WO2019013790A1

WO2019013790A1 - Antimicrobial compounds and uses thereof

Info

Publication number: WO2019013790A1
Application number: PCT/US2017/041793
Authority: WO
Inventors: Hariprasada R. Kanna REDDY; Paul R. SEBAHAR; Ryan E. LOOPER
Original assignee: Curza Global, Llc; The University Of Utah Research Foundation
Priority date: 2017-07-12
Filing date: 2017-07-12
Publication date: 2019-01-17

Abstract

Disclosed are compounds of formula I: or pharmaceutically acceptable salts thereof. Compounds of formula I are anti-microbials that inhibit, for instance, Mycobacterium tuberculosis (Mtb) H37Ra. Compounds of formula I also have anti-tubercular activity, exhibit limited cytotoxicity, and inhibit protein synthesis. Processes for making compounds of formula I are also disclosed, as well as methods of using compounds of formula I for the treatment of bacterial infections, particularly tuberculosis.

Description

ANTIMICROBIAL COMPOUNDS AND USES THEREOF

Background of the Invention

[0001] Tuberculosis (TB) remains one of the world's leading causes of death from a single infectious agent, second only to Human Immunodeficiency Virus (HIV). About one third of the world's population is infected with latent TB, with over 9 million active TB cases and 1.3 million TB-related deaths in 2012. Recent years have seen an increase in the number of deadly strains of TB. As of 2012, extensively drug resistant TB (XDR-TB) has been reported in over 91 countries, as well as totally drug resistant strains in Italy, Iran, and India.

[0002] TB is the most common illness among people with HIV. The World Health Organization estimated that 12 million people living with HIV are co-infected with TB. It is the leading cause of death among people with HIV infection with about 320,000 HIV- associated TB deaths reported in 2012.

[0003] TB-HIV co-infection is aggravated by the activation of hepatic cytochromes (CYP2C9 and CYP3A4) by the current TB drugs (e.g., rifampin). There are several mechanisms by which these enzymes are upregulated. CYP2C9 and CYP3A4 are liver proteins that degrade drugs including the anti-retrovirals, especially HIV-protease inhibitors and N RTIs used in treating HIV. Activation of these proteins renders the plasma levels of the anti-retrovirals subtherapeutic, which concomitantly accelerates the progression of TB due to increased weakening of the immune system. Further, an ineffective regimen of TB therapeutics leads to increased resistance in organisms.

[0004] Current treatment regimens are long (6-24 months), complicated (IV and oral dosing) and the side-effects significant enough to preclude treatment until the patient becomes symptomatic. The reasons for TB latency are not fully understood, but it has been hypothesized that its ability to dwell in the biofilm phenotype may be, at a minimum, partially responsible. Inhibiting Mtb biofilm development (with an unrelated chemotype) may therefore hold promise to treat latent TB.

[0005] Given this global health threat and the inadequacy of currently available treatments, it is imperative to identify new drug candidates which are 1 ) active against TB and XDR-TB, 2) non-cytotoxic; and 3) compatible with antiretroviral therapeutics (ART) (i.e. non- cytochrome inducing). Summary of the Invention

[0006] These and other needs are met by the present invention which provides in one aspect a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

A is an optionally substituted monocyclic heteroarylene;

Yi is C1-C4 alkylene;

Y2 is absent or is selected from the group consisting of 0-(Ci-C6 alkylene) and -NH- (Ci-C₆ alkylene);

Ri is selected from the group consisting of NH₂ and piperidine optionally substituted with Me or NR_xR_y, wherein R_x and R_y are independently selected from Me and H;

Zi is absent or is CH₂, (CO), (C=0)NH, CH₂0, CH₂NH, CH₂N(Ci-C₆ alkyl), CH₂N(Ci-C₆ alkyNH₂),

Z₂ is absent or is optionally substituted C1-C10 alkylene, optionally substituted cycloalkylene and optionally substituted heterocycloalkylene, optionally substituted Ci-C₆ alkylene-cycloalkyiene and optionally substituted Ci-C6 alkylene-heterocycloalkylene, wherein up to two carbon atoms of optionally substituted O-C10 alkylene are replaced by O or -(C=0)-, NH, NH(Ci-C₆ alkyl), NH-(C=0)-, N(Ci-C₆ alkyl)-(C=0)-, and

wherein n is or 5, wherein " ^w " indicates the point of attachment;

R₂ is

or R₂ is selected from the group consisting of H, OH, NH₂, NH(Q- C₆ alkyl), N(Ci-C₆ alkyl)₂, and NH(Ci-C₆ alkylene-cycloalkyl), wherein "·~>~ " indicates the point of attachment;

R_2a is selected from the group consisting of hydrogen and (Ci-C₆ alkyl);

R_2b is selected from the group consisting of hydrogen, (Ci-C₆ alkyl), (C₂-C6 alkenyl), aryl, and arylalkyl; and

R3 is H or F. [0007] Compounds of formula I are structurally related to amicetin, a ribosomal antibiotic isolated from Streptomyces vinaceusdrappus. Amicetin is a known inhibitor of protein synthesis that is active against a number of acid-fast gram-positive bacteria including Mycobacterium tuberculosis (Mtb). Amicetin exhibits an IC50 of 0.24 μΜ (0.15 g mL) against Mtb H37Ra and an EC50 of 4.4 μΜ (2.8 μg mL) against CEM/TART T-Cell leukemia lineage, respectively, corresponding to almost 20-fold selectivity index. Amicetin was also found to be a poor inducer of CYP2C9 and CYP3A4 (< 2 fold induction as measured by qPCR in the HepG2 cell line), making it potentially compatible with ART. However, due to its chemical complexity and instability it remains a poor drug candidate. Most notably the cytosine-glycal linkage is labile and hydrolysis produces two fragments (amicetamine and cytimidine) which are not active against MTb.

[0008] We surprisingly found that while compounds of formula 1 selectively inhibit Mtb H37Ra, they exhibit limited cytotoxicity against mammalian cells and low CYP induction.

[0009] In another aspect, the invention provides methods of using compounds of formula I for the treatment of bacterial infections.

[0010] In a further aspect, the invention provides processes for making compounds of formula I as depicted in the synthetic schemes.

Detailed Description of the Invention

[0011] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety, including U.S. Pat. Publ. No. 2013/0090326. In case of conflict, the present specification, including these definitions, will control.

[0012] The terms "a," "an," and "the" as used herein not only include aspects with one member, but also include aspects with more than one member.

[0013] The term "about" as used herein means "approximately" and is used to modify a numerical value indicates a defined range around that value. If "X" were the value, "about X" would generally indicate a value from 0.95X to 1.05X. Any reference to "about X" specifically indicates at least the values X, 0.95X, 0.96X, 0.97X, 0.98X, 0.99X, 1.0 I X, 1.02X, 1.03X, 1.04X, and 1.05X. Thus, "about X" is intended to teach and provide written description support for a claim limitation of, e.g., "0.98X." When the quantity "X" only includes whole-integer values (e.g., "X carbons"), "about X" indicates from (X-l ) to (X+l). In this case, "about X" as used herein specifically indicates at least the values X, X-l , and X+l .

[0014] When "about" is applied to the beginning of a numerical range, it applies to both ends of the range. Thus, "from about 5 to 20%" is equivalent to "from about 5% to about 20%." When "about" is applied to the first value of a set of values, it applies to all values in that set. Thus, "about 7, 9, or 1 1 %" is equivalent to "about 7%, about 9%, or about 1 1%."

[0015] The term "acyl" as used herein includes an alkanoyl, aroyl, heterocycloyl, or heteroaroyl group as defined herein. Examples of acyl groups include, but are not limited to, acetyl, benzoyl, and nicotinoyl.

[0016] The term "alkanoyl" as used herein includes an alkyl-C(O)- group wherein the alkyl group is as defined herein. Examples of alkanoyl groups include, but are not limited to, acetyl and propanoyl.

[0017] The term "agent" as used herein includes a compound or mixture of compounds that, when added to a composition, tend to produce a particular effect on the composition's properties. For example, a composition comprising a thickening agent is likely to be more viscous than an otherwise identical comparative composition that lacks the thickening agent.

[0018] The term "alkenyl" as used herein includes a straight or branched chain

hydrocarbon containing at least one carbon-carbon double bond. The chain may contain an indicated number of carbon atoms. For example, "Ci-Ci₂ alkenyl" indicates that the group may have from 1 to 12 (inclusive) carbon atoms and at least one carbon-carbon double bond. When the indicated number of carbon atoms is 1, then the Cj alkenyl is double bonded to a carbon (i.e., a carbon equivalent to an oxo group). In certain aspects, the chain includes 1 to 12, about 2 to 15, about 2 to 12, about 2 to 8, or about 2 to 6 carbon atoms. An alkenyl group can be preferably one stereoisomer (i.e., cis- or, alternatively, trans-). Examples of an alkenyl group may include, but are not limited to, ethenyl (i.e., vinyl), allyl, propenyl, butenyl, crotyl, pentenyl, hexenyl, heptenyl, octenyl, nonenyl, decenyl, dodecenyl, cyclopentenyl, cyclohexenyl, 2-isopentenyl, allenyl, butadienyl, pentadienyl, 3-(l,4- pentadienyl), and hexadienyl.

[0019] An alkenyl group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the alkenyl group (e.g., from 1 to 4, from 1 to 2, or 1 ) may be replaced with a moiety independently selected from fluoro, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio, with the proviso that no hydrogen atom substituent on the carbon-carbon double bond is replaced by a hydroxy, amino, or thio group. In some aspects, the alkenyl group is unsubstituted or not optionally substituted.

[0020] "Alkenylene" as used herein includes an alkenyl group that is substituted at two points. An example is but-2-enyIene (-CH₂CH=CHCH2-) and the like.

[0021] The term "alkyl" as used herein includes an aliphatic hydrocarbon chain that may be straight chain or branched. The chain may contain an indicated number of carbon atoms: For example, Ci-Ci₀ indicates that the group may have from 1 to 10 (inclusive) carbon atoms in it. If not otherwise indicated, an alkyl group contains from 1 to about 20 carbon atoms. In some aspects, alkyl groups have 1 to about 10 carbon atoms. In some aspects, alkyl groups ("lower alkyl") have 1 to 8, 1 to 6, or 1 to 3 carbon atoms in the chain. Examples may include, but are not limited to, methyl, ethyl, propyl, isopropyl (iPr), 1 -butyl, 2-butyl, isobutyl (iBu), tert-butyl, pentyl, 2-methylbutyl, 1 , 1 -dimethylpropyl, hexyl, heptyl, octyl, nonyl, decyl, docecyl, cyclopentyl, or cyclohexyl.

[0022] An alkyl group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the alkyl group (e.g., from 1 to 4, from 1 to 2, or I ) may be replaced with a moiety independently selected from fluoro, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio. In some aspects, the alkyl group is unsubstituted or not optionally substituted.

[0023] "Alkylene" as used herein includes an alkyl group that is substituted at two points. An example is methylene (-CH₂-), propylene (-CH₂CH₂CH₂-), and the like.

[0024] An alkylene group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the alkylene group (e.g., from 1 to 4, from 1 to 2, or 1 ) may be replaced with a moiety independently selected from the group consisting of halo (e.g., chloro, fluoro), aryl, alkyl, hydroxyalkyl, haloalkyl, haloalkoxy, hydroxy, -C0₂H, - C0₂(Ci-6 alkyl), alkoxy, amino, alkylamino, acylamino, thio, and alkylthio. In some aspects, the alkylene group is unsubstituted or not optionally substituted.

[0025] The term "alkoxy" as used herein includes a straight or branched chain saturated or unsaturated hydrocarbon containing at least one oxygen atom in an ether group (e.g., EtO-). The chain may contain an indicated number of carbon atoms. For example, "C1 -C12 alkoxy" indicates that the group may have from 1 to 12 (inclusive) carbon atoms and at least one oxygen atom. Examples of a C1-C12 alkoxy group include, but are not limited to, methoxy, ethoxy, isopropoxy, butoxy, n-pentoxy, isopentoxy, neopentoxy, and hexoxy. [0026] An alkoxy group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the alkoxy group (e.g., from 1 to 4, from I to 2, or 1 ) may be replaced with a moiety independently selected from fluoro, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio, with the proviso that no hydrogen atom alpha to the ether oxygen is replaced by a hydroxy, amino, or thio group. In some aspects, the alkoxy group is unsubstituted or not optionally substituted.

[0027] The term "alkynyl" as used herein includes a straight, branched, or cyclic hydrocarbon containing at least one carbon-carbon triple bond. Examples may include, but are not limited to, ethynyl, propargyl, propynyl, butynyl, pentynyl, hexynyl, heptynyl, octynyl, nonynyl, decynyl, or decynyl.

[0028] "Alkynylene" as used herein includes an alkynyl group that is substituted at two points. An example is 2-butynylene (-CH₂CCCH₂-) and the like.

[0029] An alkynyl group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the alkynyl group (e.g., from 1 to 4, from 1 to 2, or 1 ) may be replaced with a moiety independently selected from fluoro, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio, with the proviso that no sp-hybridized hydrogen atom substituent is replaced by a hydroxy, amino, or thio group. In some aspects, the alkynyl group is unsubstituted or not optionally substituted.

[0030] The term "aryl" as used herein includes cyclic aromatic carbon ring systems containing from 6 to 18 carbons. Examples of an aryl group include, but are not limited to, phenyl, naphthyl, anthracenyl, tetracenyl, biphenyl and phenanthrenyl.

[0031] An aryl group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the aryl group (e.g., from 1 to 5, from 1 to 2, or 1 ) may be replaced with a moiety independently selected from alkyl, cyano, acyl, halo, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio. In some aspects, the alkoxy group is unsubstituted or not optionally substituted.

[0032] The term "arylalkyl" or "aralkyl" as used herein includes an alkyl group as defined herein where at least one hydrogen substituent has been replaced with an aryl group as defined herein. Examples include, but are not limited to, benzyl, 1 -phenylethyl, 4- methylbenzyl, and 1 , 1 , -dimethyl- 1 -phenylmethy I.

[0033] An arylalkyl or aralkyl group can be unsubstituted or optionally substituted as per its component groups. For example, but without limitation, the aryl group of an arylalkyl group can be substituted, such as in 4-methylbenzyl. In some aspects, the group is unsubstituted or not optionally substituted, especially if including a defined substituent, such as a hydroxyalkyl or alky lam inoalkoxy group.

[0034] The term "cycloalkyl" as used herein includes a cyclic hydrocarbon group that may contain an indicated number of carbon atoms: For example, C3-C 12 indicates that the group may have from 3 to 12 (inclusive) carbon atoms in it. If not otherwise indicated, a cycloalkyl group includes about 3 to about 20 carbon atoms. In some aspects, cyclo alkyl groups have 3 to about 12 carbon atoms in the group. In some aspects, cycloalkyl groups have 3 to about 7 carbon atoms in the group. Examples may include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, 4,4-dimethylcyclohexyl, and cycloheptyl.

[0035] A cycloalkyl group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the cycloalkyl group {e.g., from 1 to 4, from 1 to 2, or 1 ) may be replaced with a moiety independently selected from fluoro, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio. In some aspects, a substituted cycloalkyl group can incorporate an exo- or endocyclic alkene (e.g., cycIohex-2-en-l -yl). In some aspects, a cycloalkyl group is unsubstituted or not optionally substituted.

[0036] The terms "disorder," "disease," and "condition" are used herein interchangeably for a condition in a subject. A disorder is a disturbance or derangement that affects the normal function of the body of a subject. A disease is a pathological condition of an organ, a body part, or a system resulting from various causes, such as infection, genetic defect, or environmental stress that is characterized by an identifiable group of symptoms. A disorder or disease can refer to a biofilm-related disorder or disorder caused by a planktonic bacterial phenotype that is characterized by a disease-related growth of bacteria.

[0037] The term "effective amount" or "effective dose" as used herein includes an amount sufficient to achieve the desired result and accordingly will depend on the ingredient and its desired result. Nonetheless, once the desired effect is identified, determining the effective amount is within the skill of a person skilled in the art.

[0038] As used herein, "fluoroalkyl" includes an alkyl group wherein the alkyl group includes one or more fluoro- substituents. Examples include, but are not limited to, trifluoromethyl.

[0039] As used herein, "geminal" substitution includes two or more substituents that are directly attached to the same atom. An example is 3,3-dimethyl substitution on a cyclohexyl or spirocyclohexyl ring.

[0040] As used herein, "halo" or "halogen" includes fluoro, chloro, bromo, or iodo. [0041] The term "heteroaryl" includes 6 membered aromatic groups containing one to 4 heteroatoms. Heteroatom as used in the term heteroaryl refers to nitrogen. A nitrogen atom of a heteroaryl is optionally oxidized to the corresponding N-oxide. Examples include, but are not limited to, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, 1 ,2,4-triazinyl and tetrazinyl.

[0042] An heteroaryl group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the heteroaryl group (e.g., from 1 to 5, from 1 to 2, or 1) may be replaced with a moiety independently selected from the group consisting of alkyl, haloalkyl, cyano, acyl, halo, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio. In some aspects, the heteroaryl group is unsubstituted or not optionally substituted.

[0043] The term "heteroarylene" as used herein includes a heteroaryl group that is substituted at two points. An heteroarylene group can be unsubstituted or optionally substituted. An example of a heteroarylene group is a pyridylene group. When optionally substituted, one or more hydrogen atoms of the heteroarylene group (e.g., from 1 to 5, from 1 to 2, or 1 ) may be replaced with a moiety independently selected from the group consisting of alkyl, haloalkyl, cyano, acyl, halo, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio. In some aspects, the heteroarylene group is unsubstituted or not optionally substituted.

[0044] The term "heteroaroyl" as used herein includes a heteroaryl-C(O)- group wherein heteroaryl is as defined herein. Heteroaroyl groups include, but are not limited to, thiophenoyl, nicotinoyl, pyrrol-2-ylcarbonyl, and pyridinoyl.

[0045] The term "heterocycloyl" as used herein includes a heterocyclyl-C(O)- group wherein heterocyclyl is as defined herein. Examples include, but are not limited to, N-methyl prolinoyl and tetrahydrofuranoyl.

[0046] As used herein, "heterocyclyl" includes a non-aromatic saturated monocyclic or multicyc!ic ring system of about 3 to about 10 ring atoms (e.g., 5 to about 10 ring atoms, or 3 to about 6 ring atoms), in which one or more of the atoms in the ring system is an element or elements other than carbon, e.g., nitrogen, oxygen or sulfur. A heterocyclyl group optionally comprises at least one sp²-hybridized atom (e.g., a ring incorporating an carbonyl, endocyclic olefin, or exocyclic olefin). In some embodiments, a nitrogen or sulfur atom of the heterocyclyl is optionally oxidized to the corresponding N-oxide, S-oxide or S,S-dioxide. Examples of monocycylic heterocyclyl rings include, but are not limited to, piperidyl, pyrrolidinyl, piperazinyl, morpholinyl, thiomorpholinyl, thiazolidinyl, 1,3-dioxolanyl, 1,4- dioxanyl, tetrahydrofuranyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, azetidyl, and tetrahydropyranyl.

[0047] A heterocycyl group can be unsubstituted or optionally substituted. When optionally substituted, one or more hydrogen atoms of the group (e.g., from 1 to 4, from 1 to 2, or 1) may be replaced with a moiety independently selected from fluoro, hydroxy, alkoxy, amino, alkylamino, acylamino, thio, and alkylthio. In some aspects, a substituted heterocycyl group can incorporate an exo- or endocyclic alkene (e.g., cyclohex-2-en-l -yl). In some aspects, the heterocycyl group is unsubstituted or not optionally substituted.

[0048] As used herein, the term "hydrophilic moiety" or "hydrophilic group" includes a moiety or a functional group that has a strong affinity to water. Examples may include, but are not limited to, a charged moiety, such as a cationic moiety or an anionic moiety, or a polar uncharged moiety, such as an alkoxy group or an amine group.

[0049] As used herein, the term "hydroxyalkyi" includes an alkyl group where at least one hydrogen substituent has been replaced with an alcohol (-OH) group. In certain aspects, the hydroxyalkyi group has one alcohol group. In certain aspects, the hydroxyalkyi group has one or two alcohol groups, each on a different carbon atom. In certain aspects, the hydroxyalkyi group has 1 , 2, 3, 4, 5, or 6 alcohol groups. Examples may include, but are not limited to, hydroxymethyl, 2-hydroxyethyl, and 1 -hydroxyethyl.

[0050] When any two substituent groups or any two instances of the same substituent group are "independently selected" from a list of alternatives, the groups may be the same or different. For example, if R^a and R^b are independently selected from alkyl, fluoro, amino, and hydroxyalkyi, then a molecule with two R^a groups and two R^b groups could have all groups be an alkyl group (e.g., four different alkyl groups). Alternatively, the first R^a could be alkyl, the second R^a could be fluoro, the first R^b could be hydroxyalkyi, and the second R^b could be amino (or any other substituents taken from the group). Alternatively, both R^a and the first R could be fluoro, while the second R^b could be alkyl (i.e., some pairs of substituent groups may be the same, while other pairs may be different).

[0051] "Pharmaceutically acceptable acid addition salt" refers to those salts that retain the biological effectiveness of the free bases and that are not biologically or otherwise undesirable, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like, as well as organic acids such as acetic acid, trifluoroacetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, orotic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and the like.

[0052] "Pharmaceutically acceptable base addition salts" include those derived from inorganic bases such as sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Exemplary salts are the ammonium, potassium, sodium, calcium, and magnesium salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as isopropylamine,

trimethylamine, diethylamine, triethylamine, tripropylamine, ethanolamine,

2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, ethylenediamine, glucosamine, methylglucamine, theobromine, purines, piperazine, piperidine, N-ethylpiperidine, polyamine resins, and the like. Exemplary organic bases are isopropylamine, diethylamine,

ethanolamine, trimethylamine, dicyclohexylamine, choline, and caffeine. (See, for example, S. M. Berge, et al., "Pharmaceutical Salts," J. Pharm. Sci., 1977;66: 1 -19 which is incorporated herein by reference.)

[0053] As used herein, "or" should in general be construed non-exclusively. For example, an embodiment of "a composition comprising A or B" would typically present an aspect with a composition comprising both A and B, and an embodiment of "a method to disperse or kill biofllms" could disperse, kill, or a combination of both. "Or" should, however, be construed to exclude those aspects presented that cannot be combined without contradiction (e.g., a composition pH that is between 9 and 10 or between 7 and 8).

[0054] As used herein, "spirocycloalkyl" includes a cycloalkyl in which geminal substituents on a carbon atom are replaced to join in forming a 1 , 1 -substituted ring. For example, but without limitation, for a -C(R')( ²)- group that was part of a longer carbon chain, if R¹ and R² joined to form a cyclopropyl ring incorporating the carbon to which R' and R² were bonded, this would be a spirocycloalkyl group (i.e., spirocyclopropyl).

[0055] As used herein, "spiroheterocyclyl" includes a heterocycloalkyl in which geminal substituents on a carbon atom are replaced to join in forming a 1 , 1 -substituted ring. For example, but without limitation, for a -C(R')(R²)- group that was part of a longer carbon chain, if R¹ and R² joined to form a pyrrolidine ring incorporating the carbon to which R¹ and R² were bonded, this would be a spiroheterocyclyl group. [0056] It is to be understood that molecular fragments such as

and the like are bound to two other groups in either orientation. For example, unless otherwise indicated,

can be bound to A and B to provide both 1 and A ^Ri*

[0057] As used herein, the term "treat," "treating," or "treatment" includes administering or applying a composition (e.g., a composition described herein) in an amount, manner (e.g., schedule of administration), and mode (e.g., route of administration) that is effective to improve a disorder or a symptom thereof, or to prevent, to retard, or to slow the progression of a disorder or a symptom thereof. Such improvements can include, but are not limited to, alleviation or amelioration of one or more symptoms or conditions, diminishment of the extent of a disease, stabilizing (i.e. , not worsening) the state of disease, prevention of a disease's transmission or spread, delaying or slowing of disease progression, amelioration or palliation of the disease state, diminishment of the reoccurrence of disease, and remission, whether partial or total and whether detectable or undetectable.

[0058] "Treating" and "treatment" as used herein also include prophylactic treatment. In certain embodiments, treatment methods comprise administering to a subject a

therapeutically effective amount of a composition of the invention. The administering step may consist of a single administration or may comprise a series of administrations. The length of the treatment period depends on a variety of factors, such as the severity of the condition, the age of the patient, the concentration of active agent in the composition, the activity of the compositions used in the treatment, or a combination thereof. It will also be appreciated that the effective dosage of an agent used for the treatment or prophylaxis may increase or decrease over the course of a particular treatment or prophylaxis regime. Changes in dosage may result and become apparent by standard diagnostic assays known in the art. In some aspects, chronic administration may be required. For example, the compositions are administered to the subject in an amount, and for a duration, sufficient to treat the patient.

Embodiments

Compounds

[0059] In the first aspect, the invention provides a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

A is an optionally substituted monocyclic heteroarylene;

Yi is C1-C4 alkylene;

Y2 is absent or is selected from the group consisting of 0-(C]-C6 alkylene) and -NH- (Ci-Ce alkylene);

Zi is absent or is CH₂, (C=0), CH₂0, CH₂NH, CH₂N(Ci-C₆ alkyl), CH₂N(Ci-C₆ alkyNH₂),

Z₂ is absent or is optionally substituted Ci -Cio alkylene, optionally substituted cycloalkylene and optionally substituted heterocycioalkylene, optionally substituted Ci-C₆ alkylene-cycioalkylene and optionally substituted Ci-C6 alkylene-heterocycloalkylene, wherein up to two carbon atoms of optionally substituted C I -CIO alkylene ar replaced by O or -(CO)-, NH, NH(Ci-C₆ alkyl), NH-(C=0)-, N(Ci-C₆ alkyl)-(C=0)-, and

wherein n is 2, 3, 4, or 5, wherein indicates the point of attachment;

R₂ is

or R₂ is selected from the group consisting of H, OH, NH₂, NH(Ci- C₆ alkyl), and NH(Ci-C₆ alkylene-cycloalkyl), wherein "— " indicates the point of attachment;

R_2a is selected from the group consisting of hydrogen and (Ci-Ce alkyl);

R3 is H or F.

[0060] In one embodiment of a compound of formula I, A is pyridylene.

[0061] In another embodiment, the compound of formula 1 is a compound of formula IA or

IB:

[0062] In another embodiment of a compound of formula IA and IB and thus of formula I: Zi is absent.

(0063] In another embodiment of a compound of formula IA and IB and thus of formula I: Zi is CH₂, (C=0), (C=0)NH, CH₂0, or CH₂NH.

[0064] In another embodiment of a compound of formula IA and IB Z₂ is absent.

[0065] In another embodiment, Z₂ is optionally substituted Ci -Cio alkylene, optionally substituted cycloalkylene and optionally substituted heterocycloalkylene, optionally substituted Ci-C6 alkylene-cycloalkylene and optionally substituted Ci-Cealkylene- heterocycloalkylene, wherein up to two carbon atoms of optionally substituted Ci-Cio alkylene are replaced by O or -(C=0)-, NH, NH(Ci-C₆ alkyl), NH-(C=0)-, N(C,-C₆ alkyl)-

(C=0)-, and ^ , wherein n is 1 , 2, 3, 4, or 5, wherein "·~«~ " indicates the point of attachment. In a further embodiment, Z₂ is optionally substituted C1-C4 alkylene, wherein up to two carbon atoms of optionally substituted C1-C4 alkylene are replaced by O or -(C=0)-,

NH, NH(Ci-C₆ alkyl), NH-(C=0)-, N(Ci-C₆ alkyl)-(C=0)-, and ^¾ ^ , wherein n is 1 , 2, 3, 4, or 5. In a further embodiment, Z₂ is optionally substituted cycloalkylene. In a further embodiment, Z₂ is optionally substituted heterocycloalkylene. In a further embodiment, Z₂ is optionally substituted Ci-C₆ alkylene-cycloalkylene. In a further embodiment, Z₂ is optionally substituted Ci-Ce alkylene-heterocycloalkylene. HO

[0066] In another embodiment, R₂ is ^H2^{N R}2 . in these and other embodiments, R_2a is selected from the group consisting of hydrogen and (Ci-C₆ alkyl) and R_2b is selected from the group consisting of hydrogen, (Ci-C₆ alkyl), (C₂-C6 alkenyl), aryl, and arylalkyl.

[0067] In another embodiment of a compound of formula IA and IB and thus of formula I:

.

[0068] In another embodiment of a compound of formula I, IA and IB, R₂ is selected from the group consisting of H, OH, NH₂, NH(Ci-C₆ alkyl), N(Ci-C₆ alkyl)₂, and NH(Ci-C₆ alkylene-cycloalkyl), wherein " w " indicates the point of attachment.

[0069] In one embodiment of a compound of formula 1, IA and IB, R₃ is H.

[0070] In another embodiment of a compound of formula I, IA and IB, R₃ is F.

[0071] In another embodiment of a compound of formula I, IA and IB, Z₂ is selected from the group consisting of: C=0, -CH₂-, -CH₂CH₂-, -CH₂CH₂CH₂-, -CH₂CH₂CH₂CH₂-, - -CH₂CH₂CH₂CH₂CH₂- -CH₂CH₂ -, -CH₂CH₂CH₂NHCH₂CH CH₂-, -

and OH , wherein " ~ " indicates the point of attachment.

[0072] In another embodiment of a compound of formula I, IA and IB, Z|Z₂ is selected from the group consisting of: -CH₂0, -CH₂NHCH₂CH₂C -, -C(0)NHCH₂CH₂CH₂-,

CH₂OCH₂CH₂-, -CH₂OCH₂CH₂CH₂-, CH₂OCH₂CH₂CH₂CH₂- -CH₂OCH₂CH₂CH₂CH₂CH

CH₂OCH₂CH₂CH₂NH-CH2CH₂CH₂-,

-

(C=0)CH₂-, wherein " indicates the point of attachment.

[0073J In another embodiment of a compound of formula 1, 1A and IB, R₂Z₂ is selected

from the group consisting of: -CH2CH2CH2NH2,

V-^J , CH₃CH₂CH₂NH-_, CH3CH₂CH₂NHCH₂CH₂CH₂-, H Λ

^{N - /}^ ^IF , ^^^H , -CH2CH2NH2, -CH₂NH₂, -CH₂CH₂CH₂NH₂, -

OH O OH HN^i

CH₂CH₂CH₂CH₂CH₂NH_2, ^{Me NH}2 , ^{Me NH}2 and OH , wherein indicates a point of attachment.

[0074] In another embodiment of a compound of formula I, IA and IB, R2-Z2-Z] is selected

wherein

indicates a point of attachment.

[0075] In one embodiment of a compound of formula I, IA and IB, Yi is selected from the group consisting of CH₂CH₂CH₂CH₂, and CH₂CH₂.

[0076] In another embodiment of a compound of formula I, IA and IB, Y₂ is absent, or is selected from the group consisting -CH₂CH₂0-, -CH₂CH₂CH₂NH, and -CH₂CH₂CH₂NMe.

[0077] In another embodiment of a compound of formula I, IA and IB, Ri is selected from

the group consisting of: NH₂,

, , and , wherein

^■™ rw. indicates the point of attachment.

selected

wherein ^ w^w*. indicates a point of attachment.

[0079] In a further embodiment, the compound of formula IB and thus of formula I is a compound of formula IC:

IC [0080] In a further embodiment of a compound of formula I and thus of formula IA is a compound of formula IE:

ID

[0081] In another aspect, the invention provides a compound of formula II:

II

or a pharmaceutically acceptable salt thereof, wherein:

A is pyridylene;

Yi is selected from the group consisting of CH₂ or optionally substituted aryl;

Y₂ is absent or is selected from the group consisting of optionally substituted Ci-Cio alkylene, optionally substituted Ci-Cio alkenylene, and optionally substituted Ci-Cio alkynylene, wherein up to three carbons of the optionally substituted Ci-Cio alkylene, optionally substituted Ci-Cio alkenylene, and optionally substituted G-Cio alkynylene, are independently replaced by aryl, O, NH, N-(Ci-6 alkyl) or (C=0);

Ri is selected from the group consisting of H, halo, NRpRr, and heterocycloalkyi optionally substituted with NH₂ or Me; wherein Rr and Rr are each independently selected from H and Me;

Z[ is absent or is selected from the group consisting of CH₂, -CH₂0-, -CH₂NH-, - CH₂N(Ci-6 alkyl)-, -CH₂(C=0)-, -NH(C=0)-;

Z₂ is absent or is selected from the group consisting of optionally substituted G-Cio alkylene, optionally substituted heterocycloalkyi, and optionally substituted heteroaryl; and

R₂ is selected from H, OH, NH₂, NH(Ci-6 alkyl), N(Ci_-6 alkyl)₂, NH(cycloalkyl), N(cycloalkyl)₂.

[0082] In one embodiment of a compound of formula II, Yi is CH₂.

[0083] In another embodiment of a compound of formula II, Yi is optionally substituted aryl. In another embodiment, Yi is optionally substituted phenyl.

[0084] In one embodiment of a compound of formula II, Y₂ is absent. [0085] In another embodiment of a compound of formula II, Y₂ is optionally substituted Ci-Cio alkylene, wherein up to three carbon atoms are independently replaced by O, NH, N- (Ci-6 alkyl) or (C=0).

[0086] In another embodiment of a compound of formula II, Y₂ is optionally substituted Ci-Cio alkenylene, wherein up to three carbon atoms are independently replaced by O, NH, N-(Ci-6 alkyl) or (C=0).

[0087] In another embodiment of a compound of formula II, Y₂ and optionally substituted Ci-Cio alkynylene, wherein up to three carbon atoms are independently replaced by O, NH, N-(C 1-6 alkyl) or (CO).

[0088] In one embodiment of a compound of formula II, Ri is H.

[0089] In another embodiment of a compound of formula II, Ri is halo.

[0090] In another embodiment of a compound of formula II, Ri is NRrRr wherein Rr and

Rr are each independently selected from H and Me.

[0091] In another embodiment of a compound of formula II, Ri is heterocycloalkyl optionally substituted with NH₂ or Me.

[0092] In one embodiment of a compound of formula II, Zi is absent.

[0093] In another embodiment of a compound of formula II, Zi is CH₂.

[0094] In another embodiment of a compound of formula II, Zi is -CH₂0-.

[0095] In another embodiment of a compound of formula II, Zi is -CH₂NH-.

[0096] In another embodiment of a compound of formula II, Zi is -CH₂N(Ci-6 alkyl)-.

[0097] In another embodiment of a compound of formula II, Zi is -CH₂(C=0)-.\

[0098] In another embodiment of a compound of formula II, Zi is -NH(C=0)-.

[0099] In one embodiment of a compound of formula II, Z₂ is absent.

[00100] In another embodiment of a compound of formula II, Z₂ is optionally substituted G-

Cio alkylene.

[00101] In another embodiment of a compound of formula II, Z₂ is optionally substituted heterocycloalkyl.

[00102] In another embodiment of a compound of formula II, Z₂ is optionally substituted heteroaryl.

[00103] In one embodiment of a compound of formula II, R₂ is H.

[00104] In another embodiment of a compound of formula II, R₂ is OH.

[00105] In another embodiment of a compound of formula II, R₂ is NH₂.

[00106] In another embodiment of a compound of formula II, R₂ is NH(Ci-6 alkyl).

[00107] In another embodiment of a compound of formula II, R₂ is N(G-6 alkyl)₂. [00108] In another embodiment of a compound of formula II, R2 is NH(cycloalkyl).

[00109] In another embodiment of a compound of formula II, R₂ is N(cycloalkyl)₂.

^R2a

[00110] In one embodiment of a compound of formula II, R₂-Z2-Zi is ^{HzN R}2 , wherein R_2a is selected from the group consisting of hydrogen and (C1-C6 alkyl) and R₂b is selected from the group consisting of hydrogen, (C1-C (C₂-C6 alkenyl), aryl, and arylalkyl.

[00111] In another embodiment R₂-Z₂-Zi is

wherein R_2a and R₂b are defined as previously.

[00112] In one embodiment of a compound of

[00113] In another embodiment, the compound of formula II is a compound of formula IIA:

IIA

or a ph utically acceptable salt thereof, wherein:

is pyridylene;

Y₂ is absent or is selected from the group consisting of optionally substituted Ci-Cio alkylene, optionally substituted Ci-Cio alkenylene, and optionally substituted Ci-Cio alkynylene, wherein up to three carbons of the optionally substituted Ci-Cio alkylene, optionally substituted Ci-Cio alkenylene, and optionally substituted C1-C10 alkynylene, are independently replaced by O, NH, N-(Ci-6 alkyl) or (C=0);

Ri is selected from the group consisting of H, halo, NRi Rr, and heterocycloalkyl optionally substituted with NH₂ or Me; wherein Ry and Ri - are each independently selected from H and Me.

[00114] In a further embodiment, the compound of formula IIA is a compound of formula IIAi:

IIAi

or a ph utically acceptable salt thereof, wherein:

is pyridylene;

Y₂ is absent or is selected from the group consisting of optionally substituted Ci-Cio alkylene, optionally substituted Ci-Cio alkenylene, and optionally substituted Ci-Cio alkynylene, wherein up to three carbons of the optionally substituted Ci-Cio alkylene, optionally substituted CI -C IO alkenylene, and optionally substituted Ci -Cio alkynylene, are independently replaced by O, NH, N-(Ci-6 alkyl) or (C=0); and

Ri is selected from the group consisting of H, halo, NRrRr, and heterocycloalkyl optionally substituted with NH₂ or Me; wherein Rr and Rr are each independently selected from H and Me.

[00115] In a further embodiment, the compound of formula IIAi and thus of formula IIA and thus of formula II is a compound of formula IIA- 1 :

IIA-1

or a pharmaceutically acceptable salt thereof.

[00116] In a further embodiment, the compound of formula IIAi and thus of formula IIA and thus of formula I is a compound of formula IIA-2:

IlA-2

or a pharmaceutically acceptable salt thereof.

[00117] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula IIA-3:

_{I IA 3}. or a pharmaceutically acceptable salt thereof, wherein m is 0, 1 , or 2; and Ri is selected from the group consisting of NR1 R1 ·, and heterocycloalkyl optionally substituted with NH2 or Me; wherein Rr and Rr are each independently selected from H and Me. In one embodiment of a compound of formula IA-3, Ri is halo. In a further embodiment of a compound of formula IIA-3, Ri is chloro. In a further embodiment, Ri is N(Me)₂.

[00118] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula I1A-4:

_nA_4 or a pharmaceutically acceptable salt thereof, wherein Rx is H or methyl; and Ri is heterocycloalkyl.

[00119] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula IIA-5:

or a pharmaceutically acceptable salt thereof, wherein Rx is H or methyl; and Ri is selected from the group consisting of H, halo, NRrRr, and heterocycloalkyl optionally substituted with NH₂ or Me; wherein Rr and Rr are each independently selected from H and Me. In a further embodiment of a compound of formula IIA-4, Ri is NH₂.

[00120] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula IIA-6:

or a pharmaceutically acceptable salt thereof, wherein Ri is selected from the group consisting of H, halo, NRrRr, and heterocycloalkyl optionally substituted with NH₂ or Me; wherein Rr and Rr- are each independently selected from H and Me. In a further embodiment, Ri is heterocycloalkyl optionally substituted with NH₂ or Me.

[00121] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula IIA-7a or IIA-7b:

or a pharmaceutically acceptable salt thereof, wherein Rx is H or methyl; and R\ is heterocycloalkyl optionally substituted with NH₂ or Me. [00122] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula IIA-8:

or a pharmaceutically acceptable salt thereof, wherein R_x is H or methyl and Ri is selected from the group consisting of H, halo, NRrRr, and heterocycioalkyl optionally substituted with NH₂ or Me; wherein Rr and Rr are each independently selected from H and Me. In a further embodiment, Ri is heterocycioalkyl optionally substituted with NH₂ or Me.

[00123] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula IIA-9:

[00124] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula IIA- 10:

or a pharmaceutically acceptable salt thereof, wherein R_x is H or methyl and Ri is selected from the group consisting of H, halo, NRrRr-, and heterocycioalkyl optionally substituted with NH₂ or Me; wherein Rr and Rr are each independently selected from H and Me. In a further embodiment, Ri is heterocycioalkyl optionally substituted with NH₂ or Me. [00125] In a further embodiment, the compound of formula IIA-I and thus of formula IIA and thus of formula II is a compound of formula IIA- 1 la or IIA- 1 IB:

or a pharmaceutically acceptable salt thereof, wherein R_x is H or methyl and Ri is selected from the group consisting of H, halo, NRrRr, and heterocycloalkyl optionally substituted with NH₂ or Me; wherein Rr and Rr are each independently selected from H and Me. In a further embodiment, Ri is heterocycloalkyl optionally substituted with NH₂ or Me.

[00126] In a further embodiment, the compound of formula IIAi and thus of formula IIA and thus of formula II is a compound of formula IIA-12:

[00127] The formula II compounds de icted above are compounds having an para- substituted pyridylene core

It is also to be understood that any and all of the formula II compounds may also have a meta-substituted pyridylene core

[00128] In a further embodiment of a compound of formula IIA an thus of formula II, Ri is

XX ^NH2 , NH₂,

, wherein indicates a point of attachment.

[00129] In a further embodiment of a compound of formula IIA, Y1-Y2-R1 is selected from the group consisting of

[00130] In another aspect, the invention provides a compound which is:

7041793

or a pharmaceutically acceptable salt thereof.

In another aspect, the invention provides a compound which is:

No. Compound

2017/041793

Pharmaceutical Compositions and Administration

[00132] The present invention provides pharmaceutical compositions comprising a compound of the present invention and a pharmaceutically acceptable excipient. In certain embodiments, the compound of the present invention is provided in an effective amount in the pharmaceutical composition. In certain embodiments, the effective amount is a therapeutically effective amount. In certain embodiments, the effective amount is a prophylactically effective amount.

[00133] Pharmaceutically acceptable excipients include any and all solvents, diluents, or other liquid vehicles, dispersions, suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as 2017/041793 suited to the particular dosage form desired. General considerations in formulation and/or manufacture of pharmaceutical compositions agents can be found, for example, in

Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980), and Remington: The Science and Practice of Pharmacy, 21 st Edition (Lippincott Williams & Wilkins, 2005).

[00134] Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include the steps of bringing the compound of the present invention (the "active ingredient") into association with a carrier and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.

[0013S] Pharmaceutical compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses. As used herein, a "unit dose" is discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient. The amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.

[00136] Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition of the invention will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered. By way of example, the composition may comprise between 0.1 % and 100% (w/w) active ingredient.

[00137] Pharmaceutically acceptable excipients used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.

[00138] Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystal!ine cellulose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.

[00139] Exemplary granulating and/or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose and wood products, natural sponge, cation-exchange resins, calcium 2017/041793 carbonate, silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross- linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, quaternary ammonium compounds, and mixtures thereof.

[00140] Exemplary surface active agents and/or emulsifiers include natural emulsifiers (e.g. acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g.

bentonite [aluminum silicate] and Veegum [magnesium aluminum silicate]), long chain amino acid derivatives, high molecular weight alcohols (e.g. stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g. carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g. carboxymethy (cellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters (e.g. polyoxyethylene sorbitan monolaurate [Tween 20], polyoxyethylene sorbitan [Tween 60], polyoxyethylene sorbitan monooleate [Tween 80], sorbitan monopalmitate [Span 40], sorbitan monostearate [Span 60], sorbitan tristearate [Span 65], glyceryl monooleate, sorbitan monooleate [Span 80]), polyoxyethylene esters (e.g. polyoxyethylene monostearate [Myrj 45], polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil, polyoxymethylene stearate, and Solutol), sucrose fatty acid esters, polyethylene glycol fatty acid esters (e.g. Cremophor), polyoxyethylene ethers, (e.g.

polyoxyethylene lauryl ether [Brij 30]), poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic F 68, Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, and/or mixtures thereof.

[00141] Exemplary binding agents include starch (e.g. cornstarch and starch paste), gelatin, sugars (e.g. sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums (e.g. acacia, sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose,

ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl

methylcellulose, microcrystalline cellulose, cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate (Veegum), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, and/or mixtures thereof.

[00142] Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, alcohol preservatives, acidic preservatives, and other preservatives.

[00143] Exemplary antioxidants include alpha tocopherol, ascorbic acid, acorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium metabisulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.

[00144] Exemplary chelating agents include ethylenediaminetetraacetic acid (EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof. Exemplary antimicrobial preservatives include benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.

[00145] Exemplary antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium benzoate, sodium propionate, and sorbic acid.

[00146] Exemplary alcohol preservatives include ethanol, polyethylene glycol, phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.

[00147] Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, beta- carotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.

[00148] Other preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT),

ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant Plus, Phenonip, methylparaben, Germall 1 15, Germaben II, Neolone, Kathon, and Euxyl. In certain embodiments, the preservative is an anti-oxidant. In other embodiments, the preservative is a chelating agent. [00149] Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D-gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium acetate, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen- free water, isotonic saline, Ringer's solution, ethyl alcohol, and mixtures thereof.

[00150] Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, and mixtures thereof.

[00151] Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea buckthorn, sesame, shea butter, silicone, soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, and wheat germ oils. Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixtures thereof.

[00152] Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredients, the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1 ,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the conjugates of the invention are mixed with solubilizing agents such as Cremophor, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and mixtures thereof.

[00153] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation can be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1 ,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables. The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

[00154] A sterile injectable composition, e.g., a sterile injectable aqueous or oleaginous suspension, can be formulated according to techniques known in the art using suitable dispersing or wetting agents (such as Tween 80) and suspending agents. The sterile injectable preparation can also be a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example, as a solution in 1 ,3-butanediol. Among the acceptable vehicles and solvents that can be employed are mannitol, water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium (e.g., synthetic mono- or diglycerides). Fatty acids, such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions. These oil solutions or suspensions can also contain a long-chain alcohol diluent or dispersant, or carboxymethyl cellulose or similar dispersing agents. Other commonly used surfactants such as Tweens or Spans or other similar emulsifying agents or bioavailability enhancers which are commonly used in the manufacture of pharmaceutically acceptable solid, liquid, or other dosage forms can also be used for the purposes of formulation.

[00155] 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 can 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 which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.

[00156] Compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing the conjugates of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.

[00157] Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active ingredient 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, 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, cetyl 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 comprise buffering agents.

[00158] Solid compositions of a similar type can be employed as fillers in soft and hard- filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally comprise opacifying agents and can 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 which can be used include polymeric substances and waxes. Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.

[00159] The active ingredient can 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. In such solid dosage forms the active ingredient can be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may comprise buffering agents. They may optionally comprise opacifying agents and can 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 which can be used include polymeric substances and waxes.

[00160] Dosage forms for topical and/or transdermal administration of a compound of this invention may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches. Generally, the active ingredient is admixed under sterile conditions with a pharmaceutically acceptable carrier and/or any needed preservatives and/or buffers as can be required. Additionally, the present invention contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of an active ingredient to the body. Such dosage forms can be prepared, for example, by dissolving and/or dispensing the active ingredient in the proper medium. Alternatively or additionally, the rate can be controlled by either providing a rate controlling membrane and/or by dispersing the active ingredient in a polymer matrix and/or gel.

[00161] Suitable devices for use in delivering intradermal pharmaceutical compositions described herein include short needle devices such as those described in U.S. Pat. Nos.

4,886,499; 5, 190,521 ; 5,328,483; 5,527,288; 4,270,537; 5,015,235; 5, 141 ,496; and

5,417,662. Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin, such as those described in PCT publication WO 99/34850 and functional equivalents thereof. Jet injection devices which deliver liquid vaccines to the dermis via a liquid jet injector and/or via a needle which pierces the stratum corneum and produces a jet which reaches the dermis are suitable. Jet injection devices are described, for example, in U.S. Pat. Nos. 5,480,381 ; 5,599,302; 5,334, 144; 5,993,412;

5,649,912; 5,569, 1 89; 5,704,91 1 ; 5,383,851 ; 5,893,397; 5,466,220; 5,339,163; 5,312,335; 5,503,627; 5,064,413; 5,520,639; 4,596,556; 4,790,824; 4,941 ,880; 4,940,460; and PCT publications WO 97/37705 and WO 97/13537. Ballistic powder/particle delivery devices which use compressed gas to accelerate vaccine in powder form through the outer layers of the skin to the dermis are suitable. Alternatively or additionally, conventional syringes can be used in the classical mantoux method of intradermal administration.

[00162] A pharmaceutical composition of the invention can be prepared, packaged, and/or sold in a formulation suitable for pulmonary administration via the buccal cavity. Such a formulation may comprise dry particles which comprise the active ingredient and which have a diameter in the range from about 0.5 to about 7 nanometers or from about 1 to about 6 nanometers. Such compositions are conveniently in the form of dry powders for

administration using a device comprising a dry powder reservoir to which a stream of propellant can be directed to disperse the powder and/or using a self-propelling

solvent/powder dispensing container such as a device comprising the active ingredient dissolved and/or suspended in a low-boiling propellant in a sealed container. Such powders comprise particles wherein at least 98% of the particles by weight have a diameter greater than 0.5 nanometers and at least 95% of the particles by number have a diameter less than 7 nanometers. Alternatively, at least 95% of the particles by weight have a diameter greater than 1 nanometer and at least 90% of the particles by number have a diameter less than 6 nanometers. Dry powder compositions may include a solid fine powder diluent such as sugar and are conveniently provided in a unit dose form.

[00163] Low boiling propellants generally include liquid propellants having a boiling point of below 65 °F at atmospheric pressure. Generally the propellant may constitute 50 to 99.9% (w/w) of the composition, and the active ingredient may constitute 0.1 to 20% (w/w) of the composition. The propellant may further comprise additional ingredients such as a liquid non-ionic and/or solid anionic surfactant and/or a solid diluent (which may have a particle size of the same order as particles comprising the active ingredient).

[00164] Pharmaceutical compositions of the invention formulated for pulmonary delivery may provide the active ingredient in the form of droplets of a solution and/or suspension. Such formulations can be prepared, packaged, and/or sold as aqueous and/or dilute alcoholic solutions and/or suspensions, optionally sterile, comprising the active ingredient, and may conveniently be administered using any nebulization and/or atomization device. Such formulations may further comprise one or more additional ingredients including, but not limited to, a flavoring agent such as saccharin sodium, a volatile oil, a buffering agent, a surface active agent, and/or a preservative such as methy (hydrox benzoate. The droplets provided by this route of administration may have an average diameter in the range from about 0.1 to about 200 nanometers.

[00165] Formulations described herein as being useful for pulmonary delivery are useful for intranasal delivery of a pharmaceutical composition of the invention. Another formulation suitable for intranasal administration is a coarse powder comprising the active ingredient and having an average particle from about 0.2 to 500 micrometers. Such a formulation is administered by rapid inhalation through the nasal passage from a container of the powder held close to the nares.

[00166] Formulations for nasal administration may, for example, comprise from about as little as 0.1% (w/w) and as much as 100% (w/w) of the active ingredient, and may comprise one or more of the additional ingredients described herein. A pharmaceutical composition of the invention can be prepared, packaged, and/or sold in a formulation for buccal

administration. Such formulations may, for example, be in the form of tablets and/or lozenges made using conventional methods, and may contain, for example, 0.1 to 20% (w/w) active ingredient, the balance comprising an orally dissolvable and/or degradable composition and, optionally, one or more of the additional ingredients described herein. Alternately, formulations for buccal administration may comprise a powder and/or an aerosolized and/or atomized solution and/or suspension comprising the active ingredient. Such powdered, aerosolized, and/or aerosolized formulations, when dispersed, may have an average particle and/or droplet size in the range from about 0.1 to about 200 nanometers, and may further comprise one or more of the additional ingredients described herein.

[00167] Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.

[00168] Compounds provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the 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 subject or organism will depend upon a variety of factors including the disease, disorder, or condition being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.

[00169] To practice the method of this invention, the above-described compound or its pharmaceutical composition can be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally, rectally, or via an implanted reservoir. The term "parenteral" as used herein includes subcutaneous, intracutaneous, intravenous, intramuscular, intraarticular, intraarterial, intrasynovial, intrastemal, intrathecal, intraiesional, and intracranial injection or infusion techniques. In general the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g., its stability in the environment of the gastrointestinal tract), and/or the condition of the subject (e.g., whether the subject is able to tolerate oral administration).

[00170] The exact amount of a compound required to achieve an effective amount will vary from subject to subject, depending, for example, on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound(s), mode of administration, and the like. The desired dosage can be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage can be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).

[00171] In certain embodiments, an effective amount of a compound for administration one or more times a day to a 70 kg adult human may comprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000 mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg, about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1 mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about 1000 mg, or about 100 mg to about 1000 mg, of a compound per unit dosage form.

[00172] In certain embodiments, the compounds of the invention may be administered orally or parenterally at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg kg to about 50 mg/kg, preferably from about 0.1 mg kg to about 40 mg kg, preferably from about 0.5 mg/kg to about 30 mg kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg kg, and more preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.

[00173] It will be appreciated that dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult. The amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.

[00174] It will be also appreciated that a compound or composition, as described herein, can be administered in combination with one or more additional therapeutically active agents. The compounds or compositions can be administered in combination with additional therapeutically active agents that improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body. It will also be appreciated that the therapy employed may achieve a desired effect for the same disorder, and/or it may achieve different effects.

[00175] The compound or composition can be administered concurrently with, prior to, or subsequent to, one or more additional therapeutically active agents. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent. In will further be appreciated that the additional therapeutically active agent utilized in this combination can be administered together in a single composition or administered separately in different compositions. The particular combination to employ in a regimen will take into account compatibility of the inventive compound with the additional therapeutically active agent and/or the desired therapeutic effect to be achieved. In general, it is expected that additional therapeutically active agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually. Additional therapeutically active agents include antibiotic agents, e.g., antibiotics useful for treating tuberculosis. Exemplary antibiotics include, but are not limited to, isoniazid, rifampin, pyrazinamide, ethambutol, and streptomycin.

[00176] Also encompassed by the invention are kits (e.g., pharmaceutical packs). The kits provided may comprise an inventive pharmaceutical composition or compound and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or compound. In some embodiments, the inventive

pharmaceutical composition or compound provided in the container and the second container are combined to form one unit dosage form.

Methods of Use and Treatment

[00177] In another aspect, the invention provides a method of treating a bacterial infection in a patient in need of such treatment, comprising administering an effective amount of a compound of formula I or a composition comprising a compound of formula I. In certain embodiments, the effective amount is a therapeutically effective amount. In certain other embodiments, the effective amount is a prophylactically effective amount.

[00178] In one embodiment, the bacterial infection is tuberculosis. In certain embodiments, the tuberculosis infection is a Mycobacterium tuberculosis infection. In certain embodiments, the tuberculosis infection is multi-drug-resistant tuberculosis (MDR-TB) infection, e.g., resistant to first-line TB drugs rifampicin and/or isoniazid. In certain embodiments, the tuberculosis infection is extensively-drug-resistant tuberculosis (XDR-TB) infection, e.g., also resistant to three or more of the six classes of second-line drugs (see, e.g., Centers for Disease Control and Prevention (CDC) (2006). "Emergence of Mycobacterium tuberculosis with extensive resistance to second-line drugs worldwide, 2000-2004". MMWR Morb Mortal Wkly Rep 55 (l l): 301 -5).

[00179] In some embodiments, the compounds of the invention can be active against a wide range of both Gram-positive and Gram-negative organisms. In these and other embodiments, the compounds of the invention can be used to treat infections and to inhibit microbial growth. Thus, the compounds of the invention can be used to treat humans and animals having a broad spectrum of bacterial infections such as impetigo, pneumonia, bronchitis, pharyngitis, endocarditis, urinary tract infections, diabetes foot ulcers, gastro-intestinal infections and bacteremia. These bacterial infections could be caused by any of the following bacteria-Staphylococcus aureus, coagulase negative staphylococci, methicillin-resistant Staphylococcus aureus, methicillin-resistant coagulase negative staphylococci, enterococci, beta-haemolytic streptococci, viridans group of streptococci, Bacillus mycobacterial infections due to multi-drug resistant M. tuberculosis and other atypical mycobacteria such as M. intracellulare and M. avium, as well as newly emerging Gram-negative pathogens such as Chryseobacterium meningosepticum, Chryseobacterium indologense and other Gram- negative pathogens such as E. coli, Klebsiella, Proteus, Serratia, Citrobacter, Pseudomonas, Burkholderia, Brucella, Yersinia, Francisella, Coxiella, Chlamydia, Salmonella, Rickettsia, Shigella and Campylobacter.

[00180] In another embodiment, the bacterial infection is a gram negative or gram positive bacterial infection.

[00181] In a further embodiment, the bacterial infection is a gram negative bacterial infection. In a further embodiment, the gram negative infection is selected from the group consisting of E. coli, Acinetobacter baumanii, Pseudomonas aeruginosa, Klebisella pneumonia, and Neisseria gonorrhoeae.

[00182] In a further embodiment, the gram positive bacterial infection is selected from the group consisting of a Methicillin resistant staphylococcus aureus ( RSA) infection and an M. smegmatis infection.

Processes

[00183] In another aspect, the invention provides processes for preparing compounds of formula I. The process is depicted in the synthetic schemes in the following section.

Examples

[00184] The invention will now be demonstrated by the following non-limiting examples.

[00185] All reactions requiring anhydrous conditions were conducted in flame-dried glassware under a positive pressure of either nitrogen or argon. Commercially available reagents were used as received; otherwise, materials were purified according to Purification of Laboratory Chemicals. Dichloromethane (CH2CI2), N,N'-dimethylformamide (DMF), and tetrahydrofuran (THF) were degassed with nitrogen and passed through a solvent purification system (Innovative Technologies Pure Solv). Dry 1 ,4-dioxane was purchased from Acros Organics in a Acros Seal™ bottle. Reverse phase HPLC was conducted on a Gilson 322 using a Vydac CI 8 column eluting with H₂0 (0. 1 % TFA) and 10%H₂O:90 CH3CN (0.1 % TFA).

[00186] Melting points were determined using Mel-Temp® Capillary Melting Point Apparatus. Infrared spectra were obtained using Nicolet 380-FT IR spectrometer fitted with a Smart Orbit sample system. Optical rotations were obtained at ambient temperature on a Perkin Elmer Model 343 polarimeter (Na D line) using a microcell with a 1 decimeter path length. Mass spectra were determined on a Micromass Quattro II (ESI/APCI-TOF) for HRMS at the University of Utah Mass Spectrometry Facility or LCMS were collected on Thermo Scientific™ UltiMate™ 3000 UHPLC with electrochemical detector with a fluorescence detector monitored at either 214 or 254 nm. Ή NMR spectra were recorded at 500 MHz, 400 MHz, and 300 MHz, and ¹³C at 125 MHz. Proton resonances were reported relative to the deuterated solvent peak: 7.27 ppm for CDCb, 3.31 ppm (center line signal) for CD₃OD, 2.50 for D6-DMSO and 4.79 for D₂0 using the following format: chemical shift (δ) [multiplicity (s= singlet, br s= broad singlet, d= doublet, t= tripletq= quartet, m= multiplet)]. Carbon resonances were reported as chemical shifts (δ) in parts per million, relative to the center line signal of the respective solvent peak: 77.23 ppm for CDCb and 49.15 ppm for CD3OD. All the commercially available chemicals are purchased from Sigma-Aldrich, Acros, TCI America, Combi-Blocks, Alfa-Aesar, Ark Pharma, Strem Chemicals, Frontier Scientific, and AstaTech, Inc.

Example 1

Example 1: l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((4-(hydroxymethyl)pyridin-2- yI)amino)pyrimidin-2(lH)-one

[00187] Example I was prepared as provided in Synthetic Scheme 1.

Synthetic Scheme 1

Reagents: Step 1) CS2CO3, CH₃CN, reflux, 2h (2) K2CO3, CH₃CN,70 °C, 2h (3) ΝΗ,ΟΗ, MeOH, 12h

(4) Pd2(dba)₃,B!NAP,NaOtBu, toluene, 80 °C, MW, 200W, 20Min.

Step 1: iV-fl-(4-Bromobutvn-2-oxo-l,2-dihvdropyriniidiii-4-vnacetamide; [00188] To a pre-heated (at 50 °C, 15 minutes) suspension of N-(2-oxo-l ,2- dihydropyrimidin-4-yI)acetamide (0.30g, 2.0 mmol) and Cs₂C0₃ (0.79g, 2.4 mmol) in dry CH3CN (20 mL), 1 ,4-dibromobutane (518 mg, 2.4 mmol) was added under an atmosphere of nitrogen. After, the reaction mixture was stirred for 0.5h at 50 °C, filtered and the filtrate was concentrated under reduced pressure. Purification on silica gel using flash chromatography afforded the desired product as a pale yellow colored solid.

Step 2: fert-Butyl (l-(4-(4-acetamido-2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4- vDcarbamate;

[00189] To a stirring suspension of N-( l -(4-bromobutyl)-2-oxo-l ,2-dihydropyrimidin-4- yl)acetamide (220 mg, 0.77 mmol), and potassiumcarbonate (21 1 mg, 1.53 mmol) in acetonitrile (12 mL), 4-Boc amino piperidine (150 mg, 0.75 mmol) dissolved on DMF (1 mL) was added. The reaction mixture was allowed to stir under heating conditions (70 °C) for 2h, then filtered and concentrated under reduced pressure. The compound was used in the next step without further purification.

Step 3: fert-Butyl (l-(4-(4-amino-2-oxopyrimidin-l(2H)-yl)butvnpiperidin-4- vOcarbamate:

[00190] The stating material ter/-butyl ( l -(4-(4-acetamido-2-oxopyrimidin-l (2H)- yl)butyl)piperidin-4-yl)carbamate (220 mg, 0.54 mmol) was dissolved in MeOH ( 10 mL) followed by the addition of ammonium hydroxide (2 mL). The reaction mixture was allowed to stir at room temperature for 16h, then the solvent was evaporated. The residue upon flash column chromatography afforded the desired compound as a white solid.

Step 4: fert-Butyl (l-(4-(4-((4-(((fg ^,/-butyldimethylsilvnoxy)methvnpyridin-2-vnamino)- 2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4-vncarbamate;

[00191] An oven dried microwave reaction tube was charged with 2-bromo-4-(((/er/- butyldimethylsilyl)oxy)methyl)pyridine (75 mg, 0.25 mmol), /ert-butyl ( l -(4-(4-amino-2- oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate (92 mg, 025 mmol), NaO'Bu (48 mg, 0.50 mmol), Pd₃(dba)₂ (23 mg, 25.0 μιηοΐ), rac-BINAP (23 mg, 37. μηιοΐ) and dry toluene. The reaction mixture was degased and purged with nitrogen 3 times and stirred and heated in a focused CEM microwave reactor microwave conditions (80 °C 200 W) for 20 minutes. After which the reaction mixture is diluted with EtOAc (1 mL) and filtered through a pad of celite and concentrated under reduced pressure. Purification on silica gel using flash chromatography (2% MeOH/CHCb) afforded the desired product as a yellow colored solid.

Step 5: l-(4-(4-Aminopiperidin-l-yl)butyl)-4- 4-(hvdroxYmethvnpyridin-2- vhamino)pyrimidin-2(lH)-one; 41793

[00192] tert-Butyl (l-(4-(4-((4-(((/ert-butyldimethylsilyl)oxy)methyl)pyridin-2-yl)amino)-2- oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate (50 mg, 85.0 μιτιοΐ) was dissolved in 50% TFA in dichloromethane (1 mL) and stirred for 16h at room temperature. The solvent was evaporated and neutralized with Et₃N. The compound was purified using MPLC to afford title compound l -(4-(4-Aminopiperidin-l -yl)butyl)-4-((4-(hydroxymethyl)pyridin-2- yl)amino)pyrimidin-2(lH)-one (25 mg, 79%) as a brown colored solid. Ή NMR (500 MHz, CD₃OD) δ ppm 8.23-8.19 (m, 2H), 7.75 (d, 1 H), 7.08 (t, 1 H), 6.51 (br s, 1 H), 4.67 (s, 2H), 3.86 (t, 2H), 2.90 (d, 2H), 2.65-2.60 (m, 1 H), 2.39-2.37 (m, 2H), 2.04-1.98 (m, 2H), 1.83- 1.79 (m, 2H), 1.76- 1.70 (m, 2H), 1.57- 1.5 1 (m, 2H), 1.44- 1.36 (m, 2H). ^,3C NMR (100 MHz,) 6 ^{l 3}C NMR (125 MHz, CD3OD) δ ppm 163.9, 158.9, 155.0, 153.8, 148.7, 147.9, 1 18.0, 1 13.7, 97.7, 79.5, 63.8, 59.0, 53.5, 51 .1 , 35.3, 28.1, 24.7.

Example 2

2-((l-(4-(4-Aminopiperidin-l-yl)butyl)-2-oxo-l,2-di ydropyrimidin-4-yl)amino)-N-(3- aminopropyl)isonicotinamide hydrochloride salt

[00193] Example 2 was prepared as provided in Synthetic Scheme 2.

Synthetic Scheme 2

R=NHCH₂CH₂CH₂NHBoc

Reagents: Step 1) Pd₂(dba)₃,BINAP,NaOtBu, toluene, 80 °C, MW, 200W, 20 in (2) Methanolic HCI

[00194] Example 2 was prepared in a similar fashion to Example 1 from /ert-butyl (l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl (3-(2- chloroisonicotinamido)propyl) carbamate. Ή NMR (500 MHz, CD3OD) 5 ppm 8.59 (br s, 1 H), 8.31 (d, 1 H), 7.71 (d, 1 H), 7.37 (d, 1 H), 6.29 (d, 1 H), 3.79 (t, 2H), 3.42-3.38 (m, 2H), 2.82 (d, 2H), 2.69-2.65 (m, 2H), 2.57-2.51 (m, 1 H), 2.29 (t, 2H), 1.93 (t, 2H), 1.76- 1.70 (m, 4H), 1.69-1.63 (m, 2H), 1.49- 1.43 (m, 2H), 1.36-1.27 (m, 4H). ¹³C NMR (100 MHz,) δ ^l3C NMR (120 MHz, CD₃OD) 5 ppm 167.9, 163.8, 159.0, 154.3, 149.9, 148.1, 144.8, 1 18.3, 1 13.0, 97.8, 59.0, 53.5, 51 .2, 39.7, 38.4, 35.2, 32.8, 28.2, 28.1, 24.7.

Example 3

l-(4-(4-aminopiperidin-l-yl)bur l)-4-((4-(((3-aminopropyl)amino)methyl)pyridin-2- yl)amino)pyrimidin-2(l//)-one;

[00195] Example 3 was prepared in a similar fashion to Example 1 from tert-butyl (l-(4-(4- amino-2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4-yl)carbamate and /er/-butyl ((2- bromopyridin-4-yl)methyl)(3-((/er/-butoxycarbonyl)amino)propyl)carbamate as yellow colored solid. ^lH NMR (400 MHz, D₂0) δ ppm 8.50 (d, 1 H), 8.13 (d, 1 H), 7.52 (br s 1 H), 6.47 (d, 1 H), 4.45 (s, 2H), 4.00 (br s, 2H), 3.73 (d, 2H), 3.61 -3.44 (m, 1 H), 3.32-3.28 (m, 2H), 3.22 (br s, 2H), 3.17-3.1 1 (m, 2H), 2.35 (d, 2H), 2.21-2.12 (m, 2H), 1.20-1.92 (m, 2H), 1.90-1.84 (m, 4H).

Example 4

6-((l-(4-(4-aminopiperidin-l-yl)butyl)-2-oxo-l,2-dihydropyrimidin-4-yI)amino)-N-(3- aminopropyl)nicotinamide hydrochloride salt

[00196] Example 4 was prepared as provided in Synthetic Scheme 3.

Synthetic Scheme 3

Reagents; Step 1) Pd(dba)₂, Xantphos, Cs₂C0₃, dry 1 ,4-dioxane, 110 oC, 16h (2) Methanolic HCI

[00197] Step 1 : fert-Butyl (1-(4-(4-((5-(Γ3-( ftert- butoxycarbonyl)aniino)propyl)carbamoyl) pyridine-2-yl)aminQ)-2-oxopyrimidin-lC2H>- v0butyl)piperidin-4-vDcarbamate; An oven dried pressure flask was charged with tert- butyl (3-(6-chloronicotinamido)propyl) carbamate ( 1 .0 eq.), /<?/Y-butyl ( l -(4-(4-amino-2- oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate (1.01 eq.), cesium carbonate (2 eq.), Pd(dba)₂ (0.1 eq.), Xantphos (0.2 eq.) and dry dioxane (12 mL). The reaction mixture was degassed and purged with nitrogen 3 times and stirred at 1 10 °C for 16h. The reaction mixture was diluted with CHC (25 mL), filtered through a pad of celite and concentrated under reduced pressure. Purification on silica gel using flash chromatography afforded tert- Butyl (l -(4-(4-((4-((3-((tert-butoxycarbonyl)amino)propyl)carbamoyl) phenyl)amino)-2- oxopyrimidin-l (2H)-yl)butyl) piperidin-4-yl)carbamate as an yellow solid.

[00198] Step 2 ; 6-(( l-( 4-(4-Am inopiperidin- 1 -vUbutyl)- 2-oxo-l ,2-dihvdropyrimidin-4- yl)amino)-N-(3-aminopropyhnicotinamide: ter/-Butyl (l-(4-(4-((5-((3-((tert- butoxycarbonyl)amino)propyl)carbamoyl) pyridinr-2-yl)amino)-2-oxopyrimidin- 1 (2H)- yl)butyl) piperidin-4-yl)carbamate was dissolved in methanolic HCI and stirred for 4h. The methanol was evaporated and the resultant solid was triturated with ether and dried under vacuum to afford the desired product as a yellow solid. Ή NMR (500 MHz, CD₃OD) δ 8.77

(d, 1 H), 8.35 (br s, 1 H), 8.17 (dd, 1 H), 7.85 (d, 1 H), 6.56 (d, 1 H), 3.89 (t, 2H), 3.50 (t, 2H), 2.96 (d, 2H), 2.92 (t, 2H), 2.89-2.84 (m, 1 H), 2.41 (t, 2H), 2.07 (t, 2H), 1.92-1.89 (m, 4H), 1.78-1.70 (m, 2H), 1.59-1.47 (m, 4H). ^{I 3}C NMR ( 125 MHz, CD3OD) δ 168.3, 164.0, 158.9, 156.1, 149.0, 148.6, 138.2, 125.9, 1 15.1, 98.1, 58.9, 53.1, 51.3, 49.6, 39.0, 37.9, 33.3, 30.7, 28.2, 24.8 ppm. LC-MS [M+H] 443.3. Example 5

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((4-((3-(cycIopropylamino)propoxy) methyl)pyridin-2-yl)amino)pyrimidin-2(l H)-one hydrochloride salt

[00199] Example 5 was prepared in a similar fashion to Example 4 from ter/-butyl (l-(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl (3-((2- chloropyridin-4-yl)methoxy)propyl)(cyclopropyl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D2O) δ 8.29 (d, 1 H), 8.04 (d, 1 H), 7.42 (d, 1 H), 7.40 (s, 1 H), 6.40 (d, 1 H), 4.76 (s, 2H), 3.96 (t, 2H), 3.75-3.67 (m, 4H)₅ 3.57-3.51 (m, 1 H), 3.29 (t, 2H), 3.19 (t, 2H), 3.09 (t, 2H), 2.74 (t, 1 H), 2.32 (d, 2H), 2.09-2.01 (m, 2H), 1.97-1.87 (m, 2H), 1.80 (br s, 4H), 0.84-0.76 (m, 4H). ^l C NMR (125 MHz, D₂0) 8 161.9, 158.0, 155.4, 150.1 , 148.9, 137.5, 1 17.7, 1 12.9, 97.1, 70.0, 68.2, 56.2, 50.6, 50.0, 45.8, 45.3, 30.0, 27.0, 25.4, 25.1 , 20.6, 2.9 ppm. LC-MS [M+H] 470.3

Example 6

l-(4-(4-Aminopiperidin-l-yI)butyl)-4-((5-(((3-aminopropyl)amino)methyl) pyridin-2- yl)amino)pyrimidin-2(lH)-one

[00200] Example 6 was prepared in a similar fashion to Example 4 from /ert-butyl (l-(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl ((6- bromopyridin-3-yl)methyl)(3-((tert-butoxycarbonyl)amino)propyl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, CD3OD) δ 8.26 (s, 1 H), 8.23 (br s, 1 H), 7.78 (d, 2H), 6.50 (bs, 1 H), 3.87 (t, 2H), 3.75 (s, 2H), 2.94 (d, 2H), 2.84 (t, 2H), 2.75- 2.66 (m, 3H), 2.40 (t, 2H), 2.06 (t, 2H), 1.86 (d, 2H), 1.79-1.71 (m, 4H), 1.59-1.53 (m, 2H), 1.50-1 .42 (m, 2H). ^{I 3}C NMR (125 MHz, CD3OD) δ 164.0, 159.0, 153.0, 149.1 , 148.1; 139.8, 131.7, 1 16.2, 97.9, 59. 1, 53.5, 51.3, 51.2, 49.6, 46.7, 40.4, 34.7, 31.3, 28.3, 24.8 ppm. LC-MS [M+H] 429.3

(R)- 1-(4-(4- Am inopiperidi n- l-yl) buty l)-4-((4-(3-hyd roxy pyrrolidine- 1- carbonyl)pyridin-2-yl)amino)pyrimidin-2(lH)-one

[00201] Example 7 was prepared in a similar fashion to Example 4 from 2-(( 1 -(4-(4-((tert- butoxycarbonyl)amino)piperidin-l-yl)butyl)-2-oxo- l ,2-dihydropyrimidin-4- yl)amino)isonicotinic acid and (R)-pyrrolidin-3-ol.

Example 8

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((4-(4-(hydroxymethyl)piperazine-l-carbonyl) pyridin-2-yl)amino)pyrimidin-2(lH)-one

[00202] Example 8 was prepared in a similar fashion to Example 4 from 2-((l-(4-(4-((tert- butoxycarbonyl)amino)piperidin-l -yl)butyl)-2-oxo- l ,2-dihydropyrimidin-4- yl)amino)isonicotinic acid and 2-(piperazin-l -yl)ethan-l -ol.

Example 9

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((4-(4-(hydroxymethyl)piperidine-l- carbonyl)pyridin-2-yl)amino)pyrimidin-2(lH)-one

[00203] Example 9 was prepared in a similar fashion to Example 4 from 2-((l-(4-(4-((tert- butoxycarbonyl)amino)piperidin- l -yl)butyl)-2-oxo-l ,2-dihydropyrimidin-4- yl)amino)isonicotinic acid and piperidin-4-ylmethanol. Example 10

l-(4-(4-Aminopiperidin-l-yl)but )-4-((5-((piperidin-4-ylamino)methyl) pyridine-2- yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00204] Example 10 was prepared in a similar fashion to Example 4 from /er/-butyl (l-(4-(4- amino-2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl 4-((tert- butoxycarbonyl) ((6-chloropyridin-3-yl)methyl)amino)piperidine- l -carboxylate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.61 (s, I H), 8.27 (d, I H), 8.17 (d, I H), 7.47 (d, I H), 6.50 (d, I H), 4.49 (s, 2H), 4.04 (t, 2H), 3.80-3.55 (m, 6H), 3.30-3.1 1 (m, 6H), 2.53 (d, 2H), 2.37 (d, 2H), 2.08-1.79 (m, 8H). ¹³C NMR ( 125 MHz, D₂0) δ 158.8, 151.1, 150.9, 144.5, 143.6, 123.9, 1 16.0, 1 15.8, 96.2, 56.1 , 52.6, 50.7, 50.0, 45.4, 45.0, 42.3, 27.1, 26.9, 25.1, 25.0, 20.6 ppm. LC-MS [M+H] 455.3

Example 11

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((5-((piperidin-4-ylamino)methyl) pyridin-2- yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00205] Example 1 1 was prepared in a similar fashion to Example 4 from tert-butyl (l-(4-(4- amino-2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl (l -((6- chloropyridin-3-yl)methyl)piperidin-4-yl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.58 (s, I H), 8.22 (dd, I H), 8.16 (d, I H), 7.43 (d, IH), 6.46 (d, I H), 4.48 (s, 2H), 4.00 (t, 2H), 3.70 (t, 4H), 3.59-3.53 (m, 2H), 3.27-3.20 (m, 4H), 3.12 (t, 2H), 2.33 (d, 4H), 1.94 (q, 4H), 1.83 (br s, 4H). ¹³C NMR (125 MHz, D₂0) δ 158.5, 151.6, 151.2, 150.2, 146.2, 144.4, 121.7, 1 15.9, 1 15.8, 96.2, 56.5, 56.1, 50.7, 50.4, 49.9, 45.4, 45.3, 27.0, 26.9, 25.0, 20.6 ppm. LC-MS [M+H] 455.3

Example 12

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((5-((azetidin-3-ylamino)methyl) pyridin-2- yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00206] Example 12 was prepared in a similar fashion to Example 4 from ½r/-butyl (l-(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl azetidin-3- yl((6-chloropyridin-3-yl)methyl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.59 (s, I H), 8.23 (dd, I H), 8.17 (d, I H), 7.45 (d, I H), 6.47 (d, I H), 4.62 (p, IH), 4.50 (d, 4H), 4.42 (br s, 2H), 4.01 (t, 2H), 3.73 (d, 2H), 3.61 -3.54 (m, I H), 3.22 (t, 2H), 3.14 (t, 2H), 2.35 (d, 2H), 1.96 (dq, 2H), 1 .85 (d, 4H). ¹³C NMR (125 MHz, D₂0) δ 158.5, 151.4, 151. 1 , 150.3, 145.0, 143.3, 123.2, 1 16.0, 96.1 , 56.1 , 50.7, 49.9, 48.8, 47.5, 45.9, 45.3, 27.0, 25.0, 20.6 ppm. LC-MS [ +H] 427.3

Example 13

(-S -2-Amino-N-((6-((l-(4-(4-aminopiperidin-l-yl)butyl)-2-oxo-l,2-dihydropyrimidin-4- yI)amino)pyridin-3-yl)methyl)-3-hydroxypropanamide hydrochloride salt

[00207] Example 13 was prepared in a similar fashion to Example 4 from /er/-butyl (l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl (S)-4-(((6- chloropyridin-3-yI)methyl)carbamoyl)-2,2-dimethyloxazolidine-3-carboxylate to afford the desired product as a yellow solid. Ή NMR (500 MHz, 1¾0) δ 8.33 (s, I H), 8.19 (d, I H), 8.09 (d, I H), 7.44 (d, I H), 6.43 (d, I H), 4.56 (d, 2H), 4.22 (t, I H), 4.05-3.97 (m, 4H), 3.73 (d, 2H), 3.58 (t, I H), 3.22 (t, 2H), 3.14 (t, 2H), 3.36 (d, 2H), 2.01 -1 .92 (m, 2H), 1.84 (br s, 4H). ^{, 3}C NMR (125 MHz, D₂0) δ 168.1 , 160.8, 154.0, 150.3, 148.7, 143.7, 137.8, 130.5, 1 16.1 , 96.8, 60.1 , 56.2, 54.5, 50.7, 50.0, 45.4, 39.8, 27.1, 25.1 , 20.7 ppm. LC-MS [M+H] 459.3

Example 14

(S)-2-Amino-N-((6-((l-(4-(4-aminopiperidin-l-yl)buryl)-2-oxo-l,2-dihydropyrimidin-4- yI)amino)pyridin-3-yl)methyl)propenamide hydrochloride salt

[00208] Example 14 was prepared in a similar fashion to Example 4 from /m-butyl (l -(4-(4- amino-2-oxopyrimidin- l (2H)-yl)butyl)piperidin-4-yl)carbamate and /er/-butyl (iS -(l -(((6- chloropyridin-3-yl)methyl)amino)-l -oxopropan-2-yl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.29 (s, I H), 8. 13 (dd, I H), 8.05 (d, I H), 7.47 (d, I H), 6.42 (d, I H), 4.72 (s, 2H), 4.15 (q, I H), 3.98 (br s, 2H), 3.73 (d, 2H), 3.58 (t, I H), 3.22-3.16 (m, 2H), 3.14 (t, 2H), 2.33 (d, 2H), 1.96 (q, 2H), 1.84 (br s, 4H), 1.55 (d, 3H). ^{, 3}C NMR (125 MHz, D2O) 5 171.0, 161 .0, 154.3, 150.0, 148.8, 143.1 , 138.7, 130.4, 1 16.1 , 96.8, 56.2, 50.7, 49.9, 49.0, 45.4, 39.8, 27.1 , 25.1, 20.7, 16.4 ppm. LC-MS [M+H] 443.3

Example 15

4-((5-(Aminomethyl)pyridin-2-yl)amino)-l-(4-(4-aminopiperidin-l-yl)butyl)pyriinidin-

2(lH)-one hydrochloride salt

[00209] Example 15 was prepared in a similar fashion to Example 4 from tert-butyl (l -(4-(4- amino-2-oxop rimidin- l (2H)-yl)butyl)piperidin-4-yl)carbamate and ter/-butyl ((6- chloropyridin-3-yl)methyl)carbamate to afford the desired product as a yellow solid. Ή NMR (400 MHz, D₂0) δ 8.55 (s, I H), 8.24 (d, I H), 8.14 (d, I H), 7.52 (d, I H), 6.50 (d, IH), 4.34 (s, 2H), 4.03 (br s, 2H), 3.76 (d, 2H), 3.68-3.62 (m, IH), 3.25 (t, 2H), 3.16 (t, 2H), 2.38 (d, 2H), 2.03-1.94 (m, 2H), 1.87 (br s, 4H) ppm. LC-MS [M+H] 372.2

Example 16

-((l-(4-(4-Aminopiperidin-l-yl)butyl)-2-oxo-l,2-dihydropyrimidin-4-yl)amino

(azetidin-3-yl)isonicotinamide trifluoroacetate salt

[00210] Example 16 was prepared in a similar fashion to Example 4 from ter/-butyl ( l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl 3-(2- chloroisonicoti-namido)azetidine- l -carboxylate to afford the desired product as a yellow solid. Ή NMR (500 MHz, CD3OD) δ 8.72 (br s, I H), 8.42 (d, I H), 7.82 (d, I H), 7.47 (d, I H), 6.40 (br s, I H), 4.95-4.89 (m, I H), 4.00-3.83 (m, 6H), 2.97 (d, 2H), 2.90-2.85 (m, I H), 2.42-2.10 (m, 2H), 2.08 (t, 2H), 1.91 (d, 2H), 1.78-1.72 (m, 2H), 1.58-1.49 (m, 4H). ^I3C NMR (125 MHz, CD3OD) δ 167.7, 164.0, 159.2, 154.4, 150.1 , 148.3, 144.5, 1 18.5, 1 13.5, 98.0, 58.9, 54.2, 53.1 , 51.3, 45.8, 33.2, 28.2, 24.8 ppm. Example 17

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((4-(piperazine-l-carbonyI)pyridin-2- yl)amino)pyrimidin-2(lH)-one trifluoroacetate salt

[00211] Example 17 was prepared in a similar fashion to Example 4 from /er/-butyl ( l -(4-(4 amino-2-oxopyrimidin- l (2H)-yl)butyl)piperidin-4-yl)carbamate and /i?r/-butyl 4-(2- chloroisonicotinoyl) piperazine-l -carbox late to afford the desired product as a yellow solid. LC-MS [Μ+Η]

Example 18

2-((l-(2-(2-(4-Aminopiperidin-l-yl)ethoxy)ethyl)-2-oxo-l,2-dihydropyriniidin-4- yl)amino)-N-(3-aminopropyl)isonicotinamide hydrochloride salt

[00212] Example 18 was prepared in a similar fashion to Example 4 from tert-butyl (l-(2-(2- (4-amino-2-oxopyrimidin- l (2H)-yl)ethoxy)ethyl)piperidin-4-yl)carbamate and tert-butyl (3- (2-chloroisonicotinamido)propyl)carbamate to afford the desired product as a yellow solid. LC-MS [M+H]

Example 19

l-(2-(2-(4-aminopiperidin-l-yl)ethoxy)ethyl)-4-((4-(((3- aminopropyl)amino)methyl)pyridin-2-yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00213] Example 19 was prepared in a similar fashion to Example 4 from ter/-butyl ( l -(2-(2- (4-amino-2-oxopyrimidin-l (2H)-yl)ethoxy)ethyl)piperidin-4-yl)carbamate and ter/-butyl (3- (((2-chloropyridin-4-yl)methyl)amino)propyl)carbamate to afford the desired product as a yellow solid. LC-MS [M+H] Example 20

l-(2-(2-(4-aminopiperidin-l-yl)ethoxy)ethyI)-4-((5-(((3- aminopropyl)amino)methyl)pyridin-2-yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00214J Example 20 was prepared in a similar fashion to Example 4 from (ert-butyl (l-(2-(2- (4-amino-2-oxopyrimidin-l (2H)-yl)ethoxy)ethyl)piperidin-4-yl)carbamate and ter/-butyl (3- (((6-chloropyridin-3-yl)methyl)amino)propyl)carbamate to afford the desired product as a yellow solid. LC-MS [M+H]

Example 21

(S)-2-Amino-N-((6-((l-(4-(4-aminopiperidin-l-yl)butyl)-2-oxo-l,2-dihydropyriinidin-4- yl)amino)pyridin-3-yl)methyl)-3-hydroxy-2-methylpropanamide

[00215] Example 21 was prepared in a similar fashion to Example 4 from tm-butyl (l-(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-bufyl (2Λ,45)-2- (tert-butyl)-4-(((6-chloropyridin-3-yl)methyl)carbamoyl)-4-methyloxazolidine-3-carboxylate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.37 (d, 1 H), 8.23 (dd, 1 H), 8.15 (d, 1 H), 7.49 (d, 1 H), 6.49 (d, 1 H), 4.61 (s, 2H), 4.07-4.02 (m, 3H), 3.92 (d, I H), 3.79 (d, 2H), 3.64 (p, 1 H), 3.28 (t, 2H), 3.20 (dt, 2H), 2.42 (d, 2H), 2.02 (dq, 2H), 1.90 (d, 4H), 1.65 (s, 3H). ¹³C NMR ( 125 MHz, D₂0) δ 171.1 , 160.8, 154.0, 150.3, 148.7, 143.7, 137.8, 130.7, 1 16.2, 96.9, 64.4, 61.4, 56.3, 50.8, 50.0, 45.5, 40.0, 27.1 , 25.2, 20.7, 18.1 ppm. LC-MS [M+H] 473.3

Example 22

(5)-4-((5-(((2-Amino-3-hydroxypropyl)amino)methyl)pyridin-2-yl)amino)-l-(4-(4- amino-piperidin-l-yl)butyl)pyrimidin-2(lH)-one hydrochloride salt [00216] Example 22 was prepared in a similar fashion to Example 4 from /er/-butyl (l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and (S)-3-(tert- butoxycarbonyl)-2,2-dimethyloxazolidine-4-carboxylic acid to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.61 (br s, I H), 8.25 (d, I H), 8.15 (d, I H), 7.50 (d, I H), 6.49 (br s, I H), 4.49 (br s, 2H), 4.03 (br s, 2H), 3.98-3.92 (m, I H), 3.90-3.82 (m, 2H), 3.75 (d, 2H), 3.63-3.51 (m, 3H), 3.24 (t, 2H), 3.15 (t, 2H), 2.37 (d, 2H), 2.04-1.90 (m, 2H), 1.87 (br s, 4H). LC-MS [M⁺H] 445.3

Example 23

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((5-((3-aminopropoxy)methyl)pyridin-2- yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00217] Example 23 was prepared in a similar fashion to Example 4 from tert-butyl (l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl (3-((6- chloropyridin-3-yl)methoxy)propyl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.36 (s, I H), 8.26 (d, I H), 8.09 (d, 1 H), 7.45 (d, I H), 6.42 (d, I H), 4.67 (s, 2H), 3.99 (br s, 2H), 3.73 (t, 2H), 3.58 (t, I H), 3.22 (br s, 2H), 3. 17-3.10 (m, 4H), 2.35 (d, 2H), 2.04- 1.92 (m, 4H), 1.84 (br s, 4H). ^I3C NMR (125 MHz, D₂0) δ 160.9, 154.2, 150.3, 148.9, 144.4, 137.9, 130.3, 1 16.0, 96.8, 68.5, 67.9, 56.2, 50.7, 50.0, 45.3, 37.4, 27.1 , 26.6, 25.1 , 20.6 ppm. LC-MS [M+H] 430.3

Example 24

(5)-l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((5-((pyrrolidin-2-ylmethoxy)methyl) pyridin-

2-yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00218] Example 24 was prepared in a similar fashion to Example 4 from /<?r/-butyl (l-(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl (S)-2-(((6- chloropyridin-3-yl)methoxy)methyl)pyrrolidine-l -carboxylate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.37 (s, I H), 8.24 (d, I H), 8.05 (d, I H), 7.44 (d, I H), 6.40 (d, I H), 4.69 (s, 2H), 3.96 (br s, 2H), 3.87 (t, 2H), 3.70 (d, 3H), 3.54 (t, I H), 3.31 (t, 2H), 3.19 (br s, 2H), 3.10 (t, 2H), 2.32 (d, 2H), 2.16-2.05 (m, 2H), 2.04-1 .96 (m, 2H), 1.95-1.86 (m, 2H), 1.81 (br s, 4H). ^I3C NMR (125 MHz, D₂0) δ 160.7, 153.9, 150.0, 148.7, 144.0, 137.6, 129.8, 1 15.8, 96.6, 68.6, 68.5, 58.9, 55.9, 50.4, 49.8, 45.4, 45.1 , 26.8, 25.6, 24.8, 23.0, 20.4 ppm. LC-MS [M+H] 456.3

Example 25

1 -(4-(4-Aminopiperidin- 1 -yl)b utyl)-4-((5-((3-(propy lam ino)propoxy)methy l)py ridin-2- yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00219] Example 25 was prepared in a similar fashion to Example 4 from /er/-butyl (l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and ter/-butyl (3-((6- chloropyridin-3-yl)methoxy)propyl)(propyl)carbamate to afford the desired product as a yellow solid. ^l3C NMR (125 MHz, D₂0) δ 160.4, 153.5, 149.7, 148.5, 143.7, 137.6, 129.6, 1 15.5, 96.3, 68.0, 67.3, 55.7, 50.2, 49.5, 48.7, 44.9, 44.7, 26.5, 25.0, 24.5, 20.1, 18.5, 9.55 ppm. LC-MS [M+H] 472.3

Example 26

6-((l-(4-(4-aminopiperidin-l-yl)butyl)-2-oxo-l,2-dihydropyrimidin-4-yl)amino)-N- (azetidin-3-yI)nicotinamide hydrochloride salt

[00220] Example 26 was prepared in a similar fashion to Example 4 from ter/-butyl ( l -(4-(4- amino-2-oxopyrimidin- l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl 3-(6- chloronicotinamido)azetidine-l -carboxylate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.84 (d, 1 H), 8.41 (dd, 1 H), 8.19 (d, 1 H), 7.43 (d, 1 H), 6.49 (d, 1 H), 4.98-4.91 (m, 1 H), 4.46 (t, 2H), 4.37 (t, 2H), 4.02 (t, 2H), 3.73 (d, 2H), 3.60-3.54 (m, 1 H), 3.22 (t, 2H), 3.13 (t, 2H), 2.34 (d, 2H), 2.00-1.90 (m, 2H), 1.85 (br s, 4H). ^,3C NMR ( 125 MHz, D₂0) δ 166.4, 158.5, 152.6, 151.4, 150.1, 143.8, 140.3, 125.9, 1 15.3, 96.1, 56.2, 52.0, 50.7, 50.0, 45.3, 42.3, 27.1 , 25.0, 20.6 ppm. LC-MS Calculated for m/z, Obsd. LC-MS [M+H] 441.3 3

Example 27

2-((l-(4-(4-aminopiperidin-l-yl)butyl)-2-oxo-l,2-dihydropyrimidin-4-yl)amino)-N-

(azetidin-3-yl) -3-fluoroisonicotinamide hydrochloride salt

[00221] Example 27 was prepared in a similar fashion to Example 4 from /er/-butyl (l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl 3-(2-chloro-3- fluoronicotinamido)azetidine- l -carboxylate to afford the desired product as a yellow solid. Ή NMR (500 MHz, CD₃OD) δ 8.86 (d, I H), 8.31 (d, I H), 7.84 (d, I H), 7.02 (d, I H), 4.56 (t, 2H), 4.50 (t, 2H), 4.26 (br s, 2H), 3.56 (d, 2H), 3.74 (t, I H), 3.40-3.35 (m, I H), 3.28-3.20 (m, 4H), 2.34 (d, 2H), 2.16-2.09 (m, 2H), 1.98 (br s, 4H). ¹³C NMR ( 125 MHz, CD₃OD) δ 166.8, 157.6, 152.0, 147.4, 146.3, 140.6, 138.7, 134.0 (d, J_C-F=228.8 Hz), 130.0 (d, J_c-F=12.4 Hz), 123.0, 1 18.9, 97.4, 57.4, 53.4, 51.9, 50.7, 46.9, 43.4, 28.5, 27.0, 22.0 ppm. LC-MS [M+H] 459.3

Example 28

(S 2-Amino-N-(6-((l-(4-(4-aminopiperidin-l-yl)b^

yl) amino)pyridin-3-yl)-3-hydroxy-2-methylpropanamide hydrochloride salt

[00222] Example 28 was prepared in a similar fashion to Example 4 from tert-butyl ( l-(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl (2R,4S)-2- (tert-butyl)-4-((6-chloropyridin-3-yl)carbamoyl)-4-methyloxazolidine-3-carboxylate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.66 (s, I H), 8.19 (d, IH), 8.10 (d, I H), 7.37 (d, I H), 6.41 (d, I H), 4.16 (d, I H), 3.99 (br s, 2H), 3.92 (d, IH), 3.72 (d, 2H), 3.57 (t, 2H), 3.21 (br s, I H), 3.12 (t, 2H), 2.34 (d, 2H), 1.99-1.89 (m, 2H), 1.83 (br s, 4H), 1.70 (s, 3H). ^{I 3}C NMR ( 125 MHz, D₂0) δ 169.6, 158.3, 150.7, 150.5, 147.3, 136.3, 135.8, 131.0, 1 15.8, 96.1 , 64.1, 62.1 , 56.2, 50.7, 49.8, 45.3, 27.1 , 25.0, 20.6, 17.8 ppm. LC- MS [M+H] 459.3 T U 2017/041793

Example 29

l-(4-(4-Aminopiperidin-l-yI)bulyI)-4-((5-(((l-((methyIamino) methyl)cycIopropyI)methoxy) methyl)pyridin-2-yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00223] Example 29 was prepared in a similar fashion to Example 4 from tert-buty\ (l-(4-(4- amino-2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl ((l-(((6- chloropyridin-3-yl)methoxy)methyl)cyclopropyl)methyl)(methyl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.37 (s, I H), 8.25 (d, IH), 8.08 (d, I H), 7.45 (d, IH), 6.43 (d, I H), 4.67 (s, 2H), 3.99 (t, 2H), 3.72 (d, 2H), 3.57 (t, I H), 3.52 (s, 2H), 3.21 (t, 2H), 3.13 (d, 2H), 3.09 (s, 2H), 2.67 (s, 3H), 2.35 (d, 2H), 1.99-1.88 (m, 2H), 1.83 (d, 4H), 0.70 (q, 4H). ^{, 3}C NMR (125 MHz, D₂0) 5 161.0, 154.2, 150.2, 149.0, 144.3, 137.9, 130.3, 1 16.1, 96.9, 75.4, 68.5, 56.2, 55.3, 50.7, 50.0, 45.3, 33.3, 27.1, 25.1, 20.6, 17.5, 9.6 ppm. LC-MS [M+H] 470.3

Example 30

l.(4-(4-Aminopiperidin-l-yl)butyl)-4-((5-((2-((cyclopropylmethyl)amino)ethoxy)methyl) pyridin-2-yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00224] Example 30 was prepared in a similar fashion to Example 4 from ter/-butyl (l-(4-(4- amino-2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4-yl)carbamate and tert-butyl (2-((6- chloropyridin-3-yl)methoxy)ethyl)(cyclopropylmethyl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.39 (d, IH), 8.26 (dd, IH), 8.07 (d, I H), 7.45 (d, I H), 6.42 (d, I H), 4.70 (s, 2H), 3.98 (t, 2H), 3.84 (t, 2H), 3.71 (d, 2H), 3.56 (p, IH), 3.33 (t, 2H), 3.20 (t, 2H), 3.14-3.08 (m, 2H), 2.96 (d, 2H), 2.34 (d, 2H), 1.98-1.89 (m, 2H), 1.88-1.80 (m, 4H), 1.08-1.04 (m, I H), 0.66 (q, 2H), 0.33 (q, 2H). ¹³C NMR (125 MHz, D₂0) 5 160.9, 154.1, 150.3, 149.0, 144.3, 138.1, 130.0, 1 16.1, 96.9, 68.7, 65.1, 56.2, 52.3, 50.7, 50.0, 46.2, 45.3, 27.1, 25.1, 20.6, 6.4, 3.3 ppm. LC-MS [M+H] 470.3 Example 31

4-((5-((2-Aminoethoxy)methyl)pyridin-2-yl)amino)-l-(4-(4-aminopiperidin-l-yl)butyl) pyrimidin-2(lH)-one hydrochloride salt

[00225] Example 31 was prepared in a similar fashion to Example 4 from /er/-butyl (l-(4-(4- amino-2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4-yl)carbamate tert-butyl (2-((6- chloropyridin-3-yl)methoxy)ethyl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) 6 8.40 (s, 1H), 8.27 (d, 1H), 8.07 (d, 1 H), 7.47 (d, 1 H), 6.43 (d, 1H), 4.72 (s, 2H), 3.99 (br s, 2H), 3.82 (t, 2H), 3.72 (d, 2H), 3.60-3.52 (m, 1H), 3.26 (br s, 2H), 3.21 (br s, 2H), 3.12 (t, 2H), 3.34 (d, 2H), 1.98-1.90 (m, 2H), 1.83 (br s, 4H). ¹³C NMR (125 MHz, D₂0) δ 161.0, 154.3, 150.2, 144.2, 138.0, 130.1, 1 16.1, 96.9, 68.6, 66.0, 56.2, 50.7, 50.0, 45.3, 39.0, 27.1, 25.1, 20.7 ppm. LC-MS [M+H] 416.3

Example 32

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((5-((3- ((cyclopropylmethyl)amino)propoxy)methyl) pyridin-2-yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00226] Example 32 was prepared in a similar fashion to Example 4 from /m-butyl (l-(4-(4- amino-2-oxopyrimidin-l(2H)-yl)butyl)piperidin-4-yl)carbamate tert-butyl (3-((6- chloropyridin-3-yl)methoxy)propyl)(cyclopropylmethyl)carbamate to afford the desired product as a yellow solid. LC-MS [Μ+Η] 484.3

Example 33

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((5-((3-(methylamino)propoxy)methyl)pyridin-2- yl)amino)pyrimidin-2(lH)-one hydrochloride salt [00227] Example 33 was prepared in a similar fashion to Example 4 from tert-butyl (l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate tert-butyl (3-((6- chloropyridin-3-yl)methoxy)propyl)(methyl)carbamate to afford the desired product as a yellow solid. LC-MS [Μ+Η] 444.3

Example 34

l-(4-(4-Aminopiperidin-l-yl)butyl)-4-((5-(4-hydroxypiperidin-4-yl)pyridin-2- yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00228] Example 34 was prepared in a similar fashion to Example 4 from tert-butyl (l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate tert-butyl 4-(6- chloropyridin-3-yl)-4-hydroxypiperidine-l -carboxylate to afford the desired product as a yellow solid. LC-MS [Μ+Η] 442.3

Example 35

l-(4-(4-Aminopiperidin-l-yl)buryl)-4-((5-glycylpyridin-2-yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00229] Example 35 was prepared in a similar fashion to Example 4 from tert-butyl ( l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)carbamate tert-butyl (2-(6- chloropyridin-3-yl)-2-oxoethyl)carbamate to afford the desired product as a yellow solid. LC- MS [Μ+Η] 400.2

Example 36

l-(4-(4-aminopiperidin-l-yl)butyl)-4-((5-(((3-aminopropyl)amino)methyl)pyridin-2- yl)amino)-5-fluoropyrimidin-2(lH)-one hydrochloride salt [00230] Example 36 was prepared in a similar fashion to Example 4 from tert-butyl ( l -(4-(4- amino-5-fluoro-2-oxopyrimidin-l (2H)-yI)butyl)piperidin-4-yl)carbamate and tert-butyl (3- ((tert-butoxycarbonyl)amino)propyl)(3-chloro-4-fluoro-5-iodobenzyl)carbamate to afford the desired product as a yellow solid. LC-MS [M+H] 447.3

Example 37

l-(4-(4-amino-4-methylpiperidin-l-yl)butyl)-4-((5-(((3- aminopropyl)amino)methyl)pyridin-2-yl)amino)pyrimidin-2(lH)-one hydrochloride salt

[00231] Example 37 was prepared in a similar fashion to Example 4 from tert-butyl ( l -(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)-4-methylpiperidin-4-yl)carbamate and tert-butyl (3- ((tert-butoxycarbonyl)amino)propyl)(3-chloro-4-fluoro-5-iodobenzyl)carbamate to afford the desired product as a yellow solid. LC-MS [M+H] 443.3

Example 38

l-(4-(4-aminopiperidin-l-yl)butyl)-4-((5-(((3-aminopropyl)amino)methyl)pyridin-2- yl)amino)-5-fluoropyrimidin-2(l H)-one hydrochloride salt

[00232] Example 38 was prepared in a similar fashion to Example 4 from tert-butyl ( l-(4-(4- amino-2-oxopyrimidin-l (2H)-yl)butyl)piperidin-4-yl)(methyl)carbamate and tert-butyl (3- ((tert-butoxycarbonyl)amino)propyl)(3-chloro-4-fluoro-5-iodobenzyl)carbamate to afford the desired product as a yellow solid. Ή NMR (500 MHz, D₂0) δ 8.55 (br s, 1 H), 8.19 (d, 1 H), 8.1 1 (d, 1 H), 7.48 (d, 1 H), 6.46 (d, 1 H), 4.39 (br s, 2H), 3.99 (t, 2H), 3.76 (d, 2H), 3.48-3.42 (m, 3H), 3.25 (t, 2H), 3.10 (t, 4H), 2.74 (s, 3H), 2.43 (d, 2H), 2.15-2.09 (m, 2H), 1.95-1.87 (m, 2H), 1.84 (br s, 4H) ppm. LC-MS [M+H] 443.3.

Biological Examples

Standard Microbiological Activity:

[00233] A certified BSL-2 laboratory was used for testing. Compounds were evaluated using the microdilution minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays defined by Clinical and Laboratory Standards Institute (CLSI) in the M26-A guideline against Mtb H37Ra, M. smegmatus, M. bovis BCG, RSA, E. coli, and P. aeruginosa.

[00234] E. coli S30: Inhibition of bacterial protein synthesis was determined using the E. coli S30 Extract System for Circular DNA (Promega catalog #L-2010) and Luciferase Assay

Reagent (Promega catalog #E1500) with slight modifications to a published protocol. Fyfe,

C, Sutcliffe, J.A. and Grossman, T.H. (2012) "Development and characterization of a

Pseudomonas aeruginosa in vitro coupled transcription-translation assay system for evaluation of translation inhibitors" J. Microbiol. Methods 90(3), 256-261.

[00235] Compounds were serial diluted in 0.5 mL microcentrifuge tubes by mixing and transferring 50 μΐ, from the highest concentration to 50 of water, mixing and transferring

50 μΐ, of this 2-fold dilution to 50 μL· of water. This mixing and transferring was repeated so that there are a total of 8 tubes with serial dilutions of compound at 1 Ox the desired screening concentration that are ultimately diluted to l by the addition of S30 luciferase synthesis mixture. Serial dilutions of compounds were added (2 μί) to wells in a black round bottom

96-well plate. Water (2 μί) was used as a "no inhibitor" control in 4 wells/plate. No DNA control reaction mixture (20 μί; see below) was used as a control in 4 wells/plate for background luminescence. S30 luciferase synthesis mixture ( 18 μΙ_; see below) was added to wells with compounds or water mixture and incubated at 37 °C for 1 hour. Reactions were stopped by transferring to 4 °C refrigerator for 5 minutes then 25 μL· of luciferase activity mix was added. Luminescence was measured using a BioTek Synergy HTX plate reader. %

Inhibition was determined relative to no inhibitor controls.

S30 luciferase synthesis mixture:

445 μί S30 extract, circular

712 S30 Premix without amino acids

4.45 μΐ pBESTlucTM DNA (1 μg μί)

78 μL· complete amino acid mixture

267 μΐ, water

No DNA control:

20 μΐ, S30 extract, circular

32 μΐ. S30 Premix without amino acids

7 μΐ, complete amino acid mixture

21 μΐ, water

Rabbit Reticulocyte lysate

[00236] Inhibition of eukaryotic protein synthesis was determined using the Rabbit Reticulocyte Lysate System, Nuclease-Treated from Promega (catalog #L-4960) with slight modifications to the manufacturer's protocol. Compounds were serial diluted in 0.5 mL microcentrifuge tubes by mixing and transferring 50 from the highest concentration to 50 of water, mixing and transferring 50 μL· of this 2-fold dilution to 50 μΐ-, of water. This mixing and transferring was repeated so that there are a total of 8 tubes with serial dilutions of compound at l Ox the desired screening concentration that are ultimately diluted to l x by the addition of rabbit reticulocyte luciferase synthesis mixture. Serial dilutions of compounds were added (2.5 μΙ_) to wells in a black round bottom 96-well plate. Water (2.5 μί) was used as a "no inhibitor" control in 4 wells/plate. No RNA control reaction mixture (2 μΙ_; see below) was used as a control in 4 wells/plate for background luminescence. Rabbit reticulocyte luciferase synthesis mixture (22.5 μί; see below) was added to wells with compounds or water mixture and incubated at 30 °C for 90 minutes. Luciferase assay reagent

(25 μ1_ was added with luminescence measured using a BioTek Synergy HTX plate reader.

% Inhibition was determined relative to no inhibitor controls.

Rabbit reticulocyte luciferase synthesis mixture:

1,000 μΐ rabbit reticulocyte lysate

5.7 μL· Luciferase Control RNA (1 μg/ μί)

26 μL· complete amino acid mixture

395 μί water

No RNA Control

70 μΐ. rabbit reticulocyte lysate

2 μΐ, complete amino acid mixture

28 μί water

Minimum Inhibitory Concentration (MIC)

[00237] MICs were determined using the Clinical Laboratory and Standards Institute (CLSI) Broth Microdilution Method with slight modification. Clinical and Laboratory Standards Institute (2012). "Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically; approved standard, 9th ed. M07-A9. Clinical and Laboratory Standards Institute, Wayne, PA." Serial two-fold dilutions of compounds are prepared in sterile clear round- bottom 96-well plates.

[00238] To prepare microdilution trays, two-fold dilutions of antimicrobial agent are prepared by adding 200 μΐ. of the highest concentration, prepared in Cation-Adjusted Mueller-Hinton Broth (CAMHB), to be tested (64 μg/mL, for example) in row A, mixing and transferring 100 μL from row A to 100 μί CAMHB in row B, then repeating the mixing and transferring through row H of the 96-well plate, discarding the excess 100 μΐ, remaining. This slight modification to the CLSI protocol enables evaluation of MICs for 3 compounds per plate in triplicate, albeit with only 8 compound dilutions (CLSI protocol enables 2 compounds in triplicate with 10 dilutions). Bacterial suspensions are added to a final concentration of 5 x 104 CFU/well by adding 5 μί, of a 1 : 10 dilution of a 0.5 McFarland suspension (1 ^χ 108 CFU/mL) for each bacterium evaluated. Bacterial suspensions were prepared using the growth method described by CLSI. Well-isolated colonies (3-5 from an agar plate) were selected using a sterile loop and used to inoculate a tube containing 4 mL of tr ptic soy broth. The cultures are incubated at 35 ± 2°C until it achieves or exceeds the turbidity of the 0.5 McFarland standard, determined by measuring A600nm (usually two to six hours). When growth exceeds a 0.5 McFarland standard, the turbidity is adjusted with broth to be equivalent to a 0.5 McFarland standard.

Data for compounds is provided in Table 1. An ICso value that is 1 μΜ or greater is designated by a "+". An IC50 value that is 0.5 μΜ or greater and less than 1 μΜ is designated by a "++". An IC50 value that is less than 0.5 μΜ is designated by "+++". An MIC value that is 32 μg/mL or greater and less than 128 μg/mL is designated by a "+". An MIC value that is 8 μg/mL or greater and less than 32 μg/mL is designated by a "++". An MIC value that is less than 8 g/mL is designated by "+++".

Table 1.

Biological Activity of Compounds of Formula I

P T/US2017/041793

[00239] The foregoing disclosure has been described in some detail by way of illustration and example, for purposes of clarity and understanding. The invention has been described with reference to various specific and preferred embodiments and techniques. However, it should be understood that many variations and modifications can be made while remaining within the spirit and scope of the invention. It will be obvious to one of skill in the art that changes and modifications can be practiced within the scope of the appended claims. Therefore, it is to be understood that the above description is intended to be illustrative and not restrictive. The scope of the invention should, therefore, be determined not with reference to the above description, but should instead be determined with reference to the following appended claims, along with the full scope of equivalents to which such claims are entitled.

Claims

1. A compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

A is an optionally substituted six-membered heteroarylene;

Yi is C1-C4 alkylene;

Y2 is absent or is selected from the group consisting of 0-(Ci-C₆ alkylene) and -NH-(Ci- C₆ alkylene);

Ri is selected from the group consisting of NH2 and piperidine optionally substituted with Me or NRxRy, wherein R_x and R_y are independently selected from Me and H;

Zi is absent or is CH₂, (C=0), (C=0)NH CH₂0, CH₂NH, CH₂N(Ci-C₆ alkyl), CH₂N(Ci- C₆ alkyNH₂),

Z₂ is absent or is optionally substituted Ci-Cio alkylene, optionally substituted

cycloalkylene and optionally substituted heterocycloalkylene, optionally substituted Ci-C₆ alkylene-cycloalkylene and optionally substituted Ci-Ce alkylene-heterocycloalkylene, wherein up to two carbon atoms of optionally substituted C1-C10 alkylen replaced by O or -(C=0)-,

NH, NH(Ci-C₆ alkyl), NH-(C=0)-, N(Ci-C₆ alkyl)-(C=0)-, and

wherein n is 1, 2, 3, 4, or 5, wherein " -~w " indicates the point of attachment;

R₂ is

or R₂ is selected from the group consisting of H, OH, NH₂, NH(Ci-C₆ alkyl), N(Ci-C₆ alkyl)₂, and NH(Ci-C₆ alkylene-cycloalkyl), wherein " w " indicates the point of attachment;

R_2a is selected from the group consisting of hydrogen and (Ci-C₆ alkyl); R₂b is selected from the group consisting of hydrogen, (Ci-C₆ alkyl), (C2-C6 alkenyl), ryl, and arylalkyl; and

R3 is H or F.

The compound of claim 1 which is a compound of formula I A or IB:

IB.

3. The compound of claims 1-2, wherein Zi is CH₂, (C=0), (C=0)NH, CH2O, or CH₂NH.

4. The compound of claims 1-2, wherein Z₂ is absent.

5. The compound of claims 1-2, wherein Z₂ is optionally substituted C1-G0 alkylene, optionally substituted cycloalkylene and optionally substituted heterocycloalkylene, optionally substituted Ci-C₆ alkylene-cycloaIkylene and optionally substituted Ci-C₆ alkylene- heterocycloalkylene, wherein up to two carbon atoms of optionally substituted G-Go alkylene re replaced by O or -(C=0)-, NH, NH(G-C₆ alkyl), NH-(C=0)-, N(G-C₆ alkyl)-(C=0)-, and

, wherein n is 1, 2, 3, 4, or 5, wherein " indicates the point of attachment.

R2a

6. The compound of claims 1-3, wherein R₂ is ^{2N Rzb} and R_2a is selected from the group consisting of hydrogen and (G-C₆ alkyl) and R₂b is selected from the group consisting of hydrogen, (Ci-C₆ alkyl), (C2-C6 alkenyl), aryl, and arylalkyl, wherein indicates the point of attachment.

7. The compound of claims 1 -2, wherein R₂ is selected from the group consisting of H, OH, NH₂, NH(Ci-C₆ alkyl), and NH(Ci-C₆ alkylene-cycloalkyl), wherein indicates the point of attachment.

8. The compound of claims 1-2, wherein Z₂ is selected from the group consisting of: C=0, -CH2-, -CH2CH2-, -CH₂CH₂CH₂-, -CH2CH2CH2CH2-, -

-CH2CH2CH2CH2CH2-, -CH2CH2NHCH2CH2C -, -CH2CH2CH2NHCH2CH2CH2-, -

OH _> wherein "— " indicates the point of attachment.

9. The compound of claims 1-2, wherein Z1Z2 is selected from the group consisting of: -

-CH2NHCH2 -, -C(=0)NHCH₂CH₂CH₂-,

O -CH₂NH(C=0)-, -CH2OCH2CH2-, -CH2OCH2CH2CH2-, CH2OCH2CH2CH2CH2-, -CH2OCH2CH2CH2CH2CH -,

CH2OCH2CH2CH2NH-CH2CH2CH2-,

(C=0)CH₂-, wherein " -~w " indicates the point of attachment.

10. The com ound of claims 1 -2, wherein R2Z2 is selected from the group consisting of: -

CH3CH2CH2NHCH2CH2CH2-, ^H . ^ "^ H

CH -CH2NH2, -CH2CH2CH2NH2, -CH₂CH2CH₂CH2CH₂NH2,

and

indicates a point of attachment.

The compound of claims 1-2, wherein R₂-Z2-Z₁ is selected from the group consisting

_{H N} -^ OH O OH

HN T . Me⁷ NH₂ ^{H '} H N H₂ ^H _ H₂N^'

₅ wherein -~www. indicates a point of attachment.

12. The compound of claims 1-12, wherein Yi is selected from the group consisting of CH₂CH₂CH₂CH2, and CH₂CH₂.

13. The compound of claims 1-12, wherein Y₂ is absent, or is selected from the group consisting -CH₂CH₂0-, -CH₂CH₂CH₂NH, and -CH₂CH₂CH₂NMe. The c m und of claims 1 -13 wherein R is selected from the group consisting of:

and , wherein indicates the point of attachment

15. The compound of claims 1-14, wherein Ri - Y₂- Y ι is selected from the group consisting

, wherein .~ ww indicates a point of attachment. compound of claims 1-2 which is a com ound of formula IC:

compound of cl im 16 which is a co ound of formula ID:

ID.

18. A compound of formula II:

II

or a pharmaceutically acceptable salt thereof, wherein:

A is pyridylene;

Y₂ is absent or is selected from the group consisting of optionally substituted Ci-Cio alkylene, optionally substituted Ci-Ci₀ alkenylene, and optionally substituted Ci-Cio alkynylene, wherein up to three carbons of the optionally substituted O-Cio alkylene, optionally substituted Ci-Ci₀ alkenylene, and optionally substituted Ci-Cio alkynylene, are independently replaced by aryl, O, NH, N-(Ci_-6 alkyl) or (CO); Ri is selected from the group consisting of H, halo, NRrRr, and heterocycloalkyl optionally substituted with NH₂ or Me; wherein Rr and Ri - are each independently selected from H and Me;

Zi is absent or is selected from the group consisting of CH_2> -CH₂0-, -CH2NH-, - CH₂N(Ci-6 alkyl)-, -CH₂(C=0)-, -NH(C=0)-;

Z₂ is absent or is selected from the group consisting of optionally substituted C1-C10 alkylene, optionally substituted heterocycloalkyl, and optionally substituted heteroaryl; and

R₂ is selected from H, OH, NH₂, NH(C|.₆ alkyl), N(C,.₆ alkyl)₂, NH(cycloalkyl), N(cycloalkyl)₂.

19. The compound of claim 18 which is a compound of formula IIA:

or a pharmaceutically acceptable salt thereof, wherein:

is pyridylene;

Y₂ is absent or is selected from the group consisting of optionally substituted C1-C10 alkylene, optionally substituted Ci-Cio alkenylene, and optionally substituted C1-C 10 alkynylene, wherein up to three carbons of the optionally substituted C1-O0 alkylene, optionally substituted C 1-C10 alkenylene, and optionally substituted Ci-Cio alkynylene, are independently replaced by O, NH, N-(Ci-₆ alkyl) or (C=0);

Ri is selected from the group consisting of H, halo, NRpRr, and heterocycloalkyl optionally substituted with NH₂ or Me; wherein Rr and Rr- are each independently selected from H and Me.

20. A compound which is:

or a pharmaceutically acceptable salt thereof. 21. A compound which is:

PCT/US2017/041793

PCT/US2017/041793

No. Compound

38

^H 3HCI

22 A pharmaceutical composition comprising a compound of claims 1 -21 and a

pharmaceutically acceptable excipient.

23. A method of treating a bacterial infection in a patient in need of such treatment, comprising administering the composition of any one of claims 1-21 or the pharmaceutical composition of claim 22.

24. The method of claim 23, wherein the bacterial infection is tuberculosis.

25. The method of claim 23, wherein the bacterial infection is a gram negative or gram positive bacterial infection.

26. The method of claim 24, wherein the bacterial infection is a gram negative bacterial infection.

27. The method of claim 25, wherein the gram negative infection is selected from the group consisting of E. coli, Acinetobacter baumanii, Pseudomonas aeruginosa, Klebisella pneumonia, and Neisseria gonorrhoeae.

28. The method of claim 25, wherein the bacterial infection is a gram positive bacterial infection.

29. Thee method of claim 28, wherein the gram positive bacterial infection is selected from the group consisting of an Methicillin resistant staphylococcus aureus (MRSA) infection and an M. smegmatis infection.