(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)

(19) World Intellectual Property Organization International Bureau

(10) International Publication Number (43) International Publication Date PCT 16 October 2008 (16.10.2008) WO 2008/122988 Al

(51) International Patent Classification: (74) Agents: SUBRAMANIAM, Hariharan et al; SUBRA- C07C 46/10 (2006.01) C07C 50/32 (2006.01) MANIAM, NATARAJ & ASSOCIATES, Patent & Trade mark Attorneys, E 556, Greater Kailash-II, New Dehli 110 (21) International Application Number: 048 (IN). PCT/IN2008/000216 (81) Designated States (unless otherwise indicated, for every (22) International Filing Date: 3 April 2008 (03.04.2008) kind of national protection available): AE, AG, AL, AM, AO, AT,AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, (25) Filing Language: English CH, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, (26) Publication Language: English IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, (30) Priority Data: MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PG, PH, 686/MUM/2007 5 April 2007 (05.04.2007) IN PL, PT, RO, RS, RU, SC, SD, SE, SG, SK, SL, SM, SV, SY, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, (71) Applicant and ZA, ZM, ZW (72) Inventor: CADILA HEALTHCARE LIMITED (84) Designated States (unless otherwise indicated, for every [IN/IN]; Zydus Tower, Satellite Cross Roads, Amedad- kind of regional protection available): ARIPO (BW, GH, abad 380 015, Gujara (IN). GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, TM), (72) Inventors; and European (AT,BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, (75) Inventors/Applicants (for US only): VERMA, Shyam, FR, GB, GR, HR, HU, IE, IS, IT, LT,LU, LV,MC, MT, NL, Sunder [IN/IN]; Zydus Tower, Satellite Cross Roads, NO, PL, PT, RO, SE, SI, SK, TR), OAPI (BF, BJ, CF, CG, Ahmedabad 380 015, Gujarat (IN). PATEL, Dhi- CI, CM, GA, GN, GQ, GW, ML, MR, NE, SN, TD, TG). πiant, Jasubhai [IN/IN]; Zydus Tower, Satellite Cross Roads, Ahmedabad 380 015, Gujarat (IN). DWIVEDI, Declaration under Rule 4.17: Shriprakash, Dhar [IN/IN]; Zydus Tower, Satellite Cross — as to applicant's entitlement to applyfor and be granted a Roads, Ahmedabad 380 015, Gujarat (IN). patent (Rule 4.17(U)) [Continued on next page]

(54) Title: PROCESS FOR PREPARATION OF ATOVAQUONE AND THE CONVERSION OF CIS-ISOMER TO TRANS- ISO MER

FIGURE I

(57) Abstract: Substantially pure atovaquone and parocess for the preparation thereof is disclosed. Published: PROCESS FOR PREPARATION OF ATOVAQUONE AND THE CONVERSION OF CIS-ISOMER TO TRANS- ISOMER

The present invention relates a process for the preparation of Atovaquone of formula (I).

More particularly, the present invention relates to the process for the preparation of Atovaquone substantially free from its cis isomer. The present invention also provides the process for the preparation of purification of Atovaquone. BACKGROUND OF THE INVENTION Pneumocystis carinii is a parasite, which has a natural habitat in lung tissue, in a host with normal immune system. Without treatment Pneumocystis carinii pneumonia is almost always fatal in immune compromised host. U.S. Pat. No. 4,981,874 discloses the process of preparation and the activity of the Atovaquone. U.S. Pat. No. 5053432 disclosed route of synthesis of atovaquone. In condensation of 2-chloro-l, 4-naphthoquinone and 4-(4-chlorophenyl) cyclohexane-1- carboxylic acid in presence of silver nitrate and ammonium persulphate then extracted with chloroform also treated with acetonitrile gives a poor yield 35%. Here cis-isomer more generated, another disadvantage is last steps treated with KOH give 57% yield. Thus obtained Atovaquone so in this patent several disadvantages. The process for the preparation of Atovaquone was also reported in Tetrahedron Letters, Vol. 39, 7629-7632 (1998), article as shown in below scheme:

As above disclosed process suffers with several drawbacks, as it requires to purification by recrystallization from acetonitrile. The solubility of Atovaquone in acetonitrile is very less and the high amount acetonitrile required. Moreover, it provides crystalline floppy material, which is difficult to handle at formulation development end. WO2006008752 discloses three polymorphic forms of Atovaquone designated as Form-I, Form-II and Form-Ill. The patent application discloses that Form-I is prior art form. OBJECTS OF THE INVENTION It is an important object of the present invention to provide a process for the preparation of Atovaquone of formula (I). Another object of the present invention is to provide a process for the preparation of Atovaquone substantially free of its c/s-ismer. Yet another object of the present invention is to provide a process for the purification of Atovaquone of formula (I). Another embodiment of invention cis-isomer converted to trans-isomer. BRIEF DESCRIPTION OF THE DRAWINGS FIG. I XRPD of cis-isomer of 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyI]- [1,4]naphthoquinone. FIG. π DSC of cis-isomer of 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]- [1,4]naphthoquinone. FIG. π i XRPD of trans-isomer of 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]- [1,4]naphthoquinone. FIG. IV DSC of trans-isomer of 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]- [1,4]naphthoquinone. FIG. V XRPD of Cis-isomer of Atovaquone. FIG. VI DSC of Cis-isomer of Atovaquone. FIG. VII XRPD of trans-isomer of Atovaquone. FIG. Vi π DSC of trans-isomer of Atovaquone. FIG. IX particle size of trans-isomer of 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]- [l,4]naphthoquinone. FIG. X Particle size of Cis-isomer of Atovaquone. FIG. XI Particle size of trans-isomer of Atovaquone. FIG. XII HPLC graph of free from cis-isomer. DETAILED DESCRIPTION OF THE INVENTION As used herein the term "substantially pure atovaquone" means it contains less than about 0.1% of individual impurity. As used here in the term "atovaquone substantially Pure" means it atovaquone containing less than about 0.1% of cis-atovaquone. According to the present invention, there is provided a process for the preparation of Atovaquone of formula (I), which comprises the steps of (i) condensing 2-chloro-l,4-naphthoquinone of formula (II) with 4-(4- chlorophenyl)cyclohexane-l-carboxylic acid of formula (III) in presence of silver nitrate and ammonium persulfate to provide 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-1,4-naphthoquinone of formula (IV)

(II) (III) (ii) treating 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone of formula (IV) with alkali base in mixture of alcoholic solvent and halogenated solvent followed by treatment with mineral acid to provide Atovaquone of formula (I). (IV) The step of preparing the compound of formula (IV) by reacting 2-chloro-l,4- naphthoquinone of formula (II) with 4-(4-chlorophenyl)cyclohexane-l-carboxylic acid of formula (III) is carried out at a temperature in the range of 70-1000C, preferably, temperature range of 75-85°C. It is preferable to avoid solvent like sulpholane. This reaction condition gives high yield and purity. According to an embodiment of the present invention, 2-chloro-l,4-naphthoquinone of formula (II) is reacted with 4-(4-chlorophenyl)cyclohexane-l-carboxylic acid of formula (III) in the presence of silver nitrate and ammonium persulfate to provide 2-[4- (4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone of formula (IV). The reaction is preferably carried out in polar solvent such as acetonitrile. Thus obtained 2- [4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone of formula (IV) may contain a mixture of cis and trans isomer. The ratio of trans: cis isomer may be in the range of 99:1 to about 1:99, preferably it may be in the range of 70:30 to 60:40 In another embodiment of present invention is formula (IV), any cis-isomer produced is converted to trans-isomer by dissolving it in organic solvent and heating it to reflux temperature.

The organic solventa are selected from group comprising of ketones like acetone, methyl ethyl ketone, methyl isobutyl ketone, methyl isopropyl ketone and methyl tert-butyl ketone; alcohols like , ethanol, isopropyl alcohol and tert- butyl alcohol etc., esters like methyl acetate, ethyl acetate, n-butyl acetate, tert-butyl acetate, halogenated alkanes like dichloromethane, aromatic hydrocarbons like toluene, xylene etc., preferably xylene. The alkali metal base is selected from , hydroxide, sodium methoxide, sodium ethoxide, potassium methoxide, potassium ethoxide, potassium tert-butoxide. The preferred alkali metal base is . According to an embodiment of the present invention, the solvent system of step (i) comprises of a mixture of alcoholic solvent and halogenated solvent. The preferred alcoholic solvent is selected from methanol, ethanol, n-propanol, isopropanol, n-butanol and halogenated solvent selected from methylene dichloride, ethylene dichloride, chloroform, carbon tetrachloride. An another embodiment of the invention is treating 2-[4-(4-chlorophenyl) cyclohexyl]-3-chloro-l,4-naphthoquinone of formula (IV) with alkali base in mixture of alcoholic solvent and halogenated solvent followed by treatment with mineral acid to provide Atovaquone of formula (I). In another embodiment of present invention is formula (IV), any cis-isomer produced is converted to trans-isomer by dissolving it in organic solvent and heating it to reflux temperature.

m-Atovaquone rαns-Atovaquone

The organic solvents are selected from group comprising of ketones like acetone, methyl ethyl ketone, methyl isobutyl ketone, methyl isopropyl ketone and methyl tert-butyl ketone; alcohols like methanol, ethanol, isopropyl alcohol and tert- butyl alcohol etc., esters like methyl acetate, ethyl acetate, n-butyl acetate, tert-butyl acetate, halogenated alkanes like dichloromethane, aromatic hydrocarbons like toluene, xylene etc., preferably xylene. The alkali metal base is selected from sodium hydroxide, potassium hydroxide, sodium methoxide, sodium ethoxide, potassium methoxide, potassium ethoxide, potassium ter/-butoxide. The preferred alkali metal base is potassium hydroxide. According to embodiment of the present invention, the solvent system of step (ii) comprised of mixture of alcoholic solvent and halogenated solvent. The preferred alcoholic solvent is selected from methanol, ethanol, n-propanol, isopropanol, n-butanol and halogenated solvent selected from methylene dichloride, ethylene dichloride, chloroform, carbon tetrachloride. The present invention further provides a process for the purification of atovaquone, which comprises treating atovaquone with alkali base in suitable solvent to form solution of alkali salt of atovaquone and treating it with acid to provide "substantially pure atovaquone". According to the preferred embodiment of the present invention, atovaquone is treated with alkali base selected from sodium hydroxide, potassium hydroxide, sodium methoxide, sodium ethoxide, potassium methoxide, potassium ethoxide, potassium tert- butoxide to form solution of alkali salt of atovaquone. The reaction is preferably carried out in suitable solvent. The solvent system is preferably selected so as to facilitate the salt reaction and to provide solution of alkali salt of atovaquone or subsequent separation of the alkali salt of atovaquone. Advantageously, both atovaquone and the alkali base are dissolvable, at least partly, in the solvent system, at least at elevated temperatures. In the process, a mixture, slurry, or solution of atovaquone and a solvent may be contacted with alkali base, or conversely, a mixture, slurry, or solution of alkali base and a solvent may be contacted with atovaquone. In another embodiment, both atovaquone and alkali base combined with a solvent system prior to being contacted together, whereby the solvent system used for alkali base may be identical with or different from the solvent system used for atovaquone. The solvent system can be comprised of a single solvent or a mixture of solvents. Suitable solvents include water, a lower alcohol (Cl- C6) such as methanol, ethanol, isopropanol, n-propanol, n-butanol, iso-butanol, /er/-butanol; ester such as ethyl acetate, isopropyl acetate, butyl acetate, iso-butyl acetate; ketone such as acetone, methyl ethyl ketone, methyl /ert-butyl ketone; ether such as tetrahydrofuran, di ethyl ether, diisoproipyl ether, dioxane and the like. The temperature of contact of atovaquone and alkali base in the solvent system is from ambient to the boiling point of the solvent system, with elevated temperatures, but generally less than the boiling point, being preferred. It is not required that a complete solution is formed in this step, i.e. a slurry is also possible, though a single solution is generally preferred. The atovaquone alkali salt can be isolated or recovered from the salt forming reaction by any convenient means. For example, the atovaquone alkali metal salt can be precipitated out of a solution or reaction mixture. The precipitation may be spontaneous depending upon the solvent system used and the conditions. Alternatively, the precipitation can be induced by reducing the temperature of the solvent, especially if the initial temperature at contact is elevated. Thus obtained alkali salt of atovaquone is treated with mineral acid or organic acid such as HCl, H2SO4, HNO3, and acetic acid to provide substantially pure atovaquone. Thus obtained atovaquone is substantially pure from and having individual impurities less than 0.1%. Figure-XII typically shows the HPLC chromatogram of the substantially pure Atovaquone. According to the another embodiment of the present invention, there is provided a process for the preparation of cis- isomer of 2-[4-(4-chlorophenyl) cyclohexyl]-3- chloro-l,4-naphthoquinone of formula (IV). 2-[4-(4-chlorophenyl) cyclohexyl]-3- chloro-l,4-naphthoquinone treated with organic solvent and then treated with alcoholic solvent. The preferred alcoholic solvent is selected from methanol, ethanol, n-propanol, isopropanol, n-butanol and organic solvent is a halogenated solvent selected from methylene dichloride, ethylene dichloride, chloroform, carbon tetrachloride, preferably methylene dichloride and methanol. According to the another embodiment of the present invention, there is provided a process for the preparation of trans- isomer of 2-[4-(4-chlorophenyl) cyclohexyl]-3- chloro-l,4-naphthoquinone of formula (IV). 2-[4-(4-chlorophenyl) cyclohexyl]-3- chloro-l,4-naphthoquinone treated with organic solvent. The preferred organic solvent is selected from group comprising of ketones like acetone, methyl ethyl ketone, methyl isobutyl ketone, methyl isopropyl ketone and methyl tert-butyl ketone; alcohols like methanol, ethanol, isopropyl alcohol and tert- butyl alcohol etc., esters like methyl acetate, ethyl acetate, n-butyl acetate, tert-butyl acetate, halogenated alkanes like dichloromethane, ether such as tetrahydrofuran, diethyl ether, disopropyl ether, dioxane and the like, nitriles such as acetonitrile preferably tetrahydro furan and acetonitrile. According to the another embodiment of the present invention, there is provided a process for the preparation of cis isomer of Atovaquone formula (I). Cis/trans isomer of Atovaquone treated with organic solvent . The organic solvent is selected from halogenated alkanes like dichloromethane and nitriles such as acetonitrile preferably dichloromethane and acetonitrile. According to another embodiment of the present invention, there is provided control synthesis of atovaquone drug substance to insure that level of cw-atovaquone is at low levels. According to the present invention, a level of not greater than about 0.1% of cw-atovaquone. The present invention pertains to atovaquone compositions comprising levels of c/s-atovaquone of up to but not greater than about 0.1% and to methods for controlling the levels of cw-atovaquone to up to but not greater than about 0.1% in a atovaquone composition. The preset invention further relates to atovaquone composition comprising low levels of cw-atovaquone, preferably not greater than about 0.1% c/s-atovaquone, more preferably not greater than about 0.05% c/s-atovaquone, and even more preferably not greater than about cis-Atovaquone 0.01% c/s-atovaquone. In a more specific embodiment, this invention provides a method of synthesizing atovaquone composition that comprises an amount of c/s-atovaquone of not greater than about 0.1%, which method comprises: a) obtaining one or more samples of one or more 2-[4-(4-chlorophenyl)cyclohexyl]-3- chloro-1,4-naphthoquinone batches; b) measuring the level of c/s-2-[4-(4-chlorophenyl)cyc!ohexyl]-3-chloro-l,4- naphthoquinone impurity in each of the samples of (a); c) selecting a 2-[4-(4-chlorophenyI)cyclohexyl]-3-chloro-l,4-naphthoquinone batch that comprises a level of cis isomeric impurity of not greater than about 0.4% based on the measurement or measurements conducted in (b); and d) using the batch selected in (c) to synthesize said atovaquone composition. In one embodiment, step (c) comprises selecting a 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone batch that comprises a level of c/s-isomeric impurity of not greater than about 0.15%. In a preferred embodiment, step (c) comprises selecting a 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4- naphthoquinone batch that comprises a level of c/s-isomeric impurity of not greater than about 0.05%. The level of cw-isomeric impurity in a sample of a batch of 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone can be determined using Standard analytical techniques known to those of ordinary skill in the art. For example, the level of cw-isomeric impurity may be determined by normal phase HPLC, reverse phase HPLC, or gas chromatography methods. This invention also provides a method of synthesizing atovaquone composition that comprises an amount of cw-atovaquone of not greater than about 0.1%, which method comprises: a) condensing 2-chloro-l,4-naphthoquinone of formula (II) or its salts with 4-(4- chlorophenyl)cyclohexane-l-carboxylic acid of formula (III) or its salts in presence of silver nitrate and ammonium persulfate to provide 2-[4-(4-chlorophenyl)cyclohexyl]-3- chloro-l,4-naphthoquinone of formula (IV); b) isolating a sample of the composition resulting from (a); c) measuring the quantity of cis- 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4- naphthoquinone impurity in the isolated sample from (b); d) determining whether or not the quantity in (c) is not greater than about 0.40%; and e) purifying by treating the composition resulting from (a) with organic solvent, if the quantity measured in (c) is greater than about 0.40% until the quantity of cis- 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone impurity is not greater than about 0.40%, and synthesizing a atovaquone composition from the composition so purified; or, f) if the quantity in (c) is not greater than about 0.40%, synthesizing a atovaquone composition from the composition of (a). In one embodiment, the purification of a composition comprising 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone in step (e) is carried out by slurrying or suspending or dissolving in organic solvent at about 0° C to elevated temperature for sufficient time. According to the present invention, there is provided a process for the preparation of atovaquone substantially free from cw-atovaquone impurity, which comprises treating crude atovaquone with organic solvent selected from ketones, Cl- C5 alcohols, esters, halogenated solvent, aromatic hydrocarbons and isolating atovaquone substantially free from cw-isomer. According to the preferred embodiment of the present invention, crude atovaquone is slurried or suspended or dissolved in organic solvent selected from ketones, C1-C5 alcohols, esters, halogenated solvent, aromatic hydrocarbons at about 0° C to elevated temperature for sufficient time to form atovaquone substantially free from c/s-isomer, which is isolated by conventional process such as evaporation of solvent, cooling followed by filtration, by addition of anti solvent or freeze drying. The present invention further relates to the substantially pure cw-isomer of 2-[4- (4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone, which can be used as reference marker for the determination of purity of 2-[4-(4-chlorophenyl)cyclohexyl]-3- chloro-l,4-naphthoquinone. The substantially pure c/s-isomer of 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone is characterized by its powder X-ray diffraction pattern having peaks expressed as 2Θat about 7.3, 15.0, 17.9, 20.0, 25.4±0.2 degrees. The substantially pure e/s-isomer of 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone is further characterized by its powder X-ray diffraction pattern as shown in Figure- 1. FIG. 2 shows DSC analysis of typical substantially pure c/s-isomer of 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4- naphthoquinone. The present invention further relates to the substantially pure trans-isomer of 2- [4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone, which can be used for the formation of substantially pure atovaquone. The substantially pure trans-isomer 2- [4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone is characterized by its powder X-ray diffraction pattern having peaks expressed as 2Θat about 7.2, 21.6, 25.2, 28.9±0.2 degrees. The substantially pure trans-isomer of 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone is further characterized by its powder X-ray diffraction pattern as shown in Figure-Ill. FIG. IV shows DSC analysis of typical substantially pure trans-isomer of 2-[4-(4-chlorophenyl)cyclohexyl]-3- chloro-l,4-naphthoquinone. The particle size of trans-isomer of 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone is analyzed and found to be D(0.50):25.33 µm, D(0.90):91.83 µm as shown in Fig.IX. The present invention further relates to the substantially pure cw-atovaquone, which can be used as reference marker for the determination of purity. The substantially pure cw-atovaquone is characterized by its powder X-ray diffraction pattern having peaks expressed as 2Θat about 11.1, 17.9, 23.1, 24.3, 27.8±0.2 degrees. The substantially pure cw-atovaquone is further characterized by its powder X-ray diffraction pattern as shown in Figure-V. FIG. VI shows DSC analysis of typical substantially pure c/s-atovaquone. The particle size of cis isomer of Atovaquone is analyzed and found to be D(0.50):81.03 µm, D(0.90):183.04 µm as shown in Fig.X. The present invention further relates to the substantially pure Atovaquone. The substantially pure Atovaquone is characterized by its powder X-ray diffraction pattern having peaks expressed as 2Θ at about 10.7, 19.3, 19.9, 21.1, 24.6±0.2 degrees. The substantially pure atovaquone is further characterized by its powder X-ray diffraction pattern as shown in Figure- VII. FIG. VIII shows DSC analysis of typical substantially pure atovaquone. The particle size of atovaquone is analyzed and found to be D(0.50):81.03 µm, D(0.90):183.04 µm as shown in Fig.X. The HPLC analysis performed as follows: Column & Packing : Kromosil C 18 (250 x 4.6 mm, 5µ) Mobile Phase : Acetonitrile :Methanol : water : ortho phosphoric acid (500:175:325:5) Flow rate : 30 mL/min Wavelength : 220 nm Injection Volume : 2 1µL Run time : 60 min Diluent : Acetonitrile: water (80:20)

The present invention is demonstrated in examples illustrated below. These examples are provided as illustration only and therefore should not be construed as limitation of the scope of invention. Working Examples: Example-1 (a): Process for preparation of 2-Chloro-3-[4-(4-chIoro-phenyl)- cyclohexyl]-[l,4]naphthoquinone (cis/trans isomer). 2-Chloro-[l,4]naphthoquinone(600g 1.0 mole), trans-4-(p-chlorophenyl)- cyclohexane carboxylic acid (75Og 1.0 mole) ,water(3L) and acetonitrile(6L) were added to the reaction vessel and stirred at 25-350C. Silver nitrate (160.5g 0.3mole) was added and heated 75-85°C after then aq. Ammonium persulphate(1837.5g 2.6mole)was added at reflux temperature 75-850C for 5 hours. Then stirred for lhrours, after reaction was completed the acetonitrile was distilled, then cooled at, 10-200C and washed with water (500ml). Product was dried at 50-550C for 12 hours and 579g of dry product was obtained. (47% Yield) Example-1 (b): Purification of 2-ChIoro-3-[4-(4-chloro-phenyl)-cyclohexyl]- [l,4]naphthoqui πone (trans isomer). 579g of cured product of of 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]- [l,4]naphthoquinone dissolved in dichloromethane (2.8 liter) at 25-35 0C and stirred for 1 hour. Filter the product, filtrate use for next step. Example-2(a): Preparation of Atovaquone (cis/trans isomer). As per example 1 collect the MDC then added methanol (3.8 lit) at 25-35°C. Prepare the KOH solution (KOH (374 g 7.0v/w) added water (1.5Ht)), then this solution added for lor 2 hours time at 25-35 0C. Then stirred for 18 hours at 35-4O0C, after the complies of reaction then added con. HCl (450ml) adjust PH=2 then stirred for 30 min. Filter and wash with water (500ml). Dry the product at 50-550C for 12 hours. 600mg Yield = 67%.

Example-2 (b): Purification of Atovaquone (trans isomer). As per example 2 dissolved in THF (3 Lit) stirred for 30 min, added charcoal (15g) stirred for 1 hrs, filter and distilled THF at temperature 65-7O0C. added acetonitrile (6 lit.) and stirred for 1 hours cooled then filter it wash with acetonitrile (300 ml) for two times. Dry the product at 55-650C for 12 hours, 126g product obtains. Yield 22%. Example 3: Preparation of Atovaquone (Form I). To the compound of disclosed in example 2(b) (332g dissolved in methanol (2Lit)) was added a solution of methanolic KOH (102g in 1 Lit, 10% solution) slowly for 1 hour at temperature of 20-30 0C followed by filtration. The filtrate was neutralized with the help of cone. HCl (PH=2) then water was added (675 ml) and stirred for 1 hours till solid was obtained. It was filtered and washed with water (200ml) and acetone (100 ml). The product was dried at 50-550C for 12 hours. Yield 98%. Example 4: Preparation of conversion of Cis 2-Chloro-3-[4-(4-chloro-phenyl)- cyclohexyl]-[l,4]naphthoquinone to trans 2-Chloro-3-[4-(4-chloro-phenyl)- cyclohexyl]- [1,4]naphthoquinone. 2.0g of2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]-[l,4]naphthoquinone(cis) was added to xylene(10 ml) at temperature 20-300C, then refluxed at 120-1360C for 18 hours. Cooled at 20-300C and the product was filtered. Yield: 1.8-g. 90%, Purity 96.91%. Example 5: Preparation of conversion of Cis Atovaquone to trans Atovaquone. To 5.0g of Atovaquone (cis) xylene (30 ml) was added at temperature 20-300C, then refluxed at 120-1360C for 24 hours. Cooled at 20-300C and filtered the product 3.6-g. Yield 72% Purity 83.20%. Example 6: Preparation of trans 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]- [1,4]naphthoquinone. 32.2 g 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]-[l,4]naphthoquinone was taken and to it THF (162 ml) added at temperature 20-300C, then refluxed at 63-66°C for 1 hour. Added acetonitrile (324 ml) at temperature 63-650C. Cooled at 20-300C and again cooled to 0-100C. The product was filtered. 16.4-g. Yield 50.6%.[99.61 % trans isomer/ 0.06 cis isomer] Example 7: Preparation of cis 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]- [l,4]naphthoquinone. 14.8 g 2-Chloro-3-[4-(4-chloro-phenyl)-cyclohexyl]-[l,4]naphthoquinone was taken and to it, MDC (70 ml) was added at temperature 20-300C, then refluxed at 30- 42°C for 1 hour. It was cooled at 0-100C again. Filtered the product 3.6-g wash with methanol. Yield 24.3%.[75.7 % cis isomer/ 6.04 trans isomer] Example 8: Preparation of cis-isomer of Atovaquone a) 40 g cis/trans isomer mixture was taken and to it MDC (70 ml) was added. The reaction mass was stirred for 30 min. Further, charcoal 92.0 g) was added and the reaction mixture was filtered and solvent was distilled. To the reaction mixture acetonitrile (40 mL) was added and stirred. Finally, reaction mixture was filtered to obtain cis-isomer of Atovaquone (86% cis and 12% trans). b) 27 g of crude cis isomer of Atovaquone as obtained in a) was taken and treated with acetonitrile and refluxed at 75-81 0C. The reaction mass was filtered to obtain the cis-isomer of Atovaquone. (93.4% cis and 6.3% trans). We claim: 1. Substantially pure atovaquone.

2. Substantially pure atovaquone as claimed in claim 1, having cis-isomer not more than 0.5%., preferably not more than than 0.3%. 3. Substantially pure atovaquone as claimed in claim 1, having each individual impurity less than 0.1%. 4. A process for preparing frø«s-atovaquone which comprises : a) dissolving c/s-atovaquone in a suitable organic solvent; b) heating the reaction mixture to a temperature in the range of 25°C-160°C; c) cooling the reaction mixture to precipitate nms-atovaquone; and d) recovering /raws-atovaqoune. 5. A process for preparing rα/w-2-chloro-3-[4-(4-chlorophenyl)-cyclohexyl]-[l,4] naphthoquinone which comprises: a) dissolving cw-2-chloro-3-[4-(4-chlorophenyl)-cyclohexyl]-[ 1,4]naphthoquinone dissolved in a suitable organic solvent; b) heating the reaction mixture to a temperature in the range of 25°C-160°C; c) cooling the reaction mixture to precipitate frøws-atovaquone; and d) recovering /rørø-2-chloro-3-[4-(4-chlorophenyl)-cyclohexyl]-[l,4] naphthoquinone. 6. A process as claimed in claim 4 or 5 wherein suitable organic solvent is selected from the group consisting of non-polar organic solvents like toluene, xylene, hexane, heptane, cyclohexane and polar organic solvents like ketones like acetone, methyl ethyl ketone, methyl isobutyl ketone, methyl isopropyl ketone and methyl tert-butyl ketone; alcohols like methanol, ethanol, isopropyl alcohol and tert-butyl alcohol etc., esters like methyl acetate, ethyl acetate, n-butyl acetate, tert-butyl acetate, halogenated alkanes like dichloromethane, preferably xylene. 7. A process as claimed in claim 4 or 5 wherein step (b) is carried out at a temperature in the range of 125-1400C. 8. A process for the preparation of Atovaquone of formula (I), which comprises the steps of

(i) condensing 2-chloro-l,4-naphthoquinone of formula (II)

with 4-(4-chlorophenyl)cyclohexane-l-carboxylic acid of formula (III)

in presence of silver nitrate and ammonium persulfate in a suitable organic solvent

at temperature in the range of from 7O0C to 1000C to provide 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone of formula (IV), in absence of sulpholane;

(ii) treating 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone of formula (IV) with base in mixture of alcoholic solvent and halogenated solvent followed by treatment with mineral acid to provide Atovaquone of formula (I). 9. A process as claimed in claim 8 wherein suitable organic solvent is mixture of acetonitrile and water. 10. A process as claimed in claim 8 wherein the preferable temperature range is 75- 850C. 11. A process as claimed in claim 8 wherein base is selected from sodium hydroxide, potassium hydroxide, sodium methoxide, sodium ethoxide, potassium methoxide, potassium ethoxide, potassium tert-butoxide, preferably potassium hydroxide. 12. A process as claimed in claim 8 wherein said solvent system is comprised of mixture of alcoholic solvent and halogenated solvent. 13. A process as claimed in claim 12, wherein said alcoholic solvent is selected from methanol, ethanol, n-propanol, isopropanol, n-butanol and halogenated solvent selected from methylene dichloride, ethylene dichloride, chloroform, carbon tetrachloride. 14. A process for preparing atovaquone which comprises: a) dissolving atovaquone in a suitable organic solvent; b) adding base or alcoholic base at a suitable temperature; c) neutralizing the product of step (b) mineral acid or organic acid or water to isolate atovaqoune; and c) washing with water or organic solvent to provide pure atovaquone. 15. A process as claimed in claim 14 wherein said suitable organic solvent is selected from alcohols or ketones or esters, preferably, methanol.

16. A process as claimed in claim 15 wherein said base is NaOH, KOH and alcoholic base is methanolic NaOH, methanolic KOH, preferably methanolic KOH.

17. A process as claimed in claim 13 wherein the mineral acid or organic acid in step c)

is HCl, H2SO4, HNO3 or acetic acid, preferably, HCl. 18. A method of synthesizing atovaquone composition that comprises an amount of cis- atovaquone of not greater than about 0.1%, which method comprises: a) obtaining one or more samples of one or more 2-[4-(4-chlorophenyl)cyclohexyl]-3- chloro-l,4-naphthoquinone batches; b) measuring the level of c/s-isomer of 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro- 1,4- naphthoquinone impurity in each of the samples of (a); c) selecting a 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone batch that comprises a level of c/s-isomeric impurity of not greater than about 0.4% based on the measurement or measurements conducted in (b); and d) using the batch selected in (c) to synthesize said atovaquone composition. 19. A method as claimed in claim 18, wherein said step (c) comprises selecting a 2-[4- (4-chlorophenyl) cyclohexyl]-3-chloro-l,4-naphthoquinone batch that comprises a level of c/s-isomeric impurity of not greater than about 0.15%, preferably not greater than about 0.05%. 20. A method of synthesizing atovaquone composition that comprises an amount of cis- atovaquone of not greater than about 0.1%, which method comprises: a) condensing 2-chloro-l,4-naphthoquinone of formula (II) or its salts with 4-(4- chlorophenyl)cyclohexane-l-carboxylic acid of formula (III) or its salts in presence of silver nitrate and ammonium persulfate to provide 2-[4-(4- chlorophenyl)cyclohexyl]-3-chloro- 1,4-naphthoquinone of formula (IV); b) isolating a sample of the composition resulting from (a); c) measuring the quantity of cw-isomer of 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro- 1,4-naphthoquinone impurity in the isolated sample from (b); d) determining whether or not the quantity in (c) is not greater than about 0.40%; and e) purifying by treating the composition resulting from (a) with organic solvent, if the quantity measured in (c) is greater than about 0.40% until the quantity of c/s-isomer of 2-[4-(4-chlorophenyl)cyclohexyl]-3-chloro-l,4-naphthoquinone impurity is not greater than about 0.40%, and synthesizing a atovaquone composition from the composition so purified; or, f) if the quantity in (c) is not greater than about 0.40%, synthesizing atovaquone composition from the composition of (a). 21. A method as claimed in claim 20 wherein said step (e) is performed by slurrying or suspending or dissolving in organic solvent at about O0C to elevated temperature for sufficient time. 22. A process for the preparation of atovaquone substantially free from c/s-atovaquone impurity, which comprises treating crude atovaquone with organic solvent selected from ketones, C1-C5 alcohols, esters, halogenated solvent, aromatic hydrocarbons and isolating Atovaquone substantially free from c/s-isomer. 23. A process as claimed in claim 22, wherein said organic solvent is ketones selected from acetone, methyl ethyl ketone, methyl isobutyl ketone, methyl isopropyl ketone and methyl ter/-butyl ketone; alcohols selected from methanol, ethanol, isopropyl alcohol and /erf-butyl alcohol, esters selected from methyl acetate, ethyl acetate, n- butyl acetate, ter/-butyl acetate, halogenated solvents like dichloromethane, aromatic hydrocarbons like toluene, xylene. 24. A process for preparing c«-2-Chloro-3-[4-(4-chlorophenyl)-cyclohexyl]-[l,4] naphthoquinone which comprises: a) dissolving 2-chloro-3-[4-(4-chlorophenyl)-cyclohexyl]-[l,4]naphthoquinone in a suitable organic solvent. b) heating the reaction mixture at a suitable temperature; c) cool the reaction mixture; and d) wash with suitable organic solvent to obtain pure c/s-2-Chloro-3-[4-(4- chlorophenyl)-cyclohexyl]-[ 1,4] naphthoquinone. 25. A process as claimed in claim 24 wherein said organic solvent is halogenated

alkanes like CHCl 3, CH2Cl2 preferably CH2Cl2. 26. A process as claimed in claim 24 wherein suitable temperature in step (b) is in the range of 25-60 0C, preferably, 30-420C. 27. A process as claimed in claim 24 wherein the organic solvent comprises alcohols like methanol, ethanol, propanol, and butanol preferably methanol. 28. Pure c/s-isomer of 2-[4-(4-chlorophenyl) cyclohexyl]-3-chloro-l,4- naphthoquinone. 29. Pure c/s-isomer of 2-[4-(4-chlorophenyl) cyclohexyl]-3-chloro-l,4-naphthoquinone characterized by its powder X-ray diffraction pattern having peaks expressed as 2Θ at about 7.3, 15.0, 17.9, 20.0, 25.4+0.2 degrees. 30. Pure /rørø-isomer of 2-[4-(4-chlorophenyl) cyclohexyl]-3-chloro-l,4- naphthoquinone. 31. Pure trans-isomer of 2-[4-(4-chlorophenyl) cyclohexyl]-3-chloro-l,4- naphthoquinone characterized by its powder X-ray diffraction pattern having peaks expressed as 2Θat about 7.2, 21.6, 25.2, 28.9+0.2 degrees. 32. Pure c/s-atovaquone. 33. Pure cw-atovaquone characterized by its powder X-ray diffraction pattern having peaks expressed as 2Θat about 11.1, 17.9, 23.1, 24.3, 27.8±0.2 degrees. 34. Substantially pure atovaquone having individual impurities less than 0.1%. 35. The c/5-atovaquone having particle size less than about 200 µm. 36. The cw-atovaquone having particle size of less than about 50 µm . 37. Substantially pure atovaquone having particle size of less than 200 µm. 38. Substantially pure atovaquone having particle size of less than 150 µm . 39. Substantially pure atovaquone having particle size of less than 50 µm . 40. Atovaquone and its process for the preparation and purification such as here in described in accordance with the accompanying text, description, drawings and examples.

A. CLASSIFlC ATION OF SUBJECT MATTER INV . C07C46/10 C07C50/32

According to International Patent Classification (IPC) or to both national classification and IPC

B. FIELDS SEARCHED Minimum documentation searched (classification system followed by classification symbols) C07C

Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched

Electronic data base consulted during the international search (name of data base and, where practical, search terms used) EPO-Internal , WPI Data, BEILSTEIN Data, CHEM ABS Data

C. DOCUMENTS CONSIDERED TO BE RELEVANT

Category * Citation of document, with indication, where appropriate, of the relevant passages Relevant to claim No.

WILLIAMS D R ET AL: "Synthesis of 1-3,34, Atovaquone" 37-40 TETRAHEDRON LETTERS, ELSEVIER, AMSTERDAM, vol. 39, no. 42, 15 October 1998 (1998-10-15), pages 7629-7632, XP004134267 ISSN: 0040-4039 .4-33,35, 36

WO 2006/008752 A (USV LTD [IN]; TARUR 1-3,34, VENKATASUBRAMANIAN RADHA [IN]; SATHE 37-40 DHANANJAY GOV) 26 January 2006 (2006-01-26) claims 1-23 4-33,35, 36

-/--

Further documents are listed in the continuation of Box C. See patent family annex.

* Special categories of cited documents : 'T' later document published after the international filing date or priority date and not in conflict with the application but 'A' document defining the general state of the art which is not cited to understand the principle or theory underlying the considered to be of particular relevance invention 'E' earlier document but published on or after the international 'X' document of particular relevance, the claimed invention filing date cannot be considered novel or cannot be considered to "L" document which may throw doubts on priority claιm(s) or involve an inventive step when the document is taken alone which is cited to establish the publication date of another 1Y' document of particular relevance; the claimed invention citation or other special reason (as specified) cannot be considered to involve an inventive step when the "O" document referring to an oral disclosure, use, exhibition or document is combined with one or more other such docu¬ other means ments, such combination being obvious to a person skilled 'P' document published prior to the international filing date but in the art. later than the priority date claimed '&' document member of the same patent family

Date of the actual completion of the international search Date of mailing of the international search report

17 July 2008 24/07/2008

Name and mailing address of the ISA/ Authorized officer European Patent Office, P.B. 5818 Patentlaan 2 NL - 2280 HV Rijswijk TeI. (+31-70) 340-2040, Tx. 3 1 651 epo nl, Fax (+31-70) 340-3016 Butkowskyj-Wal kiw, T

Form PCT/ISA/210 (second sheet) (April 2005) C(Contlnuatlon). DOCUMENTS CONSIDERED TO BE RELEVANT

Category * Citation of document, with indication, where appropriate, of the relevant passages Relevant to claim No.

F .DALENCON ET AL: "Atovaquone and 1-3,34, rifabuti ne-1 oaded nanocapsul e s" 37-40 INTERNATIONAL JOURNAL OF PHARMACEUTICS, vol. 153, 1997, pages 127-130, XP009103321 the whole document 4-33 ,35, 36

US 4 981 874 A (LATTER VICTORIA S [GB] ET 1-3, 34, AL) 1 January 1991 (1991-01-01) 37-40 claims 1-20 4-33 ,35, 36

GB 782 316 A (HOFFMANN LA ROCHE) 1-40 4 September 1957 (1957-09-04) page 4 , line 119 - page 5 , line 9 ; claim 8

GB 1 076 306 A (HOFFMANN LA ROCHE) 1-40 19 July 1967 (1967-07-19) page 3 , line 45 - line 55

GB 840 272 A (UNION CARBIDE CORP) 1-40 6 July 1960 (1960-07-06) page 7 , line 64 - line 75

L .SEK ET AL: "Examination of the impact of a range of Pluronic surfactants on the in-vitro solubilization behaviour and oral bioavailability of lipidic formulations of atovaquone" JOURNAL OF PHARMACY AND PHARMACOLOGY, 2006, pages 809-820, XP009103340 the whole document

Form PCT/ISA/210 (continuation of second sheet) (April 2005) Patent document Publication Patent family Publication cited in search report date member(s) date

WO 2006008752 26-01-2006 CA 2549871 A l 26-01-2006 CN 1878741 A 13-12-2006 EP 1768944 A l 04-04-2007 JP 2007510715 T 26-04-2007 US 2006241311 A l 26-10-2006

US 4981874 A 01-01-1991 AP 111 A 23-02-1991 ZA 8906227 A 24-04-1991

GB 782316 A 04-09-1957 NONE

GB 1076306 A 19-07-1967 BE 680076 A 26-10-1966 NL 6605422 A 31-10-1966

GB 840272 A 06-07-1960 NONE

Form PCT/ISA/210 (patent family annex) (Apπl 2005)