-2′-deoxyuridine (Robins, M. J. et al. (1983)) (565 mg, 2 mmol) in 40 mL of anhydrous THF under argon was treated with 4-nitrophenol (696 mg, 5 mmol), triphenylphosphine (787 mg, 3 mmol), and diisopropyl azodicarboxylate (590 liters, 3 mmol), and the reaction mixture heated at 60° C. until the solution was clear, and then 1 hour longer. The mixture was allowed to cool to 23° C. and then it was evaporated onto SiO2 and purified by chromatography using MeOH/CH2Cl2 as eluent to afford 107 mg (13%) of the desired ether product: melting point 112-118° C. H NMR ((CD3)2SO) δ11.65 (s, exchanges with D2O, 1, NH), 8.29 (s, 1, H6), 8.24 (d, J=9.3 Hz, 2, m-ArH), 7.23 (d, J=9.3 Hz, 2, o-ArH), 6.09 (pseudo-t, 1, H1′), 5.17 (s, 2, propargyl-CH2), 4.22 (m, 1, H3′), 3.80 (m, 1, H4′), 3.59 (m, 2, 5′-CH2), 2.13 (pseudo-t, 2, 2′-CH2). Low-resolution mass spectrum (DCI—NH3) onper-trimethylsilyated material, m/z 547 [M(TMS)2H+], 565 [M(TMS)2NH4+], 620 [M(TMS)3H+].

EXAMPLE 9

5-(4-Carbethoxy-1,3-butadienyl)-2′-dexoyuridine

[0245] (a) 5-(Carbomethoxyvinyl)-2′-deoxyuridine-3′,5′-bis(tetrahydro-2H-pyran-2-yl)ether (I)

[0246] A slurry of 5-(carbomethoxyvinyl)-2′-deoxyuridine (3.0 g, 9.6 mmol), 3,4-dihydro-2H-pyran (22 mL, 21.3 mmol) and pyridinium p-toluenesulfonate (PPTS, 0.242 g, 0.96 mmol) in dimethylformamide (DMF, 5 mL) was stirred at 50° C. for 18 hours. The resulting solution was concentrated in vacuo (bath temperature 45° C.) to give a thick, pale yellow oil. The oil was dissolved in EtOAc and the solid was filtered. The solution was again concentrated. The oil obtained was purified by column chromatography on silica gel using 50-75% EtOAc/hexane as eluent to give 3.81 g (85%) of pure product as a colorless oil.

[0247] (b) 5-(3-Hydroxyprop-1-enyl)-2′-deoxyuridine-3 ′,5′-bis(tetrahydro-2H-pyran-2-yl)ether (II)

[0248] A solution of (I) (3.5 g, 7.27 mmol) in CH2Cl2 (14 mL) was cooled to −78° C. in a dry ice/acetone bath. Diisobutylaluminum hydride (DIBAL-H) in toluene (1.0M, 24 mL, 24.0 mmol) was added dropwise over 2 hours while the temperature was maintained at −78° C. The solution was stirred at −78° C. for an additional 2 hours and MeOH (2.5 mL) was added dropwise to destroy any excess DIBAL-H. The reaction mixture was cannulated into a mixture of 30% citric acid solution (50 mL), ice (25 g) and EtOAc (30 mL) over ca. 20 minutes. The phases were separated and the aqueous phase was extracted with EtOAc (2×25 mL). The combined organic phase was washed with saturated NaHCO3 (20 mL) and brine (20 mL), dried over MgSO4 and concentrated to give 3.288 g (100%) of colorless oil

[0249] (c) 5-(3-Oxoprop-1-enyl)-2′-dexoyuridine-3′,5′-bis(tetrahydro-2H-pyran-2-yl)ether (III)

[0250] To a solution of crude (II) obtained from above (1.988 g, 4.4 mmol) in CH2Cl2 (9 mL) was added solid pyridinium dichromate (PDC; 1.82 g, 4.8 mmol) with water cooling. The suspension was stirred while acetic acid (0.4 mL) was added dropwise. The water bath was removed and the reaction was stirred at room temperature for 1 hour. The crude product was filtered through a pad of florisil (2×2.5 cm) and the florisil washed with 35 mL EtOAc. The brown solution obtained was filtered through another column of florisil (3.5 cm diam×2.5 cm height). The filtrate was concentrated to give 1.273 g (64% yield) of very light brown oil.

[0251] (d) 5-(4-Carbethoxy-1,3-butadienyl)-2′-dexoyuridine-3′,5′-bis(tetrahydro-2H-pyran-2-yl)ether (IV)

[0252] (Carbethoxymethylene)triphenylphosphorane (0.32 mg, 0.92 mmol) was added to a solution of the crude aldehyde (III) (0.344 g, 0.77 mmol). The solution darkened and turned rust color. After 1 hour, (III) was completely consumed as judged by thin layer chromatography. The solvent was evaporated and the crude product was purified by column chromatography on silica gel using 35-45% EtOAc/hexane as eluent. The pure product (0.310 g, 78% yield) was obtained as colorless oil.

[0253] (e) 5-(4-Carbethoxy-1,3-butadienyl)-2′-dexoyuridine (V)

[0254] 5-(4-Carbethoxy-1,3-butadienyl)-2′ -dexoyuridine-3′,5′-bis(tetrahydro-2H-pyran-2-yl)ether (IV) (0.637 g, 1.22 mmol) was dissolved in MeOH (1.5 mL) and PPTS (0.049 g, 0.16 mmol) was added. The solution was stirred at 50° C. for 7.5 hours and left at room temperature overnight. A white precipitate was formed. The reaction mixture was cooled to 0° C. and filtered to give pure (V) as a white solid (0.188 g). The filtrate was concentrated and chromatographed on silica gel using 50-100% EtOAc/hexane as eluent to give a further 0.180 g product. The total yield of the product was 0.368 g (86%).

[0255] 1 H NMR (DMSO-d6): 1.22 (3H, t, J=7 Hz), 2.17 (2H, br t, J=5.5 Hz), 3.55-3.75 (2H, m), 3.81 (1H, m), 4.12 (2H, q, J=7 Hz), 4.25-4.28 (1H, m), 5.19 (1H, t, J=4.8 Hz), 5.27 (1H, d, J=4.1 Hz), 5.98 (1H, d, J=14.5 Hz), 6.14 (1H, t, J=6.3 Hz), 6.75 (1H, d, J=14.5 Hz), 7.18-7.30 (2H, m), 8.30 (1H, s), 11.56 (1H, s).

EXAMPLE 10

5-(4-Carbomethoxy-1,3-butadienyl)-2′-dexoyuridine (Va)

[0256] A solution of triethylamine (3.9 mL, 28.2 mmol) in dioxane (12 mL) was deareated by bubbling nitrogen through for 15 minutes. Palladium acetate (0.60 g, 0.26 mmol) and triphenylphosphine (0.183 g, 0.70 mmol) were added and the solution was heated at 70° C. for 20 minutes to give a dark brown solution. 5-Iodo-3′-deoxyuridine (5.0 g, 14.1 mmol) and methyl 2,4-pentadienoate (2.5 g, 22.3 mmol) were added and the mixture was heated under reflux for 15 hours. The solvent and volatile components were evaporated in vacuo and the residue was partitioned between water (15 mL) and EtOAc (15 mL). The phases were separated and the aqueous phase was extracted twice with EtOAc (10 mL each). The combined organic phase was washed with brine and concentrated. The residue was dissolved in MeOH (15 mL) and allowed to cool to room temperature. The solid formed was collected by filtration, washed with a small quantity of MeOH and dried in vacuo to give 0.38 g brown powder.

[0257] 1 H NMR (DMSO-d6): 2.17 (2H, t, J=6.4 Hz), 3.55-3.70 (2H, m), 3.66 (3H, s), 3.82 (1H, q, J=3.6 Hz), 4.27 (1H, m), 5.18 (1H, t, J=4.9 Hz), 5.26 (1H, d, J=4.5 Hz), 5.99 (1H, d, J=14.4 Hz), 6.14 (1H, d, J=6.4 Hz), 6.74 (1H, d, J=14.8 Hz), 7.20-7.35 (2H, m), 8.30 (1H, s), 11.56 (1H, s).

[0258] The filtrate from above was concentrated and chromatographed on silica gel using 60-100% EtOAc/hexanes as eluent to give another 0.70 g of product as a brown foam. The combined yield was 1.08 g (22.6%).

EXAMPLE 11

5-(4-Carboxy-1,3-butadienyl)-2′-dexoyuridine (VI)

Method I

[0259] 5-(4-Carbethoxy-1,3-butadienyl)-2′-dexoyuridine (V, from Example 9) (0.449 g, 1.28 mmol) was dissolved in 2N NaOH (3 mL) and stirred at 25° C. After 20 minutes, a precipitate was formed and TLC showed that the starting material was completely consumed. The mixture was cooled to 0° C. and acidified to pH 1 with 2N HCl. The resulting off-white solid was filtered off, washed with water and dried in vacuo to give 0.225 g (54%) product.

[0260] 1 H NMR (DMSO-d6): 2.12-2.19 (2H, m), 3.50-3.70 (2H, m), 3.75-3.85 (1H, m), 4.24-4.29 (1H, m), 5.19 (1H, t, J=4.8 Hz), 5.27 (1H, d, J=4.2 Hz), 5.80-5.95 (1H, m), 6.14 (1H, t, J=6.4 Hz), 6.60-6.75 (1H, m), 7.15-7.25 (2H, m), 8.26 (1H, s), 11.56 (1H, s), 12.16 (1H, br s).

[0261] The filtrate and washings were combined and evaporated to dryness. The resulting sticky yellow solid was dissolved in MeOH from which a white precipitate was formed. The solid was filtered off to give an additional 0.200 g of product.

Method II

[0262] The title compound can also be prepared from 5-(4-carbomethoxy-1,3-butadienyl)-2′-dexoyuridine (Va, from Example 10) in comparable yield as mentioned above.

EXAMPLE 12

5-(4-Bromo-1E,3E-butadienyl)-2′-dexoyuridine (VIIa) and 5-(4-Bromo-1E,3Z-butadienyl)-2′-dexoyuridine (VIIb)

[0263] To a solution of 5-(4-carboxy-1,3-butadienyl)-2′-dexoyuridine (VI) (0.200 g, 0.62 mmol) in DMF (1 mL) was added KHCO3 (0.185 g, 1.84 mmol) and the mixture was stirred for 20 minutes at 25° C. A solution of N-bromosuccinimide (0.117 g, 0.65 mmol) in DMF (0.3 mL) was added dropwise. Smooth gas evolution (CO2) occurred throughout the addition. The resulting brown suspension was stirred for 2 hours at 25° C. at which time TLC showed that (VI) was completely consumed. Water (10 mL) was added to the suspension and the resulting solution was extracted with EtOAc (2×15 mL). The extract was dried over MgSO4 and the solvent was evaporated in vacuo to give a yellow solid (178 mg, 80% yield) consisting of a mixture of two isomers as shown by 1H NMR. The crude product was separated by semi-preparative HPLC (reversed phase C18 column) using 20% acetonitrile in water as the mobile phase to give the following isomers:

[0264] 5-(4-Bromo-1E,3Z-butadienyl)-2′-dexoyuridine: retention time 10.5 minutes; 1H NMR: (DMSO-d6): 2.11-2.18 (2H, m), 3.50-3.70 (2H, m), 3.80 (1H, distorted q, J=3.5 Hz), 4.25 (1H, br s), 5.08 (1H, br s), 5.25 (1H, br s), 6.15 (1H, t, J=6.5 Hz), 6.40 (1H, d, J=7 Hz), 6.53 (1H, d, J=15.6 Hz), 6.83 (1H, dd, J=7, 10 Hz), 7.39 (1H, dd, J =10, 15.6 Hz).

[0265] 5-(4-Bromo-1E,3E-butadienyl)-2′-dexoyuridine: retention time 15.1 minutes; 1H NMR (DMSO-d6): 2.12-2.16 (2H, m), 3.50-3.70 (2H, m), 3.80 (1H, q, J=3.2 Hz), 4.26 (1H, m), 5.13 (1H, br s), 5.25 (1H, br s), 6.14 (1H, t, J=6.5 Hz), 6.36 (1H, d, J=15.6 Hz), 6.67 (1H, d, J=13.1 Hz), 6.84(1H, dd, J=11, 13.1 Hz), 7.04 (1H, dd, J=11, 15.6 Hz).

EXAMPLE 13

[0266] Using the procedures mentioned in Example 11, Method II, the following compounds can be obtained in a similar fashion: 5-(4-chloro-1,3-butadienyl)-2′-dexoyuridine (using N-chlorosuccinimide in place of N-bromosuccinimide in Step B); 5-(4-iodo-1,3-butadienyl)-2′-dexoyuridine (using iodine in sodium idodide in place of N-bromosuccinimide).

EXAMPLE 14

Phenyl N-methoxy-L-alaninyl Phosphorochloridate

[0267] L-alanine methyl ester hydrochloride (245.8 g; 1.76 mol) was placed in a 12 liter three-neck round bottom flask (equipped with a mechanical stirrer and thermometer) followed by 4.0 liters of dichloromethane. The mixture was stirred for 15 minutes at room temperature. Phenyl phosphodichloridate (370.0 g; 1.76 mol) was added to the mixture and stirring was continued for 15 minutes at room temperature. The flask was placed in the bath with dry ice and the stirring was continued for 20 minutes until a uniform suspension was formed.

[0268] Freshly distilled tri-n-butylamine (626.5 g; 3.38 mol) was added dropwise (˜90 minutes) with vigorous stirring to the reaction mixture so that the temperature inside the flask was held at ˜0° C. The bath was removed and the stirring was continued for 6 hours at room temperature. The solution was concentrated to ˜2.84 liters by evaporating several portions of the mixture on a rotary evaporator and the mixture was sealed under argon and stored at −20° C. The product was 85% pure by phosphorus NMR to give an estimated concentration of phenylmethoxyalaninyl phosphochloridate of ˜0.5M.

EXAMPLE 15

5-(2-Bromovinyl)-2′-deoxyuridine phenyl N-methoxy-L-alaninyl phosphoramidate (NB1011)

[0269] The reaction was performed under argon atmosphere. 5-(2-bromovinyl)-2′-deoxyuridine (BVdU) (204 g; 612 mmol) was placed in three-neck 3 liter round bottom flask equipped with mechanical stirrer. The flask was placed in ice-water bath and 1600 mL (˜800 mmol) of phenylmethoxyalaninyl phosphochloridate reagent were added using an addition funnel over 15 minutes with vigorous stirring of the reaction mixture, followed by the addition of 100 mL of N-methylimidazole over 5 minutes using syringe. After 5 minutes the mixture became clear and after 10 minutes the ice-water bath was removed to allow the mixture to warm up to room temperature while stirring was continued. The reaction was monitored by reversed phase HPLC and was complete in 3 hours. The reaction was quenched by the addition of 100 mL of methanol and the mixture was evaporated to an oil, re-dissolved in 6 liters of dichloromethane and passed through 800 g of silica gel. The major portion of BVdU-PA, referred to herein as NB1011, was passed through the column during the loading and finally the elution of NB1011 was completed by passing 5 liters of 5% methanol in dichloromethane. All fractions containing NB1011 were combined and evaporated to an oil, the residue was dissolved in 4 liters of ethyl acetate and the mixture was extracted with water (2×2 liters). The organic layer was dried with sodium sulfate, filtered, and washed with ethyl acetate (3×300 mL). The combined filtrate and washings were evaporated to produce a lightly colored white foam; total weight ˜540 g.

[0270] The crude product was purified by two silica gel chromatography using 0-5% MeOH in CH2Cl2 and 10% MeOH in CH2Cl2, respectively, as eluent. The yield of product (>98% pure) was 64 g.

EXAMPLE 16

[0271] Using the methods described in Example 15, the phenyl N-methoxy-L-alanyl phosphoramidates of the following nucleosides were prepared:

[0272] 5-(4,4-dibromo-1,3-butadienyl)-2′-deoxyuridine;

[0273] 5-(2-chlorovinyl)-2′-deoxyuridine;

[0274] 5-trifluoromethyl-2′-deoxyuridine;

[0275] 5-(4-carbethoxy-1,3-butadienyl)-2′-deoxyuridine;

[0276] 5-(4-carbomethoxy-1,3-butadienyl)-2′-dexoyuridine;

[0277] 5-(4-bromo-1E,3E-butadienyl)-2′-deoxyuridine;

[0278] 5-(4-bromo-1E,3Z-butadienyl)-2′-deoxyuridine;

[0279] 5-(trimethylsilylethynyl)-2′-deoxyuridine;

[0280] 5-(ethynyl)-2′-deoxyuridine;

[0281] 5-(1-decynyl)-2′-deoxyuridine;

[0282] 3-(2′-deoxy-β-D-ribofuranosyl)-2,3-dihydrofuro[2,3-d]pyrimidin-2-one; and

[0283] 3-(2′-deoxy-β-D-ribofuranosyl)-6-octyl-2,3-dihydrofuro[2,3-d]pyrimidin-2-one.

EXAMPLE 17

[0284] Using the methods described in Examples 14 and 15, the following amino acid phosphoramidate derivatives of 5-(2-bromovinyl)-2′-deoxyuridine were prepared:

[0285] Phenyl (benzoxy-L-alaninyl) phosphoramidate;

[0286] Phenyl (methylene cyclopropoxy-L-alaninyl) phosphoramidate;

[0287] Phenyl (cyclohexoxy-L-alaninyl) phosphoramidate;

[0288] Phenyl (iso-propoxy-L-alaninyl) phosphoramidate;

[0289] Phenyl (methylene tert-butoxy-L-alaninyl) phosphoramidate;

[0290] Phenyl (cycloheptoxy-L-alaninyl) phosphoramidate;

[0291] Phenyl (cyclooctoxy-L-alaninyl) phosphoramidate;

[0292] Phenyl (methylene adamantoxy-L-alaninyl) phosphoramidate; and

[0293] Phenyl (methoxy-L-tryptophanyl) phosphoramidate.

[0294] Chemical assays for products, for example, where a reaction product is an anti-metabolite of the bromovinyl-derivatives of dUMP, are described in the Examples provided below or by Barr, P. J. et al. (1983).

EXAMPLE 18

Cell and Enzyme Based Assays

[0295] Expression of thymidylate synthase in human normal tissues. The TS expression level in normal human tissues was examined in order to estimate the systemic toxicity of the compound(s) activated by thymidylate synthase. The relative TS mRNA levels in brain, heart, kidney, spleen, liver, colon lung, small intestine, stomach muscle, testis, ovary, uterus, prostate, thyroid gland, salivary gland, adrenal gland, skin, PBL and bone marrow tissues were determined by using RT-PCR. It has been shown that TS mRNA levels in most of these tissues were equal to or less than that in colon tissue, except that in bone marrow (1.25 fold), ovary (1.38 fold) and testis tissues (2.13 fold). However, the average TS mRNA level in colon cancer samples was 4.6 fold more than that in their matched normal colon tissue samples. This result suggests that compounds which are activated by overexpressed TS in colon cancer would have no or little toxicity to normal human tissues.

[0296] Transcript levels of human thymidylate synthase in multiple normal tissues were investigated by PCR amplification. Panel of cDNAs of human tissues were obtained from OriGene Technologics, Inc. (Rockville, Md.). PCR reactions were perfromed in a volume of 25 μl, containing cDNA (100×), 3 mM MgCl2,, 50 mM KCl 20 mM Tris-Cl, pH 8.4, 0.2 mM of each dNTP, 0.2 μM of thymidylate synthase sense and antisense primers and 1.25 units of Taq DNA polymerase (obtained from Promega, Madison, Wis.). The reaction mixtures were incubated at 94° C. for 2 min, followed by 12 cycles of 40 sec incubations at 94° C., 1 min incubation at 58° C., and then 1 min incubation at 72° C.25 μl reaction buffer contained 0.2 μM β-actin primers, 0.2 μM of thymidylate synthase primers, 3 mM MgCl2, 50 mM KCl, 20 mM Tris-cl, pH 8.4, 0.2 mM of each dNTP and 1.25 units of Taq DNA polymerase were added to achieve a final concentration of 0.2 μM of thymidylate synthase primers and 0.1 μM β-actin primers, bringing the reaction volume to 50 μl. PCR reaction was continued to a total of 36 cycles, followed by a 7 min incubation at 72° C.

[0297] 10 μL of PCR products were resolved by electrophoresis in a 2% agarose gel, followed by staining with SYBR Gold nucleie acid gel stain (obtained from Molecular probes, Eugene, Oreg.). The DNA bands corresponding to thymidylate synthase were quantified and normalized to that of β-actin by Molecular Dynamics Storm. The quantified expression levels were expressed as values relative to that of colon.

[0298] RT-PCR analysis of matched normal and tumor tissues. Transcript levels of human thymidylate synthase in colon cancer tissues and matched normal colon tissues were quantified by using Reverse RT-PCR amplification. Oligonucleotide primers for amplification of the human thymidylate synthase and β-actin were designed as following: thymidylate synthase sense primer 5′-GGGCAGATCCAACACATCC-3′ (SEQ ID NO. 1) (corresponding to bases 208-226 of thymidylate synthase cDNA sequence, Genbank Accession No. X02308), antisense primer 5′-GGTCAACTCCCTGTCCTGAA-3′ (SEQ ID NO. 2) (corresponding to bases 564-583), β-actin sense primer 5′-GCCAACACAGTGCTGTCTG-3′ (SEQ ID NO. 3) (corresponding to bases 2643-2661 of β-actin gene sequence, Genbank Accession No. M10277) and antisense primer 5′-CTCCTGCTTGCTGATCCAC-3′ (SEQ ID NO. 4) (corresponding to bases 2937-2955).

[0299] Human colon tumor tissues and matched normal tissues were obtained from Cooperative Human Tissue Network (CHTN, Western Division, Cleveland, Ohio). Total RNAs were isolated using Tri pure isolation reagent (obtained from Boehringer Mannheim Corp., Indianapolis, Ind.), followed manufactureis protocol. To monitor for possible DNA contamination, the primers for amplification of β-actin were designed to span the exon4/intron5/exon5 junction. Genomic DNA template leads to a 313 bp β-actin fragment, and cDNA template generates a 210 bp product.

[0300] Reverse transcriptions were performed, using SuperScript preamplification system (Gibco/BRL, Gaithersburg, Md.). 3 μg total RNA was applied in a volume of 20 μl buffer to conduct reverse transcription reaction, followed manufacture's protocol.

[0301] PCR reactions were performed in a volume of 96 μl, containing 5 μl of cDNA mixture from reverse transcription reaction, 3 mM MgCl2, 50 mM KCl, 20 mM Tris-Cl, pH 8.4, 0.2 mM of each dNTP, 0.3 μM of thymidylate synthase sense and antisense primers and 5 units of Tag DNA polymerase (obtained from Promega, Madison, Wis.). The reaction mixtures were incubated at 94° C. for 3 min, followed by 9 cycles of 1 min incubation at 94° C., 1 min incubation at 58° C., and then 1 min incubation at 72° C. After 9 cycles, human β-actin primers in 4 μl were added to achieve a final concentration of 0.2 μM, bringing the final reaction volume to 100 μl. PCR reaction was continued to a total of 30, 32 or 34 cycles, followed by a 7 min incubation at 72° C.

[0302] 10 82 L of PCR products were resolved by electrophoresis in 2% agarose gel, followed by staining with SYBR Gold nucleic acid gel stain (obtained from Molecular probes, Eugene, Oreg.). Result of quantification indicated that amplification of thymidylate synthase and β-actin was linear between cycles 30 and 34. The DNA bands corresponding to thymidylate synthase were quantified and normalized to that of actin by Molecular Dynamics Storm. The quantified expression levels were expressed as values of ratio between TS and β-actin.

[0303] Cell lines and transfection. HT1080 cells were grown in PRM11640 medium supplemented with 10% fetal calf serum, and transfected with GFP-TS expression vector. 48 hours after, transfection cells were tripsinized and replated in culture medium containing 750 μg/ml G418. After selection with G418 for two weeks, surviving cells were sorted based upon fluorescence expression. One clone with higher fluorescence expression (named as TSH/HT1080) and one clone with lower fluorescence expression (named as TSL/HT1080) were selected and expanded into cells lines. The stable HT1080 cells transfected with pEGFP-C3 were used as control.

[0304] Construction of GFP-TS expression vector. A cDNA fragment encoding conserved region of human thymidylate synthase (amino acids 23 to 313) was obtained by PCR amplification using following primers: Sense primer, 5′-CGGAAGCTTGAGCCGCGTCCGCCGCA-3′ (SEQ ID NO. 6) and antisense primer, 5′-GAAGGTACCCTAAACAGCCATTTCCA-3′ (SEQ ID NO. 7). The cDNA was cloned into HindIII and KpnI sites of mammalian expression vector pEGFP-C3 ( Clontech Laboratories. Inc., Palo Alto, Calif.), in-frame with GFP sequence. The cDNA insert was confirmed by DNA sequencing.

[0305] Western blot analysis. Human normal and cancer cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum. Cells were grown till confluent in 100 mm culture dish and lysed in 0.5 ml of RIPA buffer ( 50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.5% Triton X-100, 0.1% SDS, 0.5% Deoxycholic acid, sodium salt and protease inhibitors ). Protein concentrations were determined by using BCA-200 protein assay kit (obtained from Pierce, Rockford, Ill.). 15 μg of total protein from each cell strain/line was resolved by 12% SDS-PAGE. The separated proteins were transferred onto PVDF membrane, followed by immunoblot with human thymidylate synthase monoclonal primary antibody (manufactured by NeoMarkers, Fremont, Calif.) and horseradish peroxidase linked sheep anti-mouse Ig secondary antibody (obtained from Amersham, England). The ECL plus kit (Amersham) was used for detection of immunoreactivity. The bands corresponding to thymidylate synthase were quantified and normalized to that of tubulin by Molecular Dynamics Storm. The quantified expression levels were expressed as values relative to that of cell strain CCD 18co.

[0306] TS Activity Assay by Tritium Release from dUMP-3H. Cells were plated in 24 well plates to a density of 30,000 cells/plate and incubated for 16 hours to allow adhesion to the plastic surface of the plate.

[0307] Immediately prior to the thymidylate synthase assay, the media was replaced with RPMI+10% dialyzed fetal calf serum. 0.5 μCi of 5-[3H]deoxyuridine was added to each well, and plates were incubated for 60 minutes at 37° C. without additional CO2. [3H] release was measured by adsorbing 5-[3H]deoxyuridine to activated charcoal (10% in 1×PBS) for 5 minutes at room temperature. After centrifugation for 5 minutes at 13,000 RPM, the amount of [3H] in the supernatant was determined by liquid scintillation counting.

[0308] Growth Inhibition Studies. Cells growing exponentially were transferred to 384-well flat bottom tissue culture plates. All cell types were plated at a density of 500 cells per well in 25 μL of complete medium (RPMI 1640+10% fetal bovine serum+antibiotics/antimycotics). After 24 hours (day 0), 25 μL of complete medium containing the experimental compounds over the dose range of 10ñ3 to 10ñ10 M were added in triplicate. Drug exposure time was 120 hours (day 5), after which growth inhibition was assayed. 5 μL of the redox indicator, alamarBlue, was added to each well (10% v/v). After 4 hours incubation at 37° C., fluorescence was monitored at 535 nm excitation and 595 nm emission.

[0309] Concentration vs. relative fluorescence units (RFU) were plotted, and sigmoid curves were fit using the Hill equation. IC50, indicated by the inflection point of the curve, is the concentration at which growth is inhibited by 50%.

[0310] Enzyme Preparation. Cloned human thymidylate synthase plasmid pBCHTS was subcloned into E. coli. BL21 (DE3)/pET-28a(+) (Novagen) using the Ndel ñSacI insertion site, in order to add an amino terminal His tag. Enzyme was expressed in E. coli. by induction with IPTG, and purified by affinity chromatography on a Ni2+ His Bind metal chelation resin (Novagen). The column Ni2+ His Bind metal chelation column was washed with 20 mM Tris pH 7.9, 5 mM imidazole, 0.5M NaCl; thymidylate synthase activity was eluted with 20 mM Tris pH 7.9, 60 mM imidazole, 0.5M NaCl.

[0311] Enzyme Assays and Kinetic Measurements. Thymidylate synthase assays were done in 96 well Costar UV transparent plates in a reaction volume of 200 μL, consisting of 40 mM Tris pH 7.5, 25 mM MgCl2, 1 mM EDTA, 25 mM-mercaptoethanol, 125M dUMP, and 65 μM N5, N10-methylene tetrahydrofolate indicated. Tetrahydrofolate stock solutions were prepared by dissolving tetrahydrofolic acid (Sigma) directly into 0.2M Tris pH 7.5, 0.5 M-mercaptoethanol; stock solutions were stored at −80° C. N5, N10-methylene tetrahydrofolate was prepared by adding 12 μl of 3.8% formaldehyde to 1 ml of a 0.65 mM solution of tetrahydrofolate and incubating for 5 minutes at 37° C. N5, N10-methylene tetrahydrofolate was kept on ice and used within 2 hours of preparation.

[0312] Conversion of BVdUMP to fluorescent product(s) by thymidylate synthase was measured in 200 μl thymidylate synthase reactions containing 125M BVdUMP in 96 well Dynex Microfluor Black “U” bottom microtiter plates using an excitation wavelength of 340 nm and emission wavelength of 595 nm. Fluorescence was measured with a Tecan Spectrafluor Plus fluorimeter.

[0313] Enzyme kinetic constants (Km and Vmax) were determined for the human thymidylate synthase substrates dUMP and BVdUMP using the enzyme assay conditions described above. Results are shown in Table 3. The initial rates of the enzyme reactions was determined by measuring the increase in A340 for the reaction with dUMP, and decrease in A294 for the reaction with BVdUMP. The catalytic efficiency of the enzyme (Kcat/Km) was calculated from the kinetic constants Km and Vmax.

[0314] Liquid Chromatography/Mass Spectroscopy. Cells were washed three times with PBS at room temperature, then subjected to freeze/thaw lysis in 5 ml PBS. Cell extracts were centrifuged for 10 minutes at 10KRPM, then adsorbed to Sep-Pak C18 and washed with 10 ml PBS. BVdUMP was eluted with 1 ml distilled water. LC/MS samples were analyzed by reverse phase chromatography on a C18 column using a linear gradient of 0.1% formic acid-0.1% formic acid/95% acetonitrile. Mass spectroscopy was done with a Micromass Quattro II triple quadropole spectrometer.

[0315] Tomudex Inhibition of NB1011 Cytotoxicity. MCF7-TDX were transferred to a 384 well assay plate at 500 cells in 25 μL complete medium per well. After 24 hours (day 0), 25 μL complete medium containing a combination of NB1011 in doubling serial dilutions from 1 mM and tomudex at discrete concentrations (0,1,10,100,1000 nM) were added in duplicate. Drug exposure time was 120 hours (day 5) after which growth inhibition was measured with alamarBlue as described above in Growth Inhibition Studies (above).

[0316] Reversal of Resistance. The origin and characteristics of the human breast cancer MCF7 TDX cell line have been previously described (Drake, et al. (1996)). Briefly, MCF-7 breast cancer cells were selected in vitro for resistance to Tomudex by continuous exposure to stepwise increases in TDX concentrations up to 2.0 μM. A resistant subline was selected for resistance to NB1011 by continuous exposure of the parental MCF7 TDX cell line to medium supplemented without TDX but with 50 μM NB1011, a concentration approximately 16 times higher than the IC50 for NB1011 in the parental MCF7 TDX cell line. After a dramatic initial cell killing effect, resistant colonies emerged, and vigorously growing monolayers were formed. TS protein level and IC50 for 5-FU, TDX, and NB1011 were determined for the resultant MCF7 TDX/1011 cell line as described in above by western blot and the alamarBlue cytotoxicity assay, respectively.

[0317] Analysis of NB1011 in TS-expressing, 5-FU resistant, H630-10 colon carcinoma xenografts in vivo. H630-10 colon cancer cells, selected for resistance to 5-FU in vitro, express high levels of thymidylate synthase, and form xenografts in athymic mice. Following cell expansion ex-vivo H630-10 were injected subcutaneously (S.Q.) at 1.5×107 cells/tumor in the mid-back region of 4-6 week old, female, CD-1 (nu/nu), athymic mice (Charles River Laboratories, Wilmington, Mass.). Tumor volumes, calculated as the product of length, width, and depth, were monitored twice weekly by serial micrometer measurements by a single observer. Six animals were randomly assigned to each treatment group and statistical tests were performed (single-factor ANOVA) to assure uniformity in starting tumor volumes between treatment and control groups at the beginning of the experiment. NB1011 was administered by intraperitoneal (I.P.) or intratumoral (IT) injection. The dosage of experimental agents tested were as follows: Group 1: DMSO vehicle control solution (IP), Group 2: 5-FU (15 mg/kg×5 days IP=the MTD for 5-FU in this model), Group 3: NB1011=1.25 mg×5 days (IP), Group 4: NB1011=2.5 mg×5 days (IP), Group 5: NB1011=3.5 mg×5 days (IP), Group 6: DMSO control (IT), Group 7: NB1011=1.25 mg×5 days (IT), and Group 8: NB1011=2.5 mg×5 days (IT). These doses were based on independent dose-finding experiments conducted in our laboratory and were near the maximum-tolerated dose of NB1011 for this specific age and strain of female athymic mice. To assure accurate dosing, drug doses were individualized based upon animal weights determined immediately prior to each injection. Treatment with control solution or NB1011 was initiated 10 days status post xenograft inoculation at which time xenograft volumes measured 45-68 mm3. Differences in day 25 xenograft volumes between groups were analyzed by single-factor ANOVA of the log transformed tumor volume data. Experimental athymic mice were maintained under aseptic conditions in a dedicated room in the UCLA Animal Care Facility. The University of California, Los Angeles has an Animal Welfare Assurance document on file with the Office of Protection from Research Risks, Laboratory Animal Safety Assurance Number A-3196-01. All experiments were closely supervised by the UCLA veterinarian. Euthanasia techniques employed by UCLA are supported by the Panel of the American Veterinary Medical Association. The University of California, Los Angeles experimental animal program and facilities are accredited by the American Association for the Accreditation of Laboratory Animal Care. The personnel performing the animal procedures/manipulations described in this protocol are technically competent in those procedures and have received their training on the use of animals in research, as required by the Animal Welfare Act of 1985.

In vitro Reaction of BVdUMP with Human Thymidylate Synthase

[0318] 1. The Cell-free Processing of BVdUMP by rHuTS Generates Fluorescent Product(s)

[0319] The cell-free processing of BVdUMP by L. casei TS has been shown to create potentially reactive intermediates (Barr, et al. (1983)). For this reason it has been thought that processing of BVdUMP by TS leads to irreversible inactivation of human TS (Balzarini (1987)). The cell-based experiments by DeClercq, Balzarini and colleagues (Balzarini (1987); Balzarini (1993); and Balzarini (1995)) support the concept that, once BVDU is converted to the monophosphate in cells (via herpes virus thymidine kinase), then it binds to and inactivates the Hu TS enzyme during processing. However, the actual reaction of human TS with BVdUMP has never been adequately characterized. Santi and colleagues (Barr, P. J. et al. (1983)) utilized a bacterial TS for their work to show generation of product from the BVdUMP+TS reaction, and DeClercq and colleagues utilized cells and cell lysates, not purified human TS (Balzarini (1987)); Balzarini, (1993); and Balzarini (1995)).

[0320] The interaction of BVdUMP with purified recombinant human TS (rHuTS) was revisited. When BVdUMP was incubated with rHuTS in the standard reaction mixture, the reaction results in the formation of fluorescent product(s) (FIG. 1). The time dependent increase in fluorescence is accompanied by a decrease in the initial BVdUMP concentration. The product(s) produced have been partially characterized, and appear to be exocyclic pyrimidine nucleotide derivatives.

[0321] This result is surprising because previous results supported the idea that TS reaction with BVdUMP should inactivate the human TS enzyme (Balzarini, et al. (1987), (1993), and (1995)). Because the reactions described above were done in a cell-free system with purified components, it remained possible that the intracellular milieu could provide components that would result in TS inactivation following conversion of NB1011 to the free nucleotide monophosphate inside the cell. This issue is addressed in more detail below.

[0322] 2. Comparative Reaction Kinetics of dUMP and BVdUMP with rHuTS

[0323] Previously reported work by Barr, et al.(1983), utilizing the L. casei TS (Balzarini (1987), (1993), (1995) and (1995b)) using cells and cell lysates, leaves unclear whether the reaction of BVdUMP with human TS will result in irreversible inactivation of the enzyme. To address this question, the kinetics of interaction of BVdUMP with rHuTS, in the presence or absence of dUMP, were determined.

[0324] Competitive inhibition is most consistent with a reaction in which BVdUMP does not inactivate the TS enzyme. To help further clarify this situation, an extended incubation of rHuTS with BVdUMP was done in order to measure any inactivation that may occur over a period of time longer than that in which the kinetics were performed (FIG. 2).

[0325] These data show that even after a 20 hour incubation of rHuTS with BVdUMP, little or no enzymatic inactivation is apparent as measured by rate of conversion of THF DHP dUMP as substrate. This result is consistent with the hope for ability of overexpressed TS to convert BVdUMP into cytotoxic metabolites in cells, preferentially in cells which overexpress TS, and finally, without inactivating the enzyme.

[0326] 3. Characterization of BVdUMP reaction with TS: Cofactors and Inhibitors

[0327] The best characterized reaction of TS is the conversion of dUMP to dTMP. This reaction involves the transfer of a methylene group from N5,N10-methylene tetrahydrofolate (THF) to the C-5 position of dUMP (Carreras, C. W. and Santi, D. V. (1995)). This reaction is dependent upon the cofactor (THF), and is inhibited by the uridylate mimic, 5F-dUMP, which, upon reaction with the enzyme, results in the formation of a stable complex and loss of enzymatic activity. A second well characterized inhibitor of TS activity is Tomudex, which occupies the folate binding site of the TS homodimer, prevents the binding of THF, and blocks TS activity in the cell (Drake (1996) and Touroutoglou and Pazdur (1996)). As part of a preliminary effort to characterize the reaction of rHuTS with BVdUMP, the effects of 5F-dUMP, Tomudex and cofactor were compared on the reaction of the enzyme with dUMP and BVdUMP. These experiments (Table 3) show that, similarly to the case of dUMP, 5F-dUMP can prevent conversion of BVdUMP to fluorescent product(s). In addition, Tomudex can also prevent product formation from both dUMP and BVdUMP. However, consistent with earlier reported results with L. casei TS (Barr, et al. (1983)), THF is not required for the conversion of BVdUMP to fluorescent product(s). In addition, the data shown in Table 3 also demonstrate that THF stimulates the production of fluorescent product(s) in the BVdUMP reaction with rHuTS. This result is not expected from the earlier data reporting that THF has no effect on this reaction (Barr, P. J. et al. (1983)), and illustrates a potentially important possibility that cofactors, or cofactor agonists, like leucovorin, could modulate the reaction of BVdUMP with human TS.

[0328] Analysis of the Michaelis-Menton kinetics of this reaction showed that inhibition of BVdUMP by dUMP fits the expected form for competitive inhibition, consistent with both nucleotides behaving as substrates for rHuTS.

[0329] Previously reported data with the L. casei TS indicated that BVdUMP is 385 times less efficient a substrate as dUMP (Barr, P. J. et al. (1983); Santi, D. V. (1980)). The experiments reported herein have shown that this situation is quite different with the human enzyme. For rHuTS the relative catalytic efficiency of dUMP compared with BVdUMP is 60×. This represents a >6.4 fold increase in catalytic efficiency as compared to endogenous substrate. The previous result with L. casei TS leads to the prediction that the efficiency of enzymatic reaction within the cell would be too low for NB1011 to be an effective therapeutic substrate, since it would have to compete with large amounts of endogenous dUMP. The discovery reported herein, ie. that the human enzyme has a >6.4-fold improved efficiency of conversion of BVdUMP, is an important factor enabling utility of NB1011. The increased efficiency of BVdUMP utilization by the human enzyme as compared to the L. casei enzyme also establishes that species specific substrates are possible and can be designed. The ability to specifically inhibit heterologous enzymes via binding to species specific regions on the surface of L. casei vs. human TS has recently been reported (Stout (1999) and Costi, et al. (1999)). Differences in specificity relating to the active site of TS, which is composed of the most highly conserved regions of the protein (Carreras, C. W. and Santi, D. V. (1995)) is surprising and has not been reported previously.

[0330] Products of the cell-free enzymatic reaction of rHuTS with BVdUMP were analyzed by mass spectroscopy. The two molecular structures of the products have masses that are consistent with the mass of molecular ions detected in TS reaction mixtures following incubation of BVdUMP with purified rHuTS. Knowledge of the products of this reaction may be used to understand the final mechanism of action of NB1011. In addition, this information could be used to design novel chemotherapeutics, since the products of the TS-BVdUMP reaction could, themselves, be potentially used as chemotherapeutics.

[0331] 4. NB1011 is Converted to the Monophosphate in Tumor Cells

[0332] NB1011 is converted from the phosphoramidate to the monophosphate form in cells, as a prerequisite for binding to TS. To determine whether this crucial step in conversion was taking place advantage was taken of an unusual property of the bromine atom, i.e. that it exists in nature in two equally abundant isotopic forms. This situation allows detection of the bromine containing monophosphate by focusing the mass spectrometry analysis on the predicted mass ions of BVdUMP (411 and 413 daltons). H630 R10 tumor cells (which express high levels of TS) were incubated with 100 FM NB1011. Extracts of treated cell lysates were prepared as described herein. Detection using mass spectroscopy, following an initial purification with liquid chromatography relied upon formation of the unprotected nucleotide mass ions of BVdUMP which have identical retention times on reverse phase chromatography. Results are shown in FIGS. 3A and 3B.

Characterization of the Cytotoxic Activity of NB1011

[0333] 1. The Tumor/normal Cell Screen

[0334] As an initial step in characterizing the biological activity of NB1011, a large series of normal and tumor cell types were tested in the alamarBlue assay for sensitivity to both NB1011 and 5-fluorouracil.

[0335] Assays were carried out as described in Methods, above. Therapeutic index is calculated as the ratio of the average IC50 for normal cells to the average IC50 for tumor cells. All assays were done at least three times. See Table 5.

[0336] These data show that NB1011 has met the primary design goal for TS ECTA compounds, i.e. increased potency on tumor cells vs. normal cell types. Overall, NB1011 is about 2-fold more cytotoxic to tumor cells vs. normal cells, while 5-FU is 3-fold more toxic to normal cells than it is to tumor cells. The total benefit of NB1011 is therefore (2)×(3)=6-fold improvement in therapeutic index for NB1011 as compared with 5-FU. A critical tactic that allows for selection of chemotheraputics with a positive therapeutic index is screening of activity on both normal and tumor cell types. This approach has not been consistently employed in the field of new cancer drug discovery. For instance, screening of new candidate compounds on normal cell types is part of the National Cancer Institute's screening procedure (Curt (1996)).

[0337] 2. NB1011 Does Not Inactivate TS in Vivo

[0338] The results described above indicate that BVdUMP, generated intracellularly from NB1011, is unlikely to inactivate TS during its transformation to product(s). However, the cell free system is different from the intracellular milieu. In order to further explore this question, cell-based assays for TS activity were performed. In these experiments exogenous 5-(3H) deoxyuridine is added to cell culture medium and the release of tritiated water is monitored (Carreras, C. W. and Santi, D. V. (1995) and Roberts (1966)). FIG. 4 shows that the presence of NB1011 in cell culture media reduces the rate at which [3H]2O is released from 5-[3H]dUMP. In order to determine whether this is the result of irreversible inhibition of TS, NB1011-treated cells were allowed to briefly recover in fresh culture media, then assayed for TS activity. Cells that have been allowed to recover in culture media lacking NB1011 have the same level of TS activity as untreated cells. This result supports the proposal that NB1011 does not irreversibly inactivate the TS enzyme following intracellular processing.

[0339] An additional approach was taken to understanding whether NB1011 might interfere with cell growth primarily by inactivating TS. This approach is based upon thymidine rescue of TS-blocked cells. Cells which are blocked by Tomudex or by 5FdUMP (following treatment by 5FdUrd) do not make dTMP by de novo synthesis. For this reason, they survive only by scavenger mechanisms. One of the important scavenger mechanisms is utilization of extracellular thymidine. Thymidine incorporated by target cells can be converted to dTMP, usually by thymidine kinase, and thus continue DNA synthesis. Other pathways for use of exogenous thymidine have also been described If an important mechanism for NB1011 activity is via inhibition of endogenous TS, then the cytotoxicity should be relieved when thymidine is added to the cell culture media. For this experiment, a number of tumor cell lines were screened for their sensitivity to Tomudex and 5FdUrd, and ability to be rescued from these agents via thymidine supplementation. The normal colon epthelial cell, CCD18co, was used because of its measurable sensitivity to NB1011, 5FUdR and Tomudex. Experiments were carried out as described by (Patterson, et al. (1998)) with or without 10 μM thymidine, except that the alamarBlue assay was employed to determine cytotoxicity. The results showed a 15-fold rescue from Tomudex (IC50 change from 6.5 nM to 95 nM), a greater than 590-fold rescue from 5FudR (from an IC50 of less than 0.01 μM to greater than 5.9 μM), and a slight decrease in the absence of thymidine to 223 μM in the presence of 10 μM thymidine.

[0340] 3. Relationship Between TS Level and NB1011-mediated Cytotoxicity on Tumor Cell Lines

[0341] Confirmation that TS participates in NB1011-mediated cytotoxicity was established using several approaches: 1). The activity of NB1011 was examined on normal colon cells vs. high TS expressing, 5FU-resistant, tumor cells; 2). transfection of TS into a tumor cell background, and generating clonal derivatives which differ primarily by TS expression level, but are otherwise very similar; and 3). Use of a specific inhibitor of TS, Tomudex, to decrease intracellular TS activity.

[0342] In the initial analysis, of NB1011 and 5FUdR-mediated cytotoxicity were compared on the CCD18co normal colon epithelial cell type and H630R10, 5FU-resistant colon tumor cell line (Copur, S. et al. (1995)). This allows a determination of cytotoxicity vs. normal cells (CCD18co) as well as a measure of cytotoxicity vs. drug-resistant tumor cells (H630R10), which overexpress TS. This is important because a significant limitation to current chemotherapeutics is their toxicity to normal tissues. The results are presented in Table 5.

[0343] This experiment shows that 5FUdR is about 18-fold more toxic to normal colon cells (CCD18co) than to 5FU-resistant H630R10 tumor cells. This negative therapeutic index characterizes the major limitation of current chemotherapy, i.e. its toxicity to normal tissue. Such a negative therapeutic index has also been reported for doxorubicin (Smith, et al. (1985) and Smith, et al. (1990)). In contrast to 5FUdR, however, NB1011 has more than an 11 -fold improved activity on drug-resistant H630R10 cells (IC50=216.7 μM) vs. normal colon epithelial cells (IC50 greater than 2500 μM). This result suggests that: 1). Activity of NB1011 is more pronounced on high TS expressing tumor cells; and 2). A total improvement in therapeutic index of (18)×(11)=198-fold is achievable using TS ECTA compounds vs. 5FUdR.

[0344] 4. Overexpression of TS in HT1080 Tumor Cells Enhances Their Sensitivity to NB1011

[0345] Activation of NB1011 requires several steps. These include cell penetration conversion to the nucleotide monophosphate, binding to TS, and subsequent toxic metabolism. The precise mechanisms of cell penetration and conversion are not fully defined. Cell entry may depend in part on nucleoside transport mechanisms (Cass, et al. (1998)). Similarly, processing from the phosphoramidate to the monophosphate employs poorly defined mechanisms (Abraham, et al. (1996)).

[0346] These results are particularly significant because they demonstrate, in a fairly uniform genetic background, that increasing TS levels predicts enhanced sensitivity to NB1011. In addition, the data also show that increasing TS levels predicts resistance to fluoropyrimidines, a result consistent with reports in the literature (Copur, et al. (1995); Banerjee, et al. (1998)).

[0347] 5. Inhibitors of NB1011-mediated Cytotoxicity

[0348] Tomudex is a chemotherapeutic that acts primarily via inhibition of TS. If NB1011 exerts cytotoxicity via the TS enzyme, then inhibition of TS with Tomudex should decrease NB1011-mediated cytotoxicity. To test this hypothesis directly, Tomudex-resistant MCF7 cells, which overexpress TS 11-fold compared to the parental MCF7 cell line, were exposed to NB1011 in the presence of increasing concentrations of TDX. Cells were plated and exposed to indicated concentrations of compound(s) as described above. Results are shown in Table 7.

[0349] The data show that blockade of TS using the specific inhibitor Tomudex, results in up to about 25-fold inhibition of NB1011 -mediated cytotoxicity. These results support the concept that activity of NB1011 results from its metabolism by TS.

[0350] To further characterize the intracellular metabolism of NB1011, combination experiments with leucovorin (LV; 5-formyltetrahydrofolate) were performed. This experiment was initiated because we had observed that THF stimulates production of fluorescent product(s) in the cell-free reaction of BVdUMP and rHuTS. It was hypothesized that if the fluorescent products are related to the cytotoxic effects of NB1011, then enhancing intracellular levels of THF by providing LV in the culture media would also enhance NB1011-mediated cytotoxic effects. Surprisingly, in the presence of 3 μM LV, NB1011 activity on the H630R10 cell line was diminished by more than 90%, compared to NB1011 alone, as determined in the alamarBlue assay. The fact that NB1011 activity is abolished by LV, which supplements intracellular reduced folate pools, suggests that NB1011 may work in part by diminishing these pools. Alternatively, LV (or a metabolite) could directly impact the metabolism of BVdUMP by interfering with its interaction with TS.

[0351] To explore whether LV could directly impact the reaction of BVdUMP with TS, reactions were carried out+/−THF with BVdUMP, or with THF+dUMP, and+/−Methotrexate (MTX), LV or Tomudex (TDX).

[0352] The results (Table 8) are surprising in two respects: 1). Although an increase in fluorescent product was noted from BVdUMP in the presence of THF, a decreased rate of substrate consumption (BVdUMP) utilization occurs in the presence of the cofactor; and 2). In the presence of cofactor, all three compounds tested (MTX, TDX and LV) dramatically inhibited the BVdUMP+rHuTS reaction. In each case, the inhibition was more pronounced than that seen in the dUMP+rHuTS reaction, or the reactions with BVdUMP in the absence of THF.

[0353] The results described above, demonstrating inhibition of the BVdUMP+TS reaction by LV, MTX and TDX, and further, that this effect is more pronounced in the presence of cofactor (THF), suggests that NB1011 activity may be modulated by other chemotherapeutics. Importantly, rescue of NB1011-treated cells is feasible by providing LV, similar to the LV rescue from MTX. In the case of MLX, LV rescue occurs via supplementation of intracellular folate pools, which are diminished via MTX inhibition of dihydrofolate reductase and TS. If reduced folates are diminished within the cell during BVdUMP reaction with TS, then other compounds that diminish intracellular thymidine or purine nucleotide pools by distinct mechanisms may give additive or synergistic anti-cellular effects when used together with NB1011. Examples of such compounds (Dorr and Von Hoff (1994)),include 6-mercaptopurine, thioguanine and 2i-deoxycoformycin, all of which interfere with purine metabolism. Azacytidine-mediated inhibition of orotidylate decarboxylase blocks pyrimidine biosynthesis, and so could lower intracellular thymidine levels in a cell by a mechanism distinct from that of NB 1011.

[0354] Pharmacogenomics of TS ECTA

[0355] 1. Comparison of TS and HER2

[0356] An important aspect of the current approach to discovery and development of novel therapeutics is the ability to identify patients who are most likely to respond to treatment (a positive pharmacogenomics selection). One of the pioneering drugs in this area is Herceptin, now used to treat breast cancers which overexpress the HER2 protooncogene. Early data with anti-HER2 antibodies showed that activity on randomly selected tumor cells and normal cells was minimal. However, if tumor cell lines were selected that had at least a 4-fold increased expression of HER2, then a significant activity and anti-HER2 antibody could be demonstrated, as compared to normal cells or tumor cells expressing lower amounts of the HER2 gene product (Shepard, et al. (1991) and (Lewis (1993)). The data shown in FIGS. 5A and 5B demonstrate that, similarly to the case with Herceptin.

[0357] The cell line results shown in FIG. 2 may suggest an additional similarity between the TS and HER2/NEU systems. The similarity is that each has a similar overexpression requirement (about 4-fold) which predicts more aggressive disease for both TS and HER2/NEU overexpressing patients (Johnston, et al. (1994)).

[0358] 2. NB1011 is Active Against 5FU and Tomudex-resistant Colon and Breast Tumor Cell Lines

[0359] Because NB1011 has promising anticancer activity, it is important to compare it with other chemotherapeutics with respect to safety. The utility of NB1011 in the treatment of cancer is further strengthened when it is compared with Tomudex, a chemotherapeutic which, like 5FU, is often used to treat colon and breast cancer, among other malignancies.

[0360] The results (FIG. 10) show that while NB1011 is more than 10-fold less toxic than TDX vs. normal cells (CCD18co), it is more than 30-fold more potent than TDX on MCF7-TDX resistant tumor cells. Similar results have been obtained for other TDX-resistant tumor cell lines. The low level of toxicity vs. normal cells and the high activity vs. TDXR tumor cells supports the application of NB1011 to drug resistant cancers that overexpress TS.

[0361] 3. NB1011 is More Dependent Upon TS Protein Levels than TS Activity as Measured by Tritium Release from dUMP-3H

[0362] Four types of assays have been used to characterize TS levels in cells and tissues. Most commonly used is the antibody-based technique (Johnston (1994) and (Johnston (1995)) but RT-PCR, 5FdUMP-binding and tritium release (van Laar (1996), van Triest (1999), Jackman (1995), Larsson (1996), Komaki (1995) and Mulder (1994)) have also been measured in various studies. For characterization of cell lines we have focused on Western blotting and tritium release from 3H-dUMP. These assays were chosen because antibody-detection is commonly used for clinical samples and tritium release from labeled deoxyuridine is a direct measure of TS catalytic activity in cells.

[0363] Cells were grown and characterized as described above. TS expression level is relative to CCD18co, a normal colon epithelial cell line. Tritium release is background substracted as described in Methods. ND=Not detectable above background.

[0364] Analysis of the data presented in Table 7 indicates that there is a closer relationship between TS protein level and sensitivity to NB1011 than between TS activity (tritium release from 3H-dUMP) and NB1011 sensitivity. In each set of matched parental and drug-resistant tumor cell types, the drug-resistant derivatives, each with more TS protein than the parent, also have an increased sensitivity to NB1011. However, when the same comparison is done with respect to TS activity, the parental cell lines often have comparable, or greater, TS activity and are less sensitive to NB1011 -mediated cytotoxicity.

[0365] While these results could occur via a number of different mechanisms, or combinations of mechanisms, it is likely that 3H-dUMP conversion to dTMP (and accompanying tritium release) may be subject to limitation by some component, perhaps cofactor availability. However, since conversion of BVdUMP is not dependent upon cofactor, then its reaction with TS can continue even in a cellular milieu in which cofactor is limiting. This observation is important because TS substrates as therapeutics would not be attempted based upon the results of typical tritium release assays for TS activity in which the most aggressive, and drug-resistant, tumor cells are observed to have a lower TS activity than their precursors. These results lend additional support to the proposal of selecting patients for TS ECTA therapy based simply on the level of TS detected by antibody staining.

[0366] 4. TS Levels in Tumor Samples Often Exceed a 4-fold Increase Over Normal Tissue

[0367] The results shown above suggest that TS ECTA therapy, at least with NB1011, will be most effective when used in patients whose cancers overexpress TS at least four-fold.

[0368] The literature (Johnston (1994), Bathe (1999), Leichman (1998) and Lenz (1995)) suggests that overexpression in the range of 4-fold occurs in about 50% of cancers, and furthermore, that this level of overexpression predicts a more aggressive disease. To confirm the frequency of at least 4-fold overexpression of TS in human colon cancer, we obtained matched normal and tumor samples from the Cooperative Human Tissue Network. These samples were analyzed for TS mRNA level via RT-PCR, which gives results comparable to immunohistochemistry (Johnston, et al. (1994)). The results of the RT-PCR evaluation of the samples is shown in FIG. 9.

[0369] Five of the seven samples analyzed above have at least a 4-fold level of overexpressed TS as determined by the RT-PCR assay. None of these patients were previously treated with chemotherapy, which suggests that this frequency and level of overexpression is associated with invasive disease and not due to selection by chemotherapy. It is expected that cancer cells that have been exposed to TS inhibitors such as Tomudex or the anabolic derivative of 5FU or 5-FdUrd, 5FdUMP, may be selected for increased expression (Lonn, et al. (1996)). The average degree of overexpression, as measured by RT-PCR for all 7 samples, is about 4.7-fold. These data suggest that greater than 4-fold overexpression of TS in tumor foci is a common event.

[0370] 5. Experimental Therapy of 5FU-resistant Human Colon Cancer

[0371] The most important diseases for new compounds that target TS are the gastrointestinal cancers. To study the activity of NB1011 in an in vivo model, H630R10, 5FU-resistant human colon cancer cells, were grown subcutaneously to an average tumor size of 50 mm3 in nude mice. The mice were then treated, with excipient (DMSO, 5FU or NB1011).

[0372] Doses of 3.5 mg, 2.5 mg, and 1.25 mg of NB1011 were administered daily for 5 days, either peritumorally or intraperitoneally to tumor-bearing mice. FIG. 8A shows the initial block in tumor growth induced by treatment for 5 days with NB1011, as compared to excipient or 5FU treated animals. Although no statistically significant dose response relationship is evident among the NB1011 groups, there is a significant difference between the NB1011 groups vs. either the 5FU or excipient controls, starting with Day 6. This difference is maintained (FIG. 9B) until the control animals were sacrificed at Day 25, even though therapy was discontinued after Day 5.

TABLE 3
Comparison of Kinetic Parameters of Bacterial and rHuTS
	Kinetic Constants	Lactobacillus casei	rHuTS
	dump
	Km	3.0	μM	7.7	μM
	Kcat	6.4	s−1	0.2	s−1
	Kcat/Km	2.1 × 106 M−1 s−1	2.6 × 104 M−1 s−1
	Kl (of BVdUMP)	0.6	μM	4.5	μM
	BVdUMP
	Km	3.3	μM	16	μM
	Kcat	0.018	s−1	0.0067	s−1
	Kcat/Km	5.6 × 103 M−1 s−1	4.2 × 103 M−1s−1
	Kl (of dUMP)	2.0	μM	17.5	μM
	Relative catalytic	385-fold	60-fold
	efficiency
	(dUMP vs
	BVdUMP)
	Enzyme kinetics were done as described in Methods. Data for Lactobacillus casei are derived from Barr, et al. (1983) supra. The rHuTS was prepared as described in Materials and Methods, above.

[0373]

TABLE 4
Inhibition of rHuTS reactions by Tomudex and 5-FdUMP
		Tomusdex
Substrate + Cofactor	No Inhibitor	(500 nM)	5-FdUMP (500 nM)
BVdUMP + THF	109 ± 16	67 ± 3	44 ± 2
	RFU/min	(61%)	(40%)
	(100%)
BVdUMP − THF	75 ± 11	34 ± 3	93 ± 13
	(100%)	(45%)	(129%)
dUMP + THF	1500 ± 20	690 ± 40	290 ± 70
	nmoles/min	(46%)	(19%)
	(100%)
Inhibition of rHuTS reactions by Tomudex and 5-FdUMP. Thymidylate synthase reactions containing enzyme inhibitors or cofactor were incubated at 30° C. as described in Materials and Methods, and the initial rates of the enzyme reaction were determined by measuring the increase in relative fluorescence units at 340 nm excitation, 595 nm emission for the BVdUMP reactions, or increase in A340 for the dUMP reaction.

[0374]

TABLE 5
Cytotoxicity of NB1011 vs. 5FU on Normal and Tumor Cell Strains
IC50 (μM)		IC50 (μM)
Normal Cells	NB101.1	5FU	Tumor Cells	NB101.1	5FU
CCD1800 (Colon)	562	2.0	H630R10 (Colon)	65	41.6
DET551 (Skin)	262	0.8	HT1080 (Colon)	449	0.8
NHDF (Skin)	359	0.8	COLO320 (Colon)	401	1.5
H527 (Skin)	273	1.6	COLO205 (Colon)	105	1.3
W138 (Lung)	335	1.0	SW620 (Colon)	374	4.6
MRC9 (Lung)	303	1.1	SKCO1 (Colon)	184	1.4
NHLF (Lung)	139	0.9	HCTC (Colon)	280	2.8
NHA (Brain)	839	0.9	MCF7 (Breast)	141	1.0
NHOST (Bone)	642	4.7	MDAMB361 (Breast	365	5.0
NPRSC (Prostate)	369	1.7	MDAMB468 (Breast)	172	4.4
NHEPF (Liver)	2085	1.7	SW527 (Breast)	431	4.3
Average	561	1.6	NCI H520 (Lung)	135	0.6
			SKLU1 (Lung)	270	7.9
			SOAS2 (Bone)	232	1.4
			PANC1 (Pancreas)	492	1.9
			SKOV3 (Ovary)	484	3.0
			PC3 (Prostate)	184	0.9
			HEPG2 (Liver)	704	22.8
			SKHEP1 (Liver)	247	1.7
			A431 (Skin)	266	0.2
			MCIxc (Brain)	61.	1.2
			Average	288	5.3
	NB101.1	5FU
Therapeutic index (N/T)	1.95	0.30
Cells were analyzed for response to either NB1011 or 5FU in the alamarBlue assay (Methods). All assays were performed at least three times. The standard deviation is less than 20%. Therapeutic index was calculated as the ratio of IC50 (mean of all cell types) to IC50 (mean of all tumor cell lines).

[0375]

TABLE 6
NB1011 cytotoxicity on cell lines engineered to express HuTS.
	IC50
	TS Level	NB1011	FUDR	5-FU	TDX
Cell Line	(%)*	(μM)	(μM)	(μM)	(μM)
C/HT1080	100	320	<0.1	1.0	3.6
TSL/HT1080	409	196	2.2	1.7	24
TSL/HT1080	702	0.8	3.1	3.5	153
A cDNA encoding rHuTS was subcloned into ventor pEGFP-C3, in-frame with GFP. The construct was transfected into HT1080 cells and selected with G418 (750 ug/ml) in order to obtain clones that stably express fusion rHuTS. Individual cells were cloned based upon high or low fluorescence expression as described in Methods.
*TS levels were determined by using Western blot analysis, the quantified expression levels were expressed as values relative to that of cell strain CCD18co.

[0376]

TABLE 7
Tomudex Inhibits NB1011 Mediated Cytotoxicity
[Tomudex]
(nM)	0 nM	1 nM	10 nM	100 nM	1000 nM
NB1011IC50	5.7	25.5	87.7	140.3	103.0
(μM)
Fold Protection	1	4.5×	15.4×	24.6×	18.1×
The Tomudex rescue assay (alamarBlue) was done with TDX-resistant MCF7 breast tumor cells as described in Methods.
“Fold Protection” was calculated as the ratio of IC50 with and without added TDX.

[0377]

TABLE 8
Impact of Folate Inhibitors
	BVdUMP,
Inhibitor	with THF	BVdUMP, w/o THF	dUMP, with THF
None	100%	138%	100%
MTX	10%	24%	31%
LV	17%	97%	77%
TDX	0%	25%	18%
Cell-free assays using rHuTS, the appropriate substrate and other components were combined as described in Methods. MTX (140 μM), LV (140 μM) or TDX (5 μM) were added to evaluate their inhibitory activity. Utilization of substrate (either BVdUMP or THF) was employed as a measure of reaction rate. The numbers indicate remaining activity.

[0378]

TABLE 9
NB1011 activity is more associated with TS protein than with tritium
release
	Drug		Tritium	NB1011-
Cell Line	Selection	TS Protein	Release	IC50
H630	None	288	3206	414
Colon cancer	5FU	2350	1840	65
	TDX	671	3980	2.3
RKO	None	142	4920	136
Colon cancer	TDX	279	1625	28
MCF7	None	178	5185	327
Breast cancer	TDX	1980	875	2.8
N1S1	None	197	12,565	494
	5FU	1241	ND	204

[0379]

TABLE 10
MDF7 TDX cells selected for resistance to NB1011 are more sensitive to
5-Fluorouracil and Tomudex
	IC50 (micromolar)*	Relative TS
	5-FU	Tomudex	NB1011	Protein Level
MCF7	10−	.026−	291−	1X−
MCF7 TDX	32	>10	2	11X
MCF7 TDX/1011	2	.041	240	4X
*= as determined by the alamarBlue assay described in Materials and Methods
TDX = Tomudex;
1011 = NB 1011

EXAMPLE 19

Co-Administration

[0380] Cell lines: Normal human colon epithelial cells (CCD18co) and skin fibroblasts (Det55 1) were purchased from ATCC (Rockville,Md.). MCF7TDX, human breast carcinoma cells resistant to 2 μM Tomudex were obtained from Dr. Patrick Johnston, Queens University, Belfast. H630R10, human colorectal carcinoma cells resistant to 10 μM 5-Fluorouracil were obtained from Dr. Edward Chu (Yale Cancer Center) and Dr. Dennis Slamon (UCLA). The MCF7TDX and the H630R10 cell lines have been previously described in Drake, J. C. et al. (1996) and Copur, S. et al. (1995) respectively.

[0381] Chemicals: Dipyridamole and nitrobenzylthioinosine were purchased from ICN Biomedicals (Aurora, Ohio). 5-Fluorouracil was purchased from Sigma (St. Louis, MO). Tomudex was provided by Zeneca (Wilmington, Del.).

[0382] Culture Conditions: All cells were cultured under standard conditions of 37° C., 95% humidified air, 5% CO2 in RPMI 1640 culture medium containing 10% fetal calf serum (Life Technologies) and penicillin/streptomycin/fungizone. MCF7TDX cells were maintained continuously in 2 μM Tomudex, and H630R10 cells were maintained continuously in 10 μM 5-FU. The medium was renewed or the cells were passaged about every three days to maintain optimal growth conditions. Normal cells were passaged a maximum of 15 times to avoid senescence.

[0383] Cytotoxicity Studies: 384-well interaction screening assay. 500 cells per well were transferred to a 384-well tissue culture plate (Corning Inc., Corning, N.Y.) and allowed to attach for 24 hours in standard culture conditions. Compounds were then applied in a bidirectional (checker board) pattern (Chou, T. C. and Talalay, P. (1984)). Following a 5-day incubation, the redox indicator dye, alamarBlue (AccuMed International, Westlake, Ohio) was added to each well at a 10% v/v ratio, and fluorescence was monitored at 535 excitation, 595 emission. Cytotoxic effect levels and drug interactions were assessed by the combination index method (Chou, T. C. and Talalay, P. (1984) and Bible, K. C. et al. (1997)), described briefly below. 96-well combination cytotoxicity assay. Exponentially growing cells were transferred at a density of 1.0-5.5×103 cells per well to a 96-well tissue culture plate and allowed to attach for 24 hours. Compounds were then applied in duplicate half log serial dilutions. Each compound was tested separately, and mixed together at a single molar ratio approximately equal to the ratio of the individual IC50 values. After an additional 72 hour incubation, cells were washed once with PBS and stained with 0.5% crystal violet in methanol. Plates were washed gently in water to remove unbound stain and allowed to dry overnight. Crystal violet stain bound to the total protein of attached cells was redissolved in Sorenson's buffer (0.025M sodium citrate, 0.025M citric acid in 50% ethanol), and absorbance monitored at 535 nM. Sigmoid curves were fit according to the Hill inhibitory Emax model, and IC50 calculated as the average of three or more separate determinations. Where applicable, the combination index for multiple drug effects was calculated according to the median-effect principle (Chou, T. C. and Talalay, P. (1984)) using the CalcuSyn software from Biosoft (Ferguson, Mo.). Briefly, the ICso and the slope parameter (m) for each agent alone were determined from the median effect plot, an x,y plot of log(D) vs log (fa/fu) based on Chou's median effect equation:

f a /f u =(D/Dm)m  [Equation 1]

[0384] where D=dose of the drug, Dm=IC50 as determined from the x-intercept of the median effect plot, fa=fraction of cells affected, fu=fraction of cells unaffected (fu =1−fa), and m=an exponent signifying the steepness of the sigmoid dose-effect curve. Only experiments with linear correlation coefficients (r) >0.9 were accepted for analysis. A combination index (CI) was then calculated to assess synergism or antagonism according to the following equation which assumes an independent mechanism of drug action (mutual exclusivity):

CI=(D)1/(Dx)1+(D)2/(Dx)2+(D)1(D)2/(Dx)1 (Dx)2  [Equation 2]

[0385] where (D)1 and (D)2 are the concentrations of drug 1 and drug 2 which combined produce x% inhibition, and (Dx)1 and (Dx)2 are the concentrations of each drug which alone produce x% inhibition. CI=1 indicates an additive interaction, CI<1 indicates synergy, and CI>1 indicates antagonism. For each experiment Cl's from several different effect levels and concentrations of a constant molar ratio were averaged. Student t-tests were applied to determine if the average differed significantly from 1.

[0386] Results:

[0387] 384-well screening studies. To identify drugs which potentially synergize with NB1011, combination cytotoxicity experiments were performed with NB1011 and each of 10 antitumor agents from several different mechanistic classes using MCF7TDX and H630R10 tumor cells. Results from these initial 384-well alamarBlue screening assays are shown in Table 11. In general, a combination index of <1 indicates synergy, ˜1 indicates additivity, and >1 indicates antagonism (Pegram, M. D. et al. (1999)).

TABLE 11
Drugs screened for interaction with NB1011
	Combination Index ± s.e.m.
Drug	Class	MCF7 TDX	H630R10
Irinotecan	Inhibition of topoisomerase I	1.36 ± 0.38	1.26 ± 0.20
topotecan		2.45 ± 0.85	ND
Etoposide	Inhibition of topoisomerase II	3.13 ± 0.58	1.96 ± 0.28
Vinblastine	Inhibition of microtubule	1.09 ± 0.16	0.78 ± 0.32
	assembly
Taxol	Stabilization of microtubules	1.41 ± 0.32	0.99 ± 0.15
Cisplatin	DNA damage	1.51 ± 0.35	ND
Thiotepa	Alkylation	2.23 ± 0.45	ND
Doxorubicin	Inhibition of nucleic acid	0.55 ± 0.06	1.05 ± 0.13
	synthesis
5-fluoro-	Inhibition of TS, DNA/RNA	3.19 ± 0.35	ND
uracil	incorporation
Methotrexate	Antifolate, inhibition of	1.78 ± 0.44	ND
	DHFR, TS
ND = not determined.
Combination Index (CI) = 1 indicates additivity, CI < 1 indicates synergy, and CI > 1 indicates antagonism. CI calculated as the average of at least 4 consecutive dose / effect levels. Class of drugs as indicated by Dorr, R. T. and Van Hoff, D. D. (1994).

[0388] Two of the ten agents screened, vinblastine and doxorubicin, showed potential synergy (CI≦1.1) with NB1011 in MCF7TDX and H630R10 cell. Two of the remaining 8 agents, irinotecan and taxol showed an additive or antagonistic interaction (CI=1-1.4) with NB1011, while all the other agents showed antagonism (CI>1.5). The most antagonistic interaction was observed with 5-Fluorouracil which gave CI=3.19 in MCF7TDX cells. In light of these results, vinblastine and doxorubicin were chosen for further study using a 96-well crystal violet combination cytotoxicity assay. 96-well combination cytotoxicity studies. The 96-well format was chosen for more detailed drug interaction studies. Three additional agents were included in the 96-well assay: oxaliplatin, a new platinum analog DNA damaging agent; dipyridamole (DP) and p-nitrobenzylthioinosine (NBMPR), both potent inhibitors of equilibrative nucleoside transport processes. Oxaliplatin was tested to confirm the antagonism results for cisplatin. The nucleoside transport inhibitors were tested because published data (Tsavaris, N. et al.(1990), Grem, J. L. (1992) and Wright, A. M. et al. (2000)) suggested they may modulate the activity of nucleoside based drugs. To analyze whether any of these drugs would enhance the activity of NB1011 specifically in tumor cells, two normal cell types, Det551 and CCD18co, were included in the assays. Results of these experiments are shown in Table 12.

TABLE 12
Average combination index (CI) values for drugs tested in combination
with NB1011 in tumor and normal cells
				P	Molar	NB1011	Drug Dose	Inter-
Drug	Cell Line	CI	±SEM	value	Ratioa	Dose (μM)	(μM)	actionb
Dipyridamole	H630R10	0.75	0.11	0.052	2	11-150	5.5-75	Syn
	MCF7TDX	0.51	0.06	0.001	0.2	1.1-3.2	5.5-16	Syn
	Det551	1.17	0.23	0.484	5	5.8-375	1.2-75	Add
	CCD18co	1.30	0.08	0.008	5	81-375	16-75	Ant
p-Nitrobenzyl-	H630R10	0.35	0.07	0.001	1	1.5-500	1.5-500	Syn
Thioinosine	MCF7TDX	0.57	0.17	0.029	3.33	0.15-150	0.045-45	Syn
(NBMPR)	Det551	1.43	0.16	0.026	3.33	32-300	9.7-90	Ant
	CCD18co	3.93	1.00	0.019	3.33	32-300	9.7-90	Ant
Vinblastine	H630R10	0.63	0.10	0.003	6000	4.1-54	0.0005-0.015	Syn
	MCF7TDX	1.44	0.29	0.186	2000	0.4-1.9	0.0005-0.015	Ant
	Det551	0.54	0.10	0.003	50000	2.9-47	0.0005-0.015	Syn
	CCD18co	0.65	0.10	0.008	50000	17-135	0.0005-0.015	Syn
Oxaliplatin	H630R10	1.78	0.06	0.001	120	6.9-150	0.1-1.3	Ant
	MCF7TDX	2.24	0.33	0.004	12	0.6-15	0.1-1.3	Ant
Doxorubicin	H630R10	1.39	0.13	0.012	300	117-150	0.039-0.5	Ant
	MCF7TDX	1.96	0.25	0.004	600	1.9-15	0.001-0.025	Ant
aMolar ratio of NB1011:Drug.
bSyn = synergy,
Ant = antagonism,
Add = additivity.

[0389] As can be seen in Table 12, doxorubicin, although promising in the initial screening assay, failed to synergize in the more detailed 96 well cytotoxicity assay (CI =1.39 and 1.96 in H630R10 and MCF7TDX cells, respectively). Oxaliplatin had an antagonistic interaction in the tumor cells (CI=1.78 and 2.24, respectively). Since both oxaliplatin and doxorubicin antagonized NB1011 in the tumor cells, they were not tested in the normal cell assays. Consistent with the initial screening data, vinblastine synergized with NB1011 in H630R10 cells (CI=0.63), however it antagonized NB1011 in MCF7TDX cells (CI=1.44). Furthermore, in Det551 and CCD18co normal cells, vinblastine interacted synergistically with NB1011 to a similar extent as in H630R10 cells (CI=0.54 and 0.65, respectively). This lack of selectivity in the potentiation of NB1011 by vinblastine would most likely limit the use of this combination in the clinic. The nucleoside transport inhibitor, dipyridamole, synergized with NB1011 in the tumor cells (CI=0.75 and 0.51), but failed to synergize with NB1011 in the normal cells (CI=1.17 and 1.30). Similarly, NBMPR, another NT inhibitor, showed synergy with NB31011 in the tumor cells (CI=0.35 and 0.57), but produced no synergy in the normal cells (CI=1.43 and 3.93). Taken together this data indicate that 2 of the 13 agents tested, DP and NBMPR, which are both inhibitors of equilibrative nucleoside transport, potentiate the activity of NB1011. This enhancement of NB1011 activity by DP and NBMPR appears specific for the tumor cells tested, since no synergy was observed for these combinations in the two normal cell types analyzed.

EXAMPLE 20

[0390] Induction and Assessment of Arthritis

[0391] Arthritis was induced in male DBA/1 mice (8-10 weeks old) by intradermal injection of bovine type II collagen, purified in-house at the Kennedy Institute of Rheumatology as previously described (Miller, E. J. et al. (1972)). Collagen was administered in complete Freund's adjuvant (Difco, Detroit, Mich.). Onset of arthritis is expected to be variable. Arthritis onset is considered to occur on the day that swelling and/or erythema were observed. Clinical score is a composite of disease severity and the number of limbs affected, and is monitored daily from onset of disease and used as an assessment of disease progress. An example for scoring is: 0, Normal; 1, slight swelling with erythema; 2, pronounced swelling; 3, joint rigidity. In addition, the extent of paw swelling reflects the degree of edema in affected limbs.

[0392] Anti-TNF antibody used in these experiments was as described by Marinova-Mutafchieva, L. et al. (2000). NB1011 was administered daily by intraperitoneal administration at 2.5 mg total dose per day. Anti-TNF antibody was compared with NB1011 because, at present, antiTNF antibody is the optimal single agent for treatment of collagen induced arthritis (Marinova-Mutafchieva, L. et al. (2000)).

[0393] Success in this model has been shown to be predictive for clinical success in the development of new agents to treat inflammatory disease, especially rheumatoid arthritis (Elliott et al. (1994) and Feldmann et al. (1998)). This model therefore represents an ideal setting for establishing proof of concept for new agents to treat rheumatoid arthritis, and potentially other autoimmune and inflammatory diseases.

[0394] Following immunization with collagen, mice were maintained until a significant clinical score for disease progression was achieved (between 2.5 and 3.5). Mice were then treated with control saline injections, NB1011, or with anti-TNF antibody as a positive control. The results showed that the NB1011-treated group exhibited significant disease suppression (p<0.05), similar to the anti-TNF control, when compared with the saline-treated control group. There was no significant difference between the NB1011 and anti-TNF groups with regard to clinical score. Paw swelling is an alternative measure of CIA disease severity. When paw swelling was used as a criteria for disease suppression, comparable results were observed. In this second measure of efficacy, both the NB1011 and anti-TNF groups demonstrated significant disease suppression as compared to the saline-treated control group (p<0.05). Again, there was no significant difference between the NB1011 and anti-TNF groups, although suppression of swelling may have been less dramatic with NB1011. A further significant outcome of this work is that by comparison with earlier reported work, NB1011 appears to have activity superior to anti-angiogenesis agents, an anti-CD4 immunosuppressive agent, and cannabidiol, a third experimental agent currently being considered for use to treat rheumatoid arthritis, and potentially other autoimmune and inflammatory disorders (Malfait, A. M. et al. (2000); Miotla, J. et al. (2000); Marinova-Mutafchieva, L. et al. (2000)).

[0395] Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be apparent to those skilled in the art that certain changes and modifications will be practiced. Therefore, the description and examples should not be construed as limiting the scope of the invention, which is delineated by the appended claims.

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Claims

1. A compound having the formula:

2. The compound of claim 1, wherein R8 is the side chain of a naturally occurring amino acid, its analogue or isomer, selected from the group consisting of alanine, glycine, tryptophan, leucine and aspartic acid.

3. The compound of claim 1, wherein R1 is a halogen-substituted vinyl derivative.

4. The compound of claim 3, wherein R1 is bromovinyl.

5. The compound of claim 4, wherein R8 is alanine, with the proviso that R9 is not methyl.

6. The compound of claim 5, wherein R9 is selected from the group consisting of —CH2-phenyl, —CH3, —CH2-cyclopropyl, cyclohexyl, iso-propyl, —CH2-tert-butyl, cycloheptyl, cyclooctyl and —CH2-adamantyl.

7. The compound of claim 1, wherein the compound has the formula:

8. The compound of claim 1, wherein the compound has the formula:

9. The compound of claim 1, wherein the compound has the formula:

10. The compound of claim 1, wherein the compound has the formula:

11. The compound of claim 1, wherein the compound has the formula:

12. The compound of claim 1, wherein the compound has the formula:

13. The compound of claim 1, wherein the compound has the formula:

14. The compound of claim 1, wherein the compound has the formula:

15. The compound of claim 1, wherein the compound has the formula:

16. The compound of claim 1, wherein the compound has the formula:

17. The compound of claim 1, wherein the compound has the formula:

18. The compound of claim 1, wherein the compound has the formula:

19. The compound of claim 1, wherein the compound has the formula:

20. The compound of claim 1, wherein the compound has the formula:

21. The compound of claim 1, wherein the compound has the formula:

22. The compound of claim 1, wherein the compound has the formula:

23. The compound of claim 1, wherein the compound has the formula:

24. The compound of claim 1, wherein the compound has the formula:

25. The compound of claim 1, wherein the compound has the formula:

26. The compound of claim 1, wherein the compound has the formula:

27. A composition comprising the compound of claim 1 and a carrier.

28. A pharmaceutical composition comprising the compound of claim 1 and a pharmaceutically acceptable carrier.

29. A method of inhibiting the proliferation of a cell selected from the group consisting of a cancer cell or a cell infected with an infectious agent, comprising contacting the cell with an effective amount of the compound of claim 1.

30. A method for treating a cell or tissue related to an autoimmune disorder or inflammatory condition, comprising contacting the cell or tissue with an effective amount of the compound of claim 1.