USRE40245E1 - Gyrase inhibitors and uses thereof - Google Patents

Gyrase inhibitors and uses thereof Download PDF

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USRE40245E1
USRE40245E1 US10/833,995 US83399504A USRE40245E US RE40245 E1 USRE40245 E1 US RE40245E1 US 83399504 A US83399504 A US 83399504A US RE40245 E USRE40245 E US RE40245E
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con
halogen
cor
ring
optionally substituted
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Anne-Laure Grillot
Paul S. Charifson
Dean Stamos
Yusheng Liao
Michael C. Badia
Martin Trudeau
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Vertex Pharmaceuticals Inc
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Vertex Pharmaceuticals Inc
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Definitions

  • This invention is in the field of medicinal chemistry and relates to compounds, and pharmaceutical compositions thereof, that inhibit bacterial gyrases.
  • the compounds are useful as inhibitors of bacterial gyrase activity.
  • the present invention also relates to methods for treating bacterial infections in mammals.
  • the present invention also relates to methods for decreasing bacterial quantity in a biological sample.
  • Gyrase is one of the topoisomerases, a group of enzymes which catalyze the interconversion of topological isomers of DNA (see generally, Kornberg and Baker, DNA Replication, 2d Ed., Chapter 12, 1992, W. H. Freeman and Co.; Drlica, Molecular Microbiology, 1992, 6, 425; Drlica and Zhao, Microbiology and Molecular Biology Reviews, 1997, 61, 377). Gyrase itself controls DNA supercoiling and relieves topological stress that occurs when the DNA strands of a parental duplex are untwisted during the replication process. Gyrase also catalyzes the conversion of relaxed, closed circular duplex DNA to a negatively superhelical form which is more favorable for recombination.
  • the mechanism of the supercoiling reaction involves the wrapping of gyrase around a region of the DNA, double strand breaking in that region, passing a second region of the DNA through the break, and rejoining the broken strands.
  • a cleavage mechanism is characteristic of a type II topoisomerase.
  • the supercoiling reaction is driven by the binding of ATP to gyrase.
  • the ATP is then hydrolyzed during the reaction.
  • This ATP binding and subsequent hydrolysis cause conformational changes in the DNA-bound gyrase that are necessary for its activity.
  • the level of DNA supercoiling or relaxation
  • gyrase is only capable of relaxing supercoiled DNA.
  • Bacterial DNA gyrase is a 400 kilodalton protein tetramer consisting of two A (GyrA) and two B subunits (GyrB). Binding and cleavage of the DNA is associated with GyrA, whereas ATP is bound and hydrolyzed by the GyrB protein. GyrB consists of an amino-terminal domain which has the ATPase activity, and a carboxy-terminal domain which interacts with GyrA and DNA.
  • eukaryotic type II topoisomerases are homodimers that can relax negative and positive supercoils, but cannot introduce negative supercoils.
  • an antibiotic based on the inhibition of bacterial DNA gyrase would be selective for this enzyme and be relatively inactive against the eukaryotic type II topoisomerases.
  • the widely-used quinolone antibiotics inhibit bacterial DNA gyrase.
  • the quinolones include the early compounds such as nalidixic acid and oxolinic acid, as well as the later, more potent fluoroquinolones such as norfloxacin, ciprofloxacin, and trovafloxacin. These compounds bind to GyrA and stabilize the cleaved complex, thus inhibiting overall gyrase function, leading to cell death.
  • drug resistance has also been recognized as a problem for this class of compounds (WHO Report, “Use of Quinolones in Food Animals and Potential Impact on Human Health”, 1998).
  • bacteria exposed to earlier compounds often quickly develop cross-resistance to more potent compounds in the same class.
  • GyrB There are fewer known inhibitors that bind to GyrB. Examples include the coumarins, novobiocin and coumermycin A1, cyclothialidine, cinodine, and clerocidin. The coumarins have been shown to bind to GyrB very tightly. For example, novobiocin makes a network of hydrogen bonds with the protein and several hydrophobic contacts. While novobiocin and ATP do appear to bind within the ATP binding site, there is minimal overlap in the bound orientation of the two compounds. The overlapping portions are the sugar unit of novobiocin and the ATP adenine (Maxwell, Trends in Microbiology, 1997, 5, 102).
  • the coumarins Despite being potent inhibitors of gyrase supercoiling, the coumarins have not been widely used as antibiotics. They are generally not suitable due to their low permeability in bacteria, eukaryotic toxicity, and poor water solubility (Maxwell, Trends in Microbiology, 1997, 5, 102). It would be desirable to have a new, effective GyrB inhibitor that overcomes these drawbacks and, preferably does not rely on binding to Arg136 for activity. Such an inhibitor would be an attractive antibiotic candidate, without a history of resistance problems that plague other classes of antibiotics.
  • antibiotics that represent a new class of compounds not previously used to treat bacterial infection. Such compounds would be particularly useful in treating nosocomial infections in hospitals where the formation and transmission of resistant bacteria are becoming increasingly prevalent.
  • One embodiment of this invention relates to a method of treating a bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a compound of formula I: or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
  • aliphatic as used herein means straight-chain, branched or cyclic C 1 -C 12 hydrocarbons which are completely saturated or which contain one or more units of unsaturation but which are not aromatic.
  • suitable aliphatic groups include substituted or unsubstituted linear, branched or cyclic alkyl, alkenyl, alkynyl groups and hybrids thereof such as (cycloalkyl)alkyl, (cycloalkenyl) alkyl or (cycloalkyl)alkenyl.
  • alkyl used alone or as part of a larger moiety includes both straight and branched chains containing one to twelve carbon atoms.
  • alkenyl and “alkynyl” used alone or as part of a larger moiety shall include both straight and branched chains containing two to twelve carbon atoms.
  • cycloalkyl used alone or as part of a larger moiety shall include cyclic C 3 -C 12 hydrocarbons which are completely saturated or which contain one or more units of unsaturation, but which are not aromatic.
  • haloalkyl means alkyl, alkenyl or alkoxy, as the case may be, substituted with one or more halogen atoms.
  • halogen means F, Cl, Br, or I.
  • heteroatom means N, O, or S and includes any oxidized form of nitrogen and sulfur, and the quaternized form of any basic nitrogen.
  • carrier means an aliphatic ring system having three to fourteen members.
  • the terms “carbocyclyl”or “carbocyclic” also include aliphatic rings that are fused to one or more aromatic or nonaromatic rings, such as in a decahydronaphthyl or tetrahydronaphthyl, where the radical or point of attachment is on the aliphatic ring.
  • aryl used alone or as part of a larger moiety as in “aralkyl”, “aralkoxy”, or “aryloxyalkyl”, refers to aromatic ring groups having five to fourteen members, such as phenyl, benzyl, phenethyl, 1-naphthyl, 2-naphthyl, 1-anthracyl and 2-anthracyl.
  • aryl also refers to rings that are optionally substituted.
  • aryl may be used interchangeably with the term “aryl ring”.
  • Aryl also includes fused polycyclic aromatic ring systems in which an aromatic ring is fused to one or more rings.
  • aryl is a group in which an aromatic ring is fused to one or more non-aromatic rings, such as in a indanyl, phenanthridinyl, or tetrahydronaphthyl, where the radical or point of attachment is on the aromatic ring.
  • heterocycle includes non-aromatic ring systems having five to fourteen members, preferably five to ten, in which one or more ring carbons, preferably one to four, are each replaced by a heteroatom such as N, O, or S.
  • heterocyclic rings include 3-1H-benzimidazol-2-one, (1-substituted)-2-oxo-benzimidazol-3-yl, 2-tetrahydrofuranyl, 3-tetrahydrofuranyl, 2-tetrahydrothiophenyl, 3-tetrahydrothiophenyl, 2-morpholinyl, 3-morpholinyl, 4-morpholinyl, 2-thiomorpholinyl, 3-thiomorpholinyl, 4-thiomorpholinyl, 1-pyrrolidinyl, 2-pyrrolidinyl, 3-pyrrolidinyl, 1-piperazinyl, 2-piperazinyl, 1-piperidinyl, 1-piperidinyl, 3-piperidinyl, 4-piperidinyl, 4-thiazolidinyl, diazolonyl, N-substituted diazolonyl, 1-phthalimidinyl, benzoxanyl, benzopyrrolidinyl, benzopiperidinyl,
  • heterocyclyl or “heterocyclic”, as it is used herein, is a group in which a non-aromatic heteroatom-containing ring is fused to one or more aromatic or non-aromatic rings, such as in an indolinyl, chromanyl, phenanthridinyl, or tetrahydroquinolinyl, where the radical or point of attachment is on the non-aromatic heteroatom-containing ring.
  • heterocycle “heterocyclyl”, or “heterocyclic” whether saturated or partially unsaturated, also refers to rings that are optionally substituted.
  • heteroaryl used alone or as part of a larger moiety as in “heteroaralkyl” or “heteroarylalkoxy”, refers to heteroaromatic ring groups having five to fourteen members.
  • heteroaryl rings include 2-furanyl, 3-furanyl, 3-furazanyl, N-imidazolyl, 2-imidazolyl, 4-imidazolyl, 5-imidazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-oxadiazolyl, 5-oxadiazolyl, 2-oxazolyl, 4-oxazolyl, 5-oxazolyl, 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 1-pyrazolyl, 3-pyrazolyl, 4-pyrazolyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-pyrimidyl, 3-pyridazin
  • heteroaryl is a group in which a heteroatomic ring is fused to one or more aromatic or nonaromatic rings where the radical or point of attachment is on the heteroaromatic ring. Examples include tetrahydroquinoline, tetrahydroisoquinoline, and pyrido[3,4-d]pyrimidinyl.
  • heteroaryl also refers to rings that are optionally substituted.
  • heteroaryl may be used interchangeably with the term “heteroaryl ring” or the term “heteroaromatic”.
  • An aryl (including aralkyls, aralkoxy, aryloxyalkyl and the like) or heteroaryl (including heteroaralkyl and heteroarylalkoxy and the like) group may contain one or more substituents.
  • suitable substituents on the unsaturated carbon atom of an aryl, heteroaryl, aralkyl, or heteroaralkyl group include a halogen, —R o , —OR o , —SR o , 1,2-methylene-dioxy, 1,2-ethylenedioxy, protected OH (such as acyloxy), phenyl (Ph), substituted Ph, —O(Ph), substituted —O(Ph), —CH 2 (Ph), substituted —CH 2 (Ph), —CH 2 CH 2 (Ph), substituted —CH 2 CH 2 (Ph), —NO 2 , —CN, —N(R o ) 2 , —NR 0 C(O)R
  • substituents on the aliphatic group or the phenyl ring include amino, alkylamino, dialkylamino, aminocarbonyl, halogen, alkyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylaminocarbonyloxy, dialkylaminocarbonyloxy, alkoxy, nitro, cyano, carboxy, alkoxycarbonyl, alkylcarbonyl, hydroxy, haloalkoxy, or haloalkyl.
  • An aliphatic group or a non-aromatic heterocyclic ring may contain one or more substituents.
  • suitable substituents on the saturated carbon of an aliphatic group or of a non-aromatic heterocyclic ring include those listed above for the unsaturated carbon of an aryl or heteroaryl group and the following: ⁇ O, ⁇ S, ⁇ NNHR*, ⁇ NN(R*) 2 , ⁇ N—, ⁇ NNHC(O)R*, ⁇ NNHCO 2 (alkyl), ⁇ NNHSO 2 (alkyl), or ⁇ NR*, where each R* is independently selected from hydrogen, an unsubstituted aliphatic group or a substituted aliphatic group.
  • substituents on the aliphatic group include amino, alkylamino, dialkylamino, aminocarbonyl, halogen, alkyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylaminocarbonyloxy, dialkylaminocarbonyloxy, alkoxy, nitro, cyano, carboxy, alkoxycarbonyl, alkylcarbonyl, hydroxy, haloalkoxy, or haloalkyl.
  • Suitable substituents on the nitrogen of an aromatic or non-aromatic heterocyclic ring include —R + , —N(R + ) 2 , —C(O)R + , —CO 2 R + , C(O)C(O)R + , —C(O)CH 2 C(O)R + , —SO 2 R + , —SO 2 N(R + ) 2 , —C( ⁇ S)N(R + ) 2 , —C( ⁇ NH)—N (R + ) 2 , and —NR + SO 2 R + ; wherein R + is H, an aliphatic group, a substituted aliphatic group, phenyl (Ph), substituted Ph, —O(Ph), substituted —O(Ph), CH 2 (Ph), substituted CH 2 (Ph), or an unsubstituted heteroaryl or heterocyclic ring.
  • substituents on the aliphatic group or the phenyl ring include amino, alkylamino, dialkylamino, aminocarbonyl, halogen, alkyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylaminocarbonyloxy, dialkylaminocarbonyloxy, alkoxy, nitro, cyano, carboxy, alkoxycarbonyl, alkylcarbonyl, hydroxy, haloalkoxy, or haloalkyl.
  • linker group means an organic moiety that connects two parts of a compound.
  • Linkers are typically comprised of an atom such as oxygen or sulfur, a unit such as —NH—, —CH 2 —, —C(O)—, —C(O)NH—, or a chain of atoms, such as an alkylidene chain.
  • the molecular mass of a linker is typically in the range of about 14 to 200.
  • linkers include a saturated or unsaturated C 1-6 alkylidene chain which is optionally substituted, and wherein one or two saturated carbons of the chain are optionally replaced by —C(O)—, —C(O)C(O)—, —CONH—, —CONHNH—, —CO 2 —, —OC(O)—, —NHCO 2 —, —O—, —NHCONH—, —OC(O)NH—, —NHNH—, —NHCO—, —S—, —SO—, —SO 2 —, —NH—, —SO 2 NH—, or —NHSO 2 —.
  • alkylidene chain refers to an optionally substituted, straight or branched carbon chain that may be fully saturated or have one or more units of unsaturation.
  • the optional substituents are as described above for an aliphatic group.
  • a combination of substituents or variables is permissible only if such a combination results in a stable or chemically feasible compound.
  • a stable compound or chemically feasible compound is one that is not substantially altered when kept at a temperature of 40° C. or less, in the absence of moisture or other chemically reactive conditions, for at least a week.
  • structures depicted herein are also meant to include all stereochemical forms of the structure; i.e., the R and S configurations for each asymmetric center. Therefore, single stereochemical isomers as well as enantiomeric and diastereomeric mixtures of the present compounds are within the scope of the invention.
  • structures depicted herein are also meant to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of a hydrogen by a deuterium or tritium, or the replacement of a carbon by a 13 C- or 14 C-enriched carbon are within the scope of this invention.
  • One preferred embodiment of this invention relates to a method of treating a bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a compound having the formula Ia or Ib: or a pharmaceutically acceptable derivative or prodrug thereof, wherein R 1 , R 2 , R 3 , R 4 , and R 5 are as described above.
  • R 1 examples include optionally substituted phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, thienyl, pyrimidyl, imidazol-1-yl, imidazol-2-yl, pyrazol-1-yl, aminopyrimidinyl, quinolinyl, aminobenzimidazole, and indolyl.
  • R 9 if present, on the R 1 aryl or heteroaryl ring include halogen, CN, oxo, R 6 , SR 6 , OR 6 , N(R 6 ) 2 , CON(R 6 ) 2 , CO 2 R 6 , CON(R)COR 6 , N(R)T n CO 2 R 6 , N(R) T n NRCO 2 R 6 , N(R)T n N(R 6 ) 2 , NO 2 , T n (haloalkyl), CO 2 N (R 6 ) 2 , COR 6 , SO 2 R 6 , or SO 2 N(R 6 ) 2 .
  • R 9 groups include, but are not limited to, pyrrol-2,5-dione, NR 2 , OR, CO 2 H, NO 2 , OH, NHCOR, NHCO 2 R, NHCH 2 CO 2 R, NH(CH 2 ) 2 NHCO 2 R, CH 2 CO 2 R, CF 3 , SO 2 R, NHCH(CH 2 OH)CO 2 H, N—SO 2 Me-piperidinyl, SMe, NH(CH 2 ) 2 NH 2 , and piperidinyl.
  • R 2 and R 3 groups include halogen, CN, CO 2 R 6 , OR 6 , and R 6 .
  • preferred R 3 groups include Br, F, Cl, COOH, CN, OMe, methyl, ethyl, t-butyl, CF 3 , OH, and OBn.
  • R 5 examples include CO 2 (aliphatic), C( ⁇ NH)—NH 2 , and CON(R 7 ) 2 such as CO(piperidin-1-yl), CONHEt, CONHMe, CONH(cyclopropyl), CONH (isopropyl), CONH(propyl), CONH(pyrrolidinyl), CO 2 Et, and CO 2 Me.
  • CON(R 7 ) 2 such as CO(piperidin-1-yl), CONHEt, CONHMe, CONH(cyclopropyl), CONH (isopropyl), CONH(propyl), CONH(pyrrolidinyl), CO 2 Et, and CO 2 Me.
  • Preferred compounds of formula Ia and Ib include those having one or more, or most preferably all, of the features selected from the group consisting of:
  • More preferred compounds of formula Ia and Ib include those having one or more, or most preferably all, of the features selected from the group consisting of:
  • Another embodiment of this invention relates to compounds of formula IIa or IIb or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
  • R 1 examples include optionally substituted phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, thienyl, pyrimidyl, imidazol-1-yl, imidazol-2-yl, pyrazol-1-yl, aminopyrimidinyl, quinolinyl, aminobenzimidazole, and indolyl.
  • R 9 if present, on the R 1 aryl or heteroaryl ring of formula IIa or IIb include halogen, CN, oxo, R 6 , SR 6 , OR 6 , N(R 6 ) 2 , CON(R 6 ) 2 , CO 2 R 6 , CON(R)COR 6 , and N(R)T n CO 2 R 6 .
  • R 9 groups include, but are not limited to, pyrrol-2,5-dione, NR 2 , OR, CO 2 H, NO 2 , OH, NHCOR, NHCO 2 R, NHCH 2 CO 2 R, NH(CH 2 ) 2 NHCO 2 R, CH 2 CO 2 R, CF 3 , SO 2 R, NHCH(CH 2 OH)CO 2 H, N—SO 2 Me-piperidinyl, SMe, NH(CH 2 ) 2 NH 2 , and piperidinyl.
  • R 2 and R 3 groups include halogen, CN, CO 2 R 6 , OR 6 , and R 6 .
  • preferred R 3 groups include Br, F, Cl, COOH, CN, OMe, methyl, ethyl, t-butyl, CF 3 , OH, and OBn.
  • Preferred compounds of formula IIa and IIb include those having one or more, or most preferably all, of the features selected from the group consisting of:
  • More preferred compounds of formula IIa and IIb include those having one or more, or most preferably all, of the features selected from the group consisting of:
  • Another embodiment of this invention relates to compounds of formula IIIa or IIIb: or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
  • Preferred R 9 , if present, on Ring A of formulae IIIa and IIIb include halogen, CN, oxo, R 6 , SR 6 , OR 6 , N(R 6 ) 2 , CON(R 6 ) 2 , CO 2 R 6 , CON(R)COR 6 , and N(R)T n CO 2 R 6 .
  • R 9 groups include, but are not limited to, pyrrol-2,5-dione, NR 2 , OR, CO 2 H, NO 2 , OH, NHCOR, NHCO 2 R, NHCH 2 CO 2 R, NH(CH 2 ) 2 NHCO 2 R, CH 2 CO 2 R, CF 3 , SO 2 R, NHCH(CH 2 OH)CO 2 H, N—SO 2 Me-piperidinyl, SMe, NH(CH 2 ) 2 NH 2 , and piperidinyl.
  • R 2 and R 3 groups include halogen, CN, CO 2 R 6 , OR 6 , and R 6 .
  • preferred R 3 groups include Br, F, Cl, COOH, CN, OMe, methyl, ethyl, t-butyl, CF 3 , OH, and OBn.
  • R 5 examples include CO 2 (aliphatic), C( ⁇ NH)—NH 2 , and CON(R 7 ) 2 such as CO(piperidin-1-yl), CONHEt, CONHMe, CONH(cyclopropyl), CONH (isopropyl), CONH(propyl), CONH(pyrrolidinyl), CO 2 Et, and CO 2 Me.
  • CON(R 7 ) 2 such as CO(piperidin-1-yl), CONHEt, CONHMe, CONH(cyclopropyl), CONH (isopropyl), CONH(propyl), CONH(pyrrolidinyl), CO 2 Et, and CO 2 Me.
  • Preferred compounds of formulae IIIa and IIIb include those having one or more, or most preferably all, of the features selected from the group consisting of:
  • More preferred compounds of formula IIIa and IIIb include those having one or more, or most preferably all, of the features selected from the group consisting of:
  • the compounds of this invention may be prepared in general by methods known to those skilled in the art for analogous compounds, as illustrated by the general Schemes I through VII shown below. The details of the conditions used for preparing these compounds are set forth in the Examples. Reagents and conditions: (a) Ar-boronic acid, PdCl 2 (dppf), K 3 PO 4 , DMF, 95° C., 18 hours; (b) 40 psi H 2 , 10% Pd/C, EtOAc; (c) ROCOCl, NaOH, H 2 O, 0° C.; (d) p-TsOH, ROH, reflux, 1 hour.
  • the compounds 2 are prepared by treating a solution of 4-bromo-2-nitroaniline (1) in DMF with an arylboronic acid (1.2 equivalents), potassium phosphate (1.3 equivalents), and dichloro-(diphenylphosphinoferrocene)palladium (0.1 equivalent). The resulting mixture is heated at 95° C. for 18 hours then cooled to room temperature and diluted with ethyl acetate. The crude product is isolated by aqueous work-up then concentrated in vacuo. The concentrate is purified by silica gel chromatography to afford 2. A wide variety of substitutions on the aryl ring are amenable to this reaction. Examples of suitable substituted and unsubstituted aryl groups include, but are not limited to, those set forth in Table 1 above.
  • Compound 3 is prepared by treating a solution of 2 in ethyl acetate with 10% palladium on carbon (0.1 g/mmol) and the resulting suspension hydrogenated at 40 psi while shaking at ambient temperature for 2 hours. The catalyst is removed by filtration and the filtrate concentrated in vacuo to afford 3.
  • Compounds of formula 5 are prepared by first preparing a solution of 2-methyl-2-thiopseudourea (4, 1 equivalent) and alkylchloroformate (2 equivalents) in water at 0° C. To this solution is added 25% aqueous sodium hydroxide in a dropwise fashion over 1 hour until the pH stabilized at 8. Acetic acid is then added to achieve pH 5 then sodium acetate trihydrate (1 eauivalent) and a solution of 3 (1 equivalent) in ROH are added. p-Toluenesulfonic acid (catalytic amount) is added and the resulting mixture heated at reflux for 1 hour. The reaction mixture is then cooled to ambient temperature and diluted with ethyl acetate.
  • Scheme II above shows an alternative method for preparing compound 2.
  • Starting material 1 (1 equivalent) is combined with bis(pinacolato)diboron (1.2 equivalents), PdCl 2 (dppf) (0.1 equivalent), and KOAc (3 equivalents) in DMSO, and the resulting mixture is heated at 80° C. for 18 hours.
  • the reaction mixture is cooled to ambient temperature then the aryl bromide (1.1 equivalents) is added followed by the further addition of K 3 PO 4 (3 equivalents) and PdCl 2 (dppf) (0.1 equivalent).
  • the resulting mixture is heated at 95° C. for another 72 hours then allowed to cool to room temperature. Purification by chromatography affords compound 2.
  • Reagents and conditions (a) BrCN, THF, MeOH, water, room temperature; (b) EtNCO, THF, reflux.
  • Scheme III shows the general method used for preparing compounds of formula IIa.
  • Starting material 6 is prepared according to the method described in Scheme I at steps (a) and (b).
  • Compound 7 is prepared by treating 6 with cyanogen bromide in acetonitrile at room temperature over night. Aqueous work-up affords 7.
  • Compound Ia-84 is prepared from 7 by treating with ethyl isocyanate in THF at reflux over night. The crude product is purified by preparation chromatography to afford Ia-84.
  • Reagents and conditions (a) EtOH, 80° C., 4 hours; (b) PdCl 2 (dppf), K 3 PO 4 , 95° C., 48 hours; (c) Pd/C, H 2 , 50 psi, 6 hours; (d) 2-methyl-2-thiopseudourea (14), EtOCOCl, 80° C., 18 hours.
  • Scheme IV above shows a general method that may be used for preparing compounds of formula IIIa.
  • Compound 10 is prepared from 5-bromo-2-chloropyrimidine (8) and N-Boc-ethylenediamine (9) by heating a mixture of 8 and 9 in ethanol at 80° C. for 4 hours.
  • Compound 12 is prepared from 10 and 11 according to the method described in Scheme II.
  • Compound 12 is used to prepare Ia-86 via steps (c) and (d) according to steps (b) and (c) of Scheme I.
  • Reagents and conditions (a) BrCN, THF, MeOH, water, room temperature; (b) EtOCOCl, pyridine.
  • Scheme V above shows a general method that may be used for preparing compounds of formula Ib.
  • Compound 16 is prepared from 15 according to the method described in Scheme III, step (a).
  • Compound Ib-1 is prepared by treating 16 with ethylchloroformate in pyridine. Reagents and conditions: (a) (b) EtNCO, THF, reflux.
  • Scheme VI shows a general method that may be used for preparing compounds of formula IIb.
  • Compound 16 is treated ethyl isocyanate in THF at reflux according to Scheme III step, (b) to afford Ib-3.
  • Reagents and conditions (a) NaH, THF, 0° C.; (b) H 2 (45 psi), Pd-C, MeOH; (c) BrCN, MeCN, MeOH, room temperature; (d) i EtNCO, DMSO, 80° C., ii NH 3 , MeOH, 80° C.
  • step (a) dinitrofluorobenzene (17) is combined with methyl-4-imidazolecarboxylate (18) in THF and treated with sodium hydride at 0° C. After 3 hours, the reaction mixture is diluted with toluene and acidified with HCl. The phases are separated and the aqueous phase washed with toluene, cooled to 0° C., and basified with conc. NH 4 OH. Ethyl acetate is added and the resulting mixture stirred until all solids dissolved.
  • the phases are separated and the organic phase washed with brine, dried over Na 2 SO 4 , then filtered and the filtrate concentrated in vacuo.
  • the mixture of regioisomers are separated and purified via flash chromatography (silica gel, 5% ⁇ >20% ethanol/ethyl acetate gradient) to afford the desired adduct 19 as an off-white solid.
  • Compound 19 is used to prepare compounds Ia-156, Ia-157, and Ia-170 in a manner substantially similar to the methods described above for Scheme III.
  • a preferred embodiment of this invention relates to a method of treating a bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a compound having the formula IIa or IIb: or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
  • Another preferred embodiment of this invention relates to a method of treating a bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a compound of formula IIIa or IIIb: or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
  • the invention provides a method of decreasing bacterial quantity in a biological sample.
  • This method comprises the step of contacting said biological sample with a compound of formula I: or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
  • biological sample includes cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof.
  • biological sample also includes living organisms, in which case “contacting a compound of this invention with a biological sample” is synonymous with the term “administrating said compound for composition comprising said compound) to a mammal”.
  • a preferred embodiment comprises contacting said biological sample with a compound of formula Ia, Ib, IIa, IIb, IIIa, IIIb, or a compound listed in either of Tables 1 and 2.
  • Pharmaceutical compositions useful for such methods are described below.
  • the compounds of this invention are potent inhibitors of gyrase as determined by enzymatic assay. These compounds have also been shown to have antimicrobial activity in an antimicrobial susceptibility assay. The details of the conditions used for both the enzymatic and the antimicrobial susceptibility assays are set forth in the Examples below.
  • the gyrase inhibitors of this invention may be formulated into pharmaceutical compositions for administration to animals or humans.
  • These pharmaceutical compositions effective to treat or prevent a bacterial infection which comprise the gyrase inhibitor in an amount sufficient to measurably decrease bacterial quantity and a pharmaceutically acceptable carrier, are another embodiment of the present invention.
  • the term “measurably decrease bacterial quantity”, as used herein means a measurable change in the number of bacteria between a sample containing said inhibitor and a sample containing only bacteria.
  • Another preferred embodiment of this invention relates to a method, as described above, of treating a bacterial infection in a mammal in need thereof, but further comprising the step of administering to said mammal an agent which increases the susceptibility of bacterial organisms to antbiotics.
  • the invention provides a method, as described above, of decreasing bacterial quantity in a biological sample, but further comprising the step of contacting said biological sample with an agent which increases the susceptibility of bacterial organisms to antibiotics.
  • compositions and methods of this invention will be useful generally for controlling bacterial infections in vivo.
  • bacterial organisms that may be controlled by the compositions and methods of this invention include, but are not limited to the following organisms: Streptococcus pneumoniae, Streptococcus pyrogenes, Enterococcus fecalis, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sps. Proteus sps. Pseudomonas aeruginosa, E. coli, Serratia marcesens, Staphylococcus aureus, Coag. Neg.
  • nosocomial uses include, but are not limited to, urinary tract infections, pneumonia, surgical wound infections, and bacteremia.
  • non-nosocomial uses include but are not limited to urinary tract infections, pneumonia, prostatitis, skin and soft tissue infections, intra-abdominal infections, and therapy for febrile neutropenic patients.
  • compositions to treat or prevent the above-identified disorders.
  • a “pharmaceutically acceptable derivative or prodrug” means any pharmaceutically acceptable salt, ester, salt of an ester or other derivative of a compound of this invention which, upon administration to a recipient, is capable of providing, either directly or indirectly, a compound of this invention or an inhibitorily active metabolite or residue thereof.
  • Particularly favored derivatives or prodrugs are those that increase the bioavailability of the compounds of this invention when such compounds are administered to a mammal (e.g., by allowing an orally administered compound to be more readily absorbed into the blood) or which enhance delivery of the parent compound to a biological compartment (e.g., the brain or lymphatic system) relative to the parent species.
  • compositions of this invention include, without limitation, esters, amino acid esters, phosphate esters, metal salts and sulfonate esters.
  • Pharmaceutically acceptable salts of the compounds of this invention include those derived from pharmaceutically acceptable inorganic and organic acids and bases.
  • suitable acid salts include acetate, adipate, alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptanoate, glycerophosphate, glycolate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, lactate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, palmoate, pectinate, persul
  • Salts derived from appropriate bases include alkali metal (e.g., sodium and potassium), alkaline earth metal (e.g., magnesium), ammonium and N + (C 1-4 alkyl) 4 salts.
  • alkali metal e.g., sodium and potassium
  • alkaline earth metal e.g., magnesium
  • ammonium and N + (C 1-4 alkyl) 4 salts This invention also envisions the quaternization of any basic nitrogen-containing groups of the compounds disclosed herein. Water or oil-soluble or dispersible products may be obtained by such quaternization.
  • compositions of this invention comprise a compound of formula I or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable carrier.
  • Such compositions may optionally comprise an additional therapeutic agent.
  • agents include, but are not limited to, an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant, an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound.
  • pharmaceutically acceptable carrier refers to a non-toxic carrier that may be administered to a patient, together with a compound of this invention, and which does not destroy the pharmacological activity thereof.
  • Pharmaceutically acceptable carriers that may be used in the pharmaceutical compositions of this invention include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, wool fat and self-emulsifying drug delivery systems (SEDDS) such as ⁇ -tocopherol, polyethyleneglycol 1000 succinate, or other similar polymeric delivery matrices.
  • SEDDS self-e
  • pharmaceutically effective amount refers to an amount effective in treating or ameliorating a bacterial infection in a patient.
  • prophylactically effective amount refers to an amount effective in preventing or substantially lessening a bacterial infection in a patient.
  • additional therapeutic agents which are normally administered to treat or prevent that condition, may be administered together with the inhibitors of this invention.
  • therapeutic agents include, but are not limited to, an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant, an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound.
  • the compounds of this invention may be employed in a conventional manner for controlling bacterial infections levels in vivo and for treating diseases or reducing the advancement or severity of effects which are mediated by bacteria. Such methods of treatment, their dosage levels and requirements may be selected by those of ordinary skill in the art from available methods and techniques.
  • a compound of this invention may be combined with a pharmaceutically acceptable adjuvant for administration to a patient suffering from a bacterial infection or disease in a pharmaceutically acceptable manner and in an amount effective to lessen the severity of that infection or disease.
  • the compounds of this invention may be used in compositions and methods for treating or protecting individuals against bacterial infections or diseases over extended periods of time.
  • the compounds may be employed in such compositions either alone or together with other compounds of this invention in a manner consistent with the conventional utilization of enzyme inhibitors in pharmaceutical compositions.
  • a compound of this invention may be combined with pharmaceutically acceptable adjuvants conventionally employed in vaccines and administered in prophylactically effective amounts to protect individuals over an extended period of time against bacterial infections or diseases.
  • the compounds of formula I may also be co-administered with other antibiotics to increase the effect of therapy or prophylaxis against various bacterial infections.
  • the compounds of this invention are administered in combination therapies with other agents, they may be administered sequentially or concurrently to the patient.
  • pharmaceutical or prophylactic compositions according to this invention comprise a combination of a compound of formula I and another therapeutic or prophylactic agent.
  • the additional therapeutic agents described above may be administered separately, as part of a multiple dosage regimen, from the inhibitor-containing composition. Alternatively, these agents may be part of a single dosage form, mixed together with the inhibitor in a single composition.
  • compositions of this invention may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir.
  • the pharmaceutical compositions of this invention may contain any conventional non-toxic pharmaceutically-acceptable carriers, adjuvants or vehicles.
  • the pH of the formulation may be adjusted with pharmaceutically acceptable acids, bases or buffers to enhance the stability of the formulated compound or its delivery form.
  • parenteral as used herein includes subcutaneous, intracutaneous, intravenous, intramuscular, intra-articular, intrasynovial, intrasternal, intrathecal, intralesional and intracranial injection or infusion techniques.
  • the pharmaceutical, compositions may be in the form of a sterile injectable preparation, for example, as a sterile injectable aqueous or oleaginous suspension.
  • This suspension may be formulated according to techniques known in the art using suitable dispersing or wetting agents (such as, for example, Tween 80) and suspending agents.
  • the sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
  • suitable vehicles and solvents that may be employed are mannitol, water, Ringer's solution and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil may be employed including synthetic mono- or diglycerides.
  • Fatty acids, such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions.
  • These oil solutions or suspensions may also contain a long-chain alcohol diluent or dispersant, such as those described in Pharmacopeia Helvetica, or a similar alcohol.
  • compositions of this invention may be orally administered in any orally acceptable dosage form including, but not limited to, capsules, tablets, and aqueous suspensions and solutions.
  • carriers which are commonly used include lactose and corn starch.
  • Lubricating agents such as magnesium stearate, are also typically added.
  • useful diluents include lactose and dried corn starch.
  • compositions of this invention may also be administered in the form of suppositories for rectal administration.
  • These compositions can be prepared by mixing a compound of this invention with a suitable non-irritating excipient which is solid at room temperature but liquid at the rectal temperature and therefore will melt in the rectum to release the active components.
  • suitable non-irritating excipient include, but are not limited to, cocoa butter, beeswax and polyethylene glycols.
  • Topical administration of the pharmaceutical compositions of this invention is especially useful when the desired treatment involves areas or organs readily accessible by topical application.
  • the pharmaceutical composition should be formulated with a suitable ointment containing the active components suspended or dissolved in a carrier.
  • Carriers for topical administration of the compounds of this invention include, but are not limited to, mineral oil, liquid petroleum, white petroleum, propylene glycol, polyoxyethylene polyoxypropylene compound, emulsifying wax and water.
  • the pharmaceutical composition can be formulated with a suitable lotion or cream containing the active compound suspended or dissolved in a carrier.
  • Suitable carriers include, but are not limited to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol and water.
  • the pharmaceutical compositions of this invention may also be topically applied to the lower intestinal tract by rectal suppository formulation or in a suitable enema formulation. Topically-administered transdermal patches are also included in this invention.
  • compositions of this invention may be administered by nasal aerosol or inhalation.
  • Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and may be prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other solubilizing or dispersing agents known in the art.
  • Dosage levels of between about 0.01 and about 100 mg/kg body weight per day, preferably between 0.5 and about 75 mg/kg body weight per day and most preferably between about 1 and 50 mg/kg body weight per day of the active ingredient compound are useful in a monotherapy for the prevention and treatment of bacterial infections caused by bacteria such as Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus fecalis, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sps. Proteus sps. Pseudomonas aeruginosa, E. coli, Serratia marcesens, S. aureus, and Coag. Neg. Staph.
  • bacteria such as Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus fecalis, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter
  • the pharmaceutical compositions of this invention will be administered from about 1 to 5 times per day or alternatively, as a continuous infusion. Or, alternatively, the compositions of the present invention may be administered in a pulsatile formulation. Such administration can be used as a chronic or acute therapy.
  • the amount of active ingredient that may be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration.
  • a typical preparation will contain from about 5% to about 95% active compound (w/w).
  • such preparations contain from about 20% to about 80% active compound.
  • compositions of this invention comprise a combination of a compound of formula I and one or more additional therapeutic or prophylactic agents
  • both the compound and the additional agent should be present at dosage levels of between about 10% to 80% of the dosage normally administered in a monotherapy regime.
  • a maintenance dose of a compound, composition or combination of this invention may be administered, if necessary. Subsequently, the dosage or frequency of administration, or both, may be reduced, as a function of the symptoms, to a level at which the improved condition is retained when the symptoms have been alleviated to the desired level, treatment should cease. Patients may, however, require intermittent treatment on a long-term basis upon any recurrence or disease symptoms.
  • the invention provides methods for treating or preventing a bacterial infection, or disease state, comprising the step of administering to a patient any compound, pharmaceutical composition, or combination described herein.
  • patient means an animal, preferably a mammal, and most preferably a human.
  • the compounds of this invention are also useful as commercial reagents which effectively bind to the gyrase B enzyme.
  • the compounds of this invention, and their derivatives may be used to block gyrase B activity in biochemical or cellular assays for bacterial gyrase B or its homologs or may be derivatized to bind to a stable resin as a tethered substrate for affinity chromatography applications.
  • the purified aminobenzimidazole was diluted in DMSO (1 mL), treated with excess ethyl-isocyanate (0.5 mL) and heated to 80° C. for 3 hours.
  • the reaction was cooled to room temperature, excess ethyl isocyanate removed in vacuo, azeotroped with MeOH (thrice), diluted with MeOH (5 mL), treated with NH4OH (2 mL), and heated to 80° C. for 3 hours.
  • the mixture was cooled to room temperature, concentrated in vacuo, diluted with 1/1 water/brine, and extracted twice with 4/1 ethyl acetate/ethanol.
  • Ia-157 A solution of Ia-156 (95 mg, 0.289 mmole) in 6N HCl (2 mL) was refluxed for 6 hours. The solution was then cooled to room temperature, concentrated in vacuo, and azeotroped sequentially with MeOH (twice) and acetone (twice).
  • the ATP hydrolysis activity of DNA gyrase was measure by coupling the production of ADP through pyruvate kinase/lactate dehydrogenase to the oxidation of NADH. This method has been described previously (Tamura and Gellert, 1990, J. Biol. Chem., 265, 21342).
  • ATPase assays are carried out at 30° C. in buffered solutions containing 100 mM TRIS pH 7.6, 1.5 mM MgCl 2 , 50 mM KCl.
  • the coupling system contains (final concentrations) 2.5 mM phosphoenol pyruvate, 200 ⁇ M nicotinamide adenine dinucleotide (NADH), 1 mM DTT, 30 ug pyruvate kinase, and 10 ug/ml lactate dehydrogenase.
  • nanomolar enzyme (374 kDa Gyr A2B2 subunit from Staphylococcus aureus) and a DMSO solution of the inhibitor to a final concentration of 4% are added and the reaction mixture is allowed to incubate for 10 minutes at 30° C.
  • the reaction is then started by the addition of ATP to a final concentration of 0.9 mM and the rate of NADH disappearance at 340 nanometers is measured over the course of 10 minutes.
  • the percent inhibition values are determined from rate versus concentration profiles and are reported as the average of duplicate values.
  • Table 4 shows the results of the percent inhibition activity of selected compounds of this invention in the Gyrase inhibition assay at 10 ⁇ M concentration.
  • the compound numbers correspond to the compound numbers in Table 1.
  • Compounds having an activity designated as “A” provided a percent inhibition value below 50 percent; compounds having an activity designated as “B” provided a percent inhibition value between 50 and 75 percent; and compounds having an activity designated as “C” provided a percent inhibition value greater than 75 percent.
  • the freshly picked colonies can be incubated at 37° C. for about 4 to 8 hrs until the culture equals or exceeds a turbidity of a 0.5 McFarland standard (approximately 1.5 ⁇ 10 8 cells per mL) and diluted to give the same CFU per mL as above.
  • the inoculum was prepared using a commercially available mechanical device (the BBL PROMPT System) that involves touching five colonies directly with a wand, containing crosshatch grooves at its bottom, followed by suspension of the bacteria in an appropriate volume of saline. Dilution to the appropriate inoculum cell density was made from this cell suspension.
  • the broth used for testing consists of MHB supplemented with 50 mg per L of Ca 2+ and 25 mg per L of Mg 2+ .
  • Standard dilution panels of control antibiotics were made and stored as in the NCCLS standard M7-A5, the dilution range typically being in the 128 ⁇ g per mL to 0.015 ⁇ g per mL (by 2-fold serial dilution).
  • test compounds were dissolved and diluted fresh for experimentation on the same day; the same or similar ranges of concentration as above being used.
  • the test compounds and controls were dispensed into a multiwell plate and test bacteria added such that the final inoculation was approximately 5 ⁇ 10 4 CFU per well and the final volume was 100 ⁇ L.
  • the plates were incubated at 35° C. overnight (16 to 20 hr) and checked by eye for turbidity or quantitated with a multiwell plate reader.
  • the endpoint minimal inhibitory concentration (MIC) is the lowest concentration of drug at which the microorganism tested does not grow.
  • Table 5 shows the results of the MIC assay for selected compounds of this invention.
  • the compound numbers correspond respond to the compound numbers in Table 1.
  • Compounds having an activity level designated as “A” provided an MIC of less than 10 ⁇ g/mL; compounds having an activity level designated as “B” provided an MIC of between 10 and 40 ⁇ g/mL; compounds having an activity level designated as “C” provided an MIC of greater than 40 ⁇ g/mL.

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Abstract

The present invention relates to compounds of the formula I:
Figure USRE040245-20080415-C00001
or a pharmaceutically acceptable derivative or prodrug thereof. The compounds are useful as inhibitors of bacterial gyrase activity. The present invention also relates to methods for treating bacterial infections in mammala. The present invention also relates to methods for decreasing bacterial quantity in a biological sample.

Description

CROSS REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Patent Application No. 60/256,094 filed Dec. 15, 2000 and U.S. Provisional Patent Application No. 60/275,292 filed Mar. 13, 2001, the contents of which are incorporated herein by reference.
FIELD OF THE INVENTION
This invention is in the field of medicinal chemistry and relates to compounds, and pharmaceutical compositions thereof, that inhibit bacterial gyrases. The compounds are useful as inhibitors of bacterial gyrase activity. The present invention also relates to methods for treating bacterial infections in mammals. The present invention also relates to methods for decreasing bacterial quantity in a biological sample.
BACKGROUND OF THE INVENTION
Bacterial resistance to antibiotics has long been recognized, and it is today considered to be a serious worldwide health problem. As a result of resistance, some bacterial infections are either difficult to treat with antibiotics or even untreatable. This problem has become especially serious with the recent development of multiple drug resistance in certain strains of bacteria, such as Streptococcus pneumoniae (SP), Mycobacterium tuberculosis, and Enterococcus. The appearance of vancomycin resistant enterococcus was particularly alarming because vancomycin was formerly the only effective antibiotic for treating this infection, and had been considered for many infections to be the drug of “last resort”. While many other drug-resistant bacteria do not cause life-threatening disease, such as enterococci, there is the fear that the genes which induce resistance might spread to more deadly organisms such as Staphylococcus aureus, where methicillin resistance is already prevalent (De Clerq, et al., Current Opinion in Anti-infective Investigational Drugs, 1999, 1, 1; Levy, “The Challenge of Antibiotic Resistance”, Scientific American, March, 1998).
Another concern is how quickly antibiotic resistance can spread. For example, until the 1960's SP was universally sensitive to penicillin, and in 1987 only 0.02% of the SP strains in the U.S. were resistant. However, by 1995 it was reported that SP resistance to penicillin was about seven percent and as high as 30% in some parts of the U.S. (Lewis, FDA Consumer magazine (September, 1995); Gershman in The Medical Reporter, 1997).
Hospitals, in particular, serve as centers for the formation and transmission of drug-resistant organisms. Infections occurring in hospitals, known as nosocomial infections, are becoming an increasingly serious problem. Of the two million Americans infected in hospitals each year, more than half of these infections resist at least one antibiotic. The Center for Disease Control reported that in 1992, over 13,000 hospital patients died of bacterial infections that were resistant to antibiotic treatment (Lewis, “The Rise of Antibiotic-Resistant Infections”, FDA Consumer magazine, September 1995).
As a result of the need to combat drug-resistant bacteria and the increasing failure of the available drugs, there has been a resurgent interest in discovering new antibiotics. One attractive strategy for developing new antibiotics is to inhibit DNA gyrase, a bacterial enzyme necessary for DNA replication, and therefore, necessary for bacterial cell growth and division. Gyrase activity is also associated with events in DNA transcription, repair and recombination.
Gyrase is one of the topoisomerases, a group of enzymes which catalyze the interconversion of topological isomers of DNA (see generally, Kornberg and Baker, DNA Replication, 2d Ed., Chapter 12, 1992, W. H. Freeman and Co.; Drlica, Molecular Microbiology, 1992, 6, 425; Drlica and Zhao, Microbiology and Molecular Biology Reviews, 1997, 61, 377). Gyrase itself controls DNA supercoiling and relieves topological stress that occurs when the DNA strands of a parental duplex are untwisted during the replication process. Gyrase also catalyzes the conversion of relaxed, closed circular duplex DNA to a negatively superhelical form which is more favorable for recombination. The mechanism of the supercoiling reaction involves the wrapping of gyrase around a region of the DNA, double strand breaking in that region, passing a second region of the DNA through the break, and rejoining the broken strands. Such a cleavage mechanism is characteristic of a type II topoisomerase. The supercoiling reaction is driven by the binding of ATP to gyrase. The ATP is then hydrolyzed during the reaction. This ATP binding and subsequent hydrolysis cause conformational changes in the DNA-bound gyrase that are necessary for its activity. It has also been found that the level of DNA supercoiling (or relaxation) is dependent on the ATP/ADP ratio. In the absence of ATP, gyrase is only capable of relaxing supercoiled DNA.
Bacterial DNA gyrase is a 400 kilodalton protein tetramer consisting of two A (GyrA) and two B subunits (GyrB). Binding and cleavage of the DNA is associated with GyrA, whereas ATP is bound and hydrolyzed by the GyrB protein. GyrB consists of an amino-terminal domain which has the ATPase activity, and a carboxy-terminal domain which interacts with GyrA and DNA. By contrast, eukaryotic type II topoisomerases are homodimers that can relax negative and positive supercoils, but cannot introduce negative supercoils. Ideally, an antibiotic based on the inhibition of bacterial DNA gyrase would be selective for this enzyme and be relatively inactive against the eukaryotic type II topoisomerases.
The widely-used quinolone antibiotics inhibit bacterial DNA gyrase. Examples of the quinolones include the early compounds such as nalidixic acid and oxolinic acid, as well as the later, more potent fluoroquinolones such as norfloxacin, ciprofloxacin, and trovafloxacin. These compounds bind to GyrA and stabilize the cleaved complex, thus inhibiting overall gyrase function, leading to cell death. However, drug resistance has also been recognized as a problem for this class of compounds (WHO Report, “Use of Quinolones in Food Animals and Potential Impact on Human Health”, 1998). With the quinolones, as with other classes of antibiotics, bacteria exposed to earlier compounds often quickly develop cross-resistance to more potent compounds in the same class.
There are fewer known inhibitors that bind to GyrB. Examples include the coumarins, novobiocin and coumermycin A1, cyclothialidine, cinodine, and clerocidin. The coumarins have been shown to bind to GyrB very tightly. For example, novobiocin makes a network of hydrogen bonds with the protein and several hydrophobic contacts. While novobiocin and ATP do appear to bind within the ATP binding site, there is minimal overlap in the bound orientation of the two compounds. The overlapping portions are the sugar unit of novobiocin and the ATP adenine (Maxwell, Trends in Microbiology, 1997, 5, 102).
For coumarin-resistant bacteria, the most prevalent point mutation is at a surface arginine residue that binds to the carbonyl of the coumarin ring (Arg136 in E. coli GyrB). While enzymes with this mutation show lower supercoiling and ATPase activity, they are also less sensitive to inhibition by coumarin drugs (Maxwell, Mol. Microbiol., 1993, 9, 681).
Despite being potent inhibitors of gyrase supercoiling, the coumarins have not been widely used as antibiotics. They are generally not suitable due to their low permeability in bacteria, eukaryotic toxicity, and poor water solubility (Maxwell, Trends in Microbiology, 1997, 5, 102). It would be desirable to have a new, effective GyrB inhibitor that overcomes these drawbacks and, preferably does not rely on binding to Arg136 for activity. Such an inhibitor would be an attractive antibiotic candidate, without a history of resistance problems that plague other classes of antibiotics.
As bacterial resistance to antibiotics has become an important public health problem, there is a continuing need to develop newer and more potent antibiotics. More particularly, there is a need for antibiotics that represent a new class of compounds not previously used to treat bacterial infection. Such compounds would be particularly useful in treating nosocomial infections in hospitals where the formation and transmission of resistant bacteria are becoming increasingly prevalent.
DESCRIPTION OF THE INVENTION
It has now been found that compounds of this invention and pharmaceutical compositions thereof are useful in treating bacterial infections. One embodiment of this invention relates to a method of treating a bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a compound of formula I:
Figure USRE040245-20080415-C00002
or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
    • Z is O or N—R4;
    • W is nitrogen or CRa;
    • Ra is selected from hydrogen, halogen, —CF3, R7, —OR7, or —N(R7)2;
    • R1 is an aryl or heteroaryl ring, wherein said ring is optionally substituted by up to four R9; wherein an R9 substituent in the ortho-position of R1 taken together with R2 may form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring having 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R2 and R3 are each independently selected from R6, halogen, CN, SR6, OR6, N(R6)2, NRCO2R6, NRCON (R6)2, CON(R6)2, NRCOR6, NRN(R6)2, COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or NRSO2R6; or R2 and R3 are taken together to form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R4 is selected from R6, CON(R6), COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or (CH2)yR2;
    • y is 1-6;
    • R5 is selected from R7, Ar, COAr, CON(R7)Ar, (CH2)yCO2R, (CH2)yN(R7)2, C(═NR10)—N(R7)2, C(═NR10)—NRCOR, C(═S)—N(R7)2, CON(R7)2, COR, SO2R, or SO2N(R7)2;
    • Ar is a five membered heteroaryl, heterocyclyl, or carbocyclyl ring, wherein said ring is optionally substituted by up to three substituents selected from oxo, halogen, CN, NO2, R8, OR8, NHR8, NHCOR8, NHCONHR8, COR8, CONHR8, SO2R8, NHSO2NHR8 or SO2NHR8;
    • each R6 is independently selected from R7 or an optionally substituted group selected from alkoxy, hydroxylalkyl, heterocyclyl, heterocyclcylalkyl, aryl, aralkyl, aralkoxy, aryloxyalkyl, heteroaryl, heteroaralkyl, heteroaralkoxy, or heteroarayloxyalkyl;
    • each R7 is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons, or two R7 on the same nitrogen taken together with the nitrogen optionally form a four to six member, saturated or unsaturated heterocyclic ring having one to three heteroatoms;
    • R8 is a C1-C4 aliphatic group, wherein two R8 on adjacent positions of Ar, or an aryl or heteroaryl ring, may be taken together with their intervening atoms to form a three to six membered fused ring;
    • each R9 is independently selected from oxo, halogen, CN, NO2, Tn(haloalkyl), R6, SR6, OR6, OR8, N(R6)2, CON (R6)2, CON(R)COR6, COR6, CO2R6, CO2N(R6)2, COCOR6, SO2R6, SO2N(R6)2, N(R)TnCO2R6, N(R) TnCON(R6)2, N(R)TnN(R6)2, N(R)TnNRCO2R6, N(R) TnNRCON(R6)2, N(R)TnCOR6, N(R)TnNRCOR6, N(R)TnSO2N(R6)2, N(R)TnSO2R6, TnPO(OR7)2, TnOPO(OR7)2, TnSP(OR7)2, TnPO(OR7)2, or TnNPO (OR7)2;
    • each Q is an independently selected C1-C3 branched or straight alkyl;
    • T is selected from —Q— or —Qm—CH(Qm—R2)—;
    • each m and n are independently selected from zero or one;
    • and R10 is selected from R7 or Ar.
As used herein, the following definitions shall apply unless otherwise indicated. In addition, unless otherwise indicated, functional group radicals are independently selected.
The term “aliphatic” as used herein means straight-chain, branched or cyclic C1-C12 hydrocarbons which are completely saturated or which contain one or more units of unsaturation but which are not aromatic. For example, suitable aliphatic groups include substituted or unsubstituted linear, branched or cyclic alkyl, alkenyl, alkynyl groups and hybrids thereof such as (cycloalkyl)alkyl, (cycloalkenyl) alkyl or (cycloalkyl)alkenyl. The terms “alkyl”, “alkoxy”, “hydroxyalkyl”, “alkoxyalkyl”, and “alkoxycarbonyl”, used alone or as part of a larger moiety includes both straight and branched chains containing one to twelve carbon atoms. The terms “alkenyl” and “alkynyl” used alone or as part of a larger moiety shall include both straight and branched chains containing two to twelve carbon atoms. The term “cycloalkyl” used alone or as part of a larger moiety shall include cyclic C3-C12 hydrocarbons which are completely saturated or which contain one or more units of unsaturation, but which are not aromatic.
The terms “haloalkyl”, “haloalkenyl” and “haloalkoxy” means alkyl, alkenyl or alkoxy, as the case may be, substituted with one or more halogen atoms. The term “halogen” means F, Cl, Br, or I.
The term “heteroatom” means N, O, or S and includes any oxidized form of nitrogen and sulfur, and the quaternized form of any basic nitrogen.
The term “carbocycle”, “carbocyclyl”, or “carbocyclic” as used herein means an aliphatic ring system having three to fourteen members. The term “carbocycle”, “carbocyclyl”, or “carbocyclic” whether saturated or partially unsaturated, also refers to rings that are optionally substituted. The terms “carbocyclyl”or “carbocyclic” also include aliphatic rings that are fused to one or more aromatic or nonaromatic rings, such as in a decahydronaphthyl or tetrahydronaphthyl, where the radical or point of attachment is on the aliphatic ring.
The term “aryl” used alone or as part of a larger moiety as in “aralkyl”, “aralkoxy”, or “aryloxyalkyl”, refers to aromatic ring groups having five to fourteen members, such as phenyl, benzyl, phenethyl, 1-naphthyl, 2-naphthyl, 1-anthracyl and 2-anthracyl. The term “aryl” also refers to rings that are optionally substituted. The term “aryl” may be used interchangeably with the term “aryl ring”. “Aryl” also includes fused polycyclic aromatic ring systems in which an aromatic ring is fused to one or more rings. Examples include 1-naphthyl, 2-naphthyl, 1-anthracyl and 2-anthracyl. Also included within the scope of the term “aryl”, as it is used herein, is a group in which an aromatic ring is fused to one or more non-aromatic rings, such as in a indanyl, phenanthridinyl, or tetrahydronaphthyl, where the radical or point of attachment is on the aromatic ring.
The term “heterocycle”, “heterocyclyl”, or “heterocyclic” as used herein includes non-aromatic ring systems having five to fourteen members, preferably five to ten, in which one or more ring carbons, preferably one to four, are each replaced by a heteroatom such as N, O, or S. Examples of heterocyclic rings include 3-1H-benzimidazol-2-one, (1-substituted)-2-oxo-benzimidazol-3-yl, 2-tetrahydrofuranyl, 3-tetrahydrofuranyl, 2-tetrahydrothiophenyl, 3-tetrahydrothiophenyl, 2-morpholinyl, 3-morpholinyl, 4-morpholinyl, 2-thiomorpholinyl, 3-thiomorpholinyl, 4-thiomorpholinyl, 1-pyrrolidinyl, 2-pyrrolidinyl, 3-pyrrolidinyl, 1-piperazinyl, 2-piperazinyl, 1-piperidinyl, 1-piperidinyl, 3-piperidinyl, 4-piperidinyl, 4-thiazolidinyl, diazolonyl, N-substituted diazolonyl, 1-phthalimidinyl, benzoxanyl, benzopyrrolidinyl, benzopiperidinyl, benzoxolanyl, benzothiolanyl, and benzothianyl. Also included within the scope of the term “heterocyclyl” or “heterocyclic”, as it is used herein, is a group in which a non-aromatic heteroatom-containing ring is fused to one or more aromatic or non-aromatic rings, such as in an indolinyl, chromanyl, phenanthridinyl, or tetrahydroquinolinyl, where the radical or point of attachment is on the non-aromatic heteroatom-containing ring. The term “heterocycle”, “heterocyclyl”, or “heterocyclic” whether saturated or partially unsaturated, also refers to rings that are optionally substituted.
The term “heteroaryl”, used alone or as part of a larger moiety as in “heteroaralkyl” or “heteroarylalkoxy”, refers to heteroaromatic ring groups having five to fourteen members. Examples of heteroaryl rings include 2-furanyl, 3-furanyl, 3-furazanyl, N-imidazolyl, 2-imidazolyl, 4-imidazolyl, 5-imidazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-oxadiazolyl, 5-oxadiazolyl, 2-oxazolyl, 4-oxazolyl, 5-oxazolyl, 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 1-pyrazolyl, 3-pyrazolyl, 4-pyrazolyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-pyrimidyl, 3-pyridazinyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, 5-tetrazolyl, 2-triazolyl, 5-triazolyl, 2-thienyl, 3-thienyl, carbazolyl, benzimidazolyl, benzothienyl, benzofuranyl, indolyl, quinolinyl, benzotriazolyl, benzothiazolyl, benzooxazolyl, benzimidazolyl, isoquinolinyl, indolyl, isoindolyl, acridinyl, or benzoisoxazolyl. Also included within the scope of the term “heteroaryl”, as it is used herein, is a group in which a heteroatomic ring is fused to one or more aromatic or nonaromatic rings where the radical or point of attachment is on the heteroaromatic ring. Examples include tetrahydroquinoline, tetrahydroisoquinoline, and pyrido[3,4-d]pyrimidinyl. The term “heteroaryl” also refers to rings that are optionally substituted. The term “heteroaryl” may be used interchangeably with the term “heteroaryl ring” or the term “heteroaromatic”.
An aryl (including aralkyls, aralkoxy, aryloxyalkyl and the like) or heteroaryl (including heteroaralkyl and heteroarylalkoxy and the like) group may contain one or more substituents. Examples of suitable substituents on the unsaturated carbon atom of an aryl, heteroaryl, aralkyl, or heteroaralkyl group include a halogen, —Ro, —ORo, —SRo, 1,2-methylene-dioxy, 1,2-ethylenedioxy, protected OH (such as acyloxy), phenyl (Ph), substituted Ph, —O(Ph), substituted —O(Ph), —CH2(Ph), substituted —CH2(Ph), —CH2CH2(Ph), substituted —CH2CH2(Ph), —NO2, —CN, —N(Ro)2, —NR0C(O)Ro, —NRoC(O)N(Ro)2, —NRoCO2Ro, —NRoNRoC(O)Ro, —NRoNRoC(O)N(Ro)2, —NRoNRoCO2Ro, —C(O)C(O)Ro, —C(O)CH2C(O)Ro, —CO2Ro, —C(O)Ro, —C(O)N(Ro)2, —OC(O)N(Ro)2, —S(O)2Ro, —SO2N(Ro)2, —S(O)Ro, —NRoSO2N(Ro)2, —NRoSO2Ro, —C(═S)N(Ro)2, —C(═NH)—N(Ro)2, —(CH2)yNHC(O)Ro, —(CH2)yNHC(O)CH(V—Ro)(Ro); wherein Ro is H, a substituted or unsubstituted aliphatic group, an unsubstituted heteroaryl or heterocyclic ring, phenyl (Ph), substituted Ph, —O(Ph), substituted —O(Ph), —CH2(Ph), or substituted —CH2(Ph); y is 0-6; and V is a linker group. Examples of substituents on the aliphatic group or the phenyl ring include amino, alkylamino, dialkylamino, aminocarbonyl, halogen, alkyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylaminocarbonyloxy, dialkylaminocarbonyloxy, alkoxy, nitro, cyano, carboxy, alkoxycarbonyl, alkylcarbonyl, hydroxy, haloalkoxy, or haloalkyl.
An aliphatic group or a non-aromatic heterocyclic ring may contain one or more substituents. Examples of suitable substituents on the saturated carbon of an aliphatic group or of a non-aromatic heterocyclic ring include those listed above for the unsaturated carbon of an aryl or heteroaryl group and the following: ═O, ═S, ═NNHR*, ═NN(R*)2, ═N—, ═NNHC(O)R*, ═NNHCO2(alkyl), ═NNHSO2 (alkyl), or ═NR*, where each R* is independently selected from hydrogen, an unsubstituted aliphatic group or a substituted aliphatic group. Examples of substituents on the aliphatic group include amino, alkylamino, dialkylamino, aminocarbonyl, halogen, alkyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylaminocarbonyloxy, dialkylaminocarbonyloxy, alkoxy, nitro, cyano, carboxy, alkoxycarbonyl, alkylcarbonyl, hydroxy, haloalkoxy, or haloalkyl.
Suitable substituents on the nitrogen of an aromatic or non-aromatic heterocyclic ring include —R+, —N(R+)2, —C(O)R+, —CO2R+, C(O)C(O)R+, —C(O)CH2C(O)R+, —SO2R+, —SO2N(R+)2, —C(═S)N(R+)2, —C(═NH)—N (R+)2, and —NR+SO2R+; wherein R+ is H, an aliphatic group, a substituted aliphatic group, phenyl (Ph), substituted Ph, —O(Ph), substituted —O(Ph), CH2(Ph), substituted CH2(Ph), or an unsubstituted heteroaryl or heterocyclic ring. Examples of substituents on the aliphatic group or the phenyl ring include amino, alkylamino, dialkylamino, aminocarbonyl, halogen, alkyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylaminocarbonyloxy, dialkylaminocarbonyloxy, alkoxy, nitro, cyano, carboxy, alkoxycarbonyl, alkylcarbonyl, hydroxy, haloalkoxy, or haloalkyl.
The term “linker group” or “linker” means an organic moiety that connects two parts of a compound. Linkers are typically comprised of an atom such as oxygen or sulfur, a unit such as —NH—, —CH2—, —C(O)—, —C(O)NH—, or a chain of atoms, such as an alkylidene chain. The molecular mass of a linker is typically in the range of about 14 to 200. Examples of linkers include a saturated or unsaturated C1-6 alkylidene chain which is optionally substituted, and wherein one or two saturated carbons of the chain are optionally replaced by —C(O)—, —C(O)C(O)—, —CONH—, —CONHNH—, —CO2—, —OC(O)—, —NHCO2—, —O—, —NHCONH—, —OC(O)NH—, —NHNH—, —NHCO—, —S—, —SO—, —SO2—, —NH—, —SO2NH—, or —NHSO2—.
The term “alkylidene chain” refers to an optionally substituted, straight or branched carbon chain that may be fully saturated or have one or more units of unsaturation. The optional substituents are as described above for an aliphatic group.
A combination of substituents or variables is permissible only if such a combination results in a stable or chemically feasible compound. A stable compound or chemically feasible compound is one that is not substantially altered when kept at a temperature of 40° C. or less, in the absence of moisture or other chemically reactive conditions, for at least a week.
It will be apparent to one skilled in the art that certain compounds of this invention may exist in tautomeric forms, all such tautomeric forms of the compounds being within the scope of the invention.
Unless otherwise stated, structures depicted herein are also meant to include all stereochemical forms of the structure; i.e., the R and S configurations for each asymmetric center. Therefore, single stereochemical isomers as well as enantiomeric and diastereomeric mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, structures depicted herein are also meant to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of a hydrogen by a deuterium or tritium, or the replacement of a carbon by a 13C- or 14C-enriched carbon are within the scope of this invention.
One preferred embodiment of this invention relates to a method of treating a bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a compound having the formula Ia or Ib:
Figure USRE040245-20080415-C00003
or a pharmaceutically acceptable derivative or prodrug thereof, wherein R1, R2, R3, R4, and R5 are as described above.
Examples of preferred R1 include optionally substituted phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, thienyl, pyrimidyl, imidazol-1-yl, imidazol-2-yl, pyrazol-1-yl, aminopyrimidinyl, quinolinyl, aminobenzimidazole, and indolyl. Preferred R9, if present, on the R1 aryl or heteroaryl ring include halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, N(R)TnCO2R6, N(R) TnNRCO2R6, N(R)TnN(R6)2, NO2, Tn(haloalkyl), CO2N (R6)2, COR6, SO2R6, or SO2N(R6)2. Examples of such R9 groups include, but are not limited to, pyrrol-2,5-dione, NR2, OR, CO2H, NO2, OH, NHCOR, NHCO2R, NHCH2CO2R, NH(CH2)2NHCO2R, CH2CO2R, CF3, SO2R, NHCH(CH2OH)CO2H, N—SO2Me-piperidinyl, SMe, NH(CH2)2NH2, and piperidinyl.
Preferred R2 and R3 groups include halogen, CN, CO2R6, OR6, and R6. Examples of preferred R3 groups include Br, F, Cl, COOH, CN, OMe, methyl, ethyl, t-butyl, CF3, OH, and OBn.
Examples of preferred R5 include CO2(aliphatic), C(═NH)—NH2, and CON(R7)2 such as CO(piperidin-1-yl), CONHEt, CONHMe, CONH(cyclopropyl), CONH (isopropyl), CONH(propyl), CONH(pyrrolidinyl), CO2Et, and CO2Me.
Preferred compounds of formula Ia and Ib include those having one or more, or most preferably all, of the features selected from the group consisting of:
    • (a) R1 is an optionally substituted aryl or heteroaryl ring;
    • (b) R2 and R3 are each independently selected from halogen, CN, CO2R6, OR6, or R6;
    • (c) R5 is CO2R, COAr, COR, CON(R7)2, Ar, (CH2)yCO2R, or (CH2)yN(R7)2; and
    • (d) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, N(R)TnCO2R6, N(R)TnNRCO2R6, N(R)TnN(R6)2, NO2, Tn(haloalkyl), CO2N(R6)2, COR6, SO2R6, or SO2N(R6)2.
More preferred compounds of formula Ia and Ib include those having one or more, or most preferably all, of the features selected from the group consisting of:
    • (a) R1 is an optionally substituted ring selected from phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, thienyl, pyrimidyl, imidazol-1-yl, imidazol-2-yl, pyrazol-1-yl, amino-pyrimidinyl, quinolinyl, aminobenzimidazole, or indolyl;
    • (b) R2 is hydrogen, alkoxy, aminoalkyl, or halogen;
    • (c) R3 is hydrogen, alkoxy, aralkoxy, or halogen;
    • (d) R4 is hydrogen or (CH2)yR2;
    • (e) R5 is CON(R7)2, Ar, (CH2)yCO2R, or (CH2)yN(R7)2; and
    • (f) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, or N(R)TnCO2R6.
Selected compounds of formula Ia are set forth in Table 1 below.
TABLE 1
No. Ia- Structure
1
Figure USRE040245-20080415-C00004
2
Figure USRE040245-20080415-C00005
3
Figure USRE040245-20080415-C00006
4
Figure USRE040245-20080415-C00007
5
Figure USRE040245-20080415-C00008
6
Figure USRE040245-20080415-C00009
7
Figure USRE040245-20080415-C00010
8
Figure USRE040245-20080415-C00011
9
Figure USRE040245-20080415-C00012
10
Figure USRE040245-20080415-C00013
11
Figure USRE040245-20080415-C00014
12
Figure USRE040245-20080415-C00015
13
Figure USRE040245-20080415-C00016
14
Figure USRE040245-20080415-C00017
15
Figure USRE040245-20080415-C00018
16
Figure USRE040245-20080415-C00019
17
Figure USRE040245-20080415-C00020
18
Figure USRE040245-20080415-C00021
19
Figure USRE040245-20080415-C00022
20
Figure USRE040245-20080415-C00023
21
Figure USRE040245-20080415-C00024
22
Figure USRE040245-20080415-C00025
23
Figure USRE040245-20080415-C00026
24
Figure USRE040245-20080415-C00027
25
Figure USRE040245-20080415-C00028
26
Figure USRE040245-20080415-C00029
27
Figure USRE040245-20080415-C00030
28
Figure USRE040245-20080415-C00031
29
Figure USRE040245-20080415-C00032
30
Figure USRE040245-20080415-C00033
31
Figure USRE040245-20080415-C00034
32
Figure USRE040245-20080415-C00035
33
Figure USRE040245-20080415-C00036
34
Figure USRE040245-20080415-C00037
35
Figure USRE040245-20080415-C00038
36
Figure USRE040245-20080415-C00039
37
Figure USRE040245-20080415-C00040
38
Figure USRE040245-20080415-C00041
39
Figure USRE040245-20080415-C00042
40
Figure USRE040245-20080415-C00043
41
Figure USRE040245-20080415-C00044
42
Figure USRE040245-20080415-C00045
43
Figure USRE040245-20080415-C00046
44
Figure USRE040245-20080415-C00047
45
Figure USRE040245-20080415-C00048
46
Figure USRE040245-20080415-C00049
47
Figure USRE040245-20080415-C00050
48
Figure USRE040245-20080415-C00051
49
Figure USRE040245-20080415-C00052
50
Figure USRE040245-20080415-C00053
51
Figure USRE040245-20080415-C00054
52
Figure USRE040245-20080415-C00055
53
Figure USRE040245-20080415-C00056
54
Figure USRE040245-20080415-C00057
55
Figure USRE040245-20080415-C00058
56
Figure USRE040245-20080415-C00059
57
Figure USRE040245-20080415-C00060
58
Figure USRE040245-20080415-C00061
59
Figure USRE040245-20080415-C00062
60
Figure USRE040245-20080415-C00063
61
Figure USRE040245-20080415-C00064
62
Figure USRE040245-20080415-C00065
63
Figure USRE040245-20080415-C00066
64
Figure USRE040245-20080415-C00067
65
Figure USRE040245-20080415-C00068
66
Figure USRE040245-20080415-C00069
67
Figure USRE040245-20080415-C00070
68
Figure USRE040245-20080415-C00071
69
Figure USRE040245-20080415-C00072
70
Figure USRE040245-20080415-C00073
71
Figure USRE040245-20080415-C00074
72
Figure USRE040245-20080415-C00075
73
Figure USRE040245-20080415-C00076
74
Figure USRE040245-20080415-C00077
75
Figure USRE040245-20080415-C00078
76
Figure USRE040245-20080415-C00079
77
Figure USRE040245-20080415-C00080
78
Figure USRE040245-20080415-C00081
79
Figure USRE040245-20080415-C00082
80
Figure USRE040245-20080415-C00083
81
Figure USRE040245-20080415-C00084
82
Figure USRE040245-20080415-C00085
83
Figure USRE040245-20080415-C00086
84
Figure USRE040245-20080415-C00087
85
Figure USRE040245-20080415-C00088
86
Figure USRE040245-20080415-C00089
87
Figure USRE040245-20080415-C00090
88
Figure USRE040245-20080415-C00091
89
Figure USRE040245-20080415-C00092
90
Figure USRE040245-20080415-C00093
91
Figure USRE040245-20080415-C00094
92
Figure USRE040245-20080415-C00095
93
Figure USRE040245-20080415-C00096
94
Figure USRE040245-20080415-C00097
95
Figure USRE040245-20080415-C00098
96
Figure USRE040245-20080415-C00099
97
Figure USRE040245-20080415-C00100
98
Figure USRE040245-20080415-C00101
99
Figure USRE040245-20080415-C00102
100
Figure USRE040245-20080415-C00103
101
Figure USRE040245-20080415-C00104
102
Figure USRE040245-20080415-C00105
103
Figure USRE040245-20080415-C00106
104
Figure USRE040245-20080415-C00107
105
Figure USRE040245-20080415-C00108
106
Figure USRE040245-20080415-C00109
107
Figure USRE040245-20080415-C00110
108
Figure USRE040245-20080415-C00111
109
Figure USRE040245-20080415-C00112
110
Figure USRE040245-20080415-C00113
111
Figure USRE040245-20080415-C00114
112
Figure USRE040245-20080415-C00115
113
Figure USRE040245-20080415-C00116
114
Figure USRE040245-20080415-C00117
115
Figure USRE040245-20080415-C00118
116
Figure USRE040245-20080415-C00119
117
Figure USRE040245-20080415-C00120
118
Figure USRE040245-20080415-C00121
119
Figure USRE040245-20080415-C00122
120
Figure USRE040245-20080415-C00123
121
Figure USRE040245-20080415-C00124
122
Figure USRE040245-20080415-C00125
123
Figure USRE040245-20080415-C00126
124
Figure USRE040245-20080415-C00127
125
Figure USRE040245-20080415-C00128
126
Figure USRE040245-20080415-C00129
127
Figure USRE040245-20080415-C00130
128
Figure USRE040245-20080415-C00131
129
Figure USRE040245-20080415-C00132
130
Figure USRE040245-20080415-C00133
131
Figure USRE040245-20080415-C00134
132
Figure USRE040245-20080415-C00135
133
Figure USRE040245-20080415-C00136
134
Figure USRE040245-20080415-C00137
135
Figure USRE040245-20080415-C00138
136
Figure USRE040245-20080415-C00139
137
Figure USRE040245-20080415-C00140
138
Figure USRE040245-20080415-C00141
139
Figure USRE040245-20080415-C00142
140
Figure USRE040245-20080415-C00143
141
Figure USRE040245-20080415-C00144
142
Figure USRE040245-20080415-C00145
143
Figure USRE040245-20080415-C00146
144
Figure USRE040245-20080415-C00147
145
Figure USRE040245-20080415-C00148
146
Figure USRE040245-20080415-C00149
147
Figure USRE040245-20080415-C00150
148
Figure USRE040245-20080415-C00151
149
Figure USRE040245-20080415-C00152
150
Figure USRE040245-20080415-C00153
151
Figure USRE040245-20080415-C00154
152
Figure USRE040245-20080415-C00155
153
Figure USRE040245-20080415-C00156
154
Figure USRE040245-20080415-C00157
155
Figure USRE040245-20080415-C00158
156
Figure USRE040245-20080415-C00159
157
Figure USRE040245-20080415-C00160
158
Figure USRE040245-20080415-C00161
159
Figure USRE040245-20080415-C00162
160
Figure USRE040245-20080415-C00163
161
Figure USRE040245-20080415-C00164
162
Figure USRE040245-20080415-C00165
163
Figure USRE040245-20080415-C00166
164
Figure USRE040245-20080415-C00167
165
Figure USRE040245-20080415-C00168
166
Figure USRE040245-20080415-C00169
167
Figure USRE040245-20080415-C00170
168
Figure USRE040245-20080415-C00171
169
Figure USRE040245-20080415-C00172
170
Figure USRE040245-20080415-C00173
171
Figure USRE040245-20080415-C00174
172
Figure USRE040245-20080415-C00175
173
Figure USRE040245-20080415-C00176
174
Figure USRE040245-20080415-C00177
175
Figure USRE040245-20080415-C00178
176
Figure USRE040245-20080415-C00179
177
Figure USRE040245-20080415-C00180
178
Figure USRE040245-20080415-C00181
179
Figure USRE040245-20080415-C00182
180
Figure USRE040245-20080415-C00183
181
Figure USRE040245-20080415-C00184
182
Figure USRE040245-20080415-C00185
183
Figure USRE040245-20080415-C00186
184
Figure USRE040245-20080415-C00187
185
Figure USRE040245-20080415-C00188
186
Figure USRE040245-20080415-C00189
187
Figure USRE040245-20080415-C00190
188
Figure USRE040245-20080415-C00191
189
Figure USRE040245-20080415-C00192
190
Figure USRE040245-20080415-C00193
191
Figure USRE040245-20080415-C00194
192
Figure USRE040245-20080415-C00195
193
Figure USRE040245-20080415-C00196
194
Figure USRE040245-20080415-C00197
195
Figure USRE040245-20080415-C00198
196
Figure USRE040245-20080415-C00199
197
Figure USRE040245-20080415-C00200
198
Figure USRE040245-20080415-C00201
199
Figure USRE040245-20080415-C00202
200
Figure USRE040245-20080415-C00203
Selected compounds of formula Ib are shown in Table 2 below.
TABLE 2
No. Ib- Structure
1
Figure USRE040245-20080415-C00204
2
Figure USRE040245-20080415-C00205
3
Figure USRE040245-20080415-C00206
4
Figure USRE040245-20080415-C00207
5
Figure USRE040245-20080415-C00208
6
Figure USRE040245-20080415-C00209
7
Figure USRE040245-20080415-C00210
8
Figure USRE040245-20080415-C00211
9
Figure USRE040245-20080415-C00212
10
Figure USRE040245-20080415-C00213
11
Figure USRE040245-20080415-C00214
12
Figure USRE040245-20080415-C00215
13
Figure USRE040245-20080415-C00216
14
Figure USRE040245-20080415-C00217
15
Figure USRE040245-20080415-C00218
16
Figure USRE040245-20080415-C00219
17
Figure USRE040245-20080415-C00220
18
Figure USRE040245-20080415-C00221
19
Figure USRE040245-20080415-C00222
20
Figure USRE040245-20080415-C00223
21
Figure USRE040245-20080415-C00224
22
Figure USRE040245-20080415-C00225
23
Figure USRE040245-20080415-C00226
24
Figure USRE040245-20080415-C00227
25
Figure USRE040245-20080415-C00228
26
Figure USRE040245-20080415-C00229
27
Figure USRE040245-20080415-C00230
28
Figure USRE040245-20080415-C00231
Another embodiment of this invention relates to compounds of formula IIa or IIb
Figure USRE040245-20080415-C00232
or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
    • W is nitrogen or CRa;
    • Ra is selected from hydrogen, halogen, —CF3, R7, —OR7, or —N(R7)2;
    • R1 is an aryl or heteroaryl ring, wherein said ring is optionally substituted by up to four R9; wherein an R9 substituent in the ortho-position of R1 taken together with R2 may form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring having 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R2 and R3 are each independently selected from R6, halogen, CN, SR6, OR6, N(R6)2, NRCO2R6, NRCON (R6)2, CON(R6)2, NRCOR6, NRN(R6)2, COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or NRSO2R6; or R2 and R3 are taken together to form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R4 is selected from R6, CON(R6), COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or (CH2)yR2;
    • y is 1-6;
    • Ar is a five membered heteroaryl, heterocyclyl, or carbocyclyl ring, wherein said ring is optionally substituted by up to three substituents selected from oxo, halogen, CN, NO2, R8, OR8, NHR8, NHCOR8, NHCONHR8, COR8, CONHR8, SO2R8, NHSO2NHR8 or SO2NHR8;
    • each R6 is independently selected from R7 or an optionally substituted group selected from alkoxy, hydroxyalkyl, heterocyclyl, heterocyclcylalkyl, aryl, aralkyl, aralkoxy, aryloxyalkyl, heteroaryl, heteroaralkyl, heteroaralkoxy, or heteroarayloxyalkyl;
    • each R7 is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons, or two R7 on the same nitrogen taken together with the nitrogen optionally form a four to six member, saturated or unsaturated heterocyclic ring having one to three heteroatoms;
    • R8 is a C1-C4 aliphatic group, wherein two R8 on adjacent positions of Ar, or an aryl or heteroaryl ring, may be taken together with their intervening atoms to form a three to six membered fused ring;
    • each R9 is independently selected from oxo, halogen, CN, NO2, Tn(haloalkyl), R6, SR6, OR6, OR8, N(R6)2, CON (R6)2, CON(R)COR6, COR6, CO2R6, CO2N(R6)2, COCOR6, SO2R6, SO2N(R6)2, N(R)TnCO2R6, N(R) TnCON(R6)2, N(R)TnN(R6)2, N(R)TnNRCO2R6, N(R) TnNRCON(R6)2, N(R)TnCOR6, N(R)TnNRCOR6, N(R)TnSO2N(R6)2, N(R)TnSO2R6, TnPO(OR7)2, TnOPO(OR7)2, TnSP(OR7)2, TnPO(OR7)2, or TnNPO (OR7)2;
    • each Q is an independently selected C1-C3 branched or straight alkyl;
    • T is selected from —Q— or —Qm—CH(Qm—R2)—; and
    • each m and n are independently selected from zero or one.
Examples of preferred R1 include optionally substituted phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, thienyl, pyrimidyl, imidazol-1-yl, imidazol-2-yl, pyrazol-1-yl, aminopyrimidinyl, quinolinyl, aminobenzimidazole, and indolyl. Preferred R9, if present, on the R1 aryl or heteroaryl ring of formula IIa or IIb include halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, and N(R)TnCO2R6. Examples of such R9 groups include, but are not limited to, pyrrol-2,5-dione, NR2, OR, CO2H, NO2, OH, NHCOR, NHCO2R, NHCH2CO2R, NH(CH2)2NHCO2R, CH2CO2R, CF3, SO2R, NHCH(CH2OH)CO2H, N—SO2Me-piperidinyl, SMe, NH(CH2)2NH2, and piperidinyl.
Preferred R2 and R3 groups include halogen, CN, CO2R6, OR6, and R6. Examples of preferred R3 groups include Br, F, Cl, COOH, CN, OMe, methyl, ethyl, t-butyl, CF3, OH, and OBn.
Preferred compounds of formula IIa and IIb include those having one or more, or most preferably all, of the features selected from the group consisting of:
    • (a) R1 is an optionally substituted aryl or heteroaryl ring;
    • (b) R2 and R3 are each independently selected from halogen, CN, CO2R6, OR6, or R6;
    • (c) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, N(R)TnCO2R6, N(R)TnNRCO2R6, N(R)TnN(R6)2, NO2, Tn(haloalkyl), CO2N(R6)2, COR6, SO2R6, or SO2N(R6)2.
More preferred compounds of formula IIa and IIb include those having one or more, or most preferably all, of the features selected from the group consisting of:
    • (a) R1 is an optionally substituted ring selected from phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, thienyl, pyrimidyl, imidazol-1-yl, imidazol-2-yl, pyrazol-1-yl, amino-pyrimidinyl, quinolinyl, aminobenzimidazole, or indolyl;
    • (b) R2 is hydrogen, alkoxy, aminoalkyl, or halogen;
    • (c) R3 is hydrogen, alkoxy, aralkoxy, or halogen;
    • (d) R4 is hydrogen or (CH2)yR2; and
    • (e) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, or N(R)TnCO2R6.
Another embodiment of this invention relates to compounds of formula IIIa or IIIb:
Figure USRE040245-20080415-C00233
or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
    • W is nitrogen or CRa;
    • Ra is selected from hydrogen, halogen, —CF3, R7, —OR7, or —N(R7)2;
    • Ring A is optionally substituted with up to three R9; wherein when an R9 substituent is in the ortho-position of Ring A, said R9 substituent may be taken together with R2 to form an optionally substituted 5-7 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R2 and R3 are each independently selected from R6, halogen, CN, SR6, OR6, N(R6)2, NRCO2R6, NRCON (R6)2, CON(R6)2, NRCOR6, NRN(R6)2, COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or NRSO2R6; or R2 and R3 are taken together to form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R4 is selected from R6, CON(R6), COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or (CH2)yR2;
    • y is 1-6;
    • R5 is selected from R7, Ar, COAr, CON(R7)Ar, (CH2)yCO2R, (CH2)yN(R7)2, C(═NR10)—N(R7)2, C(═NR10)—NRCOR, C(═S)—N(R7)2, CON(R7)2, COR, SO2R, or SO2N(R7)2;
    • Ar is a five membered heteroaryl, heterocyclyl, or carbocyclyl ring, wherein said ring is optionally substituted by up to three substituents selected from oxo, halogen, CN, NO2, R8, OR8, NHR8, NHCOR8, NHCONHR8, COR8, CONHR8, SO2R8, NHSO2NHR8 or SO2NHR8;
    • each R6 is independently selected from R7 or an optionally substituted group selected from alkoxy, hydroxylalkyl, heterocyclyl, heterocyclcylalkyl, aryl, aralkyl, aralkoxy, aryloxyalkyl, heteroaryl, heteroaralkyl, heteroaralkoxy, or heteroarayloxyalkyl;
    • each R7 is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons, or two R7 on the same nitrogen taken together with the nitrogen optionally form a four to six member, saturated or unsaturated heterocyclic ring having one to three heteroatoms;
    • R8 is a C1-C4 aliphatic group, wherein two R8 on adjacent positions of Ar, or an aryl or heteroaryl ring, may be taken together with their intervening atoms to form a three to six membered fused ring;
    • each R9 is independently selected from oxo, halogen, CN, NO2, Tn(haloalkyl), R6, SR6, OR6, OR8, N(R6)2, CON (R6)2, CON(R)COR6, COR6, CO2R6, CO2N(R6)2, COCOR6, SO2R6, SO2N(R6)2, N(R)TnCO2R6, N(R) TnCON(R6)2, N(R)TnN(R6)2, N(R)TnNRCO2R6, N(R) TnNRCON(R6)2, N(R)TnCOR6, N(R)TnNRCOR6, N(R)TnSO2N(R6)2, N(R)TnSO2R6, TnPO(OR7)2, TnOPO(OR7)2, TnSP(OR7)2, TnPO(OR7)2, or TnNPO (OR7)2;
    • each Q is an independently selected C1-C3 branched or straight alkyl;
    • T is selected from —Q— or —Qm—CH(Qm—R2)—;
    • each m and n are independently selected from zero or one;
    • and R10 is selected from R7 or Ar.
Preferred R9, if present, on Ring A of formulae IIIa and IIIb include halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, and N(R)TnCO2R6. Examples of such R9 groups include, but are not limited to, pyrrol-2,5-dione, NR2, OR, CO2H, NO2, OH, NHCOR, NHCO2R, NHCH2CO2R, NH(CH2)2NHCO2R, CH2CO2R, CF3, SO2R, NHCH(CH2OH)CO2H, N—SO2Me-piperidinyl, SMe, NH(CH2)2NH2, and piperidinyl.
Preferred R2 and R3 groups include halogen, CN, CO2R6, OR6, and R6. Examples of preferred R3 groups include Br, F, Cl, COOH, CN, OMe, methyl, ethyl, t-butyl, CF3, OH, and OBn.
Examples of preferred R5 include CO2(aliphatic), C(═NH)—NH2, and CON(R7)2 such as CO(piperidin-1-yl), CONHEt, CONHMe, CONH(cyclopropyl), CONH (isopropyl), CONH(propyl), CONH(pyrrolidinyl), CO2Et, and CO2Me.
Preferred compounds of formulae IIIa and IIIb include those having one or more, or most preferably all, of the features selected from the group consisting of:
    • (a) R2 and R3 are each independently selected from halogen, CN, CO2R6, OR6, or R6;
    • (b) R5 is CO2R, COAr, COR, CON(R7)2, Ar, (CH2)yCO2R, or (CH2)yN(R7)2; and
    • (c) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, N(R)TnCO2R6, N(R)TnNRCO2R6, N(R)TnN(R6)2, NO2, Tn(haloalkyl), CO2N(R6)2, COR6, SO2R6, or SO2N(R6)2.
More preferred compounds of formula IIIa and IIIb include those having one or more, or most preferably all, of the features selected from the group consisting of:
    • (a) R2 is hydrogen, alkoxy, aminoalkyl, or halogen;
    • (b) R3 is hydrogen, alkoxy, aralkoxy, or halogen;
    • (c) R4 is hydrogen or (CH2)yR2;
    • (d) R5 is CON(R7)2, Ar, (CH2)yCO2R, or (CH2)yN(R7)2; and
    • (e) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, or N(R)TnCO2R6.
The compounds of this invention may be prepared in general by methods known to those skilled in the art for analogous compounds, as illustrated by the general Schemes I through VII shown below. The details of the conditions used for preparing these compounds are set forth in the Examples.
Figure USRE040245-20080415-C00234
Reagents and conditions: (a) Ar-boronic acid, PdCl2(dppf), K3PO4, DMF, 95° C., 18 hours; (b) 40 psi H2, 10% Pd/C, EtOAc; (c) ROCOCl, NaOH, H2O, 0° C.; (d) p-TsOH, ROH, reflux, 1 hour.
The compounds 2 are prepared by treating a solution of 4-bromo-2-nitroaniline (1) in DMF with an arylboronic acid (1.2 equivalents), potassium phosphate (1.3 equivalents), and dichloro-(diphenylphosphinoferrocene)palladium (0.1 equivalent). The resulting mixture is heated at 95° C. for 18 hours then cooled to room temperature and diluted with ethyl acetate. The crude product is isolated by aqueous work-up then concentrated in vacuo. The concentrate is purified by silica gel chromatography to afford 2. A wide variety of substitutions on the aryl ring are amenable to this reaction. Examples of suitable substituted and unsubstituted aryl groups include, but are not limited to, those set forth in Table 1 above.
Compound 3 is prepared by treating a solution of 2 in ethyl acetate with 10% palladium on carbon (0.1 g/mmol) and the resulting suspension hydrogenated at 40 psi while shaking at ambient temperature for 2 hours. The catalyst is removed by filtration and the filtrate concentrated in vacuo to afford 3.
Compounds of formula 5 are prepared by first preparing a solution of 2-methyl-2-thiopseudourea (4, 1 equivalent) and alkylchloroformate (2 equivalents) in water at 0° C. To this solution is added 25% aqueous sodium hydroxide in a dropwise fashion over 1 hour until the pH stabilized at 8. Acetic acid is then added to achieve pH 5 then sodium acetate trihydrate (1 eauivalent) and a solution of 3 (1 equivalent) in ROH are added. p-Toluenesulfonic acid (catalytic amount) is added and the resulting mixture heated at reflux for 1 hour. The reaction mixture is then cooled to ambient temperature and diluted with ethyl acetate. After aqueous work-up, the crude product is purified by preparative HPLC to afford 5.
Figure USRE040245-20080415-C00235
Reagents and conditions: (a) bis(pinacolato)diboron, KOAc, PdCl2(dppf), DMSO, 80° C.; (b) ArBr, K3PO4, PdCl2(dppf), DMSO, 95° C;
Scheme II above shows an alternative method for preparing compound 2. Starting material 1 (1 equivalent) is combined with bis(pinacolato)diboron (1.2 equivalents), PdCl2 (dppf) (0.1 equivalent), and KOAc (3 equivalents) in DMSO, and the resulting mixture is heated at 80° C. for 18 hours. The reaction mixture is cooled to ambient temperature then the aryl bromide (1.1 equivalents) is added followed by the further addition of K3PO4 (3 equivalents) and PdCl2(dppf) (0.1 equivalent). The resulting mixture is heated at 95° C. for another 72 hours then allowed to cool to room temperature. Purification by chromatography affords compound 2.
Figure USRE040245-20080415-C00236
Reagents and conditions: (a) BrCN, THF, MeOH, water, room temperature; (b) EtNCO, THF, reflux.
Using the preparation of compound number Ia-84 to illustrate, Scheme III above shows the general method used for preparing compounds of formula IIa. Starting material 6 is prepared according to the method described in Scheme I at steps (a) and (b). Compound 7 is prepared by treating 6 with cyanogen bromide in acetonitrile at room temperature over night. Aqueous work-up affords 7. Compound Ia-84 is prepared from 7 by treating with ethyl isocyanate in THF at reflux over night. The crude product is purified by preparation chromatography to afford Ia-84.
Figure USRE040245-20080415-C00237
Reagents and conditions: (a) EtOH, 80° C., 4 hours; (b) PdCl2(dppf), K3PO4, 95° C., 48 hours; (c) Pd/C, H2, 50 psi, 6 hours; (d) 2-methyl-2-thiopseudourea (14), EtOCOCl, 80° C., 18 hours.
Using the preparation of compound number Ia-86 to illustrate, Scheme IV above shows a general method that may be used for preparing compounds of formula IIIa. Compound 10 is prepared from 5-bromo-2-chloropyrimidine (8) and N-Boc-ethylenediamine (9) by heating a mixture of 8 and 9 in ethanol at 80° C. for 4 hours. Compound 12 is prepared from 10 and 11 according to the method described in Scheme II. Compound 12 is used to prepare Ia-86 via steps (c) and (d) according to steps (b) and (c) of Scheme I.
Figure USRE040245-20080415-C00238
Reagents and conditions: (a) BrCN, THF, MeOH, water, room temperature; (b) EtOCOCl, pyridine.
Using the preparation of compound number Ib-1 to illustrate, Scheme V above shows a general method that may be used for preparing compounds of formula Ib. Compound 16 is prepared from 15 according to the method described in Scheme III, step (a). Compound Ib-1 is prepared by treating 16 with ethylchloroformate in pyridine.
Figure USRE040245-20080415-C00239
Reagents and conditions: (a) (b) EtNCO, THF, reflux.
Using the preparation of compound number Ib-3 to illustrate, Scheme VI above shows a general method that may be used for preparing compounds of formula IIb. Compound 16 is treated ethyl isocyanate in THF at reflux according to Scheme III step, (b) to afford Ib-3.
Figure USRE040245-20080415-C00240
Figure USRE040245-20080415-C00241
Reagents and conditions: (a) NaH, THF, 0° C.; (b) H2 (45 psi), Pd-C, MeOH; (c) BrCN, MeCN, MeOH, room temperature; (d) i EtNCO, DMSO, 80° C., ii NH3, MeOH, 80° C.
Scheme VII above shows a general method for preparing compounds of this invention wherein R1 is imidazol-1-yl. In step (a), dinitrofluorobenzene (17) is combined with methyl-4-imidazolecarboxylate (18) in THF and treated with sodium hydride at 0° C. After 3 hours, the reaction mixture is diluted with toluene and acidified with HCl. The phases are separated and the aqueous phase washed with toluene, cooled to 0° C., and basified with conc. NH4OH. Ethyl acetate is added and the resulting mixture stirred until all solids dissolved. The phases are separated and the organic phase washed with brine, dried over Na2SO4, then filtered and the filtrate concentrated in vacuo. The mixture of regioisomers are separated and purified via flash chromatography (silica gel, 5%→>20% ethanol/ethyl acetate gradient) to afford the desired adduct 19 as an off-white solid.
Compound 19 is used to prepare compounds Ia-156, Ia-157, and Ia-170 in a manner substantially similar to the methods described above for Scheme III.
A preferred embodiment of this invention relates to a method of treating a bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a compound having the formula IIa or IIb:
Figure USRE040245-20080415-C00242
or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
    • W is nitrogen or CRa;
    • Ra is selected from hydrogen, halogen, —CF3, R7, —OR7, or —N(R7)2;
    • R1 is an aryl or heteroaryl ring, wherein said ring is optionally substituted by up to four R9; wherein an R9 substituent in the ortho-position of R1 taken together with R2 may form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring having 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R2 and R3 are each independently selected from R6, halogen, CN, SR6, OR6, N(R6)2, NRCO2R6, NRCON (R6)2, CON(R6)2, NRCOR6, NRN(R6)2, COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2 or NRSO2R6; or R2 and R3 are taken together to form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R4 is selected from R6, CON(R6), COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or (CH2)yR2;
    • y is 1-6;
    • Ar is a five membered heteroaryl, heterocyclyl, or carbocyclyl ring, wherein said ring is optionally substituted by up to three substituents selected from oxo, halogen, CN, NO2, R8, OR8, NHR8, NHCOR8, NHCONHR8, COR8, CONHR8, SO2R8, NHSO2NHR8 or SO2NHR8;
    • each R6 is independently selected from R7 or an optionally substituted group selected from alkoxy, hydroxyalkyl, heterocyclyl, heterocyclcylalkyl, aryl, aralkyl, aralkoxy, aryloxyalkyl, heteroaryl, heteroaralkyl, heteroaralkoxy, or heteroarayloxyalkyl;
    • each R7 is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons, or two R7 on the same nitrogen taken together with the nitrogen optionally form a four to six member, saturated or unsaturated heterocyclic ring having one to three heteroatoms;
    • R8 is a C1-C4 aliphatic group, wherein two R8 on adjacent positions of Ar, or an aryl or heteroaryl ring, may be taken together with their intervening atoms to form a three to six membered fused ring;
    • each R9 is independently selected from oxo, halogen, CN, NO2, Tn(haloalkyl), R6, SR6, OR6, OR8, N(R6)2, CON (R6)2, CON(R)COR6, COR6, CO2R6, CO2N(R6)2, COCOR6, SO2R6, SO2N(R6)2, N(R)TnCO2R6, N(R) TnCON(R6)2, N(R)TnN(R6)2, N(R)TnNRCO2R6, N(R) TnNRCON(R6)2, N(R)TnCOR6, N(R)TnNRCOR6, N(R)TnSO2N(R6)2, N(R)TnSO2R6, TnPO(OR7)2, TnOPO(OR7)2, TnSP(OR7)2, TnPO(OR7)2, or TnNPO (OR7)2;
    • each Q is an independently selected C1-C3 branched or straight alkyl;
    • T is selected from —Q— or —Qm—CH(Qm—R2)—; and
    • each m and n are independently selected from zero or one.
Another preferred embodiment of this invention relates to a method of treating a bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a compound of formula IIIa or IIIb:
Figure USRE040245-20080415-C00243
or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
    • W is nitrogen or CRa;
    • Ra is selected from hydrogen, halogen, —CF3, R7, —OR7, or —N(R7)2;
    • Ring A is optionally substituted with up to three R9; wherein when an R9 substituent is in the ortho-position of Ring A, said R9 substituent may be taken together with R2 to form an optionally substituted 5-7 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R2 and R3 are each independently selected from R6, halogen, CN, SR6, OR6, N(R6)2, NRCO2R6, NRCON (R6)2, CON(R6)2, NRCOR6, NRN(R6)2, COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or NRSO2R6; or R2 and R3 are taken together to form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R4 is selected from R6, CON(R6), COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or (CH2)yR2;
    • y is 1-6;
    • R5 is selected from R7, Ar, COAr, CON(R7)Ar, (CH2)yCO2R, (CH2)yN(R7)2, C(═NR10)—N(R7)2, C(═NR10)—NRCOR, C(═S)—N(R7)2, CON(R7)2, COR, SO2R, or SO2N(R7)2;
    • Ar is a five membered heteroaryl, heterocyclyl, or carbocyclyl ring, wherein said ring is optionally substituted by up to three substituents selected from oxo, halogen, CN, NO2, R8, OR8, NHR8, NHCOR8, NHCONHR8, COR8, CONHR8, SO2R8, NHSO2NHR8 or SO2NHR8;
    • each R6 is independently selected from R7 or an optionally substituted group selected from alkoxy, hydroxyalkyl, heterocyclyl, heterocyclcylalkyl, aryl, aralkyl, aralkoxy, aryloxyalkyl, heteroaryl, heteroaralkyl, heteroaralkoxy, or heteroarayloxyalkyl;
    • each R7 is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons, or two R7 on the same nitrogen taken together with the nitrogen optionally form a four to six member, saturated or unsaturated heterocyclic ring having one to three heteroatoms;
    • R8 is a C1-C4 aliphatic group, wherein two R8 on adjacent positions of Ar, or an aryl or heteroaryl ring, may be taken together with their intervening atoms to form a three to six membered fused ring;
    • each R9 is independently selected from oxo, halogen, CN, NO2, Tn(haloalkyl), R6, SR6, OR6, OR8, N(R6)2, CON (R6)2, CON(R)COR6, COR6, CO2R6, CO2N(R6)2, COCOR6, SO2R6, SO2N(R6)2, N(R)TnCO2R6, N(R) TnCON(R6)2, N(R)TnN(R6)2, N(R)TnNRCO2R6, N(R) TnNRCON(R6)2, N(R)TnCOR6, N(R)TnNRCOR6, N(R)TnSO2N(R6)2, N(R)TnSO2R6, TnPO(OR7)2, TnOPO(OR7)2, TnSP(OR7)2, TnPO(OR7)2, or TnNPO (OR7)2;
    • each Q is an independently selected C1-C3 branched or straight alkyl;
    • T is selected from —Q— or —Qm—CH(Qm—R2)—;
    • each m and n are independently selected from zero or one;
    • and R10 is selected from R7 or Ar.
According to another embodiment, the invention provides a method of decreasing bacterial quantity in a biological sample. This method comprises the step of contacting said biological sample with a compound of formula I:
Figure USRE040245-20080415-C00244
or a pharmaceutically acceptable derivative or prodrug thereof, wherein:
    • Z is O or N—R4;
    • W is nitrogen or CRa;
    • Ra is selected from hydrogen, halogen, —CF3, R7, —OR7, or —N(R7)2;
    • R1 is an aryl or heteroaryl ring, wherein said ring is optionally substituted by up to four R9; wherein an R9 substituent in the ortho-position of R1 taken together with R2 may form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring having 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R2 and R3 are each independently selected from R6, halogen, CN, SR6, OR6, N(R6)2, NRCO2R6, NRCON (R6)2, CON(R6)2, NRCOR6, NRN(R6)2, COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or NRSO2R6; or R2 and R3 are taken together to form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
    • R4 is selected from R6, CON(R6), COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or (CH2)yR2;
    • y is 1-6;
    • R5 is selected from R7, Ar, COAr, CON(R7)Ar, (CH2)yCO2R, (CH2)yN(R7)2, C(═NR10)—N(R7)2, C(═NR10)—NRCOR, C(═S)—N(R7)2, CON(R7)2, COR, SO2R, or SO2N(R7)2;
    • Ar is a five membered heteroaryl, heterocyclyl, or carbocyclyl ring, wherein said ring is optionally substituted by up to three substituents selected from oxo, halogen, CN, NO2, R8, OR8, NHR8, NHCOR8, NHCONHR8, COR8, CONHR8, SO2R8, NHSO2NHR8 or SO2NHR8;
    • each R6 is independently selected from R7 or an optionally substituted group selected from alkoxy, hydroxylalkyl, heterocyclyl, heterocyclcylalkyl, aryl, aralkyl, aralkoxy, aryloxyalkyl, heteroaryl, heteroaralkyl, heteroaralkoxy, or heteroarayloxyalkyl;
    • each R7 is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons, or two R7 on the same nitrogen taken together with the nitrogen optionally form a four to six member, saturated or unsaturated heterocyclic ring having one to three heteroatoms;
    • R8 is a C1-C4 aliphatic group, wherein two R8 on adjacent positions of Ar, or an aryl or heteroaryl ring, may be taken together with their intervening atoms to form a three to six membered fused ring;
    • each R9 is independently selected from oxo, halogen, CN, NO2, Tn(haloalkyl), R6, SR6, OR6, OR8, N(R6)2, CON (R6)2, CON(R)COR6, COR6, CO2R6, CO2N(R6)2, COCOR6, SO2R6, SO2N(R6)2, N(R)TnCO2R6, N(R) TnCON(R6)2, N(R)TnN(R6)2, N(R)TnNRCO2R6, N(R) TnNRCON(R6)2, N(R)TnCOR6, N(R)TnNRCOR6, N(R)TnSO2N(R6)2, N(R)TnSO2R6, TnPO(OR7)2, TnOP(OR7)2, TnSP(OR7)2, TnPO(OR7)2, or TnNPO (OR7)2;
    • each Q is an independently selected C1-C3 branched or straight alkyl;
    • T is selected from —Q— or —Qm—CH(Qm—R2)—;
    • each m and n are independently selected from zero or one;
    • and R10 is selected from R7 or Ar.
The term “biological sample”, as used herein, includes cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof. The term “biological sample” also includes living organisms, in which case “contacting a compound of this invention with a biological sample” is synonymous with the term “administrating said compound for composition comprising said compound) to a mammal”.
A preferred embodiment comprises contacting said biological sample with a compound of formula Ia, Ib, IIa, IIb, IIIa, IIIb, or a compound listed in either of Tables 1 and 2. Pharmaceutical compositions useful for such methods are described below.
The compounds of this invention are potent inhibitors of gyrase as determined by enzymatic assay. These compounds have also been shown to have antimicrobial activity in an antimicrobial susceptibility assay. The details of the conditions used for both the enzymatic and the antimicrobial susceptibility assays are set forth in the Examples below.
The gyrase inhibitors of this invention, or pharmaceutical salts thereof, may be formulated into pharmaceutical compositions for administration to animals or humans. These pharmaceutical compositions effective to treat or prevent a bacterial infection which comprise the gyrase inhibitor in an amount sufficient to measurably decrease bacterial quantity and a pharmaceutically acceptable carrier, are another embodiment of the present invention. The term “measurably decrease bacterial quantity”, as used herein means a measurable change in the number of bacteria between a sample containing said inhibitor and a sample containing only bacteria.
Agents which increase the susceptibility of bacterial organisms to antibiotics are known. For example, U.S. Pat. No. 5,523,288, U.S. Pat. No. 5,783,561 and U.S. Pat. No. 6,140,306 describe methods of using bactericidal/permeability-increasing protein (BPI) for increasing antibiotic susceptibility of gram-positive and gram-negative bacteria. Agents that increase the permeability of the outer membrane of bacterial organisms have been described by Vaara, M. in Microbiological Reviews (1992) pp. 395-411, and the sensitization of gram-negative bacteria has been described by Tsubery, H., et al, in J. Med. Chem. (2000) pp. 3085-3092.
Another preferred embodiment of this invention relates to a method, as described above, of treating a bacterial infection in a mammal in need thereof, but further comprising the step of administering to said mammal an agent which increases the susceptibility of bacterial organisms to antbiotics.
According to another preferred embodiment, the invention provides a method, as described above, of decreasing bacterial quantity in a biological sample, but further comprising the step of contacting said biological sample with an agent which increases the susceptibility of bacterial organisms to antibiotics.
The pharmaceutical compositions and methods of this invention will be useful generally for controlling bacterial infections in vivo. Examples of bacterial organisms that may be controlled by the compositions and methods of this invention include, but are not limited to the following organisms: Streptococcus pneumoniae, Streptococcus pyrogenes, Enterococcus fecalis, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sps. Proteus sps. Pseudomonas aeruginosa, E. coli, Serratia marcesens, Staphylococcus aureus, Coag. Neg. Staph, Haemophilus infuenzae, Bacillus anthracis, Mycoplasma pneumoniae, and Staphylococcus epidermitidis. The compositions and methods will therefore be useful for controlling, treating or reducing the advancement, severity or effects of nosocomial or non-nosocomial infections. Examples of nosocomial uses include, but are not limited to, urinary tract infections, pneumonia, surgical wound infections, and bacteremia. Examples of non-nosocomial uses include but are not limited to urinary tract infections, pneumonia, prostatitis, skin and soft tissue infections, intra-abdominal infections, and therapy for febrile neutropenic patients.
In addition to the compounds of this invention, pharmaceutically acceptable derivatives or prodrugs of the compounds of this invention may also be employed in compositions to treat or prevent the above-identified disorders.
A “pharmaceutically acceptable derivative or prodrug” means any pharmaceutically acceptable salt, ester, salt of an ester or other derivative of a compound of this invention which, upon administration to a recipient, is capable of providing, either directly or indirectly, a compound of this invention or an inhibitorily active metabolite or residue thereof. Particularly favored derivatives or prodrugs are those that increase the bioavailability of the compounds of this invention when such compounds are administered to a mammal (e.g., by allowing an orally administered compound to be more readily absorbed into the blood) or which enhance delivery of the parent compound to a biological compartment (e.g., the brain or lymphatic system) relative to the parent species.
Pharmaceutically acceptable prodrugs of the compounds of this invention include, without limitation, esters, amino acid esters, phosphate esters, metal salts and sulfonate esters.
Pharmaceutically acceptable salts of the compounds of this invention include those derived from pharmaceutically acceptable inorganic and organic acids and bases. Examples of suitable acid salts include acetate, adipate, alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptanoate, glycerophosphate, glycolate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, lactate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, palmoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, salicylate, succinate, sulfate, tartrate, thiocyanate, tosylate and undecanoate. Other acids, such as oxalic, while not in themselves pharmaceutically acceptable, may be employed in the preparation of salts useful as intermediates in obtaining the compounds of the invention and their pharmaceutically acceptable acid addition salts.
Salts derived from appropriate bases include alkali metal (e.g., sodium and potassium), alkaline earth metal (e.g., magnesium), ammonium and N+(C1-4 alkyl)4 salts. This invention also envisions the quaternization of any basic nitrogen-containing groups of the compounds disclosed herein. Water or oil-soluble or dispersible products may be obtained by such quaternization.
Pharmaceutical compositions of this invention comprise a compound of formula I or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable carrier. Such compositions may optionally comprise an additional therapeutic agent. Such agents include, but are not limited to, an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant, an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound.
The term “pharmaceutically acceptable carrier” refers to a non-toxic carrier that may be administered to a patient, together with a compound of this invention, and which does not destroy the pharmacological activity thereof.
Pharmaceutically acceptable carriers that may be used in the pharmaceutical compositions of this invention include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, wool fat and self-emulsifying drug delivery systems (SEDDS) such as α-tocopherol, polyethyleneglycol 1000 succinate, or other similar polymeric delivery matrices.
The term “pharmaceutically effective amount” refers to an amount effective in treating or ameliorating a bacterial infection in a patient. The term “prophylactically effective amount” refers to an amount effective in preventing or substantially lessening a bacterial infection in a patient.
Depending upon the particular condition, or disease state, to be treated or prevented, additional therapeutic agents, which are normally administered to treat or prevent that condition, may be administered together with the inhibitors of this invention. Such therapeutic agents include, but are not limited to, an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant, an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound.
The compounds of this invention may be employed in a conventional manner for controlling bacterial infections levels in vivo and for treating diseases or reducing the advancement or severity of effects which are mediated by bacteria. Such methods of treatment, their dosage levels and requirements may be selected by those of ordinary skill in the art from available methods and techniques.
For example, a compound of this invention may be combined with a pharmaceutically acceptable adjuvant for administration to a patient suffering from a bacterial infection or disease in a pharmaceutically acceptable manner and in an amount effective to lessen the severity of that infection or disease.
Alternatively, the compounds of this invention may be used in compositions and methods for treating or protecting individuals against bacterial infections or diseases over extended periods of time. The compounds may be employed in such compositions either alone or together with other compounds of this invention in a manner consistent with the conventional utilization of enzyme inhibitors in pharmaceutical compositions. For example, a compound of this invention may be combined with pharmaceutically acceptable adjuvants conventionally employed in vaccines and administered in prophylactically effective amounts to protect individuals over an extended period of time against bacterial infections or diseases.
The compounds of formula I may also be co-administered with other antibiotics to increase the effect of therapy or prophylaxis against various bacterial infections. When the compounds of this invention are administered in combination therapies with other agents, they may be administered sequentially or concurrently to the patient. Alternatively, pharmaceutical or prophylactic compositions according to this invention comprise a combination of a compound of formula I and another therapeutic or prophylactic agent.
The additional therapeutic agents described above may be administered separately, as part of a multiple dosage regimen, from the inhibitor-containing composition. Alternatively, these agents may be part of a single dosage form, mixed together with the inhibitor in a single composition.
The pharmaceutical compositions of this invention may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir. The pharmaceutical compositions of this invention may contain any conventional non-toxic pharmaceutically-acceptable carriers, adjuvants or vehicles. In some cases, the pH of the formulation may be adjusted with pharmaceutically acceptable acids, bases or buffers to enhance the stability of the formulated compound or its delivery form. The term parenteral as used herein includes subcutaneous, intracutaneous, intravenous, intramuscular, intra-articular, intrasynovial, intrasternal, intrathecal, intralesional and intracranial injection or infusion techniques.
The pharmaceutical, compositions may be in the form of a sterile injectable preparation, for example, as a sterile injectable aqueous or oleaginous suspension. This suspension may be formulated according to techniques known in the art using suitable dispersing or wetting agents (such as, for example, Tween 80) and suspending agents. The sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are mannitol, water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil may be employed including synthetic mono- or diglycerides. Fatty acids, such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions. These oil solutions or suspensions may also contain a long-chain alcohol diluent or dispersant, such as those described in Pharmacopeia Helvetica, or a similar alcohol.
The pharmaceutical compositions of this invention may be orally administered in any orally acceptable dosage form including, but not limited to, capsules, tablets, and aqueous suspensions and solutions. In the case of tablets for oral use, carriers which are commonly used include lactose and corn starch. Lubricating agents, such as magnesium stearate, are also typically added. For oral administration in a capsule form, useful diluents include lactose and dried corn starch. When aqueous suspensions and solutions and propylene glycol are administered orally, the active ingredient is combined with emulsifying and suspending agents. If desired, certain sweetening and/or flavoring and/or coloring agents may be added.
The pharmaceutical compositions of this invention may also be administered in the form of suppositories for rectal administration. These compositions can be prepared by mixing a compound of this invention with a suitable non-irritating excipient which is solid at room temperature but liquid at the rectal temperature and therefore will melt in the rectum to release the active components. Such materials include, but are not limited to, cocoa butter, beeswax and polyethylene glycols.
Topical administration of the pharmaceutical compositions of this invention is especially useful when the desired treatment involves areas or organs readily accessible by topical application. For application topically to the skin, the pharmaceutical composition should be formulated with a suitable ointment containing the active components suspended or dissolved in a carrier. Carriers for topical administration of the compounds of this invention include, but are not limited to, mineral oil, liquid petroleum, white petroleum, propylene glycol, polyoxyethylene polyoxypropylene compound, emulsifying wax and water. Alternatively, the pharmaceutical composition can be formulated with a suitable lotion or cream containing the active compound suspended or dissolved in a carrier. Suitable carriers include, but are not limited to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol and water. The pharmaceutical compositions of this invention may also be topically applied to the lower intestinal tract by rectal suppository formulation or in a suitable enema formulation. Topically-administered transdermal patches are also included in this invention.
The pharmaceutical compositions of this invention may be administered by nasal aerosol or inhalation. Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and may be prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other solubilizing or dispersing agents known in the art.
Dosage levels of between about 0.01 and about 100 mg/kg body weight per day, preferably between 0.5 and about 75 mg/kg body weight per day and most preferably between about 1 and 50 mg/kg body weight per day of the active ingredient compound are useful in a monotherapy for the prevention and treatment of bacterial infections caused by bacteria such as Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus fecalis, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sps. Proteus sps. Pseudomonas aeruginosa, E. coli, Serratia marcesens, S. aureus, and Coag. Neg. Staph.
Typically, the pharmaceutical compositions of this invention will be administered from about 1 to 5 times per day or alternatively, as a continuous infusion. Or, alternatively, the compositions of the present invention may be administered in a pulsatile formulation. Such administration can be used as a chronic or acute therapy. The amount of active ingredient that may be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration. A typical preparation will contain from about 5% to about 95% active compound (w/w). Preferably, such preparations contain from about 20% to about 80% active compound.
When the compositions of this invention comprise a combination of a compound of formula I and one or more additional therapeutic or prophylactic agents, both the compound and the additional agent should be present at dosage levels of between about 10% to 80% of the dosage normally administered in a monotherapy regime.
Upon improvement of a patient's condition, a maintenance dose of a compound, composition or combination of this invention may be administered, if necessary. Subsequently, the dosage or frequency of administration, or both, may be reduced, as a function of the symptoms, to a level at which the improved condition is retained when the symptoms have been alleviated to the desired level, treatment should cease. Patients may, however, require intermittent treatment on a long-term basis upon any recurrence or disease symptoms.
As the skilled artisan will appreciate, lower or higher doses than those recited above may be required. Specific dosage and treatment regimens for any particular patient will depend upon a variety of factors, including the activity of the specific compound employed, the age, body weight, general health status, sex, diet, time of administration, rate of excretion, drug combination, the severity and course of the disease, and the patient's disposition to the disease and the judgment of the treating physician.
According to another embodiment, the invention provides methods for treating or preventing a bacterial infection, or disease state, comprising the step of administering to a patient any compound, pharmaceutical composition, or combination described herein. The term “patient”, as used herein, means an animal, preferably a mammal, and most preferably a human.
The compounds of this invention are also useful as commercial reagents which effectively bind to the gyrase B enzyme. As commercial reagents, the compounds of this invention, and their derivatives, may be used to block gyrase B activity in biochemical or cellular assays for bacterial gyrase B or its homologs or may be derivatized to bind to a stable resin as a tethered substrate for affinity chromatography applications. These and other uses which characterize commercial gyrase B inhibitors will be evident to those of ordinary skill in the art.
In order that this invention be more fully understood, the following examples are set forth. These examples are for the purpose of illustration only and are not to be construed as limiting the scope of the invention in any way.
EXAMPLES Example 1
Figure USRE040245-20080415-C00245
4-(Pyridin-3-yl)-2-nitroaniline (2): To a solution of 4-bromo-2-nitroaniline (217 mg, 1 mmol) in DMF (6 mL) was added 3-pyridine boronic acid (148 mg, 1.2 mmol), potassium phosphate (276 mg, 1.3 mmol), and dichloro(diphenylphosphinoferrocene)palladium (75 mg, 0.1 mmol).
The resulting mixture was heated at 95° C. for 18 hours then cooled to room temperature and diluted with ethyl acetate (80 mL). The resulting solution was washed successively with saturated aqueous sodium bicarbonate, water, and brine, dried over magnesium sulfate then concentrated in vacuo. The concentrate was purified by chromatography [Silica Gel, ethyl acetate: hexanes (1:3)→(1:2)] to afford compound 2 (117 mg, 54%). 1H NMR (CDCl3) δ 8.8 (d, 1H), 8.55 (m, 1H), 8.35 (d, 1H), 7.85 (dd, 1H), 7.65 (dd, 1H), 7.35 (m, 1H), 6.95 (d, 1H), 6.25 (br s, 2H).
Example 2
Figure USRE040245-20080415-C00246
4-Pyridin-3-yl-benzene-1,2-diamine (3): To a solution of compound 2 (117 mg, 0.54 mmol) in ethyl acetate (13 mL) was added 10% palladium on carbon (51 mg). The resulting suspension was placed in a Parr hydrogenation apparatus under 40 psi hydrogen gas while shaking at ambient temperature for 2 hours. The catalyst was removed by filtration and the filtrate concentrated in vacuo to afford compound 2 (115 mg, quantitative yield). 1H NMR (CDCl3) δ 8.8 (m, 1H), 8.45 (m, 1H), 7.75 (m, 1H), 7.25 (m, 1H), 6.95 (m, 2H), 6.80 (m, 1H), 3.25 (br s, 4H).
Example 3
Figure USRE040245-20080415-C00247
(5-Pyridin-3-yl-1H-benzoimidazol-2-yl)-carbamic acid ethyl ester (Ia-11): To a solution of 2-methyl-2-thiopseudourea (151 mg, 0.54 mmol) and ethylchloroformate (0.103 mL, 1.08 mmol) in water (2 mL) at 0° C. was added 25% aqueous sodium hydroxide in a dropwise fashion over 1 hour until the pH stabilized at 8. Enough acetic acid was then added to achieve pH 5 then sodium acetate trihydrate (74 mg, 0.54 mmol) and a solution of 2 (0.54 mmol) in ethanol (3 mL) were added. A catalytic amount of p-toluenesulfonic acid was added and the resulting mixture was heated at reflux for 1 hour. The reaction mixture was then cooled to ambient temperature and diluted with ethyl acetate (50 mL). The organic solution was washed with aqueous NaOH, water, and brine then dried over magnesium sulfate and concentrated in vacuo. The crude product was purified by preparative HPLC to afford compound Ia-11. 1H NMR (CDCl3) δ 9.1 (s, 1H), 8.75 (d, 1H), 8.5 (d, 1H), 7.9 (s, 1H), 7.8 (m, 1H), 7.65 (m, 2H), 4.3 (q, 2H), 1.3 (t, 3H). (M+1)283.
Example 4
Figure USRE040245-20080415-C00248
5-Phenyl-1H-benzoimidazol-2-ylamine (7): To a solution of biphenyl-3,4-diamine (0.99 mmol) in THF:MeOH:water (5 mL:10 mL:10 mL) was added cyanogen bromide (5M solution in acetonitrile, 1.06 mmol). The resulting mixture was stirred at room temperature overnight. The reaction was partitioned between EtOAc and aqueous sodium hydroxide and the aqueous layer re-extracted with EtOAc.
The combined EtOAc extracts were washed with water, brine, dried over MgSO2, then concentrated in vacuo to afford 7 (147 mg, 71%) as an off-white solid.
Example 5
Figure USRE040245-20080415-C00249
1-Ethyl-3-(5-phenyl-1H-benzoimidazol-2-yl)-urea (Ia-84): To a solution of 7 (40 mg, 0.19 mmol) in THF (1 mL) was added ethyl isocyanate (27 μL, 0.34 mmol) as a solution in THF (0.5 mL). The reaction was heated to reflux overnight then concentrated in vacuo. The crude product was purified by preparative HPLC to afford Ia-84.
Example 6
Figure USRE040245-20080415-C00250
[2-(5-Bromo-pyrimidin-2-ylamino)-ethyl]-carbamic acid tert-butyl ester (10): A mixture of 5-bromo-2-chloropyrimidine (500 mg), N-Boc-ethylenediamine (496 mg), and triethylamine (1 mL) in ethanol (10 mL) was heated at 80° C. for 4 hours. The reaction was then concentrated in vacuo and the residue purified by preparative HPLC (hexanes:EtOAc; 60:40) to afford compound 10 (700 mg) as a white solid.
Example 7
Figure USRE040245-20080415-C00251
1-(3,4-Dinitro-phenyl)-1H-imidazole-4-carboxylic acid methyl ester (19): To a stirred, 0° C. solution of 1,2-dinitro-4-fluorobenzene (325 mg, 1.74 mmole) and methyl-4-imidazolecarboxylate (200 mg, 1.59 mmole) in THF (5 mL) was added NaH (70 mg, 1.74 mmole) in one portion. The resulting mixture was stirred at 0° C. for 3 hours, then diluted with toluene and acidified with 6N HCl. The phases were separated and the aqueous phase washed with toluene, cooled to 0° C., and basified with conc. NH4OH. Ethyl acetate was added and the resulting mixture stirred until all solids dissolved. Phases separated, organic phase washed with brine, dried over Na2SO4, filtered, concentrated in vacuo. The mixture of regioisomers were separated and purified via flash chromatography (silica gel, 5%→>20% ethanol/ethyl acetate gradient) to fford the desired adduct 19 (225 mg, 48%) as an off-white solid. 1H NMR (500 MHz, dmso d6): 8.41 (1H, d); 8.13 (1H, d); 7.5 (1H, broad s); 7.28 (1H, s); 7.02 (1H, d); 3.80 (3H, s)
Example 8
Figure USRE040245-20080415-C00252
1-[2-(3-Ethyl-ureido)-3H-benzoimidazol-5-yl]-1H-imiazole-4-carboxylic acid methyl ester (Ia-156): A mixture of 19 (225 mg, 0.770 mmole) and 10% Pd-C. (catalytic amount) in MeOH (10 mL) was placed under 45 psi of H2 (Parr Shaker) overnight. The mixture was filtered, concentrated in vacuo, re-diluted with MeCN and MeOH (5 mL/5 mL), and treated with cyanogen bromide (168 mg, 1.54 mmole) at room temperature. The resulting mixture was stirred for 4 hours (precipitate formed), then quenched by the addition of 7N NH3-MeOH. The crude reaction was concentrated in vacuo and directly flash chromatographed (silica gel, 10%→>35% 7N NH3-MeOH/CH2Cl2 gradient) to give the pure aminobenzimidazole as a white solid.
The purified aminobenzimidazole was diluted in DMSO (1 mL), treated with excess ethyl-isocyanate (0.5 mL) and heated to 80° C. for 3 hours. The reaction was cooled to room temperature, excess ethyl isocyanate removed in vacuo, azeotroped with MeOH (thrice), diluted with MeOH (5 mL), treated with NH4OH (2 mL), and heated to 80° C. for 3 hours. The mixture was cooled to room temperature, concentrated in vacuo, diluted with 1/1 water/brine, and extracted twice with 4/1 ethyl acetate/ethanol. The combined organic extracts were dried over Na2SO4, filtered, concentrated in vacuo, and flash chromatographed (silica gel, 5%→>30% 2N NH3-EtOH/CH2Cl2 gradient) to give the desired produce la-156 contaminated with ethyl urea. The solid was triturated with water and filtered to give pure Ia-156 (115 mg, 41% over four steps) as a white solid. 1H NMR (500 MHz, dmso-d6): 11.81 (1H, br s); 9.94 (1H, br d); 8.32 (1H, br d); 8.26 (1H, br d); 7.58 (1H, br d); 7.48 (1H, m); 7.28 (1H, d); 7.12 (1H, br d); 3.78 (3H, s); 3.20 (2H, dq); 1.12 (3H, t).
Example 9
Figure USRE040245-20080415-C00253
1-[2-(3-Ethyl-ureido)-3H-benzoimidazol-5-yl]-1H-imiazole-4-carboxylic acid 1-[2-(Ethyl-ureido)-3H-benzoimidazol-5-yl]-1H-imizaole-4-carboxylic acid (Ia-157): A solution of Ia-156 (95 mg, 0.289 mmole) in 6N HCl (2 mL) was refluxed for 6 hours. The solution was then cooled to room temperature, concentrated in vacuo, and azeotroped sequentially with MeOH (twice) and acetone (twice). The resulting solids were suspended in acetone, filtered, and washed with acetone followed by hexanes to give Ia-157 (115 mg, 100%) as a white solid. 1H NMR (500 MHz, dmso-d6): 8.77 (1H, m); 8.52 (1H, m); 7.79 (1H, s); 7.72 (1H, m); 7.65 (2H, m); 5.6-4.0 (2H, br s); 3.20 (2H, dt); 1.11 (3H, t).
Example 10
Figure USRE040245-20080415-C00254
A solution of Ia-157 (20 mg, 0.051 mmole) and morpholine (0.050 mL, excess) in DMF (1 mL) was treated with PyBrop (20 mg, excess) at room temperature. The resulting mixture was stirred overnight, then diluted with 4:1 ethyl acetate:ethanol, washed with 1:1 brine:water (five times), dried over Na2SO4, filtered, and flash chromatographed (silica gel, 5%→>20% 2N NH3-EtOH/CH2Cl2 gradient) to give Ia-170 (13 mg, 72%) as a white solid. LRMS: 384.5 (M+H)
Example 11
We have prepared other compounds of formula I by methods substantially similar to those described in the above Examples 1-6 and those illustrated in Schemes I—VI. The characterization data for these compounds is summarized in Table 3 below and includes mass spectral (as M+1) and 1H NMR data.
1H NMR data is summarized in Table 3 below wherein “Y” designates 1H NMR data is available and was found to be consistant with structure. Compound numbers correspond to the compound numbers listed in Table 1.
TABLE 3
Characterization Data for Selected Compounds
No. Ia- M + 1 1H NMR
1 282 Y
2 288 Y
3 283 Y
4 283 Y
6 210 Y
7 268 Y
8 292 —
9 350 Y
10 296 Y
11 283 Y
12 325 Y
13 324 Y
14 336 Y
15 326 Y
16 344 Y
17 361 Y
18 313 Y
19 360 Y
20 399 Y
21 284 Y
22 314 Y
23 312 Y
24 215 Y
26 342 Y
33 249 Y
34 298 Y
35 356 Y
36 283 Y
37 428 Y
38 294 Y
39 272 Y
40 498 Y
41 452 Y
42 312 Y
43 295.1 Y
44 338 —
45 386 Y
46 320 Y
47 382 —
48 389 —
49 418 —
50 311 Y
51 299 Y
52 343 Y
53 368 Y
54 298 Y
55 395 Y
56 406 —
57 366 Y
58 296 Y
59 354 Y
60 326 Y
61 440 Y
62 300 Y
63 403 —
64 381 —
65 352 —
66 326 —
67 409 Y
69 468 Y
70 368 Y
71 299 Y
72 299 Y
73 267 —
74 253 —
75 297 —
76 413 Y
77 371 —
78 282 Y
79 296 Y
80 357 Y
81 340 Y
82 280 Y
84 281 Y
85 321 —
86 442 Y
87 370 Y
88 342 —
89 359 Y
90 298 Y
91 446 Y
92 329 —
93 499 Y
94 387 Y
97 294 Y
98 389 —
100 370 —
101 280 —
102 370 —
103 312 Y
106 409 —
108 300 Y
109 394 —
110 467 Y
111 367 Y
112 343 Y
113 409 —
115 298 Y
116 343 —
117 369 —
116 282 Y
119 296 Y
120 296 Y
121 322 Y
122 340 Y
124 445 —
125 382 —
126 328 Y
127 394 —
128 432 —
129 368 —
130 396 Y
131 316 Y
132 312 Y
133 296 Y
134 316 Y
135 410 Y
136 300 Y
137 310 Y
138 388 —
139 352 Y
140 401 Y
141 384 Y
142 310 Y
143 511 Y
144 311 Y
145 353 —
146 400 Y
147 326 Y
148 411 Y
149 370 Y
150 — —
151 — —
152 317 Y
153 362 Y
154 389 Y
155 299 —
156 — —
157 — —
158 — —
159 328 —
160 — —
161 — —
162 — —
163 326 Y
164 367 Y
165 297 Y
166 367 Y
167 350 —
168 298 Y
169 — Y
170 — —
171 — —
172 — —
173 — —
174 — —
175 365 Y
176 — Y
177 — —
178 — Y
179 367 Y
180 — Y
181 315 Y
182 366 Y
183 330 Y
184 — —
185 — —
186 — —
187 — —
188 — —
Example 12
Gyrase ATPase Assay
The ATP hydrolysis activity of DNA gyrase was measure by coupling the production of ADP through pyruvate kinase/lactate dehydrogenase to the oxidation of NADH. This method has been described previously (Tamura and Gellert, 1990, J. Biol. Chem., 265, 21342).
ATPase assays are carried out at 30° C. in buffered solutions containing 100 mM TRIS pH 7.6, 1.5 mM MgCl2, 50 mM KCl. The coupling system contains (final concentrations) 2.5 mM phosphoenol pyruvate, 200 μM nicotinamide adenine dinucleotide (NADH), 1 mM DTT, 30 ug pyruvate kinase, and 10 ug/ml lactate dehydrogenase. 40 nanomolar enzyme (374 kDa Gyr A2B2 subunit from Staphylococcus aureus) and a DMSO solution of the inhibitor to a final concentration of 4% are added and the reaction mixture is allowed to incubate for 10 minutes at 30° C. The reaction is then started by the addition of ATP to a final concentration of 0.9 mM and the rate of NADH disappearance at 340 nanometers is measured over the course of 10 minutes. The percent inhibition values are determined from rate versus concentration profiles and are reported as the average of duplicate values.
Table 4 shows the results of the percent inhibition activity of selected compounds of this invention in the Gyrase inhibition assay at 10 μM concentration. The compound numbers correspond to the compound numbers in Table 1. Compounds having an activity designated as “A” provided a percent inhibition value below 50 percent; compounds having an activity designated as “B” provided a percent inhibition value between 50 and 75 percent; and compounds having an activity designated as “C” provided a percent inhibition value greater than 75 percent.
TABLE 4
Gyrase Inhibitory Activity of Selected Compounds
No. Ia- Activity
 1 B
 2 B
 3 B
 4 C
 6 A
 7 A
 8 A
 9 A
 10 A
 11 C
 12 B
 13 A
 14 B
 15 B
 16 C
 17 C
 18 C
 19 C
 20 A
 21 C
 22 C
 23 C
 24 C
 26 B
 33 A
 34 C
 35 C
 36 A
 37 C
 38 B
 39 C
 40 C
 41 A
 42 C
 43 C
 44 C
 45 C
 46 A
 47 C
 48 C
 49 C
 50 B
 52 C
 53 C
 54 C
 55 C
 56 C
 57 C
 58 C
 59 C
 60 C
 61 C
 62 C
 63 C
 64 C
 65 C
 66 C
 67 C
 69 B
 70 C
 71 A
 72 C
 73 A
 74 A
 75 A
 76 C
 77 C
 78 A
 79 A
 80 C
 81 B
 82 A
 84 C
 85 A
 86 C
 87 C
 88 C
 89 C
 90 C
 91 A
 92 C
 93 C
 94 C
 97 A
 98 C
100 C
101 A
102 C
103 C
106 C
108 C
109 C
110 C
111 C
112 C
113 C
115 A
116 B
117 A
118 C
119 C
120 B
121 A
122 C
124 B
125 C
126 C
127 C
128 C
129 C
130 C
131 C
132 C
133 C
134 C
135 C
136 C
137 C
138 C
139 C
140 C
141 C
142 C
143 C
144 C
145 C
146 C
147 B
148 C
149 C
150 B
151 C
152 C
153 B
154 C
155 A
156 C
157 C
158 C
159 A
160 C
161 A
162 C
163 C
164 C
165 C
166 C
167 C
168 C
169 C
170 C
171 C
172 C
173 C
174 C
175 C
176 A
177 C
178 C
179 C
180 C
181 B
182 C
183 B
184 B
185 C
186 C
187 C
188 C
— —
Example 13
Susceptibility Testing in Liquid Media
Compounds of this invention were also tested for antimicrobial activity by susceptibility testing in liquid media. Such assays were performed within the guidelines of the latest NCCLS document governing such practices: “M7-A5 Methods for dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically; Approved Standard—Fifth Edition (2000)”. Other publications such as “Antibiotics in Laboratory Medicine” (Edited by V. Lorian, Publishers Williams and Wilkins, 1996) provide essential practical techniques in laboratory antibiotic testing. Essentially several discrete bacterial colonies (3 to 7) from a freshly streaked plate were transferred to an appropriate rich broth medium such as MHB, supplemented where appropriate for the more fastidious organisms. This was grown overnight to high density followed by a 1 or 2-thousand-fold dilution to give an inoculation density of between 5×105 and 5×106 CFU per mL. Alternatively, the freshly picked colonies can be incubated at 37° C. for about 4 to 8 hrs until the culture equals or exceeds a turbidity of a 0.5 McFarland standard (approximately 1.5×108 cells per mL) and diluted to give the same CFU per mL as above. In a more convenient method, the inoculum was prepared using a commercially available mechanical device (the BBL PROMPT System) that involves touching five colonies directly with a wand, containing crosshatch grooves at its bottom, followed by suspension of the bacteria in an appropriate volume of saline. Dilution to the appropriate inoculum cell density was made from this cell suspension. The broth used for testing consists of MHB supplemented with 50 mg per L of Ca2+ and 25 mg per L of Mg2+. Standard dilution panels of control antibiotics were made and stored as in the NCCLS standard M7-A5, the dilution range typically being in the 128 μg per mL to 0.015 μg per mL (by 2-fold serial dilution). The test compounds were dissolved and diluted fresh for experimentation on the same day; the same or similar ranges of concentration as above being used. The test compounds and controls were dispensed into a multiwell plate and test bacteria added such that the final inoculation was approximately 5×104 CFU per well and the final volume was 100 μL. The plates were incubated at 35° C. overnight (16 to 20 hr) and checked by eye for turbidity or quantitated with a multiwell plate reader. The endpoint minimal inhibitory concentration (MIC) is the lowest concentration of drug at which the microorganism tested does not grow. Such determinations were also compared to the appropriate tables contained in the above two publications to ensure that the range of antibacterial activity is within the acceptable range for this standardized assay.
Table 5 shows the results of the MIC assay for selected compounds of this invention. The compound numbers correspond respond to the compound numbers in Table 1. Compounds having an activity level designated as “A” provided an MIC of less than 10 μg/mL; compounds having an activity level designated as “B” provided an MIC of between 10 and 40 μg/mL; compounds having an activity level designated as “C” provided an MIC of greater than 40 μg/mL.
TABLE 5
MIC Values of Selected Compounds
No. Ia- Activity
 42 B
 58 A
 90 A
 92 A
 98 B
112 A
116 C
117 C
118 A
119 C
120 C
121 C
122 C
133 A
137 C
138 C
139 C
140 A
141 A
142 A
144 B
145 B
146 A
147 C
148 B
149 C
150 C
151 C
152 B
153 C
154 C
156 B
157 C
158 C
159 C
160 C
161 C
162 C
163 A
164 C
165 B
166 C
167 C
168 A
169 B
170 C
171 B
173 B
174 C
175 C
177 C
178 A
179 C
180 B
181 C
182 C
183 C
184 C
185 C
186 A
187 B
188 A
196 B
197 B
198 B
— —
While we have described a number of embodiments of this invention, it is apparent that our basic constructions may be altered to provide other embodiments which utilize the products and processes of this invention.

Claims (26)

1. A compound of formula IIa or IIb:
Figure USRE040245-20080415-C00255
or a pharmaceutically acceptable salt thereof, wherein:
W is nitrogen or CRa;
Ra is selected from hydrogen, halogen, —CF3, R7, —OR7, or —N(R7)2;
R1 is an aryl or heteroaryl ring, wherein said ring is optionally substituted by up to four R9; wherein an R9 substituent in the ortho-position of R1 taken together with R2 may form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring having 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
R2 and R3 are each independently selected from R6, halogen, CN, SR6, OR6, N(R6)2, NRCO2R6, NRCON (R6)2, CON(R6)2, NRCOR6, NRN(R6)2, COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or NRSO2R6; or R2 and R3 are taken together to form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
R4 is selected from R6, CON(R6), COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or (CH2)yR2;
y is 1-6;
each R is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons;
Ar is a five membered heteroaryl, heterocyclyl, or carbocyclyl ring, wherein said ring is optionally substituted by up to three substituents selected from oxo, halogen, CN, NO2, R8, OR8, NHR8, NHCOR8, NHCONHR8, COR8, CONHR8, SO2R8, NHSO2NHR8 or SO2NHR8;
each R6 is independently selected from R7 or an optionally substituted group selected from alkoxy, hydroxyalkyl, heterocyclyl, heterocyclcylalkyl heterocyclylalkyl, aryl, aralkyl, aralkoxy, aryloxyalkyl, heteroaryl, heteroaralkyl, heteroaralkoxy, or heteroarayloxyalkyl heteroaryloxyalkyl;
each R7 is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons, or two R7 on the same nitrogen taken together with the nitrogen optionally form a four to six member, saturated or unsaturated heterocyclic ring having one to three heteroatoms;
R8 is a C1-C4 aliphatic group, wherein two R8 on adjacent positions of Ar, or an aryl or heteroaryl ring, may be taken together with their intervening atoms to form a three to six membered fused ring ;
each R9 is independently selected from oxo, halogen, CN, NO2, Tn(haloalkyl), R6, SR6, OR6, OR8, N(R6)2, CON (R6)2, CON(R)COR6, COR6, CO2R6, CO2N(R6)2, COCOR6, SO2R6, SO2N(R6)2, N(R)TnCO2R6, N(R) TnCON(R6)2, N(R)TnN(R6)2, N(R)TnNRCO2R6, N(R) TnNRCON(R6)2, N(R)TnCOR6, N(R)TNNRCOR6 N(R)T n NRCOR 6, N(R)TnSO2N(R6)2, N(R)TnSO2R6, TnPO(OR7)2, TnOPO(OR7)2, TnSP(OR7)2, TnPO(OR7)2, or TnNPO (OR7)2;
each Q is an independently selected C1-C3 branched or straight alkyl;
T is selected from —Q— or —Qm—CH(Qm—R2)—; and
each m and n are independently selected from zero or one.
2. The compound according to claim 1, wherein said compound has one or more features selected from the group consisting of:
(a) R1 is an optionally substituted aryl or heteroaryl ring;
(b) R2 and R3 are each independently selected from halogen, CN, CO2R6, OR6, or R6; and
(c) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, N(R)TnCO2R6, N(R)TnNRCO2R6, N(R)TnN(R6)2, NO2, Tn(haloalkyl), CO2N(R6)2, COR6, SO2R6, or SO2N(R6)2.
3. The compound according to claim 2, wherein:
(a) R1 is an optionally substituted aryl or heteroaryl ring;
(b) R2 and R3 are each independently selected from halogen, CN, CO2R6, OR6, or R6; and
(c) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, N(R)TnCO2R6, N(R)TnNRCO2R6, N(R)TnN(R6)2, NO2, Tn(haloalkyl), CO2N(R6)2, COR6, SO2R6, or SO2N(R6)2.
4. The compound according to claim 2, wherein said compound has one or more features selected from the group consisting of:
(a) R1 is an optionally substituted ring selected from phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, thienyl, pyrimidyl, imidazol-1-yl, imidazol-2-yl, pyrazol-1-yl, amino-pyrimidinyl, quinolinyl, aminobenzimidazole, or indolyl;
(b) R2 is hydrogen, alkoxy, aminoalkyl, or halogen;
(c) R3 is hydrogen, alkoxy, aralkoxy, or halogen;
(d) R4 is hydrogen or (CH2)yR2; and
(e) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, or N(R)TnCO2R6.
5. The compound according to claim 4, wherein:
(a) R1 is an optionally substituted ring selected from phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, thienyl, pyrimidyl, imidazol-1-yl, imidazol-2-yl, pyrazol-1-yl, amino-pyrimidinyl, quinolinyl, aminobenzimidazole, or indolyl;
(b) R2 is hydrogen, alkoxy, aminoalkyl, or halogen;
(c) R3 is hydrogen, alkoxy, aralkoxy, or halogen;
(d) R4 is hydrogen or (CH2)yR2; and
(e) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, or N(R)TnCO2R6.
6. A compound of formula IIIa or IIIb:
Figure USRE040245-20080415-C00256
or a pharmaceutically acceptable salt thereof, wherein:
W is nitrogen or CRa;
Ra is selected from hydrogen, halogen, —CF3, R7, —OR7, or —N(R7)2;
Ring A is optionally substituted with up to three R9; wherein when an R9 substituent is in the ortho-position of Ring A, said R9 substituent may be taken together with R2 to form an optionally substituted 5-7 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
R2 and R3 are each independently selected from R6, halogen, CN, SR6, OR6, N(R6)2, NRCO2R6, NRCON (R6)2, CON(R6)2, NRCOR6, NRN(R6)2, COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or NRSO2R6; or R2 and R3 are taken together to form a fused, unsaturated or partially unsaturated, optionally substituted 5-8 membered ring containing 0-2 ring heteroatoms selected from nitrogen, oxygen, or sulfur;
R4 is selected from R6, CON(R6), COR6, CO2R6, COCOR6, SO2R6, SO2N(R6)2, or (CH2)yR2;
y is 1-6;
R5 is selected from R7, Ar, COAr, CON(R7)Ar, CO2 R, (CH2)yCO2R, (CH2)yN(R7)2, C(═NR10)—N(R7)2, C(═NR10)—NRCOR, C(═S)—N(R7)2, CON(R7)2, COR, SO2R, or SO2N(R7)2;
Ar is a five membered heteroaryl, heterocyclyl, or carbocyclyl ring, wherein said ring is optionally substituted by up to three substituents selected from oxo, halogen, CN, NO2, R8, OR8, NHR8, NHCOR8, NHCONHR8, COR8, CONHR8, SO2R8, NHSO2NHR8 or SO2NHR8;
each R is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons;
each R6 is independently selected from R7 or an optionally substituted group selected from alkoxy, hydroxyalkyl, heterocyclyl, heterocyclcylalkyl heterocyclylalkyl, aryl, aralkyl, aralkoxy, aryloxyalkyl, heteroaryl, heteroaralkyl, heteroaralkoxy, or heteroarayloxyalkyl heteroaryloxyalkyl;
each R7 is independently selected from hydrogen or an optionally substituted aliphatic group having one to six carbons, or two R7 on the same nitrogen taken together with the nitrogen optionally form a four to six member, saturated or unsaturated heterocyclic ring having one to three heteroatoms;
R8 is a C1-C4 aliphatic group, wherein two R8 on adjacent positions of Ar, or an aryl or heteroaryl ring, may be taken together with their intervening atoms to form a three to six membered fused ring;
each R9 is independently selected from oxo, halogen, CN, NO2, Tn(haloalkyl), R6, SR6, OR6, OR8, N(R6)2, CON (R6)2, CON(R)COR6, COR6, CO2R6, CO2N(R6)2, COCOR6, SO2R6, SO2N(R6)2, N(R)TnCO2R6, N(R) TnCON(R6)2, N(R)TnN(R6)2, N(R)TnNRCO2R6, N(R) TnNRCON(R6)2, N(R)TnCOR6, N(R)TnNRCOR6, N(R)TnSO2N(R6)2, N(R)TnSO2R6, TnPO(OR7)2, TnOPO(OR7)2, TnSP(OR 7)2 Tn SP(OR 7)2, TnPO(OR7)2, or TnNPO (OR7)2;
each Q is an independently selected C1-C3 branched or straight alkyl;
T is selected from —Q— or —Qm—CH(Qm—R2)—;
each m and n are independently selected from zero or one; and R10 is selected from R7 or Ar.
7. The compound according to claim 6, wherein said compound has one or more features selected from the group consisting of:
(a) R2 and R3 are each independently selected from halogen, CN, CO2R6, OR6, or R6;
(b) R5 is CO2R, COAr, COR, CON(R7)2, Ar, (CH2)yCO2R, or (CH2)yN(R7)2; and
(c) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, N(R)TnCO2R6, N(R)TnNRCO2R6, N(R)TnN(R6)2, NO2, Tn(haloalkyl), CO2N(R6)2, COR6, SO2R6, or SO2N(R6)2.
8. The compound according to claim 7, wherein:
(a) R2 and R3 are each independently selected from halogen, CN, CO2R6, OR6, or R6;
(b) R5 is CO2R, COAr, COR, CON(R7)2, Ar, (CH2)CO2R, or (CH2)yN(R7)2; and
(c) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, N(R)TnCO2R6, N(R)TnNRCO2R6, N(R)TnN(R6)2, NO2, Tn(haloalkyl), CO2N(R6)2, COR6, SO2R6, or SO2N(R6)2.
9. The compound according to claim 7, wherein said compound has one or more features selected from the group consisting of:
(a) R2 is hydrogen, alkoxy, aminoalkyl, or halogen;
(b) R3 is hydrogen, alkoxy, aralkoxy, or halogen;
(c) R4 is hydrogen or (CH2)yR2;
(d) R5 is CON(R7)2, Ar, (CH2)yCO2R, or (CH2)yN(R7)2; and
(e) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, or N(R)TnCO2R6.
10. The compound according to claim 9, wherein:
(a) R2 is hydrogen, alkoxy, aminoalkyl, or halogen;
(b) R3 is hydrogen, alkoxy, aralkoxy, or halogen;
(c) R4 is hydrogen or (CH2)yR2;
(d) R5 is CON(R7)2, Ar, (CH2)yCO2R, or (CH2)yN(R7)2; and
(e) R9 is halogen, CN, oxo, R6, SR6, OR6, N(R6)2, CON(R6)2, CO2R6, CON(R)COR6, or N(R)TnCO2R6.
11. A compound selected from the group consisting of:
No. Ia- Structure 20
Figure USRE040245-20080415-C00257
 21
Figure USRE040245-20080415-C00258
 22
Figure USRE040245-20080415-C00259
 25
Figure USRE040245-20080415-C00260
 28
Figure USRE040245-20080415-C00261
 29
Figure USRE040245-20080415-C00262
 33
Figure USRE040245-20080415-C00263
 35
Figure USRE040245-20080415-C00264
 37
Figure USRE040245-20080415-C00265
 38
Figure USRE040245-20080415-C00266
 39
Figure USRE040245-20080415-C00267
 40
Figure USRE040245-20080415-C00268
 — — 42
Figure USRE040245-20080415-C00269
 43
Figure USRE040245-20080415-C00270
 44
Figure USRE040245-20080415-C00271
 45
Figure USRE040245-20080415-C00272
 46
Figure USRE040245-20080415-C00273
 47
Figure USRE040245-20080415-C00274
 48
Figure USRE040245-20080415-C00275
 49
Figure USRE040245-20080415-C00276
 50
Figure USRE040245-20080415-C00277
 51
Figure USRE040245-20080415-C00278
 52
Figure USRE040245-20080415-C00279
 53
Figure USRE040245-20080415-C00280
 54
Figure USRE040245-20080415-C00281
 55
Figure USRE040245-20080415-C00282
 56
Figure USRE040245-20080415-C00283
 57
Figure USRE040245-20080415-C00284
 58
Figure USRE040245-20080415-C00285
 59
Figure USRE040245-20080415-C00286
 60
Figure USRE040245-20080415-C00287
 61
Figure USRE040245-20080415-C00288
 62
Figure USRE040245-20080415-C00289
 63
Figure USRE040245-20080415-C00290
 64
Figure USRE040245-20080415-C00291
 65
Figure USRE040245-20080415-C00292
 66
Figure USRE040245-20080415-C00293
 68
Figure USRE040245-20080415-C00294
 69
Figure USRE040245-20080415-C00295
 70
Figure USRE040245-20080415-C00296
 72
Figure USRE040245-20080415-C00297
 76
Figure USRE040245-20080415-C00298
 77
Figure USRE040245-20080415-C00299
 80
Figure USRE040245-20080415-C00300
 83
Figure USRE040245-20080415-C00301
 84
Figure USRE040245-20080415-C00302
 86
Figure USRE040245-20080415-C00303
 88
Figure USRE040245-20080415-C00304
 89
Figure USRE040245-20080415-C00305
 91
Figure USRE040245-20080415-C00306
 92
Figure USRE040245-20080415-C00307
 93
Figure USRE040245-20080415-C00308
 94
Figure USRE040245-20080415-C00309
 98
Figure USRE040245-20080415-C00310
 99
Figure USRE040245-20080415-C00311
 100
Figure USRE040245-20080415-C00312
 102
Figure USRE040245-20080415-C00313
 103
Figure USRE040245-20080415-C00314
 104
Figure USRE040245-20080415-C00315
 105
Figure USRE040245-20080415-C00316
 106
Figure USRE040245-20080415-C00317
 107
Figure USRE040245-20080415-C00318
 108
Figure USRE040245-20080415-C00319
 109
Figure USRE040245-20080415-C00320
 110
Figure USRE040245-20080415-C00321
 111
Figure USRE040245-20080415-C00322
 112
Figure USRE040245-20080415-C00323
 113
Figure USRE040245-20080415-C00324
 116
Figure USRE040245-20080415-C00325
 117
Figure USRE040245-20080415-C00326
 118
Figure USRE040245-20080415-C00327
 119
Figure USRE040245-20080415-C00328
 120
Figure USRE040245-20080415-C00329
 121
Figure USRE040245-20080415-C00330
 — — 123
Figure USRE040245-20080415-C00331
 124
Figure USRE040245-20080415-C00332
 125
Figure USRE040245-20080415-C00333
 126
Figure USRE040245-20080415-C00334
 127
Figure USRE040245-20080415-C00335
 128
Figure USRE040245-20080415-C00336
 129
Figure USRE040245-20080415-C00337
 130
Figure USRE040245-20080415-C00338
 131
Figure USRE040245-20080415-C00339
 132
Figure USRE040245-20080415-C00340
 133
Figure USRE040245-20080415-C00341
 134
Figure USRE040245-20080415-C00342
 135
Figure USRE040245-20080415-C00343
 136
Figure USRE040245-20080415-C00344
 137
Figure USRE040245-20080415-C00345
 138
Figure USRE040245-20080415-C00346
 139
Figure USRE040245-20080415-C00347
 140
Figure USRE040245-20080415-C00348
 141
Figure USRE040245-20080415-C00349
 142
Figure USRE040245-20080415-C00350
 143
Figure USRE040245-20080415-C00351
 144
Figure USRE040245-20080415-C00352
 145
Figure USRE040245-20080415-C00353
 146
Figure USRE040245-20080415-C00354
 147
Figure USRE040245-20080415-C00355
 148
Figure USRE040245-20080415-C00356
 149
Figure USRE040245-20080415-C00357
 150
Figure USRE040245-20080415-C00358
 151
Figure USRE040245-20080415-C00359
 152
Figure USRE040245-20080415-C00360
 153
Figure USRE040245-20080415-C00361
 154
Figure USRE040245-20080415-C00362
 155
Figure USRE040245-20080415-C00363
 156
Figure USRE040245-20080415-C00364
 157
Figure USRE040245-20080415-C00365
 158
Figure USRE040245-20080415-C00366
 159
Figure USRE040245-20080415-C00367
 160
Figure USRE040245-20080415-C00368
 161
Figure USRE040245-20080415-C00369
 162
Figure USRE040245-20080415-C00370
 163
Figure USRE040245-20080415-C00371
 164
Figure USRE040245-20080415-C00372
 165
Figure USRE040245-20080415-C00373
 166
Figure USRE040245-20080415-C00374
 167
Figure USRE040245-20080415-C00375
 168
Figure USRE040245-20080415-C00376
 169
Figure USRE040245-20080415-C00377
 170
Figure USRE040245-20080415-C00378
 171
Figure USRE040245-20080415-C00379
 172
Figure USRE040245-20080415-C00380
 173
Figure USRE040245-20080415-C00381
 174
Figure USRE040245-20080415-C00382
 175
Figure USRE040245-20080415-C00383
 176
Figure USRE040245-20080415-C00384
 177
Figure USRE040245-20080415-C00385
 178
Figure USRE040245-20080415-C00386
 179
Figure USRE040245-20080415-C00387
 180
Figure USRE040245-20080415-C00388
 181
Figure USRE040245-20080415-C00389
 182
Figure USRE040245-20080415-C00390
 183
Figure USRE040245-20080415-C00391
 184
Figure USRE040245-20080415-C00392
 185
Figure USRE040245-20080415-C00393
 186
Figure USRE040245-20080415-C00394
 187
Figure USRE040245-20080415-C00395
 188
Figure USRE040245-20080415-C00396
 189
Figure USRE040245-20080415-C00397
 190
Figure USRE040245-20080415-C00398
 191
Figure USRE040245-20080415-C00399
 192
Figure USRE040245-20080415-C00400
 193
Figure USRE040245-20080415-C00401
 194
Figure USRE040245-20080415-C00402
 195
Figure USRE040245-20080415-C00403
 196
Figure USRE040245-20080415-C00404
 197
Figure USRE040245-20080415-C00405
 198
Figure USRE040245-20080415-C00406
 199
Figure USRE040245-20080415-C00407
 and 200
Figure USRE040245-20080415-C00408
12. A compound selected from the group consisting of:
No. Ib- Structure 3
Figure USRE040245-20080415-C00409
 4
Figure USRE040245-20080415-C00410
 5
Figure USRE040245-20080415-C00411
 6
Figure USRE040245-20080415-C00412
 7
Figure USRE040245-20080415-C00413
 8
Figure USRE040245-20080415-C00414
 9
Figure USRE040245-20080415-C00415
 10
Figure USRE040245-20080415-C00416
 11
Figure USRE040245-20080415-C00417
 12
Figure USRE040245-20080415-C00418
 13
Figure USRE040245-20080415-C00419
 14
Figure USRE040245-20080415-C00420
 15
Figure USRE040245-20080415-C00421
 16
Figure USRE040245-20080415-C00422
 17
Figure USRE040245-20080415-C00423
 20
Figure USRE040245-20080415-C00424
 21
Figure USRE040245-20080415-C00425
 22
Figure USRE040245-20080415-C00426
 23
Figure USRE040245-20080415-C00427
 24
Figure USRE040245-20080415-C00428
 25
Figure USRE040245-20080415-C00429
 26
Figure USRE040245-20080415-C00430
 27
Figure USRE040245-20080415-C00431
 and 28
Figure USRE040245-20080415-C00432
13. A composition comprising an effective amount of a compound according to any one of claims 1 to 10 1- 2, 4, 6 - 7 and 9 , and a pharmaceutically acceptable carrier.
14. A composition according to claim 13, wherein said compound is formulated in a pharmaceutically acceptable manner for administration to a patient.
15. The composition according to claim 13 further comprising an additional therapeutic agent selected from an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant, an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound.
16. The composition according to claim 14 further comprising an additional therapeutic agent selected from an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant, an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound.
17. The composition according to claim 13 further comprising an agent that increases the susceptibility of bacterial organisms to antibiotics.
18. The composition according to claim 15 further comprising an agent that increases the susceptibility of bacterial organisms to antibiotics.
19. A method of decreasing Staphylococcus aureus, E. faecalis, or S. pneumoniae bacterial quantity in a biological sample comprising the step of contacting said biological sample with a compound according to either of claims 1 or 6.
20. The method according to claim 19 further comprising the step of contacting said biological sample with an agent which increases the susceptibility of bacterial organisms to antibiotics.
21. A method of inhibiting gyrase Staphylococcus aureus, E. faecalis, or S. pneumoniae in a mammal, comprising the step of administering to said mammal a composition according to claim 13.
22. A method of treating a Staphylococcus aureus, E. faecalis, or an S. pneumoniae bacterial infection in a mammal in need thereof, comprising the step of administering to said mammal a therapeutically effective amount of a composition according to claim 13.
23. The method according to claim 22, wherein the bacterial infection to be treated is characterized by the presence of one or more of the following: Streptococcus pneumoniae, Streptococcus pyrogenes, Enterococcus fecalis, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sps. Proteus sps. Pseudomonas aeruginosa, E. coli, Serratia marcesens, S. aureus, or Coag. Neg. Staph.
24. The method according to claim 22, wherein the bacterial infection to be treated is selected from one or more of the following: urinary tract infections, pneumonia, prostatitis skin, and soft tissue infections, intra-abdominal infections, or infections of febrile neutropenic patients.
25. The method according to claim 22 further comprising the step of administering to said patient an antibiotic, an anti-inflammatory agent, a matrix metalloprotease inhibitor, a lipoxygenase inhibitor, a cytokine antagonist, an immunosuppressant, an anti-cancer agent, an anti-viral agent, a cytokine, a growth factor, an immunomodulator, a prostaglandin or an anti-vascular hyperproliferation compound, either as part of a multiple dosage form together with said compound or as a separate dosage form.
26. The method according to claim 22 further comprising the step of administering to said patient an agent that increases the susceptibility of bacterial organisms to antibiotics.
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