WO2000036099A1

WO2000036099A1 - New medical use of gene and vector encoding a multisubstrate deoxyribonucleosidase

Info

Publication number: WO2000036099A1
Application number: PCT/SE1999/002314
Authority: WO
Inventors: Anna Karlsson; Magnus Johansson
Original assignee: Biovici
Priority date: 1998-12-11
Filing date: 1999-12-10
Publication date: 2000-06-22
Also published as: AU778376B2; DE69924003D1; DE69924003T2; ATE290071T1; SE9804298D0; EP1137764A1; US6582947B1; EP1137764B1; ES2239475T3; JP2002532090A; AU2018500A

Abstract

By inserting a DNA or RNA sequence comprising a subsequence showing a homology of at least 60 %, preferably at least 80 %, and most preferably at least 90 % of the DNA sequence of SEQ.ID.NO.1 into a cell, that cell will obtain a broad specificity for changing nucleoside analog prodrugs to active drugs by phosphorylation. Likewise this changement will occur at a high catalytic rate. Preferably the DNA sequence is inserted into the cell by transformation with a suitable virus or another suitable vector. Such viruses and vectors also constitute a part of the present invention.

Description

NEW MEDICAL USE OF GENE AND VECTOR ENCODING A MULTISUBSTRATE DEOXYRIBONUCLEOSIDASE

The present invention relates to a gene encoding a multisubs rate deoxyribonucleo-. side kinase of Drosophila melanogaster, and vectors and recombinant viruses con- taining said gene, as well as pharmaceutical compositions comprising such a vector and/or a virus. It also relates to production of said multisubstrate deoxyribonucleoside kinase and a process for phosphorylating nucleosides and nucleoside analogs.

Technical background

Nucleoside analogs are commonly used in treatment of virus infections and cancer. The therapeutic nucleoside analogs are inactive prodrugs that are dependent on in- tracellular phosphorylation for pharmacological activity. The majority of nucleoside analogs in clinical use are phosphorylated by deoxyribonucleoside kinases (Arner et al., (1995) Pharmac. Ther. 61, 155-186). These enzymes are intensively studied since they catalyze the rate limiting step in the pharmacological activation of the nucleoside analogs. There are four major deoxyribonucleoside kinases in human cells: deoxycytidine kinase (dCK), deoxyguanosine kinase (dGK), thymidine kinase 1 (TK1) and thymidine kinase 2 (TK2) (1995) Pharmac. Ther. 61, 155-186). DCK, dGK and TK2 are closely sequence-related enzymes whereas TK1 has low similarity with the other deoxyribonucleoside kinases (Johansson et al., (1996) Proc. Natl. Acad. Set USA. 93, 7258-7262; Johansson et al., (1997) J. Biol. Chem. 272, 8454- 8458; Chottiner et al., ( 1991) Proc. Natl. Acad. Sci. USA. 88, 1531-1535). The human deoxyribonucleoside kinases have distinct substrate specificities in regard to phosphorylation of both deoxyribonucleosides as well as nucleoside analogs.

WO95/14102 discloses recombinant adenoviruses comprising a DNA sequence coding for herpes simplex thymidine kinase under the control of a heterologous expression signal that can be associated with certain form of cancer. These recombi- nant viruses are then used to infect tumours of such a cancer. As a result, thymidine kinase is expressed in the cancer tumour. Subsequently, a therapeutic nucleoside analog prodmg, such as acyclovir (ACN, 9-(hydroxy ethoxymethyl)-guanine) and gancyclovir (GCN), is administred. Due to the enhanced expression of thymidine kinase in the tumor, the prodmg is only converted to the active form in the tumour, resulting in death of the tumour. However, the ability of thymidine kinase to phosphorylate potentially useful nucleoside analog prodrugs is limited.

W097/29196 also relates to recombinant adenoviruses comprising a DΝA sequence encoding herpes simplex thymidine kinase (HSN-TK). The kinase is mutated in or- der to increase the phosphorylation rate and to broaden the substrate specificity.

WO96/21724 discloses recombinant virus particles, such as recombinant retroviru- ses, contaning RΝA encoding human deoxycytidine kinase 2. These virus particles are used for the same purposes as the vims particles described in W097/29196 and WO95/14102, but the enzyme has another substrate specificity.

Accordingly, it is known to insert a "suicide" nucleic acid sequence, such as a nucleic acid sequence encoding a nucleoside kinase, into the genome of a vims or some other kind of vector capable of transferring nucleic acid sequences into tumour cells of a human or animal patient, and subsequently administer a therapeutic nucleoside analog prodmg. Known nucleoside kinases have a limited substrate specificity. HSV-TK, which is described in the above cited WO97/29196 and WO95/14102, cannot phosphorylate 2',2'-difluorodeoxycytidine, 2-chloro-2'-deoxyadenosine, 1- β-D-arabinofuranosylcytosine, 2',3 '-dideoxycytidine and 2'-deoxy-3-thiacytidine. Also deoxyguanosine kinase disclosed in the above cited W096/21724 has been shown to have a limited substiate specificity. This enzyme does not phosphorylate ), (E)-5-(2-bromovinyl)-2'-deoxyuridine, (E)-5-(2-bromovinyl)- 1-β-D- arabinofuranosyl-uracil, 2',2'-difluoiOdeoxycytidine, 1-β-D- arabinofuranosylcytosine, 2',3'-dideoxycytidine or 3TC. Consequently, there is a need for a DNA sequence encoding a nucleotide kinase having a broad specificity and a high catalytic rate of phosphorylation, in order to obtain flexibility regarding the use possible nucleoside analog prodrugs, and in order to reduce the dose amount required to obtain a sufficient therapeutic effect, resulting in a minimized risk for undesired side effects in the patient.

When comercially producing phosphorylated nucleoside analogs, there is also a need for a nucleotide kinase having a broad specificity and a high catalytic rate of phosphorylation.

Summary of the invention

It has now turned out that by inserting a DNA or RNA sequence comprising a subsequence showing a homology of at least 60 %, preferably at least 80 % , and most preferably at least 90 % of the DNA sequence of SEQ.ID.NO.1 into a cell, that cell will obtain a broad specificity for changing nucleoside analog prodmgs to active drugs by phosphorylation. Likewise this changement will occur at a high catalytic rate. Preferably the DNA sequence is inserted into the cell by transformation with a suitable vims or another suitable vector. Such viruses and vectors also constitute a part of the present invention.

Detailed description ofthe invention

A recent report (Munch-Petersen et al, (1998) J. Biol. Chem. 273, 3926-3931) shows that cell lines from the fruit fly Drosophila melanogaster contains only a single deoxyribonucleoside kinase. The report does neither reveal anything about the aminoacid sequence of the enzyme, nor about any DNA sequence encoding it. This enzyme, namned -dNK, is in contrast to the human deoxyribonucleoside kinases a multisubstrate enzyme. Although pyrimidine nucleosides are the preferred substrates of this enzyme, it catalyzes phosphorylation of both pyrimidine and puri- ne deoxyribonucleosides. The enzyme also efficiently phosphorylates several anti- viral and anti-cancer nucleoside analogs. The catalytic rates of deoxyribonucleoside and nucleoside analog phosphorylation are, depending on the substrate, 10- to 100- folds higher than the maximal catalytic rates reported for the mammalian enzymes. The broad substrate specificity and high catalytic rate in phosphorylation of deoxy- ribonucleosides render -dNK unique among the family members of deoxyribonucleoside kinases.

Accordingly, an object of the present invention is to provide a nucleic acid sequence encoding a multisubstrate deoxyribonucleoside kinase showing at least 70% homo- logy, preferably at least 90% homology with the amino acid sequence of

SEQ.ID.NO.2. Depending on the vector into which the nucleic acid sequence is intended to be inserted, the nucleic acid sequence can be a DNA sequence or a RNA sequence. The DNA may be cDNA, genomic DNA and synthetic DNA. It may also be double-stranded or single-stranded, and if single-stranded it may be the coding strand or the anti-sense strand. SEQ.ID.NO.1 discloses a cDNA sequence encoding the multisubstrate deoxyribonucleoside kinase. However, because of the fact that the genetic code is degenerated, other nucleic acid sequences encoding the same enzyme can be used in connection to the present invention.

Another object of the present invention is to provide a nucleic acid sequence comprising a disease-associated promoter and/or signal sequence operatively linked to a nucleic acid subsequence encoding a multisubstrate deoxyribonucleoside kinase showing at least 70% homology, preferably at least 90% homology with the amino acid sequence of SEQ.ID.NO.2. Depending on the vector into which the nucleic acid sequence is intended to be inserted, the nucleic acid sequence can be a DNA sequence or a RNA sequence. It is also possible to inject an expression cassette comprising such a DNA sequence directly into cells that are to be killed.

Yet another object of the present invention is to provide a vector, such as a plasmid, cosmid or a bacteriophage, which vector contains a DNA sequence encoding a multisubstrate deoxyribonucleoside kinase showing at least 70% homology, preferably at least 90% homology with the amino acid sequence of SEQ.ID.NO.2. Optionally, the vector also contains a disease-associated promoter and/or signal sequence operatively linked to the DNA sequence encoding a multisubstrate deoxyribonucleoside kinase. The invention also relates to host cells including these vectors.

Host cells are genetically engineered (transduced, transformed or transfected) with the vectors of this invention, which may be, for example, a cloning vector or an expression vector. The vector may be, for example, in the form of a plasmid, a viral particle, a phage, etc. The engineered host cells can be cultured in conventional nu- trient media modified as appropriate for activating promoters, selecting transfor- mants or amplifying the genes encoding the multisubstrate deoxyribonucleoside kinase. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent for the skilled artisan.

The polynucleotides of the present invention may be employed for producing poly- peptides by recombinant techniques. Thus, for example, the polynucleotide may be included in anyone of a variety of expression vectors for expressing a polypeptide. Such vectors include chromosomal, non-chromosomal (such as cDNA) and synthe- tic DNA sequences, e.g. derivatives of SV40, bacterial plasmids, phage DNA, ba- culovirus, yeast plasmids, vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox vims, and pseudorabies. However, any other vector may be used as long as it is replicable and viable in the host.

The appropriate DNA sequences may be inserted into the vector by a variety of procedures. In general, the DNA sequence is inserted into an appropriate restriction en- donuclease site(s) by procedures known in the art. Such procedures and others are deemed to be within the scope of those skilled in the art. The DNA sequence in the expression vector is operatively linked to an appropriate expression control sequence(s) (promoter) to direct mRNA synthesis. As representative examples of such promoters, there may be mentioned: LTR or SN40 promoter, the E. coli lac (lad, lacZ) or trp, the phage lambda P_L promoter and other pro- moters known to control expression of genes in prokaryotic or eukaryotic cells or their vimses, such as the promoters T3, T7, gpt, lambda P_R, CMN immediate early, HSV thymidine kinase, early and late SN40 and late LTRs from retrovirus and mouse metallothionein-I. The expression vector also contains a ribosome binding site for translation initiation and a franscription terminator. The vector may also include ap- propriate sequences for amplifying expression.

In addition, the expression vectors preferably contain one ore more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli.

Yet another object of the present invention is to provide a process for producing a multisubstrate deoxyribonucleoside kinase by recombinant techniques comprising culturing recombinant prokaryotic and/or eukaryotic host cells containing and ca- pable of expressing a nucleic acid sequence showing at least 70% homology, preferably at least 90% homology with the amino acid sequence of SEQ.ID.ΝO.2, under conditions promoting expression of said multisubstrate deoxyribonucleoside kinase and subsequent recovery of said multisubstrate deoxyribonucleoside kinase.

As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as E. coli, Streptomyces, Salmonella typhimiirhim; fungal cells, such as yeast; insect cells, such as Drosophila S2 and Spodoptera Sf9; animal cells such as CHO, COS or Bowes melanoma; adenovims; plant cells etc. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein. Yet another object of the present invention is to provide a process for utilizing said multisubstrate deoxyribonucleoside kinase, or nucleic acid encoding such multisubstrate deoxyribonucleoside kinase, for example, to phosphorylate deoxyribonucleo- sides to ribonucleotides to activate specific anti-cancer and anti-viral drugs, and to preserve the fidelty of the deoxynucleotide pool.

Yet another object of the present invention is to provide a recombinant vims, such as a retrovims or an adenovims, whose genome comprises a disease-associated promoter and/or signal sequence operatively linked to a DNA sequence or a RNA sequence encoding a multisubstrate deoxyribonucleoside kinase showing at least

70% homology, preferably at least 90 % homology with the amino acid sequence of SEQ.ID.NO.2.

Yet another object of the present invention is to provide a pharmaceutical compri- sing a recombinant vims, such as a retrovims or an adenovims, whose genome comprises a disease-associated promoter and/or signal sequence operatively linked to a DNA sequence or a RNA sequence encoding a multisubstrate deoxyribonucleoside kinase showing at least 70% homology, preferably at least 90 % homology with the amino acid sequence of SEQ.ID.NO.2, together with a pharmaceutically accep- table carrier, excipient or diluent.

Yet another object of the present invention is to provide a conjugated multisubstrate deoxyribonucleoside kinase showing at least 70 % homology, preferably at least 90% homology with the amino acid sequence of SEQ.ID.NO.2, which deoxyribo- nucleoside kinase is conjugated to a targeting group, such as a magnetic group or an antibody which specifically binds to an antigen associated with a disease, such as cancer or a vims infection.

Yet another object of the present invention is to provide a pharmaceutical composi- tion comprising a conjugated multisubstrate deoxyribonucleoside kinase showing at least 70 % homology, preferably at least 90% homology with the amino acid se- quence of SEQ.ID.NO.2, which deoxyribonucleoside kinase is conjugated to a tar- getting group, such as a magnetic group or an antibody which specifically binds to an antigen associated with a disease, such as cancer or a vims infection, together with a pharmaceutically acceptable carrier, excipient or diluent.

As disclosed here, the term "multi substiate deoxyribonucleoside kinase" relates to a deoxyribonuleoside kinase showing at least 70 % homology, preferably at least 90% homology with the amino acid sequence of SEQ.ID.NO.2. The deoxyribonucleoside kinase is derived from Drosophila melanogaster and has a broad specificity for changing nucleoside analog prodrugs to active drugs by phosphorylation. Likewise this changement will occur at a high catalytic rate.

As disclosed herein, the terms "therapeutic nucleoside analog prodmg", "therapeutic nucleoside analog", and "nucleoside analog", relates to nucleosides and analogs of nucleosides which are non-toxic and/or lack useful pharmaceutical characteristics, but which are transformed to potent pharmaceutically useful compounds when they are phosphorylated. Typically, they become cytotoxic after such a phosphorylation. Examples of such compounds include 9-(hydroxyethoxymethyl)-guanine (ACV), 1- β-D-arabinofuranosyladenine (AraA), 1-β-D-arabinofuranosylcytosine (AraC), 1- β-D-arabinofuranosylguanine (AraG), 1-β-D-aιabinofuranosylthymine (AraT), 3'- azido-2',3'-dideoxythymidine (AZT), 5-biOmo-2'-deoxyuridine (BrdU), (E)-5-(2- bromovinyl)-2'-deoxyuridine (BNDU), 2-chloro-2'-deoxyadenosine (CdA), 2', 3'- didehydro-2',3'-dideoxythymidine (D4T), 2',3'-dideoxycytidine (ddC), dideox- ythymidine (ddT), 2',2'-difluorodeoxycytidine (dFdC), l-(2-deoxy-2-fluoro-β-D- arabinofuranosyl)-5-iodouracil (FIAU), 3 '-fluoro-2',3'-dideoxythymidine (FLT), (E)-5-(2-bromovinyl)-l-β-D-arabinofuranosyl-uracil (BNaraU), 5- fluorodeoxyuridine (FdU), and 2'-deoxy-3-thiacytidine, 2 ',2'- difluorodeoxyguanosine (dFdG), 2-fluoro-9-β-D-arabinofuranosyladenine (FaraA), 5-aza-2'-deoxycytidine (5-AzadC), 5-fluoro-2'-deoxycytidine (5-FdC), 5-methyl- deoxycytidine (5-metdC), granciclovir (GCN), l-(2-deoxy-2-fluoro-l-β-D- arabinofuranosyl)-5-thymine (FMAU) and 5-(2-bromovinyl)-2'-deoxycytidine (BNDC).

As disclosed herein, the term "disease-associated promoter and/or signal sequence" relates to a promoter or a signal sequence that is active in a cell affected by a disease, such as cancer or a vims infection. It is not a requirement that the promoter controls a gene that actively causes the disease, but it is a requirement that the gene that is controlled by the promoter is active in a cell affected by the disease. Preferably, the gene is not active in surrounding cells not affected by the disease. Likewise, it is not necessaiy that the signal sequence is directly involved in the mechanisms behind the disease. However, it is a requirement that the signal sequence actively taigets the gene encoding the multifunctional nucleoside kinase to a cell affected by the disease. Examples are promoters and signal sequences originating from viruses such as human immunodeficiency vims (HIN), hepatitis C vims (HIN), the promoter of the TK gene of herpes simplex vims type I, promoters of the adenovims genes El A, and MLP, the LTR promoter of Ross Sarcoma Nims, promoters of ubiquitous euca- ryotic genes such as HPRT, PGK, alpha-actine, tubuline and DHFR, promoters from genes encoding filamentous proteins such as GFAP, desmine, vimentine, neu- rofϊlaments and keratine, promoters from therapeutically interesting genes such as MDR, CFTR, factor VIII, and ApoAI, promoters from genes that are specifically associated with certain tissues, such as the pymvate kinase promoter, and promoters of intestinal fatty acid-binding proteins, promoters controlling the expression of on- cogenes, etc. Signal sequences that can be used in relation to the present invention are nucleic acid sequences encoding a peptide sequence having the ability of direc- ting the transport of a certain protein to the mitochondria (Zhu et al. (1998), J. Biol. Che ., vol. 273, 14707-14711; Johansson et al. (1996), Proc. Natl. Acad. Sci. USA, vol. 93, 7258-7262) or the cell nucleus (Johansson et al. (1997), Proc. Natl. Acad. Sci. USA, vo\. 94, 11941-11945).

The invention also relates to novel pharmaceutical and therapeutical agents which render it possible to specifically kill cells affected by a certain disease, such as can- cer or a vims infection. Expression cassettes comprising a cDNA encoding the multisubstrate deoxynucleoside kinase of the present invention operatively linked to a disease-associated promoter or a signal sequence can be directly injected per se into the tissue to be treated. However, it is preferred to use some kind of vector to introduce DNA into the cells to be treated. Examples of such vectors are DEAE-dextran (Pagano et al., (1967) J. Virol. Vol. 1, p.891), nuclear proteins (Kaneda et al., (1989) Science, Vol. 243, p. 375), lipids (Feigner et al., (1987) Proc. Natl. Acad. Sci. USA, vol. 84, p. 7413) and liposomes (Fraley et al., (1980) J. Biol. Chem. Vol. 255, p. 10431).

In a preferred embodiment of the present invention, the DNA or RNA sequence is fransferred to the cells by using a recombinant vims comprising a nucleic acid encoding the multisubstrate deoxynucleoside kinase of the present invention as a vector. Examples of such vims are retroviruses (RS V, HMS, MMS, etc) and adenovi- ms.

The expression cassette or the vims comprising a nucleic acid sequence encoding the multisubstrate deoxynucleosidase kinase according to the present invention can be formulated into pharmaceutical compositions suitable for various administration routes, such as topical, oral, parenteral, intranasal, intravenous, intramuscular, intravenous, subcutanous, intraocular and transdermal administration. Preferably, the pharmaceutical compositions are used in an injectable form. Accordingly, the pharmaceutical compositions comprise an expression cassette or a vims containing a nucleic acid sequence encoding the multisubstrate deoxynucleosidase kinase accor- ding to the present invention together with a pharmaceutically acceptable vehicle which is suitable for an injectable solution which preferably can be injected directly inte the tissue to be treated. Examples of formulations are sterile isotonic aqueous solutions, or dry, in particular lyophilized, compositions which can be transformed into injectable solutions by adding e.g. sterile water or semm. According to the present invention, cells may be engineered in vivo for expression of a polypeptide in vivo by, for example, procedures known in the art. As known in the art, a producer cell for producing a retroviral particle containing RNA encoding the polypeptide of the present invention may be administred to a patient for enginee- ring cells in vivo and expression of the polypeptide in vivo. These and other methods for administering a multisubstrate deoxynucleoside kinase of the present invention by such method should be apparent to those skilled in the art from the teachings ofthe present invention. For example, the expression vehicle for engineering cells may be a retiovims or an adenovims which may be used to engineering cells in vivo after combination with a suitable delivery vehicle.

Once the multisubstrate deoxynucleoside kinase is being expressed intracellularly via gene therapy, it may be employed to treat malignancies, e.g. tumours, cancer, leukemias and lymphomas and viral infections, since the multisubstrate deoxynuc- leoside kinase catalyses the initial phosphorylation step of a therapeutic nucleoside analog prodmg. Examples of diseases that can be treated according to the principles outlined in the present application are: cancer in buccal cavity and pharynx, cancer in digestive organs (esophagus, stomach, small intestine, colon-rectum, liver, and biliary passages, pancreas), lung cancer, cancer of connective tissue, melanoma of skin, basal and squamous cell cancers, breast cancer, cancer in genital organs (cervix uteri, corpus uteri, ovary, prostate, testis), cancer in urinary organs (bladder, kidney), cancer of brain and central nervous system, cancer of endocrine glands (thyroid and other endocrine glands), leukemia and other cancers of blood and lymph tissues (Hodgkin's disease, Non-Hodgkins's lymphoma, multiple myeloma), human immunodeficiency vims (HIV) associated diseases, viral hepatitis, cytome- galovirus disease and other chronic infections caused by vimses.

A suitable dose of expression cassette or recombinant vims in relation to the present invention is a function of different parameters such as the vector/recombinant vims used, administration route, the particular pathology, or the duration of the treatment. A typical dose may be within the range from 10⁹-10¹² vims particles. When the phaπnaceutical composition comprising the expression cassette and/or the recombinant vims has been administred to suitable cells, these cells start to express the multisubstrate deoxyribonucleoside kinase. Then, a second pharmaceutical com- position comprising a therapeutic nucleoside analog together with a pharmaceutically acceptable vehicle, excipient or diluent, preferably an injectable sterile aqueous solution is administred. The multisubstrate deoxyribonucleoside kinase according to the invention converts the therapeutic nucleoside analog to the active cytotoxic form resulting in cell death. A suitable dose of expression cassette or recombinant vims in relation to the present invention is a function of different parameters such as the vector/recombinant vims used, administration route, the particular pathology, or the duration of the treatment. A typical dose may be within the range of 100 mg - 5000 mg.

The invention will now be described with reference to the enclosed figures in which

Fig. 1 shows similarities and homologies between the amino acid sequence ofthe kinase of the present invention ( w-dNK) and human TK2, human dCK, and human dGK, respectively. The aminoacid sequences of these enzymes are aligned to- gether and homologies are marked white text on black background;

Fig. 2 presents retroviral vector pLXSN used to construct a retrovims expressing /w-dNK cDNA (dNK-pLXSN). LTR, P_Sv₄₀, and Neo^R, respectively, means long terminal repeat, SV40 large T-antigen promoter, and neomycine resistance gene, re- spectively;

Fig. 3 discloses Western blot analysis of Drø-dNK expression in cancer cells with mouse polyclonal anti- -dNK antibodies. (A) The antibodies detected recombinant rø-dNK and without any cross-reactivity to the human nucleoside kinases dCK, dGK, and TK2. (B) Western blot analysis of protein extracts from osteosar- coma cell lines transfected with the pLXSN vector or the vector expressing Dm- dNK;

Fig. 4 is a diagram showing nucleoside kinase activity in crude extracts of cells ex- pressing D -άMK. Phosphorylation of dThd and CdA were assayed;

Fig. 5 present autoradiographies of TK-deficient cells transduced with pLXSN or dNK-pLXSN incubated with ^"H-dThd. Wt means wild-type; and

Fig. 6 discloses diagrams showing sensitivity of osteosarcoma cells to the nucleoside analogs BVDU, FdUrd, araC and dFdC.

The invention will now be described with reference to the following examples, which are given for the purpose of illustration, and are not intended to limit the sco- pe of the present invention.

Example 1: Cloning of Pm-dNK cDNA

The expressed sequence tag library of the GeneBank database at the National Insti- tute for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) was searched with the Basic Local Alignment Search Tool (BLAST) to identify Drosophila mela- nogaster cDNA clones that encoded enzymes similar to human dCK, dGK and TK2. An EST clone deposited by D. Harvey and coworkers (LD 15983) was identified. A plasmid comprising the expressed sequence tag inserted in the vector pBlu- escript SK+/- (Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory Press) was obtained from D. Harvey (Howard Hughes Medical Institute, University of California, USA) and the DNA sequence of the expressed sequence tag was con- fimed with an automatic laser fluorescent (A.L.F.) sequencer (Amersham Pharmacia Biotech) according to the manufacturer's instructions. The DNA sequence determi- nation of the full length 1001 bp cDNA showed that it encoded a protein of 250 amino acid residues (SEQ.ID.NO.2). The calculated molecular mass of the protein was 29 kDa. The greatest similarity of the protein was to human TK2 that had 38 % identical amino acids at best alignment (figure 1 ). Human dCK and dGK were both 28 % identical to Dw-dNK.

Example 2: Expression and purification of recombinant D -dNK

The cDNA-encoded protein was expressed in Escherichia coli as a fusion protein to glutathione-S-transferase. Two oligonucleotide primers that flanked the open reading frame of the cDNA were designed with EcoRl and Sail restiiction enzyme sites (5'-AAGAATTCGGACTGATGGCGGAGGCAGCATCC (SEQ.ID.NO.3) and 5'- AAGTCGACGTACTAATGGGATAATGGTTATCT (SEQ.ID.NO.4)). The oligo- nucleotides were used in a PCR and the amplified DNA fragment was cloned into the EcoRl-Satl sites of the pGEX-5X-l plasmid vector (Amersham Pharmacia Biotech). The plasmid was transformed into the Escherichia coli strain BL21(DE3)pLysS (Stratagene). A tiansformed colony was inoculated i 2YT medium (Sambrook., (1989) Molecular Cloning, Cold Spring Harbor Laboratory Press) supplemented with 100 μg/ml ampicillin and 34 μg/ml chloramphenicol. Protein expression was induced at OD₅₉₅ = 0.9 with 1 mM isopropyl- 1-thio-β-D- galactopyranoside for 3 h at 37° C. The cells were harvested by centrifugation at 7,700 x g for 10 min and resuspended in phosphate-buffered saline. The bacteria were lysed by addition of 1 mg/ml lysozyme and by sonication. Triton X-100 was added to a final concentration of 1 % (v/v) and the sample was incubated for 30 min at room temperature. The protein extract was centrifuged at 12,000 x g for 10 min and loaded onto a glutathione-Sepharose 4B column (Amersham Pharmacia Bio- tech). The purified recombinant protein was eluted in 50 mM Tris, pH 8.0 supplemented with 10 mMreduced glutathione (Sigma). The size and purity of the recombinant protein was determined by sodium dodecyl sulfate-polyacrylamide gel elec- trophoresis (Phast system, Amersham Pharmacia Biotech). The protein concentration was determined with Bradford Protein Assay (BIO-RAD) and bovine serum al- bumen was used as the concentration standard. About lOmg of fusion protein per liter of bacterial culture was obtained. The electrophoresis showed a single band of the purified protein.

Example 3: Characterization of Pm-dNK

A phosphor transferase assay was used to determine the substrate specificity of the putative deoxyribonucleoside kinase. The phosphoryl transfer assay was performed using [γ-³²P]ATP (3000 Ci/mmol, Amersham Pharmacia Biotech) as described (Eriksson et al., (1991) Biochem. Biophys. Res. Commun., vol. 176, pp. 586-592). The nucleosides were added to 50 mM Tris, pH 8, 5 mM MgCl₂, 1 mM unlabeled ATP, 100 μCi of _[γ-³²P] ATP and 1 μg recombinant D -dNK. The samples were incubated 30 min at 37°C. 2 μl of the reaction mixtures were spotted on poly(ethyleneimine) cellulose F thin layer chromatography sheets (Merck Inc.) and the nucleotide separated in a buffer containing NH^OHisobutyric acid:dH₂O (1:66:33). The sheets were autoradiographed using phosphoimaging plates (BAS 1000, Fujix). Among the naturally occurring deoxyribonucleosides, the enzyme efficiently phosphorylated both the pyrimidines deoxycytidine and deoxythymidine as well as the purines deoxyadenosine and deoxyguanosine. The enzyme did not phosphorylate ribonucleosides. The results are disclosed in table 1 below:

Table 1 : Substrate specificity of recombinant Dm-dNK.

Substrate Relative ph osphorylation 100 μM deoxyadenosine 1.7 deoxycytidine 1.6 deoxyguanosine 1.5 deoxythymidine 1.0 deoxyinosine 0.0 The enzyme's phosphorylation of several nucleoside analogs was also studied. At 100 μM, all investigated nucleoside analogs were efficiently phosphoiylated. It was also determined how efficiently the nucleoside analogs competed with deoxythymidine phosphorylation.

The competion experiments were carried out in the following way: The standard reaction mixture contained 2.5 mM MgCl₂, 10 mM dithio threitol, 1 mg/ml bovine se- rum albumin, 2.5 mM ATP, 10 mM NaF, 2 μM methyl- H-thymidine, an appropriate amount of a nucleoside analog and the multisubstrate deoxyribonucleoside kina- se in an amount resulting in a linear conversion of he substrate, in a total reaction mixture of 50 μl of 50 mM Tris-HCl, pH 8.0. The reaction mixture was incubated at 37 °C for 30 min, and the reaction was terminated by spotting on to DE-81 discs (Whatman). The discs were instantly immersed and washed in ethanol (70%). The filters were dried and assayed for radioactivity in a tuluene-based scintillant. The concentration resulting in 50% inhibition of phosphorylation of 2 μM deoxythymidine was determined as a mean value of three independent experiments.

The results are presented in tables 2 and 3 below:

Table 2: Phosphorylation of nucleoside analogs by the multisubstrate deoxynucleoside kinase. The relative phosphorylation of the nucleoside analogs is correlated to deoxythymidine phosphorylation.

Substrate Relative phosphorylation at 100 μM substrate

AraA 1.5

AraC 1.9

AraG 1.7

AraT 1.5 AZT 1.3

BrdU 4.0

CdA 1.8 ddC 1.6 ddT 1.9 dFdC

FdU 1.5

FLT 1.7

Table 3 : . Nucleoside analog concentration resulting in 50% competitive inhibition (IC₅o) of phosphorylation of 2 μM deoxythymidine by the multisubstrate deoxynucleoside kinase and HSV-1 TK

Nucleoside analog multisubstrate deoxyHSV-1 TK nucleoside kinase

BVaraU 20 4

AraC 53 >1000

AraT 84 N.D.

AZT 51 N.D.

BVDU 3 3

CdA 120 >1000 ddC 755 >1000 ddT 422 N.D. dFdC 144 >1000

FdU 25 58

FIAU 16 2

FLT 105 N.D.

3TC 700 >1000

N.D. = not determined

The table shows that the multisubstiate deoxynucleoside kinase of the invention is able to phosphorylate a large amount of nucleoside analogs. The previously used enzyme HSV-1 TK shows a more limited substrate specificity.

Example 4: Construction of a retrovims expressing Dm-dNK

TK-deficient osteosarcoma cells were obtained from the American Type Culture Collection. The cells were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10 % (v/v) fetal calf semm (Gibco BRL), 100 U/ml penicillin, and 0.1 mg/ml streptomycin. The cells were grown at 37 °C in a humidified incubator with a gas phase of 5 % CO .

A retrovims vector based on the Moloney murine leukemia vims was used to gene- rate a replicon-deficient recombinant retrovims to introduce the cDNA of Drø-dNK in mammalian cells. Oligonucleotide primers containing engineered EcoRl and Xhol restriction enzyme sites were designed flanking the open reading frame of m-dNK cDNA (5'-AAGAATTCGGACTGATGGCGGAGGCAGCATCC (SEQ.ID.NO.4) and 5'-TTCTCGAGTGGTTATCTGGCGACCCTCTGGC (SEQ.ID.NO.8)). The primers were used in a PCR and the DNA fragment was cloned into the EcoRl-Xhol site of the pLXSN plasmid vector (Clontech). The plasmid was purified using the Nucleobond plasmid purification kit (Clontech). The DNA sequence of the constructed plasmid was verified by DNA sequence determination using a ABI310 automated DNA sequencer (Perkin-Elmer). Fig. 2 outlines replicon-deficient recombi- nant retroviridae with (dNK-pLXSN) and without the D -dNK cDNA (pLSNX).

RetroPack PT67 packaging cells (Clontech) were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10 % (v/v) fetal calf serum (Gibco BRL), 100 U/ml penicillin, and 0.1 mg/ml streptomycin. The pLXSN plasmid vectors were transfected into the packaging cells using LipofectAmine (Life Technology Inc.) according to the protocol provided by the supplier. 48 hours after transfection, medium from packaging cells were collected, filtered through a 0.45 μm filter, diluted 2- fold with fresh medium, and added to the osteosarcoma cells. Polybrene was added to the culture to a final concentration of 4 μg/ml. The cells were incubated for another 48 hours and then cultured for 3 weeks in the presence of 1.0 mg/ml Gene- ticin to generate a polpulation of stable transfected cells.

To verify that the Drø-dNK retained its enzymatic activity when expressed in human cells, the activity of dThd phosphorylation in crude cell protein extracts was deter- mined. Cell protein extracts were prepared of the transfected osteosarcoma cells ac- cording to well-known methods. Deoxyribonucleoside kinase assays were performed in 50 mM Tris-HCl pH 7.6, 5 mM MgCl₂, 5 mM ATP, 5 mM dithiothreitol, 15 mM nAf, 100 mM KCl and 0.5 mg/ml bovine semm albumin. 2.5 μM unlabelled dThd, and 2.5 μM [8- H]-dThd (Moravek Biochemicals Inc.) or 2 μM unlabelled CdA and 3 μM [8-³H]-CdA (Moravek Biochemicals Inc.) were added together with 20 μg of protein extract in a total volume of 35 μl. Aliquots of the reaction mixture were spotted on Whatman DE-81 filters after 10, 20 and 30 min incubation, respectively, at 37 °C. The filters were washed three times in 50 mM ammonium formate, dTMP was eluted from the filter with 0.5 M KCl, and radioactivity was determined by scintillation counting.

The results are disclosed in fig. 4. Untransfected osteosarcoma cells deficient in cytosolic TK1 expression showed low level of dThd phosphorylation, probably catalysed by mitochondrial TK2. The cells transfected with the pLXSN retroviral vector alone showed similar levels of dThd phosphorylation as the wild-type cells, whereas the cells transfected with dNK-pLXSN exhibited ~ 100-fold higher enzymatic activity than the parent cell line.

Example 5: Western blot and autoradiography using mouse polyclonal antibodies

The D -dNK cDNA was expressed in the BL21 E. Coli strain with an N-terminal poly-histidine tag and the recombinant protein was purified by affinity chromato- graphy. 2.0 μg protein diluted in 300 μl phosphate-buffered saline was injected sub- cutaneously in four-week-old female BALB/c mice with an equal volume of Freund's complete adjuvant (Sigma). A booster injection containing the same amount of protein was given ten days later together with Freund's incomplete adjuvant (Sigma). Two weeks after the booster injection, 3 ml of blood was retrieved and allowed to clot. The serum was collected and stored at -20 °C. To verify the specificity of the antibodies, a Western blot analysis was performed with recombinant Dm-άNK and the sequence-related human deoxyribonucleoside kinases dCK, dGK and TK2. Protein extracts of the transfected osteosarcoma cells in example 4. The protein concentration of the extracts was determined by Bio-Rad protein assay. The protein extracts were separated by 1.2 % SDS/PAGE gel electrophoresis. The proteins were electiOtransferred to a nitrocellulose membrane at 35 V overnight. The membranes were blocked for 1 h at room temperature with the Drø-dNK mouse antisera and washed three times with TBS buffer. A secondary alkaline phosphatase conjugated anti-mouse IgG antibody diluted 1 :5000 (Sigma) was applied for 1 h and the membrane was washed in TBS buffer. The alkaline phosphatase immobilised on the membrane was developed with BCIP/NBT (Sigma).

The results of the Western blot analysis are shown in fig. 3 A. The anti-Dw-dNK antibodies detected the Dw-dNK protein and did not cross-react with the human nucleoside kinases. The antibodies were used to analyse the expression of Dw-dNK in the transfected cells (fig. 3B). A band of 28 kDa was detected in the cells transduced with the dNK-pLXSN vector, but not in the cells transduced with pLSNX.

Autoradiography was further used to visualise incorporation of dThd in situ. The cells were cultured on poly-L-lysine-coated chamber slides (Nunc, Inc.) for 24 h. Cells were labelled with [³H]-dThd (Moravek Biochem) for 12 hours. The slides were rinsed with PBS twice, fixed ten minutes in methanol: acetic acid (3: 1), washed three times with ice-cold 10 % TCA, and then air-dried. The slides were coated with photoemulsion (Amersham) and exposed 1-4 weeks at 4 °C. The autoradiographs were developed using a developer.

The results of the autoradiography are presented in fig. 5. The TK-deficient cells incubated with [^~H]-dThd showed a dotted autoradiography pattern distributed thro- ughout the cells, indicating phosphorylation of dThd by mitochondrial TK2 and its subsequent incorporation into mitochondial DNA. The cells expressing Dw-dNK exhibited incorporation of [ H]-dThd into nuclear DNA. ~ 90 % of the cells in the population showed this pattern, indicating that the majority of cells expressed the Dw-dNK. In summary, the experiments described in examples 4 and 5 show that cancer cells infected with the dNK-pLXSN retroviral vector express Dw-dNK and that the enzyme retained its enzymatic activity when expressed in human cells.

Example 6: Cell proliferation assays

The sensitivities of the transduced cancer cells to the nucleoside analogs BVDU, FdUrd, araC and dFdC were determined. AraC, and FdUrd were obtained from Sigma Inc. DFdC and dFdG were obtained from Lilly Research Laboratories. BVDU was a gift from Prof. J. Balzarini, Leuven, Belgium. 2000 cells were plated in 96-well microtiter plates and indicated concentrations of nucleoside analogs were added after 24 h. Cell survival was assayed by the MTT assay (Boehringer Mannheim) after four days of dmg exposure. Each experiment was performed in triplicate. Statistical analysis was performed using the student's paired t test.

The results are disclosed in fig. 6. The wild-type parent cell line is represented by filled circles, cells transduced with pLXSN vector alone is represented by filled squares, and cells transduced with dNK-pLXSN is represented by open circles. The diagrams of fig. 6 show that the wild-type parent cell line and cells transduced with the LXSN vector alone were equally sensitive to the investigated nucleoside analogs. The cells transduced with dNK-LXSN showed 10- to 1000-fold higher sensiti- vity to BVDU, FdUrd, araC and dFdC.

Claims

1. A nucleic acid sequence, such as a DNA sequence or a RNA sequence encoding a multisubstrate deoxyribonucleosidase having a sequence showing at least 70 % homology, preferably at least 90 % homology with the amino acid sequence of

SEQ.ID.NO.2.

2. A nucleic acid sequence according to claim 1, characterized in that the multisubstrate deoxyribonucleosidase encoded by the sequence, has an amino acid se- quence according to SEQ.ID.NO.2.

3. A nucleic acid sequence according to claim 1, characterized in that the sequence shows at least 70% homology, preferably at least 90% homology with the DNA sequence of SEQ.ID.NO. l.

4. A nucleic acid sequence according to anyone of claims 1 - 3, for medical use.

5. A vector comprising a DNA sequence according to anyone of claims 1-3.

6. A vector according to claim 5, characterized in that said nucleic acid sequence according to anyone of claims 1 - 3 is functionally linked to a disease-associated promoter and/or signal sequence.

7. A vector according to claim 6, for medical use.

8. A recombinant vims comprising a nucleic acid sequence according to anyone of claims 1-3.

9. A recombinant vims according to claim 8, characterized in that that said nucleic acid sequence according to anyone of claims 1 - 3 is functionally linked to a disease-associated promoter and/or signal sequence.

10. A recombinant vims according to claim 9, for medical use.

11. A pharmaceutical composition comprising a vector according to claim 6 or a recombinant vims according to claim 9, together with a pharmaceutically acceptable carrier, excipient and/or diluent.

12. A multisubstrate deoxynucleoside kinase having a sequence showing at least 70 % homology, preferably at least 90 % homology with the amino acid sequence of SEQ.ID.NO.2, for medical use.

13. A method for producing a multisubstrate deoxyribonucleoside kinase comprising the steps of inserting a vector according to claim 5 into a suitable procaryotic or eucaryotic host cell, culturing said host cell under conditions causing expression of said multisubstiate deoxyribonucleoside kinase and subsequently recovering said multisubstiate deoxyribonucleoside kinase from the host cell or the culture medium.

14. A method of phosphoiylating a nucleoside or a nucleoside analog, comprising the steps of: a) providing a multisubstrate deoxyribonucleoside kinase showing showing at least 70 % homology, preferably at least 90 % homology with the amino acid sequence of SEQ.ID.NO.2, and a sufficient amount of a suitable co-factor, such as ATP; b) contacting said nucleoside or nucleoside analog with the multisubstrate deoxyribonucleoside kinase and the co-factor of step a) in a suitable buffer solution; c) recovering the phosphorylated nucleoside or nucleoside analog.

15. Use of a multisubstrate deoxyribonucleoside kinase showing showing at least 70 % homology, preferably at least 90 % homology with the amino acid sequence of SEQ.ID.NO.2, for phosphoryl ating nucleosides or nucleoside analogs.