AU6358900A - Enzyme catalyzed anti-infective therapeutic agents - Google Patents

Description

WO 01/07087 PCT/USOO/19844 ENZYME CATALYZED ANTI-INFECTIVE THERAPEUTIC AGENTS CROSS-REFERENCE TO RELATED APPLICATIONS This appliation claims priority under 35 U.S.C. § 119(e) to the following U.S. 5 provisional applications, Serial Nos. 60/153,101, filed September 9, 1999 and 60/145,364, filed July 22, 1999, the contents of which are hereby incorporated by reference into the present disclosure. TECHNICAL FIELD 10 This invention relates to the field of therapies for infectious diseases, and in particular, compositions and methods for the treatment of therapy-resistant infectious diseases. BACKGROUND 15 Throughout and within this disclosure, various publications are referenced by first author and date, patent number or publication number. The full bibliographic citation for each reference can be found within the specification. The disclosures of these publications are hereby incorporated by reference into this disclosure to more fully describe the state of the art to which this invention pertains. 20 Resistance to chemotherapeutic and antibiotic treatments for infectious disease 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 activity. In infectious disease, amplified expression of beta-lactamases accounts for 25 more than one-third of all beta-lactam antibiotic resistant isolates (Felmingham and Washington (1999) J. Chemother. 11 Suppl 1:5-21), 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 30 in populations of infectious organisms. Recently, infectious agents carrying sets of genes simultaneously conferring resistance to multiple antibiotic agents have arisen 1 WO 01/07087 PCT/USOO/19844 making treatment by traditional antibiotic therapy difficult. Applicant has developed a novel approach to development of therapeutics targeting well characterized enzymes which are expressed by infectious agents. This technology is distinct from prior and historical approaches to therapy for infectious diseases and is referred to as 5 "ECTA," for Enzyme Catalyzed Therapeutic Agent. DISCLOSURE OF THE INVENTION This invention provides a method for selectively inhibiting the proliferation of an infectious agent or a cell infected by the infectious agent. Infectious agents 10 suitably treated by the method of this invention express an activating agent that selectively activates or converts a prodrug to a toxin. The enzyme is not inactivated or inhibited by the substrate prodrug compound. The method requires contacting the cell or the agent with an effective amount of the substrate compound thereby selectively inhibiting the proliferation of the infectious agent, the cell or the 15 infectious agent within the cell. This invention also provides a method for screening for prodrugs selectively converted to a toxin in a cell by an activating enzyme expressed by an infectious agent. The screen requires contacting an infectious agent or a cell infected with the infectious agent with a candidate prodrug and assaying for activation of the prodrug 20 into toxic agents by the activating enzyme. Alternatively, activation of the prodrug is determined by noting inhibition of the proliferation or growth of the infectious agent or the cell infected with the agent. BRIEF DESCRIPTION OF THE FIGURES 25 Figure 1 schematically shows the mechanism of action of the ECTA prodrugs of this invention. Figure 2 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 30 results in a time and enzyme dependent generation of fluorescent product(s). BVdUMP was incubated with the indicated amounts of rHuTS in the standard 2 WO 01/07087 PCT/USOO/19844 reaction mixture at 30* C (See Materials and Methods below), except that N5, N1O methylenetetrahydrofolate was omitted from the reaction. The numbers adjacent to each data curve refer to TS enzyme units. Figure 3 shows that BVdUMP is competitive with deoxyuridine 5 monophosphate (dUMP) in rHuTS. Thymidylate synthase catalyzed reaction of converting dUMP into dTMP was run in vitro in the absence (triangles) and in the presence of 20 pM BVdUMP (squares). dUMP concentration was varied from 10 to 100 pM, N5, N1O-methylene tetrahydrofolate concentration was 140 pM and the enzyme concentration was 0.1 AM. Enzyme activity was determined by measuring 10 the increase in A 4 ,. Figure 4 is the structures of products of in vitro reaction of BVdUMP catalyzed by rHuTS. Structures I and II are consistent with mass ions identified in cell free reaction mixtures. Figure 5 is a proposed mechanism of NB 1011 activation. NB 1011 must be 15 able to enter cells and convert to BVdUMP before interacting with TS. Structures generated following transformation by TS are proposed to be exocyclic pyrimidine nucleotide monophosphates. These compounds may be cytotoxic to cells by a variety of mechanisms including interference with nucleotide and nucleic acid metabolism. 20 Figure 6 shows detection of BVdUMP in H630R10 cells treated with NB10 11. H630 R10 cells were treated with 100 pM NB10 11 for 5 days, then analyzed by liquid chromatograph/mass spectroscopy as described in the Materials and Methods, below. Figure 7 demonstrates that NB 1011 does not irreversibly inactivate TS in 25 vivo. The effect of NB 1011 on TS activity in intact cells is completely reversible. TS activity was measured in intact RKO cells by release of [ 3

H]

2 0 from 5-[ 3 H]deoxyuridine as described in Materials and Methods. NB1O1 1 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 30 washing procedure. 3 WO 01/07087 PCT/USOO/19844 Figure 8 shows TS expression level in cells selected with Tomudex or NB 1011, as estimated by SDS PAGE Western blot developed with antibody against thymidylate synthase and tubilin. Lane 1 shows MCF7 cells, no selection with drug; lane 2 shows MCF7 cells selected with 2pM tomudex; lane 3 shows MCF7 cells as 5 in lane 2, but after a subsequent selection using NB 1011 as the selective agent; lane 4 shows MCF7 cells as in lane 2, after a subsequent passaging without tomudex. MODE(S) FOR CARRYING OUT THE INVENTION The practice of the present invention will employ, unless otherwise indicated, 10 conventional techniques of molecular biology, microbiology, cell biology and recombinant DNA, which are within the skill of the art. See, e.g., Sambrook, Fritsch and Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL, 2 n edition (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel et al. eds., (1987)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.): 15 PCR 2: A PRACTICAL APPROACH (M.J. MacPherson, B.D. Hames and G.R. Taylor eds. (1995)) and ANIvAL CELL CULTURE (R.I. Freshney, ed. (1987)). 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. 20 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 25 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 30 invention. 4 WO 01/07087 PCT/USOO/19844 An "infectious agent" or a "pathogen" is a organism that is pathological to a cell or organism that it infects. Examples of pathogenic organisms include, but are not limited to, bacteria, parasites, viruses or yeast. Examples of viruses include but are not limited to Herpes, Varicella zoster, Hepatitis C and Epstein Barr virus. 5 Examples of parasites include but are not limited to T. brucei, T. cruzi, and Plasmodium falcipurum. 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.. And, from among these, preferred pathogens are those which have become resistant to 10 common antibiotics (see reveiw by Murray, BE "Antibiotic Resistance" (1997) Adv. Int. Med. 42:339-367.) A "composition" is intended to mean a combination of active agent and another compound or composition, inert (for example, a detectable agent or label or a pharmaceutically acceptable carrier) or active, such as an adjuvant. 15 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. As used herein, the term "pharmaceutically acceptable carrier" encompasses any of the standard pharmaceutical carriers, such as a phosphate buffered saline 20 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 PHARM. SCI., 15th Ed. (Mack Publ. Co., Easton (1975)). An "effective amount" is an amount sufficient to effect beneficial or desired 25 results. An effective amount can be administered in one or more administrations, applications or dosages. A "subject," "individual" or "patient" is used interchangeably herein, which refers to a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport 30 animals, and pets. 5 WO 01/07087 PCTUSOO/19844 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 an altered expression level of a gene with a particular type of pathogenic agent, it is generally preferable to 5 use a positive control (a subject or a sample from a subject, carrying such alteration and exhibiting syndromes characteristic of that infection), and a negative control (a subject or a sample from a subject lacking the altered expression and clinical syndrome of that disease). The term "activating enzyme" as used herein means an enzyme that is 10 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. As used herein, the terms "pathological cells, "target cells", and "test cells" encompass cells characterized by the presence of an activating enzyme. The expression of the activating enzyme occurs as a consequence of infection by a 15 pathogenic organism, as defined above. Enzymes expressed by the pathogen or within an infected cell providing targets for this therapy include, but are not limited to thymidylate synthase and dihydrofolate reductase. Additional examples are listed below. 20 Therapeutic Methods 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 substrate prodrug that is selectively converted to a toxin in the cell by an activating enzyme expressed by the infectious 25 agent. 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 prodrug to the activating enzyme expressed by the 30 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 prodrug is 6 WO 01/07087 PCT/USOO/19844 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) 5 J. Virol. 70(11):8010-8018). Examples of activating enzymes that are selective targets for the prodrugs and methods of this invention include, but are not limited to, thymidylate synthase (TS), dihydrofolate reductase (DHFR) and P-lactamase activating enzymes. The concepts of this invention are illustrated using the activating enzyme 10 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) Annu. Rev. Biochem. 64:721-726), the fact that it is 15 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. 20 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) J. Mol. Biol. 285:1-32), the picornaviruses (eg., Hepatitis A virus, Wang Q.M. (1999) Prog. Drug Res. 52:197-219), and Hepatitis C virus (Kwong A.D. et al. 25 (1999) Antiviral Res. 41:67-84). Early clinical success observed with anti-HIVI reverse transciptase and protease inhibitors (reviewed by Shafer R.W. and Vuitton D.A. (1999) Biomed. Pharamcother. 53:73-86.) has been tempered by the development of resistance, largely due to mutations in the virally-enoded enzymes (Catucci M. et al. (1999) J. Acquir. Immune Defic. Syndr. 21:203-208; Mahalingam 30 B. et al. (1999) Eur. J. Biochem. 263:238-44; and Palmer, S. et al. (1999) AIDS 13(6): 661-667. Highly drug-resistant HIV-1 clinical isolates are cross-resistant to 7 WO 01/07087 PCT/USOO/19844 many anti-retroviral compounds in current clinical development. Hooker et al. (1996) supra. 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 prodrugs of this invention are specifically 5 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 substrate prodrug, referred to as an ECTA compound, which require the activating enzyme to generate toxin in the infected cell. NB 1011 is an example of such a compound, directed against TS expressed by mammalian and human cells as well as pathogens. 10 In one embodiment, the prodrug is a compound having a structure as defined in more detail herein. The term prodrug refers to precursors of active therapeutics. The perfect prodrug is one that is pharmacologically inert until activated by the intended mechanism. Prodrug strategies are meant to target potentially toxic therapies to the site of disease, thereby avoiding systemic toxicity. A number of 15 approaches have been made to this goal. One of the first attempts at a prodrug for cancer therapy was reported by Mead et al. (1966) Cancer Res. 26:2374-2379 and Nichol and Hakala (1966) Biochem. Pharmacol. 15:1621-1623. The guiding principle of this effort was to target overexpressed dihydrofolate reductase in methotrexate-resistant leukemia. Self-poisoning of tumor cells was hoped for as the 20 elevated dihydrofolate reductase in methotrexate-resistant tumor cells was supposed to convert homofolate into metabolic poison directed to thymidylate synthase. It was later discovered that the modest antitumor effects of homofolate are not due to metabolic activation, but more likely to inhibition of folate transport into cells (Livingston et al. (1968) Biochem 7(8):2814-2818.) This, and subsequent, prodrug 25 like attempts to leverage tumor selective targets for therapeutics development are summarized in Table 1, infra. One or more of the following issues has confounded these approaches: a) locating the activating enzyme appropriately and/or lack of tumor selectivity of the targeted enzyme; b) systemic distribution and resulting toxicity of the activated prodrug; and c) achieving the needed substrate enzyme 30 specificity to prevent activation by enzymes other than the ones targeted. For instance, the glutathione-s-transferase (GST) prodrug that has been described by 8 WO 01/07087 PCT/USOO/19844 Morgan et al. (1998) Cancer Res. 58:2568-2575, while "specific" for GST, it also is activated by by the tumor overexpressed GST-P1-1 and can be activated by GST-Al 1. This leads to inappropriate drug activation and potential toxicity. Many of these issues are discussed in more detail in the publications cited in Table 1, infra. The 5 methods and compositions disclosed herein avoid the prior prodrug failures by developing prodrugs that target enzymes that have appropriate properties to specifically activate the produgs only in the appropriate target cells, without priming the cells by prior adminstration of activating enzymes. In an additional aspect of the prodrugs is that they are essentially non-toxic to 10 normal, uninfected cells. This aspect further enhances the selectivity of the prodrugs and increases the overall safety of the therapy. The prodrug can selectively kill the cell because only infected cells provide an effective amount of the toxic metabolite of the prodrug to inhibit proliferation of the pathogen or the cell infected with the pathogen. In other words, the ultimate efficacy of the prodrugs of this invention are 15 related to the origin of the activating enzyme. For example, the efficacy of NB1011 is unexpectedly more potent as a substrate for human TS than microbial TS, as would be expected from published studies. (Barr (1983) J. Biol. Chem. 258(22):13637 1363 1) summarized in Table 2, infra. Various methods are available to determine if the object of the therapeutic 20 method has been met. This include, but are not limited to RT-PCR analysis, growth inhibition study (alamar blue assay) and plaque assays. These methods are well known in the art and described herein. Applicant also has discovered that cells which have been treated with the substrate prodrugs may revert to a prior phenotype which is suitably treated by 25 conventional therapies. Using TS as an example, Applicant has shown that tumor cells treated with 5-FU became resistant to the drug. At that time, the cells were treated with NB 1011. A subpopulation survived and became resistant to NB1011 but regained sensitivity to 5-FU (see Table 9 and Figure 8). Thus, this invention provides the methods described above wherein an effective amount of another anti 30 infective agent is co-administered with the substrate prodrug of this invention. In one aspect, the second or third agent is the drug to which the pathogen had 9 WO 01/07087 PCT/USOO/19844 previously developed resistance. The additional agent can be administered concurrently or subsequent to administration of the substrate prodrug. This invention further provides prodrugs that are selectively converted by an activating enzyme produced or expressed by an infectious agent or pathogen as 5 compared to the uninfected cell, e.g., an animal cell, a mammalian cell, or a human cell. Applicant has discovered several preferential prodrugs for the practice of this invention. The structures and synthetic methods for these compounds are provided in Materials and Methods, below. As used herein, the term "contacting" includes in vitro, ex vivo and in vivo 10 administration of prodrug. When done in vivo, the prodrug is administered to a subject in an effective amount. As used herein, the term "subject" is intended to include any appropriate animal model, e.g., mouse, rat, rabbit, simian. It also includes administration to humans patients. Another aspect of this invention is a method for treating a subject infected with 15 a pathogen by administering to the subject a therapeutically effective amount of a prodrug that is selectively converted to a toxin in a cell by an activating enzyme as defined herein. The enzyme is not necessarily overexpressed. In a father aspect, an effective amount of at least one additional therapeutic agent is co-administered concurrently, previously or subsequently to administration of the substrate prodrug. 20 When the prodrug is administered to a subject such as a mouse, a rat or a human patient, the agent can be added to a pharmaceutically acceptable carrier and systemically or topically administered to the subject. Administration in vivo can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most 25 effective means and dosage of administration are well 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. Suitable dosage formulations and methods of administering 30 the agents can be found below. 10 WO 01/07087 PCT/USOO/19844 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 5 aqueous or nonaqueous diluents, syrups, granulates or powders. In addition to a compound of the present invention, the pharmaceutical compositions can also contain other pharmaceutically active compounds or a plurality of compounds of the invention. More particularly, a compound of the formula of the present invention also 10 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, parental (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 15 being treated. In general, a suitable dose for each of the above-named compounds, is in the range of about 1 to about 100 mg per kilogram body weight of the recipient per day, preferably in the range of about 1 to about 50 mg per kilogram body weight per day and most preferably in the range of about 1 to about 25 mg per kilogram body weight 20 per day. Unless otherwise indicated, all weights of active ingredient are calculated as the parent compound of the formula of the present invention for salts or esters thereof, the weights would be increased proportionately. The desired dose is preferably presented as two, three, four, five, six or more sub-doses administered at appropriate intervals throughout the day. These sub-doses may be administered in 25 unit dosage forms, for example, containing about 1 to about 100 mg, preferably about 1 to above about 25 mg, and most preferably about 5 to above about 25 mg of active ingredient per unit dosage form. It will be appreciated that appropriate dosages of the compounds and compositions of the invention may depend on the type and severity and stage of the disease and can vary from patient to patient. Determining 30 the optimal dosage will generally involve the balancing of the level of therapeutic 11 WO 01/07087 PCT/USOO/19844 benefit against any risk or deleterious side effects of the treatments of the present invention. Ideally, the prodrug should be administered to achieve peak concentrations of the active compound at sites of disease. This may be achieved, for example, by the 5 intravenous injection of the prodrug, optionally in saline, or orally administered, for example, as a tablet, capsule or syrup containing the active ingredient. Desirable blood levels of the prodrug may be maintained by a continuous infusion to provide a therapeutic amount of the active ingredient within disease tissue. The use of operative combinations is contemplated to provide therapeutic combinations 10 requiring a lower total dosage of each drug that may be required when each individual therapeutic compound or drug is used alone, thereby reducing adverse effects. It is a further aspect of this invention to combine the prodrugs described herein with additional therapies as described above. For example, the prodrugs 15 described herein are preferentially combined with drugs that exert their toxic effect by a means other that that of the invention prodrugs. While it is possible for the prodrug 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 20 carriers therefor 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. Formulations include those suitable for oral, recta, nasal, topical (including transdermal, buccal and sublingual), vaginal, parenteral (including subcutaneous, 25 intramuscular, intravenous and intradermal) and pulmonary administration. The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. Such methods include the step of bringing into association the active ingredient with the carrier which constitutes one or more accessory ingredients. In general, the formulations are 30 prepared by uniformly and intimately bringing into association the active ingredient 12 WO 01/07087 PCTIUSOO/19844 with liquid carriers or finely divided solid carriers or both, and then if necessary shaping the product. Formulations of the present invention suitable for oral administration may be presented as discrete units such as capsules, cachets or tablets, each containing a 5 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. A tablet may be made by compression or molding, optionally with one or 10 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 15 carboxymethyl cellulose) 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 20 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. Formulations suitable for topical administration in the mouth include lozenges comprising the active ingredient in a flavored basis, usually sucrose and 25 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. Pharmaceutical compositions for topical administration according to the present invention may be formulated as an ointment, cream, suspension, lotion, 30 powder, solution, past, gel, spray, aerosol or oil. Alternatively, a formulation may 13 WO 01/07087 PCT/US00/19844 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. 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 5 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 prodrug may be employed with either a paraffinic or a water-miscible ointment base. Alternatively, the prodrug ingredients may be formulated in a cream with an oil-in-water cream base. 10 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 which enhances absorption or penetration of the 15 prodrug ingredient through the skin or other affected areas. Examples of such dermal penetration enhancers include dimethylsulfoxide and related analogues. The oily phase of the emulsions of this invention may be constituted from known ingredients in an known manner. While this phase may comprise merely an emulsifier (otherwise known as an emulgent), it desirably comprises a mixture of at 20 lease 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 which 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 25 ointment base which forms the oily dispersed phase of the cream formulations. 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 sulphate. The choice of suitable oils or fats for the formulation is based on achieving 30 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 14 WO 01/07087 PCT/USOO/19844 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, 5 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. 10 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 prodrug ingredient. The prodrug ingredient is 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. 15 Formulations for rectal administration may be presented as a suppository with a suitable base comprising, for example, cocoa butter or a salicylate. Formulations suitable for vaginal administration may be presented as suppositories, tampons, creams, gels, pastes, foams or spray formulations containing in addition to the prodrug ingredient, such carriers as are known in the art to be 20 appropriate. 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 25 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 prodrug ingredient. Formulations suitable for parenteral administration include aqueous and non aqueous isotonic sterile injection solutions which may contain anti-oxidants, buffers, 30 bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may 15 WO 01/07087 PCT/USOO/19844 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 5 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. Preferred unit dosage formulations are those containing a daily dose or unit, 10 daily subdose, as herein above-recited, or an appropriate fraction thereof, of a prodrug ingredient. 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 15 example, those suitable of oral administration may include such further agents as sweeteners, thickeners and flavoring agents. Prodrugs and 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, for example, by methods that are conventional in the art. 20 The agents and compositions of the present invention can be used in the manufacture of medicaments and for the treatment of humans and other animals by administration in accordance with conventional procedures, such as an active ingredient in pharmaceutical compositions. 25 Screening Assays This invention further provides a method for screening for prodrugs 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 prodrug. At least one test cell expresses the pathogen's version of the enzyme (wild-type or mutated) and 30 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 prodrug into 16 WO 01/07087 PCT/USOO/19844 toxic agents by the activating enzyme produced by the pathogen. As used herein, the test cells can be procaryotic or eucaryotic cells infected with the pathogen or alternatively, transformed to express the activating enzyme. For example, a procaryotic E. coli which does not endogenously express the activating enzyme TS is 5 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 10 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. 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 15 compounds shown below, which have been shown to be potent prodrugs. 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 20 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, CA 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 25 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. 30 The test cells can be grown in small multi-well plates and is used to detect the biologic activity of test prodrugs. For the purposes of this invention, the successful 17 WO 01/07087 PCTUSOO/19844 candidate drug will block the growth or kill the pathogen but leave the control cell type unharmed. The candidate prodrug 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 5 the media. Methods of conjugation for cell specific delivery are well known in the art, see e.g., U.S. Patent Nos. 5,459,127; 5,264,618; and published patent specification WO 91/17424 (published November 14, 1991). The leaving group of the candidate prodrug 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 prodrug. 10 Alternatively, cellular uptake may be enhanced by packaging the prodrug into liposomes using the method described in Lasic, D.D. (1996) Nature 380:561-562 or combined with cytofectins as described in Lewis, J.G. et al. (1996) Proc. Natl. Acad. Sci. USA 93:3176-3181. It should be understood, although not always explicitly stated, each 15 embodiment can be further modified by providing a separate target cell to act as a control by receiving an effective amount of a compound, such as, for example, the compounds shown below, which have been shown to be potent prodrugs. Agents identified by this method are further provided herein. In one embodiment, the assay of the effect of the prodrug is provided by 20 analysis of intracellular metabolites of the prodrug, as described in the Materials and Methods and Experimental Section below; the results of which are shown in Figure 4. In this embodiment, the prodrug contains a detectable label that is monitored during conversion of the prodrug to toxic agent by the activating enzyme. In an alternative embodiment, the candidate substrate prodrug is detectably labeled, e.g., e.g., 25 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 prodrug 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, the 30 results of which are shown in Figure 6. 18 WO 01/07087 PCT/USOO/19844 Using the above screen, one also can pre-screen several prodrugs against samples taken from a subject such as a human patient. One can use the screen to determine the most effective substrate prodrug and therapy for each pathogen and subject. 5 I. MATERIALS AND METHODS A. Synthetic Methodology. (E)-5-(2-Bromovinyl)-2'-deoxyuridine (BVdU), was prepared by the method of Dyer et al. (Dyer et al. (1991) Nucleic Acid Chemistry: Improved and 10 New Synthetic Procedures, Methods and Techniques, Townsend et al. (eds) John Wiley & Sons, Inc., New York, pp.79-83). This and commercial (Fisher/Acros) 5 fluoro-2'-deoxyuridine (5FdU) were each dried in vacuo at 75 *C adjacent to P205 immediately prior to use. Radial chromatography was performed on a Chromatotron instrument (Harrison Research, Palo Alto, CA), using Merck silica gel-60 with 15 fluorescent indicator as adsorbant. (E)-5-(2-Bromovinyl)-2'-deoxyuridine 5' monophosphate (BVdUMP), was prepared by standard chemical phosphorylation of BVdU. NMR 1H NMR spectra were recorded on a Varian Associates Gemini spectrometer at 300 MHz, using hexadeuterio-dimethyl sulfoxide (C2H 3 )2SO 20 solutions. Chemical shifts are reported relative to internal tetramethylsilane reference at d = 0.0 ppm. "C NMR spectra were recorded at 75 MHz, with chemical shifts reported relative to internal pentadeuterio-dimethyl sulfoxide at d = 39.5 ppm. "P NMR spectra were recorded at 202 MHz on a Bruker spectrometer, with chemical shifts reported relative to external 85%H 2 0/15%H 3

PO

4 , vol/vol, at d = 0.0 ppm. 25 NB1 011 ((E)-5-(2-Bromovinyl)-2'-deoxy-5'-uridyl phenyl L alaninylphosphoramidate (BVdU-PA, "NB1011")) was prepared as follows. A solution of BVdU (420 mg, 1.26 mmol) and imidazole (103 mg, 1.51 mmol) in 2 mL of anhydrous DMF under argon was treated dropwise with phenyl L methoxyalaninyl phosphorochloridate (McGuigan et al. (1996) J. Med. Chem. 30 39:1748-1753(15 drops, 350 mg, 1.26 mmol) and the reaction mixture was stirred at 23 *C under argon for 24 hours. By TLC on silica gel using 10%MeOH/90%CH 2 Cl 2 , 19 WO 01/07087 PCT/US00/19844 vol/vol, as eluent, the generation of the conversion product (Rf= 0.70) from the starting material (Rf = 0.53) had occurred but only to a partial extent (ca. 15%), so additional imidazole (52 mg, 0.75 mmol) and phosphorochloridate reagent (8 drops, 175 mg, 0.63 mmol) was added and the mixture stirred at 23 *C under argon another 5 24 hours. By TLC, the conversion had increased to ca. 30% extent. Subsequent treatment with additional phosphorochloridate and imidazole did little to promote the progress of the reaction. The solution was reduced in volume to 0.75 mL by rotary evaporation in vacuo at ~ 40 *C, and then an equal volume of CH 2 Cl 2 was added and the solution was applied directly to a dry 4 mm silica gel Chromatotron plate. At this 10 point, the subsequent separation was facilitated if the bulk of the remaining DMF was removed by placing the plate in a vacuum desiccator for 30 min. Radial chromatography using 250 mL of CH2Cl 2 (to elute residual reagents and DMF) followed by 10%MeOH/90%CH 2 Cl 2 , vol/vol, (to elute the product and then the starting material) gave 144 mg (20%) of the conversion product and 294 mg of the 15 starting material, for a 67% yield of conversion product based on unrecovered starting material. If the presence of contaminating imidazole (d = 7.65 and 7.01) or DMF (d = 7.95, 2.89, and 2.73) was detected by 'H NMR, an additional radial chromatographic purification was performed. In this way, 3 with a purity of =98% by TLC and 1H NMR was obtained as a nearly equimolar mixture of phosphorus 20 center-based diastereomers, in oil/gum or foam-powder form: 'H NMR ((C 2

H

3

)

2 SO) d = 11.4 (bs, exchanges with 2

H

2 0, 1, N3H), 8.28 (pseudo-t, 1, H6), 7.35 (pseudo-t, 2, o-Ph), 7.31 (d, 1, vinyl 'H), 7.20 (pseudo-t, 3, m- and p-Ph), 6.89 (d, 1, vinyl 2H), 6.19 (t, 1, Hi'), 6.08 (t, exchanges with 2

H

2 0, 1, alaninyl NH), 5.45 (bs, exchanges with 2

H

2 0, 1, O3'H), 4.32 (m, 1, H3'), 4.22 (m, 2, 5'CH2), 3.97 (m, 1, H4'), 3.86 (t, 1, 25 alaninyl CH), 3.58 (two s, 3, CO 2 Me), 2.15 (m, 2, 2'CH2), 1.23 (pseudo-t, 3, alaninyl CH3). Jvinyl CH-vinyl CH = 13.5, JH1'-H2'~ 6.8, JH2'-H3'~ 5, JH3'-H4'~ 0, Jalaninyl CH-alaninyl NH - 6 Hz. Spectral assignments were confirmed by 1H/1H COSY 2D NMR analysis. 3 C NMR ((C 2

H

3

)

2 SO)) d = 173.7 and 173.6 (alaninyl C0 2 ), 162.1 and 161.6 (C2), 150.6, 150.5 (ipso-Ph), 149.2 (C4), 139.4 and 139.2 30 (C6), 129.8 and 129.6 (m-Ph), 124.7 (p-Ph), 120.3, 120.2 (o-Ph), 107.1 (vinyl C1), 87.5 (vinyl C2), 84.8 (C4'), 83.8 (C1'), 70.1 (C3'), 66.1 (C5'), 51.9 (alaninyl OMe), 20 WO 01/07087 PCT/USOO/19844 49.7 (alaninyl a-H), 29.5 (C2'), 19.6 (alaninyl a-Me). 3JP-C4'= 7.8, 2JP-C5' = 4.4, 2JP-ipso-Ph = 6.5 Hz. 31P NMR d = 3.99, 3.69. Low-resolution DCI (NH 3 ) mass: 593/591 (MNH4*), 576/574 (MH*). For convenience only, the generic structures of exemplar prodrugs useful in 5 the methods of this invention have been classified as Class I and Class II. General Synthesis of Compounds of Class I The L and D isomers of the compounds of Class I have the structure: 0 OH 0 R1 R1 R, 4 5 NH 4 N 4 N 6 or 6 or 6 2 N 0 N 0 N OH Q Q Q 10 In the above formulae, R, (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 the activating enzyme, e.g., thymidylate synthase, and which upon release from the pyrimidine ring by the enzyme, has the ability to inhibit the proliferation of the agent or cell. 15 In the above formulae, Q can be a moiety such as a sugar, carbocylic or acyclic compound, a masked phosphate or phosphoramidate derivative containing a chemical entity selected from the group consisting of sugar groups, thio-sugar groups, carbocyclic groups, and derivatives thereof. Examples of sugar groups include, but are not listed to, monosaccharide cyclic sugar groups such as those derived from oxetanes 20 (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, 25 a five-carbon sugar); and lyxo-furanosyl (from lyxose, a five-carbon sugar). Examples of sugar group derivatives include "deoxy", "keto", and "dehydro" derivatives as well as substituted derivatives. Examples of thio sugar groups include 21 WO 01/07087 PCT/USO0/19844 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 C 4 carbocyclic groups, C, carbocyclic groups, and C 6 carbocyclic groups that may further have one or more subsituents, such as -OH groups. 5 In one embodiment, Q is a p-D-ribofuranosyl group of the formula:

R

7

-O--CH

2 0

R

3 R 2 wherein R, is attached to the furane at the 5' position and is selected from the group consisting of H, a masked phosphate or a phosphoramidate and derivatives thereof, and wherein R 2 and R 3 are the same or different and are independently -H or 10 OH. In some embodiments, R, may contain an alkenyl group, i.e., (-CH=CH)n-R 4 , wherein n is 0 or is an integer from 1 to 10, and R 4 is a halogen such as is I- or Br~, CN or mercury; wherein R 2 is H and R3 is -OH; wherein R2 is OH and R3 is H; wherein R2 and R3 are H; or wherein R 2 and R3 are OH. In another aspect, R4 is or contains a group 15 selected from the group consisting of H, a halogen, alkyl, alkene, alkyne, hydroxy, -0-alkyl, -0-aryl, 0-heteroaryl, -S-alkyl, -S-aryl, a cyanide, cyanate and thiocyanate halovinyl group, a halomercuric group, -S-heteroaryl, -NH2, -NH-alkyl, -N(alkyl)2, -NHCHO, -NHOH, -NHO-alkyl, NH 2 CONHO-, and NHNH 2 . In these embodiments, further aspects include: wherein R2 and R3 are H; wherein R2 is OH and R3 is H; herein 20 R2 is H and R 3 is OH; or wherein R2 and R 3 are OH. A preferred embodiment for the substituent in the R, position is one that could undergo an allylic interchange. 22 WO 01/07087 PCT/USOO/19844 In a still further aspect, the candidate therapeutic agent is a compound of the formula: 0 H **(CH=CH),-CH 2 -O-A O N Q wherein n is 0 or an integer from 1 to 10; wherein A is a phosphorous 5 derivative, or a compound of the formula: 0

-P-N(CH

2

CH

2

CI)

2

NH

2 and wherein Q is as defined above. Additionally, in a further aspect, the candidate therapeutic agent is a compound of the formula: 10

NH

2 C=O R-(CH=CH)n-(CH 2 )m--O H wherein R = 2'-deoxy-5-uridyl, m is 0 or 1, and n is an integer from 0 to 10. Where appropriate, the compounds can be in any of their enantiomeric, 15 diasteriomeric, or stereoisomeric forms, including, for example, D- or L-forms, and can be in any stereochemical configuration, including, for example, a- or P-anomeric form. Synthesis of the above noted 5-substituted pyrimidine nucleosides and 5 substituted pyrimidine nucleoside monophosphates can be accomplished by methods 23 WO 01/07087 PCT/USOO/19844 that are well-known in the art. For example, treatment of 5-chloromercuri-2' deoxyuridine with haloalkyl compounds, haloacetates or haloalkenes in the presence of Li 2 PdCl 4 results in the formation, through an organopalladium intermediate, of the 5-alkyl, 5-acetyl or 5-alkene derivative, respectively. Another example of C5 5 modification of pyrimidine nucleosides and nucleotides is the fonnation 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 Li 2 PdCl 4 . Bigge et al. (1980) J. Am. Chem. Soc. 102(6):2033-2038. Pyrimidine deoxyribonucleoside triphosphates were derivatized with mercury at the 5 position of 10 the pyrimidine ring by treatment with mercuric acetate in acetate buffer at 500 for 3 hours. Dale et al. (1973) PNAS 70(8):238-2242. Such treatment would also be expected to be effective for modification of monophosphates; alternatively, a modified triphosphate could be converted enzymatically to a modified monophosphate, for example, by controlled treatment with alkaline phosphatase 15 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, for example, U.S. Patent Nos. 4,247,544; 4,267,171; and 4,948,882; and Bergstrom et al. (1981) J. Org. Chem. 46(7):1432-1441. The above methods would 20 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 et al. (1983) J. Biol. Chem. 25 258(22):1367-13631 and Biochem. 22:1696-1703. 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, CA (USA), ICN, Costa Mesa, CA (USA) and New England 30 Nuclear, Boston, MA (USA). Commercially-available 5-bromodeoxyuridine and 5 iododeoxyuridine can be converted to their monophosphates either chemically or 24 WO 01/07087 PCT/USOO/19844 enzymatically, though the action of a kinase enzyme using commercial available reagents from Glen Research, Sterling, VA (USA) and ICN, Costa Mesa, CA (USA). These halogen derivatives could be combined with other substituents to create novel and more potent antimetabolites. 5 General Synthesis of Compounds of Class II In this embodiment, the present invention involves four classes of compounds activated by enzymes such as TS. Each class is defined by the structure of the uricil base, or modified uricil base present. These classes are ECTA compounds wherein: 10 I) the base is a furano-pyrimidinone derivative of uracil; II) the base is 6-fluoro uracil; and III) the base is 4-hydrazone substituted uracil derivative, or IV) the base is uracil. 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 15 the electron conduit and the toxic leaving group. The ECTA 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 20 suitable chemical protecting groups. Protection of 5-substituted deoxyuridine monophosphate derivatives can improve solubility, facilitate cellular penetration, facilitate passage across the blood-brain barrier, and prevent action of cellular or extracellular phosphatases, which might otherwise result in loss of the phosphate group. In another embodiment, 5-substituted uracil or uridine derivatives are 25 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. Action of thymidylate synthase upon 5-substituted uridine monophosphate 30 derivatives can release the substituent attached to the 5-position ("leaving group") of the pyrimidine ring. The released substituent is then capable, either inherently or 25 WO 01/07087 PCTUSOO/19844 following reaction with another cellular component, of acting as a toxin or an inhibitor of cellular proliferation. In one embodiment, the L and D isomers of the compounds of this invention are selected from the group consisting of the compounds having the structures shown 5 below: I. or II. or III.

H

2 N 0 NH NN N. 0 = R 1 0N R , 0N R , Q Q F Q < / N/ Iv. N R In the above formulae, R' has the formula: R2 3 4 10 ' ' m In the above formulae, R 2 is or contains a divalent electron conduit moiety. In one embodiment, R 2 is or contains a mono- or polyunsaturated electron conduit acting to conduct electrons away from the pyrimidine ring and toward the leaving group R 1 15 with the proviso that in compounds of class I, n can be zero. In one 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. 26 WO 01/07087 PCT/USOO/19844 In one embodiment, R 2 is an unsaturated hydrocarbyl group having a structure selected from the group consisting of: and 5 In one embodiment, R 2 and R 3 , taken together form a structure selected from the group consisting of: and In one embodiment, R 2 is an aromatic hydrocarbyl group having a structure selected from the group consisting of: 1 lt and In an alternative embodiment, R 2 is a heteroaromatic group having a structure selected from the group consisting of: Jj J and wherein J is a heteroatom, such as -0-, -S-, or -Se-, or a heteroatom group, such 15 as -NH- or -NR -, where RAI is a linear or branched alkyl having 1 to 10 carbon atoms or a cycloalkyl group having 3 to 10 carbon atoms. In the above formulae, R 3 is a divalent spacer moiety, also referred to as a spacer unit. In one embodiment, R 3 is a divalent spacer moiety having a structure selected from the group consisting of: 27 WO 01/07087 PCT/USOO/19844 R3

-CH

2 0- -CH 2 S- -N=N O O S

-CH

2 0-- CH 2 S-C- CH 2 0-C S -CH2SC

-CH

2 - -CHR 5 - -C(R52 -- S- -NH- and -NR5_ 5 wherein R 5 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 or R' is a halogen (F, Cl, Br, I). In one embodiment, R 3 is a divalent spacer moiety having a structure selected from the group consisting of: 10

-

-- S-- -- NH- and -- NR5_ In one embodiment, R3 is a divalent spacer moiety having a structure selected from the group consisting of: 28 WO 01/07087 PCTIUSOO/19844 R 3 CH2C CH 2 S- N=N

-CH

2 0-C-

-CH

2 S-C

CH

2 0-C S -CH2S~C In the above formula, n is an integer from 0 to 10 and, m is 0 or 1. In one embodiment, n is 0 or an integer from 0 to 10 and, m is 1. In one embodiment, n is 0 and m is 0. In one embodiment, when R 7 is -H, then n is not zero. In one embodiment, when R 7 is -H, then m is not zero. In one embodiment, when R 7 is -H, then n is not zero and m is not zero. In one embodiment, when R 7 is -H, then R 4 is not a halogen (i.e., -F, -Cl, -Br, -I). In one embodiment, when R 7 is -H, and m is zero, then R 4 is not a halogen (i.e., -F, -Cl, -Br, -I). In one embodiment, when R 7 is H, and m is zero and n is zero, then R 4 is not a halogen (i.e., -F, -Cl, -Br, -I). In the above formula, R 4 is a toxophore moiety. As used herein, the term "toxophore" shall mean a moiety which 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 thymidylate synthase, and which upon release from the pyrimidine ring by thymidylate synthase, has the ability to inhibit the proliferation of the cell or kill the cell. 29 WO 01/07087 PCT/USOO/19844 In one embodiment, the toxophore is or contains a leaving group that is activated or released by an intracellular enzyme overexpressed in the cell. In one embodiment, R 4 is or contains a group having a structure selected from the group consisting of: x

R

8 0

R

8 0 O2R -- ZzF - Z

R

1 0 x o 0 5 - o R-0 x z z -Z-P-N -Z-P-N /N NH 2 0

-O-NH-C-NH

2

CH

2 C=0 NH OH - Z-CH 2 -CH-CH-CH= CH-- (CH 2

)

1 2

CH

3 0 1I -- Z-CF 2

-CH

2 ~-CHF-C-OH 0 10 -Z-CF 2 -CHF-CH 2 -C-OH 0 II

-Z-CF

2

-CH

2 -C--OH 30 WO 01/07087 PCT/USOO/19844

CH

3 0 I __ _ 1I

-Z-CF

2 -CH C-OH Y -Z-CF 2 -~-Y Y

-Z-CF

2

-CH

2

-CH

2

-NO

2 and -- Z\NNO2 5 wherein X is -Cl, -Br, -I, or other potent leaving group (including, but not limited to, -CN, -OCN, and -SCN); Y is the same or different, and is independently H or -F; and Z is the same or different and is independently -0- or -S-, R 8 and R' are lower alkyls, and R' is H or CH 3 . 10 In one embodiment, R 4 is or contains a chemical entity selected from the group consisting of: -Br, -I, -0-alkyl, -0-aryl, 0-heteroaryl, -S-alkyl, -S-aryl, -S-heteroaryl, -CN, -OCN, -SCN, -NH 2 , -NH-alkyl, -N(alkyl) 2 , -NHCHO, -NHOH, -NHO-alkyl,

NH

2 CONHO-, NHNH 2 , -N 3 , and a derivative of cis-platin, such as: O=C C=O I I Pt

H

3 N NH 31 WO 01/07087 PCTIUSOO/19844 In the above formulae, Q is or contains a group which supports functional binding of the prodrug to the enzyme, e.g., TS or TK. In one embodiment, Q is selected from the group consisting of:

R

7 -O R 7 -O R 7 -- O 0 S R6 R6 R R 6 6

R

7

-CH

2

R

7 -O and 0< 5 wherein R' is the same or different and is independently -H, F, -OH, OC(=0)CH 3 , or other protected hydroxyl group (including, but not limited to, benzoyl,

-COC

6 H., and toluoyl, -COC 6

H

4

CH

3 ); and, R7, attached at the 5' position of Q, is hydrogen, a phosphate group, a phosphodiester group, a phosphoramidate group, or other phosphorus containing group. 10 In one embodiment, R' is a phosphoramidate group derived from an amino acid, including, for example, the twenty naturally occurring amino acids. In one embodiment, R7 is a phosphoramidate group derived from alanine. In one embodiment, R 7 is or contains a group having the structure: O NH .CH

CH

3

COOCH

3 15 The above group, and methods for its preparation, are described in McGuigan et al. (1993) J. Med. Chem. 36:1048-1052 and McGuigan et al. (1996) J. Med. Chem. 39:1748-1753. 32 WO 01/07087 PCT/USOO/19844 In one embodiment, R 7 is a phosphoramidate group derived from tryptophan. In one embodiment, R' is or contains a group having the structure: O

HO-P

NH NH .CH

COOCH

3 The above group, and methods for its preparation, are described in 5 Abraham et al., (1996) J. Med. Chem. 39:4569-4575. In one embodiment, R' is a phosphate group. In one embodiment, R 7 is or contains a group having a structure selected from the group consisting of: 0 0 a0 0 0 O-P-- 0-p O O and O O S The first of the two above groups, and methods for its preparation, are 10 described in Freed et al. (1989) Biochem. Pharmacol. 38:3193-3198; Sastry et al. (1992) Mol. Pharmacol 41:441-445; Farquhar et al. (1994) J. Med. Chem. 37:3902 3909; and Farquhar et al. (1995) J. Med. Chem. 38:448-495. The second of the two above groups, and methods for its preparation, are described in Valette et al. (1996) J. Med. Chem. 39:1981; and Benzaria et al. (1996) J. Med. Chem. 39:4958. 15 In one embodiment, R' is or contains a group having a structure selected from the group consisting of (where R is an aromatic substituent): 0 1 OO 0 and O 0 0(CH 2

)

17

CH

3 OH R 33 WO 01/07087 PCT/USOO/19844 The first of the two above groups, and methods for its preparation, are described in Meier et al. (1997) Bioorg. Med. Chem. Lett. 7:1577; Meier et al. (1997) Bioorg. Med. Chem. Lett 7:99; and Meier et al. (1997) International Antiviral News. 5:183. The second of the two above groups, and methods for its preparation, are 5 described in Hostetler et al. (1997) Biochem. Pharmcol. 53:1815; and Hostetler et al., published International Patent Application No. WO 96/40088 (1996). In one embodiment, the R 7 forms a cyclic group within Q. One such embodiment, and a method for its preparation, is shown below (where DMTr is 4,4'-dimethoxytrityl, Boc is t-butyloxycarbonyl, DCC is 1,3-dicyclohexylcarbodiimide, 10 and 4-DMvAP is 4-dimethylaminopyridine): DMTr-O 0 HO DMTr-O B DMTr-CI Boc-L-alanine Boc NH H H DCC, cat. 4-DMAP C,. 0 OH OH H 3 0 HO 1. HCI PhOP(O)Cl 2 I

NH

2 NH 2. Base Imidazole -H' 0 0 O O In one embodiment, the compound may be in any enantiomeric, diasteriomeric, or stereoisomeric form, including, D-form, L-form, a-anomeric form, and p-anomeric form. 15 In one embodiment, the compound 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. 34 WO 01/07087 PCT/USOO/19844 In a separate embodiment, the above structures are further modified to possess thiophosphodiaziridine instead of phosphodiaziridine groups, using the methods described below. Synthesis of the above noted 5-substituted pyrimidine derivatives can be 5 accomplished by methods that are well-known in the art, and as described above. 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, CA (USA), ICN, Costa Mesa, CA (USA) and New 10 England Nuclear, Boston, MA (USA). Commercially-available 5 bromodeoxyuridine and 5-iododeoxyuridine can be converted to their monophosphates either chemically or enzymatically, though the action of a kinase enzyme using commercial available reagents from Glen Research, Sterling, VA (USA) and ICN, Costa Mesa, CA (USA). These halogen derivatives could be 15 combined with other substituents to create novel and more potent antimetabolites. The structures at the 5-position of uracil are referred to as the tethers because they connect the proposed leaving group (toxophore) to the heterocycle. Upon activation of the heterocycle by reaction with a Cys residue in the active site of human TS, a negative charge is conducted from the 6-position of uracil into the 20 tether. This mechanism has been described for the 5'-monophosphorylated versions of (E)-5-(bromovinyl)-2'-deoxyuridine (BVDU) by Barr et al. (1983) Biochemistry 22(7):1696-1703 and of (E)-5-(3,3,3-trifluoro-l-propenyl)-2'-deoxyuridine (TFPe dUrd) by Wataya et al. (1979) J. Med. Chem. 22:339-340; Santi (1980) J. Med. Chem. 23:103-111; and Bergstrom et al. (1984) J. Med. Chem. 27:279-284. 25 The tether "spacer" between the toxin and dNMP must be unsaturated so that it can conduct the toxin-labilizing negative charge supplied by the TS-Cysteine sulfhydryl attack. Of the many unsaturated organic functionalities available for this purpose, the 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 30 in either of two non-interconvertible geometric isomeric forms. Thus, they can be used as "probes" of prodrug accommodation by the TS active site. On the other 35 WO 01/07087 PCTIUS00/19844 hand, the propargyl unit has the advantage of being cylindrically symmetrical, so that TS-catalyzed toxin release from this type of tether does not depend upon its orientation with respect to dUMP's uracil ring, as is the case with the vinyl and allyl molecules. 5 Two distinct approaches have been taken to design several of the nucleotide based prodrugs of this invention. One is based on the structure of BVDU monophosphate and features a leaving group/toxin directly attached to the terminus of a (poly)vinyl substituent at C5 of dUMP. This is the vinyl tether approach. The other is based on the structure of TFPe-dUMP and is similar to the first but has a 10 methylene unit separating the leaving group/toxin and the unsaturated unit and thus contains an allyl or propargyl unit. This is the allyl tether approach. The mechanism of activation of a propargyl version of the allyl tether approach has a precedent in the interaction of both 5-ethynyl-2'-deoxyuridine 5' monophosphate (EdUMP) and 5-(3-hydroxy-l-propynyl)-2'deoxyuridine 5' 15 monophosphate (HOPdUMP) with TS (Barr et al. (1981) J. Med. Chem. 24:1385 1388 and Barr et al. (1983) supra.) EdUMP is a potent inhibitor of TS (Ki = 0.1 pM), and likely forms an allene-based species at the active site. HOPdUMP (Ki = 3.0 pM) shows unusual inhibition kinetics, which might be due to formation of a cumulene-based species at the active site. 20 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 et al. (1996) J. Heterocycl. Chem. 33:1259-1270). These were shown to be highly electrophilic. Their ready reaction with ethanol to generate 5-(ethoxymethyl)uracils is a precedent for the water addition that 25 regenerates catalytically competent TS. Even more recently, the existence of the long-elusive C5 methylene intermediate produced by TS was demonstrated by trapping studies (Barrett et al. (1998) J. Am. Chem. Soc. 120:449-450). Synthesis of ECTA compounds with propargyl tethers. The synthesis of propargylic and allylic alcohol-equipped 2'-deoxyuridines is straightforward. Many 30 of these and their close derivatives are reported in the literature, and some have even been studied in connection with TS. For example, 5-alkynyl-dUMPs including the 5 36 WO 01/07087 PCTIUSOO/19844 (3-methoxy-l-propynyl) and 5-(3-hydroxy-l-propynyl) ones have been examined as TS inhibitors (Barr et al. (1981) J. Med. Chem. 24:1385-1388) and some of these have been shown to become incorporated into the DNA of TS-deficient cancer cells (Balzarini et al. (1985) FEBS Lett 373(1):41-4). 5 Both 5-mercuri- (Ruth et al. (1978) J. Org. Chem. 43:2870-2876) and 5 iodouridines (Robins et al. (1981) Tetrahedron Lett 22:421-424) 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 et al. (1982) Can. J. Chem. 60:554-557; Asakura (1988) Tetrahedron Lett. 29:2855-2858; and 10 Asakura (1990) J. Org. Chem. 55:4928-4933). High-yielding condensations of protected 5-iodo-2'-deoxyuridines with t-butyidimethylsilyl propargyl ether (Graham et al. (1998) J. Chem. Soc. Perk. Trans. 1:1131-1138 and De Clercq et al. (1983) J. Med. Chem. 26:661-666), methyl propargyl ether (Tolstikov et al. (1997) Nucleosides Nucleotides 16:215-225) and even propargyl alcohol itself (Chaudhuri et 15 al. (1995) J. Am. Chem. Soc. 117:10434-10442 and Goodwin et al. (1993) Tetrahedron Lett. 34:5549-5552) have been achieved. The 3-hydroxy-l-propynyl substituent introduced by the latter reaction can also be accessed by DIBAL-H reduction of a methacrylate group (Cho et al. (1994) Tetrahedron Lett. 25:1149 1152), itself arising from the same Heck reaction used in the synthesis of BVDU. 20 These palladium-catalyzed reactions are so versatile that they can used to condense very long and elaborately-functionalized propargyl-based tethers to 5-iodo-2' deoxyuridines (Livak et al. (1992) Nucleic Acids Res. 20:4831-4837 and Hobbs (1989) J. Org. Chem. 54:3420-3422). (Z)-Allyl-based tethers are generated by the partial hydrogenation of a propargylic precursor over Undiar catalyst (Robins (1983) 25 J. Org. Chem 5(11):3546-3548 and Barr (1983) J. Biol. Chem. 258(22):13627-13631 and Biochem. 22:1696-1703) whereas the (E)-allyl-based ones are best prepared by Heck coupling of an (E)-tributylstannylated ethylene (Crisp (1989) Synth. Commun. 19:2117-2123). Closely following the literature procedures, a t-butyldimethylsilyl propargyl 30 ether-equipped 3', 5'-di-0-protected 2'-deoxyuridine (Graham et al. (1998) supra; De Clercq et al. (1983) J. Med. Chem. 26:661-666) is prepared and a portion of it, 37 WO 01/07087 PCT/USOO/19844 converted to the corresponding (Z)-allyl ether, (Barr et al. (1983) supra) 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 will serve as convenient precursors to some of the toxophore 5 equipped targets. For the (E)-allyl alcohol equipped nucleoside, the known 0 tetrahydropyranyl ether derivative is prepared by the literature Heck coupling of an (E)-tributylstannylated ethylene (Crisp (1989) supra). N N O= / -I O=< / C= =C-CH 2 -OH PG-O . PG-O N propargyhc, (E)-allylic, or (Z)-allylic PG-0 PG-O 10 Using a two step literature protocol (Phelps et al. (1980) J. Med. Chem. 23:1229-1232; and Hsiao and Bardos (1981) J. Med. Chem. 24:887-889), the propargylic and (E) and (Z)-allylic alcohols are converted to their corresponding bis 15 aziridinyl phosphoramidates or thiophosphoramidates so that TS processing of the 5'-mononucleotide versions will release an active metabolite of the cytostatic drugs TEPA or ThioTEPA (Dirven et al. (1995) Cancer Res. 55:1701-1706), respectively. 38 WO 01/07087 PCTIUSOO/19844 H 0 N O== C= =C-C d-0 H PG-O 0 N propargylic, (E)-allylic, or (Z)-allylic PG-O H N 0(S) O= = =C-C PG-O N propargylic (E)-allylic, or ()-allylic PG-O Bis-aziridin-1-yl-phosphinic acid 3-[2-deoxyuridin-5-yl]-prop-2-ynyl ester 5 (TEPA) was synthesized and analyzed by 'H NMR to yield the following result: 'H NMR ((CD 3

)

2 SO) complicated due to noise. Salient features: 8 8.28 (d, 1, H6), 6.10 (pseudo-t, 1, Hi'), 5.26 (m, exchanges with D 2 0, 1, 3'-OH), 5.13 (m, exchanges with D 2 0, 1, 5'-OH), 4.81 (q or dd, 2, propargyl-CH 2 ), 4.24 (m, 1, H3'), 3.57 (m, 2, 5'-CH 2 ), 2.15-2.0 (m, 8, aziridine-CH 2

)

10 Bis-aziridin-1-yl-phosphinothioic acid 3-[2-deoxyuridin-5-yl]-prop-2-ynyl ester (Thio TEPA) was also synthesized and analyzed by 'H NMR to yield the following result: 'H NMR ((CD 3

)

2 SO) complicated due to noise. Salient features: 6 8.29 (d, 1, H6), 6.10 (pseudo-t, 1, Hi'), 5.22 (m, exchanges with D 2 0, 1, 3'-OH), 5.10 (m, exchanges 15 with D 2 0, 1, 5'-OH), 4.88 (q or dd, 2, propargyl-CH 2 ), 4.31 (m, 1, H3'), 3.52 (m, 2, 5'-CH 2 ), 2.15-2.0 (m, 8, aziridine-CH 2 ). Synthesis of furano-pyrimidinones. Synthesis of furano-pyrimidinones begins with synthesis of a C5 propargylic -alcohol-equipped 2'-deoxyuridine. Furano-pyrmidinone compounds are then be formed from the 0-tetrahydropyranyl 39 WO 01/07087 PCT/USOO/19844 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 5 synthesis of ECTA compounds through various combinations of specific electron conduits, spacers and toxic leaving groups. O R1 N Q 10 The furo[2,3-d]pyrimidinone nucleosides were prepared by condensing 2',3' di-0-p-toluoyl or 2',3'-di-O-acetyl-5-iodo-2'-deoxyuridine with 1 (tetrahydropyranyloxy)-2-propyne (Jones and Mann (1953) J. Am. Chem. Soc. 75:4048-4052) under conditions known to promote the formation of these fluorescent compounds (Barr et al. (1983) supra). Base-catalyzed removal of the carbohydrate 15 protecting groups gave the 6-(tetrahydropyran-2-yloxymethyl)-substituted bicyclic nucleoside which was either subjected to standard acidic THP group hydrolysis (TFA in CH2C1 2 ) or was regioselectively 5'-phosphoramidated by the same procedure used to prepare BVDU-PA and 5FUdR-PA. After the phosphoramidation, the THP group could be removed by acidic hydrolysis. 40 WO 01/07087 PCT/USOO/19844 H 00 0N N 0 N- 0a RO N RO N HO O N O N (Ph3P)2PdCI, CuI, Et 3 N : N RO /RO HO R = 4-CH3C 6

H

4 C(0) or CH 3 C(=0) OH 0 I 0=6N OH PhO- - N N / Me. NH M% N HO N r HH MeOMC H H MeO 2 C HO 3-(2-Deoxy-p-D-ribofuranosyl)-6-(tetrahydropyran-2 yloxymethyl)furo[2,3-d]pyrimidin-2(3H)-one. 'H NMR ((CD 3

)

2 SO) 6 8.80 (s, 1, 5 H4), 6.74 (s, 1, H5), 6.16 (pseudo-t, 1, Hi'), 5.27 (d, exchanges with D 2 0, 1, 3'-OH), 5.12 (t, exchanges with DO, 1, 5'-OH), 4.72 (m, 1, THP-H2), 4.56 (q, 2, CH 2 OTHP), 3.92 (m, 1, H4'), 3.64 (m, 2, 5'-CH 2 ), 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-NH 3 ) on bis-TMS derivative, m/z 323 (B+TMS+H*), 511 (MH*), 583 (M+TMS*). 10 3-(2-Deoxy-p-D-ribofuranosyl)-6-(hydroxymethyl)furo[2,3-d]pyrimidin 2(3H)-one. 'H NMR ((CD 3

)

2 SO) 6 12.0 (bs, 1, OH), 8.24 (s, 1, H4), 6.53 (s, 1, H5), 5.51 (pseudo-t, 1, Hi'), 4.42 (m, 2, CH 2 OH). Low-resolution mass spectrum (DCI

NH

3 ), m/z 167 (B+2H*), 184 (B+NH4*). 1-[6-(Tetrahydropyran-2-yloxymethyl)furo[2,3-d]pyrimidin-2(3H)-on-3-yl] 15 2-deoxy-p-D-ribofuranos-5-yl phenyl methoxy-L-alaninylphosphoramidate. 1H NMR ((CD3)2SO) complicated due to presence of diastereomers. Salient features: 6 8.62 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, Hi'), 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-ax-Me). Low-resolution mass 20 spectrum (DCI-NH3), m/z 167 (B+2H*), 184 (B+H*+NH4+-THP). 1-[6-(Hydroxymethyl)furo[2,3-dpyrimidin-2(3H)-on-3-ylJ-2-deoxy-p-D ribofuranos-5-yl phenyl methoxy-L-alaninylphosphoramidate. 'H NMR (CDCl 3 ) complicated due to presence of diastereomers. Salient features: 6 8.5 (s, 1, H4), 7.4 41 WO 01/07087 PCTIUSOO/19844 7.1 (m, 5, PhO), 6.36 and 6.30 (each s, each 1, H5), 6.23 (m, 1, Hi'), 3.67 and 3.65 (each s, each 3, CO 2 Me), 2.69 (m, 1, H2'a), 2.10 (m, 1, H2'b), 1.35 (m, 3, alaninyl-a Me). Low-resolution mass spectrum (DCI-NH 3 ), m/z 525 (MH*), 595 (MNH4*). The 4-nitrophenyl ether derivative of 5-(3-hydroxy-1-propynyl)-2' 5 deoxyuridine was prepared according to a standard ether synthesis as shown below. N 02NOH H N O N OHOH N O /K /n/ K N N Ph 3 P 02N 5-[3-(4-Nitrophenoxy)-1-propynyl]-2'-deoxyuridine. A solution of pre dried 5-(3-hydroxy-1-propynyl)-2'-deoxyuridine ("Nucleic Acid Compounds. 39. Efficient Conversion of 5-Iodo to 5-Alkynyl and Derived 5-Substituted Uracil Bases 10 and Nucleosides" (Barr et al.(1983) supra) (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 L, 3 mmol), and the reaction mixture heated at 60 "C until the solution was clear, and then 1 h longer. The mixture was allowed to cool to 23 *C and then it was evaporated 15 onto SiO2 and purified by chromatography using MeOH/CH 2 Cl 2 as eluent to afford 107 mg (13%) of the desired ether product: mp 112-118 "C. 'H NMR ((CD 3

)

2 SO) 6 11.65 (s, exchanges with D 2 0, 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, Hi'), 5.17 (s, 2, propargyl

CH

2 ), 4.22 (m, 1, H3'), 3.80 (m, 1, H4'), 3.59 (m, 2, 5'-CH 2 ), 2.13 (pseudo-t, 2, 2' 20 CH 2 ). Low-resolution mass spectrum (DCI-NH 3 ) on per-trimethylsilyated material, m/z 547 [M(TMS) 2 H*], 565 [M(TMS) 2

NH

4 *], 620 [M(TMS) 3 H*]. TS ECTA compounds based on furano-pyrimidinones. Toxic R 4 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 25 compound, as explained with the synthesis of the TEPA and ThioTEPA derivatives described above. A variety of alternative toxic leaving groups, apparent to one 42 WO 01/07087 PCT/USOO/19844 skilled in the art, are envisioned. In addition, modifications to the length and composition of the R 2 electron conduit component and of the composition of the R 3 spacer element are also envisioned. TS ECTA compounds based on furano-pyrimidinones can also consist of 5 variously modified "Q" moeities. Many 5-substituted 2'-deoxyuridines are not substrates for human TK, but interestingly 5-(4-hydroxy-l-butynyl)-2'-deoxyuridine was found to be an exception (Barr et al. (1981) supra). Thus, it is expected that some of the toxophore equipped nucleosides will also possess propitious TK substrate activity. Thus, the ECTA compounds can have a free 5' hydroxyl, a 5' 10 monophosphate, or a 5' phosphoramidate group attached to alternative carbohydrate groups. A novel 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 HCl scavenger. In a preferred embodiment, the phosphochloridate comprises a phosphorus substituent which is 15 derived from an amino acid such as alanine. For example, the phosphochloridate can be phenyl-L-methoxyalanine phosphorochloridate. C6 Fluoro uridine and C4 hydozone based compounds. The neutral thiol addition to the pyrimidine C5-C6 double bond proceeds as an exothermic reaction (3 9 kcal per mol; see review by (Les et al (1998) Biomolecular Structure and Dynamics 20 15(4):703-715) in the normal TS reaction with dUMP. Alternative substituents to the TS reactive hydrogen at the 6 position that can facilitate the formation of the sulfydryl bond with the enzyme, via an active human TS cysteine (homologous with cys-198 of L. casei), include fluorine. Such substituents at other positions in the pyrimidine ring can also facilitate the reaction between the substrate and TS. For 25 instance, a 4-hydrazone substitution on the uracil (as described by Les et al. (1998), supra) facilitates formation of the thiol with TS. It is important that the resulting nucleotide-thiol (TS) intermediate rearranges in such a way as to release the altered nucleotide which can be accomplished passively via hydrolysis. 43 WO 01/07087 PCTIUSOO/19844 OH N== N / Q F The introduction of fluorine at the C6 position has not been previously reported, but it can be synthesized by following the synthetic descriptions of Krajewskas and Shugar (1982) Biochem. Pharmacol. 31(6):1097-102, who describe 5 the synthesis of a number of 6 substituted uracil and uridine analogues. Chemistry facilitating substitutions at the C4 position of the pyrimidine base are well known by those skilled in the art. Examples of literature descriptions include Wallis et al. (1999) Pharmaco. 54(1-2):83-89; Negishi et al. (1996) Nucleic Acids Symp. Ser. 35 (Twentythird Symposium on Nucleic Acids Chemistry) 137 10 138; Barbato et al. (1991) Nucleosides Nucleotides 10(4):853-66; Barbato et al. (1989) Nucleosides Nucleotides 8(4):515-528; and Holy et al. (1999) J. Med. Chem. 42(12):2064-2086. These synthetic techniques also enable combinations of substitutions, for instance at the C4 and C5 positions of the pyrimidine ring (Pluta et al. (1999) Boll. Chim. Farm. 138(1):30-33) or the C2 and C4 positions of the 15 pyrimidine ring (Zeid et al. (1999) Nucleosides Nucleotides 18(1):95-1 11).

H

2 N NH

N

N Q 44 WO 01/07087 PCT/USOO/19844 In another embodiment of the invention, ECTA 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 ECTA compounds 5 can again be employed for synthesis of such molecules. B. Derivatives of the Compounds of Class I and II Salts, esters, and ethers of the above compounds disclosed herein are also within the scope of this invention. Salts of the prodrugs of the present invention may 10 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 15 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 NW,, wherein W is C, alkyl. 20 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, 25 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', NH, and NW,' (wherein W is a C, 4 alkyl group). 30 For therapeutic use, salts of the compounds of the present invention will be pharmaceutically acceptable. However, salts of acids and bases which are non 45 WO 01/07087 PCT/USOO/19844 pharmaceutically acceptable may also find use, for example, in the preparation or purification of a pharmaceutically acceptable compound. Esters of the prodrugs or compounds identified by the method of this invention include carboxylic acid esters (i.e., -O-C(=O)R) obtained by esterification 5 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, C 1 _alkyl, or C 1 alkoxy or amino); (2) sulfonate esters, such as alkylsulfonyl 10 (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

C,

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 15 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 prodrug derivatives of the present invention include, for example, those with 20 chemically protected hydroxyl groups (e.g., with O-acetyl groups), such as 2'-0 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. Ethers of the compounds of the present invention include methyl, ethyl, propyl, butyl, isobutyl, and sec-butyl ethers. 25 In a further embodiment, the substrate may not be chemically related to pyrimidines or folates, but rather synthesized based upon known parameters of rational drug design. (See Dunn et al. (1996) J. Med. Chem. 39:4825). Chemical assays for products, for example, where a reaction product is an anti-metabolite of the bromovinyl-derivatives of dUMP, are described in the 30 Examples provided below or by (Barr et al. (1983) supra). 46 WO 01/07087 PCT/USOO/19844 C. 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 P 5 actin were designed as following: thymidylate synthase sense primer 5' GGGCAGATCCAACACATCC-3' (corresponding to bases 208-226 of thymidylate synthase cDNA sequence, Genbank Accession No. X02308), antisense primer 5' GGTCAACTCCCTGTCCTGAA-3' (corresponding to bases 564-583), p-actin sense primer 5'-GCCAACACAGTGCTGTCTG-3' (corresponding to bases 2643-2661 of 10 p-actin gene sequence, Genbank Accession No. M10277) and antisense primer 5' CTCCTGCTTGCTGATCCAC-3' (corresponding to bases 2937-2955). Human colon tumor tissues and matched normal tissues were obtained from Cooperative Human Tissue Network (CHTN, Western Division, Cleveland, OH). Total RNAs were isolated using Tri pure isolation reagent (obtained from Boehringer 15 Mannheim Corp., Indianapolis, IN), followed manufactureis protocol. To monitor for possible DNA contamination, the primers for amplification of p-actin were designed to span the exon4/intron5/exon5 junction. Genomic DNA template leads to a 313 bp p-actin fragment, and cDNA template generates a 210 bp product. Reverse transcriptions were performed, using SuperScript preamplification 20 system (Gibco/BRL, Gaithersburg, MD). 3 pg total RNA was applied in a volume of 20 pl buffer to conduct reverse transcription reaction, followed manufacture's protocol. PCR reactions were performed in a volume of 96 pl, containing 5pl of cDNA mixture from reverse transcription reaction, 3 mM MgCl 2 , 50 mM KCl, 20 mM Tris 25 Cl, pH 8.4, 0.2 mM of each dNTP, 0.3 pM of thymidylate synthase sense and antisense primers and 5 units of Tag DNA polymerase (obtained from Promega, Madison, WI). 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 p-actin primers in 4 pl were added to 30 achieve a final concentration of 0.2 pM, bringing the final reaction volume to 100 ptl. 47 WO 01/07087 PCTIUSOO/19844 PCR reaction was continued to a total of 30, 32 or 34 cycles, followed by a 7 min incubation at 72 *C. 10 ptL of PCR products were resolved by electrophoresis in 2% agarose gel, followed by staining with SYBR Gold nucleic acid gel stain (obtained from 5 Molecular probes, Eugene, OR). Result of quantification indicated that amplification of thymidylate synthase and p-actin was linear between cycles 30 and 34. The DNA bands corresponding to thymidylate synthase were quantified and normalized to that of p-actin by Molecular Dynamics Storm. The quantified expression levels were expressed as values of ratio between TS and p-actin. This assay is also useful for 10 detecting pathogens in mammalian cells, as described in Nagata et al. (1999) J. Hepatol-30:965-969. D. Cell lines and transfection. HT1080 cells were grown in PRMI1640 medium supplemented with 10% fetal calf serum, and transfected with GFP-TS 15 expression vector. 48 hours after, transfection cells were tripsinized and replated in culture medium containing 750 pg/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 20 into cells lines. The stable HT1080 cells transfected with pEGFP-C3 were used as control. E. Construction of GFP-TS expression vector. A cDNA fragment encoding conserved region of human thymidylate synthase (amino acids 23 to 313) 25 was obtained by PCR amplification using following primers: Sense primer, 5' CGGAAGCTTGAGCCGCGTCCGCCGCA-3' and antisense primer, 5' GAAGGTACCCTAAACAGCCATTTCCA-3'. The cDNA was cloned into HindIII and KpnI sites of mammalian expression vector pEGFP-C3 ( Clontech Laboratories. Inc., Palo Alto, CA), in-frame with GFP sequence. The cDNA insert was confirmed 30 by DNA sequencing. 48 WO 01/07087 PCT/USOO/19844 F. Western Blot analysis. Human normal and cancer cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum. Cells were grown until 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 5 acid, sodium salt and protease inhibitors ). Protein concentrations were determined by using BCA-200 protein assay kit (obtained from Pierce, Rockford, IL). 15 pg 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 10 NeoMarkers, Fremont, CA) 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 15 values relative to that of cell strain CCD 1 8co. G. TS Activity Assay by Tritium Release from dUMP- 3 H. 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. 20 Immediately prior to the thymidylate synthase assay, the media was replaced with RPMI+10% dialyzed fetal calf serum. 0.5 gCi of 5-[ 3 H]deoxyuridine was added to each well, and plates were incubated for 60 minutes at 37 *C without additional CO 2 . [ 3 H] release was measured by adsorbing 5-[ 3 H]deoxyuridine to activated charcoal (10% in 1 x PBS) for 5 minutes at room temperature. After 25 centrifugation for 5 minutes at 13,000 RPM, the amount of [ 3 H] in the supernatant was determined by liquid scintillation counting. H. Growth Inhibition Studies. Cells growing exponentially were transferred to 384-well flat bottom tissue culture plates. All cell types were plated at 30 a density of 500 cells per well in 25 iL of complete medium (RPMI 1640 + 10% fetal bovine serum + antibiotics/antimycotics). After 24 hours (day 0), 25pL of 49 WO 01/07087 PCT/USOO/19844 complete medium containing the experimental compounds over the dose range of 10 3 to 10 "' 0 M were added in triplicate. Drug exposure time was 120 hours (day 5), after which growth inhibition was assayed. 5p.L of the redox indicator, alamarBlue, was added to each well (10% v/v). After 4 hours incubation at 37 *C, fluorescence 5 was monitored at 535 nm excitation and 595 nm emission. Concentration vs. relative fluorescence units (RFU) were plotted, and sigmoid curves were fit using the Hill equation. ICO, indicated by the inflection point of the curve, is the concentration at which growth is inhibited by 50%. The same growth inhibition/cytotoxicity assays can be used to measure 10 cytotoxicity of toxins released from ECTA compounds by activating enzymes encoded by infectious agents as described in the patent. As noted above, infectious agents of this class include, but are not limited to, Mycobacterium sp., Chlamydia sp., Rickettsia sp. And Pheumocystis sp. pathogenic Enterococcus sp., Moraxella sp., Haemophilis sp., and Staphylococcus sp. Colony formation assays can be used to 15 measure cytotoxicty of metabolized ECTA compounds on extracellular pathogenic bacteria or other pathogens on plates or in liquid media (Miller, J.H. A Short Course in Bacterial Genetics: A Laboratory Manual and Hardbook for E. Coli and Related Bacteria, Cold Spring Harbor Press (1992)). 20 . Tomudex Inhibition of NB1011 Cytotoxicity. MCF7-TDX were transferred to a 384 well assay plate at 500 cells in 25 pL complete medium per well. After 24 hours (day 0), 25 pL complete medium containing a combination of NB 1011 in doubling serial dilutions from 1mM and tomudex at discrete concentrations (0,1,10,100,1000 nM) were added in duplicate. Drug exposure time 25 was 120 hours (day 5) after which growth inhibition was measured with alamarBlue as described above in Growth Inhibition Studies. J. Enzyme Preparation. Cloned human thymidylate synthase plasmid pBCHTS was subcloned into E. coli. BL21 (DE3)/pET-28a(+) (Novagen) using the 30 NdeI iSacl 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 50 WO 01/07087 PCTIUSOO/19844 chromatography on a Ni 2 + His Bind metal chelation resin (Novagen). The column Ni 2 + His Bind metal chelation column was washed with 20 mM Tris pH 7.9, 5 mM imidazole, 0.5 M NaCl; thymidylate synthase activity was eluted with 20 mM Tris pH 7.9, 60 mM imidazole, 0.5 M NaCl. 5 K. Enzyme Assays and Kinetic Measurements. Thymidylate synthase assays were done in 96 well Costar UV transparent plates in a reaction volume of 200 pl, consisting of 40 mM Tris pH 7.5, 25 mM MgCl 2 , 1 mM EDTA, 25 mM mercaptoethanol, 125 M dUMP, and 65 pM N5, N1O-methylene tetrahydrofolate 10 indicated. Tetrahydrofolate stock solutions were prepared by dissolving tetrahydrofolic acid (Sigma) directly into 0.2 M Tris pH 7.5, 0.5 M-mercaptoethanol; stock solutions were stored at -80 *C. N5, N1O-methylene tetrahydrofolate was prepared by adding 12 p1 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 15 tetrahydrofolate was kept on ice and used within 2 hours of preparation. Conversion of BVdUMP to fluorescent product(s) by thymidylate synthase was measured in 200 thymidylate synthase reactions containing 125 M 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 20 measured with a Tecan Spectrafluor Plus fluorimeter. Enzyme kinetic constants (Km and V.) were determined for the human thymidylate synthase substrates dUMP and BVdUMP using the enzyme assay conditions described above. The initial rates of the enzyme reactions was determined by measuring the increase in A 340 for the reaction with dUMP, and decrease in A 29 4 25 for the reaction with BVdUMP. The catalytic efficiency of the enzyme (KaIK.) was calculated from the kinetic constants K. and V. L. Liquid Chromatography/Mass Spectroscopy. Cells were washed three times with PBS at room temperature, then subjected to freeze/thaw lysis in 5 ml PBS. 30 Cell extracts were centrifuged for 10 minutes at 1OKRPM, then adsorbed to Sep-Pak

C

1 , and washed with 10 ml PBS. BVdUMP was eluted with 1 ml distilled water. 51 WO 01/07087 PCT/USOO/19844 LC/MS samples were analyzed by reverse phase chromatography on a C,, 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. 5 M. Reversal of Resistance. The origin and characteristics of the human breast cancer MCF7 TDX cell line have been previously described (Drake et al. (1996) Biochem. Pharmcol. 51(10):1349-1355). 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 ptM. A resistant subline was selected for 10 resistance to NB 1011 by continuous exposure of the parental MCF7 TDX cell line to medium supplemented without TDX but with 50 pLM NB 1011, a concentration approximately 16 times higher than the IC 0 for NB 1011 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 IC 50 for 5-FU, 15 TDX, and NB 1011 were determined for the resultant MCF7 TDX/101 1 cell line as described in "Materials and Methods" by western blot and the alamarBlue cytotoxicity assay, respectively. II. EXPERIMENTAL 20 A. In vitro Reaction of BVdUMP with Human Thymidylate Synthase 1. The cell-free processing of BVdUMP by rHuTS generates fluorescent product(s). The cell-free processing of BVdUMP by L. casei TS has been shown to create potentially reactive intermediates (Barr et al. (1983) supra). For this reason it 25 has been thought that processing of BVdUMP by TS leads to irreversible inactivation of human TS (Balzarini (1987) Mol. Pharmacol. 32(3):410-6). The cell-based experiments by DeClercq, Balzarini and colleagues (Balzarini (1987) supra; Balzarini (1993) J. Biol. Chem. 268(a):6332-7; Balzarini (1995) FEBS Lett 373(1):41-4) support the concept that, once BVDU is converted to the 30 monophosphate in cells (e.g. via herpes virus thymidine kinase), then it binds to and inactivates the HuTS enzyme during processing. However, the actual reaction of 52 WO 01/07087 PCT/USOO/19844 human TS with BVdUMP has never been adequately characterized. Santi and colleagues (Barr et al. (1983) supra) 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) 5 supra); Balzarini (1993) supra; Balzarini (1995) supra). Because of Applicant's interest in generating therapeutic substrates that can be specifically activated by TS, 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 10 fluorescent product(s) (Figure 2). 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 (see below). This result is surprising because previous results supported the idea that TS 15 reaction with BVdUMP should inactivate the human TS enzyme (Balzarini et al. (1987), (1993) supra and Balzarini et al. (1995) supra). 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 NB 1011 to the free nucleotide 20 monophosphate inside the cell. This issue is addressed in more detail below. 2. Comparative reaction kinetics of dUMP and BVdUMP with rHuTS. Previously reported work by Barr et al., utilizing the L. casei TS (Balzarini (1995) supra; Balzarini (1987) supra; and Balzarini (1993) supra) using cells and 25 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. Competitive inhibition is most consistent with a reaction in which BVdUMP 30 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 53 WO 01/07087 PCT/USOO/19844 that may occur over a period of time longer than that in which the kinetics were performed (Figure 4). 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 5 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. 10 3. Characterization of BVdUMP reaction with TS: Cofactors and Inhibitors The best characterized reaction of TS is the conversion of dUMP to dTMP. This reaction involves the transfer of a methylene group from N5,N1O-methylene tetrahydrofolate (THF) to the C-5 position of dUMP (Carreras CW (1995) supra). 15 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 et 20 al. (1996) Biochem. Pharmacol. 51(10):1349-1355; Touroutoglou and Pazdur (1996) Clin. Cancer Res. 2(2):227-243). 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 1) have shown that, similarly to the case of dUMP, 5F-dUMP can 25 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) supra), THF is not required for the conversion of BVdUMP to fluorescent product(s). In addition, the data shown in Table 1 also demonstrate that THF stimulates the 30 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 54 WO 01/07087 PCT/USOO/19844 reaction (Barr et al. (1983) supra), and illustrates a potentially important possibility that cofactors, or cofactor agonists, like leucovorin , could modulate the reaction of BVdUMP with human TS. Analysis of the Michaelis-Menton kinetics of this reaction showed that 5 inhibition of BVdUMP by dUMP fits the expected form for competitive inhibition, consistent with both nucleotides behaving as substrates for rHuTS. As shown in Table 2, infra, previously reported data with the L. casei TS indicated that BVdUMP is 385 times less efficient a substrate as dUMP (Barr et al. (1983) supra and Santi (1980) supra). The experiments reported herein have shown 10 that this situation is quite different with the human enzyme. For rHuTS the relative catalytic efficiency of dUMP compared with BVdUMP is 60x. 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 NB 1011 to be an effective 15 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 greater than 6.4-fold improved efficiency of conversion of BVdUMP, is an important factor enabling utility of NB 1011 as a selective anti-infective. The increased efficiency of BVdUMP utilization by the human enzyme as compared to the L. casei 20 enzyme also establishes that species specific substrates are possible and can be designed. These substrates are applied in the treatment of infections (either viral or cell-mediated) in which the infectious agent expresses a TS enzyme distinct from that encoded by the host. Examples of viral infections that can be treated using this approach include hepatitis virus, herpesviruses, or other viruses that express their 25 own TS enzyme; and bacterial infections, especially drug resistant bacteria like multiply resistant staphyloccoccus aureus, and other infectious agents for example Pneumocystis carnii and Plasmodium falciparum. 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) Biochemistry 30 38(5):1607-17 and Costi et al. (1999) J. Med. Chem. 42(12):2112-2124). Differences in specificity relating to the active site of TS, which is composed of the 55 WO 01/07087 PCT/USOO/19844 most highly conserved regions of the protein (Carreras (1995) supra) is surprising and has not been reported previously. Products of the cell-free enzymatic reaction of rHuTS with BVdUMP were analyzed by mass spectroscopy. The molecular structures I and II shown in Figure 5 5 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 NB101 1. In addition, this information could be used to design novel chemotherapeutics, since the products of the TS-BVdUMP reaction 10 could, themselves, be potentially used as chemotherapeutics. 4. NB 1011 is converted to the monophosphate in tumor cells NB 1011 is converted from the phosphoramidate to the monophosphate form in cells, as a prerequisite for binding to TS. The proposed pathway for unmasking the 15 phosphate of NB 1011, its binding to TS and conversion to toxic metabolites is shown in Figure 5. To determine whether this crucial step in conversion was taking place advantage was taken of an unusual property of the bromine atom, ie. that it exists in nature in two equally abundant isotopic forms. This situation allows detection of the 20 bromine containing monophosphate by focusing the mass spectrometry analysis on the predicted mass ions of BVdUMP (411 and 413 daltons). H630 RIO tumor cells (which express high levels of TS) were incubated with 1 OOuM NB 1011. Extracts of treated cell lysates were prepared as described in Materials and Methods, above. Detection using mass spectroscopy, following an initial purification with liquid 25 chromatography relied upon formation of the unprotected nucleotide mass ions of BVdUMP which have identical retention times on reverse phase chromatography. These results (Figure 6) are consistent with NB 1011 following the first step in the activation pathway. 30 B. Characterization of the cytotoxic activity of NB1011. 1. The tumor/normal cell screen. 56 WO 01/07087 PCTIUSOO/19844 As an initial step in characterizing the biological activity of NB 1011, a large series of normal and tumor cell types were tested in the alamar blue assay for sensitivity to both NB 1011 and 5-fluorouracil. Assays were carried out as described in Methods, above. Therapeutic index is 5 calculated as the ratio of the average IC 50 for normal cells to the average IC 50 for tumor cells. All assays were done at least three times. These data show that NB10 11 has met the primary design goal for TS ECTA compounds, i.e. increased potency on tumor cells vs. normal cell types. Overall, NB10 11 is about 2-fold more cytotoxic to tumor cells vs. normal cells, while 5FU is 10 3-fold more toxic to normal cells than it is to tumor cells. The total benefit of NB10 11 is therefore (2) x (3) = 6-fold improvement in therapeutic index for NB10 11 as compared with 5FU. 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 15 cancer drug discovery. For instance, screening of new candidate compounds on normal cell types is not part of the National Cancer Institute's screening procedure (Curt (1996) Oncologist 1 (3):II-III). 2. NB10 11 does not inactivate TS in vivo 20 The results described above indicate that BVdUMP, generated intracellularly from NB10 11, 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-('H) deoxyuridine is added to cell culture medium 25 and the release of tritiated water is monitored (Carreras et al. (1995) supra, and Roberts (1966) Biochem. 5(11) 3546-3548). Figure 7 shows that the presence of NB101 1 in cell culture media reduces the rate at which [ 3

H]

2 0 is released from 5-[ 3 H]dUMP. In order to determine whether this is the result of irreversible inhibition of TS, NB101 1-treated cells were allowed to briefly recover in fresh culture media, 30 then assayed for TS activity. Cells that have been allowed to recover in culture media lacking NB 1011 have the same level of TS activity as untreated cells. This 57 WO 01/07087 PCTUSOO/19844 result supports the proposal that NB 1011 does not irreversibly inactivate the TS enzyme following intracellular processing. An additional approach was taken to understanding whether NB 1011 might interfere with cell growth primarily by inactivating TS. This approach is based upon 5 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, 10 and thus continue DNA synthesis. Other pathways for use of exogenous thymidine have also been described If an important mechanism for NB 1011 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 15 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) Cancer Res. 58:2737-2740) with or without 1OuM thymidine, except that the alamar blue assay (see Materials and Methods) was employed to determine 20 cytotoxicity. The results showed a 15-fold rescue from Tomudex (IC 50 change from 6.5nM to 95 nM), a greater than 590-fold rescue from 5FudR (from an IC, 0 of less than 0.01 gM to greater than 5.9 piM), and a slight decrease in the absence of thymidine to 223 ptM in the presence of 10 gM thymidine. 25 3. Relationship between TS level and NB1011-mediated cytotoxicity on tumor cell lines. Confirmation that TS participates in NB101 1-mediated cytotoxicity was established using several approaches: 1). the activity of NB 1011 was examined on normal colon cells vs. high TS expressing, 5FU-resistant, tumor cells; 2). transfection 30 of TS into a tumor cell background, and generating clonal derivatives which differ 58 WO 01/07087 PCT/USOO/19844 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. In the initial analysis, of NB 1011 and 5FUdR-mediated cytotoxicity were compared on the CCD18co normal colon epithelial cell type and H630R10, 5FU 5 resistant colon tumor cell line (Copur S. et al. (1995) Biochem Pharm. 49(10):1419 1426). 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 10 Table 4. 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, ie. its' toxicity to normal tissue. Such a negative therapeutic index has also been reported 15 for doxorubicin (Smith et al. (1985) J. Natl. Cancer Inst. 74(2):341-7 and Smith et al. (1990) Cancer Res. 50(10):2943-2948). In contrast to 5FUdR, however, NB1011 has more than an 11-fold improved activity on drug-resistant H630R10 cells (IC 50 = 216.7 gM) vs. normal colon epithelial cells (ICo greater than 2500 gM). This result suggests that: 1). activity of NB 1011 is more pronounced on high TS expressing 20 tumor cells; and 2). a total improvement in therapeutic index of (18) x (11) = 198 fold is achievable using TS ECTA compounds vs. 5FUdR. 4. Overexpression of TS in HT1080 tumor cells enhances their sensitivity to NB1011. 25 Activation of NB 1011 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) Biochem. Cell Biol. 76(5):761-70). Similarly, processing from the 30 phosphoramidat+e to the monophosphate employs poorly defined mechanisms (Abraham et al. (1996) J. Med. Chem. 8:39(23):4589-4575. 59 WO 01/07087 PCTUSOO/19844 These results are particularly significant because they demonstrate, in a fairly uniform genetic background, that increasing TS levels predicts enhanced sensitivity to NB 1011. In addition, the data also show that increasing TS levels predicts resistance to fluoropyrimidines, a result consistent with reports in the literature 5 (Copur et al. (1995) Bioche. Pharm. 49(10):1419-1426 and Banerjee et al. (1998) Cancer Res. 58:4292-4296). 5. Inhibitors of NB 1011-mediated cytotoxicity. Tomudex is a chemotherapeutic that acts primarily via inhibition of TS. If 10 NB10 11 exerts cytotoxicity via the TS enzyme, then inhibition of TS with Tomudex should decrease NB 1011-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 NB 1011 in the presence of increasing concentrations of TDX. 15 Cells were plated and exposed to indicated concentrations of compound(s) as described in the Materials and Methods, above. The data show that blockade of TS using the specific inhibitor Tomudex, results in up to about 25-fold inhibition of NB 1011-mediated cytotoxicity. These results support the concept that activity of NB 1011 results from its metabolism by 20 TS. To further characterize the intracellular metabolism of NB 1011, 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 25 hypothesized that if the fluorescent products are related to the cytotoxic effects of NB10 11, 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 3iM LV, NB10 11 activity on the H630R10 cell line was diminished by more than 90%, compared to NB 1011 alone, as determined in the alamar blue assay. 30 The fact that NB 1011 activity is abolished by LV, which supplements intracellular reduced folate pools, suggests that NB10 11 may work in part by diminishing these 60 WO 01/07087 PCT/USOO/19844 pools. Alternatively, LV (or a metabolite) could directly impact the metabolism of BVdUMP by interfering with its interaction with TS. 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 5 +/ Methotrexate (MTX), LV or Tomudex (TDX). The results (Table 6) 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 10 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. The results described above, demonstrating inhibition of the BVdUMP + TS 15 reaction by LV, MTX and TDX, and further, that this effect is more pronounced in the presence of cofactor (THF), suggests that NB10 11 activity may be modulated by other chemotherapeutics. Importantly, rescue of NB 1011-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 20 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) supra),include 25 6-mercaptopurine, thioguanine and 2'-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 NB1011. 30 C. Pharmacogenomics of TS ECTA 1. Comparison of TS and HER2. 61 WO 01/07087 PCT/USOO/19844 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 5 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 10 (Shepard et al. (1991) J. Nat. Cancer Inst. 74(2):341-347 and Lewis (1993) Cancer Immural. Immunother. 37(4):255-63). The cell line results shown in Figure 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 15 for both TS and HER2/NEU overexpressing patients (Johnston et al. (1994) J. Clin. Oncol. 12:2640-2647). 2. NB 1011 is active against 5FU and Tomudex-resistant colon and breast tumor cell lines. 20 Because NB 1011 has promising anticancer activity, it is important to compare it with other chemotherapeutics with respect to safety. The utility of NB 1011 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. 25 The results show that while NB10 11 is more than 10-fold less toxic than TDX vs. normal cells (CCD1 8co), 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 NB 1011 to drug resistant 30 cancers that overexpress TS. 62 WO 01/07087 PCT/USOO/19844 3. NB 1011 is more dependent upon TS protein levels than TS activity as measured by tritium release from dUMP- 3 H. 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) J. 5 Clin. Oncol. 12:2640-2647; Johnston and Allegra (1995) Cancer Res. 55:1407-1412) but RT-PCR, 5FdUMP-binding and tritium release (van Laar (1996) Clin Cancer Res 2(8):1327-33; van Triest (1999) Clin. Cancer. Res. 5(3):643-54; Jackman (1995) Ann. Oncol. 6(9):871-81; Larsson (1996) Acta. Oncol. 35(4):469-72; Komaki (1995) Breast Cancer Res. Treat. 35(2):157-62; and Mulder (1994) Anticancer Res. 10 14(6B):2677-80) have also been measured in various studies. For characterization of cell lines Applicants have focused on western blotting and tritium release from 3

H

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. 15 Cells were grown and characterized as described in Methods. 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. Analysis of the data presented in Table 7 indicates that there is a closer 20 relationship between TS protein level and sensitivity to NB 1011 than between TS activity (tritium release from 'H-dUMP) and NB 1011 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, 25 the parental cell lines often have comparable, or greater, TS activity and are less sensitive to NB 1011-mediated cytotoxicity. While these results could occur via a number of different mechanisms, or combinations of mechanisms, it is likely that 3 H-dUMP conversion to dTMP (and accompanying tritium release) may be subject to limitation by some component, 30 perhaps cofactor availability. However, since conversion of BVdUMP is not dependent upon cofactor, then its reaction with TS can continue even in a cellular 63 WO 01/07087 PCT/USOO/19844 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. 5 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. 64 WO 01/07087 PCTIUSO0/19844 Table 1. Comparison of Prodrug Strategies Technology Acronym Description Key References Metabolic activation None Conversion of folate analogs to Mead et al. toxins via 'lethal synthesis.' (1966) supra. Antibody directed ADEPT Antibody-enzyme complex Syrigos and prodrug therapy binds to tumor selective antigen. Epenetos (1999) Prodrug is administered and Anticancer Res. activated when it encounters the 19(1A):605-13 antibody bound enzyme. Gene directed prodrug ADEPT Gene encoding activating Connors and therapy enzyme is transduced into large t Knox (1995) cells Stem Cells 13:501-511 Enzyme directed prodrug EDEPT Prodrugs are administered which Breistol et al. therapy are activated by extracellular (1998) enzymes present a high levels Eur. J. Cancer only at tumor site. 34(19):1602 1606 and Bosslet et al. (1998) Cancer Res. 58:1195-1201. Tumor Activated 'TAC' Prodrugs activated by Morgan et al. Cytotoxin glutathione-s-transferase (1998) supra Enzyme catalyzed ECTA Prodrugs are activated by As disclosed therapeutic agents enzymes overexpressed as a herein result of tumor suppressor gene loss and in vivo selection by chemotherapy 5 Table 2. Comparison of Kenetic Parameters of Bacterial and rHuTS Kinetic Constants Lactobacillus casei rHuTS DUMP Km 3.0gM 7.7gM K. 6.4s-' 0.2s' K.Km 2.1 x 10 6 M-'s' 2.6 x 10 4 M-'s K;(of BVdUMP) 0.6pM 4.5gM BvdUMP Km 3.3gM 16gM K.. 0.018s-1 0.0067s' KzavKm 5.6 x 10 3 M-'s-' 4.2 x 10 3 M's-' K, (of dUMP) 2.0gM 17.5pM Relative catalytic 385-fold 60-fold efficiency (dUMP vs BVdUMP) 65 WO 01/07087 PCT/USOO/19844 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 Methods, above. 5 Table 3. Inhibition of rHuTS reactions by Tomudex and 5-FdUMP Substrate + Cofactor No Inhibitor Tomusdex (500 nM) 5-FdUMP (500 nM) 109+16 67+3 44+2 BvdUMP + THF RFU/min (61%) (40%) (100%) 75+11 34+3 93+13 BvdUMP - THF (100%) (45%) (129%) 1500+20 690+40 290+70 dUMP + THF nmoles/min (46%) (100%) (19%) 10 Inhibition of rHuTS reactions by Tomudex and 5-FdUMP. Thymidylate synthase reactions containing enzyme inhibitors or cofactor were incubated at 30 0 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 A 340 for the 15 dUMP reaction. 66 WO 01/07087 PCT/USOO/19844 Table 4 Cytotoxicity of NB1011 vs. 5FU on Normal and Tumor Cell Strains Normal Cells IC 50 (M) Tumor Cells 1C 50 (M) NB1O.L 5FU 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 COL0320 (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 NRA (Brain) 839 0.9 MCF7 (Breast) 141 1.0 NHOST (Bone) 642 4.7 MDAMB (Breast 365 5.0 361 NPRSC (Prostat 369 1.7 MDAMB (Breast) 172 4.4 e) 468 NHEPF (Liver) 2085 1.7 SW527 (Breast) 431 4.3 NCI H520 (Lung) 135 0.6 Average 561 1.6 SKLU1 (Lung)' 270 7.9 SOAS2 (Bone) 232 1.4 PANCI (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 NBIO1.1 5FU Therapeutic index (N/T) 1.95 0.30 5 Cells were analyzed for response to either NB 1011 or 5FU in the alamar blue 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 IC 50 (mean of all cell types) to ICO (mean of all tumor cell lines). 10 67 WO 01/07087 PCT/USOO/19844 Table 5 NB1011 cytotoxicity on cell lines engineered to express HuTS Cell Line TS Level

IC

50 NB1011 FUDR 5-FU TDX (pM) (pM) (pM) (M) 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 5 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 10 to that of cell strain CCD18co. Table 6 Tomudex Inhibits NB1011 Mediated Cytotoxicity 15 [Tomudex] OnM lnM lOnM 100nM 1000nM (nM) NB1011IC 50 5.7 25.5 87.7 140.3 103.0 (M) Fold Protection 1 4.5x 15.4x 24.6x 18.1x The Tomudex rescue assay (alamar blue) was done with TDX-resistant MCF7 breast tumor cells as described in Methods. "Fold Protection" was calculated as the ratio of IC 50 with and 20 without added TDX. 68 WO 01/07087 PCT/USOO/19844 Table 7 Impact of Folate Inhibitors Inhibitor BVdUMP, 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% 5 Cell-free assays using rHuTS, the appropriate substrate and other components were combined as described in Methods. MTX (140gM), LV (140 M) or TDX (5pM) 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. 10 Table 8 NB1011 activity is more associated with TS protein than with tritium release Cell Line Drug TS Protein Tritium NB1011 Selection Release IC 50 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 15 69 WO 01/07087 PCT/USOO/19844 Table 9 MDF7 TDX cells selected for resistance to NB1011 are more sensitive to 5-Fluorouracil and Tomudex 5 ICo (micromolar)* Relative TS 5- FU Tomudex NB1011 Protein Level MCF7 10- .026- 291- lx MCF7 TDX 32 >10 2 lix MCF7 TDX/1011 2 .041 240 4X * = as determined by the alamar blue assay described in Materials and Methods TDX = Tomudex; 1011 = NB 1011 10 The preceding discussion and examples are intended merely to illustrate the invention of the claims. As is apparent to one of skill in the art, various modifications can be made to the examples and claimswithout departing from the spirit and scope of this invention. 70

Claims (16)

1. 2. The method of claim 1, wherein the substrate prodrug is an L or D compound of the structure: 0 OH 0 ~54NH or or R1 11R N 0 N 0 N OH Q Q Q 15 wherein R, 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 the activating enzyme, and which upon release from the pyrimidine ring by the activating enzyme, 20 has the ability to inhibit the proliferation of the agent or the cell; and wherein Q is a moiety selected from the group consisting of a sugar, a carbocylic, an acyclic compound and masked phosphate or phosphoramidate derivatives thereof. 71 WO 01/07087 PCT/USOO/19844
2. 3. The method of claim 1, wherein the compound has the structure: I. or II. or III. H 2 N R1 O NH NNN-.. N N N / N/ N/N Q Q F Q or IV. 0 N O = R1 N Q wherein: 5 R' is a moiety of the formula: R2n R3 R4 with the proviso that in compound I, n can be 0. R 2 is a divalent electron conduit moiety selected from the group consisting of: 10 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; 15 R2 is a divalent spacer moiety selected from the group consisting of: 72 WO 01/07087 PCTUSOO/19844 -CH2 -CHR 5 - -C(R5)2 -- O- -S- -NH- and -- NRs_ CH 2 0- CH 2 S- -NN O O S -CH20 C CH2S- CH20- C S - -CH2 R 5 may be the same or different and is independently a linear or branched alkyl group 5 having from 1 to 10 carbon atoms, or a cycloalkyl group having from 3 to 10 carbon atoms, or a halogen (F, Cl, Br, I); n is an integer from 0 to 10; m is 0 or 1; R 4 is a toxophore moiety selected from the group consisting of: 10 x RBO R80 CO 2 R9 -N -Z F -z Rio x O O -0 R0 73 WO 01/07087 PCT/USOO/19844 x -- Z-P-N -Z-P--N N \NH 2 0 -0-NH-C-NH 2 CH 2 C=O NH OH I I -Z-CH 2 -CH--CH-CH=CH-(CH 2 ) 12 CH 3 0 5 -Z-CF 2 -CH 2 -CHF-C-OH 0 -Z-CF 2 -CHF-CH 2 -- C--OH 0 S II -Z-CF 2 -CH 2 -C-OH CH 3 0 I II -Z-CF 2 -CH--C-OH Y -Z-CF 2 - -Y Y .0 -Z-CF 2 -CH 2 -CH 2 -NO 2 and -Z\,/NNO2 R 8 and R! are lower alkyls and R' is H or CH 3 X is -Cl, -Br, -I, or other potent leaving group, with the proviso that 5 when R' is -H, and m is zero, then R 4 is not a halogen or when m is zero and n is zero, then R 4 is not a halogen; Y is independently -H or -F; Z is independently -0- or -S-; Q is a moiety selected from the group consisting of: 74 WO 01/07087 PCTUSOO/19844 R7-O R7-O RI-O 0 S 6 R R R 6 6 R 7 -CH 2 R 7 -O and 6 6 RS is independently -H, -OH, -OC(=O)CH 3 , F, or other protected 5 hydroxyl group; and, R 7 is hydrogen, a phosphate group, a phosphodiester group, or a phosphoramidate group; and wherein said compound may be in any enantiomeric, diasteriomeric, or stereoisomeric form, including, D-form, L-form, a-anomeric form, and 10 p-anomeric form.
3. 4. The method of claim 1, wherein the infectious agent is selected from the group consisting of a bacteria, a parasite, a virus, and a yeast.
4. 5. The method of any of claims 1 to 4, wherein the activating enzyme is thymidylate synthase. 15 6. The method of any of claims 1 to 4, wherein the activating enzyme is selected from the group consisting of thymidylate synthase, beta-lactamase, viral proteases, dihydrofolate reductase or viral reverse transcriptase.
5. 7. The method of any of claims 1 to 4, wherein the contacting is in vitro, ex vivo or in vivo. 20 8. The method of claim 1, wherein the contacting is in vivo.
6. 9. The method of any of claims 1 to 4, further comprising contacting the agent or the cell with an effective amount of a second agent that inhibits proliferation of the infectious agent.
7. 10. A method for screening for prodrugs selectively converted to a toxin by an activating enzyme expressed by an infectious agent, wherein the prodrug is not inactivated by the 25 prodrug, comprising contacting a candidate prodrug with the infectious agent or a cell 75 WO 01/07087 PCTIUS0O/19844 infected with the infectious agent that expresses the activating enzyme and assaying for inhibition of proliferation of the infectious agent or the cell infected by the infectious agent.
8. 11. The method of claim 10, further comprising contacting a normal, unifected cell with the candidate prodrug and assaying for inhibition of growth or proliferation fo the normal cell 5 by the candidate prodrug.
9. 12. The method of claim 10, wherein the activating enzyme is thymidylate synthase expressed by the infectious agent.
10. 13. The method of any of claims 1 to 4, wherein the activating enzyme is selected from the group consisting of thymidylate synthase, beta-lactamase, viral proteases, dihydrofolate 10 reductase or viral reverse transcriptase.
11. 14. The method of any of claims claims 10 to 13, wherein the assay comprises analysis of intracellular metabolites of the candidate prodrug by mass spectrometry.
12. 15. The method of any of claims 10 to 13, wherein the candidate agent comprises a detectable agent. 15 16. The method of claim 15, wherein the detectable agent is a fluorescent marker.
13. 17. The method of claims 1 or 10, wherein the activating enzyme is wild-type enzyme.
14. 18. The method of claims 1 or 10, wherein the activating enzyme is a mutated version of the enzyme.
15. 19. The method of claim 18, wherein the activating enzyme is a mutated version that is 20 resistant to a therapy.
16. 20. The method of claim 18, wherein the activating enzyme is a mutated version of HIV- 1 reverse transcriptase that exhibits resistant to 3'-axido-3'-deoxythymidine (AZT). 76