# Patent

## Title
Synthesis of novel inhibitors of isoprenoid biosynthesis

## Abstract

Antibacterial IspF inhibitor compounds and compositions are described. Methods include administering described compounds and compositions to treat bacterial or parasitic infections and to inhibit or parasite or bacterial growth.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a U.S. nationalization under 35 U.S.C. §371 of International Application No. PCT/US2013/037765, Apr. 23, 2013, which claims the benefit of priority under 35 U.S.C. §119(e) to U.S. Provisional Patent Application No. 61/637,642, filed Apr. 24, 2012, Application No. 61/701,269, filed Sep. 14, 2012, and Application No. 61/703,145, filed Sep. 19, 2012. The disclosures set forth in the referenced applications are incorporated herein by reference in their entireties.


BACKGROUND
The fight against malaria, tuberculosis, and other infectious disease is growing more difficult due to the emergence of drug resistant forms of these diseases. One strategy to address the resistance problem is to develop novel anti-infective agents that employ new mechanisms of action. In recent studies, it has been shown that bacterial and parasitic organisms, such as those involved in malaria, tuberculosis, and melioidosis, use the methylerythritol isoprenoid (MEP) biosynthetic pathway, to produce isoprenoids, which are the basic building blocks of many essential substances found in plants and animals. Fortunately, humans do not use this process, which means any foreign pathogen in the human body that uses the MEP pathway can be targeted due to the different enzymes it puts to use.
SUMMARY
Materials and methods to design and create different analogs of oxdihydropyrimidine carboxylic acid, 4-(1H-imidazol-1-yl)phenol and 4-(1H-imidazol-5-yl)phenol that inhibit the 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MECDP) synthase, or IspF, enzymes of the MEP pathway, are described. In completing these objectives, the use of docking software software (SYBYL) was used for the theoretical design of compounds.
Compounds were designed to inhibit the enzyme IspF present in the MEP pathway. The MEP pathway is a non-mevalonate pathway or 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate pathway (MEP/DOXP pathway) of isoprenoid biosynthesis. Analogs from the claimed chemical series were found to inhibit the enzyme IspF from Burkholderia pseudomallei using SPR and NMR assays at micromolar concentrations. Selected compounds were shown to have anti-bacterial activity in Burkholderia thailandensis, a non-fermenting motile gram-negative bacteria that is often used as a model for Burkholderia pseudomallei, a BSL-3 pathogen. Burkholderia pseudomallei is a class B pathogen and is considered a biosecurity threat. Selected analogs were screened against Burkolderia pseudomallei and found to have anti-bacterial activity.
Anti-infective 2-amino-1,6-dihydro-6-oxo-5-pyrimidinecarboxylic acid derivatives are disclosed. The anti-infective 2-amino-1,6-dihydro-6-oxo-5-pyrimidinecarboxylic acid derivatives are administered to a subject, such as a mammal, such as a human or a horse, to treat a bacterial infection. Compounds and compositions as disclosed herein are administered to a subject to inhibit bacterial growth, such as Burkholderia spp. or Mycobacterium spp., and to treat subjects infected by such bacteria. The compounds disclosed in this application inhibit the enzymes IspD and or IspF and will be useful for the treatment of microbial infections. Compounds in this application have demonstrated anti-bacterial activity against Burkholderia psuedomallei, Burkholderia thailandenesis and Plasmodium falciparum. 
Embodiments include compounds of Formula I:




wherein
X is N and Y is C, or X is C and Y is N;
R1 is OH or OR5, wherein R5 is lower alkyl, acyl, CH2OCOCH3, or a prodrug;
R2 is alkyl, aryl, alkylaryl, arylheteroaryl, or heteroaryl;
R3 is H or lower alkyl; and
R4 is H or lower alkyl.
Embodiments include compounds of Formula II:




wherein
R1 is H or lower alkyl;
R2 is H or lower alkyl; and
R3 is alkyl, aryl, alkylaryl, arylheteroaryl, or heteroaryl.
Embodiments include compounds of Formula III:




wherein
R1 is H or lower alkyl;
R2 is H or lower alkyl; and
R3 is alkyl, aryl, alkylaryl, arylheteroaryl, or heteroaryl.
The most potent anti-bacterial compound, against Burkholderia in initial tests was HGN-0118 from the pyrimidine series with 94.5% inhibition at 1 mM.
The most potent antimalarial compound in initial tests was HGN-0049, submicromolar for all three strains of drug resistant malaria. Another potent compound was HGN-0051.
Another potent antibacterial compound against Burkholderia is from the imidazole series, HGN-0095 with 88.3% inhibition.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a graph depicting B. pseudomallei growth rates (as measured by absorbance at OD600) over time (min) in the presence of IspF inhibitor compounds HGN-0005, -0013, -0015, -0017, -0020, -0023, -0024, -0025, -0026, -0027, -0028, -0029, -0030, -0031, and -0032, and a negative control of no inhibitor.
FIG. 2 shows a graph depicting B. pseudomallei growth rates (as measured by absorbance at OD600) over time (min) in the presence of IspF inhibitor compounds HGN-0023, -0027, -0028, and -0029.
FIG. 3 shows a graph depicting B. pseudomallei growth rates (as measured by absorbance at OD600) over time (min) in the presence of the IspF inhibitor compound HGN-0023 at concentrations of 1 mM, 500 μM, 250 μM, 125 μM, and 62.5 μM; Controls included (a) DMSO and medium without bacteria (the blank); (b) DMSO, and (c) 300 μg/ml of kanamycin.
FIG. 4 shows a graph depicting B. pseudomallei growth rates (as measured by absorbance at OD600) over time (min) in the presence of the IspF inhibitor compound HGN-0027 at concentrations of 1 mM, 500 μM, 250 μM, 125 μM, and 62.5 μM. Controls included (a) DMSO and medium without bacteria (the blank); (b) DMSO, and c) 300 μg/ml of kanamycin.
FIG. 5 shows a graph depicting B. pseudomallei growth rates (as measured by absorbance at OD600) over time (min) in the presence of the IspF inhibitor compound HGN-0028 at concentrations of 1 mM, 500 μM, 250 μM, 125 μM, and 62.5 μM. Controls included (a) DMSO and medium without bacteria (the blank); (b) DMSO, and (c) 300 μg/ml of kanamycin.
FIG. 6 shows a graph depicting B. pseudomallei growth rates (as measured by absorbance at OD600) over time (min) in the presence of the IspF inhibitor compound HGN-0029 at concentrations of 1 mM, 500 μM, 250 μM, 125 μM, and 62.5 μM. Controls included (a) DMSO and medium without bacteria (the blank); (b) DMSO, and (c) 300 μg/ml of kanamycin.
FIG. 7 shows a graph depicting B. pseudomallei strain 1026b growth rates (as measured by absorbance at OD600) over time (min) in the presence of the IspF inhibitor compound HGN-0027 at concentrations of 1 mM, 500 μM, 250 μM, 125 μM, 62.5 μM, and 31.25 μM. Controls included (a) DMSO and medium without bacteria (the blank); (b) DMSO, and (c) 300 μg/ml of kanamycin.
FIG. 8 shows a graph depicting B. pseudomallei strain 340 growth rates (as measured by absorbance at OD600) over time (min) in the presence of the IspF inhibitor compound HGN-0027 at concentrations of 1 mM, 500 μM, 250 μM, 125 μM, 62.5 μM, and 31.25 μM. Controls included (a) DMSO and medium without bacteria (the blank); (b) DMSO, and (c) 300 μg/ml of kanamycin.
FIG. 9 shows a graph depicting B. pseudomallei strain 1026b growth rates (as measured by absorbance at OD600) over time (min) in the presence of the IspF inhibitor compound HGN-0028 at concentrations of 1 mM, 500 μM, 250 μM, 125 μM, 62.5 μM, and 31.25 μM. Controls included (a) DMSO and medium without bacteria (the blank); (b) DMSO, and (c) 300 μg/ml of kanamycin.
FIG. 10 shows a graph depicting B. pseudomallei strain 340 growth rates (as measured by absorbance at OD600) over time (min) in the presence of the IspF inhibitor compound HGN-0028 at concentrations of 1 mM, 500 μM, 250 μM, 125 μM, 62.5 μM, and 31.25 μM. Controls included (a) DMSO and medium without bacteria (the blank); (b) DMSO, and (c) 300 μg/ml of kanamycin.
FIG. 11 shows a schematic of isoprenoid metabolism through the non-mevalonate pathway. The non-mevalonate pathway is the exclusive route to isoprenoid biosynthesis in eubacteria and the malaria parasite, P. falciparum. This pathway generates the basic isoprenoid building blocks IPP and DMAPP, which are elaborated to create diverse downstream products. Enzyme names are in bold.



DETAILED DESCRIPTION
Antimicrobial drug resistance is an urgent problem in the control and treatment of many of the world's most serious infections, including Plasmodium falciparum malaria, tuberculosis, and healthcare associated infections with Gram-negative bacteria. Because the nonmevalonate pathway of isoprenoid biosynthesis is essential in eubacteria and P. falciparum and this pathway is not present in humans, there is great interest in targeting the enzymes of non-mevalonate metabolism for antibacterial and antiparasitic drug development.
Isoprenoids include a large, diverse group of intracellular metabolites with multiple cellular functions, including roles in membrane structure, cellular respiration, and cell signaling [Zhang et al. (2011); Gershenzon and Dudareva (2007)]. There are two distinct biosynthetic routes for producing isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the basic isoprenoid building blocks. Mammals, including humans, exclusively utilize the classic metabolic route through mevalonate. In contrast, eubacteria, cyanobacteria, and plant chloroplasts use an alternative route that produces the key intermediate 1-D-deoxyxylulose 5-phosphate (DOXP) from pyruvate (FIG. 11) (Hunter, 2007). In bacteria that use this pathway, including Escherichia coli, Burkholderia pseudomallei and Mycobacterium tuberculosis, genetic studies have demonstrated that non-mevalonate isoprenoid biosynthesis is essential.
The malaria parasite Plasmodium falciparum annually kills nearly 1 million people, primarily young children. There is widespread resistance to older antimalarial drugs, such as chloroquine, and emerging resistance to new artemisinin-based therapies. P. falciparum also utilizes non-mevalonate isoprenoid biosynthesis, which is essential to the parasite. Novel non-mevalonate pathway inhibitors therefore hold great promise as antimicrobial agents with broad activity against major human pathogens, including P. falciparum, B. pseudomallei, M. tuberculosis, and enterobacteria, for which global drug resistance has created an urgent need.
Compounds
The development of multi-drug resistance in bacteria and parasites that cause human disease is a growing problem in world health. The claimed compounds inhibit a unique enzyme pathway that is only found in certain types of infectious disease agents, but not in human beings. Compounds from this series will lead to improved drugs and other treatments for infectious diseases such as malaria and a range of bacterial infections. Members have shown antibacterial activity against Burkholderia thailandensis. 
Materials and methods to design and create different analogs of oxdihydropyrimidine carboxylic acid that inhibit the IspF enzymes of the MEP pathway are described. Embodiments include substituted pyrimidine and imidazole derivatives, compositions containing the pyrimidine and imidazole derivatives, and methods of treatment using therapeutically effective amounts of the pyrimidine and imidazole derivatives. Compounds and compositions disclosed herein can be used to treat bacterial disease, wherein the bacteria utilitze the non-mevalonate pathway, such as Burkholderia spp. and Mycobacterium spp.
Embodiments include compounds of Formula I:




wherein
X is N and Y is C, or X is C and Y is N;
R1 is OH or OR5, wherein R5 is lower alkyl, acyl, CH2OCOCH3, or prodrugs for phenolic groups;
R2 is alkyl, aryl, alkylaryl, arylheteroaryl, or heteroaryl;
R3 is H or lower alkyl; and
R4 is H or lower alkyl.
Embodiments include compounds of Formula II:




wherein
R1 is H or lower alkyl;
R2 is H or lower alkyl; and
R3 is alkyl, aryl, alkylaryl, arylheteroaryl, or heteroaryl.
Embodiments also include compounds of Formula III:




wherein
R1 is H or lower alkyl;
R2 is H or lower alkyl; and
R3 is alkyl, aryl, alkylaryl, arylheteroaryl, or heteroaryl
Anti-infective 2-amino-1,6-dihydro-6-oxo-5-pyrimidinecarboxylic acid derivatives are disclosed.
Specific compounds are disclosed in Tables 2-5 of Example 37 and Tables 6-9 of Example 38 herein.
Pharmaceutical Compositions
Although it is possible for compounds to be administered alone in a unit dosage form, compounds are typically administered in admixture with a carrier as a pharmaceutical composition to provide a unit dosage form. A pharmaceutical composition comprises a pharmaceutically acceptable carrier in combination with a compound disclosed herein or a pharmaceutically acceptable salt thereof.
A pharmaceutically acceptable carrier includes, but is not limited to, physiological saline, ringers, phosphate-buffered saline, and other carriers known in the art. Pharmaceutical compositions can also include additives such as, for example, stabilizers, antioxidants, colorants, excipients, binders, thickeners, dispersing agents, readsorpotion enhancers, buffers, surfactants, preservatives, emulsifiers, isotonizing agents, and diluents. Pharmaceutically acceptable carriers and additives are chosen such that side effects from the pharmaceutical compound are minimized and the performance of the compound is not canceled or inhibited to such an extent that treatment is ineffective.
Methods of preparing pharmaceutical compositions containing a pharmaceutically acceptable carrier in combination with a therapeutic compound or a pharmaceutically acceptable acid addition salt of a compound are known to those of skill in the art. The invention also includes pharmaceutically acceptable salts of the compounds of the invention. The compounds of the invention are capable of forming both pharmaceutically acceptable acid addition and/or base salts.
All methods can include the step of bringing one of the compounds disclosed herein in association with a carrier and one or more additives. Formulations generally are prepared by uniformly and intimately bringing a compound into association with a liquid carrier or a finely divided solid carrier or both, and then, if necessary, shaping the product into the desired unit dosage forms.
As used herein, the term “pharmaceutically acceptable carrier” means a non-toxic, inert solid, semi-solid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type.
Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents.
In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution that, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form may be accomplished by dissolving or suspending the drug in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the drug in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio of drug to polymer and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations may also be prepared by entrapping the drug in liposomes or microemulsions that are compatible with body tissues.
Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid; b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, acetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may also comprise buffering agents.
The active compounds can also be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.
Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches.
Compositions may also be formulated for delivery as a liquid aerosol or inhalable dry powder.
The compounds may also be formulated for use as topical powders and sprays that can contain, in addition to the compounds of this invention, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances.
Transdermal patches have the added advantage of providing controlled delivery of a compound to the body.
According to the methods of treatment of the present invention, bacterial infections are treated or prevented in a patient such as a human or lower mammal by administering to the patient a therapeutically effective amount of a compound of the invention, in such amounts and for such time as is necessary to achieve the desired result. By a “therapeutically effective amount” of a compound of the invention is meant a sufficient amount of the compound to treat bacterial or parasitic infections, at a reasonable benefit/risk ratio applicable to any medical treatment. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular patient will depend upon a variety of factors including the disorder being treated and the severity of the disorder, the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors well known in the medical arts.
A “kit” used in the instant application can include a container comprising the pharmaceutical compositions and may also include divided containers such as a divided bottle or a divided foil packet. The container can be in any conventional shape or form as known in the art that is made of a pharmaceutically acceptable material, for example a paper or cardboard box, a glass or plastic bottle or jar, a resealable bag (for example, to hold a “refill” of tablets for placement into a different container), or a blister pack with individual doses for pressing out of the pack according to a therapeutic schedule. The container employed can depend on the exact dosage form involved, for example a conventional cardboard box would not generally be used to hold a liquid suspension. It is feasible that more than one container can be used together in a single package to market a single dosage form. For example, tablets may be contained in a bottle that is in turn contained within a box.
A “daily dose” can be a single tablet or capsule or several tablets or capsules to be taken on a given day.
The kits of the present invention may also include, in addition to ISPF inhibitors, one or more additional pharmaceutically active compounds. Preferably, the additional compound is another ISPF inhibitor or another compound useful to treat bacterial or parasitic infections. The additional compounds may be administered in the same dosage form as the ISPF inhibitor compound or in different dosage forms. Likewise, the additional compounds can be administered at the same time as the ISPF inhibitor compound(s) or at different times.
Methods of Treatment
Burkholderia spp. cause a number of diseases. For instance, Burkholderia mallei is the etiologic agent of glanders. While glanders primarily affects horses, humans, dogs, cats, goats, mules, and donkeys can also contract glanders. Glanders often manifests itself as pulmonary infection. In pulmonary infections, pneumonia, pulmonary abscesses, and pleural effusion can occur. Glanders can also be a localized infection of open wounds and of mucus membranes in the eyes, nose, and respiratory tract. Burkholderia thailandensis is an opportunistic pathogen that can cause pneumonia and septicemia. Burkholderia pseudomallei the causative agent of melioidosis.
In an embodiment, a compound or composition disclosed herein can be administered to a subject to treat a Burkholderia infection. In an embodiment, compounds and compositions disclosed herein can be administered to a subject to treat glanders. An embodiment includes administering a compound or composition disclosed herein to a subject concurrently with the administration of at least one of tetracycline, ciprofloxacin, streptomycin, novobiocin, gentamicin, imipenem, ceftrazidime, or a sulfonamide. In another embodiment, compounds and compositions disclosed herein can be administered to a subject to treat melioidosis.
Multidrug resistant tuberculosis (MDR-TB), and even extensively drug resistant tuberculosis (XDR-TB) has become more prevalent in the last 20 to 40 years. New treatments are sought to battle the rising rates of drug resistant TB cases. Mycobacterium tuberculosis, the etiologic agent of tuberculosis, generates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) via the non-mevalonate pathway. Thus, M. tuberculosis is a target for the compounds and compositions disclosed herein. Treatment with compounds and compositions as disclosed herein represent new treatments for tuberculosis. As such, an embodiment includes administering a compound or composition as disclosed herein to a subject with tuberculosis. The treatment with the compounds and compositions disclosed herein may optionally be administered with at least one of the first line drugs ethambutol, isoniazid, rifampicin, or pyrazinamide. The treatment with the compounds and compositions disclosed herein may optionally be administered with at least one of the second line drugs an aminoglycoside (e.g., streptomycin, kanamycin, amikacin), a fluoroquinolone (e.g., ciprofloxacin, ofloxacin, sparfloxacin, moxifloxacin, etc.), capreomycin, viomycin, enviomycin, a thioamide (e.g., ethionamide and protionamide), cycloserine, para-aminosalicylic acid, thiacetazone, clofazimine, linezolid, a macrolide (e.g., clarithromycin, azithromycin), or amoxicillin/clavulanate.
Methods of treating bacterial or parasitic infection include administering a compound or composition as described herein, and optionally further comprising administering at least one other antibacterial agent.
Definitions
The term “compound disclosed herein” and similar terms refers to an IspF inhibitor compound as described herein, a compound of formulae I, II, or III or compounds of Tables 2-9, or a compound described in the Examples, or a pharmaceutically acceptable salt, solvate, clathrate, hydrate, polymorph or prodrug thereof.
Compounds disclosed herein may contain one or more chiral centers and/or double bonds and, therefore, exist as stereoisomers, such as double-bond isomers (i.e., geometric isomers), enantiomers, or diastereomers. According to this invention, the chemical structures depicted herein, including the compounds of this invention, encompass all of the corresponding compounds' enantiomers, diastereomers and geometric isomers, that is, both the stereochemically pure form (e.g., geometrically pure, enantiomerically pure, or diastereomerically pure) and isomeric mixtures (e.g., enantiomeric, diastereomeric and geometric isomeric mixtures). In some cases, one enantiomer, diastereomer or geometric isomer will possess superior activity or an improved toxicity or kinetic profile compared to other isomers. In those cases, such enantiomers, diastereomers and geometric isomers of compounds of this invention are preferred.
The term “alkyl” refers to a saturated linear or branched hydrocarbon radical. In one embodiment, alkyl has from 1 to 8 carbon atoms. In another embodiment, alkyl has from 1 to 6 carbon atoms. In another embodiment, alkyl has from 1 to 4 carbon atoms. In one embodiment, alkyl has 1 carbon. The alkyl group may optionally be substituted with one or more substituents such as fluorine, chlorine, alkoxy groups having from 1 to 8 carbon atoms (e.g., methoxy or ethoxy), or amido groups having from 1 to 8 carbon atoms, such as acetamido. These substituents may themselves be substituted with one or more functional groups such as hydroxy groups, carboxy groups, acetoxy groups, or halogens.
As used herein “aryl” means a mono- or poly-nuclear aromatic hydrocarbon radical. Examples of “aryl” groups include, but are not limited to aromatic hydrocarbons such as a phenyl group or a naphthyl group. The aromatic group may optionally be substituted with one or more substituents such as fluorine, chlorine, alkyl groups having from 1 to 8 carbon atoms (e.g., methyl or ethyl), alkoxy groups having from 1 to 8 carbon atoms (e.g., methoxy or ethoxy), alkoxyalkyl groups having from 1 to 8 carbon atoms and one or more oxygen atoms, or amido groups having from 1 to 8 carbon atoms, such as acetamido. These substituents may themselves be substituted with one or more functional groups such as hydroxy groups, carboxy groups, acetoxy groups, or halogens.
In one embodiment, aryl is a phenyl group or a naphthyl group that is either unsubstituted or substituted.
In another embodiment, aryl is a heteroaryl in which one or more of the carbon atoms of an aromatic hydrocarbon is substituted with a nitrogen, sulfur, or oxygen. Examples of a “heteroaryl” include but are not limited to pyridine, pyrimidine, oxazine, and oxathiazine. Likewise, the heteroaryl may optionally be substituted with functional groups such as hydroxy groups, carboxy groups, halogens, and amino groups. Examples of a “heterocycle” include but are not limited to pyran and dioxin.
The term “lower” refers to a group having up to four atoms. For example, a “lower alkyl” refers to an alkyl radical having from 1 to 4 carbon atoms, “lower alkoxy” refers to “—O—(C1-C4)alkyl. Included in this definition is a lower group having 1 to 3 carbon atoms.
The term “cycloalkyl” refers to a saturated, mono- or polycyclic alkyl radical having from 3 to 20 carbon atoms. Representative cycloalkyls include cyclopropyl, 1-methylcyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl, cyclononyl, -cyclodecyl, octahydro-pentalenyl, and the like. Cycloalkyl groups may be optionally substituted with one or more substituents.
As used herein, the term “haloalkyl” means an alkyl group, in which one or more (including all) the hydrogen radicals are replaced by a halo group, wherein each halo group is independently selected from —F, —Cl, —Br, and —I. The term “halomethyl” means a methyl in which one to three hydrogen radical(s) have been replaced by a halo group. Representative haloalkyl groups include trifluoromethyl, bromomethyl, 1,2-dichloroethyl, 4-iodobutyl, 2-fluoropentyl, and the like.
The term “polymorph” refers to solid crystalline forms of a compound or complex thereof. Different polymorphs of the same compound can exhibit different physical, chemical and/or spectroscopic properties. Different physical properties include, but are not limited to stability (e.g., to heat or light), compressibility and density (important in formulation and product manufacturing), and dissolution rates (which can affect bioavailability). Differences in stability can result from changes in chemical reactivity (e.g., differential oxidation, such that a dosage form discolors more rapidly when comprised of one polymorph than when comprised of another polymorph) or mechanical characteristics (e.g., tablets crumble on storage as a kinetically favored polymorph converts to thermodynamically more stable polymorph) or both (e.g., tablets of one polymorph are more susceptible to breakdown at high humidity). Different physical properties of polymorphs can affect their processing. For example, one polymorph might be more likely to form solvates or might be more difficult to filter or wash free of impurities than another due to, for example, the shape or size distribution of particles of it.
The term “substituent” refers to a group “substituted” on an alkyl, cycloalkyl, aryl, heterocyclyl, or heteroaryl group at any atom of that group. Suitable substituents include, without limitation, alkyl, alkenyl, alkynyl, alkoxy, halo, hydroxy, cyano, nitro, amino, SO3H, perfluoroalkyl, perfluoroalkoxy, methylenedioxy, ethylenedioxy, carboxyl, oxo, thioxo, imino (alkyl, aryl, aralkyl), S(O)nalkyl (where n is 0-2), S(O)n aryl (where n is 0-2), S(O)n heteroaryl (where n is 0-2), S(O)n heterocyclyl (where n is 0-2), amine (mono-, di-, alkyl, cycloalkyl, aralkyl, heteroaralkyl, and combinations thereof), ester (alkyl, aralkyl, heteroaralkyl), amide (mono-, di-, alkyl, aralkyl, heteroaralkyl, and combinations thereof), sulfonamide (mono-, di-, alkyl, aralkyl, heteroaralkyl, and combinations thereof), unsubstituted aryl, unsubstituted heteroaryl, unsubstituted heterocyclyl, and unsubstituted cycloalkyl. In one aspect, the substituents on a group are independently any one single, or any subset of the aforementioned substituents.
The term “antibacterial” refers to compounds or compositions disclosed herein that have either bactericidal or bacteriostatic activity. An “antibacterial” compound or composition in this context can inhibit the growth of B. mallei, B. pseudomallei, and other Burkholderia spp., and other gram-negative bacteria. Additionally, an antibacterial compound or composition in this context can inhibit the growth of Mycobacterium tuberculosis and other Mycobacterium spp. The term “inhibiting the growth” indicates that the rate of increase in the numbers of a population of particular bacteria is reduced. Thus, the term includes situations in which the bacterial population increases but at a reduced rate, as well as situations where the growth of the population is stopped, as well as situations where the numbers of the bacteria in the population are reduced or the population even eliminated.
An “antimicrobial agent” refers to a substance that kills microbes or inhibits microbial growth or replication. Microbes are microorganisms that include bacteria, fungi, or protozoans. An antimicrobial agent can be an antibiotic (e.g., streptomycin) or can be an non-pharmaceutical antimicrobial (e.g., chlorhexidine, silver, triclosan).
The terms “treat” and “treatment” refer to therapeutic treatment, wherein the object is to inhibit or slow down (lessen) an undesired physiological change or disorder, such as the development or spread of infection. For purposes of this invention, beneficial or desired clinical results include, but are not limited to, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration, or palliation of the disease state. “Treatment” can also mean prolonging survival as compared to expected survival if not receiving treatment. Those in need of treatment include those already with the condition or disorder as well as those prone to have the condition or disorder or those in which the condition or disorder is to be prevented.
“Mammal” for purposes of treatment or therapy refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, and the like. Preferably, a mammal is human.
EXAMPLES
Example 1
Analysis of IspF
To design inhibitor compounds, IspF was analyzed to better designed compounds to inhibit its function.
IspF screening by NMR spectroscopy
To design IspF inhibitor compounds, the IspF protein was analyzed by nuclear magnetic resonance (NMR) spectroscopy. NMR samples were prepared by diluting tagless, concentrated BpIspF protein in SEC buffer to 20 μm (60 μm monomer) with NMR buffer (10 mM K-Phos (pH 7.8), 50 mM NaCl, 10% (v/v) 2H2O). Compounds were assayed at ligand concentrations of 400 μm, with 400 μm cytidine and 20 μM deuterated dimethyl sulfoxide (d6-DMSO) present in a 500 μM sample volume. All experiments were conducted on a 600-MHz Bruker AV spectrometer with TCI cryoprobe set to 280 K. Screening was done using ligand-observe, protonbased one-dimensional saturation transfer difference nuclear magnetic resonance (STD-NMR) (Mayer et al., 1999) and two-dimensional nuclear Overhauser effect spectroscopy (NOESY) according to (Begley et al, 2010).
Briefly, 32 scans and 32,000 points were acquired over a 14 ppm sweep width for STD-NMR data, with a total recycle delay of 4.0 s for each mixture. A low-power 30-ms spin-lock pulse was added to filter out low-level protein peaks, and a WATERGATE sequence added to suppress bulk water signal (Piotto et al., 1992). STD-NMR pre-saturation was done using a 3.0 s-long train of Gaussian-shaped pulses with a spectral width of 600 Hz focused at -1.0 ppm, with reference irradiation set to 30 ppm. For NOESY experiments, 2,048 9 160 points were collected with a mixing time of 500 ms and a recycle delay of 2.0 s, with WATERGATE solvent suppression for each mixture.
Sequence Analysis
The IspF from nine pathogens were aligned and studied for sequence conservation. The nine pathogens were Escherichia coli, Yersinia pestis, Haemophilus influenzae, Burkholderia pseudomallei, Mycobacterium tuberculosis, Plasmodium vivax, Brucella melitensis, Babesia bovis, and Plasmodium falciparum (IspF subunit from the bifunctional IspDF enzyme). Of note, D48 was 100% conserved in the 9 pathogens. This amino acid residue does not bind substrate and has a putative structural role and a putative functional role of assisting Zn2+ ion position during catalysis. There was also 100% conservation in having the “DIG” motif, whereby D58 binds ribose and G60 is necessary for the conserved pseudo β-turn.
Additionally screening and substrate-derived fragments were soaked into crystals of IspF from B. pseudomallei. This allowed for screening ligand binding and conformation selection as analyzed by the drug design software AutoDocks (version 4.0) (The Scripps Research Institute, La Jolla, Calif.). Through this software, specific candidate compounds and classes of candidate compounds were selected.
Example 2
Synthesis of Sodium 2-((4-chlorophenethyl)amino-4-oxidopyrimidine-5-carboxylate (HGN-0028)




A mixture of ethyl 2-((4-chlorophenethyl)amino)-6-oxo-1,6-dihydropyrmidine-5-carboxylate (60 mg, 1.86 mmol) and sodium hydroxide (1M) was heated up to reflux for 4 hours and then cooled to 40° C. overnight. After heating, the solution was completely dissolved without precipitate and condensed. 1H-NMR confirmed the product as sodium 2-((4-chlorophenethyl)amino-4-oxidopyrimidine-5-carboxylate (HGN-0028) (59 mg, 94% yield).
Example 3
Synthesis of ethyl 6-oxo-2-(((tetrahydrofuran-2-yl)methyl)amino)-1,6-dihydropyrimidine-5-carboxylate (HGN-0017)




(tetrahydrofuran-2-yl)methanamine (142 mg, 1.40 mmol) was added into ethyl 2-(methylthio)-6-oxo-1,6-dihydropyrmidine-5-carboxylate (300 mg, 1.40 mmol) in methanol and refluxed overnight. After half of the starting material was consumed, the reaction mixture was reheated again overnight. Then the reaction mixture was cooled and the precipitate filtered. 1H-NMR confirmed the product as ethyl 6-oxo-2-(((tetrahydrofuran-2-yl)methyl)amino)-1,6-dihydropyrimidine-5-carboxylate (HGN-0017) (176 mg, 47% yield).
Example 4
Synthesis of ethyl 2-((1,1′-biphenyl)-4-ylamino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (HGN-0033)




Ethyl 2-(methylthio)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (60 mg, 0.233 mmol) was added to 1,1′-biphenyl-4-amine (79 mg, 0.467 mmol) dissolved in ethanol. The solution was heated in an oil bath to 80° C., while stirring, in reflux, for 72 hours. The sample was filtered and dried. 1H-NMR confirmed the structure (31 mg, 40% yield).
Example 5
Synthesis of ethyl 6-oxo-2-((4-(piperidin-1-yl)phenyl)amino)-1,6-dihydropyrimidine-5-carboxylate (HGN-0034)




Ethyl 2-(methylthio)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (200 mg, 0.934 mmol) was added to 4-(piperidin-1-yl)aniline (158 mg, 0.934 mmol) dissolved in ethanol. The solution was heated in an oil bath to 80° C., while stiffing, in reflux, for 72 hours. The sample was filtered and dried. 1H-NMR confirmed the product (HGN-0034) (15 mg, 0.447 mmol).
Example 6
Synthesis of 2-((1,1′-biphenyl)-4-ylamino)-6-oxo-1,6-dihydropyrimidine-5-carboxylic acid (HGN-0035)




A mixture of ethyl 2-((1,1′-biphenyl)-4-ylamino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (100 mg, 0.298 mmol), sodium hydroxide (1M, aq), and methanol was stirred at 70° C. for 2 hours and for 40° C. overnight. The ester did not dissolve in 3 mL methanol. The ester was then put in 3 mL dioxane and heated to 103° C. for 4 hours with an additional 1 mL of NaOH added. The reaction mixture was then heated at 40° C. overnight. After the overnight heating, the reaction mixture was cooled and the solvent removed. The reaction mixture was diluted with water, and the pH was adjusted to about 3.0. The reaction mixture was filtered to obtain the end product. 1H-NMR confirmed the product (55 mg, 60.0% yield).
Example 7
Synthesis of 6-oxo-2-((4-(piperidin-1-yl)phenyl)amino)-1,6-dihydropyrimidine-5-carboxylic acid




A mixture of ethyl 6-oxo-2-((4-(piperidin-1-yl)phenyl)amino)-1,6-dihydropyrimidine-5-carboxylate (100 mg, 0.298 mmol), sodium hydroxide (1M, aq), and methanol was stirred at 70° C. for 2 hours and for 40° C. overnight. The reaction mixture was filtered to remove the solid precipitate to verify product. Recombined the filtrate and precipitate to concentrate by adding 3 mL dioxane and heated to 103° C. for 4 hours with an additional 1 mL of NaOH added. The reaction mixture was then heated at 40° C. overnight. After the overnight heating, the reaction mixture was cooled and the solvent removed. The reaction mixture was diluted with water, and the pH was adjusted to about 3.0. The reaction mixture was filtered to obtain the end product. 1H-NMR confirmed the product (55 mg, 60% yield).
Example 8
Synthesis of ethyl 2-((4-(morpholinophenylamino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (HGN-0037)




Ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (311 mg, 1.452 mmol) and 4-morpholinoaniline (259 mg, 1.452 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. The reaction mixture was filtered to obtain the precipitate. 1H-NMR confirmed the product (294 mg, 58.8% yield).
Example 9
Synthesis of ethyl 2-((1-(tert-butoxycarbonyl)peperidin-4-yl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate




Ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (292 mg, 1.365 mmol) and tert-butyl-4-aminopiperidine-1-carboxylate (273 mg, 1.365 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. The precipitate was not evident so the solution was heated to 90° C. overnight. The final product was then recovered.
Example 10
Synthesis of ethyl 2-((1-benzylpeperidin-4-yl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate




Ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (301 mg, 1.403 mmol) and 1-benzvvylpiperidine-4-amine (267 mg, 1.403 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. The precipitate was not evident so the solution was heated to 90° C. overnight. The final product was then recovered.
Example 11
Synthesis of ethyl 2-((1-benzylpyrrolidin-3-yl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate




Ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (313 mg, 1.460 mmol) and 1-benzylpyrrolidin-3-amine (257 mg, 1.460 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. The precipitate was not evident so the solution was heated to 90° C. overnight. The final product was then recovered.
Example 12
Synthesis of Ethyl 2-((4-chlorophenethyl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (HGN-0038)




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (333 mg, 1.554 mmol) and 2-(4-chlorophenyl)ethanamine (242 mg, 1.554 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. After heating, the solution was run on thin layer chromatography and filtered. The precipitate was collected and stored. 1H-NMR confirmed the product (126 mg, 25.2% yield).
Example 13
Synthesis of Ethyl 2-([1,1′-biphenyl]-3-ylamino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (319 mg, 1.491 mmol) and [1,1′-biphenyl]-3-amine (252 mg, 1.491 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. After heating, the solution was run on thin layer chromatography and filtered. The precipitate was collected and stored. 1H-NMR confirmed the product (246 mg, 49.2%).
Example 14
Synthesis of Ethyl 2-([1,1′-biphenyl]-2-ylamino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (319 mg, 1.491 mmol) and [1,1′-biphenyl]-2-amine (252 mg, 1.491 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. After heating, the solution was run on thin layer chromatography and filtered. The precipitate was collected and stored. 1H-NMR confirmed the product.
Example 15
Synthesis of Ethyl 6-oxo-2-((4-piperidin-1-yl)amino)-1,6-dihydropyrimidine-5-carboxylate (HGN-0034)




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (313 mg, 1.460 mmol) and 4-(piperidin-1yl)aniline (257 mg, 1.460 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. After heating, the solution was run on thin layer chromatography and filtered. The precipitate was collected and stored. 1H-NMR confirmed the product (HGN-0034) (272 mg, 54.4% yield).
Example 16
Synthesis of Ethyl 2-(methylthio)-6-oxo-1,6-dihydropyrimidine-5-carboxylate




Ethyl sodium 5-(ethoxycarbonyl)-2-(methylthio)-4-oxo-4H-pyrimidin-3-ide (3.31 g, 14.00 mmol) was dissolved in 300 mL of methanol. 2 mL of HCl was added to the solution, which was condensed to yield the product.
Example 17
Synthesis of Ethyl 2-((1H-indazol-6-yl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (HGN-0040)




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (358 mg, 1.671 mmol) and 1-H-indazol-6-amine (222 mg, 1.671 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. After heating, the solution was run on thin layer chromatography and filtered. The precipitate was collected and stored. 1H-NMR confirmed the product (227 mg, 45.4% yield).
Example 18
Synthesis of Ethyl 2-((2,3-dihydro-1H-inden-2-yl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (358 mg, 1.67 mmol) and 2,3-dihyrdro-1H-inden-2-amine (222 mg, 1.67 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. Precipitate was not evident so the solution was heated up to 90° C. overnight. The product was then recovered.
Example 19
Synthesis of 2-(4-((5-(ethoxycaronyl)-6-oxo-1,6-dihydropyrimidin-2-yl)amino)phenyl)acetic acid (HGN-0041)




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (338 mg, 1.576 mmol) and 2-(4-aminophenyl)acetic acid (238 mg, 1.576 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. After heating, the solution was run on thin layer chromatography and filtered. The precipitate was collected and stored. 1H-NMR confirmed the product (HGN-0041) (235 mg, 47%).
Example 20
Synthesis of Ethyl 2-((1H-indazol-5-yl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (HGN-0042)




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihyropyrimidine-5-carboxylate (358 mg, 1.671 mmol) and 1H-indazol-5-amine (222 mg, 1.671 mmol) were dissolved in 10 mL of ethanol and heated at 80° C. overnight. After heating, the solution was run on thin layer chromatography and filtered. The precipitate was collected and stored. 1H-NMR confirmed the product (HGN-0042) (441 mg, 88% yield).
Example 21
Synthesis of Sodium 2-((4-morpholinophenyl)amino)-4-oxidopyrimidine-5-carboxylate




The mixture of ethyl 2-((4-morpholinophenyl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (210 mg, 0.610 mmol) and sodium hydroxide (1M) were heated at 105° C. for 4 hours followed by heating at 40° C. overnight. Then the solution was condensed to recover the final product (290 mg, 132% yield). 1H-NMR confirmed the product.
Example 22
Synthesis of Sodium 2-([1,1′-biphenyl]-3-ylamino)-4-oxidopyrimidine-5-carboxylate (HGN-0044)




The mixture of ethyl 2-(([1,1′-biphenyl]-3-ylamino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (179 mg, 0.534 mmol) and sodium hydroxide (1M) were heated at 105° C. for 4 hours followed by heating at 40° C. overnight. Then the solution was condensed to recover the final product. 1H-NMR confirmed the product (HGN-0044) (170 mg, 91% yield).
Example 23
Synthesis of Sodium 4-oxido-2-((piperidin-1-yl)phenyl)amino)pyrimidine-5-carboxylate (HGN-0036)




The mixture of ethyl 6-oxo-2-((4-(piperidin-1-yl)phenyl)amino-1,6-dihydropyrimidine-5-carboxylate (219 mg, 0.64 mmol) and sodium hydroxide (1M) were heated at 105° C. for 4 hours followed by heating at 40° C. overnight. Then the solution was condensed to recover the final product. 1H-NMR confirmed the product (240 mg, 105% yield).
Example 24
Synthesis of Sodium 2-((1H-indazol-6-yl)amino)-4-oxoidopyrimidine-5-carboxylate (HGN-0045)




The mixture of ethyl 2-((1H-indazol-6-yl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (144 mg, 0.481 mmol) and sodium hydroxide (1M) were heated at 105° C. for 4 hours followed by heating at 40° C. overnight. Then the solution was condensed to recover the final product. 1H-NMR confirmed the product (140 mg, 92% yield).
Example 25
Synthesis of Sodium 2-((4-(carboxylatetomethyl)phenyl)amino)-4-oxoidopyrimidine-5-carboxylate




The mixture of 2-(4-((5-(ethoxycarbonyl)-6-oxo-1,6-dihyrdropyrimidin-2-yl)amino)phenyl)acetic acid (206 mg, 0.649 mmol) and sodium hydroxide (1M) were heated at 105° C. for 4 hours followed by heating at 40° C. overnight. Then the solution was condensed to recover the final product. 1H-NMR confirmed the product.
Example 26
Synthesis of Sodium 2-((1H-indazol-5-yl)amino)-4-oxoidopyrimidine-5-carboxylate (HGN-0046)




The mixture of ethyl 2-((1H-indazol-5-yl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (292 mg, 0.976 mmol) and sodium hydroxide (1M) were heated at 105° C. for 4 hours followed by heating at 40° C. overnight. Then the solution was condensed to recover the final product. 1H-NMR confirmed the product (300 mg, 98% yield).
Example 27
Synthesis of Ethyl 2-((furan-2-ylmethyl)amino)-6-oxo-1,6-diydropyrimidine-5-carboxylate (HGN-0047)




The mixture of ethyl 2-(methylthio)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (300 mg, 1.4 mmol) and furan-2-ylmethanamine (136 mg, 1.4 mmol) were mixed in ethanol and refluxed overnight. The precipitate was filtered to recover the final product.
1H-NMR confirmed the product (200 mg, 54.3% yield).
Example 28
Synthesis of Ethyl 2-((furan-2-ylmethyl)amino)-6-oxo-1,6-diydropyrimidine-5-carboxylic acid




Ethyl 2-((furan-2-ylmethyl)amino)-6-oxo-1,6-diydropyrimidine-5-carboxylate (HGN-0047) (150 mg, 0.57 mmol) was suspended in 5 mL of dioxane and then 1M NaOH was added dropwise. The reaction mixture was heated under reflux for 4 hours and at room temperature overnight. The solvent was removed and 1H-NMR confirmed the product (204 mg, 152% yield).
Example 29
Synthesis of 6-oxo-2-(((tetrahydrofuran-2-yl)methyl)amino)-1,6-diydropyrimidine-5-carboxylic acid




Ethyl 6-oxo-2-(((tetrahydrofuran-2-yl)methyl)amino)-1,6-diydropyrimidine-5-carboxylate (126 mg, 0.471 mmol) was suspended in 5 mL of dioxane and then 1M NaOH was added dropwise. The reaction mixture was heated under reflux for 4 hours and at room temperature overnight. The solvent was removed and 1H-NMR confirmed the product (191 mg, 169% yield).
Example 30
Synthesis of ethyl 6-oxo-2-(phenylamino)-1,6-diydropyrimidine-5-carboxylate




Ethyl 2-(methylthio)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (1 g, 4.67 mmol) was added into a stirred solution of aniline (522 mg, 5.60 mmol). The reaction mixture was heated to 160° C. for 2 hours. The reaction mixture was cooled down and recrystalized in DMF with water (1:1). The mixture was filtered and titrated the residue with ethanol. 1H-NMR confirmed the product (about 100 mg).
1H-NMR: δ1.22 (t, 3H, CH3), δ4.2 (q, 2H, CH2), δ7.1 (t, 1H, H-Ph C4), δ7.3 (t, 2H, H-Ph C3), δ7.6 (d, 2H, H-Ph C2), δ8.0 (s, 1H, NH), δ8.5 (s, 1H, H-pyrimidine)
Example 31
Synthesis of ethyl 6-oxo-2-(thiazol-2-ylamino)-1,6-diydropyrimidine-5-carboxylate




Ethyl 2-(methylthio)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (1 g, 4.67 mmol) was added into a stirred solution of thiazol-2-amine (561 mg, 5.60 mmol). The reaction mixture was heated to 160° C. for 2 hours. Then the reaction mixture was cooled down and recrystalized in DMF with water (1:1). The mixture was filtered and titrated the residue with ethanol. 1H-NMR confirmed the product (about 300 mg).
1H-NMR: δ1.35 (t, 3H, H—CH3), δ4.15 (q, 2H, H—CH2), δ7.1 (t, 1H, H-thiazol C5), δ7.4 (d, 1H, H-thiazol C4), δ8.48 (s, 1H, H-pyrimidine)
Example 32
Synthesis of 6-oxo-2-(phenylamino)-1,6-diydropyrimidine-5-carboxylic acid




Sodium hydroxide (1M) was added to ethyl 6-oxo-2-(phenylamino)-1,6-dihydropyrimidine-5-carboxylate (0.1 g, 0.386 mmol) in 1 mL methanol and stirred at 80° C. for 2 hours and then 40° C. overnight. Then the reaction mixture was cooled down, and the solvent was removed. The reaction mixture was then diluted with water and the pH was adjusted to about 3.0. The reaction mixture was filtered, and the solid was collected and dried. 1H-NMR confirmed the structure (about 10 mg).
1H-NMR: δ7.1 (t, 1H, H-Ph C4), δ7.3 (t, 2H, H-Ph C3), δ7.6 (d, 2H, H-Ph C2), δ8.0 (s, 1H, NH), δ8.5 (s, 1H, H-pyrimidine), δ9.7 (s, 1H, OH).
Example 33
Synthesis of 6-oxo-2-(thiazol-2-ylamino)-1,6-diydropyrimidine-5-carboxylic acid




Sodium hydroxide (1M) was added to ethyl 6-oxo-2-(thiazol-2-ylamino)-1,6-dihydropyrimidine-5-carboxylate (360 mg, 1.352 mmol) in 1 mL methanol and stirred at 80° C. for 2 hours and then 40° C. overnight. Then the reaction mixture was cooled down, and the solvent was removed. The reaction mixture was then diluted with water and the pH was adjusted to about 3.0. The reaction mixture was filtered, and the solid was collected and dried. 1H-NMR confirmed the structure (about 20 mg).
1H-NMR: δ7.1 (d, 1H, H-thiazol C5), δ7.4 (d, 1H, H-thiazol C4), δ8.48 (s, 1H, H-pyrimidine), 69.5 (s, 1H, OH).
Example 34
Synthesis of 2-((4-bromophenyl)amino)-6-oxo-1,6-diydropyrimidine-5-carboxylic acid




Sodium hydroxide (1M) was added to ethyl 2-((4-bromophenyl)amino)-6-oxo-1,6-dihydropyrimidine-5-carboxylate (155 mg, 0.458 mmol) in 2 mL dioxane and hydrolyzed at 80° C. for 2 hours and then 40° C. overnight. Then the reaction mixture was cooled down, and the dioxane was removed. The reaction mixture was then acidified with 1N HCl so the pH was adjusted to about 3.0. The reaction mixture was filtered, and the solid was collected and dried. 1H-NMR confirmed the structure.
Example 35
IspF Binding Inhibition
Binding affinities between IspF and compounds synthesized herein were measured by surface plasmon resonance (SPR).
Methods
The binding constants of synthesized inhibitors were analyzed using surface plasmon resonance (SPR). All SPR experiments were performed using a Reichert SR7500DC instrument (Reichert, N.Y, USA) with carboxymethyl dextran hydrogel surface sensor chips (500,000 Dalton molecular weight carboxymethyl dextran chips, Reichert, N.Y, USA). IspF was immobilized using amine-coupling chemistry. The sensor chip surface was activated with a 10 min injection of a mixture of 11.5 mg/mL N-hydroxysucciniminde and 76.5 mg/mL 1-ethyl-3-(3-dimethylamino propyl) carbodiimide hydrochloride at a flow rate of 20 μl/min. IspF was diluted to final concentration of 60 μg/ml with 5 mM acetate buffer, pH 5.0 and immobilized with a 10 min injection over the left channel at a flow rate of 20 μl/min Typically, 3000 μRIU-4000 μRIU of IspF was immobilized. To quench excess succinaminde ester groups, 1M Ethanolamine, pH 8.5 was injected for 4 min at a 50 μl/min flow rate. All SPR experiments were performed at 25° C. using PBS-D (50 mM sodium phosphate/pH 7.4, 150 mM sodium chloride, and 5% DMSO) as a running buffer at a 50 μl/min flow rate Inhibitors were initially dissolved in DMSO. Samples were diluted such that 5% DMSO was maintained in all samples. A concentration series of inhibitor, as well as periodic buffer injections, were individually injected and collected for approximately 5 minutes. Data were analyzed using Scrubber2 (Biologic Software).
Results
The binding affinity between IspF inhibitor compounds and IspF were measured by SPR. The results can be used as a screening tool to indicate which compounds should be evaluated further. The results are provided in terms of the dissociation constant (Kd) between IspF and the inhibitor compounds. No binding indicated a lack of inhibition. Lower concentrations indicated a higher degree of inhibition.







TABLE 1







BINDING AFFINITY IspF INHIBITORS AND IspF










Inhibitor
Kd






HGN-0001
no binding



HGN-0002
not soluble



HGN-0003
  82 uM



HGN-0005
 176 uM



HGN-0013
non-specific



HGN-0018
no binding



HGN-0019
 380 uM



HGN-0020
 204 uM



HGN-0024
 784 uM



HGN-0025
no binding



HGN-0026
no binding



HGN-0027
no binding



HGN-0028
 305 uM



HGN-0030
 178 uM



HGN-0035
not soluble



HGN-00037
not soluble



HGN-0038
not soluble



HGN-0039
non specific



HGN-0040
no binding



HGN-0041
not soluble



HGN-0042
not soluble



HGN-0045
non specific



HGN-0046
non specific



HGN-0048
 486 uM



HGN-0052
no binding



HGN-0055
no binding



HGN-0056
no binding



HGN-0060
not soluble



HGN-0061
no binding



HGN-0062
no binding



HGN-0063
10.7 mM









Example 36
Growth Inhibition of Burkholderia spp. by IspF Inhibitor Compounds
Growth inhibition properties of compounds HGN-0023, HGN-0027, HGN-0028, and HGN-0029 against B. thailandensis E264 and B. pseudomallei 1026b and Bp340 were evaluated.
Methods
Overnight cultures of Burkholderia strains (obtained from Herbert Schweizer at the University of Colorado) were grown in low-salt LB (LSLB; 10 g/L tryptone, 5 g/L yeast extract, 1.25 g/L NaCl) at 37° C. The Burkholderia strains were diluted to 0.2 OD600 in LSLB. Stocks of HGN compounds (40 mM in DMSO, except HGN-0028 at 20 mM) were diluted to 1 mM, then two-fold dilutions (1 mL each) in LSLB (500 μM, 250 μM, 125 μM, 62.5 μM, 31.25 μM) were prepared. In a 96-well microtiter plate, 160 μL of the inhibitor in LSLB at each concentration were added to the wells in triplicate. Then 40 μL of the 0.2 OD600 bacterial suspension to was added each well (final OD600=0.04, total well volume=200 μL). As controls, 40 μL of LSLB, DMSO, or kanamycin were added (final concentration 300 μg/mL) to wells in triplicate. The plates were incubated for 20 h at 37° C. with shaking in an Infinite M200 plate reader (Tecan Group Ltd., Männedorf, Switzerland). The plate was read at 15 min. intervals at 600 nm wavelength. The OD600 values were graphed over time (FIGS. 1-6).
Results
Initial results (FIG. 1) indicated several candidate compounds to further evaluate inhibition of the growth of B. pseudomallei. From FIG. 2, tests indicated that HGN-0027 and HGN-0028 inhibited the growth of B. pseudomallei over time. Further study tested the concentration effects of HGN-0023, -0027, -0028, and -0029 on the growth of B. pseudomallei over time. These studies confirmed that HGN-0023 (FIG. 3) and HGN-0029 (FIG. 6) did not inhibit the growth of B. pseudomallei. Whereas, HGN-0027 was a potent inhibitor, at multiple concentrations, of the growth of B. pseudomallei (FIGS. 4, 7, and 8). HGN-0028 was dose dependent in its ability to inhibit B. pseudomallei growth (FIGS. 5, 9. and 10). Lower concentrations of HGN-0028 did not inhibit B. pseudomallei growth.
Example 37
The compounds can be grouped by chemical class, Pyrimidine IspF inhibitors (Table 2), Imidazole IspF inhibitors (Table 3), Fusion IspF inhibitors (Table 4), and miscellaneous IspF inhibitors (Table 5). The tables below also summarize the bacterial inhibition of the compounds.







TABLE 2







Pyrimidine IspF inhibitors













% Growth





Inhibitiona












Chemical

Endpoint
Growth


Designation
Formula
Structure
(24 h)
Curve





HGN-0017
C12H17N3O4




ND
0.00b


 


HGN-0047
C12H13N3O4




0.00b
ND


 


HGN-0041
C15H15N3O5




0.00b
ND


 


HGN-0121
C14H14ClN3O3




0.00b
ND


 


HGN-0123
C14H14ClN3O3




0.00b
ND


 


HGN-0125
C14H14ClN3O3




23.89 ± 36.14  
ND


 


HGN-0038
C15H16ClN3O3




0.00b
ND


 


HGN-0119
C15H16ClN3O3




0.00b
ND


 


HGN-0127
C14H13Cl2N3O3




 3.47 ±  2.20  
ND


 


HGN-0129
C14H13Cl2N3O3




64.42 ±  2.77  
ND


 


HGN-0131
C15H15Cl2N3O3




0.00b
ND


 


HGN-0117
C15H15Cl2N3O3




0.00b
ND


 


HGN-0135
C15H15Cl2N3O3




0.00b
ND


 


HGN-0133
C14H14FN3O3




0.00b
ND


 


HGN-0113
C14H14FN3O3




0.00b
ND


 


HGN-0111
C15H16FN3O3




31.31 ± 39.32  
ND


 


HGN-0115
C15H16FN3O3




0.00b
ND


 


HGN-0116
C13H11ClN4O4




ND
ND


 


HGN-0040
C14H13N5O3




16.39 ±  6.29  
ND


 


HGN-0042
C14H13N5O3




20.70 ±  0.71  
ND


 


HGN-0034
C18H22N4O3




86.20 ±  0.16  
ND


 


HGN-0037
C19H17N3O3




Lc
ND


 


HGN-0033
C19H17N3O3




 5.07 ±  2.01  
ND


 


HGN-0039
C19H17N3O3




0.00b
ND


 


HGN-0015
C18H16N4O3




ND
14.43 ± 2.38  


 


HGN-0012
C8H6N4O3S




ND
ND


 


HGN-0077
C16H12N4O3




ND
ND


 


HGN-0079
C11H8BrN3O3




ND
ND


 


HGN-0011
C11H9N3O3




ND
ND


 


HGN-0035
C17H13N3O3




91.14 ±  1.18  
ND


 


HGN-0050
C10H11N3Na2O4




32.99 ±  9.22  
ND


 


HGN-0049
C10H7N3Na2O4




12.25 ±  0.40  
ND


 


HGN-0126
C12H8ClN3Na2O3




34.34 ±  3.24  
ND


 


HGN-0124
C12H8ClN3Na2O3




30.67 ±  2.67  
ND


 


HGN-0122
C12H8ClN3Na2O3




23.02 ±  8.79  
ND


 


HGN-0028
C13H10ClN3Na2O3




ND
68.20 ±  2.12  


 


HGN-0120
C13H10ClN3Na2O3




80.30 ±  0.40  
ND


 


HGN-0118
C13H9Cl2N3Na2O3




94.50 ±  4.42  
ND


 


HGN-0128
C12H7Cl2N3Na2O3




37.46 ±  0.21  
ND


 


HGN-0130
C12H7Cl2N3Na2O3




45.59 ±  2.35  
ND


 


HGN-0132
C13H9Cl2N3Na2O3




72.24 ± 11.83  
ND


 


HGN-0136
C13H9Cl2N3Na2O3




16.71 ±  5.04  
ND


 


HGN-0134
C12H8FN3Na2O3




26.05 ±  6.37  
ND


 


HGN-0114
C12H8FN3Na2O3




 5.94 ±  5.46  
ND


 


HGN-0112
C13H10FN3Na2O3




19.82 ± 16.53  
ND


 


HGN-0116
C13H10FN3Na2O3




20.46 ±  3.47  
ND


 


HGN-0014
C11H6BrN3Na2O3




15.52 ±  0.41  
ND


 


HGN-0045
C12H7N5Na2O3




0.00b 
ND


 


HGN-0046
C12H7N5Na2O3




15.12 ±  4.25  
ND


 


HGN-0036
C16H16N4Na2O3




22.38 ± 21.24  
ND


 


HGN-0013
C16H10N4Na2O3




ND
 6.26 ±  1.00  


 


HGN-0044
C17H11N3Na2O3




 1.48 ±  7.90  
ND





aGrowth inhibition calculated relative to DMSO control


bGrowth with inhibitor was equal to or greater than DMSO control


cLimited solubility prevented accurate determination of growth


ND, not done













TABLE 3







Imidazole IspF inhibitors.













% Growth





Inhibitiona












Chemical

Endpoint
Growth


Designation
Formula
Structure
(24 h)
Curve





HGN-0029 and HGN-0056
C9H8N2O




ND
23.58 ± 0.54 


 


HGN-0018
C12H14N2O




ND
ND


 


HGN-0019
C14H12N2O2




ND
ND


 


HGN-0020
C19H18ClN3O




ND
1.26 ± 2.33


 


HGN-0137
C20H19N3O2




0.00b
ND


 


HGN-0021
C16H14N2O




ND
ND


 


HGN-0022 and HGN-0052 (HCl salt)
C17H16N2O




0.00b
ND


 


HGN-0048
C17H17ClN2O2




ND
ND


 


HGN-0091
C16H13ClN2O




Lc
ND


 


HGN-0090
C16H13ClN2O




Lc
ND


 


HGN-0094
C16H13ClN2O




Lc
ND


 


HG-0108
C17H15ClN2O




Lc
ND


 


HGN-0051
C17H15ClN2O




0.00b
ND


 


HGN-0096
C17H15ClN2O




Lc
ND


 


HGN-0092
C16H12Cl2N2O




25.41 ± 2.79 
ND


 


HGN0098
C17H14Cl2N2O




0.00b
ND


 


HGN-0099
C17H14Cl2N2O




0.00b
ND


 


HGN-0100
C17H14Cl2N2O




Lc
ND


 


HGN-0109
C16H13FN2O




24.77 ± 10.79
ND


 


HGN-0106
C16H13FN2O




33.79 ± 16.09
ND


 


HGN-0093
C16H13FN2O




58.12 ± 2.17 
ND


 


HGN-0095
C17H15FN2O




88.27 ± 0.48 
ND


 


HGN-0097
C17H15FN2O




 4.27 ± 14.54
ND


 


HGN-0107
C17H15FN2O




2.75 ± 2.62
ND





aGrowth inhibition calculated relative to DMSO control


bGrowth with inhibitor was equal to or greater than DMSO control


cLimited solubility prevented accurate determination of growth


ND, not done













TABLE 4







Fusion IspF inhibitors.













% Growth





Inhibitiona












Chemical

Endpoint
Growth


Designation
Formula
Structure
(24 h)
Curve





HGN-0005
C15H17N5O5




ND
0.00b


 


HGN-0006
C15H16N6O5S




0.00b
ND


 


HGN-0007
C20H19F6N7O9




0.00b
ND


 


HGN-0008
C17H19F6N5O10S




0.00b
ND


 


HGN-0102
C16H18N6O5S




0.00b
ND





aGrowth inhibition calculated relative to DMSO control


bGrowth with inhibitor was equal to or greater than DMSO control


ND, not done













TABLE 5







Miscellaneous IspF inhibitors.













% Growth 





Inhibitiona












Chemical

Endpoint
Growth


Designation
Formula
Structure
(24 h)
Curve





HGN-0031
C11H12N2O




ND
0.00b


 


HGN-0061
C12H14N2O




ND
ND


 


HGN-0063
C17H16N2O




ND
ND


 


HGN-0060
C23H20N2O




ND
ND


 


HGN-0062
C18H18N2O




ND
ND


 


HGN-0078
C10H9N5




ND
ND


 


HGN-0080
C10H11N5O




ND
ND


 


HGN-0004
C8H7N5O2S




0.00b
ND


 


HGN-0002
C12H10N6O2




ND
ND


 


HGN-0010
C10H8N6O2S




7.22 ± 4.24
ND


 


HGN-0009
C11H10N6O2S




0.00b
ND





aGrowth inhibition calculated relative to DMSO control


bGrowth with inhibitor was equal to or greater than DMSO control


ND, not done






Example 38
Growth Inhibition of Malaria by IspF Inhibitor Compounds
The compounds described herein were also tested for their ability to inhibit the growth of the causative agent of malaria, Plasmodium falciparum, a protozoan parasite.
Methods
SYBR assay: The method of testing inhibition has been previously described (Co et al., 2009). Briefly, D6, C235 and W2 P. falciparum strains were maintained in continuous long-term cultures in tissue culture medium. Cultures and assays were grown and conducted at 37° C. under a humidified atmosphere of 5% CO2 and 5% O2, with a balance of N2 using either tissue culture medium or folic acid-free medium. Parasites at 1% parasitemia and 2% hematocrit were added to predosed 96-well plates and incubated for 72 h. Lysis buffer (20 mM Tris HCl, 5 mM EDTA, 0.008% saponin, and 0.08% Triton®-X with SYBR® green I dye was subsequently added to the plates and incubated for 1 h at ambient room temperature. Fluorescence was determined, and the plates were examined for relative fluorescence units (RFUs) per well. The drug concentrations were transformed and the data were then analyzed with Prism to yield drug 50% inhibitory concentrations (IC50s). Green D6, Green C235, and Green W2 are three strains in P. falciparum. W2 is chloroquine resistant and mefloquine sensitive, D6 is chloroquine sensitive but naturally less susceptible to mefloquine, C235 is resistant to mefloquine, chloroquine, and pyrimethamine.
Results
The data are provided in Tables 6-9 below.







TABLE 6







Anti-malarial data for pyrimidine IspF inhibitors.











SYBR
SYBR
SYBR



Green D6
Green C235
Green W2


Designation
IC50 (uM)
IC50 (uM)
IC50 (uM)













HGN-0017
>40
>40
>40


HGN-0047
>40
>40
>40


HGN-0041
>40
>40
>40


HGN-0121
34.52
>40
>40


HGN-0123
ND
ND
ND


HGN-0125
>40
19.68
16


HGN-0038
>40
>40
>40


HGN-0119
ND
ND
ND


HGN-0127
>40
>40
17.7


HGN-0129
26.95
32.98
13.19


HGN-0131
ND
ND
ND


HGN-0117
ND
ND
ND


HGN-0135
ND
ND
ND


HGN-0133
>40
>40
>40


HGN-0113
29.29
>40
>40


HGN-0111
>40
>40
>40


HGN-0115
17.45
27.58
17.59


HGN-0016
ND
ND
ND


HGN-0040
>40
>40
>40


HGN-0042
>40
>40
>40


HGN-0034
>40
>40
>40


HGN-0037
>40
>40
>40


HGN-0033
>40
>40
>40


HGN-0039
>40
>40
>40


HGN-0015
>40
>40
>40


HGN-0012
ND
ND
ND


HGN-0077
ND
ND
ND


HGN-0079
ND
ND
ND


HGN-0011
ND
ND
ND


HGN-0035
ND
ND
ND


HGN-0050
ND
ND
ND


HGN-0049
0.55
0.74
0.95


HGN-0126
>40
>40
>40


HGN-0124
ND
ND
ND


HGN-0122
ND
ND
ND


HGN-0028
>40
>40
>40


HGN-0120
ND
ND
ND


HGN-0118
ND
ND
ND


HGN-0128
ND
ND
ND


HGN-0130
ND
ND
ND


HGN-0132
ND
ND
ND


HGN-0136
ND
ND
ND


HGN-0134
ND
ND
ND


HGN-0114
ND
ND
ND


HGN-0112
ND
ND
ND


HGN-0116
ND
ND
ND


HGN-0014
>40
>40
>40


HGN-0045
>20
>20
>20


HGN-0046
ND
ND
ND


HGN-0036
ND
ND
ND


HGN-0013
>40
>40
>40


HGN-0044
>40
>40
>40
















TABLE 7







Anti-malarial data for imidazole IspF inhibitors.











SYBR
SYBR
SYBR



Green D6
Green C235
Green W2


Designation
IC50 (uM)
IC50 (uM)
IC50 (uM)













HGN-0029
>40
>40
>40


and





HGN-0056





HGN-0018
>40
>40
>40


HGN-0019
11.3
13.3
13.6


HGN-0020
4.2
7.2
5.6


HGN-0137





HGN-0021
6.0
7.7
6.0


HGN-0022
>40
>40
>40


and





HGN-0052





(HCl salt)





HGN-0048
>40
>40
>40


HGN-0091
3.175
4.874
3.526


HGN-0090
5.797
6.153
3.943


HGN-0094
8.876
9.116
6.221


HGN-0108
11.48
13.81
7.219


HGN-0051
1.7
3.4
0.59


HGN-0096
9.798
12.92
7.898


HGN-0092 
ND
ND
ND


HGN0098
10.16
14.38
8.381


HGN-0099
5.362
5.436
4.251


HGN-0100
4.275
9.366
5.647


HGN-0109
4.798
5.735
3.163


HGN-0106
3.001
3.524
4.099


HGN-0093
5.829
6.345
3.36


HGN-0095
6.1
6.594
4.048


HGN-0097
10.16
5.178
2.12


HGN-0107
5.653
7.291
4.088
















TABLE 8







Anti-malarial data for fusion series IspF inhibitors.











SYBR
SYBR
SYBR



Green D6
Green C235
Green W2


Designation
IC50 (uM)
IC50 (uM)
IC50 (uM)













HGN-0005
>40
>40
>40


HGN-0006
ND
ND
ND


HGN-0007
ND
ND
ND


HGN-0008
ND
ND
ND


HGN-0102
>40
>40
>40
















TABLE 9







Anti-malarial data for miscellaneous IspF inhibitors.











SYBR
SYBR
SYBR



Green D6
Green C235
Green W2


Designation
IC50 (uM)
IC50 (uM)
IC50 (uM)













HGN-0068
8.374
6.119
5.988


HGN-0024
>40
>40
>40


HGN-0023
12.9
>40
>40


HGN-0082
>40
>40
>40


and





HGN-0101





HGN-0054
28.9
>40
11.5


HGN-0031
>40
>40
>40


HGN-0061
6.1
8.3
6.4


HGN-0063
>40
>40
>40


HGN-0060
1.6
2.7
3.1


HGN-0062
3.8
8.3
7.3


HGN-0078





HGN-0080





HGN-0004
>40
>40
>40


HGN-0002
>40
>40
>40


HGN-0010
>40
>40
>40


HGN-0009
>40
>40
>40


HGN-0085
>40
>40
>40


HGN-0083
8.49
12.03
10.4


HGN-0084
>40
>40
>40


HGN-0055
18.8
>40
19


and





HGN-0089





HGN-0087
>40
>40
>40


HGN-0088
>40
>40
>40


HGN-0025
>40
>40
>40


HGN-0026
>40
>40
>40


HGN-0057
7.6
22.8
15.0


HGN-0058
>40
>40
>40


HGN-0059
>40
>40
>40


HGN-0030
>40
>40
>40









Publications

All publications cited in this application are herein incorporated by reference.
Begley et al. (2010) Chem. Biol. Drug Des. 76(3):218-233.
Brown, A. C., and Parish, T. (2008) BMC Microbiol. 8: 78.
Co et al. (2009) Antimicrob. Agents Chemother. 53:2557-2563.
Gershenzon, J., and Dudareva, N. (2007) Nat. Chem. Biol. 3: 408-414.
Hunter, W. N. (2007) J. Biol. Chem. 282; 21573-21577.
Kuzuyama, T. et al. (1999) Biosci., Biotechnol., Biochem. 63: 776-778.
Mayer et al. (1999) Angew Chem. Int. Ed. 38(12):1784-1788.
Piotto et al. (1992) J. Biomol. NMR 2(6):661-665.
Zhang, B. et al. (2011) Biochemistry 50: 3570-3577.

## Claims

1. A compound of Formula II:




or a compound of Formula III:



or a pharmaceutically acceptable salt thereof, wherein
R1 is H or lower alkyl;
R2 is H or lower alkyl; and
R3 is biphenyl, pyridine, pyrimidine, oxazine, oxathiazine,




 or




 each of which may be optionally substituted or R3 is substituted alkylaryl;
wherein the alkyl of the alkylaryl is comprised of 2 to 8 carbon atoms.

2. The compound of claim 1 of Formula II:



or a pharmaceutically acceptable salt thereof, wherein
R1 is H or lower alkyl;
R2 is H or lower alkyl; and
R3 is substituted alkylaryl or optionally substituted biphenyl, pyridine, pyrimidine, oxazine, or oxathiazine;
wherein the alkyl of the alkylaryl is comprised of 2 to 8 carbon atoms.

3. The compound of claim 1 of Formula III:



or a pharmaceutically acceptable salt thereof, wherein
R1 is H or lower alkyl;
R2 is H or lower alkyl; and
R3 is substituted alkylaryl, or optionally substituted biphenyl, pyridine, pyrimidine, oxazine, or oxathiazine;
wherein the alkyl of the alkylaryl is comprised of 2 to 8 carbon atoms.

4. The pharmaceutically acceptable salt of claim 2 which is

5. A pharmaceutical composition comprising a therapeutically effective amount of at least one compound according to claim 1 and a pharmaceutically acceptable carrier.

6. A method of treating a bacterial infection, the method comprising administering a therapeutically effective amount of the compound according to claim 1, wherein the bacterial infection is a Burkholderia infection.

7. A method of treating a bacterial infection, the method comprising administering a therapeutically effective amount of the compound according to claim 1, wherein the bacterial infection is a Mycobacterium infection.

8. A method of treating tuberculosis, the method comprising administering a therapeutically effective amount of the compound, of claim 1.

9. A method of treating malaria the method comprising administering a therapeutically effective amount of the compound of claim 1.

10. The compound of claim 1 or a pharmaceutically acceptable salt thereof, wherein R1 is hydrogen.

11. The compound of claim 1 or a pharmaceutically acceptable salt thereof, wherein R2 is hydrogen.

12. The compound of claim 1 of Formula II:




or a compound of Formula III:



or a pharmaceutically acceptable salt thereof, wherein
R3 is substituted alkylaryl, or optionally substituted pyridine, pyrimidine, oxazine, or oxathiazine, and
wherein the alkyl of the alkylaryl is comprised of 2 to 8 carbon atoms.

13. The compound of claim 1 or a pharmaceutically acceptable salt thereof, wherein R3 is a substituted ethylaryl.

14. The compound of claim 1 or a pharmaceutically acceptable salt thereof, wherein
R1 and R2 are hydrogen, and
R3 is a substituted ethylaryl.