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US20130045962A1 - Peptide deformylase inhibitors - Google Patents

Peptide deformylase inhibitors Download PDF

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Publication number
US20130045962A1
US20130045962A1 US12/741,641 US74164108A US2013045962A1 US 20130045962 A1 US20130045962 A1 US 20130045962A1 US 74164108 A US74164108 A US 74164108A US 2013045962 A1 US2013045962 A1 US 2013045962A1
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Prior art keywords
fluoro
hydrazino
pyrimidinyl
oxopropyl
cyclopentylmethyl
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Inventor
Donghui Qin
Beth Norton
Xiangmin Liao
Andrew Nicholson Knox
Jinhwa Lee
Yuhong Fang
Jason Christopher Dreabit
Siegfried Benjamin Christensen, IV
Andrew B. Benowitz
Kelly M. Aubart
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GlaxoSmithKline LLC
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GlaxoSmithKline LLC
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Application filed by GlaxoSmithKline LLC filed Critical GlaxoSmithKline LLC
Priority to US12/741,641 priority Critical patent/US20130045962A1/en
Assigned to SMITHKLINE BEECHAM CORPORATION reassignment SMITHKLINE BEECHAM CORPORATION ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CHRISTENSEN, SIEGFRIED BENJAMIN, IV, BENOWITZ, ANDREW B, AUBART, KELLY M, DREABIT, JASON CHRISTOPHER, FANG, YUHONG, KNOX, ANDREW NICHOLSON, LIAO, XIANGMIN, QIN, DONGHUI, NORTON, BETH, LEE, JINHWA
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    • C07D239/28—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, directly attached to ring carbon atoms
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    • C07D239/24—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members
    • C07D239/28—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, directly attached to ring carbon atoms
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    • C07D401/04—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings directly linked by a ring-member-to-ring-member bond
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    • C07D401/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a chain containing hetero atoms as chain links
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    • C07D417/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
    • C07D417/04—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings directly linked by a ring-member-to-ring-member bond
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    • C07D417/12—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
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    • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
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    • C07D491/12—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains three hetero rings
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    • C07D498/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
    • C07D498/04—Ortho-condensed systems

Definitions

  • the present invention relates to certain ⁇ 2-(alkyl)-3-[2-(5-fluoro-4-pyrimidinyl)hydrazino]-3-oxopropyl ⁇ hydroxyformamide compounds, compositions containing them, the use of such compounds in the inhibition of bacterial peptide deformylase (PDF) activity, and in the treatment of bacterial infections.
  • PDF bacterial peptide deformylase
  • Peptide deformylase PDF is a metalloenzyme that removes the N-formyl group of the polypeptides as they emerge from the ribosome during the elongation process [Adams, J. M. (1968) J. Mol. Biol. 33, 571-589; Livingston, D. M. and Leder, P. (1969) Biochemistry 8, 435-443; Ball, L. A. and Kaesberg, P.
  • MAP methionine amino peptidase
  • PDF is ubiquitous in bacteria, with at least one pdf gene present in all bacterial genomes sequenced to date.
  • PDF does not play a role in eukaryotic cytoplasmic protein synthesis which does not involve N-formylation, but nuclear-encoded PDF proteins, containing a chloroplast/mitochondria localization signal, have been identified in parasites, plants and mammals, including humans.
  • PDF is essential in plant and parasite organelles since their genomes encode for a number of proteins which require deformylation for activity, but there is evidence to suggest that this is not the case in animals.
  • characterization of human mitochondrial PDF has shown that it is much less active than its bacterial counterpart.
  • PDF inhibitors which are active against the human PDF enzyme in vitro have no effect on the growth of normal human cell lines [Nguyen, K. T., Hu, X., Colton, C., Chakrabarti, R., Zhu, M. X. and Pei, D. (2003) Biochemistry 42, 9952-9958].
  • PDF inhibitors represent a promising new class of antibacterial agents with a novel mode of action covering a broad-spectrum of pathogens.
  • the present invention is directed to certain ⁇ 2-(alkyl)-3-[2-(5-fluoro-4-pyrimidinyl)hydrazino]-3-oxopropyl ⁇ hydroxyformamide derivatives, compositions containing them, the use of such compounds in the inhibition of bacterial peptide deformylase (PDF) activity, and in the treatment of bacterial infections.
  • PDF bacterial peptide deformylase
  • the invention is directed to compounds of Formula (I):
  • R1, R2 and R3 are defined below and to pharmaceutically acceptable salts thereof.
  • the compounds of this invention are bacterial peptide deformylase inhibitors and can be useful in the treatment of bacterial infections.
  • FIG. 1 provides a FT-IR spectrum of polymorphic Form 1 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is in cm ⁇ 1 and the y-axis is absorbance.
  • FIG. 2 provides a FT-IR spectrum of polymorphic Form 2 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is in cm ⁇ 1 and the y-axis is absorbance.
  • FIG. 3 provides a FT-Raman spectrum of polymorphic Form 1 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is in cm ⁇ 1 and the y-axis is intensity.
  • FIG. 4 provides a FT-Raman spectrum of polymorphic Form 2 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is in cm ⁇ 1 and the y-axis is intensity.
  • FIG. 5 provides a FT-Raman spectrum of polymorphic Form 3 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is in cm ⁇ 1 and the y-axis is intensity.
  • FIG. 6 provides an X-ray powder diffraction pattern of polymorphic Form 1 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is in degrees 2 theta and the y-axis is intensity.
  • FIG. 7 provides an X-ray powder diffraction pattern of polymorphic Form 2 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is in degrees 2 theta and the y-axis is intensity.
  • FIG. 8 provides an X-ray powder diffraction pattern of polymorphic Form 3 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is in degrees 2 theta and the y-axis is intensity.
  • FIG. 9 provides a differential scanning calorimitry (DSC) thermogram of polymorphic Form 1 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is temperature (° C.) and the y-axis is heat flow (Watts/gram).
  • the thermal event at 132° C. corresponds to exothermic solid state form conversion of Form 1 to Form 3.
  • FIG. 10 provides a differential scanning calorimitry (DSC) thermogram of polymorphic Form 2 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is temperature (° C.) and the y-axis is heat flow (Watts/gram).
  • FIG. 11 provides a differential scanning calorimitry (DSC) thermogram of polymorphic Form 3 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is temperature (° C.) and the y-axis is heat flow (Watts/gram).
  • FIG. 12 provides a thermogravimetric analysis (TGA) trace of polymorphic Form 1 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is temperature (° C.) and the y-axis is percent weight change.
  • FIG. 13 provides a thermogravimetric analysis (TGA) trace of polymorphic Form 2 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is temperature (° C.) and the y-axis is percent weight change.
  • FIG. 14 provides a thermogravimetric analysis (TGA) trace of polymorphic Form 3 of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide.
  • the x-axis is temperature (° C.) and the y-axis is percent weight change.
  • g grams; mg (milligrams); kg (kilograms); ⁇ g (micrograms); L (liters); mL (milliliters); ⁇ L (microliters); psi (pounds per square inch); M (molar); mM (millimolar); ⁇ M (micromolar); nM (nanomolar); ⁇ M (picomolar); nm (nanometers); mm (millimeters); wt (weight); N (Normal); CFU (colony forming units); I.V.
  • HEPES (4-(2-hydroxyethyl)-1-piperazine ethane sulfonic acid); DPPA (diphenylphosphoryl azide); fHNO 3 (fuming HNO 3 ); EDTA (ethylenediaminetetraacetic acid); TMEDA (N,N,N′,N′-tetramethyl-1,2-ethanediamine); NBS (N-bromosuccinimide); dppf (1,1′-bis(diphenylphosphino)ferrocene); and NIS (N-iodsuccinimide).
  • Alkyl refers to a monovalent saturated hydrocarbon chain having the specified number of member carbon atoms.
  • C1-C7 alkyl refers to an alkyl group having from 1 to 7 member carbon atoms.
  • Alkyl groups may be optionally substituted with one or more substituents as defined herein.
  • Alkyl groups may be straight or branched. Representative branched alkyl groups have one, two, or three branches.
  • Alkyl includes methyl, ethyl, propyl (n-propyl and isopropyl), butyl (n-butyl, isobutyl, and t-butyl), pentyl (n-pentyl, isopentyl, and neopentyl), and hexyl.
  • Alkenyl refers to an unsaturated hydrocarbon chain having the specified number of member carbon atoms and having one or more carbon-carbon double bonds within the chain.
  • C2-C6 alkenyl refers to an alkenyl group having from 2 to 6 member carbon atoms.
  • alkenyl groups have one carbon-carbon double bond within the chain.
  • alkenyl groups have more than one carbon-carbon double bond within the chain.
  • Alkenyl groups may be optionally substituted with one or more substituents as defined herein.
  • Alkenyl groups may be straight or branched. Representative branched alkenyl groups have one, two, or three branches.
  • Alkenyl includes ethylenyl, propenyl, butenyl, pentenyl, and hexenyl.
  • Alkoxy refers to an alkyl moiety attached through an oxygen bridge (i.e. a O—C1-C6 alkyl group wherein C1-C6 is defined herein). Examples of such groups include methoxy, ethoxy, propoxy, butoxy, pentoxy and hexoxy.
  • Alkynyl refers to an unsaturated hydrocarbon chain having the specified number of member carbon atoms and having one or more carbon-carbon triple bonds within the chain.
  • C2-C6 alkynyl refers to an alkynyl group having from 2 to 6 member atoms.
  • alkynyl groups have one carbon-carbon triple bond within the chain.
  • alkynyl groups have more than one carbon-carbon triple bond within the chain.
  • unsaturated hydrocarbon chains having one or more carbon-carbon triple bond within the chain and one or more carbon-carbon double bond within the chain are referred to as alkynyl groups.
  • Alkynyl groups may be optionally substituted with one or more substituents as defined herein.
  • Representative branched alkynyl groups have one, two, or three branches.
  • Alkynyl includes ethynyl, propynyl, butynyl, pentynyl, and hexynyl.
  • Aryl refers to an aromatic hydrocarbon ring system.
  • Aryl groups are monocyclic ring systems or bicyclic ring systems.
  • Monocyclic aryl ring refers to phenyl.
  • Bicyclic aryl rings refer to napthyl and to rings wherein phenyl is fused to a cycloalkyl or cycloalkenyl ring having 5, 6, or 7 member carbon atoms.
  • Aryl groups may be optionally substituted with one or more substituents as defined herein.
  • Cycloalkyl refers to a saturated hydrocarbon ring having the specified number of member carbon atoms. Cycloalkyl groups are monocyclic ring systems. For example, C3-C6 cycloalkyl refers to a cycloalkyl group having from 3 to 6 member atoms. Cycloalkyl groups may be optionally substituted with one or more substituents as defined herein. Cycloalkyl includes cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
  • Cycloalkenyl refers to an unsaturated hydrocarbon ring having the specified number of member carbon atoms and having a carbon-carbon double bond within the ring.
  • C3-C6 cycloalkenyl refers to a cycloalkenyl group having from 3 to 6 member carbon atoms.
  • cycloalkenyl groups have one carbon-carbon double bond within the ring.
  • cycloalkenyl groups have more than one carbon-carbon double bonds within the ring.
  • Cycloalkenyl rings are not aromatic. Cycloalkenyl groups are monocyclic ring systems. Cycloalkenyl groups may be optionally substituted with one or more substituents as defined herein. Cycloalkenyl includes cyclopropenyl, cyclobutenyl, cyclopentenyl, cyclohexenyl, and cyclohexadienyl.
  • Enantiomeric excess or “ee” is the excess of one enantiomer over the other expressed as a percentage. As a result, since both enantiomers are present in equal amounts in a racemic mixture, the enantiomeric excess is zero (0% ee). However, if one enantiomer was enriched such that it constitutes 95% of the product, then the enantiomeric excess would be 90% ee (the amount of the enriched enantiomer, 95%, minus the amount of the other enantiomer, 5%).
  • Enantiomerically enriched refers to products whose enantiomeric excess is greater than zero.
  • enantiomerically enriched refers to products whose enantiomeric excess is greater than 50% ee, greater than 75% ee, or greater than 90% ee.
  • Enantiomerically pure refers to products whose enantiomeric excess is 99% ee or greater.
  • Halo refers to the halogen radicals fluoro, chloro, bromo, and iodo.
  • Haloalkyl refers to an alkyl group wherein at least one hydrogen atom attached to a member atom within the alkyl group is replaced with halo.
  • the number of halo substituents include but are not limited to 1, 2, 3, 4, 5, or 6 substituents.
  • Haloalkyl includes monofluoromethyl, difluoroethyl, and trifluoromethyl.
  • Heteroaryl refers to an aromatic ring containing from 1 to 5, suitably 1 to 4, more suitably 1 or 2 heteroatoms as member atoms in the ring. Heteroaryl groups containing more than one heteroatom may contain different heteroatoms. Heteroaryl groups may be optionally substituted with one or more substituents as defined herein. Heteroaryl groups are monocyclic ring systems, or are fused bicyclic ring systems. Monocyclic heteroaryl rings have from 5 to 6 member atoms. Bicyclic heteroaryl rings have from 8 to 10 member atoms.
  • Bicyclic heteroaryl rings include those rings wherein the primary heteroaryl and the secondary monocyclic cycloalkyl, cycloalkenyl, heterocycloalkyl, aryl or heteroaryl ring are attached, forming a fused bicyclic ring system.
  • Heteroaryl includes, among others, pyrrolyl, pyrazolyl, imidazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, furanyl, furazanyl, thienyl, triazolyl, pyridinyl, pyrimidinyl, pyridazinyl, pyrazinyl, triazinyl, tetrazinyl, tetrazolyl, indolyl, isoindolyl, indolizinyl, indazolyl, purinyl, quinolinyl, isoquinolinyl, quinoxalinyl, quinazolinyl, pteridinyl, cinnolinyl, benzimidazolyl, benzopyranyl, benzoxazolyl, benzisoxazolyl, benzofurany
  • Heteroatom refers to a nitrogen, sulfur, or oxygen atom.
  • Heterocycloalkyl refers to a saturated or unsaturated ring containing from 1 to 4 heteroatoms as member atoms in the ring. Heterocycloalkyl rings are not aromatic.
  • Heterocycloalkyl groups containing more than one heteroatom may contain different heteroatoms. Heterocycloalkyl groups may be optionally substituted with one or more substituents as defined herein. Heterocycloalkyl groups are monocyclic ring systems or are fused, spiro, or bridged bicyclic ring systems. Monocyclic heterocycloalkyl rings have from 4 to 7 member atoms. Bicyclic heterocycloalkyl rings have from 7 to 11 member atoms. In certain embodiments, heterocycloalkyl is saturated. In other embodiments, heterocycloalkyl is unsaturated, but not aromatic.
  • Heterocycloalkyl includes, among others, pyrrolidinyl, tetrahydrofuranyl, dihydrofuranyl, pyranyl, tetrahydropyranyl, dihydropyranyl, tetrahydrothienyl, pyrazolidinyl, oxazolidinyl, thiazolidinyl, piperidinyl, homopiperidinyl, piperazinyl, morpholinyl, thiamorpholinyl, 1-pyrazolidinyl, azepinyl, 1,3-dioxanyl, 1,4-dioxanyl, 1,3-oxathiolanyl, 1,3-dithianyl, azetidinyl, isoxazolidinyl, 3-azabicyclo[3.1.0]hexyl, azabicylo[3.2.1]octyl, azabicylo[3.3.1]nonyl, azabicylo
  • Member atoms refers to the atom or atoms that form a chain or ring. Where more than one member atom is present in a chain and within a ring, each member atom is covalently bound to an adjacent member atom in the chain or ring. Atoms that make up a substituent group on a chain or ring are not member atoms in the chain or ring.
  • Optionally substituted indicates that a group, such as alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heterocycloalkyl, or heteroaryl, may be unsubstituted, or the group may be substituted with one or more substituents as defined herein.
  • “Pharmaceutically acceptable” refers to those compounds, materials, compositions, and dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings or animals without excessive toxicity, irritation, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
  • “Substituted” in reference to a group indicates that one or more hydrogen atoms attached to a member atom within the group is replaced with a substituent selected from the group of defined substituents. It should be understood that the term “substituted” includes the implicit provision that such substitution be in accordance with the permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound (i.e. one that does not spontaneously undergo transformation such as by hydrolysis, rearrangement, cyclization, or elimination, and that is sufficiently robust to survive isolation from a reaction mixture). When it is stated that a group may contain one or more substituents, one or more (as appropriate) member atom within the group may be substituted. In addition, a single member atom within the group may be substituted with more than one substituent as long as such substitution is in accordance with the permitted valence of the atom. Suitable substituents are defined herein for each substituted or optionally substituted group.
  • “Sulfanyl” refers to an alkyl moiety attached through a sulphur bridge (i.e —S—C1-C6 alkyl group wherein C1-C6 alkyl is as defined herein). Examples of sulfanyl groups include thiomethyl and thioethyl.
  • the present invention is directed to compounds according to Formula I:
  • R1 is selected from the group consisting of C2-C7 alkyl and —(CH 2 ) n —C3-C6 cycloalkyl
  • R2 is selected from the group consisting of C1-C3 alkyl; cyclopropyl; C1-C3 alkoxy; C1-C3 haloalkyl; C1-C3 sulfanyl; 5-membered heteroaryl; 5-membered heterocycloalkyl; halo; hydroxymethyl; and NRaRb
  • R3 is selected from the group consisting of —NR4R5; halo; phenyl, optionally substituted by one to three R6 groups; and heteroaryl, optionally substituted by one to three R6 groups
  • R4 is selected from the group consisting of H; C1-C6 alkyl, optionally substituted with one or two R7 groups; C1-C6 alkoxy; C3-C6 cycloalkyl, optionally substituted with one to three
  • the compounds according to Formula I may contain one or more asymmetric centers (also referred to as a chiral center) and may, therefore, exist as individual enantiomers, diastereomers, or other stereoisomeric forms, or as mixtures thereof.
  • Chiral centers such as chiral carbon atoms, may also be present in a substituent such as an alkyl group.
  • the stereochemistry of a chiral center present in Formula I, or in any chemical structure illustrated herein, is not specified, the structure is intended to encompass all individual stereoisomers and all mixtures thereof.
  • compounds according to Formula I containing one or more chiral centers may be used as racemic mixtures, diastereomeric mixtures, enantiomerically enriched mixtures, diastereomerically enriched mixtures, or as enantiomerically and diastereomerically pure individual stereoisomers.
  • Individual stereoisomers of a compound according to Formula I which contain one or more asymmetric centers may be resolved by methods known to those skilled in the art. For example, such resolution may be carried out (1) by formation of diastereoisomeric salts, complexes or other derivatives; (2) by selective reaction with a stereoisomer-specific reagent, for example by enzymatic oxidation or reduction; or (3) by gas-liquid or liquid chromatography in a chiral environment, for example, on a chiral support such as silica with a bound chiral ligand or in the presence of a chiral solvent.
  • stereoisomers may be synthesized by asymmetric synthesis using optically active reagents, substrates, catalysts or solvents, or by converting one enantiomer to the other by asymmetric transformation.
  • the compounds according to Formula I may also contain double bonds or other centers of geometric asymmetry. Where the stereochemistry of a center of geometric asymmetry present in Formula I, or in any chemical structure illustrated herein, is not specified, the structure is intended to encompass the trans (E) geometric isomer, the cis (Z) geometric isomer, and all mixtures thereof. Likewise, all tautomeric forms are also included in Formula I whether such tautomers exist in equilibrium or predominately in one form.
  • compounds according to Formula I may contain an acidic functional group. In certain other embodiments, compounds according to Formula I may contain a basic functional group.
  • salts of the compounds according to Formula I may be prepared. Indeed, in certain embodiments of the invention, salts of the compounds according to Formula I may be preferred over the respective free base or free acid because, for example, such salts may impart greater stability or solubility to the molecule thereby facilitating formulation into a dosage form. Accordingly, the invention is further directed pharmaceutically acceptable salts of the compounds according to Formula I.
  • suitable salts see Berge et al, J. Pharm. Sci., 1977, 66, 1-19.
  • Acid salts are formed from acids which form non-toxic salts and examples are hydrochloride, hydrobromide, hydroiodide, sulphate, bisulphate, nitrate, phosphate, hydrogen phosphate, acetate, maleate, malate, fumarate, malonate, lactate, tartrate, citrate, formate, gluconate, succinate, piruvate, oxalate, oxaloacetate, trifluoroacetate, saccharate, benzoate, methanesulphonate, ethanesulphonate, benzenesulphonate, p-toluenesulphonate, methanesulphonic, ethanesulphonic, p-toluenesulphonic, and isethionate.
  • Base salts include ammonium salts, alkali metal salts such as those of sodium and potassium, alkaline earth metal salts such as those of calcium and magnesium and salts with organic bases, including salts of primary, secondary and tertiary amines, such as isopropylamine, diethylamine, ethanolamine, trimethylamine, dicyclohexyl amine and N-methyl-D-glucamine.
  • pharmaceutically acceptable salts refers to salts that retain the desired biological activity of the subject compound and exhibit minimal undesired toxicological effects. These pharmaceutically acceptable salts may be prepared in situ during the final isolation and purification of the compound, or by separately reacting the purified compound in its free acid or free base form with a suitable base or acid, respectively.
  • the term “compounds of the invention” means both the compounds according to Formula I and salts thereof, including pharmaceutically acceptable salts.
  • the term “a compound of the invention” also appears herein and refers to both a compound according to Formula I and its salts, including pharmaceutically acceptable salts.
  • the compounds of the invention may exist in solid or liquid form. In the solid state, the compounds of the invention may exist in crystalline or noncrystalline form, or as a mixture thereof.
  • pharmaceutically-acceptable solvates may be formed wherein solvent molecules are incorporated into the crystalline lattice during crystallization. Solvates may involve nonaqueous solvents such as ethanol, isopropanol, DMSO, acetic acid, ethanolamine, and ethyl acetate, or they may involve water as the solvent that is incorporated into the crystalline lattice.
  • Hydrates wherein water is the solvent that is incorporated into the crystalline lattice are typically referred to as “hydrates.” Hydrates include stoichiometric hydrates as well as compositions containing variable amounts of water. The invention includes all such solvates.
  • polymorphs may exhibit polymorphism (i.e. the capacity to occur in different crystalline structures). These different crystalline forms are typically known as “polymorphs.”
  • the invention includes all such polymorphs. Polymorphs have the same chemical composition but differ in packing, geometrical arrangement, and other descriptive properties of the crystalline solid state. Polymorphs, therefore, may have different physical properties such as shape, density, hardness, deformability, stability, and dissolution properties. Polymorphs typically exhibit different melting points, IR spectra, and X-ray powder diffraction patterns, which may be used for identification.
  • polymorphs may be produced, for example, by changing or adjusting the reaction conditions or reagents used in making the compound, or by using different isolation or purification procedures. For example, changes in temperature, pressure, or solvent may result in polymorphs. In addition, one polymorph may spontaneously convert to another polymorph under certain conditions.
  • R1 is —(CH 2 ) n —C3-C6 cycloalkyl.
  • R1 is —(CH 2 ) n —C3-C6 cycloalkyl wherein n is 1.
  • R1 is —CH 2 -cyclopentyl.
  • R2 is C1-C3 alkyl; C1-C3 alkoxy; C1-C3 haloalkyl; C1-C3 sulfanyl; or halo.
  • R2 is methyl; ethyl; thiomethyl; thioethyl; fluoromethyl; difluoromethyl; 1-fluoromethyl; chloro; cyclopropyl; or methoxy.
  • R2 is methyl; ethyl; thiomethyl; or chloro.
  • R3 is —NR4R5; C1-C6 alkoxy; or heteroaryl, optionally substituted by one to three R6 groups.
  • R3 is —NR4R5 wherein R4 is C1-C6 alkyl, optionally substituted with one or two R7 groups; or C3-C6 cycloalkyl, optionally substituted by one to three R6 groups; and R5 is H, C1-C6 alkyl, or C1-C6 alkoxy.
  • R4 is cyclopropyl; cyclobutyl; cyclopentyl; tetrahydro-2H-pyranyl; 2-oxohexahydro-1H-azepinyl; 2-oxo-2,3,4,7-tetrahydro-1H-azepinyl; 5-fluoro-pyridinyl; or C1-C6 alkyl optionally substituted with one of the following R7 groups selected from the group consisting of hydroxyl; methoxy; cyano; —C(O)NRaRb; —C(O)Rc; morpholinyl; pyridinyl; 1,3-thiazolyl; 2-amino-1,3-thiazoyl; thienyl; furanyl; phenyl; and 1-hydroxy-1H-imidazolyl; and R5 is H; C1-C3 alkyl; cyclopropyl; or piperazinyl optionally substituted with one R6 group
  • R4 is methyl; ethyl optionally substituted with one substituent selected from the group consisting of: hydroxyl, methoxy and NRaRb; propyl; isopropyl; cyclopropyl; cyclobutyl; and cyclopentyl.
  • R5 is selected from the group consisting of H; C1-C6 alkyl; C1-C6 alkoxy; and C3-C6 cycloalkyl.
  • Suitabley R5 is H; methyl; or methoxy.
  • R5 is H; C1-C3 alkyl; cyclopropyl; or piperazinyl optionally substituted with one R6 group.
  • R3 is —NR4R5 wherein R4 and R5 are joined together with the N-atom to which they are attached to form a heterocycloalkyl group optionally substituted with one to three R6 groups.
  • R3 is —NR4R5 wherein R4 and R5 are joined together with the N-atom to which they are attached forming azetidinyl; pyrrolidinyl; piperazinyl; morpholinyl; 2,5-dihydro-1H-pyrrolyl; hexahydropyrazino[2,1-c][1,4]oxazin-(1H)-yl; isoxazolidinyl; hexahydropyrrolo[1,2-a]pyrazin-(1H)-yl; or 2,5-diazabicyclo[2.2.1]heptyl each of which may be optionally substituted with one to three R6 groups.
  • R3 is —NR4R5 wherein R4 and R5 are joined together with the N-atom to which they are attached forming 1-piperidinyl; 4-thiomorpholinyl; 1-pyrazolidinyl; tetrahydro-5H-[1,3]dioxolo[4,5-c]pyrrolyl; tetrahydro-1H-furo[3,4-c]pyrrol-(3H)-yl; hexahydropyrrolo[3,4-c]pyrrol-(1H)-yl; hexahydropyrrolo[1,2-a]pyrazin-(1H)-yl; hexahydropyrazino[2,1-c][1,4]oxazin-(1H)-yl; hexahydrofuro[3,4-b]pyrazin-(2H)-yl; octahydro-2H-pyrido[1,2-a]pyrazinyl;
  • R3 is —NR4R5 wherein R4 and R5 are joined together with the N-atom to which they are attached forming azetidinyl optionally substituted with one or two R6 groups each independently selected from the group consisting of methyl; ethyl; fluoro; methoxy; hydroxyl; hydroxymethyl; cyclopropyl; dimethylamino; ethylmethylamino; —CH 2 -dimethylamino; morpholinyl; pyrrolidinyl; —CH 2 -pyrrolidinyl; and pyridinyl.
  • R3 is —NR4R5 wherein R4 and R5 are joined together with the N-atom to which they are attached forming pyrrolidinyl optionally substituted with one to three R6 groups each independently selected from the group consisting of methyl; methoxy; —CH 2 -methoxy; hydroxyl; hydroxymethyl; hydroxyethyl; dimethylamino; ethylmethylamino; —CH 2 -dimethylamino; —CH 2 -pyrrolidinyl; —CH 2 -morpholinyl; pyridinyl; 2-(dimethylamino)-1,1-dimethylethyl; fluoromethyl; —CH 2 -2-hydroxyethylmethylamino; —CH 2 -2-methoxyethylamino; cyano; —C(O)N(CH 3 ) 2 ; 1-(dimethyamino)cyclopropyl; —CH 2 -e
  • R3 is —NR4R5 wherein R4 and R5 are joined together with the N-atom to which they are attached forming piperazinyl optionally substituted with one to three R6 groups each independently selected from the group consisting of methyl; ethyl; isopropyl; hydroxymethyl; hydroxyethyl; —CH 2 —O—CH 3 ; and —COOCH 3 .
  • R3 is —NR4R5 wherein R4 and R5 are joined together with the N-atom to which they are attached forming (9aS)-octahydropyrazino[2,1-c][1,4]oxazinyl.
  • R6 is C1-C3 alkyl, optionally substituted with one to three R7 groups; hydroxy; C1-C3 alkoxy; —C(O)NRaRb; or —NRaRb.
  • R6 is methyl; ethyl; isopropyl; methoxy; hydroxyl; diethylamino; or N,N-dimethylacetamido.
  • R6 is heteroaryl.
  • R6 is a 6-membered heteroaryl.
  • R6 is pyridinyl.
  • R7 is C1-C3 alkoxy; hydroxyl; or —NRaRb.
  • R7 is methoxy.
  • R7 is heterocycloalkyl.
  • R7 is a 6-membered heterocycloalkyl.
  • R7 is morpholinyl.
  • R7 is heteroaryl.
  • R7 is pyridinyl; 1,3-thiazolyl; thienyl; furanyl; imidazolyl; 1H-benzamidazolyl; 3H-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl; or 3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl.
  • Ra and Rb are both methyl.
  • Rc is heterocycloalkyl.
  • Suitabley Rc is pyrrolidinyl.
  • Another embodiment of the present invention is a compound according to Formula (I) wherein:
  • R1 is selected from the group consisting of C2-C7 alkyl and —(CH 2 ) n —C3-C6 cycloalkyl
  • R2 is selected from the group consisting of C1-C3 alkyl; cyclopropyl; C1-C3 alkoxy; C1-C3 haloalkyl; C1-C3 sulfanyl; 5-membered heteroaryl; 5-membered heterocycloalkyl; halo; hydroxymethyl; and —NRaRb
  • R3 is selected from the group consisting of —NR4R5; halo; phenyl, optionally substituted by one to three R6 groups; and heteroaryl, optionally substituted by one to three R6 groups
  • R4 is selected from the group consisting of H; C1-C6 alkyl, optionally substituted with one or two R7 groups; C1-C6 alkoxy; C3-C6 cycloalkyl, optionally substituted with one to
  • Another embodiment of the present invention is a compound according to Formula (I) wherein:
  • R1 is —CH 2 -cyclopentyl
  • R2 is selected from the group consisting of methyl; ethyl; thiomethyl; thioethyl; fluoromethyl; difluoromethyl; 1-fluoromethyl; chloro; cyclopropyl; or methoxy;
  • R3 is —NR4R5
  • R4 is selected from the group consisting of H; C1-C3 alkyl; cyclopropyl; and piperazinyl optionally substituted with one R6 group
  • R5 is selected from the group consisting of H; C1-C6 alkyl, optionally substituted with one or two R7 groups; C1-C6 alkoxy; C3-C6 cycloalkyl, optionally substituted with one to three R6 groups; heterocycloalkyl, optionally substituted by one to three R6 groups; heteroaryl, optionally substituted by one to three R6 groups; and phenyl, optionally substituted by one to three R6 groups; or R4 and R5 are joined together with the N-atom to which they are attached, forming a heterocycloalkyl group optionally substituted with one to three R6 groups; each R6 is independently selected from the group consisting of C1-C6 alkyl, optionally substituted with one to three R7 groups; hydroxy; C1-C3 alkoxy; —
  • One embodiment of the present invention is a compound which is [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide or a salt thereof.
  • Another embodiment of the present invention is a compound which is [(2R)-3-(2- ⁇ 2-Chloro-6-[(2R)-2,4-dimethyl-1-piperazinyl]-5-fluoro-4-pyrimidinyl ⁇ hydrazino)-2-(cyclopentylmethyl)-3-oxopropyl]hydroxyformamide or a salt thereof.
  • Another embodiment of the present invention is a compound which is [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 6-[(2R)-2,4-dimethyl-1-piperazinyl]-5-fluoro-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide or a salt thereof.
  • Another embodiment of the present invention is a compound which is [(2R)-3- ⁇ 2-[2-Chloro-5-fluoro-6-(4-methyl-4,7-diazaspiro[2.5]oct-7-yl)-4-pyrimidinyl]hydrazino ⁇ -2-(cyclopentylmethyl)-3-oxopropyl]hydroxyformamide or a salt thereof.
  • Another embodiment of the present invention is a compound which is ((2R)-2-(Cyclopentylmethyl)-3- ⁇ 2-[5-fluoro-2-methyl-6-(4-methyl-4,7-diazaspiro[2.5]oct-7-yl)-4-pyrimidinyl]hydrazino ⁇ -3-oxopropyl)hydroxyformamide or a salt thereof.
  • a substituent described herein is not compatible with the synthetic methods described herein, the substituent may be protected with a suitable protecting group that is stable to the reaction conditions.
  • the protecting group may be removed at a suitable point in the reaction sequence to provide a desired intermediate or target compound.
  • suitable protecting groups and the methods for protecting and de-protecting different substituents using such suitable protecting groups are well known to those skilled in the art; examples of which may be found in T. Greene and P. Wuts, Protecting Groups in Chemical Synthesis (3rd ed.), John Wiley & Sons, NY (1999).
  • a substituent may be specifically selected to be reactive under the reaction conditions used. Under these circumstances, the reaction conditions convert the selected substituent into another substituent that is either useful as an intermediate compound or is a desired substituent in a target compound.
  • (11) can be prepared by reacting an appropriate acid chloride (2) with a chiral agent, such as (S)-( ⁇ )-4-benzyl-2-oxazolidinone (Evans' chiral oxazolidinone), in the presence of a base, such as n-butyl lithium, to afford the chiral intermediate (3).
  • a base such as diisopropylethylamine
  • a chelating agent such as titanium tetrachloride
  • a solvent such as tetrahydrofuran
  • Conversion of compound (4) to the corresponding hydroxyacid (7) can be achieved by a sequence comprising oxidative cleavage of the chiral oxazolidinone, using, for example H 2 O 2 and lithium hydroxide, to the respective intermediate (5), followed by hydrogenolysis, to afford intermediate (7).
  • Compound (3) can also be converted to intermediate (7) in an alternative two-step procedure.
  • (3) can be treated with a base, such as diisopropylethylamine, in the presence of a chelating agent, such as titanium tetrachloride, in a solvent, such as tetrahydrofuran, followed by addition of trioxane or a suitable alternative formaldehyde equivalent to provide compound (6), which is then submitted to oxidative cleavage of the chiral oxazolidinone, using, for example H 2 O 2 and lithium hydroxide, to the respective acid (7).
  • a base such as diisopropylethylamine
  • a chelating agent such as titanium tetrachloride
  • solvent such as tetrahydrofuran
  • THP-protected intermediate (15) can be prepared by hydrogenation of azetidin-2-one (9) using a catalyst, such as 10% Pd/C, in an appropriate solvent, such as ethanol to provide (12).
  • a catalyst such as 10% Pd/C
  • an appropriate solvent such as ethanol
  • acid catalysis such as pyridinium p-toluenesulfonate
  • an appropriate solvent such as methylene chloride
  • Conversion of compound (14) to the product (15) can be achieved using an appropriate formylating agent, such as formic acid/acetic anhydride or methyl formate, in neat reagents or in an appropriate solvent, such as dichloromethane. Conversion of compound (14) to product (15) can also be accomplished using 5-methyl-2-thioxo-[1,3,4]thiadiazole-3-carbaldehyde (Yazawa, Hisatoyo; Goto, Shunsuke; Tetrahedron Lett. 26; 31; 1985; 3703-3706) as a formylating agent in an appropriate solvent, such as acetone.
  • an appropriate formylating agent such as formic acid/acetic anhydride or methyl formate
  • Conversion of compound (14) to product (15) can also be accomplished using 5-methyl-2-thioxo-[1,3,4]thiadiazole-3-carbaldehyde (Yazawa, Hisatoyo; Goto, Shunsuke; Tetrahedron Lett
  • Hydrazines of general structure (16) may be prepared according to literature methods by those skilled in the art.
  • the following examples of specific structures of hydrazines (16) and the synthetic methods used to generate them are merely illustrative and are not to be construed as a limitation of the scope of the present invention.
  • Hydrazines (24) where R2 is alkyl and R3 is an amino group (R4R5N) may be prepared from the appropriate precursors as shown in Scheme 4.
  • hydrazine (24) when R2 is hydrogen or alkyl can be prepared from the condensation of commercially-available fluoromalonate (19) and the appropriate amidine (20) under basic conditions to provide pyrimidinone (21).
  • Amidines (20) are commercially available or may be prepared according to literature methods by those skilled in the art.
  • Treatment of pyrimidinone (21) with POCl 3 provides dichloropyrimidine (22).
  • hydrazines of formula (30) may be prepared as shown in Scheme 6.
  • trichloropyrimidine (26) Treatment of trichloropyrimidine (26) with the desired amine R4R5NH at room temperature in an appropriate solvent, such as DMSO, followed by further treatment with hydrazine monohydrate and heating, provides the desired product (30), as well as the regioisomeric product (32).
  • the two regioisomers can usually be separated chromatographically, such as by HPLC.
  • Amines R4R5NH may be purchased from available commercial sources, prepared according to literature methods by those skilled in the art, or prepared as disclosed in the examples herein.
  • the compounds of the invention are inhibitors of microbial peptide deformylase (PDF) and are, therefore, capable of preventing bacterial growth. These compounds are potentially useful in the treatment of infectious diseases wherein the underlying pathology is (at least in part) attributable to (i.e. caused by) a variety of prokaryotic organisms. Examples include, but are not limited to, Gram positive and Gram negative aerobic and anaerobic bacteria from the genera Streptococcus , e.g. S. pneumoniae and S. pyogenes, Staphylococcus , e.g. S. aureus, S. epidermidis , and S. saprophyticus, Moraxella , e.g. M.
  • catarrhalis Haemophilus , e.g. H. influenzae, Neisseria, Mycoplasma , e.g. M. pneumoniae, Legionella , e.g. L. pneumophila, Chlamydia , e.g. C. pneumoniae, Bacteroides, Clostridium, Fusobacterium, Propionibacterium , and Peptostreptococcus.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Streptococcus , more suitably S. pneumoniae or S. pyogenes.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Staphylococcus , more suitably S. aureus, S. epidermidis , or S. saprophyticus.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Moraxella , more suitably M. catarrhalis.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Haemophilus , more suitably H. influenzae.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Neisseria.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Mycoplasma , more suitably M. pneumoniae.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Legionella , more suitably L. pneumophila.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Chlamydia , more suitably C. pneumoniae.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Bacteroides.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Clostridium.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Fusobacterium.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Propionibacterium.
  • the compounds of the present invention may be useful in the treatment of bacterial infections caused by Peptostreptococcus.
  • the compounds of the invention may also be useful in the treatment of bacterial infections caused by bacteria that are resistant to ⁇ -lactam, quinolone, macrolides, ketolides, glycopeptide, and oxazolidinone classes of antibiotics.
  • drug resistant bacterial infections include, but are not limited to, penicillin, macrolide or levofloxacin resistant S. pneumoniae ; methicillin or macrolide resistant, and vancomycin intermediate S. aureus ; methicillin resistant S. epidermidis ; and oxazolidinone resistant S. aureus.
  • the compounds of the invention may be used to treat a bacterial infection in mammals, specifically humans.
  • infections include, but are not limited to, ear infections, sinusitis, upper and lower respiratory tract infections, genital infections, skin and soft tissue infections, and bacterial endocarditis.
  • the compounds of the invention may also be used to prevent a bacterial infection in mammals, specifically humans, such as a bacterial infection that may result from medical or dental procedures.
  • the compounds of the invention may be used to treat ear infections.
  • the compounds of the invention may be used to treat sinusitis.
  • the compounds of the invention may be used to treat upper and lower respiratory tract infections.
  • the compounds of the invention may be used to treat genital infections.
  • the compounds of the invention may be used to treat skin and soft tissue infections.
  • the compounds of the invention may be used to treat bacterial endocarditis.
  • the methods of treatment of the invention comprise administering an effective amount of a compound according to Formula I, or a pharmaceutically acceptable salt thereof, to a patient in need thereof.
  • One embodiment of the present invention provides for a method of treating a bacterial infection in humans comprising administration of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide, or a pharmaceutically acceptable salt thereof, to a human in need thereof.
  • Another embodiment of the present invention provides for a method of treating a bacterial infection in humans comprising administration of [(2R)-3-(2- ⁇ 2-Chloro-6-[(2R)-2,4-dimethyl-1-piperazinyl]-5-fluoro-4-pyrimidinyl ⁇ hydrazino)-2-(cyclopentylmethyl)-3-oxopropyl]hydroxyformamide, or a pharmaceutically acceptable salt thereof, to a human in need thereof.
  • Another embodiment of the present invention provides for a method of treating a bacterial infection in humans comprising administration of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 6-[(2R)-2,4-dimethyl-1-piperazinyl]-5-fluoro-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide, or a pharmaceutically acceptable salt thereof, to a human in need thereof.
  • Another embodiment of the present invention provides for a method of treating a bacterial infection in humans comprising administration of [(2R)-3- ⁇ 2-[2-Chloro-5-fluoro-6-(4-methyl-4,7-diazaspiro[2.5]oct-7-yl)-4-pyrimidinyl]hydrazino ⁇ -2-(cyclopentylmethyl)-3-oxopropyl]hydroxyformamide, or a pharmaceutically acceptable salt thereof, to a human in need thereof.
  • Another embodiment of the present invention provides for a method of treating a bacterial infection in humans comprising administration of ((2R)-2-(Cyclopentylmethyl)-3- ⁇ 2-[5-fluoro-2-methyl-6-(4-methyl-4,7-diazaspiro[2.5]oct-7-yl)-4-pyrimidinyl]hydrazino ⁇ -3-oxopropyl)hydroxyformamide, or a pharmaceutically acceptable salt thereof, to a human in need thereof.
  • infectious disease refers to any disease characterized by the presence of a microbial infection, such as a bacterial infection.
  • treat in reference to a condition means: (1) to ameliorate or prevent the condition or one or more of the biological manifestations of the condition, (2) to interfere with (a) one or more points in the biological cascade that leads to or is responsible for the condition or (b) one or more of the biological manifestations of the condition, (3) to alleviate one or more of the symptoms or effects associated with the condition, or (4) to slow the progression of the condition or one or more of the biological manifestations of the condition.
  • prevention includes prevention of the condition.
  • prevention is not an absolute term. In medicine, “prevention” is understood to refer to the prophylactic administration of a drug to substantially diminish the likelihood or severity of a condition or biological manifestation thereof, or to delay the onset of such condition or biological manifestation thereof.
  • an effective amount in reference to a compound of the invention means an amount of the compound sufficient to treat the patient's condition, but low enough to avoid serious side effects (at a reasonable benefit/risk ratio) within the scope of sound medical judgment.
  • An effective amount of a compound will vary with the particular compound chosen (e.g., consider the potency, efficacy, and half-life of the compound); the route of administration chosen; the condition being treated; the severity of the condition being treated; the age, size, weight, and physical condition of the patient being treated; the medical history of the patient being treated; the duration of the treatment; the nature of concurrent therapy; the desired therapeutic effect; and like factors, and can be routinely determined by the skilled artisan.
  • patient refers to a human or other mammal.
  • the compounds of the invention may be administered by any suitable route of administration, including both systemic administration and topical administration.
  • Systemic administration includes oral administration, parenteral administration, transdermal administration, rectal administration, and administration by inhalation.
  • Parenteral administration refers to routes of administration other than enteral, transdermal, or by inhalation, and is typically by injection or infusion.
  • Parenteral administration includes intravenous, intramuscular, and subcutaneous injection or infusion.
  • Inhalation refers to administration into the patient's lungs whether inhaled through the mouth or through the nasal passages.
  • Topical administration includes application to the skin as well as intraocular, intravaginal, and intranasal administration.
  • the compounds of the invention may be administered once or according to a dosing regimen wherein a number of doses are administered at varying intervals of time for a given period of time. For example, doses may be administered one, two, three, or four times per day. Doses may be administered until the desired therapeutic effect is achieved or indefinitely to maintain the desired therapeutic effect. Suitable dosing regimens for a compound of the invention depend on the pharmacokinetic properties of that compound, such as absorption, distribution, and half-life, which can be determined by the skilled artisan.
  • suitable dosing regimens including the duration such regimens are administered, for a compound of the invention depend on the condition being treated, the severity of the condition being treated, the age and physical condition of the patient being treated, the medical history of the patient being treated, the nature of concurrent therapy, the desired therapeutic effect, and like factors within the knowledge and expertise of the skilled artisan. It will be further understood by such skilled artisans that suitable dosing regimens may require adjustment given an individual patient's response to the dosing regimen or over time as individual patient needs change.
  • Typical daily dosages may vary depending upon the particular route of administration chosen. Typical daily dosages for oral administration, to a human weighing approximately 70 kg, would range from 50 mg to 3 g, suitably 100 mg to 2 g of a compound of the invention a day.
  • a “prodrug” of a compound of the invention is a functional derivative of the compound which, upon administration to a patient, eventually liberates the compound of the invention in vivo.
  • Administration of a compound of the invention as a prodrug may enable the skilled artisan to do one or more of the following: (a) modify the onset of the compound in vivo; (b) modify the duration of action of the compound in vivo; (C) modify the transportation or distribution of the compound in vivo; (d) modify the solubility of the compound in vivo; and (e) overcome a side effect or other difficulty encountered with the compound.
  • Typical functional derivatives used to prepare prodrugs include modifications of the compound that are chemically or enzymatically cleaved in vivo. Such modifications, which include the preparation of phosphates, amides, esters, thioesters, carbonates, and carbamates, are well known to those skilled in the art.
  • the invention also provides a compound of the invention for use in medical therapy, particularly in bacterial infections.
  • the invention is directed to the use of a compound according to Formula I or a pharmaceutically-acceptable salt thereof in the preparation of a medicament for the treatment of bacterial infections.
  • compounds according to Formula I are PDF inhibitors, and may be useful in the treatment of bacterial infections.
  • the biological activity of the compounds according to Formula I can be determined using suitable assays such as those measuring inhibition of the enzymatic activity of PDF and those evaluating the ability of the compounds to inhibit bacterial growth in vitro or in animal models of infection.
  • Certain Examples of the invention possess greater in vitro antibacterial activity (MIC and/or MIC90) and/or better in vivo efficacy over the examples from WO 03/101442. These Examples include, but are not limited to, the following:
  • Enzymatic activity of PDF was measured using a formate dehydrogenase (FDH)-coupled assay [Lazennec and Meinnel (1997) Anal. Biochem. 244, 180-182].
  • FDH formate dehydrogenase
  • Reactions were initiated by adding PDF to microtiter plates containing all other reaction components and were continuously monitored for 20 min at 25° C.
  • the final reaction composition for the Staphylococcus aureus PDF (SaPDF) assay was 50 mM potassium phosphate, pH 7.6, 5 units/mL FDH, 7 mM NAD, 5% DMSO, 1 nM SaPDF, and 2.9 mM formyl-Met-Ala-Ser in 50 ⁇ L total volume. Serial dilutions of inhibitors were performed in DMSO. Reagents and assay format were identical for Haemophilus influenzae PDF except that formyl-Met-Ala-Ser was 6 mM final.
  • Examples 1-281 inhibit S. aureus, H. influenzae and S. pneumoniae PDF activities with IC50s ⁇ 100 nM.
  • This panel consisted of the following laboratory strains: Staphylococcus aureus Oxford, Staphylococcus aureus WCUH29, Enterococcus faecalis I, Enterococcus faecalis 7, Haemophilus influenzae Q1, Haemophilus influenzae NEMC1, Moraxella catarrhalis 1502, Streptococcus pneumoniae 1629, Streptococcus pneumoniae N1387, Streptococcus pneumoniae Ery2, Escherichia coli 7623 (AcrABEFD+) and Escherichia coli 120 (AcrAB ⁇ ).
  • the minimum inhibitory concentration (MIC) was determined as the lowest concentration of compound that inhibited visible growth. A mirror reader was used to assist in determining the MIC endpoint.
  • Each of the Examples 1-281 have a minimal inhibitory concentration (MIC) ⁇ 4 ⁇ g/mL against at least one of the organisms listed above. For at least one strain of every organism listed above, at least one example had an MIC ⁇ 4 ⁇ g/mL, with the exception of Enterococcus faecalis I, and Enterococcus faecalis 7, for which most examples had MICs ⁇ 16 ⁇ g/mL.
  • MIC minimal inhibitory concentration
  • Antimicrobial Activity data (MIC's in ⁇ g/mL) for specific Examples is given in Table 2.
  • Example Example 24* 63* 109 172 275 Organism ⁇ g/mL ⁇ g/mL ⁇ g/mL ⁇ g/mL ⁇ g/mL ⁇ g/mL S. aureus 2 1 2 1, 2 2, 4 Oxford S. aureus 0.375 0.5 0.5 0.5 0.5, 1 WCUH29 E. faecalis I 48 16 64, >64 16 32, 64 E. faecalis 7 32 64 >64 8, 64 16, 64 H. influenzae 0.5 0.25 0.5 1, 2 0.5, 1 Q1 H. influenzae 1 0.5 1 1, 2 1 NEMC1 M. catarrhalis 0.375 0.125 0.25 ⁇ 0.06, 0.25 1502 0.125 S.
  • Rat Respiratory Tract Infection Model with H. Influenzae or S. Pneumoniae.
  • the rats were euthanized 96 h post infection and the lungs removed aseptically and homogenized in 1 mL of sterile saline with a stomacher machine. Ten fold serial dilutions were done in sterile saline to enumerate viable bacteria numbers.
  • This rat lung infection model has been shown to be able to predict human efficacy in community-acquired pneumonia (CAP) caused by S. pneumoniae [Hoover J. L., C. Mininger, R. Page, R. Straub, S. Rittenhouse, and D. Payne. (2007). Abstract A-17. Proceedings of the 47th ICAAC, Chicago, Ill.].
  • CAP community-acquired pneumonia
  • mice Male CD1, 20 g (Charles River) were infected with S. aureus in semi-solid agar (1 ⁇ 10 6 CFU/mouse) subcutaneously in the groin area (Jarvest, R. L., Berge, J. M., Berry, V., Boyd, H. F., Brown, M. J., Elder, J. S., Forrest, A. K., Fosberry, A. P., Gentry, D. R., Hibbs, M. J., Jaworski, D. D., O'Hanlon, P. J., Pope, A. J., Rittenhouse, S. Sheppard, R.
  • mice were dosed with different amounts of compound (2-fold dilution ranging from 37.5 to 300 mg/kg) by oral gavage twice daily starting 1 h after infection. Control animals were dosed with diluent on the same schedule. Mice are euthanized 96 h post infection and the abscesses are aseptically removed and homogenized. Ten fold serial dilutions were done in sterile saline to enumerate viable bacteria numbers.
  • the compounds of the invention will normally, but not necessarily, be formulated into pharmaceutical compositions prior to administration to a patient. Accordingly, in another aspect, the invention is directed to pharmaceutical compositions comprising a compound of the invention and one or more pharmaceutically acceptable excipients.
  • compositions of the invention may be prepared and packaged in bulk form wherein a safe and effective amount of a compound of the invention can be extracted and then given to the patient such as with powders or syrups.
  • the pharmaceutical compositions of the invention may be prepared and packaged in unit dosage form wherein each physically discrete unit contains a safe and effective amount of a compound of the invention.
  • the pharmaceutical compositions of the invention typically contain from 25 mg to 1.5 g, suitably 100 to 500 mg, of compound of the invention.
  • compositions of the invention typically contain one compound of the invention. However, in certain embodiments, the pharmaceutical compositions of the invention may contain more than one compound of the invention. For example, in certain embodiments the pharmaceutical compositions of the invention may contain two compounds of the invention. In addition, the pharmaceutical compositions of the invention may optionally further comprise one or more additional pharmaceutically active compounds.
  • pharmaceutically acceptable excipient means a pharmaceutically acceptable material, composition or vehicle that, for example, are involved in giving form or consistency to the pharmaceutical composition.
  • Each excipient must be compatible with the other ingredients of the pharmaceutical composition when commingled such that interactions which would substantially reduce the efficacy of the compound of the invention when administered to a patient and interactions which would result in pharmaceutical compositions that are not pharmaceutically acceptable are avoided.
  • each excipient must of course be of sufficiently high purity to render it pharmaceutically-acceptable.
  • dosage forms include those adapted for (1) oral administration such as tablets, capsules, caplets, pills, troches, powders, syrups, elixers, suspensions, solutions, emulsions, sachets, and cachets; (2) parenteral administration such as sterile solutions, suspensions, and powders for reconstitution; (3) transdermal administration such as transdermal patches; (4) rectal administration such as suppositories; (5) inhalation such as dry powders, aerosols, suspensions, and solutions; and (6) topical administration such as creams, ointments, lotions, solutions, pastes, sprays, foams, and gels.
  • oral administration such as tablets, capsules, caplets, pills, troches, powders, syrups, elixers, suspensions, solutions, emulsions, sachets, and cachets
  • parenteral administration such as sterile solutions, suspensions, and powders for reconstitution
  • transdermal administration such as transdermal patches
  • rectal administration such as
  • Suitable pharmaceutically-acceptable excipients will vary depending upon the particular dosage form chosen.
  • suitable pharmaceutically acceptable excipients may be chosen for a particular function that they may serve in the composition.
  • certain pharmaceutically-acceptable excipients may be chosen for their ability to facilitate the production of uniform dosage forms.
  • Certain pharmaceutically acceptable excipients may be chosen for their ability to facilitate the production of stable dosage forms.
  • Certain pharmaceutically-acceptable excipients may be chosen for their ability to facilitate the carrying or transporting of the compound or compounds of the invention once administered to the patient from one organ, or portion of the body, to another organ, or another portion of the body.
  • Certain pharmaceutically acceptable excipients may be chosen for their ability to enhance patient compliance.
  • Suitable pharmaceutically acceptable excipients include the following types of excipients: Diluents, fillers, binders, disintegrants, lubricants, glidants, granulating agents, coating agents, wetting agents, solvents, co-solvents, suspending agents, emulsifiers, sweetners, flavoring agents, flavor masking agents, coloring agents, anticaking agents, hemectants, chelating agents, plasticizers, viscosity increasing agents, antioxidants, preservatives, stabilizers, surfactants, and buffering agents.
  • excipients may serve more than one function and may serve alternative functions depending on how much of the excipient is present in the formulation and what other ingredients are present in the formulation.
  • Skilled artisans possess the knowledge and skill in the art to enable them to select suitable pharmaceutically-acceptable excipients in appropriate amounts for use in the invention.
  • resources that are available to the skilled artisan which describe pharmaceutically-acceptable excipients and may be useful in selecting suitable pharmaceutically-acceptable excipients. Examples include Remington's Pharmaceutical Sciences (Mack Publishing Company), The Handbook of Pharmaceutical Additives (Gower Publishing Limited), and The Handbook of Pharmaceutical Excipients (the American Pharmaceutical Association and the Pharmaceutical Press).
  • compositions of the invention are prepared using techniques and methods known to those skilled in the art. Some of the methods commonly used in the art are described in Remington's Pharmaceutical Sciences (Mack Publishing Company).
  • the invention is directed to a solid oral dosage form such as a tablet or capsule comprising a safe and effective amount of a compound of the invention and a diluent or filler.
  • Suitable diluents and fillers include lactose, sucrose, dextrose, mannitol, sorbitol, starch (e.g. corn starch, potato starch, and pre-gelatinized starch), cellulose and its derivatives (e.g. microcrystalline cellulose), calcium sulfate, and dibasic calcium phosphate.
  • the oral solid dosage form may further comprise a binder. Suitable binders include starch (e.g.
  • the oral solid dosage form may further comprise a disintegrant. Suitable disintegrants include crospovidone, sodium starch glycolate, croscarmelose, alginic acid, and sodium carboxymethyl cellulose.
  • the oral solid dosage form may further comprise a lubricant. Suitable lubricants include stearic acid, magnesium stearate, calcium stearate, and talc.
  • dosage unit formulations for oral administration can be microencapsulated.
  • the composition can also be prepared to prolong or sustain the release as for example by coating or embedding particulate material in polymers, wax or the like.
  • the compounds of the invention may also be coupled with soluble polymers as targetable drug carriers.
  • soluble polymers can include polyvinylpyrrolidone, pyran copolymer, polyhydroxypropylmethacrylamide-phenol, polyhydroxyethylaspartamidephenol, or polyethyleneoxidepolylysine substituted with palmitoyl residues.
  • the compounds of the invention may be coupled to a class of biodegradable polymers useful in achieving controlled release of a drug, for example, polylactic acid, polepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydropyrans, polycyanoacrylates and cross-linked or amphipathic block copolymers of hydrogels.
  • the invention is directed to a liquid oral dosage form.
  • Oral liquids such as solution, syrups and elixirs can be prepared in dosage unit form so that a given quantity contains a predetermined amount of a compound of the invention.
  • Syrups can be prepared by dissolving the compound of the invention in a suitably flavored aqueous solution, while elixirs are prepared through the use of a non-toxic alcoholic vehicle.
  • Suspensions can be formulated by dispersing the compound of the invention in a non-toxic vehicle.
  • Solubilizers and emulsifiers such as ethoxylated isostearyl alcohols and polyoxy ethylene sorbitol ethers, preservatives, flavor additive such as peppermint oil or natural sweeteners or saccharin or other artificial sweeteners, and the like can also be added.
  • compositions adapted for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents.
  • the compositions may be presented in unit-dose or multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example water for injections, immediately prior to use.
  • Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets.
  • the invention is directed to a pharmaceutical composition
  • a pharmaceutical composition comprising [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
  • the invention is directed to a pharmaceutical composition
  • a pharmaceutical composition comprising [(2R)-3-(2- ⁇ 2-Chloro-6-[(2R)-2,4-dimethyl-1-piperazinyl]-5-fluoro-4-pyrimidinyl ⁇ hydrazino)-2-(cyclopentylmethyl)-3-oxopropyl]hydroxyformamide, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
  • the invention is directed to a pharmaceutical composition
  • a pharmaceutical composition comprising [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 6-[(2R)-2,4-dimethyl-1-piperazinyl]-5-fluoro-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
  • the invention is directed to a pharmaceutical composition
  • a pharmaceutical composition comprising [(2R)-3- ⁇ 2-[2-Chloro-5-fluoro-6-(4-methyl-4,7-diazaspiro[2.5]oct-7-yl)-4-pyrimidinyl]hydrazino ⁇ -2-(cyclopentylmethyl)-3-oxopropyl]hydroxyformamide, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
  • the invention is directed to a pharmaceutical composition
  • a pharmaceutical composition comprising ((2R)-2-(Cyclopentylmethyl)-3- ⁇ 2-[5-fluoro-2-methyl-6-(4-methyl-4,7-diazaspiro[2.5]oct-7-yl)-4-pyrimidinyl]hydrazino ⁇ -3-oxopropyl)hydroxyformamide, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient
  • ((2R)-2-(Cyclopentylmethyl)-3- ⁇ 2-[5-fluoro-2-methyl-6-(4-methyl-4,7-diazaspiro[2.5]oct-7-yl)-4-pyrimidinyl]hydrazino ⁇ -3-oxopropyl)hydroxyformamide, or a pharmaceutically acceptable salt thereof may be formulated for oral administration, suitably in a liquid or tablet form, or for patenteral administration.
  • Form 1 is a crystalline form which may be produced from a slurry of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide in ethers, acetates, ketones, longer chain alcohols, and other solvent systems (for example, nitromethane, acetonitrile, 2-butanone, methyl acetate, ethyl acetate, diethyl ether, heptane, dimethyl carbonate, t-butyl ethyl ether, 1-methoxy-2-propanol, 2-methoxyethyl ether, chloroform, chlorobenzene, tetrahydrofuran, toluene,
  • Form 2 is a crystalline form which may be produced from a slurry of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide in water.
  • Form 3 is a crystalline form which may be produced from a slurry of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide in neat, small alcohol solvent systems, such as methanol, 1-propanol, and 1-butanol. These alcohols must contain little to no water content to avoid production of Form 2, although the exact water content threshold has not been established. Heating Form 1 to above 132° C. (but not greater than ⁇ 185° C. which would lead to decomposition of the compound) causes an exothermic solid state form conversion of Form 1 to Form 3.
  • the invention provides [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide Form 1, Form 2, or Form 3 in substantially pure form.
  • the invention further provides for mixtures of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide which comprise two or more of Form 1, Form 2, and Form 3.
  • the mixture may include both Form 1 and Form 2.
  • the composition may comprise from 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 75, 80, 85, 90, 95, 97 or greater than about 99 percent of either Form 1 or Form 2.
  • the mixture may comprise both Form 2 and Form 3.
  • the composition may comprise from 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 75, 80, 85, 90, 95, 97 or greater than about 99 percent of either Form 2 or Form 3.
  • the mixture may comprise both Form 1 and Form 3.
  • the mixture may comprise 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 75, 80, 85, 90, 95, 97 or greater than about 99 percent of either Form 1 or Form 3.
  • a composition may comprise from 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 75, 80, 85, 90, 95, 97 or greater than about 99 percent of an individual polymorphic form, be it Form 1, Form 2, or Form 3.
  • Another embodiment of the invention is the polymorph Form 1, Form 2, or Form 3 in substantially pure crystalline form.
  • the crystalline state of a compound can be described by several crystallographic parameters: unit cell dimensions, space groups, and atomic position of the atoms in the compound relative to the origin of its unit cell. These parameters are experimentally determined by crystal x-ray analysis. It is possible for a compound to form more than one type of crystal. These different crystalline forms are called polymorphs.
  • Form 1, Form 2, and Form 3 may be differentiated by X-Ray powder diffraction (XRPD) of the solid state forms, as shown herein in FIGS. 6 to 8 for Forms 1 to 3 respectively.
  • XRPD X-Ray powder diffraction
  • FT-IR, FT-Raman, Differential Scanning calorimetry (DSC), and Thermogravimetric Analysis (TGA) data may also be used to assist in differentiation of the solid state forms as are shown and described herein.
  • Characteristic powder X-ray diffraction pattern peak positions are reported for polymorphs in terms of the angular positions (two theta) with an allowable variability, generally of about 0.1+/ ⁇ ° 2-theta. The entire pattern, or most of the pattern peaks may also shift by about 0.1+/ ⁇ ° due to difference in calibration, setting, and other variations from instrument to instrument and from operator to operator.
  • the XRPD data described herein was acquired on a Bruker AXS PXRD General Area Detector Diffraction system using methods as described herein. Characteristic XRPD angles and d-spacings are recorded in Table 1 below.
  • Polymorphic Form 1 may therefore be characterized by any one, any two, any three, any four, or any five or more of the 2-theta angle peaks.
  • Polymorphic Form 2 may therefore be characterized by any one, any two, any three, any four, or any five or more of the 2-theta angle peaks.
  • Polymorphic Form 3 may therefore be characterized by any one, any two, any three, any four, or any five or more of the 2-theta angle peaks.
  • Form 1 Form 2
  • Form 3 d-spacing/ d-spacing/ d-spacing/ 2 ⁇ ⁇ 2 ⁇ ⁇ 4.1 21.8 7.8 11.3 6.1 14.5 6.1 14.5 9.5 9.3 7.5 11.7 6.9 12.8 12.3 7.2 8.2 10.8 8.1 10.9 13.2 6.7 9.1 9.7 9.5 9.3 15.6 5.7 12.0 7.4 11.2 7.9 18.3 4.8 12.8 6.9 12.9 6.9 19.0 4.7 13.4 6.6 13.8 6.4 20.6 4.3 16.0 5.6 15.6 5.7 21.4 4.1 23.3 3.8 18.3 4.8 26.7 3.3 27.6 3.2
  • the FT-IR spectrum of the solid forms was recorded using a Thermo Magna MidIR system using methods as described herein. Slight variations in observed peaks are expected based on the specific spectrometer employed and the analyst's sample preparation technique. Some margin of error is present in each of the peak assignments reported below. The margin of error in the peak assignments is approximately +/ ⁇ 1 cm ⁇ 1 .
  • Form 1 IR peaks were observed at: 1035+/ ⁇ 1 cm ⁇ 1 , 1059+/ ⁇ 1 cm ⁇ 1 , 1114+/ ⁇ 1 cm ⁇ 1 , 1155+/ ⁇ 1 cm ⁇ 1 , 1173+/ ⁇ 1 cm ⁇ 1 , 1347+/ ⁇ 1 cm ⁇ 1 , 1416+/ ⁇ 1 cm ⁇ 1 , 1443+/ ⁇ 1 cm ⁇ 1 , 1603+/ ⁇ 1 cm ⁇ 1 , and 1656+/ ⁇ 1 cm ⁇ 1 .
  • Form 1 exhibits these characteristic peaks of any one, any two, any three, any four, or any five or more peaks.
  • Form 2 IR peaks were observed at: 1036+/ ⁇ 1 cm ⁇ 1 , 1114+/ ⁇ 1 cm ⁇ 1 , 1152+/ ⁇ 1 cm ⁇ 1 , 1172+/ ⁇ 1 cm ⁇ 1 , 1310+/ ⁇ 1 cm ⁇ 1 , 1414+/ ⁇ 1 cm ⁇ 1 , 1441+/ ⁇ 1 cm ⁇ 1 , 1570+/ ⁇ 1 cm ⁇ 1 , 1601+/ ⁇ 1 cm ⁇ 1 , and 1662+/ ⁇ 1 cm ⁇ 1 .
  • Form 2 exhibits these characteristic peaks of any one, any two, any three, any four, or any five or more peaks.
  • the IR data for Forms 1 and 2 are illustrated in FIGS. 1 and 2 respectively.
  • the FT-Raman spectrum of the solid forms was recorded using a Thermo FT-Raman System 960 Spectrometer using methods as described herein. Slight variations in observed peaks are expected based on the specific spectrometer employed and the analyst's sample preparation technique. Some margin of error is present in each of the peak assignments reported below. The margin of error in the peak assignments is approximately +/ ⁇ 1 cm ⁇ 1 .
  • Form 1 Raman peaks were observed at: 506+/ ⁇ 1 cm ⁇ 1 , 760+/ ⁇ 1 cm ⁇ 1 , 796+/ ⁇ 1 cm ⁇ 1 , 884+/ ⁇ 1 cm ⁇ 1 , 1180+/ ⁇ 1 cm ⁇ 1 , 1305+/ ⁇ 1 cm ⁇ 1 , 1449+/ ⁇ 1 cm ⁇ 1 , 1606+/ ⁇ 1 cm ⁇ 1 , 1674+/ ⁇ 1 cm ⁇ 1 , and 2935+/ ⁇ 1 cm ⁇ 1 .
  • Form 1 exhibits these characteristic peaks of any one, any two, any three, any four, or any five or more peaks.
  • Form 2 Raman peaks were observed at: 273+/ ⁇ 1 cm ⁇ 1 , 483+/ ⁇ 1 cm ⁇ 1 , 507+/ ⁇ 1 cm ⁇ 1 , 764+/ ⁇ 1 cm ⁇ 1 , 847+/ ⁇ 1 cm ⁇ 1 , 1179+/ ⁇ 1 cm ⁇ 1 , 1228+/ ⁇ 1 cm ⁇ 1 , 1446+/ ⁇ 1 cm ⁇ 1 , 1673+/ ⁇ 1 cm ⁇ 1 , and 2932+/ ⁇ 1 cm ⁇ 1 .
  • Form 2 exhibits these characteristic peaks of any one, any two, any three, any four, or any five or more peaks.
  • Form 3 Raman peaks were observed at: 273+/ ⁇ 1 cm ⁇ 1 , 506+/ ⁇ 1 cm ⁇ 1 , 766+/ ⁇ 1 cm ⁇ 1 , 797+/ ⁇ 1 cm ⁇ 1 , 1176+/ ⁇ 1 cm ⁇ 1 , 1228+/ ⁇ 1 cm ⁇ 1 , 1302+/ ⁇ 1 cm ⁇ 1 , 1446+/ ⁇ 1 cm ⁇ 1 , 1672+/ ⁇ 1 cm ⁇ 1 , and 2934+/ ⁇ 1 cm ⁇ 1 .
  • Form 3 exhibits these characteristic peaks of any one, any two, any three, any four, or any five or more peaks.
  • the Raman data for Forms 1 to 3 are illustrated in FIGS. 3 to 5 respectively.
  • the DSC thermogram of the forms was obtained using a TA Instruments Thermal Analysis System, Model DSC Q100 using methods as described herein. The data are illustrated herein as FIGS. 9 to 11 for Forms 1 to 3 respectively.
  • Forms 1, 2, and 3 had a melt onset measured by DSC at approximately 187° C., 185° C., and 190° C. respectively. With respect to Form 1 ( FIG. 9 ) there was a melt at 132° C. which corresponds to exothermic solid state form conversion of Form 1 to Form 3.
  • the TGA trace of the forms was obtained using a TA Instruments Thermal Analysis System, Model TGA Q500 using methods described herein.
  • the data are illustrated herein as FIGS. 12-14 for Forms 1 to 3 respectively.
  • One embodiment of the present invention is the polymorphic form, Form 1, substantially as shown in the X-ray diffraction pattern of FIG. 6 , the FT-IR spectrum of FIG. 1 , the FT-Raman spectrum of FIG. 3 , the DSC thermogram of FIG. 9 , and the TGA trace of FIG. 12 .
  • polymorph Form 1 characterized by an X-ray diffraction pattern comprising peaks expressed in terms of two theta angles wherein the x-ray diffraction pattern comprises peaks at 4.1+/ ⁇ 0.1°, 6.1+/ ⁇ 0.1°, 6.9+/ ⁇ 0.1°, 8.1+/ ⁇ 0.1°, 9.5+/ ⁇ 0.1°, 11.2+/ ⁇ 0.1°, 12.9+/ ⁇ 0.1°, 13.8+/ ⁇ 0.1°, 15.6+/ ⁇ 0.1°, and 18.3+/ ⁇ 0.1°.
  • Form 1 is characterized by an X-ray diffraction pattern comprising of peaks at 8.1+/ ⁇ 0.1°, 9.5+/ ⁇ 0.1°, 11.2+/ ⁇ 0.1°, 12.9+/ ⁇ 0.1°, 13.8+/ ⁇ 0.1°, and 15.6+/ ⁇ 0.1°.
  • Another embodiment of the present invention is the polymorphic form, Form 1, of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide wherein said polymorphic form is characterized by an X-ray diffraction pattern comprising peaks expressed in terms of 2 theta angles, wherein:
  • Another embodiment of the present invention is a pharmaceutical composition
  • a pharmaceutical composition comprising Form 1 and a pharmaceutically acceptable excipient.
  • Another embodiment of the present invention is the polymorphic form, Form 2, substantially as shown in the X-ray diffraction pattern of FIG. 7 , the FT-IR spectrum of FIG. 2 , the FT-Raman spectrum of FIG. 4 , the DSC thermogram of FIG. 10 , and the TGA trace of FIG. 13 .
  • polymorph Form 2 characterized by an X-ray diffraction pattern comprising peaks expressed in terms of two theta angles wherein the x-ray diffraction pattern comprises peaks at 7.8+/ ⁇ 0.1°, 9.5+/ ⁇ 0.1°, 12.3+/ ⁇ 0.1°, 13.2+/ ⁇ 0.1°, 15.6+/ ⁇ 0.1°, 18.3+/ ⁇ 0.1°, 19.0+/ ⁇ 0.1°, 20.6+/ ⁇ 0.1°, 21.4+/ ⁇ 0.1°, and 26.7+/ ⁇ 0.1°.
  • Form 2 is characterized by an X-ray diffraction pattern comprising of peaks at 7.8+/ ⁇ 0.1°, 9.5+/ ⁇ 0.1°, 12.3+/ ⁇ 0.1°, 13.2+/ ⁇ 0.1°, 15.6+/ ⁇ 0.1°, 18.3+/ ⁇ 0.1°, and 19.0+/ ⁇ 0.1°.
  • Another embodiment of the present invention is the polymorphic form, Form 2, of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide wherein said polymorphic form is characterized by an X-ray diffraction pattern comprising peaks expressed in terms of 2 theta angles, wherein:
  • Another embodiment of the present invention is a pharmaceutical composition
  • a pharmaceutical composition comprising Form 2 and a pharmaceutically acceptable excipient.
  • Another embodiment of the present invention is the polymorphic form, Form 3, substantially as shown in the X-ray diffraction pattern of FIG. 8 , the FT-Raman spectrum of FIG. 5 , the DSC thermogram of FIG. 11 , and the TGA trace of FIG. 14 .
  • Another embodiment of the present invention is the polymorph Form 3 characterized by an X-ray diffraction pattern comprising peaks expressed in terms of two theta angles wherein the x-ray diffraction pattern comprises peaks at 6.1+/ ⁇ 0.1°, 7.5+/ ⁇ 0.1°, 8.2+/ ⁇ 0.1°, 9.1+/ ⁇ 0.1°, 12.0+/ ⁇ 0.1°, 12.8+/ ⁇ 0.1°, 13.4+/ ⁇ 0.1°, 16.0+/ ⁇ 0.1°, 23.3+/ ⁇ 0.1°, and 27.6+/ ⁇ 0.1°.
  • Form 3 is characterized by an X-ray diffraction pattern comprising of peaks at 7.5+/ ⁇ 0.1°, 8.2+/ ⁇ 0.1°, 9.1+/ ⁇ 0.1°, 12.8+/ ⁇ 0.1°, 13.4+/ ⁇ 0.1°, and 16.0+/ ⁇ 0.1°.
  • Another embodiment of the present invention is the polymorphic form, Form 3, of [(2R)-2-(Cyclopentylmethyl)-3-(2- ⁇ 5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methyl-4-pyrimidinyl ⁇ hydrazino)-3-oxopropyl]hydroxyformamide wherein said polymorphic form is characterized by an X-ray diffraction pattern comprising peaks expressed in terms of 2 theta angles, wherein:
  • Another embodiment of the present invention is a pharmaceutical composition
  • a pharmaceutical composition comprising Form 3 and a pharmaceutically acceptable excipient.
  • NMR 1 H NMR
  • benzyloxymethylchloride (TCI-America) (39 mL, 280 mmol) was added in a slow steady stream to the resulting titanium enolate, and the mixture was maintained at 0° C. for 3.5 h.
  • the reaction mixture was then quenched with water (400 mL).
  • the aqueous layer was extracted with dichloromethane (150 mL ⁇ 2).
  • the organic extracts were washed with saturated NaHCO 3 , were dried (MgSO 4 ) and were evaporated.
  • the (2R)-3-cyclopentyl-2-( ⁇ formyl[(phenylmethyl)oxy]amino ⁇ methyl)propanoic acid, diisopropylethylamine salt, isopropanol solvate can be prepared in the following manner:
  • the organic layer was extracted with H 2 O (100 mL) and the combined aqueous layers were cooled to 0° C. and carefully acidified with 2M citric acid ( ⁇ 525 mL) drop wise over the course of 90 min, keeping the internal temperature below 10° C.
  • the acidified material was extracted with ethyl acetate (3 ⁇ 250 mL) and the combined organic layers were washed with water (2 ⁇ ), dried over MgSO 4 , filtered, and evaporated.
  • (2R)-3-Cyclopentyl-2- ⁇ [formyl(tetrahydro-2H-pyran-2-yloxy)amino]methyl ⁇ propanoic acid can also be prepared according to literature procedures [Bracken, Bushell, Dean, Francavilla, Jain, Lee, Seepersaud, Shu, Sundram, Yuan; PCT Int. Appl. (2006), WO 2006127576 A2].
  • the (2R)-3-cyclopentyl-2- ⁇ [formyl(tetrahydro-2H-pyran-2-yloxy)amino]methyl ⁇ propanoic acid, diisopropylethylamine salt can be prepared in the following manner:
  • Propionamide hydrochloride salt (30.0 g, 276.3 mmol) and dimethyl fluoromalonate (41.4 g, 276.3 mmol) in anhydrous methanol (400 mL) were treated with solid NaOMe (45 g, 829 mmol) portion-wise at room temperature. After the addition, the white suspension was heated to 85° C. and stirred for 2 h. The solvent was then evaporated to dryness. To the residue was added 70 mL of 6 N HCl solution with vigorous stirring. The suspension was stirred for 10 min until the residue was fully neutralized. The white precipitate was collected by filtration and dried over vacuum to give 2-ethyl-5-fluoro-6-hydroxy-4(1H)-pyrimidinone as a white solid.
  • Finely powdered 5-fluoro-6-hydroxy-2,4(1H,3H)-pyrimidinedione (74 g, 0.507 mol) was added portionwise over 30 min to POCl 3 (232 mL, 2.5 mol) with stirring (exothermic). Upon complete addition, the mixture was held at 60° C. while N,N,-dimethylaniline (65 mL) was added dropwise by syringe. After addition, the mixture was heated to 100-110° C. (internal) until the reaction was judged complete, usually in 4-8 h. The mixture was cooled and the bulk of the remaining POCl 3 was removed by careful vacuum distillation at 80-90° C. (some product can be detected in the POCl 3 distillate).
  • 2,4,6-Trichloro-5-fluoropyrimidine (20.92 g, 104.1 mmol) was dissolved in THF (300 mL) at room temperature and stirred. To this stirring solution was added t-butyl carbazate (13.74 g, 104.1 mmol), followed by diisopropylethylamine (19.0 mL, 109.3 mmol). The reaction mixture turned light yellow, and after several minutes a precipitate formed. The reaction appeared complete after 1.5 h, as monitored by TLC (10% EtOAc/Hex). The reaction mixture was concentrated in vacuo to remove most of the THF, and the residue was dissolved in CH 2 Cl 2 ( ⁇ 400 mL).
  • 4,6-Dichloro-2-ethyl-5-fluoropyrimidine (195 mg, 1.0 mmol) was dissolved in 3 mL of MeOH and stirred at room temperature. Azetidine (74 ⁇ L, 1.1 mmol) was added, followed by DIPEA (383 ⁇ L, 2.2 mmol). The resulting reaction mixture was stirred at room temperature until the azetidine displacement of one chlorine was complete as monitored by LCMS. Then, the MeOH was removed in vacuo, and the remaining residue was dissolved in a mixture of 2 mL DMSO and 1 mL of hydrazine. The resulting solution was heated at 40° C. for 1 h until the reaction was deemed complete by LCMS.
  • reaction mixture was then cooled to room temperature and purified by RP-HPLC to provide 4-(2,5-dihydro-1H-pyrrol-1-yl)-5-fluoro-6-hydrazino-2-methylpyrimidine (142 mg, 68%).
  • reaction mixture was purified by RP-HPLC to provide ((2R)-2-(cyclopentylmethyl)-3- ⁇ 2-[6-(2,5-dihydro-1H-pyrrol-1-yl)-5-fluoro-2-methyl-4-pyrimidinyl]hydrazino ⁇ -3-oxopropyl)(tetrahydro-2H-pyran-2-yloxy)formamide (140 mg, 55%).
  • reaction mixture was then purified by RP-HPLC to provide the assumed (1S,4S)-2-(2-chloro-5-fluoro-6-hydrazino-4-pyrimidinyl)-5-methyl-2,5-diazabicyclo[2.2.1]heptane (first eluent), as well as the assumed 4-chloro-5-fluoro-6-[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]hept-2-yl]-2(1H)-pyrimidinone hydrazone (second eluent).
  • Example 7 was also prepared in the following manner:
  • 4,6-Dichloro-5-fluoro-2-methylpyrimidine (6 g, 33 mmol) was dissolved in 50 mL of iPrOH and stirred at room temperature.
  • Azetidine-HCl (3.25 g, 35 mmol) was added, followed by 14.4 mL of DIPEA.
  • the resulting reaction mixture was stirred for 3 h, and then hydrazine monohydrate was added (4.0 mL, 82.5 mmol) and the contents were heated to 80° C. overnight.
  • the reaction mixture was then cooled to room temperature and a precipitate formed. The precipitate was filtered, washed with iPrOH, and dried.
  • the mixture was stirred for an additional 30 min at 0° C.
  • aqueous NaOH 50% w/w
  • the mixture was stirred at 0° C. for 2 h, and then warmed to 20° C.
  • the mixture was washed with heptane (165 mL) followed by a second portion of fresh heptane (240 mL).
  • the aqueous phase was cooled to 0° C., and adjusted to pH ⁇ 2 with concentrated aqueous HCl while keeping the internal temperature less than 10° C.
  • the mixture was placed in a 0° C.
  • the resulting solution was concentrated in vacuo to approximately 10% volume, diluted with EtOAc (400 mL), and concentrated in vacuo to approximately 30% volume.
  • the resulting solid was collected by vacuum filtration and washed with EtOAc.
  • the mother liquor and EtOAc washings were concentrated in vacuo to approximately 10% volume, and the resulting solid was collected by vacuum filtration and washed with EtOAc.
  • the two crops of solid were combined and dried at 50° C.
  • the resulting solution was concentrated in vacuo to a volume of approximately 70 mL, and was then diluted with EtOAc (500 mL). The solution was concentrated in vacuo to remove approximately 100 mL of solvent. The resulting solid was collected by vacuum filtration, and washed well with EtOAc followed by hexanes. The mother liquor was concentrated in vacuo, and then diluted with EtOAc (200 mL). The mixture was concentrated in vacuo to approximately 50% volume, and the resulting solid was collected by vacuum filtration and washed well with EtOAc followed by hexanes. The two batches of solid were combined and placed under high vacuum overnight. To this material was then added approximately 466 mg of material prepared through a similar sequence, and the combined batch was heated at 50° C.
  • the Pd/C was removed by filtration through Celite, washing with MeOH and CH 2 Cl 2 .
  • the filtrate was concentrated in vacuo. As the evaporation proceeded, the product crystallized out from the remaining solution. The evaporation continued until only ⁇ 50 mL of liquid remained.
  • the crystals were then collected by filtration to provide the product as a white solid (10.0 g).
  • the filtrate was further evaporated to give a second crop of crystals (1.5 g) as the pure product. In the same way, a third crop was collected.
  • N- ⁇ (2R)-2-(Cyclopentylmethyl)-3-[2-(6- ⁇ [2-(dimethylamino)ethyl](methyl)amino ⁇ -2-ethyl-5-fluoro-4-pyrimidinyl)hydrazino]-3-oxopropyl ⁇ -N-hydroxyformamide was prepared according to General Procedure B, utilizing commercially-available N,N,N′-trimethylethylenediamine in place of azetidine in Part A.
  • the solution was then diluted with Et 2 O (1000 mL) and washed with water (1000 mL).
  • the aqueous phase was extracted with a fresh portion of Et 2 O (1000 mL), and the combined organic phase was washed with water (2 ⁇ 500 mL).
  • the organic phase was then diluted with DCM (1000 mL), dried over anhydrous Na 2 SO 4 , filtered, and concentrated in vacuo.
  • the residue was filtered through a silica gel plug (30% EtOAc in hexanes; 1% Et 3 N). The solution was then concentrated in vacuo, and the residue was azeotroped with MeOH.
  • the residue was diluted with MeOH (1000 mL), and crystallized by addition of water.
  • the mixture was stirred overnight, diluted with Et 2 O (1000 mL), and washed with water (1000 mL).
  • the aqueous phase was extracted with a fresh portion of Et 2 O (1000 mL), and the combined organic phase was washed with water (3 ⁇ 300 mL).
  • the combined aqueous phase was extracted with a fresh portion of Et 2 O (300 mL), and this Et 2 O phase was washed with water (200 mL).
  • the resulting dark filtrate was concentrated in vacuo and purified by preparative reverse phase chromatography (Luna C18 (2) column; 10 microns; 101.6 mm ⁇ 250 mm; 250 nm UV detection; 480 mL/min; 40 mg/mL sample concentration; 4 g injection mass; mobile phase A: 300 mmol aqueous ammonium formate at pH 4.0; mobile phase B: MeCN; method: 28% B for 9 min; 90% B for 9 min; 28% B for 5 min).
  • the product solution fractions were combined and adjusted to pH 6.8 with aqueous NH 4 OH, and then stirred with Darco (50% weight load based on crude product) for 30 min at room temperature. The solution was then filtered through Celite.
  • the filtrate was concentrated to a volume of 3.5 L, and the pH was adjusted from 5.6 to 8.5 with NH 4 OH, affording an orange precipitate.
  • the aqueous phase was extracted 3 times with EtOAc, and then the combined organics were washed with water and brine.
  • the organics were dried (Na 2 SO 4 ), filtered, and concentrated in vacuo to a volume of 1 L, producing a tan precipitate.
  • An equal volume of heptane (1 L) was added, and the mixture was cooled to 0° C. for 1 h. Then the product was isolated by filtration, washing with heptane, and dried under reduced pressure at 50° C.
  • (3S)-1,3-Dimethylpiperazine, dihydrochloride can be prepared in a manner similar to (3R)-1,3-dimethylpiperazine, dihydrochloride (Example 63), using CBZ-L-alanine in place of CBZ-D-alanine.
  • Phenylmethyl[2-oxo-2-(1-pyrrolidinyl)ethyl]carbamate (782 mg, 3 mmol) was dissolved in 30 mL of MeOH, degassed and placed under argon. 10% Pd/C (117 mg) was added followed by 0.5 mL 6N HCl, and the contents were thoroughly degassed and placed under a hydrogen balloon for approximately 3 hrs. The contents were then degassed and filtered through Celite, and the Celite pad was washed with DCM and MeOH. The resulting filtrate was concentrated in vacuo to provide the 2-oxo-2-(1-pyrrolidinyl)ethanamine, hydrochloride salt (491 mg, 100%). LCMS: (M+H) + : 129.1.
  • Phenylmethyl[(1R)-1-methyl-2-oxo-2-(1-pyrrolidinyl)ethyl]carbamate (496 mg, 1.8 mmol) was dissolved in 20 mL of MeOH, degassed and placed under argon. 10% Pd/C (125 mg) was added, and the contents were thoroughly degassed and placed under a hydrogen balloon overnight. The contents were then degassed and filtered through Celite, and the Celite pad was washed with DCM and MeOH. The resulting filtrate was concentrated in vacuo to provide the (2R)-1-oxo-1-(1-pyrrolidinyl)-2-propanamine (235 mg, 91%). LCMS: (M+H) + : 143.1.
  • N 1 ,N 1 -dimethyl-D-alaninamide, hydrochloride salt was prepared in a manner similar to Example 69, utilizing N—CBZ-D-alanine in place of N—CBZ-glycine, utilizing dimethylamine, hydrochloride salt in place of pyrrolidine, and using 3 equivalents of NMM.
  • N2-(6- ⁇ 2-[(2R)-3-Cyclopentyl-2- ⁇ [formyl(hydroxy)amino]methyl ⁇ propanoyl]hydrazino ⁇ -5-fluoro-2-methyl-4-pyrimidinyl)-N,N-dimethyl-D-alaninamide was prepared according to General Procedure A, utilizing N 1 ,N 1 -dimethyl-D-alaninamide, hydrochloride salt in place of pyrrolidine in Part A.
  • reaction mixture was then purified by RP-HPLC to provide ((2R)-2-(cyclopentylmethyl)-3- ⁇ 2-[6-(4-ethyl-1-piperazinyl)-5-fluoro-2-(methyloxy)-4-pyrimidinyl]hydrazino ⁇ -3-oxopropyl)[(phenylmethyl)oxy]formamide as a red solid (0.145 g, 83%).
  • LCMS: (M+H) + 558.3.
  • N2-(6- ⁇ 2-[(2R)-3-Cyclopentyl-2- ⁇ [formyl(hydroxy)amino]methyl ⁇ propanoyl]hydrazino ⁇ -2-ethyl-5-fluoro-4-pyrimidinyl)-N,N-dimethyl-D-alaninamide was prepared according to General Procedure B, utilizing N 1 ,N 1 -dimethyl-D-alaninamide (Example 74) in place of azetidine in Part A.
  • reaction was purified directly by RP-HPLC yielding the benzyl protected intermediate which was subsequently dissolved in degassed MeOH (7 mL). To this solution was added 10% Pd/C (6.3 mg) and the combined mixture was stirred under a hydrogen balloon for 2 hours. Filtration of the catalyst and evaporation of the solvent yielded a crude residue which was purified by RP-HPLC.

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