WO2011087995A2 - Organic compounds - Google Patents

Abstract

This invention provides compounds which are useful in the treatment of mycobacterial infections, pharmaceutical compositions containing the compounds, processes for their preparation, and uses of the compounds in various medicinal applications, such as the treatment or prevention of mycobacterial infections, such as those caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or the treatment or prevention of parasitic diseases, such as those caused by a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania which causes visceral leishmaniasis or kala-azar, e.g., Leishmania donovani.

Description

ORGANIC COMPOUNDS

TECHNICAL FIELD

This invention is directed to novel compounds which are useful in the treatment of mycobacterial infections. The invention is also directed to pharmaceutical compositions containing the compounds, processes for their preparation and uses of the compounds in various medicinal applications, such as the treatment or prevention of mycobacterial infections, such as those caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or the treatment or prevention of parasitic diseases, such as those caused by a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania which causes visceral leishmaniasis or kala-azar, e.g. Leishmania donovani.

BACKGROUND

Tuberculosis (TB), one of the oldest diseases known to humankind, is caused by the bacterium Mycobacterium tuberculosis (MTB). The disease is contagious and, like the common cold, can be easily spread through air by coughing and sneezing. Currently, MTB infects one-third of the world population and is the second leading cause of adult mortality by an infectious disease after AIDS, with one TB death every 15 seconds. For the last two decades, there has been a resurgence of TB cases, particularly in areas like South East Asia and sub-Saharan Africa.

The first effective anti-TB drug, streptomycin, was introduced in 1946. However, the monotherapy became rapidly ineffective because of the development of bacterial resistance. As more anti-mycobacterials were discovered, combination therapies with two or more drugs were possible to suppress the emergence of resistance. Current therapy for TB involves initial treatment with rifampicin, isoniazid, pyrazinamide and ethambutol for two months, followed by continuation therapy with rifampicin and isoniazid for another 4 months. The long treatment time involved in this regimen can make patient compliance and proper implementation a challenge. Many TB patients do not receive full and proper TB treatment, which results in a high relapse rate and emergence of drug resistance. Another problem which has come to light is the emergence of XDR and MDR TB. MDR TB bacilli are resistant to the frontline anti-TB drugs rifampicin and isoniazid, while XDR TB bacilli are resistant to these two frontline drugs as well as any of the quinoline family of drugs and at least one of kanamycin, capreomycin or amikacin.

Thus, there is an urgent need for new anti-TB drugs, including new anti-TB drugs for MDR and XDR TB.

Chagas Disease (also called American Trypanosomiasis) and sleeping sickness (also called African Trypanosomiasis) are parasitic diseases caused by parasites of the genus

Trypanosoma - Trypanosoma cruzi or Trypanosoma brucei. Both are transmitted by insect vectors.

Nifurtimox and Benznidazole are the frontline drugs currently used for treating Chagas disease. Resistance to these drugs may be an issue and Amphotericin b has been proposed as a second-line drug.

There is also a need for new treatments for Chagas Disease and sleeping sickness.

Leishmaniasis is caused by parasitic protozoa of the genus Leishmania. These parasites are also transmitted by an insect vector. Visceral leishmaniais ("kala-azar") is the most serious form and is caused by Leishmania donovani. Sodium stibogluconate (Pentostam®) and meglumine antimonite (Glucatim®) are currently used for treating leishmaniasis, but again resistance may be an issue.

There is also a need for new treatments for leishmaniasis.

Surprisingly, certain nitroimidazole compounds are useful for the treatment of mycobacterial infections, such as those caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or the treatment or prevention of parasitic diseases, such as those caused by a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania, e.g. one which causes visceral leishmaniasis or kala-azar, e.g.

Leishmania donovani. It is an object of the invention to provide novel compounds. It is also an object of the invention to provide uses of such compounds, for example, for the treatment of

mycobacterial infections or parasitic diseases.

DISCLOSURE OF THE INVENTION

The invention provides compounds and pharmaceutical compositions thereof, which are useful for the treatment of mycobacterial infections, such as those caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or the treatment or prevention of parasitic diseases, such as those caused by a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania, e.g. one which causes visceral leishmaniasis or kala-azar, e.g. Leishmania donovani.

In a first aspect, the invention provides a compound of formula (I), or a pharmaceutically acceptable salt thereof:

where:

Z is (C ²R³)_n or a radical of formula (i):

(i)

or Z may optionally be absent when A and R⁴ or R⁵ together form a 5- or 6-membered oxygen-containing heterocycle; W is O or W is absent;

Y is CR⁴R⁵ or Y is carbon spiro-linked to a cycloalkyi group;

A is O or N, or A is O and together with R⁴ or R⁵ forms a 5- or 6-membered oxygen- containing heterocycle;

R¹ is absent when A is O, or R¹ is H, alkyl, alkyl amide, aryl amide or urea;

R² and R³ are each independently selected from the group consisting of H, alkyl, heteroaryl, COOH, CONH₂, and each R² and each R³ may be the same or different;

R⁴ and R⁵ are each independently selected from the group consisting of H, alkyl, alkenyl, alkynyl, alkoxyalkyi, hydroxyalkyi, cycloalkyi, cycloalkenyl; provided that R⁴ and R⁵ are not both H;

R⁶ and R⁷ are each independently selected from the group consisting of H or alkyl;

R⁸ is halogen, cycloalkyi, heterocycio, hydroxy or alkoxy, provided that when m is 2, 3 or 4, then each R⁸ may be the same or different; and n is 1 , 2, 3 or 4; and m is 0, 1 , 2, 3 or 4; provided that the following compound is excluded:

the compound where A is N; R¹ is H; Y is C(H)CH₃; Z is CH₂; m is 0; and R⁶ and R⁷ are both H.

In some examples, the compound of formula (I) is a compound of formula (la):

where A, Z, Y, W, n, m, R¹ , R², R³, R⁴, R⁵, R⁶, R⁷ and R⁸ are all as defined above. In some examples, A is O In some examples, A is N.

In some examples, the compound of formula (I) or formula (la) is a compound where A is N, Z is (C ²R³)_n or a radical of formula (i):

(i)

and W, Y, n, m, R¹, R², R³, R⁴, R⁵, R⁶, R⁷ and R⁸ are all as defined above.

In some examples, the compound of formula (I) or formula (la) is a compound where A is O or A is O and together with R⁴ or R⁵ forms a 5- or 6-membered oxygen-containing heterocycle, and where W, Y, Z, n, m, R¹ , R², R³, R⁴, R⁵, R⁶, R⁷ and R⁸ are all as defined above.

In some examples, R is H.

In some examples, Y is CR⁴R⁵. In other examples, Y is carbon, spiro-linked to a cycloalkyl group, e.g. cyclopropyl.

In some examples, one or both of R⁴ and R⁵ is alkyl, e.g. lower alkyl, e.g. methyl, ethyl, n- propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl or tert-butyl. In other examples, one or both of R⁴ and R⁵ is cycloalkyl, e.g. cyclopropyl. In still other examples, one or both of R⁴ and R⁵ is hydroxyalkyl, e.g. hydroxyl lower alkyl, e.g. hydroxymethyl. In still other examples, one or both of R⁴ or R⁵ is alkoxyalkyl, e.g. alkoxy lower alkyl, e.g. methoxymethyl. In still other examples, one or both of R⁴ or R⁵ is alkenyl, e.g. lower alkenyl, e.g. ethenyl. In some examples, one of R⁴ and R⁵ is hydrogen.

In some examples, R⁶ and R⁷ are both H.

In some examples, R² and R³ are both H.

In some examples, Z is (CR²R³)_n, e.g. (CH₂)_n, where n is 1 or 2. In other examples, Z is a radical of formula (i) and n is 1. In some examples, Z is a radical of formula (i), R² and R³ are both H and n is 1. In still other examples, Z is a radical of formula (i), n is 1 and W is O. In still other examples, Z is a radical of formula (i), n is 1 and W is absent.

In some examples, R⁸ is halogen, e.g. F or CI. In other examples, R⁸ is hydroxy.

In some examples, A is O and together with R⁴ or R⁵ forms a 5- or 6-membered oxygen- containing heterocycle, and Z is (CR²R³)_n where n is 1. In other examples, A is O and together with R⁴ or R⁵ forms a 5- or 6-membered oxygen-containing heterocycle, and Z is absent.

In some examples, n is 1. In other examples n is 2. In some examples m is 0. In other examples m is 1.

In some examples, A is N and and Y is CR⁴R⁵ where one or both of R⁴ and R⁵ is alkyl, e.g. lower alkyl, e.g. ethyl, n-propyl, iso-butyl or t-butyl. In other examples, A is N and one of R⁴ and R⁵ is cycloalkyl, e.g. cyclopropyl. In still other examples, A is N and one or both of R⁴ and R⁵ is alkoxyalkyl, e.g. methoxymethyl, or hydroxyalkyl, e.g. hydroxymethyl.

In some examples, A is N and Z is (CR²R³)_n where n is 1 or 2. In other examples, A is N and Z is a radical of formula (i). In some examples, A is N and Z is CH₂-phenyl. In some examples, A is N, R¹ is H and Z is CH₂-phenyl.

In some examples, A is N, R¹ is H and Y is CR⁴R⁵ where one of R⁴ and R⁵ is lower alkyl, e.g. ethyl. In some examples A is N, R¹ is H, Y is CR⁴R⁵ where one of R⁴ and R⁵ is lower alkyl, e.g. ethyl, and Z is (CR²R³)_n where n is 1 or 2. In other examples A is N, R¹ is H, Y is CR⁴R⁵ where one of R⁴ and R⁵ is lower alkyl, e.g. ethyl, and Z is a radical of formula (i). In some examples, A is N and R is halogen, e.g. F or CI. In other examples, A is N and R is hydroxy.

In some examples, A is O and one of R⁴ and R⁵ is alkyi, e.g. lower alkyi, e.g. ethyl, n-propyl, iso-butyl or t-butyl. In other examples, A is O and both R⁴ and R⁵ are alkyi, e.g. lower alkyi, e.g. methyl, ethyl, n-propyl, iso-butyl or t-butyl, where R⁴ and R⁵ are the same or different. In still other examples, A is O and Y is C spiro-linked to a cycloalkyl group, e.g. a cyclopropyl group.

In some examples W is O. In other examples W is absent.

In another aspect, the invention provides a compound selected from the group consisting of:

armaceutically acceptable salt thereof.

In another aspect, the invention provides a prodrug of a compound of the invention, e.g. a prodrug of a compound of formula (I).

In another aspect the invention provides a pharmaceutical composition comprising a compound of formula (I) as defined above, in association with at least one pharmaceutically acceptable excipient, e.g. appropriate diluent and/or carrier, e.g. including fillers, binders, disintegrators, flow conditioners, lubricants, sugars or sweeteners, fragrances, preservatives, stabilizers, wetting agents and/or emulsifiers, solubilisers, salts for regulating osmotic pressure and/or buffers.

In another aspect, the invention provides a compound of formula (I) for use as a

medicament.

In another aspect the invention provides a compound of formula (I) for the manufacture of a medicament.

In another aspect the invention provides the use of a compound of formula (I) for the manufacture of a medicament, e.g. a pharmaceutical composition, for the treatment and/or prevention of a mycobacterial infection or a parasitic disease.

In another aspect the invention provides the use of a compound of formula (I) as a pharmaceutical, e.g. for the treatment and/or prevention of a mycobacterial infection or a parasitic disease.

In another aspect, the invention provides a compound of formula (I) for use in the treatment and/or prevention of a mycobacterial infection or a parasitic disease.

In another aspect, the invention provides the use of a compound of formula (I) in the manufacture of a medicament for the treatment and/or prevention of a disease caused by a mycobacterial infection or a parasitic disease.

In still another aspect, the invention provides a method of treating and/or preventing a disease caused by a mycobacterial infection or a parasitic disease, comprising administering to a patient in need thereof an effective amount of a compound of formula (I).

In yet another aspect, the invention provides a pharmaceutical composition for the treatment and/or prevention of a disease caused by a mycobacterial infection or a parasitic disease, comprising a compound of formula (I).

The mycobacterial infection is, for example, caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or the treatment or prevention of parasitic diseases, such as those caused by a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania, e.g. one which causes visceral leishmaniasis or kala-azar, e.g. Leishmania donovani.

In another aspect the invention provides a combination of a compound of formula (I) with at least one second drug substance.

In another aspect the invention provides a pharmaceutical combination, e.g. a kit, comprising a) a first agent which is a compound of formula (I) and b) at least one co-agent. The kit may comprise instructions for its administration. In the above methods for using the compounds of the invention, a compound of the invention, e.g. a compound of formula (I) may be administered to a system comprising cells or tissues. In other embodiments, a compound of the invention, e.g. a compound of formula (I) may be administered to a human or animal patient.

Compounds provided by the invention are designated herein as "compound(s) of the invention". This term is intended to encompass compounds of formula (I) as defined above. A compound of the invention includes a compound in any form, e.g. in all crystalline forms, in free form, in the form of a salt, in the form of a solvate, in the form of a salt and a solvate.

The term "alkyl" as used herein refers to branched or straight chain hydrocarbon groups, comprising preferably 1 to 15 carbon atoms. The same terminology applies to the alkyl moiety of an alkoxyalkyl group. Examples of alkyl groups include, but are not limited to, methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, nonyl, decyl etc. An alkyl group may be unsubstituted or optionally substituted with one or more substituents selected from halogen, hydroxy, amino, alkylamino, dialkylamino, alkylcarbonyl, arylcarbonyl, cyano, nitro and azido. Typically it is unsubstituted.

The term "lower alkyl" as used herein refers to branched or straight chain alkyl groups comprising 1 to 6 carbon atoms, preferably 1 to 4 carbon atoms. Examples of lower alkyl groups include, but are not limited to, methyl, ethyl, n-propyl, /^'-propyl, n-butyl, /^'-butyl, sec- butyl, fert-butyl, pentyl, and hexyl. A lower alkyl group may be unsubstituted or optionally substituted with one or more substituents selected from halogen, hydroxy, amino, alkylamino, dialkylamino, alkylcarbonyl, arylcarbonyl, cyano, nitro and azido. Typically it is unsubstituted.

The term "cycloalkyl" refers to a saturated ring comprising preferably 3 to 8 carbon atoms. Examples include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl and cycloheptyl. A cycloalkyl group is preferably a 3-, 5- or 6-membered ring. A cycloalkyl group may be unsubstituted or optionally substituted with one or more substituents selected from halogen, hydroxy, amino, alkylamino, dialkylamino, alkylcarbonyl, arylcarbonyl, cyano, nitro and azido. Typically it is unsubstituted.

The term "cycloalkenyl" refers to an unsaturated (non-aromatic) ring comprising preferably 3 to 8 carbon atoms. Examples include, but are not limited to, cyclopentenyl, cyclohexenyl and cycloheptenyl. A cycloalkenyl group is preferably a 5- or 6-membered ring. A cycloalkenyl group may be unsubstituted or optionally substituted with one or more substituents selected from halogen, hydroxy, amino, alkylamino, dialkylamino, alkylcarbonyl, arylcarbonyl, cyano, nitro and azido. Typically it is unsubstituted.

The term "alkenyl" as used herein refers to branched or straight chain groups, comprising preferably 2 to 15 carbon atoms, more preferably 2 to 6 carbon atoms, still more preferably 2 or 3 carbon atoms, and containing one or more double bonds. Examples of alkenyl groups include, but are not limited to, ethenyl, propenyl, butenyl, penentyl, hexenyl, heptenyl, nonenyl decenyl etc. An alkenyl group may be unsubstituted or optionally substituted with one or more substituents selected from halogen, hydroxy, amino, alkylamino, dialkylamino, alkylcarbonyl, arylcarbonyl, cyano, nitro and azido. Typically it is unsubstituted.

The term "alkynyl" as used herein refers to branched or straight chain groups, comprising preferably 2 to 15 carbon atoms, more preferably 2 to 6 carbon atoms still more preferably 2 or 3 carbon atoms, and most preferably 2 carbon atoms, and containing one or more triple bonds. Examples of alkynyl groups include, but are not limited to, ethynyl, propynyl, butynyl, pentyntyl, hexynyl, heptynyl, nonynyl decynyl etc. An alkenyl group may be unsubstituted or optionally substituted with one or more substituents selected from halogen, hydroxy, amino, alkylamino, dialkylamino, alkylcarbonyl, arylcarbonyl, cyano, nitro and azido. Typically it is unsubstituted.

The terms "lower alkenyl" and "lower alkynyl" have corresponding meanings to the term "lower alkyl" as defined above. Examples of lower alkenyl and lower alkynyl groups include, but are not limited to, ethenyl, propenyl, butenyl, ethynyl, propynyl and butynyl. A lower alkenyl or alkynyl group may be unsubstituted or optionally substituted with one or more substituents selected from halogen, hydroxy, amino, alkylamino, dialkylamino, alkylcarbonyl, arylcarbonyl, cyano, nitro and azido. Typically it is unsubstituted.

The term "alkoxy" as used herein refers to OR where R is alkyl as defined above. The term "lower alkoxy" has a corresponding meaning to the term "lower alkyl" as defined above. Examples of lower alkoxy groups include, but are not limited to, methoxy, ethoxy, n-propoxy, /^'so-propoxy, n-butoxy, /^'so-butoxy, sec-butoxy and fe/t-butoxy. Typical examples of lower alkoxy include methoxy, ethoxy, and ieri-butoxy.

The term "alkoxyalkyl" as used herein refers to an alkoxy group as defined above, attached to an alkylene chain, where the alkylene chain is derived from an alkyl group as defined above. Examples of alkoxyalkyl groups include, but are not limited to, methoxymethyl group. The term "halo" or "halogen" as used herein refers to F, CI, Br or I, preferably F or CI.

The term "heteroaryl" means an aromatic ring having 5 to 18 atoms, preferably 5 or 6 atoms, including at least one heteroatom, such as, but not limited to, N, O and S, within the ring. The term "heteroaryl" includes monocyclic groups as well as multicyclic groups, e.g. fused groups such as bicyclic and tricyclic groups. The heteroaryl may optionally be fused or bridged with one or more benzene rings and/or to a further heteroaryl ring and/or to an alicyclic ring.

The term "heterocyclo", "heterocycloalkyl" or "heterocyclic" means a saturated or partially saturated (non-aromatic) ring having 5 to 18 atoms, preferably 5 or 6 atoms, including at least one heteroatom, such as, but not limited to, N, O and S, within the ring. The

heterocycle may optionally be fused or bridged with one or more benzene rings and/or to a further heterocyclic ring and/or to an alicyclic ring.

Examples of heterocycloalkyl and heteroaryl groups include, but are not limited to, morpholinyl, piperazinyl, piperidinyl, pyridyl, pyrrolidinyl, pyrazinyl, pyrimidinyl, purinyl, benzimidazolyl, benzoxazolyl, benzothiazolyl, benzofuranyl, benzofurazanyl, benzopyrazolyl, benzotriazolyl, benzothiophenyl, carbazolyl, carbolinyl, cinnolinyl, indolyl, isoindolyl indolinyl, imidazolyl, indolazinyl, indazolyl, morpholinyl, quinoxalinyl, quinolyl, isoquinolyl, quinazolinyl, 1 ,2,3,4-tetrahydroquinolinyl, tetrahydropyranyl, tetrazolopyridyl, thiadiazolyl, thienyl, azetidinyl, 1 ,4-dioxanyl, hexahydroazepinyl, pyridine-2-one, thiomorpholinyl,

dihydrobenzimidazolyl, dihydrobenzofuranyl, dihydrobenzothiophenyl, dihydrobenzoxazolyl, didhydrofuranyl, dihydroimidazolyl, dihydroisoxazolyl, dihydroisothiazolyl, dihydrooxadiazolyl, dihydrooxazolyl, dihydropyrazinyl, dihydropyrazolyl, dihydropyridinyl, dihydropyrimidinyl, dihydropyrrolyl, dihydroquinolinyl, dihydrotetrazolyl, dihydrothiadiazolyl, dihydrothiazolyl, dihydrothienyl, dihydrotriazolyl, dihydroazetidinyl, methylenedioxybenzoyl, tetrahydrofuranyl, tetrahydrothienyl, thiazolyl, isothiazolyl, isoxazolyl, imidazolyl, indanyl, naphthpyridinyl, oxadiazolyl, oxazolyl, oxazoline, isoxazoline, oxetanyl, pyranyl, pyrazinyl, pyridopyridinyl, pyridazinyl, pyrrolyl, pyrazolyl, pyrrolyl, phenanthridinyl, triazolyl, thienyl, furanyl,

isobenzofuranyl, or tetrazolyl, particularly N-containing heterocycles such as pyridyl, piperidinyl, pyrimidinyl, pyrrolidinyl, piperazinyl, isoquinolyl, quinazolinyl, 2,2,6,6- tetramethylpiperidyl and morpholinyl.

The term "substituted" is intended to describe moieties having substituents replacing a hydrogen on one or more atoms, e.g. C, O or N, of a molecule. By the term "one or more substituents" is contemplated up to, for example, 3 substituents, preferably one substituent. Two or more substituents may be independently chosen.

Multicyclic moieties include those with two or more rings, e.g. cycloalkyls, heteroaryls and heterocyclyls in which two or more carbons are common to two adjoining rings ("fused" rings) or in which the rings are joined through non-adjacent/shared atoms ("bridged" rings).

The term "prodrug" as used herein means a pharmacologically acceptable derivative of a compound of the invention, such that an in vivo biotransformation of the derivative gives the compound of the invention. Prodrugs of compounds of compounds of the invention may be prepared by modifying functional groups present in the compounds, such as hydroxy or acid groups, in such a way that the modified groups are cleaved in vivo to give the parent compound. Suitable prodrugs include, for example, esters or amides.

The term "salts" includes therapeutically active non-toxic acid addition salts derived from the compounds of the invention. Acid addition salts can be obtained by treating the base form of the compounds with appropriate acids. Suitable acids include inorganic acids, for example hydrohalic acid, in particular hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid and phosphoric acid; and organic acids, for example acetic acid, hydroxyacetic acid, propanoic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, fumaric acid, malic acid, tartaric acid, citric acid, methanesulfonic acid, ethanesulfonic acid, benzenesulfonic acid, p-toluenesulfonic acid, cyclamic acid, salicyclic acid, p-aminosalicylic acid, pamoic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, tartaric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, 1 ,2-ethane-disulfonic acid, 2-hydroxyethanesulfonic acid, 4-chlorobenzene- sulfonic acid, 2-napthalenesulfonic acid, camphorsulfonic acid, 3-phenylpropionic acid, trimethylacetic acid, f-butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid and stearic acid.

The term "protecting group" means a group that masks a functional group in a molecule, so that chemoselectivity is possible during a reaction. Suitable protecting groups are preferably simple to incorporate, stable to the relevant reaction conditions and easy to remove. Such protecting groups are known to those skilled in the art and are described in Protective Groups in Organic Synthesis by Theodora W Greene (John Wiley & Sons Canada, Ltd). Suitable protecting groups include, for example, The terms "treat", "treating", "treated" or "treatment" include the diminishment or alleviation of at least one symptom associated with or caused by the state, disease or disorder being treated. For example, treatment can include diminishment of one or more of the following: weakness, tiredness, weight loss, fever, night sweats, coughing, chest pain, coughing up of sputum (material from the lungs) and/or blood, and shortness of breath.

The terms "prevent", "preventing" or "prevention" include the prevention of at least one symptom associated with or caused by the state, disease or disorder being prevented. For example, prevention can include the prevention of one or more of the following: weakness, tiredness, weight loss, fever, night sweats, coughing, chest pain, coughing up of sputum (material from the lungs) and/or blood, and shortness of breath.

The term "patient" includes organisms that are capable of suffering from, or afflicted or infected with, a mycobacterial infection or a parasitic disease, e.g. mammals such as humans, apes, monkeys, cows, horses, pigs, sheep, cats, dogs, goats, mice, rabbits, rats and transgenic non-human animals. In some embodiments the patient is a human, e.g. a human capable of suffering from, or afflicted with, a disease or condition described herein, e.g. a mycobacterial infection, e.g. an infection caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or the treatment or prevention of parasitic diseases, such as those caused by a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania, e.g. one which causes visceral leishmaniasis or kala-azar, e.g. Leishmania donovani.

A "disease caused by a mycobacterial infection" includes disorders and states that are associated with the activity of a mycobacterium, e.g. infection with a mycobacterium, e.g. infection caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans, in a patient.

A parasitic disease includes disorders and states that are associated with the activity of a parasite, e.g. a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or

Trypanosoma brucei or the genus Leishmania, e.g. Leishmania donovani The "effective amount" of a compound of the invention is the amount necessary or sufficient to treat or prevent a disease caused by a mycobacterial infections such as those caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or to treat or prevent a parasitic disease, such as those caused by a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania, e.g. one which causes visceral leishmaniasis or kala-azar, e.g. Leishmania donovani, e.g. the effective amount is the amount necessary to treat or prevent one or more symptoms of a mycobacterial infection or a parasitic disease. The effective amount can vary depending on the compound employed, the mode of administration, the treatment desired and the disease indicated, as well as other factors such as a patient's age, body weight, general health and sex. For example, the choice of the compound of the invention can affect what constitutes an "effective amount". One of ordinary skill in the art would be able to study the factors described herein and make a determination regarding the effective amount of a compound of the invention without undue experimentation. The regimen of administration can affect what constitutes an effective amount. The compound of the invention can be administered to a patient either prior to or after the onset of a disease caused by a mycobacterial infection or a parasitic disease, e.g. prior to or after infection caused by Mycobacterium tuberculosis,

Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania, e.g. one which causes visceral leishmaniasis or kala-azar, e.g. Leishmania donovani.

Furthermore, several divided dosages, as well as staggered dosages, can be administered daily or sequentially, or the dose can be continuously infused, or can be a bolus injection. Further, the dosages of the compounds of the invention can be proportionally increased or decreased as indicated by the exigencies of the therapeutic or prophylactic situation. A physician or veterinarian having ordinary skill in the art can readily determine and prescribe the effective amount required. For example, the physician or veterinarian could start doses of the compounds of the invention employed in a pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved. The term "pharmaceutical composition" includes preparations, for example medicaments, suitable for administration to mammals, e.g. humans.

The compounds of the invention containing acidic protons may also be converted into their therapeutically active non-toxic base addition salt forms by treatment with appropriate organic and inorganic bases. Appropriate base salts forms include, for example, ammonium salts, alkaline and alkaline earth metal salts, in particular lithium, sodium, potassium, magnesium and calcium salts, salts with organic bases, e.g. benzathine, N-methyl-D- glucamine and hybramine salts, and salts with amino acids, for example arginine and lysine.

Conveniently, the acid or base addition salt forms can be converted into the free forms by treatment with an appropriate base or acid.

The term addition salt as used in the present context also comprises the solvates which the compounds of the invention, as well as the salts thereof, are able to form. Such solvates include, for example, hydrates and alcoholates.

It will be appreciated that the compounds of the invention may exist in the form of optical isomers, racemates or diastereoisomers. The scope of this invention embraces all stereochemically isomeric forms of the compounds. The term "stereochemically isomeric forms" as used herein therefore means all possible isomeric forms which the compounds of the invention may possess. In particular, asymmetric carbons may have the R- or S- configuration. For example, the asymmetric carbons of the compounds of the invention may have the R- or S-configuration.

It will also be appreciated that the compounds of the invention can exist as tautomers. The scope of this invention embraces all such tautomeric forms.

The compounds of the invention, and particularly as exemplified, in free or pharmaceutically acceptable addition salt form, exhibit pharmacological activity and are useful as

pharmaceuticals, particularly for the treatment and/or prevention of mycobacterial infections such as those caused by Mycobacterium tuberculosis and parasitic diseases such as those caused by a parasite of the genus Trypanosoma or the genus Leishmania, e.g.

Trypanosoma cruzi, Trypanosoma brucei or Leishmania donovani. The compounds of the invention are indicated to exhibit advantageous properties such as improved solubility and improved aerobic and anaerobic potency against Mycobacterium tuberculosis.

The compounds 13.1-13.9, 13.1 1 -13.17, 13.20, 20.1 and 20.2 of Examples 13 and 20 are preferred compounds of the invention. It has, for example been determined that the compounds of the invention, including the compounds 13.1 , 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 13.1 1 , 13.12, 13.13, 13.14, 13.15, 13.16, 13.17 and 13.20 of Example 13 and the compounds 20.1 and 20.2 of Example 20 exhibit activity in tests against

Mycobacterium tuberculosis. For example the MIC and MAC data (against Mycobacterium tuberculosis) for some of the compounds of the invention are shown in Table 1. The tests are carried out as described in the Examples section.

Table 1

[ND = not determined]

It is therefore indicated that for the treatment of mycobacterial infections such as those caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacterium that causes multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania, e.g. one which causes visceral leishmaniasis or kala-azar, e.g.

Leishmania donovani, a compound of the invention may be administered to larger mammals, for example humans, by similar modes of administration at similar dosages to those conventionally used.

Moreover, it will be appreciated that the dosage range of a compound of the invention to be employed for treating and/or preventing a mycobacterial infection or a parasitic disease depends upon factors known to the person skilled in the art, including host, nature and severity of the condition to be treated, the mode of administration and the particular substance to be employed.

The daily dosage of the compound of the invention will vary with the compound employed, the mode of administration, the treatment desired and the disease indicated, as well as other factors such as a patient's age, body weight, general health, condition, prior medical history and sex, and like factors known in the medical arts. For example, a compound of the invention is administered at a daily dosage in the range from about 0.03 mg/kg body weight to about 20 mg/kg body weight, e.g. in the range from about 0.05 mg/kg body weight to about 15 mg/kg body weight or as appropriate based on human PK/PD data. Typically, satisfactory results can be obtained when the compound of the invention is administered at a daily dosage from about 0.5 mg to about 500 mg, e.g. not exceeding about 1 gram, e.g. from about 1 mg to about 100 mg for a 70 kg human, given up to four times daily.

For example, an indicated daily dosage for Compound 13.1 of the invention for the treatment of a mycobacterial infection or a parasitic disease is about 100-1000 mg, preferably given once daily, for a 70 kg human.

For pharmaceutical use one or more compounds of the invention may be used, e.g. one, or a combination of two or more compounds of the invention, preferably one compound of the invention, is used or as appropriate based on human PK/PD data..

When the compounds of the invention are administered as pharmaceuticals to a patient, e.g. to a mammal, e.g. a human, they can be given per se, or as a pharmaceutical composition. The compounds of the invention may be formulated into various pharmaceutical forms for such administration purposes. Any suitable compositions usually employed for systemically administering drugs may be used. The compounds of the invention may be formulated for administration by any suitable route, for example orally, parenterally, by inhalation spray, transdermally, nasally (e.g. as by a spray), topically (e.g. as by powders, ointments or drops), rectally, vaginally, sublingually, bucally or via an implanted reservoir. In some examples the compounds of the invention are administered orally.

To prepare the pharmaceutical compositions of this invention, an effective amount of a compound of the invention, as active ingredient, optionally in addition salt form, is combined in intimate admixture with a pharmaceutically acceptable carrier. In general, the formulations are prepared by uniformly and intimately bringing into association a compound of the invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product. The pharmaceutically acceptable carrier includes a pharmaceutically acceptable material, composition or vehicle, suitable for administering compounds of the invention to a patient. Carriers include liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting the compound of the invention from one organ or portion of the body to another organ or portion of the body. The carrier may take a wide variety of forms depending on the form of preparation desired for administration. Carriers may be acceptable in the sense of being compatible with the other ingredients of the formulation, and not injurious to the patient. Suitable carriers include, but are not limited to, sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol; phosphate buffer solutions; water, glycols, oils, alcohols and the like in the case of oral liquid preparations; solid carriers such as kaolin; other diluents, lubricants, binders, disintegrating agents and other non-toxic compatible substances employed in

pharmaceutical formulations.

Wetting agents, emulsifiers and lubricants, such as sodium lauryl sulfate and magnesium stearate, as well as colouring agents, release agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the

compositions. Examples of pharmaceutically acceptable antioxidants include: water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, a-tocopherol, and the like; and metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.

Preferred pharmaceutical compositions include those in unit dosage form suitable for administration orally or by parenteral injection.

For oral administration the compounds can be formulated into solid or liquid preparations such as tablets, capsules, powders, pills, solutions, suspensions, syrups, elixirs, emulsions and dispersions. In preparing these oral dosage forms, any of the usual pharmaceutical media may be employed, such as water, glycols, oils, alcohols and the like in the case of oral liquid preparations or solid carriers such as starches, sugars, kaolin, diluents, lubricants, binders, disintegrating agents and the like. Other components such as colourings, sweeteners or flavourings may be added. Because of their ease of administration, tablets and capsules represent the most advantageous oral dosage unit forms in which case solid pharmaceutical carriers may be employed.

Formulations of the invention suitable for oral administration may be in the form of capsules, cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), powders, granules, or as a solution or a suspension in an aqueous or nonaqueous liquid, or as an oil-in-water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of a compound of the present invention as an active ingredient. A compound of the present invention may also be administered as a bolus, electuary or paste.

In solid dosage forms of the invention for oral administration (capsules, tablets, pills, dragees, powders, granules and the like), the active ingredient is mixed with one or more pharmaceutically acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; humectants, such as glycerol; disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; solution retarding agents, such as paraffin; absorption accelerators, such as quaternary ammonium compounds; wetting agents, such as, for example, cetyl alcohol and glycerol monostearate; absorbents, such as kaolin and bentonite clay; lubricants, such a talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof; and colouring agents. In the case of capsules, tablets and pills, the pharmaceutical compositions may also comprise buffering agents. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.

A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared using binder (for example, gelatin or hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (for example, sodium starch glycolate or cross-linked sodium carboxymethyl cellulose), surface- active or dispersing agent. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.

The tablets, and other solid dosage forms of the pharmaceutical compositions of the present invention, such as dragees, capsules, pills and granules, may optionally be scored or prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical-formulating art. They may also be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile, other polymer matrices, liposomes and/or microspheres. They may be sterilized by, for example, filtration through a bacteria-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions that can be dissolved in sterile water, or some other sterile injectable medium immediately before use. These compositions may also optionally contain opacifying agents and may be of a composition that they release the active ingredient(s) only, or preferentially, in a certain portion of the gastrointestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. The active ingredient can also be in micro-encapsulated form, if appropriate, with one or more of the above-described excipients.

Liquid dosage forms for oral administration of the compounds of the invention include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredient, the liquid dosage forms may contain inert diluent commonly used in the art, such as, for example, water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1 ,3-butylene glycol, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.

Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, colouring, perfuming and preservative agents.

Suspensions, in addition to the active compounds, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.

Formulations of the pharmaceutical compositions of the invention for rectal or vaginal administration may be presented as a suppository, which may be prepared by mixing one or more compounds of the invention with one or more suitable nonirritating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which is solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active compound.

Formulations of the present invention which are suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such carriers as are known in the art to be appropriate.

Dosage forms for the topical or transdermal administration of a compound of this invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. The active compound may be mixed under sterile conditions with a

pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants that may be required.

The ointments, pastes, creams and gels may contain, in addition to an active compound of this invention, excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.

Powders and sprays can contain, in addition to a compound of this invention, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances. Sprays can additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane.

Transdermal patches have the added advantage of providing controlled delivery of a compound of the present invention to the body. Such dosage forms can be made by dissolving or dispersing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate of such flux can be controlled by either providing a rate controlling membrane or dispersing the active compound in a polymer matrix or gel.

Ophthalmic formulations, eye ointments, powders, solutions and the like, are also contemplated as being within the scope of this invention.

Pharmaceutical compositions of this invention suitable for parenteral administration comprise one or more compounds of the invention in combination with one or more pharmaceutically acceptable sterile isotonic aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain antioxidants, buffers, bacteriostats, solutes which render the formulation isotonic with the blood of the intended recipient or suspending or thickening agents. For parenteral compositions, the carrier will usually comprise sterile water, at least in large part, though other ingredients, for example, to aid solubility, may be included. Injectable solutions, for example, may be prepared in which the carrier comprises saline solution, glucose solution or a mixture of saline and glucose solution. Injectable suspensions may also be prepared in which case appropriate liquid carriers, suspending agents and the like may be employed. Also included are solid form preparations which are intended to be converted, shortly before use, to liquid form preparations.

Examples of suitable aqueous and nonaqueous carriers that may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

These compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents that delay absorption such as aluminum monostearate and gelatin

In some cases, in order to prolong the effect of a drug, it is desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material having poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally-administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.

Injectable depot forms are made by forming microencapsule matrices of the subject compounds in biodegradable polymers such as polylactide-polyglycolide. Depending on the ratio of drug to polymer, and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include

poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions that are compatible with body tissue.

The phrase "parenteral administration" or the like as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal,

intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrasternal injection and infusion.

Depending on the mode of administration, the pharmaceutical composition will preferably comprise from 0.05 to 99.5% by weight, more preferably from 0.1 to 70% by weight, more preferably from 30 to 70% by weight of the active ingredient, and from 0.05 to 99.95% by weight, more preferably from 30 to 99.1% by weight, more preferably from 30 to 70% by weight of a pharmaceutically acceptable carrier, all percentages being based on the total composition. The pharmaceutical composition may additionally contain various other ingredients known in the art, for example, a lubricant, stabilising agent, buffering agent, emulsifying agent, viscosity-regulating agent, surfactant or preservative.

It is especially advantageous to formulate the pharmaceutical compositions in unit dosage form for ease of administration and uniformity of dosage. Unit dosage form as used herein refers to physically discrete units suitable as unitary dosages, each unit containing a predetermined quantity of active ingredient calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. Examples of such unit dosage forms are tablets (including scored or coated tablets), capsules, pills, powder packets, wafers, suppositories, injectable solutions or suspensions and the like, and segregated multiples thereof.

The compounds of the invention can be administered alone or in combination with a second drug substance.

In another aspect the invention provides:

- A combination of a compound of the invention with at least one second drug substance;

- A pharmaceutical combination comprising a compound of the invention in combination with at least one second drug substance;

- A pharmaceutical composition comprising a compound of the invention in combination with at least one second drug substance and one or more pharmaceutically acceptable excipient(s);

- A compound of the invention in combination with at least one second drug substance, e.g. in the form of a pharmaceutical combination or composition, for use in any method as defined herein;

- A combination, a pharmaceutical combination or a pharmaceutical composition, comprising a compound of the invention and at least one second drug substance for use as a pharmaceutical;

- The use as a pharmaceutical of a compound of the invention in combination with at least one second drug substance, e.g. in the form of a pharmaceutical combination or composition;

- A method for treating and/or preventing mycobacterial infections in a patient in need thereof, comprising co-administering, concomitantly or in sequence, a therapeutically effective amount of a compound of the invention and at least one second drug substance, e.g. in the form of a pharmaceutical combination or composition;

- A compound of the invention in combination with at least one second drug substance, e.g. in the form of a pharmaceutical combination or composition, for use in the preparation of a medicament for use in treating and/or preventing mycobacterial infections.

The terms "co-administering" or "co-administration" or the like as used herein are meant to encompass administration of the selected second drug substance to a single patient, and are intended to include treatment regimens in which the second drug substance is not necessarily administered by the same route of administration or at the same time. The compound of the invention and any second drug substance may be formulated in separate dosage forms. Alternatively, to decrease the number of dosage forms administered to a patient, the compound of the invention and any second drug substance may be formulated together in any combination. For example, the compound of the invention may be formulated in one dosage form and the second drug substance may be formulated together in another dosage form. Any separate dosage forms may be administered at the same time or different times.

Combinations include fixed combinations, in which a compound of the invention and at least one second drug substance are in the same formulation; kits, in which a compound of the invention and at least one second drug substance in separate formulations are provided in the same package, e.g. with instructions for co-administration; and free combinations in which a compound of the invention and at least one second drug substance are packaged separately, but instructions for concomitant or sequential administration are given.

In another aspect the invention provides:

- A pharmaceutical package comprising a first drug substance which is a compound of the invention and at least one second drug substance, beside instructions for combined administration;

- A pharmaceutical package comprising a compound of the invention beside instructions for combined administration with at least one second drug substance;

- A pharmaceutical package comprising at least one second drug substance beside instructions for combined administration with a compound of the invention.

Treatment with combinations according to the invention may provide improvements compared with single treatment.

In another aspect the invention provides: - A pharmaceutical combination comprising an amount of a compound of the invention and an amount of a second drug substance, wherein the amounts are appropriate to produce a synergistic therapeutic effect;

- A method for improving the therapeutic utility of a compound of the invention comprising co-administering, e.g. concomitantly or in sequence, of a therapeutically effective amount of a compound of the invention and a second drug substance;

- A method for improving the therapeutic utility of a second drug substance comprising coadministering, e.g. concomitantly or in sequence, of a therapeutically effective amount of a compound of the invention and a second drug substance.

A combination of a compound of the invention and a second drug substance as a combination partner may be administered by any conventional route, for example as set out herein for a compound of the invention. A second drug may be administered in dosages as appropriate, e.g. in dosage ranges which are similar to those used for single treatment, or, e.g. in case of synergy, below conventional dosage ranges.

Pharmaceutical compositions comprising a combination of the invention and pharmaceutical compositions comprising a second drug as described herein, may be provided as appropriate, e.g. according, e.g. analogously, to a method as conventional, or as described herein for a pharmaceutical composition of the invention.

Effective dosages of two or more agents, e.g. a compound of the invention and a second drug substance, are administered together, or in alternation or sequential-step therapy, whereby an effective dosage of each agent is administered serially or sequentially. In general, the first option may typically be preferred over alternation therapy because it induces multiple simultaneous stresses on the mycobacterium. The dosages given will depend on absorption, inactivation and excretion rate of the drug as well as other factors. It is to be noted that dosage values will also vary with the severity of the condition to be alleviated. It is to be further understood that for any particular subject, specific dosage regimens and schedules may be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions.

Daily dosages required in practicing such methods will vary depending upon, for example, the compound of the invention employed, the host, the mode of administration, the severity of the condition to be treated. Suitable daily dosages and unit dosage forms for oral administration to patients are described above. The amount of second drug substance in the dosage form can vary greatly, and can be determined by routine experimentation. For example, the dose of the compound of the invention and the second drug substance are indicated, depending on the pharmacological action required, to be about the same order, e.g. half, that administered for the same compound e.g. on administration alone or with another compound.

By the term "second drug substance" is meant a chemotherapeutic drug that may or may not be another compound of the invention, especially any chemotherapeutic agent other than a compound of the invention.

For example, a second drug substance as used herein includes, e.g., rifampicin, isoniazid, pyrazinamide, streptomycin and ethambutol or any other second-line anti-TB drugs such as p-Aminosalicyclic acid (PAS), Ethionamide, Prothionamide, Thioacetazone, Capreomycin, Viomycin, Cycloserine, Kanamycin etc or other anti-TB compounds like derivatives of rifamycin, aminoglycosides, fluoroquinolones, β-lactams, Oxazolidinones, phenothiazines, TMC-207.

It will be appreciated that any of the sub-scopes disclosed herein e.g. with respect to A, Y, Z, W, m, n, R\ R², R³, R⁴, R⁵, R⁶, R⁷ and/or R⁸ may be combined with any of the other sub- scopes disclosed herein to produce further sub-scopes.

Synthesis of Compounds of the Invention

The following general methods may be used to prepare compounds of the invention. The preparation of specific compounds of the invention will be apparent to those skilled in the art by reference to the particular Examples described below. Insofar as any particular process is not specifically described herein, this may be carried out in conventional or known manner or in a manner analogous to known methods.

General Procedure 1 : Synthesis of Starting Material Epoxides neral Procedure 1 (Scheme 1 ):

Scheme 1

Sharpless asymmetric dihydroxylation (using AD-mix beta) of an α,β-unsaturated trans olefin gives rise to the corresponding chiral diol. Protection of the diol followed by reduction of the ester group mediated by reducing agents such as LiAIH₄ or DI BAL gives access to the primary alcohol. Synthesis of the epoxide is achieved by tosylation of this alcohol and deprotection of the diol followed by treatment with base such as K₂C0₃ in methanol. The secondary hydroxyl group is protected, for example as a silyl derivative, using TBSCI.

General Procedure 2: Synthesis of Starting Material Epoxides

The following epoxides are synthesised according to General Procedure 2 (Scheme 2):

OTBS OTs O

" ^■ K₂C0₃, MeOH

R ^OH

CH₂CI₂ OTBS

Sharpless asymmetric dihydroxylation (using AD-mix alpha) of an α,β-unsaturated trans olefin gives rise to the corresponding chiral diol. Selective tosylation of the reactive hydroxyl group is achieved by treatment with tosyl chloride in presence of triethylamine. Protection of the free hydroxyl group, e.g. with a silyl group such as tert-butyldimethylsilyl, followed by reduction of the ester group mediated by reducing agents such as LiAIH₄, or DIBAL, gives access to the primary alcohol. Synthesis of the epoxide is achieved by treatment with base such as K₂CO₃ in methanol or NaH in THF.

General Procedure 3: Synthesis of Starting Material Epoxides rding to General Procedure 3 (Scheme 3):

Scheme 3

Vinyl MgBr L-DIT, Ti(OiPr)₄ ^ O ^ _R _^BDMS-C_ O^

THF, n0°°rC * OH TBHP, CH,CL Ξ Imidazole, CH,CI, Ξ

OH OTBS

jBu, Benzyl

DIAD,

4-nitrobenzoic

Ph₃P, Et₃N NaOMe, MeOH ^<L> ,R TBDMS-CI ^<| >v_N ,R n 1 Imidazole *

R =Benzyl

Epoxides are also synthesised using a Sharpless epoxidation procedure. The required allylic alcohols are synthesised by addition of vinylmagnesiumbromide to corresponding aldehydes. Sharpless epoxidation in presence of L-diisopropyltartrate followed by protection, e.g. with a silyl group, for example tert-butyldimethylsilyl group, gives the corresponding epoxide derivatives. Inversion of the free secondary hydroxyl group by Mitsunobu reaction gives rise to the other diastereomer. Protection, e.g. using a silyl group, of this OH group is achieved as described above.

General Procedure 4: Synthesis of Compounds of the Invention

The compounds of the invention having a linker group Y which is NH are synthesised according to general Procedure 4 (Scheme 4).

Scheme 4

R = Et, nPr, iBu, tBu, Benzyl, phenyl, hydroxy methyl, methoxymethyl, vinyl.

Reaction of 2-chloro-4-nitroimidazole with the epoxide at elevated temperatures results in the formation of an epoxide opened secondary alcohol which is protected, e.g. as the tetrahydropyran or methoxymethyl, derivative as a mixture of diastereomers. Treatment of this mixture with TBAF at elevated temperatures gives rise to the oxazine intermediate which, under acidic conditions, undergoes THP-deprotection to provide the secondary alcohol. Derivatisation of this alcohol as a leaving group such as a mesyl or tosyl derivative, followed by treatment with sodium azide, gives rise to the azide intermediate which is reduced to an amine by methods reported in the literature, e.g. by use of Ph₃P/THF/water or by using propanethiol (Tetrahedron Lett. 1978, (39), 3633-3634). Alkylation of this amine either by reductive amination with corresponding aldehydes or by using corresponding alkyl halide in presence of base gives rise to the final product.

EXAMPLES

The invention is described with reference to the following examples. It is to be appreciated that the invention is not limited to these examples.

Abbreviations

RT room temperature

Pet ether petroleum ether

DCM dichloromethane

NMR nuclear magnetic resonance

TLC thin layer chromatography MS mass spectrometry

LC-MS liquid chromatography-mass spectrometry

HPLC high performance liquid chromatography

DMSO dimethylsulfoxide

THF tetrahydrofuran

2,2-DMP 2,2-dimethoxypropane

TBDMS tert-butyldimethylsilyl

TEA triethylamine

DIBAL diisobutylaluminium hydride

TBS tert-butyldimethylsilyl

TBHP tert-butylhydroperoxide

PPTS pyridinium-p-toluene sulfonate

DMF dimethylformamide

DHP dihydropyran

TBAF tetra-n-butylammonium fluoride

(DQHD)₂PHAL hydroquinidine 1 ,4-phthalazinediyl diether

(DHQ)₂PHAL hydroquinine 1 ,4-phthalazinediyl diether

MTB Mycobacterium tuberculosis

MDR multi-drug resistant

XDR extensively drug resistant

MIC minimum inhibitory concentration

MAC minimum anaerobic concentration

TB Tuberculosis

I. Preparation of Compounds of the Invention

Example 1 : Synthesis of Epoxides According to General Procedure 1 Step 1 : 2,3-Dihydroxy-pentanoic acid methyl ester

(1.1 ) (1.2)

To a mixture of t-BuOH (600 mL) and water (600 mL), K₂Os0₄(OH)2 (484 mg, 1.3mmol), (DHQD)₂PHAL (2.04g, 2.63 mmol), K₃Fe(CN)₆ (259.6 g, 789.3 mmol), K₂C0₃ (108.9 g, 789.3 mmol) and CH₃S0₂NH₂ (25g, 263.1 mmol) are added followed by pent-2-enoic acid methyl ester (1.1 ) (30 g, 263.1 mmol) at 0 °C. After stirring the reaction mixture for 16 h at 0 °C, saturated aqueous Na₂S0₃ solution (300 mL) is added and the reaction is stirred for 30 min at RT. The reaction mixture is extracted with ethyl acetate (5 x 200 mL), the organic layer is dried (anhydrous Na₂S0₄) and concentrated in vacuo. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) by using a solvent gradient of 0- 40% EtOAc/pet ether as eluent to afford 2,3-dihydroxy-pentanoic acid methyl ester (1.2) as a colourless oil.

The following compounds are synthesised in accordance with this method:

Ste 2: 5-Ethyl-2,2-dimethyl-[1 ,3]dioxolane-4-carboxylic acid methyl ester

(1.3)

To a stirred solution of 2,3-dihydroxy-pentanoic acid methyl ester (1.2) (45g, 304.05 mmol) in acetone (450 mL) is added 2,2-DMP (338 mL, 2.73mol) under cold conditions. Then BF₃.OEt₂ (2.5 mL) is added slowly to the reaction mixture and the reaction is stirred for 1 h at 0 °C. The reaction mixture is poured into saturated aqueous NaHC03 solution and extracted with EtOAc (2 x 150 mL). The organic layer is washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure to afford crude 5-ethyl-2,2- dimethyl-[1 ,3]dioxolane-4-carboxylic acid methyl ester (1.3) as a colourless liquid.

The following compounds are synthesised in accordance with this method:

Ste 3: (5-Ethyl-2,2-dimethyl-[1 ,3]dioxolan-4-yl)-methanol

(1.4)

To a stirred solution of 5-ethyl-2,2-dimethyl-[1 ,3]dioxolane-4-carboxylic acid methyl ester (1.3) (50 g, 290.1 mmol) in THF (400 mL) is added LiAIH₄ (1 1 g, 290.1 mmol) slowly at 0 °C and the mixture is slowly allowed to reach RT and stirred for 2 h at RT. Ice water (25 mL) is added to the reaction mixture at 0 °C and the resulting precipitate is filtered . The filtrate is extracted with EtOAc (2 x 200 mL). The organic layer is washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure to give crude (5-ethyl- 2,2-dimethyl-[1 ,3]dioxolan-4-yl)-methanol (1.4) as a colourless liquid. The following compounds are synthesised in accordance with this method:

Step 4: ((4R,5R)-5-ethyl-2,2-dimethyl-1 ,3-dioxolan-4-yl)methyl 4- meth lbenzenesulfonate

(1.5)

To a stirred solution of (5-ethyl-2,2-dimethyl-[1 ,3]dioxolan-4-yl)-methanol (1.4) (38g, 265.8 mmol) in DCM (380 mL) is added triethylamine (1 11 mL, 791.6 mmol) and TsCI (150.4g, 791.6 mmol) at 0 °C. The reaction mixture is stirred at RT overnight. The reaction mixture is diluted with DCM (300 mL). The organic layer is washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) by using a solvent gradient of 0-15% EtOAc/pet ether as eluent to afford ((4R,5R)-5-ethyl-2,2-dimethyl-1 ,3- dioxolan-4-yl)methyl 4-methylbenzenesulfonate (1.5) as a colourless liquid. The following compounds are synthesised in accordance with this method:

J

J

= 8.8 Hz, 2H), 7.23 (d, J = 8.8 Hz, 2H),

7.32 (d, J = 8.0 Hz, 2H), 7.78 (d, J = 8.4

Hz, 2H).

Step 5: (2R,3R)-2,3-dihydroxypentyl 4-methylbenzenesulfonate

(1.6)

To a stirred solution of ((4R,5R)-5-ethyl-2,2-dimethyl-1 ,3-dioxolan-4-yl)methyl 4- methylbenzenesulfonate (1.5) (59g, 187.8 mmol) in MeOH (500 mL) is added 0.5% aqueous HCI (60ml_) and the mixture is heated at reflux for 4h. The solvent is distilled off and the residue is taken up in ethyl acetate (300ml_) and washed with aqueous NaHC03 (2 x 30mL) and water and brine and dried (Na₂S0₄). After concentration, the residue is washed with pentane to give (2R,3R)-2,3-dihydroxypentyl 4-methylbenzenesulfonate (1.6) as a white solid.

The following compounds are synthesised in accordance with this method:

butyldimethyl((R)-1 -((R)-oxiran-2-yl)propoxy)silane

(1.7)

To a stirred solution of (2R,3R)-2,3-dihydroxypentyl 4-methylbenzenesulfonate (45g, 156.25mmol) in MeOH (50 mL, 1.56 mol, 10eq), DCM (300 mL) is added K₂C0₃ (43.1 g, 3 2.5 mmol) at RT and the reaction mixture is stirred for 16h. The mixture is diluted with DCM (100 mL) and washed with half saturated brine solution (2 x 50 mL). The organic layer is dried over magnesium sulfate and passed through a Na₂S0₄ pad. Solvent is carefully evaporated, the residue is cooled to 0 °C and to this is added imidazole (23.9g, 352.9 mmol) followed by TBDMSCI (53.18g, 352.9 mmol) and the reaction mixture is stirred for 2 h at RT. The reaction mixture is diluted with DCM (180 mL) and washed with brine solution (2 x 50 mL). The organic layer is dried over magnesium sulfate and evaporated carefully to afford the product which is pure enough for use in the next step.

The following compounds are synthesised in accordance with this method:

Example 2: Synthesis of Epoxides According to General Procedure 2 Step 1 : 2,3-Dihydroxy-pentanoic acid methyl ester

OH O

~o

O H I (2.1)

To a cold (0 °C) solution of methane sulfonamide (25.0 g, 263.1 mmol) in t-butanol (600 mL) and water (600 mL) are added K₂Os0₄(OH)₂ (484 mg, 1.3 mmol), (DHQ)₂PHAL (2.04 g, 2.631 mmol), K₃Fe(CN)₆ (259.6 g, 789.3 mmol) and K₂C0₃ (108.9 g, 789.3 mmol). Then pent-2-enoic acid methyl ester (30 g, 263.1 mmol) is added and the reaction mixture is stirred for 16 h at 0 °C. The reaction is quenched with aqueous saturated sodium sulfite solution (200 mL), extracted with EtOAc (3 x 300 mL) and dried over anhydrous Na₂S0₄ and concentrated to afford 2,3-dihydroxy-pentanoic acid methyl ester (2.1) as a pale green liquid.

The following compounds are synthesised in accordance with this method:

Step 2: (2R,3S)-methyl 3-hydroxy-2-(tosyloxy)pentanoate

(2.2)

To a cold solution of 2,3-dihydroxy-pentanoic acid methyl ester (2.1) (30 g, 202.7 mmol) in dry DCM (300 mL) is added TEA (65.39 mL, 446.2 mmol) then tosylchloride (46.2 g, 243.2 mmol) is added portion wise for a period of 1 h and the reaction mixture is allowed to warm to RT and is stirred for 16 h . The reaction mixture is diluted with water (200 mL) and extracted with DCM (2 x 200 mL). The organic layer is washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) using a solvent gradient of 10-12% EtOAc-pet ether as eluent to afford (2R,3S)-methyl 3-hydroxy-2-(tosyloxy)pentanoate as a pale green liquid.

The following compounds are synthesised in accordance with this method:

Step 3: (2R,3S)-methyl 3-(tert-butyldimethylsilyloxy)-2-(tosyloxy)pentanoate

(2.3)

To a solution of (2R,3S)-methyl 3-hydroxy-2-(tosyloxy)pentanoate (2.2) (17 g, 56.29 mmol) in dry pyridine (34 mL) is added AgN0₃ (28.6 g, 168.7 mmol) and the mixture is stirred for 30 min. To this TBDMS-CI (15.26 g, 101.32 mmol) is added and the mixture is stirred for another 1 h. The reaction mixture is diluted with water (100 mL), filtered through a celite pad and the filtrate is extracted with diethyl ether (2 x 200 mL). The organic layer is washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure to afford (2R,3S)-methyl 3-(tert- butyldimethylsilyloxy)-2-(tosyloxy)pentanoate as a pale green liquid. This is used for next step without further purification.

The following compounds are synthesised in accordance with this method:

Step 4: (2S,3S)-3-(tert-butyldimethylsilyloxy)-1-hydroxypent

methyl benzenesulfonate

(2.4) To a cold (-70 °C) solution of (2R,3S)-methyl 3-(tert-butyldimethylsilyloxy)-2-(tosyloxy)pentanoate (2.3) (36 g, 86.53 mmol) in dry DCM (360 mL) is added 1 M DIBAL-H in hexane (173 mL, 173 mmol) over a period of 30 min and the reaction mixture is stirred for 3 h at -65 °C. The reaction is quenched with aqueous saturated NH₄CI solution (100 mL), and filtered through a celite pad. The mixture is extracted with DCM (2 x 300 mL). The organic layer is washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) using a solvent gradient of 3-8% EtOAc-pet ether as eluent to afford (2S,3S)-3-(tert-butyldimethylsilyloxy)-1-hydroxypentan-2-yl 4- methylbenzenesulfonate as a colourless liquid.

The following compounds are synthesised in accordance with this method:

-butyldimethyl((S)-1 -((R)-oxiran-2-yl)propoxy)silane

(2.5)

To a solution of (2S,3S)-3-(tert-butyldimethylsilyloxy)-1-hydroxypentan-2-yl 4- methylbenzenesulfonate (2.4) (16 g, 36.08 mmol) in dry DCM (200 mL) and methanol (200 mL) is added dry K₂C0₃ (9.97 g, 76.12 mmol) and the reaction mixture is stirred for 16 h at T. The mixture is diluted with water (300 mL) and extracted with DCM (2 x 30 mL). The organic layer is washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) using a solvent gradient of 0-5% EtOAc - pet ether as eluent to afford tert-butyldimethyl((S)- 1-((R)-oxiran-2-yl)propoxy)silane as a colourless liquid.

The following compounds are synthesised in accordance with this method:

Example 3: Synthesis of Further Epoxides

Step 1 : ((S)-1 -((R)-oxiran-2-yl)-2-phenylethoxy)(tert-butyl)dimethylsilane

(3.1 )

To a stirred solution of (S)-1-((R)-oxiran-2-yl)-2-phenylethanol (28 g, 170.73 mmol, 1 eq) (synthesised as described in Example 4) in DCM, imidazole (23.2 g, 341.46 mmol, 2 eq) is added and the mixture is cooled to 0 °C. TBDMS-CI (51 .4 g, 341 .4 mmol, 2 eq) is added and the reaction mixture is stirred at RT for 16h. The reaction mixture is diluted with DCM and washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) using a solvent gradient of 0 - 5% EtOAc-pet ether as eluent to afford ((S)- 1-((R)-oxiran-2-yl)-2-phenylethoxy)(tert-butyl)dimethylsilane as colourless liquid.

MS: m/z 279 (M+H).

The following compounds are synthesised in accordance with this method:

Example 4: Synthesis of Further Epoxides

Example 5: (1 R,2R)-1 -(tert-Butyl -dimethyl -silanyloxy)-3-(2-chloro-4-nitro-imidazol-1 -yl)- 1 -cvclopropyl-propan-2-ol

(5.1 ) (5.2) (5.3) (5.4)

The mixture of tosylate (5.1) (5 g, 15.33 mmol), 2-chloro-4-nitro-1 H-imidazole (17.1) (4.5 g, 30.67 mmol), K₂C0₃ (4.23 g, 30.67 mmol) and Kl (2.54 g, 15.33 mmol) in DMF (20mL) is stirred at 80 °C under N₂ atmosphere for 16 h. The mixture is diluted with water (100 mL) and then extracted with EtOAc (3 x 60 mL). The combined organic layer is washed with water (30 mL), brine, dried over anhydrous Na₂S0₄ and concentrated to crude compound. The crude compound is triturated with n-pentane and then filtered to afford (5.2) as an off- white solid.

¹H NMR (400 MHz, DMSO-d₆): δ 0.30-0.32 (m, 2H), 0.45-0.55 (m, 2H), 0.92-0.98 (m, 1 H), 1.27, 1.32 (2s, 6H), 3.25-3.29 (m, 1 H), 4.14-4.34 (m, 3H), 8.58 (s, 1 H).

MS: m/z 302.3 (M+H).

The above product (5.2) is treated with 0.5% aq. HCI (3 mL) and MeOH (8 mL) at 80 °C for 3h. Solvent is distilled off and the residue is diluted with aqueous NaHC0₃ solution (20 mL) and then extracted with EtOAc (3 x 30 mL). The combined organic layer is washed with water (20 mL), brine, dried over anhydrous Na₂S0₄ and concentrated to crude compound.

The crude compound is triturated with diethyl ether to afford (5.3) as a white solid.

¹H NMR (400 MHz, DMSO-d₆): δ 0.21-0.32 (m, 2H), 0.37-0.42 (m, 2H), 0.97-1.02 (m, 1 H),

2.83-2.87 (m, 1 H), 3.75-3.80 (m, 1 H), 4.02-4.08 (m, 1 H), 4.15-4.19 (m, 1 H), 4.84-4.85 (d,

1 H, J = 5.2 Hz), 5.14-5.16 (d, 1 H, J = 5.2 Hz), 8.52 (s, 1 H).

MS: m/z 262.1 (M + H).

To a stirred solution of (5.3) obtained as described above (2 g, 7.66 mmol) in DCM (8 mL) is added imidazole (1.56 g, 22.98 mmol) and TBSCI (3.4 g, 22.98 mmol) at RT under N₂ atmosphere and the mixture is stirred at RT for 40 h. The mixture is diluted with water (30 mL) and then extracted with DCM (2 x 50 mL). The combined organic layer is washed with water (20 mL), brine, dried over anhydrous Na2S0₄ and concentrated to crude compound. The crude compound is purified by column chromatography over silica gel (100-200 mesh) using a gradient mixture of 0-10% EtOAc-pet ether as eluent to afford (5.4) as a white solid. 1H NMR (400 MHz, DMSO-d₆): δ 0.03 (s, 6H), 0.24-0.32 (m, 2H), 0.42-0.45 (m, 2H), 0.86 (s, 9H), 1.01-1.05 (m, 1 H), 3.71-3.77 (m, 1 H), 3.98-4.08 (m, 2H), 4.16-4.20 (m, 1 H), 5.28-5.29 (m, 1 H), 8.41 (s, 1 H).

The following compounds are synthesised in accordance with this method:

Example 6: (2R,3R)-3-(tert-butyldimethylsilyloxy)-1 -(2-chloro-4-nitro-1 H-imidazol-1- yl)pentan-2-ol

To a stirred solution of 2-chloro-4-nitro-1 H-imidazole (28.6g, 194.4 mmol) in dry EtOH (150 mL) is added K₂C0₃ (1.79g, 12.96 mmol) at RT and the mixture is stirred for 10 min. Then tert-butyldimethyl((R)-1-((R)-oxiran-2-yl)propoxy)silane (1.7) (14g) in dry EtOH (50 mL) is added at RT and the mixture is stirred at 75 °C for 18h.The solvent is distilled off and the obtained crude compound is dissolved in EtOAc (200 mL) and washed with water (2x 20 mL), brine (20 mL), dried (anhydrous Na₂S0₄) and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100-200 mesh) using a solvent gradient of 0-20% EtOAc-petroleum ether as eluent to afford (2R,3R)-3-(tert- butyldimethylsilyloxy)-1-(2-chloro-4-nitro-1 H-imidazol-1-yl)pentan-2-ol as a solid.

The following compounds are synthesised in accordance with this method:

Example 7: 1-((2R,3R)-3-(tert-butyldimethylsilyloxy)-2-(tetrahvdro-2H-pyran-2- yloxy)pentvn-2-chloro-4-nitro-1H-imidazole

(7.1)

To a stirred solution of (2R,3R)-3-(tert-butyldimethylsilyloxy)-1 -(2-chloro-4-nitro-1 H-imidazol- 1-yl)pentan-2-ol (6.0 g, 16.52 mmol) in dry DCM (100 mL) is added PPTS (6.21 g, 24.78 mmol), DHP (3.01 mL, 33.05 mmol) at RT and the reaction mixture is stirred overnight at RT. The mixture is diluted with DCM and washed with water, brine, dried over anhydrous Na₂S0₄ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) by using a solvent gradient of 0 - 15% EtOAc/ pet ether as eluent to afford 1-((2R,3R)-3-(tert-butyldimethylsilyloxy)-2-(tetrahydro- 2H-pyran-2-yloxy)pentyl)-2-chloro-4-nitro-1 H-imidazole (6.1) as a liquid.

The following compounds are synthesised in accordance with this method:

DMSO-d₆: δ 0.05-0.08 (m, 6H), 0.89

(s, 9H), 1.20-1.60 (ser m, 6H), 2.95- 3.10 (m, 1 H), 3.29 (s, 3H), 3.40-3.90

(m, 4H), 3.95-4.30 (m, 4H), 8.47 &

8.50 (2s, 1 H).

Example 8: (6R,7R)-7-ethyl-2-nitro-6-(tetrahvdro-2H-pyran-2-yloxy)-6,7-dihvdro-5H- imidazor2,1 -bl[1 ,31oxazine

(8.1)

To a stirred solution of (1-((2R,3R)-3-(tert-butyldimethylsilyloxy)-2-(tetrahydro-2H-pyran-2- yloxy)pentyl)-2-chloro-4-nitro-1 H-imidazole (6.1) (6.0 g, 13.42 mmol) in THF (50 mL) is added TBAF solution (1 M in THF, 53.6 mL, 53.6 mmol) at RT and the reaction mixture is stirred for 1 h at RT. The reaction mixture is then heated to 70 °C for 16h. The solvent is distilled off and the residue is dissolved in EtOAc and washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) by using a solvent gradient mixture of 0 - 40% EtOAc - pet ether as eluent to afford (6R,7R)-7-ethyl-2-nitro-6- (tetrahydro-2H-pyran-2-yloxy)-6,7-dihydro-5H-imidazo[2,1-b][1 ,3]oxazine (7.1) as a light yellowish gummy solid.

The following compounds are synthesised in accordance with this method:

Example 9: (6R,7R)-7-ethyl-2-nitro-6,7-dihvdro-5H-imidazor2,1-bin,3loxazin-6-ol

(9.1)

Brief procedure: A solution of (6R,7R)-7-ethyl-2-nitro-6-(tetrahydro-2H-pyran-2-yloxy)-6,7- dihydro-5H-imidazo[2, 1 -b][1 ,3]oxazine (7.1) (3.0 g, 101.1 mmol) in acetonitrile (15 mL), TBME (27 mL), MeOH (2.25 mL) is cooled to 0 °C and to this is added IPA/HCI (2.25 mL) and the reaction mixture is stirred for 1 h at RT. The solvent is distilled off under vacuum. The resulting residue is washed with diethyl ether to afford (6R,7R)-7-ethyl-2-nitro-6,7- dihydro-5H-imidazo[2, 1 -b][1 ,3]oxazin-6-ol (8.1) as a light yellowish solid.

The following compounds are synthesised in accordance with this method:

4.35-4.60 (m, 4H), 5.85 (brs, 1H), 6.87 (d,

Example 10: (6R,7R)-7-ethyl-2-nitro-6,7-dihvdro-5H-imidazor2,1-bin,31oxazin-6-yl methanesulfonate

(10.1)

To a cold (0 °C) stirred solution of (6R,7R)-7-ethyl-2-nitro-6,7-dihydro-5H-imidazo[2,1- b][1 ,3]oxazin-6-ol (8.1) (1.8 g, 8.45 mmol) in DMF (18 mL) is added triethylamine (3.5 mL, 25.35 mmol) followed by methane sulfonylchloride (1 .31 mL, 16.9mmol) and the reaction mixture is stirred at RT for 4 h. The solvent is distilled off under vacuum. The obtained residue is diluted with EtOAc (30 mL). The organic layer is washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure to afford (6R,7R)-7- ethyl-2-nitro-6,7-dihydro-5H-imidazo[2,1 -b][1 ,3]oxazin-6-yl methanesulfonate (9.1) as light yellowish solid.

The following compounds are synthesised in accordance with this method:

-6-azido-7-ethyl-2-nitro-6,7-dihvdro-5H-imidazor2,1 -blH ,31oxazine

(11.1)

To a stirred solution of (6R,7R)-7-ethyl-2-nitro-6,7-dihydro-5H-imidazo[2, 1-b][1 ,3]oxazin-6-yl methanesulfonate (10.1) (2.1 g, 7.20 mmol) in DMF (20 mL) is added sodium azide (4.68 g, 72.04 mmol) at RT and the reaction mixture is stirred at 70 °C for 48 h. the solvent is distilled off under vacuum and the residue is dissolved in EtOAc. The organic layer was washed with water, brine and dried over anhydrous Na₂S0₄ and concentrated under reduced pressure to afford (6S,7R)-6-azido-7-ethyl-2-nitro-6,7-dihydro-5H-imidazo[2,1-b][1 ,3]oxazine (11.1) as a brown gummy compound.

The following compounds are synthesised in accordance with this method:

301 (M+1)

267.4 (M+H).

252.8 (M+1)

253.5 (M+1)

239.4 (M+1)

301 (M+1)

266.9 (M+1)

—

311.9 (M+H)

252.8 (M+1)

237.1(M+1)

361.4 (M+1)

254.8

(M+H) -7-ethyl-2-nitro-6J-dihydro-5H-iiriidazor2,1-biri,3loxazin-6-amine

(12.1)

To a stirred solution of (6S,7R)-6-azido-7-ethyl-2-nitro-6,7-dihydro-5H-imidazo[2, 1 - b][1 ,3]oxazine (11.1) (1 .2g, 5.04 mmol) in THF (20 mL) is added triphenylphosphine (6.61 g, 2 .21 mmol) and the reaction mixture is stirred for 2 h at RT (TLC indicates absence of starting material and formation of polar spot). Then water (6.7 mL) is added to the reaction mixture and it is stirred at 70 °C for 16 h. The solvent is distilled off and the residue is diluted with water (15 mL). The aqueous layer is washed with diethyl ether (3 x 20 mL) to remove TPP and other impurities. The aqueous layer is concentrated under vacuum to afford (6S, 7R)-7-ethyl-2-nitro-6,7-dihydro-5H-imidazo[2, 1-b][1 ,3]oxazin-6-amine (12.1) as brown thick residue.

The following compounds are synthesised in accordance with this method:

DMSO-d₆: δ 3.17 (s, 3H), 3.65-3.90 (m,

N-_Sl^°^_r-^OPMB 5H), 4.00-4.50 (m, 2H), 4.30-4.70 (m,

335.4 (M+1 )

3H), 6.85-6.95 (m, 2H), 7.20-7.35 (m,

2H), 8.05 (s, 1 H).

DMSO-d₆: δ 1.98 (br s, 2H), 3.20-3.40

(m, 5H), 3.60-3.80 (m, 2H), 4.10-4.20 (m,

228.8 (M+1 ).

1 H), 4.33 (br s, 1 H), 8.05 (s, 1 H).

Example 13: (6S,7R)-7-ethyl-2-nitro-N-(4-(trifluoromethoxy)benzyl)-6,7-dihvdro-5H- imidazor2,1 -blf1 ,31oxazin-6-amine

(13.1)

A solution of (6S, 7R)-7-ethyl-2-nitro-6,7-dihydro-5H-imidazo[2,1-b][1 ,3]oxazin-6-amine (12.1) (200 mg, 0.94 mmol) and 4-trifluoromethoxy benzaldehyde (358mg, 1.88 mmol) in ethanol is heated at reflux for 2h. Then acetic acid (1 mL) and NaBH(OAc)₃ (200mg, 0.94 mmol) are added and the reaction mixture is stirred for 16h at RT. Then NaBH₃CN (56 mg, 0.94 mmol) is added and the reaction mixture is stirred for 1 h at RT. The solvent is distilled off and the residue is dissolved in ethyl acetate and washed with water and sat aqueous NaHC0₃, dried (Na₂S0₄) and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) by using a solvent gradient of 0 - 40% EtOAc - pet ether as eluent to afford (6S,7R)-7-ethyl-2-nitro-N-(4- (trifluoromethoxy)benzyl)-6,7-dihydro-5H-imidazo[2, 1-b][1 ,3]oxazin-6-amine as light yellow solid.

The following compounds are synthesised in accordance with this method:

(13.1) (brs, 1H), 3.81 (m, 2H), 3.95-3.99 (m,

1H), 4.14-4.18 (m, 1H), 4.38-4.40 (m, 1H), 7.28-7.30 (d, 2H, J = 8.0 Hz), 7.43-7.45 (d, 2H, J = 8.0 Hz), 7.99 (s, 1H).

DMSO-d₆: δ 0.85 (t, 3H, J = 7.3 Hz),

1.70-1.85 (m, 2H), 2.64-2.79 (m, 1 H),

3.09 (brs, 1H), 3.69-3.74 (m, 1H), 3.82-

387.3

3.87(m, 1H), 3.99-4.03 (m, 1H), 4.11- 2.142

(M+1) 4.15 (m, 1H), 4.38-4.41 (m, 1H), 7.29-

(13.2)

7.31 (d, 2H, J = 8.0 Hz), 7.44-7.46 (d, 2H, JH = 8.0 Hz), 8.00 (s, 1H).

DMSO-d₆: δ 0.89 (t, 3H, J = 7.3 Hz),

1.38-1.63 (m, 4H), 2.77-2.78 (m, 1 H), 3.06 (brs, 1H), 3.79-3.81 (m, 2H), 3.97- 401.3

4.00 (m, 1H), 4.14-4.16 (m, 1H), 4.48 1 1.952

(m, 1H), 7.29-7.31 (d, 2H, J = 8.0 Hz), (M+1)

(13.3)

7.43-7.45 (d, 2H, JH = 8.0 Hz), 8.00 (s, 1H).

DMSO-cfe δ 0.88 (t, 3H, J = 7.3 Hz),

1.15-1.35 (m, 4H), 1.63-1.79 (m, 2H),

2.68-2.69 (m, 1 H), 3.06 (brs, 1H),

401.4

3.72-3.83 (m, 2H), 4.01-4.13 (m, 2H), 2.545

(M+1) 4.48-4.51 (m, 1H), 7.29-7.31 (d, 2H, J =

(13.4)

8.0 Hz), 7.45-7.47 (d, 2H, J = 8.0 Hz), 8.00 (s, 1H).

DMSO-d₆: δ 0.90 (t, J=7.2 Hz, 6H),

1.49-1.54 (m, 2H), 1.76-1.79 (m, 1H), 2.79 (m, 1H), 3.03 (m 1H), 3.81 (m, 415.4

2.340 2H), 4.02 (m 1H), 4.13 (m, 1H), 4.52- (M+1)

(13.5) 4.56 (m, 1H), 7.30 (m, 2H), 7.44 (m,

2H), 8.00 (s, 1H).

CDCI₃: δ 0.94-0.98 (m, 6H), 1.44-1.51

(m, 1H), 1.80-1.94 (m, 2H), 3.83-4.08 415

2.651

V (m, 4H), 4.45-4.48 (m, 1H), 7.18-7.20 (M+1)

(d, 2H, J = 8.0 Hz), 7.33-7.35 (d, 2H, J (13.6) = 8.0 Hz), 7.38 (s, H).

CD₃OD: δ 1.60 (s, 9H), 3.43 (s, H),

3.74 (m, 1H), 3.94 - 3.99(m, 2H), 4.16

(s, 1H), 4.34-4.37 (m, H), 7.21 (d, 2H, 415.4

3.615 J=8.0 Hz), 7.44 (d, J=8.0 Hz, 2H), 7.73 (M+1)

(13.7) (brs, 1H).

DMSO-d₆: δ 0.34-0.37 (m, 1H), 0.42- 0.47 (m, 1H), 0.57-0.61 (m, 2H), 1.11-

_N¾ o ><|

1.18 (m, 1H), 2.75-2.79 (m, 1H), 3.18-

399.4

3.19 (m, 1H), 3.81-3.85 (m, 3 H), 4.02- 1.802

(M+1) 4.06 (m 1 H), 4.24-4.27 (m, 1H), 7.29- (13.8)

7.31 (d, 2H, J = 8.0 Hz), 7.43-7.45 (d,

2H, J = 8.0 Hz), 8.03 (s, 1H).

DMSO-d₆: δ 0.24-0.28 (m, 1H), 0.41- 0.50 (m, 2H), 0.66-0.67 (m, 1H), 1.48- 1.54 (m, 1H), 2.81-2.83 (m, 1H), 3.17

399

(m, 1H), 3.74-4.00 (m 4 H), 4.12-4.15 1.666

(M+1) (m, 1H), 7.29-7.31 (d, 2H, J = 8.0 Hz),

(13.9)

7.47-7.49 (d, 2H, J = 8.0 Hz), 7.98 (s,

H).

CDCI₃: δ 3.44-3.48 (m, 1H), 3.80-3.83

(m, 4H), 3.85-3.95 (m, 3H), 4.03 (m,

2H), 4.49-4.55 (m, 3H), 6.85-6.87 (d, 509.4

2H, J = 8.4 Hz), 7.13-7.15 (d, 2H, J = 6

(13.10) 8.4 Hz), 7.17-7.19 (d, 2H, J = 8.0 Hz), (M+1)

7.24-7.26 (d, 2H, J = 8.0 Hz), 7.35 (s,

1H).

DMSO-d₆: δ 0.88 (t, 3H, , J = 7.3 Hz),

1.72-1.89 (m, 2H), 2.66 (m, 1H), 3.11

(m, 1H), 3.78 (m, 1H), 3.91 (m, 1H),

463.4

4.05 (m, 1H), 4.13 (m, 1H), 4.41 (m, 2.046

(M+1) 1H), 7.44 (d, 4H, J = 8.0 Hz), 7.63 (d,

(13.11)

2H, J = 8.0 Hz), 7.77 (d, 2H, J = 8.0

Hz), 8.01 (s, 1H). CD₃OD: δ 0.97 (m, 3H), 1.74-1.83 (m,

1H), 1.86-1.95 (m, 1H), 3.23 (m, 1H), 3.79 (m, 1H), 3.91 (m, 1H), 4.04 (m, 479.4

1.621 1H), 4.20 (m, 1H), 4.40 (m, 1H), 6.97 (M+1)

(13.12) (m, 2H), 7.02 (m, 2H), 7.25 (m, 2H),

7.37 (m, 2H), 7.69 (s, 1H).

DMSO-d₆: δ 0.91 (t, 3H, , J = 7.3 Hz),

1.69-1.76 (m, 2H), 1.99 (m, 1H), 2.66-

401.4

2.75 (m, 3H), 2.87 (m, 1H), 3.21 (m, 1.958

(M+1) 1H), 4.05 (m, 2H), 4.42 (m, 1H), 7.23

(13.13) (m, 2H), 7.32 (m, 2H), 8.00 (s, 1H).

DMSO-d₆: : δ 0.95 (t, 3H, J = 7.3 Hz), 1.62-1.74 (m, 2H), 2.84 (m, 1H), 3.09 (br s, 1 H), 3.82 (br s, 2H), 3.95 (m, 1 H), 405.0

2.080 4.15 (m, 1H), 4.37-4.40 (m, 1H), 7.26 (M+1)

(13.14) (m, 1H), 7.41-7.52 (m, 2H), 7.98 (s,

1H).

DMSO-d₆: δ 1.01 (t, 3H, J = 7.2 Hz), 1.65-1.84 (m, 2H), 2.73 (br d, 1H), 3.13 (br t, 1H), 3.71-3.82 (m, 2H), 4.01 (dd,

403.4

1H), 4.20 (dd, 1H), 4.42-4.46 (m, 1H), 1.384

(M+1) 6.84 (dd, 1H, J = 1.3, 8.0 Hz), 7.03 (d,

(13.15)

1H, 1.3 Hz), 7.21 (d, 1H, J = 8.0 Hz), 8.05 (s, 1H), 10.10 (s, 1H).

DMSO-cfe δ 0.87 (t, 3H, J = 7.3 Hz),

1.72-1.87 (m, 2H), 2.76-2.81 (m, 1H),

421.2

3.11 (br s, 1 H), 3.74 (m, 1 H), 3.84 (m,

6 1.864 1H), 4.01 (m, 1H), 4.10 (m, 1H), 4.41

(M+1)

(13.16) (m, 1 H), 7.42 (m, 1 H), 7.49 (m, 1 H),

7.61 (s, 1H), 7.98 (s, 1H).

DMSO-d₆: δ 0.87 (t, 3H, J = 7.3 Hz), 1.87 (m, 2H), 2.77 (m, 1H), 3.10 (br s,

405.0

1H), 3.76 (m, 2H), 4.13 (m, 2H), 4.40 1.575

(M+1) (m, 1H), 7.28 (m, 1H), 7.45-7.52 (m,

(13.17)

2H), 7.99 (s, 1H).

Example 14: Synthesis of r(6S.7R)-2-Nitro-6-(4-trifluoromethoxy-benzylamino)-6.7-

(13.10) (14.1)

To a cold (0 °C) solution of compound (13.10) (110 mg, 0.2 mmol) in DCM (3 mL) is added TBDMOTf (0.1 1 mL, 0.44 mmol) and the reaction mixture is stirred at RT. After 1.5 h, triethylamine (70.4 μί, 0.54 mmol) is added and the mixture is stirred for 30 min. The reaction mixture is diluted with water and extracted with DCM. The organic layer is washed with water, brine, dried anhydrous Na₂SC¼ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) using a solvent gradient of 10-30% EtOAc - petroleum ether as eluent to afford [(6S,7R)-7- (tert-Butyl-dimethyl-silanyloxymethyl)-2-nitro-6,7-dihydro-5H-imidazo[2,1-b][1 ,3]oxazin-6-yl]- (4-trifluoromethoxy-benzyl)-amine as a light yellow solid. ¹H NMR (400 MHz, CDCI₃): δ 0.06 (s, 3H), 0.09 (s, 3H), 0.86 (s, 9H), 3.48-3.51 (m, 1 H), 3.90 (dd, 2H), 3.95-4.15 (m, 5H), 4.36-4.41 (m, 1 H), 7.17 (d, J=1 1.2 Hz, 2H), 7.32 (d, J=1 1.2 Hz, 2H), 7.37 (s, 1 H). MS: m/z 503.0 (M+H).

The above compound (85 mg) is dissolved in DCM (3 mL) and to this is added HCI/ether (1 ml_). After stirring for 30 min at RT, the solvent is removed and the residue is washed with diethyl ether and dried under vacuum to afford (14.1 ) as a yellow solid.

1H NMR (400 MHz, CD₃OD): 5 4.08 (m, 1 H), 4.12 (m, 1 H), 4.34 (br s, 1 H), 4.41 (m, 1 H), 4.47-4.58 (m, 2H), 4.65 (m, 1 H), 4.74 (br s, 1 H), 7.40 (d, J=8.4 Hz, 2H), 7.64 (d, J=8.4 Hz, 2H), 7.89 (s, 1 H); MS: m/z 388.9(M+H). HPLC retention time: 2.744 min.

Example 15: [(6S,7S)-2-Nitro-6-(4-trifluoromethoxy-benzylamino)-6,7-dihydro-5H- in-7-yl]-methanol

(15.1)

Following a similar route to that described in Example 13 for [(6S,7R)-2-Nitro-6-(4- trifluoromethoxy-benzylamino)-6,7-dihydro-5H-imidazo[2,1-b] [1 ,3] oxazin-7-yl]-methanol (13.1), and starting with compound (12.19), [(6S,7S)-2-Nitro-6-(4-trifluoromethoxy- benzylamino)-6,7-dihydro-5H-imidazo[2,1-b] [1 ,3] oxazin-7-yl]-methanol (15.1) is also synthesised.

¹H NMR (400 MHz, CD₃OD): δ 3.35-3.45 (m, 1 H), 3.80-4.05 (m, 5H), 4.29 (m, 1 H), 4.40-4.50 (m, 1 H), 7.22 (d, J = 8.4 Hz, 2H), 7.46 (d, J = 8.4 Hz, 2H), 7.71 (s, 1 H); MS: m/z 389.4 (M+1 ). HPLC retention time: 1.367 min.

Example 16: Synthesis of (6S,7S)-7-tert-butyl-2-nitro-N-(4-(trifluoromethoxy)benzyl)-

6.7-dihvdro-5H-imidazoi2.1-bin.31oxazin-6-amine (169)

(16.1) (16.2) (16.3)

To a stirred solution of (6 ,7S)-7-tert-butyl-2-nitro-6,7-dihydro-5H-imidazo[2, 1-b][1 ,3]oxazin- 6-ol, synthesised as described in Example 8 (100 mg, 0.4149 mmol) in DCM (10 mL) is added Dess Martin periodinane (200 mg) at RT under N₂ atmosphere and the mixture is stirred at RT for 1 h. The mixture is filtered through a celite pad and the filtrate is

concentrated to crude compound. The crude compound is purified by column

chromatography over neutral alumina using DCM as eluent to (S)-7-tert-butyl-2-nitro-5H- imidazo[2, 1-b][1 ,3]oxazin-6(7H)-one (16.2) as a white solid.

¹H NMR (400 MHz, DMSO-d₆): δ 0.99 (s, 9H), 4.62 (s, 1 H), 4.78- 4.95 (m, 2H), 8.09 (s, 1 H). MS: m/z 240.3 (M+1 ).

To a mixture of (S)-7-tert-butyl-2-nitro-5H-imidazo[2,1-b][1 ,3]oxazin-6(7H)-one (16.2) (100 mg, 0.4184 mmol), (4-(trifluoromethoxy)phenyl)methanamine (160 mg, 0.836 mmol) and 4 A molecular sieves (100 mg) in MeOH (4 mL) is added AcOH (0.1 mL) at RT under N₂ atmosphere and the mixture is stirred at 80 °C for 6h. The mixture is then cooled to RT and to this is added NaCNBH₃ (107 mg, 1.6736 mmol) at RT and the mixture is stirred at RT for 3h. The mixture is neutralized with aqueous NaHC03 solution (10 mL) and then filtered through a celite pad. The filtrate is extracted with EtOAc (3 x 10 mL). The combined organic layer is washed with water (10 mL), brine and dried with anhydrous Na₂S0₄ then concentrated to crude compound. The crude compound is purified by chiral preparative HPLC to afford (6S,7S)-7-tert-butyl-2-nitro-N-(4-(trifluoromethoxy)benzyl)-6,7-dihydro-5H- imidazo[2, 1-b][1 ,3]oxazin-6-amine (16.3) as a light yellow solid.

¹H NMR (400 MHz, CD₃OD): δ 1.60 (s, 9H), 3.43 (s, 1 H), 3.74 (m, J=14.0Hz, 1 H), 3.94 (m, J=13.6Hz, 1 H), 3.97 (m, 1 H), 4.16 (s, 1 H), 4.34 (m, 1 H), 7.21 (d, 2H, J=8.0 Hz), 7.44 (d, , 2H, J=8.0 Hz), 7.73 (br s, 1 H); MS: m/z 415.4 (M+1 ). HPLC retention time: 3.615 min.

Example 17: Synthesis of (6S,7R)-7-Ethyl-2-nitro-6-(4-trifluoromethoxy-benzyloxy)-6,7- dihvdro-5H-imidazof2.1-biri.31oxazine (172) and (6S.7S)-7-Ethyl-2-nitro-6-(4- trifluoromethoxy-benzyloxy)-6.7-dihvdro-5H-imidazor2.1-biri.3loxazine

Step 1 : Synthesis of (2S,3R)-1 -(2-Chloro-4-nitro-imidazol-1 -yl)-3-(1 -methyl-1 - trimethylsilanyl-ethoxy)-pentan-2-ol

(17.1) (17.2)

To a stirred solution of tert-butyl-dimethyl-((R)-(S)-1-oxiranyl-propoxy)-silane, synthesised as described in Example 3, (4.5 g, 20.83 mmol) and 2-chloro-4-nitro-1 H-imidazole (17.1 ) (9.1 1 g, 62.49 mmol) in EtOH (45 mL) is added K₂C0₃ (574 mg, 4.16 mmol) at RT and the reaction mixture is stirred at 75 °C for 16 h. The solvent is distilled off from the reaction mixture, and the reaction mixture is diluted with water (50 mL) and extracted with EtOAc (3 x 50 mL). The combined organic layer is washed with water (50 mL), brine (50 mL), dried over anhydrous Na₂S0₄ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) using a solvent gradient of 8-10% EtOAc - pet ether as eluent to afford (2S,3R)-1 -(2-Chloro-4-nitro-imidazol-1-yl)-3- (1-methyl-1 -trimethylsilanyl-ethoxy)-pentan-2-ol as a semi solid.

H NMR (400 MHz, DMSO-d₆): δ 0.07 (s, 3H), 0.1 1 (s, 3H), 0.80-0.90 (m, 12H), 1.47-1.63 (m, 2H), 3.60-3.72 (m, 2H), 3.95 (m, 1 H), 4.21 (m, 1 H), 5.31 (m, 1 H), 8.50 (s, 1 H).

The following compound is synthesised in accordance with this method:

Step 2: Synthesis of (6S,7R)-7-Ethyl-2-nitro-6-(4-trifluoromethoxy-benzyloxy)-6,7- dihydro-5H-imidazo[2,1 -b][1,3]oxazine

(17.2) (17.3) To a stirred cold (-78 °C) solution of (17.2) (800 mg, 2.203 mmol), 1-bromomethyl-4- trifluoromethoxy-benzene (0.53 mL, 3.305 mmol) and TBAI (81 mg, 0.22 mmol) in DMF (8 mL) is added NaH (145 mg, 3.304 mmol) and the temperature is slowly warmed to 0 °C and stirred for 2 h. The reaction mixture is quenched with ice at 0 °C and extracted with EtOAc (3 x 30 mL). The combined organic layer is washed with water (30 mL), brine (30 mL) and dried over anhydrous Na₂SC>4 and concentrated under reduced pressure and passed through a short bed of silica gel to afford 1-[(2S,3R)-3-(tert-Butyl-dimethyl-silanyloxy)-2-(4- trifluoromethoxy-benzyloxy)-pentyl]-2-chloro-4-nitro-1 H-imidazole. To a stirred solution of this residue (300 mg, 0.56 mmol) in THF (3 mL) is added TBAF (1 M in THF, 2.23 mL, 2.23 mmol) and the mixture is stirred at 70 °C for 2 h. The reaction mixture is diluted with water (200 mL) and extracted with EtOAc (3 x 30 mL). The combined organic layer is washed with water (30 mL), brine (30 mL), dried over anhydrous Na₂S0₄ and concentrated under reduced pressure. The crude compound is purified by column chromatography over silica gel (100 - 200 mesh) using a solvent gradient of 10-15% EtOAc - pet ether as eluent to afford (6S,7R)-7-Ethyl-2-nitro-6-(4-trifluoromethoxy-benzyloxy)-6,7-dihydro-5H-imidazo[2,1- b][1 ,3]oxazine (17.3) as an off-white solid.

The following compounds are synthesised in accordance with this method:

Example 18: Synthesis of (6S,7S)-7-Benzyloxymethyl-2-nitro-6-(4-trifluoromethoxy- benzyloxy)-6,7-dihvdro-5H-imidazor2,1-biri,3loxazine

A mixture of epoxide (18.1 ) ((S)-2-benzyloxy-1-(S)-oxiranyl-ethoxy)-tert-butyl-dimethyl- silane), (0.9 g, 2.9 mmol, synthesised as described in Chemistry Letters, (10), 1825-6; 1994), 2,4-dinitroimidazole (0.32g, 2.3 mmol) and anhydrous K₂C0₃ (catalytic amount) in absolute EtOH (1 ml) is heated in a sealed tube at 70 °C for 20 h. The solvent is removed and the residue re- dissolved in ethyl acetate, washed with water, brine, dried (MgSC ) and evaporated in vacuo. The residue is purified (silica gel column chromatography, 8% to 15% EtOAc in hexanes) to give intermediate (2S,3S)-4-Benzyloxy-3-(tert-butyl-dimethyl- silanyloxy)-1 -(2,4-dinitro-imidazol-1-yl)-butan-2-ol which is treated with PPTS (0.25g , LOmmol) and 3,4-dihydro-2 - -pyran (1 ml) in dry DCM (50ml) at room temperature until the completion of the reaction. The organic layer is washed with water, brine, dried (MgSCu) and evaporated to afford a residue which, upon purification (silica gel column chromatography, 5- 8 % EtOAc in hexane), affords (18.2).

¹H NMR (CDCI₃): δ 0.08-0.09(s, 6H), 0.91 -0.92 (s, 9H), 1.10-2 .95(m, 6H), 3.35-4.20 (m, 7H), 4.53-4.58 (m, 2H), 4.80-5.15 (m, 2H), 7.26-7.37 (m, 5 H), 7.80-7.86 (2s, 1 H). MS: m/z 551.0 (M+1 ).

The above product (18.2) (0.5 g, 0.1 mmol) is dissolved in dry THF (25 ml) and treated with 1.0 M TBAF (2ml) in THF at room temperature for 30 minutes and concentrated. The residue is purified via column chromatography (silica gel, 30-40 % EtOAc in hexane) to afford (18.3).

¹H NMR (CDCI₃): δ 1.40-1 .80 (m, 6H), 3.44-4.39 (m, 6H), 4.43-4.76 (m, 5H), 7.26-7.39 (m, 6H).

MS: m/z 390.0 (M+1 ).

A mixture of (18.3) (0.25 g, 0.6 mmol), glacial acetic acid (4.0 mL,), tetrahydrofuran (2.0 mL) and H₂0 (1.0 mL) is heated at 60 °C for 18 h. The solvent and extra reagents are removed under reduced pressure. The residue is triturated with CH₂CI₂ to give (18.4) as a white crystalline solid.

H NMR (CDCI3): δ 3.87-3.98 (m, 2H), 4.20-4.44 (m, 2H), 4.50 (s, OH), 4.64 (s, 2 H), 4.71- 4.96 (m, 2H), 7.29-7.38 (m, 5H), 7.79 (S, 1 H).

MS: m/z 306.0 (M+1 ).

NaH (60% dispersion in mineral oil, 10 m g, 0.235 mmol) is added to a stirred mixture of (18.4) (60 mg, 0.196 mmol) in dry DMF (7 mL) at -10 ^°C under Ar. After stirring for 1 hour 4- triflouromethoxybenzylbromide (3.6ml, 0.037mmol) is added. The reaction is stirred for 30 minutes and quenched with water. The organic layer is removed and the product is separated by preparative TLC to afford 30 mg of (18.5).

¹H NMR (CD₃COCD₃): δ 3.80-3.91 (m, 2H), 4.03-4.16 (m, 1 H), 4.17-4.21 (m, 2H), 4.47-4.67 (m, 5 H), 7.15-7.36 (m, 10H).

MS: m/z 480.1 (M+1 ).

Example 19: Alternate Method for the Synthesis of Compounds of the Invention

The examples illustrated above can be synthesised by an alternate synthetic pathway as described below:

AD- mix-beta

TBSCI imidazole

1. PPh₃, THF, water

2. reductive amination or alkylation

Alkylation of the 2-chloro-4-nitroimidazole with the respective allylic halide followed by Sharpless asymmetric dihydroxylation mediated by AD-mix beta gives rise to the diol (19.2) in high enantiomeric purity. Reaction of this diol with one equivalent of TBSCI results in monoprotection of this diol to provide compound (19.3). Hereafter, the steps follow as described above. Further treatment with DHP/PPTS converts compound (19.3) to the 1- [(2R,3R)-3-(tert-Butyl-dimethyl-silanyloxy)-2-(tetrahydro-pyran-2-yloxy)-pentyl]-2-chloro-4- nitro-1 H-imidazole. Treatment with TBAF at elevated temperatures in THF followed by deprotection of the THP ether and conversion of the OH group to an NH₂ group with inversion gives rise to the required amine intermediate which can be alkylated by trifluoromethoxybenzylbromide or by reductive amination with the respective aldehyde such as trifluoromethoxybenzaldehyde to give the final compound (13.1 ).

Step 1 : Synthesis of 2-Chloro-4-nitro-1 -((E)-pent-2-enyl)-1 H-imidazole

To a solution of (E)-1-bromo-pent-2-ene (11 .1 g, 75.4 mmol) in dry CH₃CN (80mL) is added 2-chloro-4-nitroimidazole (21.7g, 147.5 mmol) followed by K₂C0₃ (20.4g, 147.5 mmol) and the mixture is stirred at 70 °C for 16h. The solvent is distilled off and the residue is dissolved in DCM, filtered, filtrate washed with water, brine and dried (Na2S04). The mixture is concentrated and the residue was washed with pentane (to remove the less polar impurities) and dried under vacuum to give (19.1) as an off-white solid. ¹H NMR (DMSO-D₆): δ 0.93-0.97 (t, 3H, J = 7.5 Hz), 2.03-2.06 (m, 2H), 4.64-4.66 (m, 2H), 5.58-5.77 (m, 2H), 8.53 (s, 1 H); Mass: m/z 216.4 (M+1 ).

Step 2: Synthesis of (2R,3R)-1 -(2-Chloro-4-nitro-imidazol-1 -yl)-pentane-2,3-diol

To a t-BuOH (300 mL), water (300 mL) solution of K₂Os0₄(OH)₂ (68.4 mg, 0.18 mmol), (DHQD)₂PHAL (290mg, 0.37 mmol), K₃Fe(CN)₆ (36.7g, 11 1.6 mmol), K₂C0₃ (15.4 g, 1 1 1.6 mmol), CH₃SO₂NH₂ (3.5 g, 37.2 mmol) is added (19.1) (8 g, 37.2 mmol) at 0 °C. After stirring the reaction mixture for 14 h at 0 °C, saturated aqueous Na₂S0₃ solution (300 mL) is added and the reaction mixture is stirred for 30 min at RT. The organic material is extracted with ethyl acetate (5 x 200 mL). The organic layer is dried with anhydrous Na₂S04 and concentrated under reduced pressure. The crude compound is washed with pentane and dried to give (19.2) as an off-white solid.

¹H NMR (DMSO-De): δ 0.87-0.91 (t, 3H, J = 7.5 Hz), 1.36-1.53 (m, 2H), 3.30-3.63 (m, 1 H), 3.67-3.71 (m, 1 H), 4.00-4.13 (m, 2H), 4.69-4.71 (d, 1 H, J = 6.2 Hz), 5.02-5.04 (d, 1 H, J = 6.2 Hz), 8.48 (s, 1 H); Mass: m/z 250.4 (M+1 ).

Step 3: Synthesis of (2R,3R)-3-(tert-Butyl-dimethyl-silanyloxy)-1-(2-chloro-4-nitro- imidazol-1-yl)-pentan-2-ol (56)

The DCM solution of (19.2) (1.9g, 7.63mmol) is cooled to 0 °C and to this is added imidazole (1.03g, 15.26 mmol)and TBDMSCI (1.72g, 11.44 mmol) and the reaction mixture is stirred for 16 h at RT. The reaction mixture is diluted with DCM (40 mL) and washed with water and saturated brine solution (2 x 50 mL). The organic layer is dried (Na₂S0₄) and concentrated. The crude residue is purified by column chromatography over silica gel (100-200mesh) using 0-10% EtOAc/hexane as eluent to give (19.3) as a white solid and some unreacted (19.2). ¹H NMR (DMSO-de): δ 0.077, 0.084 (2s, 3H), 0.89 (s, 12 H), 1.30-1.34 (m, 1 H), 1.69-1.72 (m, 1 H), 3.60-3.63 (m, 1 H), 3.72-3.75 (m, 1 H), 3.95-4.03 (m, 1 H), 4.12-4.15 (m, 1 H), 5.23- 5.25 (d, 1 H, J = 5.0 Hz), 8.45 (s, 1 H).

MS: m/z 364.0 (M+1 ).

HPLC retention time 2.32 min.

Compound (19.3) is converted to compound (13.1) as described above.

Synthesis of the corresponding ether derivatives, i.e. those where A is O, rather than N, is carried out as described below: OCF₃

Sharpless asymmetric dihydroxylation mediated by AD-mix alpha of the alkylated product (19.1) gives rise to the diol enf-(19.2) in high enantiomeric purity. Reaction of this diol with one equivalent of TBSCI results in monoprotection. Hereafter, synthesis of final compound (19.4) follows as described above for the ether derivatives, which involves alkylation with the respective halide such as trifluoromethoxybenzyl bromide in the presence of base such as NaH in DMF followed by cyclisation to form the imidazooxazine mediated by TBAF at 70 °C in THF. For the synthesis of (19.5), alkylated product (19.6) is deprotected using TBAF in THF at room temperature followed by Mitsunobu inversion of the OH group. Further reaction with TBAF/THF at elevated temperature results in the formation of imidazooxazine diastereomer (19.5).

Example 20: Synthesis of (4aS,6R,7aS)-2-Nitro-6-(4-trifluoromethoxy-phenyl)- 4a,6,7,7a-tetrahydro-4H-5,8-dioxa-1 ,3a-diaza-s-indacene and (4aS,6S,7aS)-2-Nitro-6-(4- trifluoromethoxy-phenyl)-4a,6,7,7a-tetrahydro-4H-5,8-dioxa-1,3a-diaza-s-indacene

(20.1) (20.2)

Step 1 : 1 -(1 -Methoxymethoxy-but-3-enyl)-4-trifluoromethoxy-benzene

(20.3)

To a cooled (0 °C) solution of 4-trifluoromethoxybenzaldehyde (50 g, 263.15 mmol) in dry THF (200 mL) is added allyl magnesium bromide (210 mL, 210.5 mmol) over a period of 25 min and the reaction mixture is stirred at RT for 2h. The reaction mixture is quenched with aqueous saturated NH₄CI (200 mL) , diluted with water (200 mL) and extracted with ether (3 x 300 mL). The combined organic layer is washed with water (100 mL), brine (100 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100- 200 mesh) using a solvent gradient of 1-3% EtOAc/Hexanes to afford 1-(4-trifluoromethoxy- phenyl)-but-3-en-1 -ol as a colourless liquid which is dissolved in dry DCM (420 mL) at 0 °C and to this is added DIPEA (118.24 mL, 724.12 mmol) followed by DMAP (2.20 g, 18.1 mmol) and the mixture is stirred for 10 min. MOMCI (36.2 mL, 452.58 mmol) is added in two parts, with a time interval of 6 h between each addition, and the reaction mixture is stirred at RT for 16h. The reaction mixture is diluted with water (300 mL) and extracted with DCM (3 x 300 mL). The combined organic layer is washed with water (200 mL), brine (100 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100- 200 mesh) using a gradient of 1-3% EtOAc/Hexanes to afford 1-(1-methoxymethoxy-but-3- enyl)-4-trifluoromethoxy-benzene as a colourless liquid.

¹H NMR (400 MHz, CDCI₃): δ 2.39-2.61 (m, 2H), 3.95 (s, 3H), 4.50-4.69 (m, 3 H), 5.04-5.09 (m, 2H), 5.71-5.82 (m, 1 H), 7.17-7.19 (d, 1 H, J = 8.0 Hz), 7.32-7.34 (d, 1 H, J = 8.0 Hz). xy-5-(4-trifluoromethoxy-phenyl)-pent-2-enoic acid ethyl ester

(20.4)

To a cooled (0 °C) solution of 1 -(1-methoxymethoxy-but-3-enyl)-4-trifluoromethoxy-benzene (37 g, 134.05 mmol) in acetone (1.5 L) and water (750 mL) is added Os0₄ solution (1.0 M in 'BuOH, 1.34 mL, 1 .34 mmol) followed by Nal0₄ (85.65 g, 402.15 mmol) and the reaction mixture is stirred at RT for 16h. The reaction mixture is diluted with water (500 mL) and extracted with EtOAc (3 x 500 mL). The combined organic layer is washed with an aqueous solution of sodium metabisufite (2 x 300 mL), water (500 mL), brine (500 mL), dried

(anhydrous Na₂S0₄) and concentrated to give crude 3-methoxymethoxy-3-(4- trifluoromethoxy-phenyl)-propionaldehyde which is dissolved in dry THF (100 mL) and cooled to -10 °C. This solution is added to Wittig ylide (generated by treating

triethylphosponoacetate (36.25 mL, 181.29 mmol) in dry THF (360 mL) with NaH (6.7 g, 115.38 mmol) for 10 min at 0 °C) at -10 °C and the reaction mixture is stirred at RT for 1 h. The reaction mixture is quenched with aqueous saturated NH₄CI (100 mL),diluted with water (300 mL) and extracted with EtOAc (3 x 500 mL). The combined organic layer is washed with water (200 ml), brine (200 ml), dried over anhydrous Na₂S0₄ and concentrated. The crude compound is purified by column chromatography over silica gel (100-200 mesh) using a solvent gradient of 3-5% EtOAc/Hexanes to afford 5-methoxymethoxy-5-(4- trifluoromethoxy-phenyl)-pent-2-enoic acid ethyl ester.

¹H NMR (400 MHz, CDCI₃): δ 1.25-1.29 (m, 3H), 2.52-2.73 (m, 2H), 3.35 (s, 3H), 4.14-4.20 (m, 2H), 4.50-4.56 (m, 2 H), 4.71-4.74 (m, 1 H), 5.85-5.89 (d, 1 H, J = 15.6 Hz), 6.90-6.98 (m, 1 H), 7.19-7.21 (d, 1 H, J = 8.0 Hz), 7.33-7.35 (d, 1 H, J = 8.0 Hz).

Step 3: (2R,3S)-2,3-Dihydroxy-5-methoxymethoxy-5-(4-trifluoromethoxy-phenyl)-

(20.5)

To a cooled (0 °C) solution of compound (20.4) (23.5 g, 67.52 mmol) in 'BuOH (800 mL) and water (800 mL) is added methanesulfonamide (6.42 g,67.52 mmol) followed by

K₂Os0₄.(HO)₂ (124 mg,0.337 mmol), (DHQ)₂PHAL (525 mg, 0.675 mmol) and K₃Fe(CN)₆ (66.64 g, 202.56 mmol), K₂C0₃ (27.95 g, 202.56 mmol) and the reaction mixture is stirred at 0 °C for 36h.The reaction mixture is diluted with water (500 mL) and extracted with EtOAc (3 x 500 mL). The combined organic layer is washed with water (300 mL), brine (300 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100- 200 mesh) using a gradient of 5-30% EtOAc/Hexanes to afford (2R,3S)-2,3-Dihydroxy-5- methoxymethoxy-5-(4-trifluoromethoxy-phenyl)-pentanoic acid ethyl ester as a liquid.

1H NMR (400 MHz, DMSO-d₆): δ 1.12-1 .23 (m, 3H), 1.63-1.82 (m, 2H), 3.35 (s, 3H), 3.94- 4.13 (m, 3H), 4.37-4.55 (m, 2H), 4.67-4.78 (m, 2 H), 5.13-5.17 (m, 1 H), 7.33-7.48 (m, 4H). Step 4: (S)-3-Methoxymethoxy-1-(S)-oxiranyl-3-(4-trifluoromethoxy-phenyl)-propan-1 -

(20.6)

To a cooled (0 °C) solution (2R,3S)-2,3-dihydroxy-5-methoxymethoxy-5-(4-trifluoromethoxy- phenyl)-pentanoic acid ethyl ester (12 g, 31.41 mmol) in dry THF (120 mL) is added LiAIH₄ (1.78 g, 47.12mmol) portion wise over a period of 1 h and stirred at RT for 1 h. The reaction mixture is quenched with 0.5N aq.NaOH (15 mL) and filtered through a celite bed. The bed is thoroughly washed with EtOAc (3 x 200 mL) and the filtrate is dried (anhydrous Na₂S0₄) and concentrated to afford crude (2S,3S)-5-methoxymethoxy-5-(4-trifluoromethoxy-phenyl)- pentane-1 ,2,3-triol which is dissolved in dry DCM (100 mL) and cooled (0 °C). Et₃N (8.43 mL, 60.6 mmol) is added followed by pyridine (4.89 mL, 60.6 mmol) and tosylchloride (6.9 g, 36.36 mmol) and the reaction mixture is stirred at RT for 16h. The reaction mixture is diluted with water (100 mL) and extracted with EtOAc (3 x 100 mL). The combined organic layer is washed with water (100 mL), brine (100 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100-200 mesh) using a solvent gradient of 20-30% EtOAc/Hexanes to afford toluene-4-sulfonic acid (2S,3S)-2,3-dihydroxy-5- methoxymethoxy-5-(4-trifluoromethoxy-phenyl)-pentyl ester which is dissolved in in dry DCM (30 mL) and MeOH (30 mL) and cooled to 0 °C. K₂C0₃ (1.73 g, 12.56 mmol) is added and the reaction mixture is stirred at RT for 3h. The reaction mixture is diluted with water (30 mL) and extracted with DCM (3 x 100 mL). The combined organic layer is washed with water (30 mL), brine (30 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100-200 mesh) using a solvent gradient of 10-20% EtOAc/Hexanes to afford (S)-3-methoxymethoxy-1-(S)-oxiranyl-3-(4-trifluoromethoxy-phenyl)-propan-1-ol as a liquid.

¹H NMR (400 MHz, DMSO-d₆): δ 1.63-2.04 (m, 2H), 2.42-2.67 (m, 2H), 2.85-2.97 (m, 1 H), 3.20 (s, 3H), 3.36-3.50 (m, 1 H), 4.34-4.54 (m, 2H), 4.72-4.81 (m, 1 H), 5.01-5.03 (m, 1 H), 7.31-7.49 (m, 4H).

Step 5: (2S,3S)-3-(tert-Butyl-dimethyl-silanyloxy)-1 -(2-chloro-4-nitro-imidazol-1-yl)-5- ethoxymethoxy-5-(4-trifluoromethoxy-phenyl)-pentan-2-ol

(20.9)

To a cooled (0 °C) solution of compound (20.6) (1.3 g, 4.03 mmol) in dry DCM (13 mL) is added imidazole (548 mg, 8.07 mmol) followed by TBDMSCI (1.21 g, 8.07 mmol) and the reaction mixture is stirred at RT for 18h. The reaction mixture is diluted with water (20 mL) and extracted with DCM (3 x 20 mL). The combined organic layer is washed with water (20 mL), brine (20 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100-200 mesh) using a solvent gradient of 2-5% EtOAc/Hexanes to afford tert-butyl-[(S)-3-methoxymethoxy-1-(S)-oxiranyl-3-(4-trifluoromethoxy-phenyl)- propoxy]-dimethyl-silane.

To a stirred solution of 4-nitro-2-chloroimidazole (1.37 g, 9.28 mmol) in dry EtOH (26 mL) is added anhydrous K₂C0₃ (85 mg, 0.619 mmol) and the reaction mixture is stirred at RT for 10 min. To this tert-Butyl-[(S)-3-methoxymethoxy-1-(S)-oxiranyl-3-(4- trifluoromethoxyphenyl)propoxy]dimethylsilane (1.35 g, 3.09 mmol) in dry EtOH (3 mL) is added and the mixture is stirred at 75 °C for 16h. The excess solvent is distilled off from the reaction mixture and the obtained residue is diluted with water (30 mL) and extracted with EtOAc (3 x 40 mL). The combined organic layer is washed with water (30 mL), brine (30 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100-200 mesh) using solvent gradient of 15-20% EtOAc/Hexanes to afford (2S,3S)-3-(tert-Butyl-dimethyl-silanyloxy)-1-(2-chloro-4-nitro-imidazol-1 -yl)-5-ethoxymethoxy- 5-(4-trifluoro-methoxy-phenyl)-pentan-2-ol as a syrup.

MS: m/z 583 (M+1 ).

Step 6: (6S,7S)-7-[2-Hydroxy-2-(4-trifluoromethoxy-phenyl)-ethyl]-2-nitro-6,7-dihydro- -imidazo[2,1-b][1 ,3]oxazin-6-ol

(20.10)

To a stirred solution of (2S,3S)-3-(tert-Butyl-dimethyl-silanyloxy)-1-(2-chloro-4-nitro-imidazol- 1-yl)-5-ethoxymethoxy-5-(4-trifluoro-methoxy-phenyl)-pentan-2-ol (1.0 g, 1.71 mmol) in dry DCM (10 mL) is added DHP (0.31 mL, 3.43 mmol) followed by PPTS (215 mg, 0.86 mmol) at RT and the reaction mixture is stirred at RT for 16h. The reaction mixture is diluted with water (20 mL) and extracted with DCM (3 x 30 mL). The combined organic layer is washed with water (20 mL), brine (20 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound was filtered through a short bed of silica gel using solvent gradient of 10-15% EtOAc/Hexanes to afford 1-[3-(tert-butyl-dimethyl-silanyloxy)-5-methoxymethoxy-2- (tetrahydro-pyran-2-yloxy)-5-(4-trifluoromethoxy-phenyl)-pentyl]-2-chloro-4-nitro-1 H- imidazole which is dissolved in dry THF (10 mL) containing TBAF (5.99 mL, 5.99 mmol) at RT and heated at reflux for 6h. The reaction mixture is diluted with water (20 mL) and extracted with EtOAc (3 x 20 mL). The combined organic layer is washed with water (20 mL), brine (20 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100-200 mesh) using solvent gradient of 40-60% EtOAc/Hexanes to afford (6S,7S)-7-[2-Methoxymethoxy-2-(4-trifluoromethoxy-phenyl)-ethyl]-2-nitro-6- (tetrahydro-pyran-2-yloxy)-6,7-dihydro-5H-imidazo[2, 1 -b][1 ,3]oxazine which is dissolved in CH3CN. and MeOH (2 mL). To this is added IPA/HCI (2 mL) at RT and the reaction mixture is stirred at RT for 1 h. The reaction mixture is diluted with water (10 mL) and the pH adjusted to about 8 with saturated aqueous NaHC0₃ solution and the mixture is extracted with EtOAc (3 x 20 mL). The combined organic layer is washed with water (20 mL), brine (20 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is triturated with diethyl ether (3 x 10 mL) and filtered to afford (6S,7S)-7-[2-Hydroxy-2-(4-trifluoromethoxy-phenyl)-ethyl]- 2-nitro-6,7-dihydro-5H-imidazo[2,1 -b][1 ,3]oxazin-6-ol as a yellow solid.

MS: m/z 389.9 (M+1 )

¹H NMR (400 MHz, DMSO-d₆): δ 1.85-2.16 (m, 2H), 3.98-4.29 (m, 3H), 4.73-4.86 (m, 2H), 7.33-7.35 (d, 1 H, J = 8.0 Hz), 7.50-7.52 (d, 1 H, J = 8.0 Hz), 8.08 (s, 1 H).

Step 7: (4aS,6S,7aS)-2-Nitro-6-(4-trifluoromethoxy-phenyl)-4a,6,7,7a-tetrahydro-4H-5,8- dioxa-1,3a-diaza-s-indacene and 4aS,6R,7aS)-2-Nitro-6-(4-trifluoromethoxy-phenyl)- 4a 6,7,7a-tetrahydro-4H-5,8-dioxa-1 ,3a-diaza-s-indacene

(20.1 ) (20.2)

To a stirred solution of (6S,7S)-7-[2-hydroxy-2-(4-trifluoromethoxy-phenyl)-ethyl]-2-nitro-6,7- dihydro-5H-imidazo[2, 1 -b][1 ,3]oxazin-6-ol (180 mg, 0.46 mmol) in THF (3 mL) is added 6N aq.HCI (4 mL) at RT and the reaction mixture is stirred at 60 °C for 3h. The reaction mixture is diluted with water (10 mL) and the pH adjusted to about 8 with saturated aqueous NaHC0₃ solution and the mixture is extracted with EtOAc (3 x 20 mL). The combined organic layer is washed with water (20 mL), brine (20 mL), dried (anhydrous Na₂S0₄) and concentrated. The crude compound is purified over silica gel (100-200 mesh) using solvent gradient of 50-80% EtOAc/Hexanes to afford less polar isomer (20.1) and polar isomer of (20.2). The structure is assigned based on 2D NOESY data.

19.1 (Less-Polar): MS: m/z 372.3 (M+1 ); ¹H NMR (400 MHz, DMSO-d₆): δ 2.26-2.33 (m, 1 H), 2.76-2.81 (m, 1 H), 4.28-4.40 (m, 2H), 4.82 (br s, 1 H), 5.17-5.27 (m, 2H), 7.35-7.37 (d,

I H, J = 8.0 Hz), 7.53-7.55 (d, 1 H, J = 8.0 Hz), 8.10 (s, 1 H); ¹³C NMR (400 MHz, DMSO-d₆): 5 41.9, 43.6, 72.5, 79.4, 80.5, 1 17.5, 121.0, 127.6, 141.8, 142.1 , 146.7, 147.6.

HPLC retention time: 1.795 min

19.2 (Polar): MS: m/z 372.3 (M+1 ); ¹H NMR (400 MHz, CD₃COCD₃): δ 2.21-2.27 (m, 1 H), 3.06-3.13 (m, 1 H), 4.52-4.67 (m, 3H), 5.21-5.29 (m, 2H), 7.265-7.28 (d, 1 H, J = 8.0 Hz), 7.36-7.38 (d, 1 H, J = 8.0 Hz), 7.89 (s, 1 H); ¹³C NMR (400 MHz, DMSO-d₆): δ 41.9, 43.6, 73.5, 78.4, 79.9, 1 16.1 , 121.0, 127.8, 141.4, 143.1 , 147.2, 148.5.

HPLC retention time: 1.579 min

II. Activity of Compounds of the Invention Against Mycobacteria and Trypanosomes

The compounds of the invention are active against mycobacteria and parasites of the genus Trypanosoma and Leishmania. The activities of the compounds of the invention may be shown in standard in vitro and in vivo tests.

The MIC (minimum inhibitory concentration) is defined as the minimum concentration of the drug at which 99% reduction in growth of aerobic cells is observed by visible pellet formation.

The MAC (minimum anaerobic concentration) is defined as the minimum concentration of the drug at which 90% reduction in growth of NRP-2 cells is observed with 5 days drug exposure under anaerobic conditions.

Example 21 : Activity against Mycobacterium tuberculosis Minimum Inhibitory Concentration (MIC₉₉) determination:

A stock culture of MTB H37Rv (ATCC 27294) and Mycobacterium bovis Bacillus Calmette Guerin (BCG) Pasteur (ATCC 35745) are grown to OD 0.5 in Middlebrook 7H9 broth (Difco) supplemented with 0.05% Tween 80, 0.2% glycerol and albumin/NaCI/glucose (ADC) complex. The culture is diluted 1 :1000 in 7H9-based medium before aliquoting 50 μΙ_ into each well of a 96-well plate. The compounds of the invention are dissolved in DMSO to make stock solutions of 50 μΓηοΙ/ηη... Compounds are added to the first row of wells of the 96-well plate with 100 μΙ_ 7H9-based medium. After pipette mixing and using a multi-channel pipette, 50 μΙ_ is removed from each well in the first row and added to the second row. 2-Fold dilution in this manner is carried out to give 12 dilutions of each compound. The plates are incubated for 2 weeks at 37 °C and the MICgg values are read macroscopically using an inverted plate reader. Each measurement is made three independent times.

Minimum Anaerobicidal Concentration (MAC90) determination:

For anaerobicidal concentration estimation experiments Dubos broth is used (Wayne LG. 2001 in Mycobacterium tuberculosis Protocols, ed. T. Parish, N. Stoker. Totowa, NJ:

Humana. Press 247-269). For oxygen depletion assays early log phase MTB culture in Dubos broth is diluted 100 fold and 20 ml transferred to tubes (Pyrex 16 X 125 mm culture tubes) to maintain head space ratio of 0.5 as described previously (Wayne LG. 2001 in Mycobacterium tuberculosis Protocols, ed. T. Parish, N. Stoker. Totowa, NJ: Humana. Press 247-269). The tubes are sealed with paraplast and incubated for 20 days under uniform stirring at 180 rpm using magnetic stirring bars. 1.5 μg/ml of methylene blue is added to a reference tube to visualize oxygen depletion. 100 μΙ of Mtb NRP-2 stage cells are exposed to various concentrations of compounds of the invention in a 96 well microplate, two-fold drug dilutions in DMSO starting at 500 μΜ to 1.95 μΜ and a DMSO control were made. Handling of NRP-2 cells is done in Vinyl Anaerobic Chamber (Coy Laboratories, Michigan) fitted with Coy Model 10 gas analyzer and vacuum air lock chamber. The anaerobic chamber is maintained under 90% nitrogen and 10% Hydrogen. 96 well plates are placed in a Type A Bio-bag anaerobic chamber (Bection and Dickinson, Maryland) along with a oxygen indicator strip and incubated at 37°C for 7 days. After exposure to a compound of the invention the cells are washed thrice with fresh Dubos broth. Minimal anaerobicidal concentration against MTB is estimated by measuring Cell viability by spotting by 5 μΙ of cell suspension from each well on 7H11 agar in 96 well plate. After 3 weeks of incubation, MACgo is defined as the minimum concentration of the compound at which 90% reduction in growth is observed.

Example 22: Activity Against Trypanosoma cruzi and Trypanosoma brucei

The compounds of the invention may be tested in the following way to determine their activities against Trypanosoma brucei (Wilkinson et al. 2008 Proc Natl Acad Sci USA

195:5022-5027; Hirumi et al., (1989) J. Parasitol. 75:985-989). T. brucei BSF parasites are seeded at 1X10³ ml^"1 in 200 ul growth medium containing different concentrations of compounds of the invention. After incubation at 37°C for 3 days, 20 ul Alamar blue (Biosource UK Ltd) is added to each well and the plates are incubated for a further 16 hours. The fluorescence of each culture is then determined using a Gemini Fluorescent Plate reader (Molecular Devices) at an excitation wavelength of 530 nm, emission wavelength of 585 nm and a filter cut off at 550 nm. The colour change resulting from the reduction of Alamar blue is proportional to the number of live cells. The I C50 value for each compound is then established.

Similarly, the compounds of the invention may be tested in the following way to determine their activities against Trypanosoma cruzi (Wilkinson et al. 2008 Proc Natl Acad Sci USA 195:5022-5027; Kendall et al, (1992) EMBO J 9:2751-2758). T. cruzi BSF parasites are seeded at 1 χ 10³ ml^-1 in 200 μΙ of growth medium containing different concentrations of compounds of the invention. After incubation at 37°C for 3 days, 20 μΙ of Alamar blue is added to each well and the plates are incubated for a further 16 h. The cell density of each culture is determined as described above and the I C50 established.

Example23: Activity Against Leishmania donovani

The Leishmania donovani strain MHOM/ET/67/L82 (obtained from Dr. S. Croft, London School of Hygiene and Tropical Medicine) is used. The strain is maintained in the Syrian Golden hamster. Amastigotes are collected from the spleen of an infected hamster.

Amastigotes are grown in axenic culture at 37°C in SM medium (Cunningham I., J.

Protozool. 24, 325-329, 1977) at pH 5.4 supplemented with 10% heat-inactivated foetal bovine serum (FBS) under an atmosphere of 5% C0₂ in air.

Stock compound solutions are prepared in 100% dimethylsulfoxide (DMSO) at 10 mg/mL, and heated or sonicated if necessary to dissolve the sample. After use the stocks are kept at -20°C. For the assays, the compound is further diluted to the appropriate concentration using complete medium. The DMSO concentration in the wells with the highest drug concentration does not exceed 1%.

Assays are performed in 96-well flat-bottom microtiter plates (Costar, Corning Inc.), each well containing 100 μΐ of culture medium with 105 amastigotes from axenic culture with or without a serial drug dilution. Concentration of amastigotes is determined in a CASY cell analysing system (Scharfe System, Reutlingen, Germany). Before the amastigotes are counted, the parasite culture is passed twice through a 22 gauge needle to break up clusters of amastigotes. The highest concentration for the test compounds is 90 μg/mL. Seven 3-fold dilutions are used, covering a range from 30 μg/mL to 0.041 μg mL. Each compound is tested in duplicate. Active compounds are tested twice for confirmation. After 72 hours of incubation, the plates are inspected under an inverted microscope to assure growth of the controls and sterile conditions.

10 I of Alamar Blue (12.5 mg resazurin dissolved in 100 ml distilled water) are then added to each well and the plates areincubated for another 2 hours. Then the plates are read with a Spectramax Gemini XS microplate fluorometer (Molecular Devices Cooperation, Sunnyvale, CA, USA) using an excitation wavelength of 536 nm and an emission wavelength of 588 nm.

Data are analysed using the microplate reader software Softmax Pro (Molecular Devices Cooperation, Sunnyvale, CA, USA). Decrease of fluorescence (i.e. inhibition) is expressed as percentage of the fluorescence of control cultures and plotted against the drug concentrations. The IC₅₀ value is calculated from the sigmoidal inhibition curve by the software program.

It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims.

INDUSTRIAL APPLICABILITY

The invention relates to novel compounds that have various medicinal applications, e.g. for the treatment and/or prevention of mycobacterial infections, such as those caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae, Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacteria that cause multi-drug resistant (MDR) TB or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or the treatment or prevention of parasitic diseases, such as those caused by a parasite of the genus Trypanosoma, e.g. Trypanosoma cruzi or Trypanosoma brucei or a parasite of the genus Leishmania, e.g. one which causes visceral leishmaniasis or kala-azar, e.g. Leishmania donovani.

Claims

1. A compound of formula (I), or a pharmaceutically acceptable salt thereof:

(i)

or Z may optionally be absent when A and R⁴ or R⁵ together form a 5- or 6-membered oxygen-containing heterocycle;

W is O or W is absent;

Y is CR⁴R⁵ or Y is carbon spiro-linked to a cycloalkyl group;

A is O or N, or A is O and together with R⁴ or R⁵ forms a 5- or 6-membered oxygen- containing heterocycle;

R¹ is absent when A is O, or R¹ is H, alkyl, alkyl amide, aryl amide or urea;

R² and R³ are each independently selected from the group consisting of H, alkyl, heteroaryl, COOH, CONH₂, and each R² and each R³ may be the same or different; R⁴ and R⁵ are each independently selected from the group consisting of H, alkyl, alkenyl, alkynyl, alkoxyalkyl, hydroxyalkyl, cycloalkyi, cycloalkenyl; provided that R⁴ and R⁵ are not both H;

R⁶ and R⁷ are each independently selected from the group consisting of H, alkyl,

R⁸ is halogen, cycloalkyi, heterocycio, hydroxy, alkoxy, provided that when m is 2, 3 or 4, then each R⁸ may be the same or different; and n is 1 , 2, 3 or 4; and m is O, 1 , 2, 3 or 4; provided that the following compound is excluded:

the compound where A is N; R¹ is H; Y is C(H)CH₃; Z is CH₂; m is 0; and R⁶ and R⁷ are both H.

2. A compound as claimed in claim 1 wherein A is N, Z is (CR²R³)_n or a radical of formula

(i)

and W, Y, n, m, R¹, R², R³, R⁴, R⁵, R⁶, R⁷ and R⁸ are all as defined in claim 1.

3. A compound as claimed in claim 1 wherein A is O or A is O and together with R⁴ or R⁵ forms a 5- or 6-membered oxygen-containing heterocycle, and where W, Y, Z, n, m, R¹, R², R³, R⁴, R⁵, R⁶, R⁷ and R⁸ are all as defined in claim 1.

4. A compound as claimed in claim 1 wherein one or both of R⁴ and R⁵ is alkyl, cycloalkyi, hydroxyalkyl or alkoxyalkyl.

5. A compound as claimed in claim 1 wherein Z is (CR²R³)_n.

6. A compound as claimed in claim 1 wherein R⁶ and R⁷ are both H.

7. A compound selected from the group consisting of:

88

or a pharmaceutically acceptable salt thereof.

A pharmaceutical composition comprising a compound of formula (I) as claimed in claim 1 , in association with at least one pharmaceutically acceptable excipient.

A method of treating and/or preventing a disease caused by a mycobacterial infection or a parasitic disease, comprising administering to a patient in need thereof an effective amount of a compound of formula (I) as claimed in claim 1 .

A method as claimed in claim 9 wherein the mycobacterial infection is caused by Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium leprae,

Mycobacterium africanum, Mycobacterium avium, Mycobacterium microti, or any mycobacteria that cause multi-drug resistant TB (MDR) or extensively resistant (XDR) TB, or any other mycobacterial species known to cause disease in humans; or wherein the parasitic disease is caused by Trypanosoma cruzi, Trypanosoma brucei or Leishmania donovani.