WO1990003370A1

WO1990003370A1 - DERIVATIVES OF PYRAZOLO[3,4-d]PYRIMIDINE

Info

Publication number: WO1990003370A1
Application number: PCT/US1989/004184
Authority: WO
Inventors: Charles R. Petrie; Rich B. Meyer
Original assignee: Microprobe Corporation
Priority date: 1988-09-28
Filing date: 1989-09-26
Publication date: 1990-04-05
Also published as: CA1338379C

Abstract

This invention is directed to novel 3,4-disubstituted and 3,4,6-trisubstituted pyrazolo[3,4-d]pyrimidines and to the use of these compounds in the preparation of oligonucleotides. The invention is also directed to nucleosides and mono- and oligonucleotides comprising at least one of these pyrazolopyrimidines, and to the use of the resulting novel oligonucleotides for diagnostic purposes. More particularly, the pyrazolopyrimidines of the present invention are of formula (I), wherein R1 is hydrogen, or a sugar moiety optionally substituted at its 3' or its 5' position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; provided that when R3 is hydrogen, then R1 cannot be hydrogen; R3 is hydrogen or the group -W-(X)n-A; each of W and X is independently a chemical linker arm; A is an intercalator, an electrophilic crosslinker or a reporter group; each of R4 and R6 is independently H, OH, SR, NH2, or NH(CH2)tNH2; R is H or C1-6alkyl; n is zero or one; and t is zero to twelve. The novel oligo- and polynucleotides are useful in the identification, isolation, localization and/or detection of complementary nucleic acid sequences of interest in cell-free or cellular systems. Therefore, the invention further provides a method for identifying target nucleic acid sequences, which method comprises utilizing an oligo- or polynucleotide probe comprising at least one of a labeled pyrazolo[3,4-d]pyrimidine of the present invention.

Description

DERIVATIVES OF PYRAZOLO \3.4-dlPYRIMIDINE

BACKGROUND OF THE INVENTION This invention relates to derivatives of pyrazolo- [3,4-d]pyrimidine and to the use of these compounds for the preparation of oligonucleotides.

Oligonucleotides are useful as diagnostic 0 probes for the detection of "target" DNA or RNA sequences. In the past, such probes were made up of sequences of nucleic acid containing purine, pyrimidine or 7-deazapurine nucleotide bases (U.S. Patent 4,711,955). The method for attaching chemical moieties ₅ to these bases has been via an acetoxy- mercuration reaction, which introduces covalently bound mercury atoms into the 5-position of the pyrimidine ring, the C-8 position of the purine ring or the C-7 position of a 7-deazapurine ring (Dale et al., Proc. Natl. Acad. _Q Sci. USA 7jD:2238 (1973); Dale et al., Biochemistry

14.:2447 (1975)), or by the reaction of organomercurial compounds with olefinic compounds in the presence of palladium catalysts (Ruth et al., J. Org. Chem. 43;2870 (1978); Bergstrom et al., J. Am. Chem. Soc. 100:8106 ₅ (1978); Bigge et al., J. Am. Chem. Soc. 102:2033 (1980)) .

The sugar component of oligonucleotide probes has been, until the present, composed of nucleic acid containing ribose or deoxyribose or, in one case, _Q natural 0-arabinose (patent publication EP 227,459).

A novel class of nucleotide base, the 3,4-disubst ituted and 3, ,6-trisubstituted pyrazolo[3,4-d]pyrimidines, has now been found which offers several advantages over the prior art. The de 5 novo chemical synthesis of the pyrazolopyrimidine and the resulting nucleotide allows for the incorporation of a wide range of functional groups in a variety of different positions on the nucleotide base and for the use of different sugar moieties. Also, adenine, guanine and hypoxanthine analogs are obtained from a single nucleoside precursor. Additionally, the synthesis does not require the use of toxic heavy metals or expensive catalysts. Similar pyrazolo[3,4-d]pyrimidines are known (Kobayashi, Chem. Phar . Bull. 21:941 (1973)); however, the substituents on the group are different from those of the present invention and their only use is as pharmaceuticals, more particularly as xanthine oxidase inhibitors.

SUKKARϊ OF THE INVENTION This invention is directed to novel 3,4-disubsti- tuted and 3 ,4,6-trisubstituted pyrazolo[3,4-d]pyrimidines and to the use of these compounds in the preparation of oligonucleotides. The invention is also directed to nucleosides and mono- and oligonucleotides comprising at least one of these pyrazolopyrimidines, and to the use of the resulting novel oligonucleotides for diagnostic purposes.

More particularly, the pyrazolopyrimidines of the present invention are of the following formula (I) :

wherein, ^• l is hydrogen, or a sugar moiety optionally substituted at its 3• or its 5' position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; provided that when R₃ is hydrogen, then R*-_ cannot be hydrogen;

R₃ is hydrogen or the group -w-(X)_n-A; each of and X is independently a chemical linker arm;

A is an intercalator, an electrophilic crosslinker, a photoactivatable crosslinker, or a reporter group; each of R₄ and Rg is independently H, OH, SR,

NH₂, or NH(CH₂)t^NH2'

R is H or C₁„₆alkyl; n is zero or one; and t is zero to twelve.

The invention also provides novel nucleosides and nucleotides comprising at least one of the above pyrazolo- pyrimidines.

Nucleotides of this invention and oligo- and polynucleotides into which the nucleotides have been incorporated may be used as probes. As such, the novel oligo- and polynucleotides are useful in the identification, isolation, localization and/or detection of complementary nucleic acid sequences of interest in cell-free or cellular systems. Therefore, the invention further provides a method for identifying target nucleic acid sequences, which method comprises utilizing an oligo- or polynucleotide probe comprising at least one of a labeled pyrazolo[3,4-d]pyrimi- dine of the present invention.

DETAILED DESCRIPTION OF THE INVENTION This invention provides novel substituted pyrazolo[3,4-d]pyrimidines which are used as the nucleotide base in preparing nucleosides and nucleotides, rather than the natural purine or pyrimidine bases or the deazapurine analogs.

The synthesis of 3,4-disubstituted and 3,4,6-tri- substituted pyrazolo[3,4-d]pyrimidine nucleosides and their use as reagents for incorporation into nucleic acids either enzymatically or via chemical synthesis offers several advantages over current procedures. The de novo chemical synthesis of the nucleotide allows for the incorporation of a wide range of functional groups (e.g., NH₂, SH, OH, halogen, COOH, CN, CONH₂) and the use of different sugar moieties. Also, adenine, guanine, and hypoxanthine analogs are obtained from a single nucleoside precursor. And, the synthesis does not require the use of toxic heavy metals or expensive catalysts.

^l

wherein,

Rl is hydrogen, or a sugar moiety optionally substituted at its 3* or its 5* position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; provided that when 3 is hydrogen, then R^ cannot be hydrogen;

R₃ is hydrogen or the group - -(X)_n-A; each of W and X is independently a chemical linker arm;

A is an intercalator, an electrophilic crosslinker or a reporter group; each of R4 and is independently H, OH, SR,

NH₂, or NH^(CH₂ ⁾t^NH2' R is H or C^.galkyl; n is zero or one; and t is zero to twelve.

The sugar moiety is selected from those useful as a component of a nucleotide. Such a moiety may be selected from, for example, ribose, deoxyribose, glucose, arabinose, xylose and lyxose. The sugar moiety is preferably ribose, deoxyribose or arabinose and embraces either anomer, α or β .

A reactive group suitable for internucleotide bond formation is one which is useful during chain extension in the synthesis of an oligonucleotide. Reactive groups particularly useful in the present invention are those containing phosphorus. Phosphorus-containing groups suitable for internucleotide bond formation are preferably alkyl phosphorchloridites or alkylphosphora idites.

Alternatively, activated phosphate diesters may- be employed for this purpose.

A chemical linker arm ( alone or together with X) serves to make the functional group (A) more able to readily interact with antibodies, detector proteins, or chemical reagents, for example. The linkage holds the functional group away from the base when the base is paired with another within the double-stranded complex. Linker arms may include alkylene groups of 1 to 12 carbon atoms, alkenylene groups of 2 to 12 carbon atoms and 1 or 2 olefinic bonds, alkynylene groups of 2 to 12 carbon atoms and 1 or 2 acetylenic bonds, or such groups substituted at a terminal point with nucleophilic groups such as oxy, thio, amino or chemically blocked derivatives thereof (e.g., trifluoroacetamido) . Such functionalities, including aliphatic or aromatic amines, exhibit nucleophilic properties and are capable of serving as a point of attachment of the functional group (A) . The linker arm moiety ( alone or together with X) is preferably of at least three atoms and more preferably of at least five atoms. The terminal nucleophilic group is preferably amino or chemically blocked derivatives thereof (e.g., trifluoroacetamido) . Intercalators are planar aromatic bi-, tri- or polycyclic molecules whose dimensions are roughly the same as those of a purine-pyrimidine pair and which can insert themselves between two adjacent base pairs in a double stranded helix of nucleic acid. Intercalators have been used to cause frameshift mutations in DNA and RNA. It has also recently been shown that when an intercalator is covalently bound via a linker arm ("tethered") to the end of a deoxyoligonucleotide, it increases the binding affinity of the oligonucleotide for its target sequence, resulting in strongly enhanced stability of the complementary sequence complex. At least some of the tethered intercalators also protect the oligonucleotide against exonucleases, but not against endonucleases. See, Sun et al.. Nucleic Acids Res. 15:6149-6158 (1987); Le Doan et al. , Nucleic Acids Res. 15:7749-7760 (1987) . Examples of tetherable intercalating agents are oxazolopyridocarbazole, acridine orange, proflavine, acriflavine and derivatives of proflavine and acridine such as 3-azido-6-(3-bromopropylamino)acridine, 3-amino-6-(3-bromopentylamino)acridine, and

3-methoxy-6- chloro-9-(5-hydroxypentylamino)acridine. Oligonucleotides capable of crosslinking to the complementary sequence of target nucleic acids are valuable in chemotherapy because they increase the efficiency of inhibition of mRNA translation or gene expression control by covalent attachment of the oligonucleotide to the target sequence. This can be accomplished by crosslinking agents being covalently attached to the oligonucleotide, which can then be chemically activated to form crosslinkages which can then induce chain breaks in the target complementary sequence, thus inducing irreversible damage in the sequence. Examples of electrophilic crosslinking moieties include alpha-halocarbonyl compounds, 2-chloroethylamines and epoxides.

When oligonucleotides comprising at least one nucleotide base moiety of the invention are utilized as a probe in nucleic acid assays, a label is attached to detect the presence of hybrid polynucleotides. Such labels act as reporter groups and act as means for detecting duplex formation between the target nucleotides and their complementary oligonucleotide probes.

A reporter group as used herein is a group which has a physical or chemical characteristic which can be measured or detected. Detectability may be provided by such characteristics as color change, luminescence, fluorescence, or radioactivity; or it may be provided by the ability of the reporter group to serve as a ligand recognition site.

Probes may be labeled by any one of several methods typically used in the art. A common method of detection is the use of autoradiography with ³H, ¹²⁵I, ³⁵S, ¹ C, or ³²P labeled probes or the like. Other reporter groups include ligands which bind to antibodies labeled with fluorophores , chemiluminescent agents, and enzymes. Alternatively, probes can be conjugated directly with labels such as fluorophores, chemiluminescent agents, enzymes and enzyme substrates. Alternatively, the same components may be indirectly bonded through a ligand-antiligand complex, such as antibodies reactive with a ligand conjugated with label. The choice of label depends on sensitivity required, ease of conjugation with the probe, stability requirements, and available instrumentation.

The choice of label dictates the manner in which the label is incorporated into the probe. Radioactive probes are typically made using commercially available nucleotides containing the desired radioactive isotope. The radioactive nucleotides can be incorporated into probes, for example, by using DNA synthesizers, by nick-translation, by tailing of radioactive bases to the 3• end of probes with terminal transferase, by 8 copying M13 plasmids having specific inserts with the Klenow fragment of DNA polymerase in the presence of radioactive dNTP's, or by transcribing RNA from templates using RNA polymerase in the presence of radioactive rNTP's.

Non-radioactive probes can be labeled directly with a signal (e.g., fluorophore, chemiluminescent agent or enzyme) or labeled indirectly by conjugation with a ligand. For example, a ligand molecule is covalently bound to the probe. This ligand then binds to a receptor molecule which is either inherently detectable or covalently bound to a detectable signal, such as an enzyme or photoreactive compound. Ligands and antiligands may be varied widely. Where a ligand has a natural "antiligand", namely ligands such as biotin, thyroxine, and cortisol, it can be used in conjunction with its labeled, naturally occurring antiligand. Alternatively, any haptenic or antigenic compound can be used in combination with a suitably labeled antibody. A preferred labeling method utilizes biotin-labeled analogs of oligonucleotides, as disclosed in P. Langer et al., Proc. Natl. Acad. Sci. USA 78.:6633-6637 (1981), which is incorporated herein by reference. Enzymes of interest as reporter groups will primarily be hydrolases, particularly phosphatases, esterases, ureases and glycosidases, or oxidoreductases, particularly peroxidases. Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc. Chemiluminescers include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol.

The specific hybridization conditions are not critical and will vary in accordance with the investigators preferences and needs. Various hybridization solutions may be employed, comprising from about 20 to 60% volume, preferably 30%, of a polar organic solvent. A common hybridization solution employs about 30-60% v/v formamide, about 0.5 to 1M sodium chloride, about 0.05 to 0.1M buffers, such as sodium citrate, Tris HC1, PIPES or HEPES, about 0.05 to 0.5% detergent, such as sodium dodecylsulfate, and between 1-10 mM EDTA, 0.01 to 5% ficoll (about 300-500 kilodaltons) , 0.1 to 5% polyvinylpyrrolidone (about 250-500 kdal) , and 0.01 to 10% bovine serum albumin. Also included in the typical hybridization solution will be unlabelled carrier nucleic acids from about 0.1 to 5 mg/ml, e.σ.. partially fragmented calf thymus or salmon sperm, DNA, and/or partially fragmented yeast RNA and optionally from about 0.5 to 2% wt./vol. glycine. Other additives may also be included, such as volume exclusion agents which include a variety of polar water-soluble or swellable agents, such as anionic polyacrylate or polymethylacrylate, and charged saccharidic polymers, such as dextran sulfate.

The particular hybridization technique is not essential to the invention. Hybridization techniques are generally described in Nucleic Acid Hybridization, A Practical Approach, Ed. Hames, B.D. and Higgins, S.J., IRL Press, 1985; Gall and Pardue (1969), Proc. Natl. Acad. Sci., U.S.A., 63:378-383, and John, Burnsteil and Jones (1969) Nature, 223:582-587. As improvements are made in hybridization techniques, they can readily be applied.

The amount of labelled probe which is present in the hybridization solution may vary widely. Generally, substantial excesses of probe over the stoichio etric amount of the target nucleic acid will be employed to enhance the rate of binding of the probe to the target DNA.

Various degrees of stringency of hybridization can be employed. As the conditions for hybridization become more stringent, there must be a greater degree of complementarity between the probe and the target for the formation of a stable duplex. The degree of stringency can be controlled by temperature, ionic strength, the inclusion of polar organic solvents, and the like. For example, temperatures employed will normally be in the range of about 20 to 80 C, usually 25 to 75 C. For probes of 15- 50 nucleotides in 50% formamide, the optimal temperature range can vary from 22-65"C. With routine exper¬ imentation, one can define conditions which permit satisfactory hybridization at room temperature. The stringency of hybridization is also conveniently varied by changing the ionic strength and polarity of the reactant solution through manipulation of the concentration of formamide within the range of 20% to 50%.

Treatment with ultrasound by immersion of the reaction vessel into commercially available sonication baths can often times accelerate the hybridization rates. After hybridization at a temperature and time period appropriate for the particular hybridization solution used, the glass, plastic, or filter support to which the probe-target hybrid is attached is introduced into a wash solution typically containing similar reagents (e.g., sodium chloride, buffers, organic solvents and detergent) , as provided in the hybridization solution. These reagents may be at similar concentrations as the hybridization medium, but often they are at lower concentrations when more stringent washing conditions are desired. The time period for which the support is maintained in the wash solutions may vary from minutes to several hours or more.

Either the hybridization or the wash medium can be stringent. After appropriate stringent washing, the correct hybridization complex may now be detected in accordance with the nature of the label. The probe may be conjugated directly with the label. For example, where the label is radioactive, the support surface with associated hybridization complex substrate is exposed to X-ray film. Where the label is fluorescent, the sample is detected by first irradiating it with light of a particular wavelength. The sample absorbs this light and then emits light of a different wavelength which is picked up by a detector (Physical Biochemistry, Freifelder, D. , W.H. Freeman & Co., 1982, pp. 537-542). Where the label is an enzyme, the sample is detected by incubation an appropriate substrate for the enzyme. The signal generated may be a colored precipitate, a colored or fluorescent soluble material, or photons generated by bioluminescence or chemi-luminescence. The preferred label for dipstick assays generates a colored precipitate to indicate a positive reading. For example, alkaline phosphatase will dephosphorylate indoxyl phosphate which then will participate in a reduction reaction to convert tetrazolium salts to highly colored and insoluble formazans.

Detection of a hybridization complex may require the binding of a signal generating complex to a duplex of target and probe polynucleotides or nucleic acids. Typically, such binding occurs through ligand and anti-ligand interactions as between a ligand-conjugated probe and an anti-ligand conjugated with a signal. The binding of the signal generation complex is also readily amenable to accelerations by exposure to ultrasonic energy.

The label may also allow indirect detection of the hybridization complex. For example, where the label is a hapten or antigen, the sample can be detected by using antibodies. In these systems, a signal is generated by attaching fluorescent or enzyme molecules to the antibodies or in some cases, by attachment to a radioactive label. (Tijssen, P., 12

Practice and Theory of Enzyme Immunoassays, Laboratory Techniques in Biochemistry and Molecular Biology, Burdon, R.H. , van Knippenberg, P.H., Eds., Elsevier, 1985, pp. 9-20) . The compounds of the present invention of formula I where Ri is hydrogen may be prepared by the procedures outlined below and as set forth by Kobayashi in Chem. Pharm. Bull. 21:941-951 (1973), the disclosure of which is incorporated herein by reference.

R₃C0C1 ₊ CH₂(CN)₂ )₂

(TI) CHI)

H_?NNH_? U*. )W

^In general, malononitrile (III) is treated with acyl halide (II) in the presence of a base to yield acylmalononitrile (IV) , which is subsequently methylated with dimethyl sulfate or diazomethane, for example, to give the substituted methoxymethylenemalononitrile (V) . This compound is then reacted with hydrazine hydrate in boiling alcohol to give the

3-substituted-5-aminopyrazole-4-carbonitrile (VI) , which is treated with cold concentrated sulfuric acid to give the 3-substituted-5-aminopyrazole-4-carboxamide (VII) .

The carboxamide (VII) may alternatively be prepared by treating cyanoacetamide (XII) with acid halide (II) to give the acylcyanoacetamide (XIII) , which is then methylated and the resulting methoxy compound (XIV) is reacted with hydrazine hydrate. 13

R-C0C1 +

(ID (XII) (XIII) ⁽ X I V )

H₂NNF H₂0

f H)

Syntheses of pyrazolo[3,4-d]pyrimidines are accomplished from the two pyrazole intermediates, VI and VII. Thus, 3,4-disubstituted pyrazolo[3,4-d]pyrimidines (VIII and X) are obtained by treating the corresponding VI and VII with boiling formamide. Alternatively, VI may be treated with dialkoxymethyl ester of a carboxylic acid, at room temperature or above room temperature, and then with ammonia to give VIII, and VII may be treated with dialkoxymethyl ester of a carboxylic acid (without subsequent ammonia treatment) , at room temperature or above room temperature, to give X.

3,4,6-Trisubstituted pyrazolo- [3,4-d]pyrimidines (IX and XI) are obtained by fusing the corresponding VI and VII with urea and thiourea (H₂N) C=R₆ (where Rg is 0 or S) . Alternatively, VI and VII may be treated with an alkyl xanthate salt such as potassium ethyl xanthate and with alkyl halide such as methyl iodide, at a temperature above room temperature, followed by oxidation by a peroxide such as m-chloroperbenzoic acid (MCPBA) and subsequent treatment with ammonia to give IX and XI, respectively, where Rg is NH₂. 14

(VIII) (IX) (X) (XI)

The compounds of formula I may be recovered from the reaction mixture in which they are formed by established procedures.

In the compounds of formula I where R is a sugar moiety, the sugar may be either added to the 1-position of the pyrazole VI or VII prior to further treatment or added to the 1-position of the pyrazolo[3,4-d]pyrimidine VIII, IX, X or XI. To add the sugar, the pyrazole or pyrazolopyrimidine is treated with sodium hydride and then with the glycosyl halide of the blocked sugar. Oligonucleotides of the present invention comprise at least one and up to all of their nucleotides from the substituted pyrazolo[3,4-d]pyrimidines of formula I.

To prepare oligonucleotides, protective groups are introduced onto the nucleosides of formula I and the nucleosides are activated for use in the synthesis of oligonucleotides. The conversion to protected, activated forms follows the procedures as described for 2--deoxynucleosides in detail in several reviews. See, Sonveaux, Bioorganic Chemistry l±:274-325 (1986); Jones, in Oligonucleotide Synthesis, a Practical Approach , M.J. Gait, Ed., IRL Press, p. 23-34 (1984).

The activated nucleotides are incorporated into oligonucleotides in a manner analogous to that for DNA and RNA nucleotides, in that the correct nucleotides will be sequentially linked to form a chain of nucleotides which is complementary to a sequence of nucleotides in target DNA or RNA. The nucleotides may be incorporated either enzymatically or via chemical synthesis. In a preferred embodiment, the activated nucleotides may substitute for an adenine using the nick translation procedure, as described by Langer et al., Proc. Natl. Acad. Sci. USA 2 :6633-6637 (1981), the disclosure of which is incorporated herein by reference. In another preferred embodiment, the activated nucleotides may be used directly on an automated DNA synthesizer according to the procedures and instructions of the particular synthesizer employed. The oligonucleotides may be prepared on the synthesizer using the standard commercial phosphoramidite or H-phosphonate chemistries.

An oligonucleotide probe according to the invention includes at least one labeled substituted pyrazolo[3,4-d]pyrimidine nucleotide moiety of formula I. The amount of labeled probe present in the hybridization solution may vary widely, depending upon the nature of the label, the amount of the labeled probe that can reasonably bind to the cellular target nucleic acid, and the precise stringency of the hybridization medium and/or wash medium. Generally, substantial probe excesses over the stoichiometric amount of the target will be employed to enhance the rate of binding of the probe to the target nucleic acids. The invention is also directed to a method for identifying target nucleic acid sequences, which method comprises utilizing an oligonucleotide probe including at least one labeled substituted pyrazolo[3,4-d]pyrimidine nucleotide moiety of formula I.

In one embodiment, the method comprises the steps of: 16

(a) denaturing nucleic acids in the sample to be tested;

(b) hybridizing to the target nucleic acids an oligonucleotide probe including at least one labeled substituted pyrazolo[3,4-d]pyrimidine, wherein the probe comprises a sequence complementary to that of the target nucleic acids;

(c) washing the sample to remove unbound probe; (d) incubating the sample with detection agents; and

(e) inspecting the sample.

The above method may be conducted following procedures well known in the art. An assay for identifying target nucleic acid sequences utilizing an oligonucleotide probe including at least one labeled substituted pyrazolo[3,4-d]pyrimidine nucleotide moiety of formula I and comprising the above method is contemplated for carrying out the invention. Such an assay may be provided in kit form. For example, a typical kit will include a probe reagent component comprising an oligonucletide including at least one labeled pyrazolo[3,4-d]pyrimidine, the oligonucleotide having a sequence complementary to that of the target nucleic acids; a denaturation reagent for converting double-stranded nucleic acid to single-stranded nucleic acid; and a hybridization reaction mixture. The kit can also include a signal-generating system, such as an enzyme for example, and a substrate for the system.

The following examples are provided to illustrate the present invention without limiting same. "RT" means room temperature. EXAMPLE l :

6-(Tritylamino)caproic Acid.

6-Aminocaproic acid (26 g, 0.2 mmole) was dissolved in dichloromethane (200 mL) by the addition of triethylamine (100 L) . Trityl chloride (120 g, 0.45 mmole) was added and the solution stirred for 36h. The resulting solution was extracted with IN HC1 and the organic layer evaporated to dryness. The residue was suspended in 2-propanol/lN NaOH (300 mL/100 mL) and refluxed for 3h. The solution was evaporated to a thick syrup and added to dichloromethane (500 mL) . Water was added and acidified. The phases were separated, the organic layer dried over sodium sulfate, and evaporated to dryness. The residue was suspended in hot 2-propanol, cooled, and filtered to give 43.5 g (58%) of 6-(tritylamino)caproic acid, useful as an intermediate compound.

EXAMPLE ?:

5-(Tritylamino)pentylhydroxymethylenemalononitrile.

To a dichloromethane solution of 6-(tritylamino)caproic acid (20.0 g, 53 mmole) and triethylamine (20 L) in an ice bath was added dropwise over 30 min i-butylchloroformate (8.3 mL, 64 mmole). After stirring for 2 hr in an ice bath, freshly distilled malononitrile (4.2 g, 64 mmole) was added all at once. The solution was stirred for 2 hr in an ice bath and for 2 hr at RT. The dichloromethane solution was washed with ice cold 2N HCl (300 mL) and the biphasic mixture filtered to remove product that precipitates (13.2 g) . The phases were separated and the organic layer dried and evaporated to a thick syrup. The syrup was covered with dichloromethane and on standing deposited fine crystals of product. The crystals were filtered and dried to give 6.3 g for a total yield of 19.5 g (87%) of the product, which is useful as an intermediate.

EXAMPLE 3: 5-(Tritylamino)pentylmethoxymethylenemalononitrile.

A suspension of the malononitrile of Example 2 (13 g, 31 mmole) in ether/dichloromethane (900 mL/100 mL) , cooled in an ice bath, was treated with a freshly prepared ethereal solution of diazomethane (from 50 mmole of Diazald/ (Aldrich Chemical Company) ) . The solution was stirred for 6 hr and then neutralized with acetic acid (10 mL) . The solution was evaporated to dryness and the residue chromatographed on silica gel using dichlormethane/acetone (4/1) as the eluent.

Fractions containing product were pooled and evaporated to a syrup. The syrup was triturated with dichloromethane to induce crystallization. The crystals were filtered and dried to give 8.3 g (61%) of chromatographically pure product, useful as an intermediate compound.

EXAMPLE 4:

5-Amino-3-[(5-tritylamino)pentyl]pyrazole-4-carbonitri- I^®.

To a methanol solution (100 L) of the product of Example 3 (7.0 g, 16 mmole) in an ice bath was added hydrazine monohydrate (7.8 mL, 160 mmole) dropwise over 15 min. After stirring for 30 min in an ice bath, the solution was evaporated to dryness. The residue was suspended in cold methanol and filtered to give 7.1 g (100%) of 5-amino- 3-[ (5-tritylamino)pentyl]pyrazole-4-carbonitrile, useful as an intermediate, after drying. An analytical sample was prepared by recrystallization from water. EXAMPLE 5 :

5-Amino-l- (2-deoxy-3 , 5-di-O-toluoyl-,0-D-erythropentofu- ranos- yl) -3- [ (5-tritylamino) pentyl ]pyrazole-4-carbonitrile.

An ice cold solution of the carbonitrile from

Example 4 (3.5 g, 8 mmole) was treated with sodium hydride and stirred for 30 min at 0-4*C.

1-Chloro-l,2-dideoxy-3,5- di-O-toluoylribofuranose was added and the solution stirred for 1 hr at 0-4'C. The solution was poured into a saturated solution of sodium bicarbonate and extracted with dichloromethane. The organic layer was dried over sodium sulfate and evaporated to dryness. The residue was flash chromatographed on silica gel using toluene/ethyl acetate (5/1) as eluent. Two major products were isolated and identified as the N-l and N-2 isomers in 57% (3.6 g) and 20% N-l and N-2 (1.2 q) yields, respectively. Approximately 1 g of a mixture of NI and ^N2 isomers was also collected. Overall yield of glycosylated material was 5.8 g (92%). The NI isomer, 5-amino-l-(2-deoxy-3,5-di-0-toluoyl-,5-J3-erythro- pentofuranosyl)-3-[ (5-tritylamino)pentyl]pyrazole-4- carbonitrile, was used without further purification in Example 6.

EXAMPLE 6: l-(2-Deoxy- -£-eι_ythropentofuranosyl)-3-[5-(tritylamin- o)pentyl]pyrazolo[3,4-d]pyrimidin-4-amine.

To a toluene (100 mL) solution of the pyrazole-4- carbonitrile of Example 5 (3.5 g, 4.4 mmole) was added diethoxymethyl acetate (1.1 L, 6.7 mmole) . The solution was kept at 80-90'C for 5 hr and then evaporated to a syrup. The syrup was dissolved in dichloromethane (10 mL) and added to ice cold methanolic ammonia (100 mL) in a glass pressure bottle. After two days at RT the contents of the bottle were evaporated to dryness. The residue was dissolved in methanol and adjusted to pH 8 with freshly prepared sodium methoxide to complete the deprotection. After stirring overnight the solution was treated with Dowex»-50 H+ resin, filtered, and evaporated to dryness. The residue was chromatographed on silica gel using acetone/hexane (3/2) as eluent to give 2.0 g (77%) of analytically pure product.

EXAMPLE 7: l-(2-Deoxy- -D-erythro-pentofuranosyl)-3-[5-(tritylami¬ no)ρentyl]pyrazolo[3,4-d]pyrimidin-4-amine 5•-monophosphate.

To an ice cold solution of the pyrazolopyrimidin-4-amine of Example 6 (250 mg, 0.43 mmole) in trimethyl phosphate (5 mL) was added phosphoryl chloride (50 μL) and the solution kept at 0-4^•C. The reaction was monitored by reversed phase HPLC using a linear gradient from 0 to 100% acetonitrile in water over 25 min. After stirring for 5 hr an additional aliquot of phosphoryl chloride (25 μL) was added and the solution stirred another 30 min. The solution was poured into 0.1M ammonium bicarbonate and kept in the cold overnight. The solution was then extracted with ether and the aqueous layer evaporated to dryness. The residue was dissolved in water (5 mL) and purified by reversed phase HPLC using a 22mm X 50cm C18 column. The column was equilibrated in water and eluted with a gradient of 0 to 100% acetonitrile over 20 min. Fractions containing the desired material were pooled and lyophilized to give 160 mg (56%) of chromatographically pure nucleotide. EXAMPLE 8 :

1-(2-Deoxy-^-D-erythro-pentofuranosyl)-3-{5-[ (6-biotin- amido)hexamido]pentyl)pyrazolo[3,4-d]pyrimidin-4-amine 5•-monophosphate.

An ethanol solution (10 mL) of the nucleotide of Example 7, palladium hydroxide on carbon (50 mg) , and cyclo- hexadiene (1 L) was refluxed for 3 days, filtered, and evaporated to dryness. The residue was washed with dichloromethane, dissolved in DMF (1.5 mL) containing triethylamine (100 μL) , and treated with N-hydroxysuccinimi- dyl biotinylaminocaproate (50 mg) . After stirring overnight an additional amount of N-hydroxysuccinimidyl 6-biotinamidocaproate (50 mg) was added and the solution stirred for 18 hr. The reaction mixture was evaporated to dryness and chromatographed following the procedure in Example 7. Fractions were pooled and lyophilized to give 80 mg of chromatographically pure biotinamido-substituted nucleotide.

EXAMPLE 9:

1-(2-Deoxy-,9-D-erythro-pentofuranosyl)-3-[5-(6-biotina- mido)hexamidopentyl]pyrazolo[3,4-d]pyrimidin-4-amine 5^•-triphosphate.

The monophosphate of Example 8 (80 mg, ca. 0.1 mmole) was dissolved in DMF with the addition of triethylamine (14 μL) . Carbonyldiimidazole (81 mg, 0.5 mmole) was added and the solution stirred at RT for 18 hr. The solution was treated with methanol (40 μL) , and after stirring for 30 min tributylammonium pyrophosphate (0.5 g in 0.5 mL DMF) was added. After stirring for 24 hr another aliquot of tributylammonium pyrophosphate was added and the solution stirred overnight. The reaction mixture was evaporated to dryness and chromatographed following the procedure in Example 8. Two products were collected and were each separately treated with cone, ammonium hydroxide (1 mL) for 18 hr at 55'C. UV and HPLC analysis indicated that both products were identical after ammonia treatment and were pooled and lyophilized to give 35.2 mg of triphosphate nucleotide.

EXAMPLE 10: NICK-TRANSLATION REACTION

The triphosphate of Example 9 was incorporated into pHPV-16 using the nick tanslation protocol of Langer et al. The probe prepared with the triphosphate of Example 9 was compared with probe prepared using commercially available bio-11-dUTP

(Sigma Chemical Co) . No significant differences could be observed in both a filter hybridization and in in situ smears.

More specifically, the procedure involved the following materials and steps:

Materials:

DNase (ICN Biomedicals) - 4ug/ml DNA polymerase 1 (U.S. Biochemicals) - 8 U/ml pHPV - 16 - 2.16 mg/ml which is a plasmid containing the genomic sequence of human papillo avirus type 16. 10X-DP - 1M Tris,pH7.5(20ml) ; 0.5M

DTT(80 μl) ; 1M MgCl₂(2.8 ml) ; H₂0(17ml) Nucleotides - Mix A - 2mM each dGTP, dCTP, TTP (Pharmacia) Mix U - 2mM each dGTP, dCTP, dATP Bio-11-dUTP - 1.0 mg/ml (BRL) Bio-12-dAPPTP - 1.0 mg/ml

Steps: 5 To an ice cold mixture of 10X-DP(4μl) , pHPV-16(2μl) , nucleotide mix A (6 μl) , Bio-12-dAPPTP(2μl) , and H₂θ(20μl) was added DNase (lμl) and DNA polymerase 1 (2.4μl). The reaction mixture was incubated at 16*C for 1 hr. The procedure was repeated 0 using Bio-11-dUTP and nucleotide mix U in place of

Bio-12-dAPPTP (comprising the triphosphate of Example 9) and nucleotide mix A.

Nucleic acid was isolated by ethanol precipitation and hybridized to pHPV-16 slotted onto 5 nitrocellulose. The hybridized biotinylated probe was visualized by a streptavidin - alkaline phosphatase conjugate with BCIP/NBT substrate. Probe prepared using either biotinylated nucleotide gave identical signals. The probes were also tested in an in situ o format on cervical smears and showed no qualitative differences in signal and background.

EXAMPLE 11:

5-Amino-3-[ (5-tritylamino)pentyl]pyrazole-4-carboxamid- ^e-

Following the procedure of Example 2, except that cyanoaceta ide is used instead of malononitrile, 5-(trityl- amino)pentylhydroxymethylenecyanoacetamide is prepared from 6-(tritylamino)caproic acid. This is then treated with diazomethane to give the methoxy derivative, following the procedures of Example 3, which is then reacted with hydrazine monohydrate, as in Example 4, to give 5-amino-3- [ (5-tritylamino)pentyl]pyrazole-4-carboxamide. 24

EXAMPLE 12 :

4-Hydroxy-6-methylthio-3-[(5-tritylamino)pentyl]pyrazo- lo- [3,4-d]pyrimidine.

The carboxamide from Example 11 is reacted with potassium ethyl xanthate and ethanol at an elevated temperature to give the potassium salt of 4-hydroxypyrazolo- [3,4-d]pyrimidine-6-thiol. This salt is then reacted with iodomethane to give 4-hydroxy-6-methylthio-3-[(5-trityl- amino)pentyl]pyrazolo[3,4-d]pyrimidine.

EXAMPLE 13:

1-(2-Deoxy-^-D-erythro-pentofuranosyl)-4-hydroxy-3-[5- (tritylamino)pentyl]pyrazolo[3,4-d.]pyrimidin-6-amine.

Following the procedure of Example 5, the pyrazolopyrimidine of Example 12 is treated with sodium hydride and reacted with l-chloro-l,2-dideoxy-3,5-di-o- toluoylribofuranose. The resulting compound is reacted with MCPBA and with methanolic ammonia, and the toluoyl protecting groups are removed to give the product.

EXAMPLE 14: l-(2-Deoxy-0-JD-erythro-pentofuranosyl)-4-hydroxy-3-[5- (6-biotinamido)hexamidopentyl]pyrazolo[3,4-d]pyrimidin- -6- amine 5'-monophosphate.

Following the procedure of Example 7, the pyrazolopyrimidine of Example 13 is reacted with phosphoryl chloride to give the corresponding 5*-monophosphate.

Following the procedure of Example 8, the above 5--monophosphate is reacted with palladium/carbon and cyclohexadiene, and the residue is reacted with

N-hydroxy- succinimidyl biotinylaminocaproate to give 1-(2-deoxy-_/9-D-erythropentofuranosyl)-4-hydroxy-3-[5- (6-biotinamido)hexamidopentyl]pyrazolo[3,4-d]pyrimidin -6-amine 5'-monophosphate.

EXAMPLE 15: l-(2-Deoxy-/9-D-erythropentofuranosyl)-4-hydroxy-3-[5-(- 6-biotinamido)hexamidopentyl]pyrazolo[3,4-d]pyrimidin- 6-amine 5•-triphosphate.

Following the procedure of Example 9, the 5'-mono- phosphate of Example 14 is treated with carbonyldii idazole and then reacted with tributylammonium pyrophosphate to give the corresponding 5•-triphosphate.

EXAMPLE 16: l-(2-Deoxy-9-D-erythropentofuranosyl)-3-[5-(tritylamin- o)pentyl]pyrazolo[3,4-d]pyrimidine-4-benzoylamine.

l-(2-Deoxy- -D-erythropentofuranosyl)-3-[5-

(tritylamino)pentyl]pyrazolo[3,4-d]pyrimidine-4-amine from Example 6 is reacted with benzoyl chloride and pyridine to give l-(2-deoxy-3,5-di-Q-benzoyl- -D- erythropentofuranosyl)-3-[5-(tritylamino)pentyl] pyrazolo[3,4-d]pyrimidine-4-dibenzoylamine. This is treated with aqueous sodium hydroxide to partially deprotect the compound, giving l-(2-deoxy-,-D- erythropentofuranosyl)-3-[5-(tritylamino)- pentyl]pyrazolo[3,4-d]pyrimidine-4-benzoylamine. 26

EXAMPLE 17 :

1- (2-Deoxy-_jS-D-erythropentof uranosyl) -3- [ 5- ( trif luoroa- cet- amido) pentyl] pyrazolo [3 , 4-d]pyrimidine-4- benzoylamine .

Following the procedure of Example 8, the benzoyl- amine of Example 16 is treated with palladium hydroxide on carbon and then with trifluoroacetic anhydride to give l-(2-deoxy- -D-erythropentofuranosyl) -3-[5-(trifluoroacetamido)pentyl]pyrazolo[3,4-d] pyrimidine-4-benzoylamine.

EXAMPLE 18:

1-(2-Deoxy-5-O-dimethoxytrityl-0-D-erythropentofuranos- yl)-3-[5-(trifluoroacetamido)pentyl]pyrazolo[3,4-d] pyrimidine-4-benzoylamine 3 *-0-(N,N-diisopropyl) phosphora idite cyanoethyl ester.

The compound of Example 17 is reacted with di ethoxytrityl chloride and pyridine to give the corresponding 5*-dimethoxytrityl compound. This compound is then reacted with cyanoethyl chloro-N,N-diisopropylphosphor- amidite (according to the method of Sinha et al.. Nucleic Acids Res. 12:4539 (1984)) to give the 3'-o-activated nucleoside.

From the foregoing, it will be appreciated that the compositions of the present invention are novel and are useful for diagnostic purposes.

Although the present invention has been described in some detail by way of example for purposes of clarity and understanding, it will be apparent that other arrangements and equivalents are possible and may be employed without departing from the spirit and scope of the invention. Therefore, the description and illustrations should not be construed as limiting the scope of the invention, which is delineated by the appended claims.

Claims

WHAT IS CLAIMED IS:

1. A compound of the following formula (I) :

R_l is hydrogen, or a sugar moiety optionally substituted at its 3' or its 5* position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; provided that when R₃ is hydrogen then Ri cannot be hydrogen;

R₃ is hydrogen or the group -W-(X)_n-A; each of W and X is independently a chemical linker arm; A is an intercalator, an electrophilic crosslinker or a reporter group; each of R₄ and R₆ is independently H, OH, SR, NH₂, or NH(CH₂)_tNH₂;

R is H or Cx-galkyl; n is zero or one; and t is zero to twelve.

2. A compound according to Claim 1 wherein R3 is the group -W-(X)_n-A, and A is a reporter group.

3. A compound according to Claim 2 wherein each of W and X is independently C!_₁₂alkylene, Cι_ι alkenylene, Cι_ι alkynylene, or such groups substituted at a terminal point with an oxy, thio, or amino, or a blocked derivative thereof. 4. A compound according to Claim l wherein _l is a sugar moiety optionally substituted at its 3* or its 5' position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for c nucleotide bond formation.

5. A compound according to Claim 2 wherein l is a sugar moiety optionally substituted at its 3 ' or its 5* position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation.

6. A compound according to Claim 1 wherein each of R₄ and Rg is independently H, OH, or NH₂.

7. A compound according to Claim 1 wherein the sugar moiety is ribose, deoxyribose or arabinose.

wherein,

Rl is hydrogen, or a sugar moiety optionally substituted at its 3' or its 5' position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; each of W and X is independently a chemical linker arm;

A is a reporter group; each of R4 and Rg is independently H, OH, SR, NH₂, or NH(CH₂)_tNH₂;

R is H or Ci- alkyl; n is zero or one; and 30 t is zero to twelve.

9. A compound according to Claim 8 wherein each of W and X is independently Cι_ι alkylene,

5 Cι_ι alkenylene, C^^alkynylene, or such groups substituted at a terminal point with an oxy, thio, or amino or a blocked derivative thereof.

10. A compound according to Claim 8 wherein _Q i is a sugar moiety optionally substituted at its 3' or its 5' position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation.

11. A compound according to Claim 10 wherein the sugar moiety is ribose, deoxyribose or arabinose.

12. A compound according to Claim 8 wherein each of R₄ and Rg is independently H, OH, or NH₂. 0

13. A compound according to Claim 10 wherein each of R and Rg is independently H, OH, or NH₂.

14. A compound according to Claim 8 wherein 5 the reporter group is biotin.

15. A compound according to Claim 14 wherein the group -W-(X)_n- is -C₁_₁₂alkyl-NH-C(0)-C₁_₁₂alkyl-NH-. 0

16. An oligonucleotide sequence which comprises at least one of the following:

5 (I)

wherein ,

R_l is a sugar moiety optionally substituted at its 3' or its 5' position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation;

R3 is hydrogen or the group -W-(X)_n-A; each of W and X is independently a chemical linker arm;

A is an intercalator, an electrophilic crosslinker or a reporter group; each of R₄ and Rg is independently H, OH, SR, NH₂, or NH(CH₂)_tNH₂;

R is H or C _galkyl; and t is zero to twelve.

17. An oligonucleotide sequence according to

Claim 16 wherein R3 is the group -W-(X)_n-A, and A is a reporter group.

¹⁸- ^An oligonucleotide sequence according to

Claim 17 wherein each of W and X is independently Cι_ι₂alkylene, Cι-i2^a*-^L*'^{cen lene}' Cι_χ₂alkynylene, or such groups substituted at a terminal point with an oxy, thio, or amino or blocked derivative thereof.

19. An oligonucleotide sequence according to Claim 16 wherein each of R₄ and Rg is independently H, OH, or NH₂.

20. An oligonucleotide sequence according to

Claim 16 wherein the sugar moiety is ribose, deoxyribose or arabinose.

21. An oligonucleotide sequence which comprises at least one of the following:

Rl is a sugar moiety optionally substituted at its 3¹ or its 5* position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; 0 each of W and X is independently a chemical linker arm;

A is a reporter group; each of R₄ and Rg is independently H, OH, SR, NH₂, or NH(CH₂)_tNH₂; 5 R is H or C _₆alkyl; n is zero or one; and t is zero to twelve.

22. An oligonucleotide sequence according to o Claim 21 wherein each of W and X is independently

Cι_ι₂alkylene, Cι_ι₂alkenylene, Cι-i2^a _"-*ΥⁿY-- ^ne ' ^or such groups substituted at a terminal point with an oxy, thio, amino or blocked derivative thereof.

5 23. An oligonucleotide sequence according to

Claim 21 wherein the sugar moiety is ribose, deoxyribose or arabinose.

24. An oligonucleotide sequence according to 0 Claim 21 wherein each of R₄ and Rg is independently H,

OH, or NH₂.

25. An oligonucleotide sequence according to Claim 21 wherein the reporter group is biotin. 5 26. An oligonucleotide sequence according to Claim 25 wherein the group -w-(X)_n- is -C₁_₁₂alkyl-NH-C(0)-C₁>₁₂alkyl-NH-.

27. A method for identifying target nucleic acid sequences, which method comprises utilizing an oligonucleotide probe including at least one labeled pyrazolo[3,4-d pyri__nidiτιe of formula (la) as defined in Claim 8.

28. A method according to Claim 27 which comprises the steps of:

(a) denaturing nucleic acids in the sample to be tested; (b) hybridizing to the target nucleic acids an oligonucleotide probe including at least one labeled substituted pyrazolo[3,4-d]pyrimidine of formula (la), wherein the probe comprises a sequence complementary to that of the target nucleic acids; (^c) washing "the sample to remove unbound probe; and

(d) detecting duplex formation between the target and probe nucleic acids.

29. An assay for identifying target nucleic acid sequences, -which assay comprises utilization of an oligonucleotide probe including at least one labeled substituted pyrazolo[3,4-d]pyrimidine of formula (la) as defined in Claim 8.

30. A kit for identifying target nucleic acid sequences, which kit comprises a probe reagent component comprising an oligonucleotide including at least one labeled substituted pyrazolo[3,4-d]pyrimidine of formula (la) as defined in Claim 8, the oligonucleotide having a sequence complementary to that of the target nucleic acids; a denaturation reagent for converting double-stranded nucleic acid to single-stranded nucleic acid; and a hybridization reaction mixture.

31. A process for the synthesis of 3,4-disubstituted pyrazolo[3,4-d pyrimidines of the following formula

wherein,

R_l is hydrogen, or a sugar moiety optionally substituted at its 3' or its 5* position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; provided that when 3 is hydrogen then i cannot be hydrogen;

A is an intercalator, an electrophilic crosslinker or a reporter group; and n is zero or one; which process comprises a) reacting a

3-substituted-5-aminopyrazole-4- carbonitrile of formula VI

wherein Ri, and R₃ are as defined above, with a dialkoxymethyl ester of a carboxylic acid at room temperature or above room temperature; and b) reacting the resulting intermediate with ammoni . 32. A process for the synthesis of 3 , 4-disubstituted pyrazolo[3 , 4-d] pyrimidines of the following formula

wherein,

Rl is hydrogen, or a sugar moiety optionally substituted at its 3• or its 5' position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; provided that when R3 is hydrogen then Ri cannot be hydrogen;

R₃ is hydrogen or the group -W-(X)_n-A; each of W and X is independently a chemical linker arm;

A is an intercalator, an electrophilic crosslinker or a reporter group; and n is zero or one; which process comprises a) reacting a 3-substituted-5-aminopyrazole-4- carboxamide of formula

wherein Rχ_r and R₃ are as defined above, with a dialkoxymethyl ester of a carboxylic acid at room temperature or above room temperature.

33. A process for the synthesis of 3,4,6-tri- substituted pyrazolo[3,4-d.]pyrimidines of the following formula

wherein,

R_l is hydrogen, or a sugar moiety optionally substituted at its 3' or its 5• position with monophosphate, diphosphate, triphosphate, or a reactive group suitable for nucleotide bond formation; provided that when R₃ is hydrogen then Ri cannot be hydrogen;

A is an intercalator, an electrophilic crosslinker or a reporter group;

R₄ is OH or NH₂;

Rg is H, OH, SR, NH₂, or NH(CH₂)_tNH₂;

R is H or Cι_galkyl; n is zero or one; and t is zero to twelve; which process comprises a) reacting a 3-substituted-5-aminopyrazole-4- carbonitrile of formula VI or a 3-substituted-5-aminopyra- zole-4-carboxamide of formula VII

wherein, each of i, R3, Rg, W, X, A, R, n and t are as defined above, with an alkyl xanthate salt and with an alkyl halide, at a temperature above room temperature; b) oxidizing the subsequent intermediate with a peroxide; and c) where Rg is other than -SR, reacting the subsequent intermediate with a group Rg-H. 34. The process of Claim 33 wherein Rg is an amine.